h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/gpu_cpu_common.h0000644000175000017500000000737512137171471023771 0ustar ykeyke#ifndef GPU_CPU_COMMON_H #define GPU_CPU_COMMON_H //#include #include #include #include #define NUM_SEQUENCES 95 #define PERCENTAGE 95 #define NUM_THREADSX 64 #define NUM_THREADSX_MAX 512 #define NUM_BLOCKSX 512 #define NUM_BLOCKSX_MAX 65535 #define GPU 1 #define GPU_VERBOSE 0 #define METHOD 1 #define PITCH 16 #define CPU_THREADS 1 #define QUERY_LENGTH_MAX 32768 #define NUM_QUERIES_MAX 500 #define SUBSTITUTION_MATRIX_LENGTH 896 #define H_HITS_SIZE_BYTE 4 #define BRIEF_INFO 1 const static float IMB_factor_of_gpudb_group = 1.1; typedef struct GPUBlastInitHitList { unsigned short hsp_q; unsigned short hsp_s; unsigned short offset_from_first_position; unsigned short hsp_len; unsigned short score; } GPUBlastInitHitList; #ifdef __cplusplus extern "C" { #endif void GPU_BLASTP_pre( const BLAST_SequenceBlk* query, const BlastQueryInfo* query_info, const LookupTableWrap* lookup_wrap, const Blast_ExtendWord* ewp, const BlastInitialWordParameters* word_params, const BlastGPUOptions* gpu_options, Int4* Sequence_length_vector, const int h_Database2Dpadded_bytes, const Int4 Group_number, const Int4 h_Hits_bytes, const Int4 h_GPUBlastInitHitList_bytes); void GPU_BLASTP_get_data( Int4* h_Hits, const Int4 h_Hits_bytes, GPUBlastInitHitList* h_GPUBlastInitHitList, const Int4 h_GPUBlastInitHitList_bytes, const Int4 num_sequences); void ReadGPU_BLASTP_database(const char* GPU_volume_name, const unsigned long h_GPU_BLASTP_database_bytes); void all_gpu_abnormally_exit(int exit_code); void all_gpu_quit(); void gpu_quit(); void gpu_abnormally_exit(int exit_code); double get_gpu_walltime(); void set_max_gpu_walltime(); void init_max_and_current_gpu_walltime(); void GPU_BLASTP( const int cuda_device_id, const BLAST_SequenceBlk* query, const BlastQueryInfo* query_info, const LookupTableWrap* lookup_wrap, const Blast_ExtendWord* ewp, const BlastInitialWordParameters* word_params, const BlastGPUOptions* gpu_options, const int* Sequence_length_vector ); void GPU_BLASTP_free_memory(); Boolean GPU_BLASTP_check_memory(const LookupTableWrap* lookup_wrap, const Blast_ExtendWord* ewp, const BlastGPUOptions* gpu_options, const int h_Database2Dpadded_bytes, const Int4 h_Hits_bytes, const Int4 h_GPUBlastInitHitList_bytes, const Int4 Group_number, const Int4 num_queries, const Int4 query_length ); Boolean GPU_BLAST_check_availability(); void Round2Multiple(Int4* MaxLength); void SetNumOfGpuCards(const int expected_num_of_cards); void GPU_BLASTP_check_rehit_ratio(const Int4* _h_Hits, const Int4 _num_sequences); int get_num_of_gpu_cards_used(); void set_MAX_SUCCESSFUL_HITS_PER_SEQUENCE(const unsigned int val); unsigned int get_MAX_SUCCESSFUL_HITS_PER_SEQUENCE(); void lut_sorting(BlastAaLookupTable *lookup); #ifdef __cplusplus } #endif #endif /* GPU_CPU_COMMON_H */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blastx_args.cpp0000644000175000017500000001076512001215335023604 0ustar ykeyke/* $Id: blastx_args.cpp 170780 2009-09-16 18:25:06Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file blastx_args.cpp * Implementation of the BLASTX command line arguments */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: blastx_args.cpp 170780 2009-09-16 18:25:06Z camacho $"; #endif #include #include #include #include #include BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) USING_SCOPE(objects); CBlastxAppArgs::CBlastxAppArgs() { CRef arg; static const string kProgram("blastx"); arg.Reset(new CProgramDescriptionArgs(kProgram, "Translated Query-Protein Subject BLAST")); const bool kQueryIsProtein = false; m_Args.push_back(arg); m_ClientId = kProgram + " " + CBlastVersion().Print(); static const string kDefaultTask = "blastx"; SetTask(kDefaultTask); m_BlastDbArgs.Reset(new CBlastDatabaseArgs); m_BlastDbArgs->SetDatabaseMaskingSupport(true); arg.Reset(m_BlastDbArgs); m_Args.push_back(arg); m_StdCmdLineArgs.Reset(new CStdCmdLineArgs); arg.Reset(m_StdCmdLineArgs); m_Args.push_back(arg); // N.B.: query is not protein because the options are applied on the // translated query arg.Reset(new CGenericSearchArgs( !kQueryIsProtein )); m_Args.push_back(arg); arg.Reset(new CFrameShiftArgs); m_Args.push_back(arg); arg.Reset(new CLargestIntronSizeArgs); m_Args.push_back(arg); // N.B.: query is not protein because the filtering is applied on the // translated query arg.Reset(new CFilteringArgs( !kQueryIsProtein )); m_Args.push_back(arg); arg.Reset(new CMatrixNameArg); m_Args.push_back(arg); arg.Reset(new CWordThresholdArg); m_Args.push_back(arg); m_HspFilteringArgs.Reset(new CHspFilteringArgs); arg.Reset(m_HspFilteringArgs); m_Args.push_back(arg); arg.Reset(new CWindowSizeArg); m_Args.push_back(arg); arg.Reset(new CGappedArgs); m_Args.push_back(arg); m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein)); arg.Reset(m_QueryOptsArgs); m_Args.push_back(arg); arg.Reset(new CGeneticCodeArgs(CGeneticCodeArgs::eQuery)); m_Args.push_back(arg); m_FormattingArgs.Reset(new CFormattingArgs); arg.Reset(m_FormattingArgs); m_Args.push_back(arg); m_MTArgs.Reset(new CMTArgs); arg.Reset(m_MTArgs); m_Args.push_back(arg); m_RemoteArgs.Reset(new CRemoteArgs); arg.Reset(m_RemoteArgs); m_Args.push_back(arg); m_DebugArgs.Reset(new CDebugArgs); arg.Reset(m_DebugArgs); m_Args.push_back(arg); /* *********** START ************* */ m_GpuArgs.Reset(new CGpuArgs); arg.Reset(m_GpuArgs); m_Args.push_back(arg); /* ********** FINISH ************* */ } CRef CBlastxAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& /*args*/) { return CRef(new CBlastxOptionsHandle(locality)); } int CBlastxAppArgs::GetQueryBatchSize() const { return blast::GetQueryBatchSize(eBlastx, m_IsUngapped); } END_SCOPE(blast) END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb_volume.hpp0000644000175000017500000003123312001215336024321 0ustar ykeyke#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_VOLUME_HPP #define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_VOLUME_HPP /* $Id: writedb_volume.hpp 217084 2010-12-13 21:44:14Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb_volume.hpp /// Code for database volume construction. /// /// Defines classes: /// CWriteDBVolume /// /// Implemented for: UNIX, MS-Windows #include #include #include #include #include "writedb_column.hpp" BEGIN_NCBI_SCOPE /// Import definitions from the objects namespace. USING_SCOPE(objects); /* *********** START ************* */ //Class used to store the sequences, the headers, and the length of the sequences //in order to sort them class bioseq_class{ public: bioseq_class( string seq_in, string binhdr_in, int length_in ) { seq = seq_in; binhdr = binhdr_in; length = length_in; } bioseq_class(); string GetSequence(void) { return seq; } string GetHeader(void) { return binhdr; } int GetLength(void) { return length; } public: string seq; string binhdr; int length; }; /* ********** FINISH ************* */ /// CWriteDB_GiIndex class /// /// This class creates OID->GI lookup file class CWriteDB_GiIndex : public CWriteDB_File { public: CWriteDB_GiIndex(const string & dbname, bool protein, int index, Uint8 max_fsize) : CWriteDB_File (dbname, (protein ? "pog" : "nog"), index, max_fsize, false){ } ~CWriteDB_GiIndex() { }; void AddGi(Int4 gi) { m_Gi.push_back(gi); } private: void x_Flush() { Int4 nGi = m_Gi.size(); if (! nGi) return; Create(); WriteInt4(kVersion); WriteInt4(kFileType); WriteInt4(kGiSize); WriteInt4(nGi); for (Int4 i=0; i<4; i++) { WriteInt4(0); } for (Int4 i=0; i tmp; m_Gi.swap(tmp); } static const int kVersion = 1; static const int kFileType = 0; static const int kGiSize = 4; vector m_Gi; }; /// CWriteDB_Volume class /// /// This manufactures a blast database volume from sequences. class CWriteDB_Volume : public CObject { public: /// Whether and what kind of indices to build. typedef CWriteDB::EIndexType EIndexType; /// Type used for lists of identifiers. typedef vector< CRef > TIdList; /// Type used for lists of identifiers. typedef vector< CRef > TBlobList; // Setup and control /// Build a database volume. /// /// @param dbname Base name of the database, such as 'nr'. /// @param protein True if the database is a protein database. /// @param title Title of the database. /// @param date Creation date of the database. /// @param index Volume index (for filename). /// @param max_file_size Maximum file size for this volume. /// @param max_letters Maximum number of letters for this volume. /// @param indices Type of indices to build. CWriteDB_Volume(const string & dbname, bool protein, const string & title, const string & date, int index, Uint8 max_file_size, Uint8 max_letters, EIndexType indices); /// Destructor. /// /// The Close() method will be called if it has not already been. ~CWriteDB_Volume(); /* *********** START ************* */ static void x_ExtractDeflines(CConstRef & deflines, string & bin_hdr, int OID=-1); /// Extract a defline set from a binary ASN.1 blob. /// @param bin_hdr Binary ASN.1 encoding of defline set. [in] /// @param deflines Defline set. [out] static void x_SetDeflinesFromBinary(const string & bin_hdr, CConstRef & deflines); /* ********** FINISH ************* */ /// Add a sequence to this volume. /// /// The provided data represents all information for one /// non-redundant sequence that will be added to this volume. /// /// @param seq Sequence data in format ncbi2na or ncbistdaa. /// @param ambig Ambiguities (for protein this should be empty). /// @param binhdr Binary headers (blast deflines in binary ASN.1). /// @param ids List of identifiers for ISAM construction. /// @param pig PIG protein identifier (zero if not available.) /// @param hash Sequence Hash (zero if not available.) bool WriteSequence(const string & seq, const string & ambig, const string & binhdr, const TIdList & ids, int pig, int hash, const TBlobList & blobs, int maskcol_id=-1); /* *********** START ************* */ bool WriteSequenceSort(const string & seq, const string & ambig, const string & binhdr, const TIdList & ids, int pig, int hash, const TBlobList & blobs, int maskcol_id=-1, bool last_sequence=false); /* ********** FINISH ************* */ /// Rename all volumes files to single-volume names. /// /// When volume component files are generated by WriteDB, the /// volume names include a volume index. This method renames the /// generated files for this volume to names that do not include /// the volume index. This method should not be called until the /// volume is Close()s. void RenameSingle(); /// Close the volume. /// /// This method finalizes and closes all files associated with /// this volume. (This is not a trivial operation, because ISAM /// indices and the index file (pin or nin) cannot be written /// until all of the data has been seen.) void Close(); /// Get the name of the volume. /// /// The volume name includes the path and version (if a version is /// used) but does not include the extension. It is the name that /// would be provided to SeqDB to open this volume. This method /// should be called after RenameSingle() if that method is going /// to be called. /// /// @return The volume name. const string & GetVolumeName() const { return m_VolName; } /// Get the current OID of the volume. /// /// The current OID is needed for generating BL_ORD_ID. /// /// @return the OID const int & GetOID() const { return m_OID; } /// List all files associated with this volume. /// @param files The filenames will be appended to this vector. void ListFiles(vector & files) const; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Type used for database column meta-data. typedef CWriteDB_Column::TColumnMeta TColumnMeta; /// Create a new database column. /// /// @param title The title of the new column. /// @param meta Metadata to store in the new column. /// @return The numeric column ID. int CreateColumn(const string & title, const TColumnMeta & meta, bool mbo = true); /// Add meta data to a column. /// /// In addition to normal blob data, database columns can store a /// `dictionary' of user-defined metadata in key/value form. This /// method adds one such key/value pair to the column. Specifying /// a key a second time causes replacement of the previous value. /// Using this mechanism to store large amounts of data may have a /// negative impact on performance. /// /// @param col_id Specifies the column to add this metadata to. /// @param key A unique key string. /// @param value A value string. void AddColumnMetaData(int col_id, const string & key, const string & value); #endif private: // Configuration. string m_DbName; ///< Base name of the database. string m_VolName; ///< Database name plus version (if used). bool m_Protein; ///< True for protein; false for nucleotide. string m_Title; ///< Database title (same for all volumes). string m_Date; ///< Construct time (same for all volumes). int m_Index; ///< Index of this volume (1 based). EIndexType m_Indices; ///< Indices are sparse, full, or disabled. Uint8 m_MaxFileSize; ///< Maximum size for any component file. /* *********** START ************* */ int m_HdrDataSizeInitial; int m_IdxDataSizeInitial; int m_SeqOffsetInitial; int m_SeqLettersInitial; int m_OIDInitial; std::vector < bioseq_class > bioseq_vector; bool m_LastSequence; /// Deflines to write as header. CConstRef m_Deflines; /* ********** FINISH ************* */ // Status. int m_OID; ///< Next assigned OID. bool m_Open; ///< True if user can still append sequences. // Components CRef m_Idx; ///< Index file (pin / nin). CRef m_Hdr; ///< Header file (phr / nhr). CRef m_Seq; ///< Sequence file (psq / nsq). CRef m_AccIsam; ///< Accession index (psi+psd / nsi+nsd). CRef m_GiIsam; ///< GI index (pni+pnd / nni+nnd). CRef m_PigIsam; ///< PIG index (ppi+ppd, protein only). CRef m_TraceIsam; ///< Trace ID index (pti+ptd or nti+ntd). CRef m_HashIsam; ///< Hash index (phi+phd or nhi+nhd). CRef m_GiIndex;///< OID->GI lookup (pgx or ngx). #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Database columns. vector< CRef > m_Columns; #endif /// Included Seq_ids set m_IdSet; // Functions /// Compute base-length of compressed nucleotide sequence. /// /// Nucleotide sequences stored on disk are packed 4 bases to a byte, /// except for the last byte. That byte has 0-3 bases of real sequence /// data plus a 'remainder' value (from 0-3) that indicates how many of /// the bases of the last byte are sequence data. This method finds the /// exact length in bases for a nucleotide sequence packed in this way. /// /// @param seq Ncbi2na sequence with length remainder encoding. /// @return Length in bases of actual sequence data in this sequence. int x_FindNuclLength(const string & seq); }; END_NCBI_SCOPE #endif // OBJTOOLS_WRITERS_WRITEDB__WRITEDB_VOLUME_HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb_volume.cpp0000644000175000017500000006073712001215336024327 0ustar ykeyke/* $Id: writedb_volume.cpp 217084 2010-12-13 21:44:14Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb_volume.cpp /// Implementation for the CWriteDB_Volume class. /// class for WriteDB. #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: writedb_volume.cpp 217084 2010-12-13 21:44:14Z rafanovi $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include "writedb_volume.hpp" #include #include /* *********** START ************* */ #include #include #include #include #include /* ********** FINISH ************* */ BEGIN_NCBI_SCOPE /// Include C++ std library symbols. USING_SCOPE(std); CWriteDB_Volume::CWriteDB_Volume(const string & dbname, bool protein, const string & title, const string & date, int index, Uint8 max_file_size, Uint8 max_letters, EIndexType indices) : m_DbName (dbname), m_Protein (protein), m_Title (title), m_Date (date), m_Index (index), m_Indices (indices), m_OID (0), m_Open (true) { m_VolName = CWriteDB_File::MakeShortName(m_DbName, m_Index); m_Idx.Reset(new CWriteDB_IndexFile(dbname, protein, title, date, index, max_file_size)); m_Hdr.Reset(new CWriteDB_HeaderFile(dbname, protein, index, max_file_size)); m_Seq.Reset(new CWriteDB_SequenceFile(dbname, protein, index, max_file_size, max_letters)); if (m_Indices != CWriteDB::eNoIndex) { bool sparse = (m_Indices & CWriteDB::eSparseIndex) == CWriteDB::eSparseIndex; if (m_Protein) { m_PigIsam.Reset(new CWriteDB_Isam(ePig, dbname, protein, index, max_file_size, false)); } m_GiIsam.Reset(new CWriteDB_Isam(eGi, dbname, protein, index, max_file_size, false)); m_AccIsam.Reset(new CWriteDB_Isam(eAcc, dbname, protein, index, max_file_size, sparse)); if (m_Indices & CWriteDB::eAddTrace) { m_TraceIsam.Reset(new CWriteDB_Isam(eTrace, dbname, protein, index, max_file_size, false)); } if (m_Indices & CWriteDB::eAddHash) { m_HashIsam.Reset(new CWriteDB_Isam(eHash, dbname, protein, index, max_file_size, false)); } m_GiIndex.Reset(new CWriteDB_GiIndex(dbname, protein, index, max_file_size)); } } CWriteDB_Volume::~CWriteDB_Volume() { if (m_Open) { Close(); } } /* *********** START ************* */ //bool compare (bioseq_class* in1, bioseq_class* in2 ) bool compare (bioseq_class in1, bioseq_class in2 ) { // return (in1->GetLength() < in2->GetLength()); return (in1.GetLength() > in2.GetLength()); } static void s_CheckEmptyLists(CRef & deflines, bool owner); static CRef s_EditDeflineSet(CConstRef & deflines) { CRef bdls(new CBlast_def_line_set); SerialAssign(*bdls, *deflines); s_CheckEmptyLists(bdls, true); return bdls; } static void s_CheckEmptyLists(CRef & deflines, bool owner) { CBlast_def_line_set * bdls = 0; CConstRef here(&*deflines); if (! owner) { here = s_EditDeflineSet(here); return; } bdls = const_cast(here.GetPointer()); NON_CONST_ITERATE(list< CRef< CBlast_def_line > >, iter, bdls->Set()) { CRef defline = *iter; if (defline->CanGetMemberships() && defline->GetMemberships().size() == 0) { defline->ResetMemberships(); } if (defline->CanGetLinks() && defline->GetLinks().size() == 0) { defline->ResetLinks(); } } deflines.Reset(bdls); } void CWriteDB_Volume:: x_SetDeflinesFromBinary(const string & bin_hdr, CConstRef & deflines) { CRef bdls(new CBlast_def_line_set); istringstream iss(bin_hdr); iss >> MSerial_AsnBinary >> *bdls; s_CheckEmptyLists(bdls, true); deflines.Reset(&* bdls); } void CWriteDB_Volume::x_ExtractDeflines(CConstRef & deflines, string & bin_hdr, int OID) { if (OID>=0) { // Re-inject the BL_ORD_ID CRef gnl_id(new CSeq_id); gnl_id->SetGeneral().SetDb("BL_ORD_ID"); gnl_id->SetGeneral().SetTag().SetId(OID); CRef bdls = s_EditDeflineSet(deflines); bdls->Set().front()->SetSeqid().front() = gnl_id; deflines.Reset(&* bdls); } if (bin_hdr.empty() || OID>=0) { // Compress the deflines to binary. ostringstream oss; oss << MSerial_AsnBinary << *deflines; bin_hdr = oss.str(); } } /* ********** FINISH ************* */ /* *********** START ************* */ bool CWriteDB_Volume::WriteSequenceSort(const string & seq, const string & ambig, const string & binhdr, const TIdList & idlist, int pig, int hash, const TBlobList & blobs, int maskcol_id, bool last_sequence) { // Zero is a legal hash value, but we should not be computing the // hash value if there is no corresponding ISAM file. _ASSERT((! hash) || m_HashIsam.NotEmpty()); if (! (seq.size() && binhdr.size())) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Cannot find CBioseq or deflines."); } _ASSERT(m_Open); int length = (m_Protein ? (int) seq.size() : x_FindNuclLength(seq)); bool overfull = false; /* *********** START ************* */ if( 0 == m_OID ){ m_HdrDataSizeInitial = m_Hdr->GetDataSize(); m_IdxDataSizeInitial = m_Idx->GetDataSize(); m_SeqOffsetInitial = m_Seq->GetOffset(); m_SeqLettersInitial = m_Seq->GetLetters(); } /* ********** FINISH ************* */ if (! (m_Idx->CanFit() && m_Hdr->CanFit((int)binhdr.size()) && m_Seq->CanFit((int)(seq.size() + ambig.size()), length))) { overfull = true; } if (m_Indices != CWriteDB::eNoIndex) { int num = (int)idlist.size(); if (! (m_AccIsam->CanFit(num) && m_GiIsam->CanFit(num) && (m_TraceIsam.Empty() || m_TraceIsam->CanFit(num)))) { overfull = true; } if (m_Protein && (! m_PigIsam->CanFit(1))) { overfull = true; } if (m_HashIsam.NotEmpty() && (! m_HashIsam->CanFit(1))) { overfull = true; } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) for(int blob_i = 0; blob_i < (int) blobs.size(); blob_i++) { _ASSERT(blob_i / 2 < (int) m_Columns.size()); if (! m_Columns[blob_i / 2]->CanFit(blobs[blob_i]->Size())) { overfull = true; break; } } #endif /* *********** START ************* */ //push the last sequence in the vector if( last_sequence ){ bioseq_class bioseq_temp(seq, binhdr, length);// = new bioseq_class; bioseq_temp.seq = seq; bioseq_temp.binhdr = binhdr; bioseq_temp.length = length; bioseq_vector.push_back(bioseq_temp); m_OID++; } /* ********** FINISH ************* */ // Exception - if volume has no data, ignore the file size limits; // otherwise there would be either a hard failure or an infinite // recursion of building empty volumes. Building a volume that's // too big is considered preferable to either of these outcomes. // i.e., if m_OID == 0 (which means it is the first sequences of // this volume) the sequence will be written in the volume // regardless if the volume size is larger than the maximum allowed //if (m_OID && overfull) { // return false; //} // check the uniqueness of id if (m_Indices != CWriteDB::eNoIndex) { ITERATE(TIdList, iter, idlist) { string id = (*iter)->AsFastaString(); string id_u = NStr::ToUpper(id); if (m_IdSet.find(id_u) != m_IdSet.end() ) { CNcbiOstrstream msg; msg << "Error: Duplicate seq_ids are found: " << endl << id_u << endl; NCBI_THROW(CWriteDBException, eArgErr, CNcbiOstrstreamToString(msg)); } m_IdSet.insert(id_u); } } // int off_hdr(0), off_seq(0), off_amb(0); if ( m_OID && (overfull || last_sequence) ){ cout << "Sorting " << bioseq_vector.size() << " sequences" << endl; sort(bioseq_vector.begin(), bioseq_vector.end(), compare); cout << "Writing to Volume" << endl; /* * Reset letters, datasize etc * */ m_Hdr->SetDataSize(m_HdrDataSizeInitial); m_Seq->SetOffset(m_SeqOffsetInitial); m_Seq->SetLetters(m_SeqLettersInitial); m_OID = 0; while(!bioseq_vector.empty()) { bioseq_class bioseq_temp = bioseq_vector.back(); bioseq_vector.pop_back(); string & seq_temp = bioseq_temp.seq;//.GetSequence(); string & binhdr_temp = bioseq_temp.binhdr;//.GetHeader(); int length_temp = bioseq_temp.length;//.GetLength(); //The field in the header that declares the position of the sequences in the volume //has to change since the sequences have changer position after the sorting CConstRef deflines; x_SetDeflinesFromBinary(binhdr_temp, deflines); x_ExtractDeflines(deflines, binhdr_temp, m_OID); int off_hdr(0), off_seq(0), off_amb(0); m_Hdr->AddSequence(binhdr_temp, off_hdr); if (m_Protein) { m_Seq->AddSequence(seq_temp, off_seq, length_temp); m_Idx->AddSequence((int) seq_temp.size(), off_hdr, off_seq); } else { m_Seq->AddSequence(seq_temp, ambig, off_seq, off_amb, length_temp); m_Idx->AddSequence(length_temp, off_hdr, off_seq, off_amb); } if (m_Indices != CWriteDB::eNoIndex) { m_AccIsam->AddIds(m_OID, idlist); m_GiIsam->AddIds(m_OID, idlist); Int4 gi = -1; ITERATE(TIdList, iter, idlist) { const CSeq_id & seqid = **iter; if (seqid.IsGi()) { gi = seqid.GetGi(); break; } } m_GiIndex->AddGi(gi); if (m_Protein && pig) { m_PigIsam->AddPig(m_OID, pig); } if (m_TraceIsam.NotEmpty()) { m_TraceIsam->AddIds(m_OID, idlist); } if (m_HashIsam.NotEmpty()) { m_HashIsam->AddHash(m_OID, hash); } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) for(int col_i = 0; col_i < (int)m_Columns.size(); col_i++) { _ASSERT(col_i * 2 < (int) blobs.size()); if (col_i == maskcol_id) { m_Columns[col_i]->AddBlob(*blobs[col_i * 2], *blobs[col_i * 2 + 1]); } else { m_Columns[col_i]->AddBlob(*blobs[col_i * 2]); } } #endif m_OID ++; }//while cout << "Done Writing to Database" << endl; if( last_sequence )//return true to avoid the creation new volume return true; else // returne false to close this volume and create a new one return false; } else { bioseq_class bioseq_temp(seq, binhdr, length);// = new bioseq_class; bioseq_temp.seq = seq; bioseq_temp.binhdr = binhdr; bioseq_temp.length = length; bioseq_vector.push_back(bioseq_temp); m_Hdr->UpdateSize(binhdr); m_Seq->UpdateSize(seq, length); m_OID ++; }//else /* ********** FINISH ************* */ return true; } /* ********** FINISH ************* */ bool CWriteDB_Volume::WriteSequence(const string & seq, const string & ambig, const string & binhdr, const TIdList & idlist, int pig, int hash, const TBlobList & blobs, int maskcol_id) { // Zero is a legal hash value, but we should not be computing the // hash value if there is no corresponding ISAM file. _ASSERT((! hash) || m_HashIsam.NotEmpty()); if (! (seq.size() && binhdr.size())) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Cannot find CBioseq or deflines."); } _ASSERT(m_Open); int length = (m_Protein ? (int) seq.size() : x_FindNuclLength(seq)); bool overfull = false; if (! (m_Idx->CanFit() && m_Hdr->CanFit((int)binhdr.size()) && m_Seq->CanFit((int)(seq.size() + ambig.size()), length))) { overfull = true; } if (m_Indices != CWriteDB::eNoIndex) { int num = (int)idlist.size(); if (! (m_AccIsam->CanFit(num) && m_GiIsam->CanFit(num) && (m_TraceIsam.Empty() || m_TraceIsam->CanFit(num)))) { overfull = true; } if (m_Protein && (! m_PigIsam->CanFit(1))) { overfull = true; } if (m_HashIsam.NotEmpty() && (! m_HashIsam->CanFit(1))) { overfull = true; } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) for(int blob_i = 0; blob_i < (int) blobs.size(); blob_i++) { _ASSERT(blob_i / 2 < (int) m_Columns.size()); if (! m_Columns[blob_i / 2]->CanFit(blobs[blob_i]->Size())) { overfull = true; break; } } #endif // Exception - if volume has no data, ignore the file size limits; // otherwise there would be either a hard failure or an infinite // recursion of building empty volumes. Building a volume that's // too big is considered preferable to either of these outcomes. if (m_OID && overfull) { return false; } // check the uniqueness of id if (m_Indices != CWriteDB::eNoIndex) { ITERATE(TIdList, iter, idlist) { string id = (*iter)->AsFastaString(); string id_u = NStr::ToUpper(id); if (m_IdSet.find(id_u) != m_IdSet.end() ) { CNcbiOstrstream msg; msg << "Error: Duplicate seq_ids are found: " << endl << id_u << endl; NCBI_THROW(CWriteDBException, eArgErr, CNcbiOstrstreamToString(msg)); } m_IdSet.insert(id_u); } } int off_hdr(0), off_seq(0), off_amb(0); m_Hdr->AddSequence(binhdr, off_hdr); if (m_Protein) { m_Seq->AddSequence(seq, off_seq, length); m_Idx->AddSequence((int) seq.size(), off_hdr, off_seq); } else { m_Seq->AddSequence(seq, ambig, off_seq, off_amb, length); m_Idx->AddSequence(length, off_hdr, off_seq, off_amb); } if (m_Indices != CWriteDB::eNoIndex) { m_AccIsam->AddIds(m_OID, idlist); m_GiIsam->AddIds(m_OID, idlist); Int4 gi = -1; ITERATE(TIdList, iter, idlist) { const CSeq_id & seqid = **iter; if (seqid.IsGi()) { gi = seqid.GetGi(); break; } } m_GiIndex->AddGi(gi); if (m_Protein && pig) { m_PigIsam->AddPig(m_OID, pig); } if (m_TraceIsam.NotEmpty()) { m_TraceIsam->AddIds(m_OID, idlist); } if (m_HashIsam.NotEmpty()) { m_HashIsam->AddHash(m_OID, hash); } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) for(int col_i = 0; col_i < (int)m_Columns.size(); col_i++) { _ASSERT(col_i * 2 < (int) blobs.size()); if (col_i == maskcol_id) { m_Columns[col_i]->AddBlob(*blobs[col_i * 2], *blobs[col_i * 2 + 1]); } else { m_Columns[col_i]->AddBlob(*blobs[col_i * 2]); } } #endif m_OID ++; return true; } int CWriteDB_Volume::x_FindNuclLength(const string & seq) { _ASSERT(! m_Protein); _ASSERT(seq.size()); return WriteDB_FindSequenceLength(m_Protein, seq); } void CWriteDB_Volume::Close() { if (m_Open) { m_Open = false; // close each file. m_Idx->Close(); m_Hdr->Close(); m_Seq->Close(); if (m_Indices != CWriteDB::eNoIndex) { if (m_Protein) { m_PigIsam->Close(); } m_GiIsam->Close(); m_AccIsam->Close(); m_GiIndex->Close(); if (m_TraceIsam.NotEmpty()) { m_TraceIsam->Close(); } if (m_HashIsam.NotEmpty()) { m_HashIsam->Close(); } m_IdSet.clear(); } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) NON_CONST_ITERATE(vector< CRef >, iter, m_Columns) { (**iter).Close(); } #endif } void CWriteDB_Volume::RenameSingle() { _ASSERT(! m_Open); m_VolName = m_DbName; // rename all files to 'single volume' notation. m_Idx->RenameSingle(); m_Hdr->RenameSingle(); m_Seq->RenameSingle(); if (m_Indices != CWriteDB::eNoIndex) { if (m_Protein) { m_PigIsam->RenameSingle(); } m_GiIsam->RenameSingle(); m_AccIsam->RenameSingle(); m_GiIndex->RenameSingle(); if (m_TraceIsam.NotEmpty()) { m_TraceIsam->RenameSingle(); } if (m_HashIsam.NotEmpty()) { m_HashIsam->RenameSingle(); } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) NON_CONST_ITERATE(vector< CRef >, iter, m_Columns) { (**iter).RenameSingle(); } #endif } void CWriteDB_Volume::ListFiles(vector & files) const { files.push_back(m_Idx->GetFilename()); files.push_back(m_Hdr->GetFilename()); files.push_back(m_Seq->GetFilename()); if (m_AccIsam.NotEmpty()) { m_AccIsam->ListFiles(files); } if (m_GiIsam.NotEmpty()) { m_GiIsam->ListFiles(files); } if (m_PigIsam.NotEmpty()) { m_PigIsam->ListFiles(files); } if (m_TraceIsam.NotEmpty()) { m_TraceIsam->ListFiles(files); } if (m_HashIsam.NotEmpty()) { m_HashIsam->ListFiles(files); } if (m_GiIndex.NotEmpty()) { files.push_back(m_GiIndex->GetFilename()); } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) ITERATE(vector< CRef >, iter, m_Columns) { (**iter).ListFiles(files, true); } #endif } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) int CWriteDB_Volume::CreateColumn(const string & title, const TColumnMeta & meta, bool mbo) { int col_id = m_Columns.size(); string extn(m_Protein ? "p??" : "n??"); if (col_id >= 36) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Cannot have more than 36 columns."); } extn[1] = "abcdefghijklmnopqrstuvwxyz0123456789"[col_id]; string extn2 = extn; string extn3 = extn; extn[2] = 'a'; extn2[2] = 'b'; extn3[2] = 'c'; CRef new_col (new CWriteDB_Column(m_DbName, extn, extn2, m_Index, title, meta, m_MaxFileSize)); /* For support of multiple byte orders */ if (mbo) new_col->AddByteOrder(m_DbName, extn3, m_Index, m_MaxFileSize); // If the OID is not zero, then add all the blank records for the // prior OIDs to the new column. CBlastDbBlob blank; for(int j = 0; j < m_OID; j++) { if (mbo) new_col->AddBlob(blank, blank); else new_col->AddBlob(blank); } m_Columns.push_back(new_col); return col_id; } void CWriteDB_Volume::AddColumnMetaData(int col_id, const string & key, const string & value) { if ((col_id < 0) || (col_id >= (int) m_Columns.size())) { NCBI_THROW(CWriteDBException, eArgErr, "Error: provided column ID is not valid"); } m_Columns[col_id]->AddMetaData(key, value); } #endif END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb_impl.hpp0000644000175000017500000006243212001215336023760 0ustar ykeyke#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_IMPL_HPP #define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_IMPL_HPP /* $Id: writedb_impl.hpp 176293 2009-11-17 15:41:30Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb_impl.hpp /// Defines implementation class of WriteDB. /// /// Defines classes: /// CWriteDBHeader /// /// Implemented for: UNIX, MS-Windows #include #include #include #include #include #include "writedb_volume.hpp" #include "writedb_gimask.hpp" #include "mask_info_registry.hpp" #include #include BEGIN_NCBI_SCOPE /// Import definitions from the objects namespace. USING_SCOPE(objects); /// CWriteDB_Impl class /// /// This manufactures blast database header files from input data. class CWriteDB_Impl { public: /// Whether and what kind of indices to build. typedef CWriteDB::EIndexType EIndexType; // Setup and control /// Constructor. /// @param dbname Name of the database to create. /// @param protein True for protein, false for nucleotide. /// @param title Title string for volumes and alias file. /// @param indices Type of indexing to do for string IDs. /// @param parse_ids If true generate ISAM files /// @param use_gi_mask If true generate GI-based mask files. CWriteDB_Impl(const string & dbname, bool protein, const string & title, EIndexType indices, bool parse_ids, bool use_gi_mask, /* *********** START ************* */ bool sort_sequences); /* ********** FINISH ************* */ /// Destructor. ~CWriteDB_Impl(); /// Close the file and flush any remaining data to disk. void Close(); // Sequence Data /// Add a new sequence as raw sequence and ambiguity data. /// /// A new sequence record is started, and data from any previous /// sequence is combined and written to disk. Each sequence needs /// sequence data and header data. This method takes sequence /// data in the form of seperated sequence data and compressed /// ambiguities packed in the blast database disk format. It is /// intended for efficiently copying sequences from sources that /// provide this format, such as CSeqDBExpert(). If this method /// is used for protein data, the ambiguities string should be /// empty. If this method is used, header data must also be /// specified with a call to SetDeflines(). /// /// @param sequence Sequence data in blast db disk format. /// @param ambiguities Ambiguity data in blast db disk format. void AddSequence(const CTempString & sequence, const CTempString & ambiguities); /// Add a new sequence as a CBioseq. /// /// A new sequence record is started, and data from any previous /// sequence is combined and written to disk. Each sequence needs /// sequence data and header data. This method can extract both /// from the provided CBioseq. If other header data is preferred, /// SetDeflines() can be called after this method to replace the /// header data from the CBioseq. Note that CBioseqs from some /// sources are not guaranteed to contain sequence data; if this /// might be the case, consider the versions of AddSequence that /// take either CBioseq_Handle or CBioseq and CSeqVector. In /// order to use this method, sequence data should be accessible /// from bs.GetInst().GetSeq_data(). (Note: objects provided to /// WriteDB will be kept alive until the next AddSequence call.) /// /// @param bs Bioseq containing sequence and header data. void AddSequence(const CBioseq & bs); /// Add a new sequence as a CBioseq_Handle. /// /// A new sequence record is started, and data from any previous /// sequence is combined and written to disk. Each sequence needs /// sequence data and header data. This method can extract both /// from the provided CBioseq_Handle. If other header data is /// preferred, SetDeflines() can be called after this method to /// replace the header data from the CBioseq. (Note: objects /// provided to WriteDB will be kept alive until the next /// AddSequence call.) /// /// @param bsh Bioseq_Handle for sequence to add. void AddSequence(const CBioseq_Handle & bsh); /// Add a new sequence as a CBioseq_Handle. /// /// A new sequence record is started, and data from any previous /// sequence is combined and written to disk. Each sequence needs /// sequence data and header data. This method will extract /// header data from the provided CBioseq. If the CBioseq /// contains sequence data, it will be used; otherwise sequence /// data will be fetched from the provided CSeqVector. If other /// header data is preferred, SetDeflines() can be called after /// this method. (Note: objects provided to WriteDB will be kept /// alive until the next AddSequence call.) /// /// @param bs Bioseq_Handle for header and sequence data. /// @param sv CSeqVector for sequence data. void AddSequence(const CBioseq & bs, CSeqVector & sv); /// This method replaces any stored header data for the current /// sequence with the provided CBlast_def_line_set. Header data /// can be constructed directly by the caller, or extracted from /// an existing CBioseq using ExtractBioseqDeflines (see below). /// Once it is in the correct form, it can be attached to the /// sequence with this method. (Note: objects provided to WriteDB /// will be kept alive until the next AddSequence call.) /// /// @param deflines Header data for the most recent sequence. void SetDeflines(const CBlast_def_line_set & deflines); /// Set the PIG identifier of this sequence. /// /// For protein sequences, this sets the PIG identifier. PIG ids /// are per-sequence, so it will only be attached to the first /// defline in the set. /// /// @param pig PIG identifier as an integer. void SetPig(int pig); // Options /// Set the maximum size for any file in the database. /// /// This method sets the maximum size for any file in a database /// volume. If adding a sequence would cause any file in the /// generated database to exceed this size, the current volume is /// ended and a new volume is started. This is not a strict /// limit, inasmuch as it always puts at least one sequence in /// each volume regardless of that sequence's size. /// /// @param sz Maximum file size (in bytes). void SetMaxFileSize(Uint8 sz); /// Set the maximum letters in one volume. /// /// This method sets the maximum number of sequence letters per /// database volume. If adding a sequence would cause the volume /// to have more than this many letters, the current volume is /// ended and a new volume is started. This is not a strict /// limit, inasmuch as it always puts at least one sequence in /// each volume regardless of that sequence's size. /// /// @param sz Maximum sequence letters per volume. void SetMaxVolumeLetters(Uint8 sz); /// Extract deflines from a CBioseq. /// /// Given a CBioseq, this method extracts and returns header info /// as a defline set. The deflines will not be applied to the /// current sequence unless passed to SetDeflines. The expected /// use of this method is in cases where the caller has a CBioseq /// or CBioseq_Handle but wishes to examine and/or change the /// deflines before passing them to CWriteDB. Some elements of /// the CBioseq may be shared by the returned defline set, notably /// the Seq-ids. /// /// @param bs Bioseq from which to construct the defline set. /// @param parse_ids If we should parse seq_ids. /// @return The blast defline set. static CRef ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids); /// Set bases that should not be used in sequences. /// /// This method specifies nucelotide or protein bases that should /// not be used in the resulting database. The bases in question /// will be replaced with N (for nucleotide) or X (for protein). /// The input data is expected to be specified in the appropriate /// 'alphabetic' encoding (either IUPACAA and IUPACNA). /// /// @param masked void SetMaskedLetters(const string & masked); /// List Volumes /// /// Returns the base names of all volumes constructed by this /// class; the returned list may not be complete until Close() has /// been called. /// /// @param vols /// The set of volumes produced by this class. void ListVolumes(vector & vols); /// List Filenames /// /// Returns a list of the files constructed by this class; the /// returned list may not be complete until Close() has been /// called. /// /// @param files /// The set of resolved database path names. void ListFiles(vector & files); /// Register a type of filtering data found in this database. /// /// The BlastDb format supports storage of masking data (lists of /// masked ranges) for each database sequence, as well as an /// indication of the source (or sources) of this masking data (e.g.: /// masking algorithm used to create them). /// This method stores a description of one of these masking data /// sources in this database, including which basic algorithm was /// used, as well as the options passed to that algorithm. Each /// description is associated with a numeric `algorithm id' (return value /// of this method), which identifies that data source when adding data /// with SetMaskData. /// /// @return algorithm ID for the filtering data. /// @param program Program used to produce this masking data. [in] /// @param options Algorithm options provided to the program. [in] /// @param name Name of a GI-based mask [in] int RegisterMaskAlgorithm(EBlast_filter_program program, const string & options, const string & name = ""); /// Set filtering data for a sequence. /// /// This method specifies filtered regions for the sequence. Each /// sequence can have filtering data from various algorithms. /// /// @param ranges Filtered ranges for this sequence and algorithm. /// @param gis The GIs associated with this sequence void SetMaskData(const CMaskedRangesVector & ranges, const vector & gis); /// Set up a generic CWriteDB metadata column. /// /// This method creates a column with the specified name (title). /// The name must be unique among names provided to this database. /// An integer column descriptor is returned, which must be used /// to identify this column when applying blob data. This call /// will fail with an exception if too many user defined columns /// have already been created for this database (this limit is due /// to BlastDb file naming conventions). The title identifies /// this column and is also used to access the column with SeqDB. /// /// @param title Name identifying this column. /// @return Column identifier (a positive integer). int CreateColumn(const string & title, bool mbo=false); /// Find an existing column. /// /// This looks for an existing column with the specified title and /// returns the column ID if found. /// /// @param title The column title to look for. /// @return The column ID if this column title is already defined. int FindColumn(const string & title) const; /// Add meta data to a column. /// /// In addition to normal blob data, database columns can store a /// `dictionary' of user-defined metadata in key/value form. This /// method adds one such key/value pair to the column. Specifying /// a key a second time causes replacement of the previous value. /// Using this mechanism to store large amounts of data may have a /// negative impact on performance. /// /// @param col_id Specifies the column to add this metadata to. /// @param key A unique key string. /// @param value A value string. void AddColumnMetaData(int col_id, const string & key, const string & value); /// Get a blob to use for a given column letter. /// /// To add data for a `blob' type column, this method should be /// called to get a reference to a CBlastDbBlob object. Add the /// user-defined blob data to this object. It is not correct to /// call this more than once for the same sequence and column. /// Reading, writing, or otherwise using this object after the /// current sequence is published is an error and has undefined /// consequences. ('Publishing' of a sequence usually occurs /// during the following AddSequence(*) call or during Close().) /// /// @param col_id Indicates the column receiving the blob data. /// @return The user data should be stored in this blob. CBlastDbBlob & SetBlobData(int col_id); private: // Configuration string m_Dbname; ///< Database base name. bool m_Protein; ///< True if DB is protein. string m_Title; ///< Title field of database. string m_Date; ///< Time stamp (for all volumes.) Uint8 m_MaxFileSize; ///< Maximum size of any file. Uint8 m_MaxVolumeLetters; ///< Max letters per volume. EIndexType m_Indices; ///< Indexing mode. bool m_Closed; ///< True if database has been closed. string m_MaskedLetters; ///< Masked protein letters (IUPAC). string m_MaskByte; ///< Byte that replaced masked letters. vector m_MaskLookup; ///< Is (blast-aa) byte masked? int m_MaskDataColumn; ///< Column ID for masking data column. map m_MaskAlgoMap; ///< Mapping from algo_id to gi-mask id bool m_ParseIDs; ///< Generate ISAM files bool m_UseGiMask; ///< Generate GI-based mask files /* *********** START ************* */ bool m_LastSequence; bool m_SortSequences; /* ********** FINISH ************* */ /// Column titles. vector m_ColumnTitles; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Per-column metadata. typedef CWriteDB_Column::TColumnMeta TColumnMeta; /// Meta data for all columns. vector< TColumnMeta > m_ColumnMetas; /// Gi-based masks vector< CRef > m_GiMasks; #endif // Functions /// Flush accumulated sequence data to volume. void x_Publish(); /// Compute name of alias file produced. string x_MakeAliasName(); /// Flush accumulated sequence data to volume. void x_MakeAlias(); /// Clear sequence data from last sequence. void x_ResetSequenceData(); /// Convert and compute final data formats. void x_CookData(); /// Convert header data into usable forms. void x_CookHeader(); /// Collect ids for ISAM files. void x_CookIds(); /// Compute the length of the current sequence. int x_ComputeSeqLength(); /// Convert sequence data into usable forms. void x_CookSequence(); /// Prepare column data to be appended to disk. void x_CookColumns(); /// Replace masked input letters with m_MaskByte value. void x_MaskSequence(); /// Get binary version of deflines from 'user' data in Bioseq. /// /// Some CBioseq objects (e.g. those from CSeqDB) have an ASN.1 /// octet array containing a binary ASN.1 version of the blast /// defline set for the sequence. This method looks for that data /// and returns it if found. If not found, it returns an empty /// string. /// /// @param bioseq Bioseq from which to fetch header. [in] /// @param binhdr Header data as binary ASN.1. [out] static void x_GetBioseqBinaryHeader(const CBioseq & bioseq, string & binhdr); /// Construct deflines from a CBioseq and other meta-data. /// /// This method builds deflines from various data found in the /// Bioseq, along with other meta data (like the PIG and /// membership and linkout lists.) /// /// @param bioseq Defline data will be built from this. [in] /// @param deflines A defline set will be returned here. [out] /// @param membits Membership bits for each defline. [in] /// @param linkout Linkout bits for each defline. [in] /// @param pig PIG to attach to a protein sequence. [in] static void x_BuildDeflinesFromBioseq(const CBioseq & bioseq, CConstRef & deflines, const vector< vector > & membits, const vector< vector > & linkout, int pig); /// Extract a defline set from a binary ASN.1 blob. /// @param bin_hdr Binary ASN.1 encoding of defline set. [in] /// @param deflines Defline set. [out] static void x_SetDeflinesFromBinary(const string & bin_hdr, CConstRef & deflines); /// Extract a defline set from a CFastaReader generated CBioseq. /// /// CBioseq objects produced by CFastaReader have an internal /// 'user' field that contains the original FASTA, which can be /// used to build blast deflines. If the original FASTA deflines /// were delimited with control-A characters, then those will be /// found here too. If the caller wishes to accept '>' as an /// alternate delimiter, then accept_gt should be specified. /// /// @param bioseq Bioseq object produced by CFastaReader. [in] /// @param deflines Defline set. [out] /// @param membits Membership bits for each defline. [in] /// @param linkout Linkout bits for each defline. [in] /// @param pig PIG to attach to a protein sequence. [in] /// @param accept_gt Whether greater-than is a delimiter. [in] /// @param parse_ids Whether seq_id should not be parsed. [in] static void x_GetFastaReaderDeflines(const CBioseq & bioseq, CConstRef & deflines, const vector< vector > & membits, const vector< vector > & linkout, int pig, bool accept_gt, bool parse_ids); /// Returns true if we have unwritten sequence data. bool x_HaveSequence() const; /// Records that we now have unwritten sequence data. void x_SetHaveSequence(); /// Records that we no longer have unwritten sequence data. void x_ClearHaveSequence(); /// Get deflines from a CBioseq and other meta-data. /// /// This method extracts binary ASN.1 deflines from a CBioseq if /// possible, and otherwise builds deflines from various data /// found in the Bioseq, along with other meta data (like the PIG /// and membership and linkout lists.) It returns the result as /// a blast defline set. If a binary version of the headers is /// computed during this method, it will be returned in bin_hdr. /// /// @param bioseq Defline data will be built from this. [in] /// @param deflines A defline set will be returned here. [out] /// @param bin_hdr Binary header data may be returned here. [out] /// @param membbits Membership bits for each defline. [in] /// @param linkouts Linkout bits for each defline. [in] /// @param pig PIG to attach to a protein sequence. [in] /// @param OID the current OID for local id. [in] /// @param parse_ids whether we should not parse id. [in] static void x_ExtractDeflines(CConstRef & bioseq, CConstRef & deflines, string & bin_hdr, const vector< vector > & membbits, const vector< vector > & linkouts, int pig, int OID=-1, bool parse_ids=true); /// Compute the hash of a (raw) sequence. /// /// The hash of the provided sequence will be computed and /// assigned to the m_Hash member. The sequence and optional /// ambiguities are 'raw', meaning they are packed just as /// sequences are packed in nsq and psq files. /// /// @param sequence The sequence data. [in] /// @param ambiguities Nucleotide ambiguities are provided here. [in] void x_ComputeHash(const CTempString & sequence, const CTempString & ambiguities); /// Compute the hash of a (Bioseq) sequence. /// /// The hash of the provided sequence will be computed and /// assigned to the m_Hash member. The sequence is packed as a /// CBioseq. /// /// @param sequence The sequence as a CBioseq. [in] void x_ComputeHash(const CBioseq & sequence); /// Get the mask data column id. /// /// The mask data column is created if it does not exist, and its /// column ID number is returned. /// /// @return The column ID for the mask data column. int x_GetMaskDataColumnId(); // // Accumulated sequence data. // /// Bioseq object for next sequence to write. CConstRef m_Bioseq; /// SeqVector for next sequence to write. CSeqVector m_SeqVector; /// Deflines to write as header. CConstRef m_Deflines; /// Ids for next sequence to write, for use during ISAM construction. vector< CRef > m_Ids; /// Linkout bits - outer vector is per-defline, inner is bits. vector< vector > m_Linkouts; /// Membership bits - outer vector is per-defline, inner is bits. vector< vector > m_Memberships; /// PIG to attach to headers for protein sequences. int m_Pig; /// Sequence hash for this sequence. int m_Hash; /// When a sequence is added, this will be populated with the length of that sequence. int m_SeqLength; /// True if we have a sequence to write. bool m_HaveSequence; // Cooked /// Sequence data in format that will be written to disk. string m_Sequence; /// Ambiguities in format that will be written to disk. string m_Ambig; /// Binary header in format that will be written to disk. string m_BinHdr; // Volumes /// This volume is currently accepting sequences. CRef m_Volume; /// List of all volumes so far, up to and including m_Volume. vector< CRef > m_VolumeList; /// Blob data for the current sequence, indexed by letter. vector< CRef > m_Blobs; /// List of blob columns that are active for this sequence. vector m_HaveBlob; /// Registry for masking algorithms in this database. CMaskInfoRegistry m_MaskAlgoRegistry; }; END_NCBI_SCOPE #endif // OBJTOOLS_WRITERS_WRITEDB__WRITEDB_IMPL_HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb_impl.cpp0000644000175000017500000015615212001215336023756 0ustar ykeyke/* $Id: writedb_impl.cpp 205085 2010-09-14 19:12:29Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb_impl.cpp /// Implementation for the CWriteDB_Impl class. /// class for WriteDB. #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: writedb_impl.cpp 205085 2010-09-14 19:12:29Z maning $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include #include #include #include #include #include #include // for kAsnDeflineObjLabel #include #include #include "writedb_impl.hpp" #include #include #include BEGIN_NCBI_SCOPE /// Import C++ std namespace. USING_SCOPE(std); CWriteDB_Impl::CWriteDB_Impl(const string & dbname, bool protein, const string & title, EIndexType indices, bool parse_ids, bool use_gi_mask, /* *********** START ************* */ bool sort_sequences) /* ********** FINISH ************* */ : m_Dbname (dbname), m_Protein (protein), m_Title (title), m_MaxFileSize (0), m_MaxVolumeLetters (0), m_Indices (indices), m_Closed (false), m_MaskDataColumn (-1), m_ParseIDs (parse_ids), m_UseGiMask (use_gi_mask), m_Pig (0), m_Hash (0), m_SeqLength (0), m_HaveSequence (false), /* *********** START ************* */ m_LastSequence (false), m_SortSequences (sort_sequences) /* ********** FINISH ************* */ { CTime now(CTime::eCurrent); m_Date = now.AsString("b d, Y "); string t = now.AsString("H:m P"); if (t[0] == '0') { t.assign(t, 1, t.size() - 1); } m_Date += t; } CWriteDB_Impl::~CWriteDB_Impl() { Close(); } void CWriteDB_Impl::x_ResetSequenceData() { m_Bioseq.Reset(); m_SeqVector = CSeqVector(); m_Deflines.Reset(); m_Ids.clear(); m_Linkouts.clear(); m_Memberships.clear(); m_Pig = 0; m_Hash = 0; m_SeqLength = 0; m_Sequence.erase(); m_Ambig.erase(); m_BinHdr.erase(); NON_CONST_ITERATE(vector, iter, m_HaveBlob) { *iter = 0; } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) NON_CONST_ITERATE(vector< CRef >, iter, m_Blobs) { (**iter).Clear(); } #endif } void CWriteDB_Impl::AddSequence(const CTempString & seq, const CTempString & ambig) { // Publish previous sequence (if any) x_Publish(); // Blank slate for new sequence. x_ResetSequenceData(); m_Sequence.assign(seq.data(), seq.length()); m_Ambig.assign(ambig.data(), ambig.length()); if (m_Indices & CWriteDB::eAddHash) { x_ComputeHash(seq, ambig); } x_SetHaveSequence(); } void CWriteDB_Impl::AddSequence(const CBioseq & bs) { // Publish previous sequence x_Publish(); // Blank slate for new sequence. x_ResetSequenceData(); m_Bioseq.Reset(& bs); if (m_Indices & CWriteDB::eAddHash) { x_ComputeHash(bs); } x_SetHaveSequence(); } void CWriteDB_Impl::AddSequence(const CBioseq & bs, CSeqVector & sv) { AddSequence(bs); m_SeqVector = sv; } void CWriteDB_Impl::AddSequence(const CBioseq_Handle & bsh) { CSeqVector sv(bsh); AddSequence(*bsh.GetCompleteBioseq(), sv); } /// class to support searching for duplicate isam keys template class CWriteDB_IsamKey { public: // data member T key; CNcbiIfstream * source; // constructor CWriteDB_IsamKey(const string &fn) { source = new CNcbiIfstream(fn.c_str(), IOS_BASE::in | IOS_BASE::binary); key = x_GetNextKey(); }; ~CWriteDB_IsamKey() { delete source; }; // advance key to catch up other bool AdvanceKey(const CWriteDB_IsamKey & other) { while (!source->eof()) { T next_key = x_GetNextKey(); if (next_key >= other.key) { key = next_key; return true; } } return false; }; // less_than, used for sorting bool operator <(const CWriteDB_IsamKey &other) const { return (key < other.key); }; private: // read in the next key, for numeric id T x_GetNextKey() { #define INT4_SIZE 4 char s[INT4_SIZE] = { '\0' }; source->read(s, INT4_SIZE); if ((source->gcount() != INT4_SIZE) || source->eof()) { return T(); } source->seekg(INT4_SIZE, ios_base::cur); #ifdef WORDS_BIGENDIAN Int4 next_key = (Int4) *((Int4 *) s); #else Int4 next_key = CByteSwap::GetInt4((const unsigned char *)s); #endif return next_key; }; }; // customized string file reading template <> inline string CWriteDB_IsamKey::x_GetNextKey() { #define CHAR_BUFFER_SIZE 256 char s[CHAR_BUFFER_SIZE] = { '\0' }; source->getline(s, CHAR_BUFFER_SIZE); if ((source->gcount() == 0) || source->eof()) { return kEmptyStr; } char * p = s; while (*p != 0x02) ++p; string in(s, p); // check if the current key is PDB-like, // if so, advance for the next // PDB key must be [0-9]... if ( (in.size() == 4) && ((in[0] - '0') * (in[0] - '9') <= 0) ) { // probing the next key to make sure this is pdb id char next_token[4]; source->read(next_token, 4); source->seekg(-4, ios_base::cur); string next_key(next_token, 4); if (next_key == in) { // automatically advance to next key return x_GetNextKey(); } } return in; }; /// Comparison function for set *> template struct CWriteDB_IsamKey_Compare { bool operator() (const CWriteDB_IsamKey * lhs, const CWriteDB_IsamKey * rhs) const { return (*lhs < *rhs); } }; /// Check for duplicate ids across volumes template static void s_CheckDuplicateIds(set *, CWriteDB_IsamKey_Compare > & keys) { while (!keys.empty()) { // pick the smallest key CWriteDB_IsamKey * key = *(keys.begin()); keys.erase(key); if (keys.empty()) { delete key; return; } const CWriteDB_IsamKey * next = *(keys.begin()); if (key->AdvanceKey(*next)) { if (keys.find(key) != keys.end()) { CNcbiOstrstream msg; msg << "Error: Duplicate seq_id <" << key->key << "> is found multiple times across volumes."; NCBI_THROW(CWriteDBException, eArgErr, CNcbiOstrstreamToString(msg)); } keys.insert(key); } else { delete key; } } }; void CWriteDB_Impl::Close() { if (m_Closed) return; m_Closed = true; /* *********** START ************* */ m_LastSequence = true; /* ********** FINISH ************* */ x_Publish(); m_Sequence.erase(); m_Ambig.erase(); if (! m_Volume.Empty()) { m_Volume->Close(); if (m_UseGiMask) { for (unsigned int i=0; iClose(); } } if (m_VolumeList.size() == 1) { m_Volume->RenameSingle(); } // disable the check for duplicate ids across volumes /* else if (m_Indices != CWriteDB::eNoIndex) { set *, CWriteDB_IsamKey_Compare > sids; ITERATE(vector< CRef >, iter, m_VolumeList) { string fn = (*iter)->GetVolumeName() + (m_Protein ? ".psd" : ".nsd"); if (CFile(fn).Exists()) { sids.insert(new CWriteDB_IsamKey(fn)); } } s_CheckDuplicateIds(sids); set *, CWriteDB_IsamKey_Compare > nids; ITERATE(vector< CRef >, iter, m_VolumeList) { string fn = (*iter)->GetVolumeName() + (m_Protein ? ".pnd" : ".nnd"); if (CFile(fn).Exists()) { nids.insert(new CWriteDB_IsamKey(fn)); } } s_CheckDuplicateIds(nids); } */ if (m_VolumeList.size() > 1 || m_UseGiMask) { x_MakeAlias(); } m_Volume.Reset(); } } string CWriteDB_Impl::x_MakeAliasName() { return m_Dbname + (m_Protein ? ".pal" : ".nal"); } void CWriteDB_Impl::x_MakeAlias() { string dblist; if (m_VolumeList.size() > 1) { for(unsigned i = 0; i < m_VolumeList.size(); i++) { if (dblist.size()) dblist += " "; dblist += CWriteDB_File::MakeShortName(m_Dbname, i); } } else { dblist = m_Dbname; } string masklist(""); if (m_UseGiMask) { for (unsigned i = 0; i < m_GiMasks.size(); i++) { const string & x = m_GiMasks[i]->GetName(); if (x != "") { masklist += x + " "; } } } string nm = x_MakeAliasName(); ofstream alias(nm.c_str()); alias << "#\n# Alias file created: " << m_Date << "\n#\n" << "TITLE " << m_Title << "\n" << "DBLIST " << dblist << "\n"; if (masklist != "") { alias << "MASKLIST " << masklist << "\n"; } } void CWriteDB_Impl::x_GetBioseqBinaryHeader(const CBioseq & bioseq, string & bin_hdr) { if (! bin_hdr.empty()) { return; } if (! bioseq.CanGetDescr()) { return; } // Getting the binary headers, when they exist, is probably faster // than building new deflines from the 'visible' CBioseq parts. vector< vector< char >* > bindata; ITERATE(list< CRef< CSeqdesc > >, iter, bioseq.GetDescr().Get()) { if ((**iter).IsUser()) { const CUser_object & uo = (**iter).GetUser(); const CObject_id & oi = uo.GetType(); if (oi.IsStr() && oi.GetStr() == kAsnDeflineObjLabel) { if (uo.CanGetData()) { const vector< CRef< CUser_field > > & D = uo.GetData(); if (D.size() && D[0].NotEmpty() && D[0]->CanGetLabel() && D[0]->GetLabel().IsStr() && D[0]->GetLabel().GetStr() == kAsnDeflineObjLabel && D[0]->CanGetData() && D[0]->GetData().IsOss()) { bindata = D[0]->GetData().GetOss(); break; } } } } } if (! bindata.empty()) { if (bindata[0] && (! bindata[0]->empty())) { vector & b = *bindata[0]; bin_hdr.assign(& b[0], b.size()); } } } static void s_CheckEmptyLists(CRef & deflines, bool owner); static CRef s_EditDeflineSet(CConstRef & deflines) { CRef bdls(new CBlast_def_line_set); SerialAssign(*bdls, *deflines); s_CheckEmptyLists(bdls, true); return bdls; } static void s_CheckEmptyLists(CRef & deflines, bool owner) { CBlast_def_line_set * bdls = 0; CConstRef here(&*deflines); if (! owner) { here = s_EditDeflineSet(here); return; } bdls = const_cast(here.GetPointer()); NON_CONST_ITERATE(list< CRef< CBlast_def_line > >, iter, bdls->Set()) { CRef defline = *iter; if (defline->CanGetMemberships() && defline->GetMemberships().size() == 0) { defline->ResetMemberships(); } if (defline->CanGetLinks() && defline->GetLinks().size() == 0) { defline->ResetLinks(); } } deflines.Reset(bdls); } void CWriteDB_Impl::x_BuildDeflinesFromBioseq(const CBioseq & bioseq, CConstRef & deflines, const vector< vector > & membbits, const vector< vector > & linkouts, int pig) { if (! (bioseq.CanGetDescr() && bioseq.CanGetId())) { return; } vector taxids; string titles; // Scan the CBioseq for taxids and the title string. ITERATE(list< CRef< CSeqdesc > >, iter, bioseq.GetDescr().Get()) { const CSeqdesc & desc = **iter; if (desc.IsTitle()) { //defline->SetTitle((**iter)->GetTitle()); titles = (**iter).GetTitle(); } else if (desc.IsSource()) { if (desc.IsOrg() && desc.GetOrg().CanGetDb()) { ITERATE(vector< CRef< CDbtag > >, dbiter, desc.GetOrg().GetDb()) { if ((**dbiter).CanGetDb() && (**dbiter).GetDb() == "taxon") { const CObject_id & oi = (**dbiter).GetTag(); if (oi.IsId()) { //defline->SetTaxid(oi.GetId()); taxids.push_back(oi.GetId()); } } } } } } // The bioseq has a field contianing the ids for the first // defline. The title string contains the title for the first // defline, plus all the other defline titles and ids. This code // unpacks them and builds a normal blast defline set. list< CRef > ids = bioseq.GetId(); unsigned taxid_i(0), mship_i(0), links_i(0); bool used_pig(false); // Build the deflines. CRef bdls(new CBlast_def_line_set); CRef defline; while(! ids.empty()) { defline.Reset(new CBlast_def_line); defline->SetSeqid() = ids; ids.clear(); size_t pos = titles.find(" >"); string T; if (pos != titles.npos) { T.assign(titles, 0, pos); titles.erase(0, pos + 2); pos = titles.find(" "); string nextid; if (pos != titles.npos) { nextid.assign(titles, 0, pos); titles.erase(0, pos + 1); } else { nextid.swap(titles); } // Parse '|' seperated ids. if ( nextid.find('|') == NPOS || !isalpha((unsigned char)(nextid[0]))) { ids.push_back(CRef (new CSeq_id(CSeq_id::e_Local, nextid))); } else { CSeq_id::ParseFastaIds(ids, nextid); } } else { T = titles; } defline->SetTitle(T); if (taxid_i < taxids.size()) { defline->SetTaxid(taxids[taxid_i++]); } if (mship_i < membbits.size()) { const vector & V = membbits[mship_i++]; defline->SetMemberships().assign(V.begin(), V.end()); } if (links_i < linkouts.size()) { const vector & V = linkouts[mship_i++]; defline->SetLinks().assign(V.begin(), V.end()); } if ((! used_pig) && pig) { defline->SetOther_info().push_back(pig); used_pig = true; } bdls->Set().push_back(defline); } s_CheckEmptyLists(bdls, true); deflines = bdls; } void CWriteDB_Impl:: x_SetDeflinesFromBinary(const string & bin_hdr, CConstRef & deflines) { CRef bdls(new CBlast_def_line_set); istringstream iss(bin_hdr); iss >> MSerial_AsnBinary >> *bdls; s_CheckEmptyLists(bdls, true); deflines.Reset(&* bdls); } void CWriteDB_Impl::x_ExtractDeflines(CConstRef & bioseq, CConstRef & deflines, string & bin_hdr, const vector< vector > & membbits, const vector< vector > & linkouts, int pig, int OID, bool parse_ids) { bool use_bin = (deflines.Empty() && pig == 0); if (! bin_hdr.empty() && OID<0) { return; } if (deflines.Empty()) { // Use bioseq if deflines are not provided. if (bioseq.Empty()) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Cannot find CBioseq or deflines."); } // CBioseq objects from SeqDB have binary headers embedded in // them. If these are found, we try to use them. However, // using binary headers may not help us much if we also want // lists of sequence identifiers (for building ISAM files). if (use_bin) { x_GetBioseqBinaryHeader(*bioseq, bin_hdr); } if (bin_hdr.empty()) { x_GetFastaReaderDeflines(*bioseq, deflines, membbits, linkouts, pig, false, parse_ids); } if (bin_hdr.empty() && deflines.Empty()) { x_BuildDeflinesFromBioseq(*bioseq, deflines, membbits, linkouts, pig); } } if (bin_hdr.empty() && (deflines.Empty() || deflines->Get().empty())) { NCBI_THROW(CWriteDBException, eArgErr, "Error: No deflines provided."); } if (pig != 0) { const list * L = 0; if (deflines->Get().front()->CanGetOther_info()) { L = & deflines->Get().front()->GetOther_info(); } // If the pig does not agree with the current value, set the // new value and force a rebuild of the binary headers. If // there is more than one value in the list, leave the others // in place. if ((L == 0) || L->empty()) { CRef bdls = s_EditDeflineSet(deflines); bdls->Set().front()->SetOther_info().push_back(pig); deflines.Reset(&* bdls); bin_hdr.erase(); } else if (L->front() != pig) { CRef bdls = s_EditDeflineSet(deflines); bdls->Set().front()->SetOther_info().front() = pig; deflines.Reset(&* bdls); bin_hdr.erase(); } } if (OID>=0) { // Re-inject the BL_ORD_ID CRef gnl_id(new CSeq_id); gnl_id->SetGeneral().SetDb("BL_ORD_ID"); gnl_id->SetGeneral().SetTag().SetId(OID); CRef bdls = s_EditDeflineSet(deflines); bdls->Set().front()->SetSeqid().front() = gnl_id; deflines.Reset(&* bdls); } if (bin_hdr.empty() || OID>=0) { // Compress the deflines to binary. ostringstream oss; oss << MSerial_AsnBinary << *deflines; bin_hdr = oss.str(); } if (deflines.Empty() && (! bin_hdr.empty())) { // Uncompress the deflines from binary. x_SetDeflinesFromBinary(bin_hdr, deflines); } } void CWriteDB_Impl::x_CookHeader() { int OID = -1; if (! m_ParseIDs) { OID = (m_Volume ) ? m_Volume->GetOID() : 0; } x_ExtractDeflines(m_Bioseq, m_Deflines, m_BinHdr, m_Memberships, m_Linkouts, m_Pig, OID, m_ParseIDs); } void CWriteDB_Impl::x_CookIds() { if (! m_Ids.empty()) { return; } if (m_Deflines.Empty()) { if (m_BinHdr.empty()) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Cannot find IDs or deflines."); } x_SetDeflinesFromBinary(m_BinHdr, m_Deflines); } ITERATE(list< CRef >, iter, m_Deflines->Get()) { const list< CRef > & ids = (**iter).GetSeqid(); // m_Ids.insert(m_Ids.end(), ids.begin(), ids.end()); // Spelled out for WorkShop. :-/ m_Ids.reserve(m_Ids.size() + ids.size()); ITERATE (list >, it, ids) { m_Ids.push_back(*it); } } } void CWriteDB_Impl::x_MaskSequence() { // Scan and mask the sequence itself. for(unsigned i = 0; i < m_Sequence.size(); i++) { if (m_MaskLookup[m_Sequence[i] & 0xFF] != 0) { m_Sequence[i] = m_MaskByte[0]; } } } int CWriteDB_Impl::x_ComputeSeqLength() { if (! m_SeqLength) { if (! m_Sequence.empty()) { m_SeqLength = WriteDB_FindSequenceLength(m_Protein, m_Sequence); } else if (m_SeqVector.size()) { m_SeqLength = m_SeqVector.size(); } else if (! (m_Bioseq && m_Bioseq->CanGetInst() && m_Bioseq->GetInst().GetLength())) { NCBI_THROW(CWriteDBException, eArgErr, "Need sequence data."); } if (m_Bioseq.NotEmpty()) { const CSeq_inst & si = m_Bioseq->GetInst(); m_SeqLength = si.GetLength(); } } return m_SeqLength; } void CWriteDB_Impl::x_CookSequence() { if (! m_Sequence.empty()) return; if (! (m_Bioseq.NotEmpty() && m_Bioseq->CanGetInst())) { NCBI_THROW(CWriteDBException, eArgErr, "Need sequence data."); } const CSeq_inst & si = m_Bioseq->GetInst(); if (m_Bioseq->GetInst().CanGetSeq_data()) { const CSeq_data & sd = si.GetSeq_data(); string msg; switch(sd.Which()) { case CSeq_data::e_Ncbistdaa: WriteDB_StdaaToBinary(si, m_Sequence); break; case CSeq_data::e_Ncbieaa: WriteDB_EaaToBinary(si, m_Sequence); break; case CSeq_data::e_Iupacaa: WriteDB_IupacaaToBinary(si, m_Sequence); break; case CSeq_data::e_Ncbi2na: WriteDB_Ncbi2naToBinary(si, m_Sequence); break; case CSeq_data::e_Ncbi4na: WriteDB_Ncbi4naToBinary(si, m_Sequence, m_Ambig); break; default: msg = "Need to write conversion for data type ["; msg += NStr::IntToString((int) sd.Which()); msg += "]."; } if (! msg.empty()) { NCBI_THROW(CWriteDBException, eArgErr, msg); } } else { int sz = m_SeqVector.size(); if (sz == 0) { NCBI_THROW(CWriteDBException, eArgErr, "No sequence data in Bioseq, " "and no Bioseq_Handle available."); } if (m_Protein) { // I add one to the string length to allow the "i+1" in // the loop to be done safely. m_Sequence.reserve(sz); m_SeqVector.GetSeqData(0, sz, m_Sequence); } else { // I add one to the string length to allow the "i+1" in the // loop to be done safely. string na8; na8.reserve(sz + 1); m_SeqVector.GetSeqData(0, sz, na8); na8.resize(sz + 1); string na4; na4.resize((sz + 1) / 2); for(int i = 0; i < sz; i += 2) { na4[i/2] = (na8[i] << 4) + na8[i+1]; } WriteDB_Ncbi4naToBinary(na4.data(), (int) na4.size(), (int) si.GetLength(), m_Sequence, m_Ambig); } } } void CWriteDB_Impl::x_CookColumns() { } // The CPU should be kept at 190 degrees for 10 minutes. void CWriteDB_Impl::x_CookData() { // We need sequence, ambiguity, and binary deflines. If any of // these is missing, it is created from other data if possible. // For now I am disabling binary headers, because in normal usage // I would expect to see sequences from ID1 or similar, and the // non-binary case is slightly more complex. x_CookHeader(); x_CookIds(); x_CookSequence(); x_CookColumns(); if (m_Protein && m_MaskedLetters.size()) { x_MaskSequence(); } } bool CWriteDB_Impl::x_HaveSequence() const { return m_HaveSequence; } void CWriteDB_Impl::x_SetHaveSequence() { _ASSERT(! m_HaveSequence); m_HaveSequence = true; } void CWriteDB_Impl::x_ClearHaveSequence() { _ASSERT(m_HaveSequence); m_HaveSequence = false; } void CWriteDB_Impl::x_Publish() { // This test should fail only on the first call, or if an // exception was thrown. if (x_HaveSequence()) { _ASSERT(! (m_Bioseq.Empty() && m_Sequence.empty())); x_ClearHaveSequence(); } else { return; } x_CookData(); bool done = false; if (! m_Volume.Empty()) { /* *********** START ************* */ if( m_SortSequences ) { done = m_Volume->WriteSequenceSort(m_Sequence, m_Ambig, m_BinHdr, m_Ids, m_Pig, m_Hash, m_Blobs, m_MaskDataColumn, m_LastSequence); } else { done = m_Volume->WriteSequence(m_Sequence, m_Ambig, m_BinHdr, m_Ids, m_Pig, m_Hash, m_Blobs, m_MaskDataColumn); } /* ********** FINISH ************* */ } if (! done) { int index = (int) m_VolumeList.size(); if (m_Volume.NotEmpty()) { m_Volume->Close(); } { m_Volume.Reset(new CWriteDB_Volume(m_Dbname, m_Protein, m_Title, m_Date, index, m_MaxFileSize, m_MaxVolumeLetters, m_Indices)); m_VolumeList.push_back(m_Volume); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) _ASSERT(m_Blobs.size() == m_ColumnTitles.size() * 2); _ASSERT(m_Blobs.size() == m_ColumnMetas.size() * 2); _ASSERT(m_Blobs.size() == m_HaveBlob.size() * 2); for(size_t i = 0; i < m_ColumnTitles.size(); i++) { m_Volume->CreateColumn(m_ColumnTitles[i], m_ColumnMetas[i]); } #endif } // need to reset OID, hense recalculate the header and id x_CookHeader(); x_CookIds(); /* *********** START ************* */ if( m_SortSequences ) { done = m_Volume->WriteSequenceSort(m_Sequence, m_Ambig, m_BinHdr, m_Ids, m_Pig, m_Hash, m_Blobs, m_MaskDataColumn, m_LastSequence); } else { done = m_Volume->WriteSequence(m_Sequence, m_Ambig, m_BinHdr, m_Ids, m_Pig, m_Hash, m_Blobs, m_MaskDataColumn); } /* ********** FINISH ************* */ if (! done) { NCBI_THROW(CWriteDBException, eArgErr, "Cannot write sequence to volume."); } } } void CWriteDB_Impl::SetDeflines(const CBlast_def_line_set & deflines) { CRef bdls(const_cast(& deflines)); s_CheckEmptyLists(bdls, true); m_Deflines = bdls; } inline int s_AbsMax(int a, int b) { return std::max(((a < 0) ? -a : a), ((b < 0) ? -b : b)); } // Filtering data format on disk: // // Size of integer type for this blob (1, 2, or 4) (4 bytes). // // Array of filtering types: // Filter-type (enumeration) // Array of offsets: // Start Offset // End Offset // // The isize is one of 1, 2, or 4, written in the first byte, and // followed by 0, 1, or 3 NUL bytes to align the data offset to a // multiple of `isize'. // // All other integer values in this array use isize bytes, including // array counts and the `type' enumerations. After all the offset is // written, the blob is aligned to a multiple of 4 using the `eSimple' // method. // // Each array is an element count followed by that many elements. #if 0 // I think this is a better approach; but it needs more testing, // particularly with regard to platform portability. struct SWriteInt1 { static void WriteInt(CBlastDbBlob & blob, int value) { blob.WriteInt1(value); } }; struct SWriteInt2 { static void WriteInt(CBlastDbBlob & blob, int value) { blob.WriteInt2(value); } }; struct SWriteInt4 { static void WriteInt(CBlastDbBlob & blob, int value) { blob.WriteInt4(value); } }; template void s_WriteRanges(CBlastDbBlob & blob, int count, const TRanges & ranges) { typedef vector< pair > TPairVector; Int4 num_written = 0; TWriteSize::WriteInt(blob, count); for ( typename TRanges::const_iterator r1 = (ranges).begin(), r1_end = (ranges).end(); r1 != r1_end; ++r1 ) { if (r1->offsets.size()) { num_written ++; TWriteSize::WriteInt(blob, r1->algorithm_id); TWriteSize::WriteInt(blob, r1->offsets.size()); ITERATE(TPairVector, r2, r1->offsets) { TWriteSize::WriteInt(blob, r2->first); TWriteSize::WriteInt(blob, r2->second); } } } _ASSERT(num_written == count); } #endif #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) void CWriteDB_Impl::SetMaskData(const CMaskedRangesVector & ranges, const vector & gis) { // No GI is found for the sequence // TODO should we generate a warning? if (m_UseGiMask && !gis.size()) { return; } TSeqPos seq_length = x_ComputeSeqLength(); // Check validity of data and determine maximum integer value // stored here before writing anything. The best numeric_size // will be selected; this numeric size is applied uniformly to all // integers in this blob (except for the first one, which is the // integer size itself, and which is always a single byte.) typedef vector< pair > TPairVector; int range_list_count = 0; int offset_pairs_count = 0; ITERATE(CMaskedRangesVector, r1, ranges) { if (r1->empty()) { continue; } range_list_count ++; offset_pairs_count += r1->offsets.size(); if ( !m_MaskAlgoRegistry.IsRegistered(r1->algorithm_id) ) { string msg("Error: Algorithm IDs must be registered before use."); msg += " Unknown algorithm ID = " + NStr::IntToString((int)r1->algorithm_id); NCBI_THROW(CWriteDBException, eArgErr, msg); } ITERATE(TPairVector, r2, r1->offsets) { if ((r2->first > r2->second) || (r2->second > seq_length)) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Masked data offsets out of bounds."); } } } // We may be passed an empty list of ranges, or we might be passed // several ranges whose lists of offsets are themself empty. No // matter what is passed in, we should not emit empty lists and we // should not emit any bytes at all if there are no elements. if (offset_pairs_count == 0) { return; } // Gi-based masks if (m_UseGiMask) { ITERATE(CMaskedRangesVector, r1, ranges) { if (r1->offsets.size()) { m_GiMasks[m_MaskAlgoMap[r1->algorithm_id]] ->AddGiMask(gis, r1->offsets); } } return; } // OID-based masks const int col_id = x_GetMaskDataColumnId(); CBlastDbBlob & blob = SetBlobData(col_id); blob.Clear(); blob.WriteInt4(range_list_count); CBlastDbBlob & blob2 = SetBlobData(col_id); blob2.Clear(); blob2.WriteInt4(range_list_count); ITERATE(CMaskedRangesVector, r1, ranges) { if (r1->offsets.size()) { blob.WriteInt4(r1->algorithm_id); blob.WriteInt4(r1->offsets.size()); blob2.WriteInt4(r1->algorithm_id); blob2.WriteInt4(r1->offsets.size()); ITERATE(TPairVector, r2, r1->offsets) { blob.WriteInt4(r2->first); blob.WriteInt4(r2->second); blob2.WriteInt4_LE(r2->first); blob2.WriteInt4_LE(r2->second); } } } blob.WritePadBytes(4, CBlastDbBlob::eSimple); blob2.WritePadBytes(4, CBlastDbBlob::eSimple); } int CWriteDB_Impl:: RegisterMaskAlgorithm(EBlast_filter_program program, const string & options, const string & name) { int algorithm_id = m_MaskAlgoRegistry.Add(program, options); string key = NStr::IntToString(algorithm_id); string value = NStr::IntToString((int)program) + ":" + options; if (m_UseGiMask) { m_MaskAlgoMap[algorithm_id] = m_GiMasks.size(); m_GiMasks.push_back(CRef (new CWriteDB_GiMask(name, value, m_MaxFileSize))); } else { m_ColumnMetas[x_GetMaskDataColumnId()][key] = value; } return algorithm_id; } int CWriteDB_Impl::FindColumn(const string & title) const { for(int i = 0; i < (int) m_ColumnTitles.size(); i++) { if (title == m_ColumnTitles[i]) { return i; } } return -1; } int CWriteDB_Impl::CreateColumn(const string & title, bool mbo) { _ASSERT(FindColumn(title) == -1); size_t col_id = m_Blobs.size() / 2; _ASSERT(m_HaveBlob.size() == col_id); _ASSERT(m_ColumnTitles.size() == col_id); _ASSERT(m_ColumnMetas.size() == col_id); CRef new_blob(new CBlastDbBlob); CRef new_blob2(new CBlastDbBlob); m_Blobs .push_back(new_blob); m_Blobs .push_back(new_blob2); m_HaveBlob .push_back(0); m_ColumnTitles.push_back(title); m_ColumnMetas .push_back(TColumnMeta()); if (m_Volume.NotEmpty()) { size_t id2 = m_Volume->CreateColumn(title, m_ColumnMetas.back(), mbo); _ASSERT(id2 == col_id); (void)id2; // get rid of compiler warning } return col_id; } void CWriteDB_Impl::AddColumnMetaData(int col_id, const string & key, const string & value) { if ((col_id < 0) || (col_id >= (int) m_ColumnMetas.size())) { NCBI_THROW(CWriteDBException, eArgErr, "Error: provided column ID is not valid"); } m_ColumnMetas[col_id][key] = value; if (m_Volume.NotEmpty()) { m_Volume->AddColumnMetaData(col_id, key, value); } } CBlastDbBlob & CWriteDB_Impl::SetBlobData(int col_id) { typedef CBlastDbBlob TBlob; if ((col_id < 0) || (col_id * 2 >= (int) m_Blobs.size())) { NCBI_THROW(CWriteDBException, eArgErr, "Error: provided column ID is not valid"); } if (m_HaveBlob[col_id] > 1) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Already have blob for this sequence and column"); } ++m_HaveBlob[col_id]; // Blobs are reused to reduce buffer reallocation; a missing blob // means the corresponding column does not exist. return *m_Blobs[col_id * 2 + m_HaveBlob[col_id] - 1]; } #endif void CWriteDB_Impl::SetPig(int pig) { m_Pig = pig; } void CWriteDB_Impl::SetMaxFileSize(Uint8 sz) { m_MaxFileSize = sz; } void CWriteDB_Impl::SetMaxVolumeLetters(Uint8 sz) { m_MaxVolumeLetters = sz; } CRef CWriteDB_Impl::ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids) { // Get information CConstRef deflines; string binary_header; vector< vector > v1, v2; CConstRef bsref(& bs); x_ExtractDeflines(bsref, deflines, binary_header, v2, v2, 0, -1, parse_ids); // Convert to return type CRef bdls; bdls.Reset(const_cast(&*deflines)); return bdls; } void CWriteDB_Impl::SetMaskedLetters(const string & masked) { // Only supported for protein. if (! m_Protein) { NCBI_THROW(CWriteDBException, eArgErr, "Error: Nucleotide masking not supported."); } m_MaskedLetters = masked; if (masked.empty()) { vector none; m_MaskLookup.swap(none); return; } // Convert set of masked letters to stdaa, use the result to build // a lookup table. string mask_bytes; CSeqConvert::Convert(m_MaskedLetters, CSeqUtil::e_Iupacaa, 0, (int) m_MaskedLetters.size(), mask_bytes, CSeqUtil::e_Ncbistdaa); _ASSERT(mask_bytes.size() == m_MaskedLetters.size()); // Build a table of character-to-bool. // (Bool is represented by char 0 and 1.) m_MaskLookup.resize(256, (char)0); for (unsigned i = 0; i < mask_bytes.size(); i++) { int ch = ((int) mask_bytes[i]) & 0xFF; m_MaskLookup[ch] = (char)1; } // Convert the masking character - always 'X' - to stdaa. if (m_MaskByte.empty()) { string mask_byte = "X"; CSeqConvert::Convert(mask_byte, CSeqUtil::e_Iupacaa, 0, 1, m_MaskByte, CSeqUtil::e_Ncbistdaa); _ASSERT(m_MaskByte.size() == 1); } } void CWriteDB_Impl::ListVolumes(vector & vols) { vols.clear(); ITERATE(vector< CRef >, iter, m_VolumeList) { vols.push_back((**iter).GetVolumeName()); } } void CWriteDB_Impl::ListFiles(vector & files) { files.clear(); ITERATE(vector< CRef >, iter, m_VolumeList) { (**iter).ListFiles(files); } if (m_VolumeList.size() > 1) { files.push_back(x_MakeAliasName()); } } /// Compute the hash of a (raw) sequence. /// /// The hash of the provided sequence will be computed and assigned to /// the m_Hash field. For protein, the sequence is in the Ncbistdaa /// format. For nucleotide, the sequence and optional ambiguities are /// in 'raw' format, meaning they are packed just as sequences are /// packed in nsq files. /// /// @param sequence The sequence data. [in] /// @param ambiguities Nucleotide ambiguities are provided here. [in] void CWriteDB_Impl::x_ComputeHash(const CTempString & sequence, const CTempString & ambig) { if (m_Protein) { m_Hash = SeqDB_SequenceHash(sequence.data(), sequence.size()); } else { string na8; SeqDB_UnpackAmbiguities(sequence, ambig, na8); m_Hash = SeqDB_SequenceHash(na8.data(), na8.size()); } } /// Compute the hash of a (Bioseq) sequence. /// /// The hash of the provided sequence will be computed and /// assigned to the m_Hash member. The sequence is packed as a /// CBioseq. /// /// @param sequence The sequence as a CBioseq. [in] void CWriteDB_Impl::x_ComputeHash(const CBioseq & sequence) { m_Hash = SeqDB_SequenceHash(sequence); } void CWriteDB_Impl:: x_GetFastaReaderDeflines(const CBioseq & bioseq, CConstRef & deflines, const vector< vector > & membits, const vector< vector > & linkout, int pig, bool accept_gt, bool parse_ids) { if (! bioseq.CanGetDescr()) { return; } string fasta; // Scan the CBioseq for the CFastaReader user object. ITERATE(list< CRef< CSeqdesc > >, iter, bioseq.GetDescr().Get()) { const CSeqdesc & desc = **iter; if (desc.IsUser() && desc.GetUser().CanGetType() && desc.GetUser().GetType().IsStr() && desc.GetUser().GetType().GetStr() == "CFastaReader" && desc.GetUser().CanGetData()) { const vector< CRef< CUser_field > > & D = desc.GetUser().GetData(); ITERATE(vector< CRef< CUser_field > >, iter, D) { const CUser_field & f = **iter; if (f.CanGetLabel() && f.GetLabel().IsStr() && f.GetLabel().GetStr() == "DefLine" && f.CanGetData() && f.GetData().IsStr()) { fasta = NStr::ParseEscapes(f.GetData().GetStr()); break; } } } } if (fasta.empty()) return; // The bioseq has a field contianing the ids for the first // defline. The title string contains the title for the first // defline, plus all the other defline titles and ids. This code // unpacks them and builds a normal blast defline set. unsigned mship_i(0), links_i(0); bool used_pig(false); // Build the deflines. CRef bdls(new CBlast_def_line_set); CRef defline; if (!parse_ids) { // Generate an BL_ORD_ID in case no parse is needed CRef gnl_id(new CSeq_id()); gnl_id->SetGeneral().SetDb("BL_ORD_ID"); gnl_id->SetGeneral().SetTag().SetId(0); // will be filled later // Build the local defline. defline.Reset(new CBlast_def_line); defline->SetSeqid().push_back(gnl_id); string title(fasta, 1, fasta.size()); // Replace ^A with space for(size_t pos=0; pos < title.size(); ++pos) { if (title[pos] == '\001') title[pos] = ' '; } defline->SetTitle(title); if (mship_i < membits.size()) { const vector & V = membits[mship_i++]; defline->SetMemberships().assign(V.begin(), V.end()); } if (links_i < linkout.size()) { const vector & V = linkout[mship_i++]; defline->SetLinks().assign(V.begin(), V.end()); } if ((! used_pig) && pig) { defline->SetOther_info().push_back(pig); used_pig = true; } bdls->Set().push_back(defline); } else { int skip = 1; while(fasta.size()) { size_t id_start = skip; size_t pos_title = fasta.find(" ", skip); size_t pos_next = fasta.find("\001", skip); skip = 1; if (pos_next == fasta.npos) { if (accept_gt) { pos_next = fasta.find(" >"); skip = 2; } } else { // If there is a ^A, turn off GT checking. accept_gt = false; } if (pos_next == fasta.npos) { pos_next = fasta.size(); skip = 0; } if (pos_title == fasta.npos || pos_title >= pos_next) { // title field is missing pos_title = pos_next; } string ids(fasta, id_start, pos_title - id_start); if (pos_title == pos_next) pos_title--; string title(fasta, pos_title + 1, pos_next-pos_title - 1); string remaining(fasta, pos_next, fasta.size() - pos_next); fasta.swap(remaining); // Parse '|' seperated ids. list< CRef > seqids; if ( ids.find('|') == NPOS || !isalpha((unsigned char)(ids[0]))) { seqids.push_back(CRef (new CSeq_id(CSeq_id::e_Local, ids))); } else { CSeq_id::ParseFastaIds(seqids, ids); } // Build the actual defline. defline.Reset(new CBlast_def_line); defline->SetSeqid().swap(seqids); defline->SetTitle(title); if (mship_i < membits.size()) { const vector & V = membits[mship_i++]; defline->SetMemberships().assign(V.begin(), V.end()); } if (links_i < linkout.size()) { const vector & V = linkout[mship_i++]; defline->SetLinks().assign(V.begin(), V.end()); } if ((! used_pig) && pig) { defline->SetOther_info().push_back(pig); used_pig = true; } bdls->Set().push_back(defline); } } s_CheckEmptyLists(bdls, true); deflines = bdls; } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) int CWriteDB_Impl::x_GetMaskDataColumnId() { if (m_MaskDataColumn == -1) { m_MaskDataColumn = CreateColumn("BlastDb/MaskData", true); } return m_MaskDataColumn; } #endif END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb_files.hpp0000644000175000017500000004175312001215336024124 0ustar ykeyke#ifndef OBJTOOLS_WRITERS_WRITEDB__WRITEDB_FILES_HPP #define OBJTOOLS_WRITERS_WRITEDB__WRITEDB_FILES_HPP /* $Id: writedb_files.hpp 200354 2010-08-06 17:58:25Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb_files.hpp /// Code for database files construction. /// /// Defines classes: /// CWriteDBHeader /// /// Implemented for: UNIX, MS-Windows #include #include #include #include #include BEGIN_NCBI_SCOPE /// Import definitions from the objects namespace. USING_SCOPE(objects); /// CWriteDB_IndexFile class /// /// This manufactures blast database index files from input data. class CWriteDB_File : public CObject { public: // Setup and control /// Constructor. /// /// The filename is constructed from basename, extension, and /// index, but might be changed if the RenameSingle() method is /// called. If zero is specified for maximum file size, a default /// size is provided by this class. The maximum file size is not /// enforced by this class, instead each derived class must do its /// own enforcement. /// /// @param basename Database base name, shared by all files. [in] /// @param extension File name extension for this file. [in] /// @param index Volume index used in filename. [in] /// @param max_file_size File size limit (in bytes). [in] /// @param always_create If true the file will be created now. [in] CWriteDB_File(const string & basename, const string & extension, int index, Uint8 max_file_size, bool always_create); /// Create and open the file. /// /// This method must be called before the first time that data is /// written to the file. If the constructor is passed 'true' for /// always_create, this method will be called during construction. /// It is an error to call this method more than once (including /// via the constructor) or to not call it but to call Write. The /// rationale for making this explicit is to permit some files to /// be created optionally, such as ISAM files, which should only /// be created if the corresponding ID types are found. void Create(); /// Write contents of a string to the file. /// @param data Data to write. /// @return File offset after write. int Write(const CTempString & data); /// Write an Int4 (in bigendian order) to the file. /// @param data String to write. /// @return File offset after write. int WriteInt4(int data) { s_WriteInt4(m_RealFile, data); m_Offset += 4; return m_Offset; } /// Write an Int8 (in bigendian order) to the file. /// @param data String to write. /// @return File offset after write. int WriteInt8(Int8 data) { s_WriteInt8BE(m_RealFile, data); m_Offset += 8; return m_Offset; } /// Write contents of a string to the file, appending a NUL. /// @param data String to write. /// @return File offset after write. int WriteWithNull(const CTempString & data) { Write(data); return Write(m_Nul); } /// Close the file, flushing any remaining data to disk. void Close(); /// Rename this file, disincluding the volume index. virtual void RenameSingle(); /// Construct the short name for a volume. /// /// Volume names consist of the database base name, ".", and the /// volume index in decimal. The volume index is normally two /// digits, but if more than 100 volumes are needed, the filename /// will use three or more index digits as needed. /// /// @param base Base name to use. /// @param index Volume index. /// @return A short name. static string MakeShortName(const string & base, int index); /// Get the current filename for this file. /// /// The filename is returned. The data returned by this method /// reflects changes made by RenameSingle(), so it is probably /// best to call it after that method has been called (if it will /// be called). /// /// @return The filename. const string & GetFilename() const { return m_Fname; } protected: /// True if the file has already been opened. bool m_Created; /// Underlying 'output file' type used here. typedef ofstream TFile; /// For convenience, a string containing one NUL character. string m_Nul; // init me /// The default value for max_file_size. /// @return The max file size used if otherwise unspecified. Uint8 x_DefaultByteLimit() { // 1 gb (marketing version) - 1; about a billion return 1000*1000*1000 - 1; } /// This should flush any unwritten data to disk. /// /// This method must be implemented by derived classes to flush /// any unwritten data to disk. In the cases of sequence and /// header files, it will normally do nothing, because such files /// are written as the data is available. For index (pin/nin) and /// ISAM files, this method does most of the disk I/O. virtual void x_Flush() = 0; /// Build the filename for this file. void x_MakeFileName(); // Configuration string m_BaseName; ///< Database base name for all files. string m_Extension; ///< File extension for this file. int m_Index; ///< Volume index. int m_Offset; ///< Stream position. Uint8 m_MaxFileSize; ///< Maximum file size in bytes. // The file bool m_UseIndex; ///< True if filenames should use volume index. string m_Fname; ///< Current filename for output file. TFile m_RealFile; ///< Actual stream implementing the output file. }; // For index file format, see .cpp file. /// This class builds the volume index file (pin or nin). class CWriteDB_IndexFile : public CWriteDB_File { public: /// Constructor. /// @param dbname Database base name. /// @param protein True for protein volumes. /// @param title Database title string. /// @param date Timestamp of database construction start. /// @param index Index of this volume. /// @param max_file_size Maximum file size in bytes (or zero). CWriteDB_IndexFile(const string & dbname, bool protein, const string & title, const string & date, int index, Uint8 max_file_size); /// Returns true if another sequence can fit into the file. bool CanFit() { _ASSERT(m_MaxFileSize > 1024); if (! m_OIDs) return true; return m_DataSize < (m_MaxFileSize-12); } /// Add a sequence to a protein index file (pin). /// /// The index file does not need sequence data, so this method /// only needs offsets of the data in other files. /// /// @param Sequence length in letters. /// @param hdr Length of binary ASN.1 header data. /// @param seq Length in bytes of sequence data. void AddSequence(int length, int hdr, int seq) { if (length > m_MaxLength) { m_MaxLength = length; } m_OIDs ++; m_Letters += length; m_DataSize += 8; m_Hdr.push_back(hdr); m_Seq.push_back(seq); } /// Add a sequence to a nucleotide index file (nin). /// /// The index file does not need sequence data, so this method /// only needs offsets of the data in other files. /// /// @param Sequence length in letters. /// @param hdr Length of binary ASN.1 header data. /// @param seq Length in bytes of packed sequence data. /// @param seq Length in bytes of packed ambiguity data. void AddSequence(int length, int hdr, int seq, int amb) { if (length > m_MaxLength) { m_MaxLength = length; } m_OIDs ++; m_Letters += length; m_DataSize += 12; m_Hdr.push_back(hdr); m_Seq.push_back(amb); // Not a bug. m_Amb.push_back(seq); // Also not a bug. } /* *********** START ************* */ Uint8 GetDataSize(void) { return m_DataSize; } void SetDataSize(Uint8 datasize) { m_DataSize = datasize; } /* ********** FINISH ************* */ private: /// Compute index file overhead. This is the overhead used by all /// fields of the index file, and does account for padding. /// /// @param T Title string. /// @param D Create time string. /// @return Combined size of all meta-data fields in nin/pin file. int x_Overhead(const string & T, const string & D); /// Flush index data to disk. virtual void x_Flush(); bool m_Protein; ///< True if this is a protein database. string m_Title; ///< Title string for all database volumes. string m_Date; ///< Database creation time stamp. int m_OIDs; ///< OIDs added to database so far. int m_Overhead; ///< Amount of file used by metadata. Uint8 m_DataSize; ///< Required space for data once written to disk. Uint8 m_Letters; ///< Letters of sequence data accumulated so far. int m_MaxLength; ///< Length of longest sequence. // Because the lengths are found via "next offset - this offset", // each array has an extra element. (This is not necesary in the // case of m_Amb; the last element is never examined because of // the alternation of sequences and ambiguities.) /// Start offset in header file of each OID's headers. /// /// The end offset is given by the start offset of the following /// OID's headers. vector m_Hdr; /// Offset in sequence file of each OID's sequence data. /// /// The end of the sequence data is given by the start offset of /// the ambiguity data for the same OID. vector m_Seq; /// Offset in sequence file of each OID's ambiguity data. /// /// The end of the ambiguity data is given by the start offset of /// the sequence data for the next OID. vector m_Amb; }; /// This class builds the volume header file (phr or nhr). class CWriteDB_HeaderFile : public CWriteDB_File { public: /// Constructor. /// @param dbname Database base name. /// @param protein True for protein volumes. /// @param index Index of this volume. /// @param max_file_size Maximum file size in bytes (or zero). CWriteDB_HeaderFile(const string & dbname, bool protein, int index, Uint8 max_file_size); /// Returns true if the specified amount of data would fit. /// /// If the specified amount of data (in bytes) would fit in the /// file without exceeding the max_file_size, this method returns /// true. /// /// @param size Size of new data in bytes. bool CanFit(int size) { if (! m_DataSize) { return true; } return (m_DataSize + size) < m_MaxFileSize; } /// Add binary header data to this file. /// @param binhdr Binary ASN.1 version of header data. [in] /// @param offset Offset of end of header data. [out] void AddSequence(const string & binhdr, int & offset) { m_DataSize = offset = Write(binhdr); } /* *********** START ************* */ void UpdateSize(const string & binhdr) { m_DataSize += binhdr.size(); } Uint8 GetDataSize(void) { return m_DataSize; } void SetDataSize(Uint8 datasize) { m_DataSize = datasize; } /* ********** FINISH ************* */ private: /// Flush unwritten data to the output file. virtual void x_Flush() { // There is nothing to do here - header data is written as // soon as it is added. } /// Amount of data written so far. Uint8 m_DataSize; }; class CWriteDB_SequenceFile : public CWriteDB_File { public: /// Constructor. /// @param dbname Database base name. /// @param protein True for protein volumes. /// @param index Index of this volume. /// @param max_file_size Maximum file size in bytes (or zero). /// @param max_letter Maximum sequence letters per volume (or zero). CWriteDB_SequenceFile(const string & dbname, bool protein, int index, Uint8 max_file_size, Uint8 max_letters); /// Returns true if the specified amount of data would fit. /// /// If the specified amount of data (in bytes) would fit in the /// file without exceeding the max_file_size, and the specified /// number of letters would fit without exceeding the maximum /// letters limit, this method returns true. /// /// @param size Size of new data in bytes. /// @param letters Number of sequence letters in new data. bool CanFit(int size, int letters) { if (m_Offset <= 1) { return true; } if (m_BaseLimit && ((m_Letters + letters) > m_BaseLimit)) { return false; } return ((m_Offset + (unsigned)size) < m_MaxFileSize); } /// Add a protein sequence to this file. /// /// This method should only be called in the protein case. /// /// @param sequence Packed sequence data. [in] /// @param offset Offset of the end of the sequence data. [out] /// @param length Length of the sequence in letters. [in] void AddSequence(const string & sequence, int & offset, int length) { _ASSERT(m_Protein); offset = WriteWithNull(sequence); m_Letters += length; } /// Add a nucleotide sequence to this file. /// /// This method should only be called in the nucleotide case. /// /// @param sequence Packed sequence data. [in] /// @param ambig Packed ambiguity data. [in] /// @param off_seq Offset of the end of the sequence data. [out] /// @param off_amb Offset of the end of the ambiguity data. [out] /// @param length Length of the sequence in letters. [in] void AddSequence(const string & sequence, const string & ambig, int & off_seq, int & off_amb, int length) { _ASSERT(! m_Protein); off_seq = Write(sequence); off_amb = Write(ambig); m_Letters += length; } /* *********** START ************* */ void UpdateSize( const string & sequence, int length) { m_Offset += sequence.size() + 1; //+1 because in AddSequence WriteWithNull is used m_Letters += length; } int GetOffset(){ return m_Offset; } void SetOffset(int offset){ m_Offset = offset; } Uint8 GetLetters(void) { return m_Letters; } void SetLetters(Uint8 letters) { m_Letters = letters; } /* ********** FINISH ************* */ private: /// Flush unwritten data to the output file. virtual void x_Flush() { // There is nothing to do here - sequence data is written as // soon as it is added. } Uint8 m_Letters; ///< Letters of sequence data added so far. Uint8 m_BaseLimit; ///< Limit on letters of sequence data. bool m_Protein; ///< True if this is a protein database. }; END_NCBI_SCOPE #endif // OBJTOOLS_WRITERS_WRITEDB__WRITEDB_FILES_HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb.hpp0000644000175000017500000006002612001215336022734 0ustar ykeyke#ifndef OBJTOOLS_BLAST_SEQDB_WRITER___WRITEDB__HPP #define OBJTOOLS_BLAST_SEQDB_WRITER___WRITEDB__HPP /* $Id: writedb.hpp 204621 2010-09-09 14:55:38Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb.hpp /// Defines BLAST database construction classes. /// /// Defines classes: /// CWriteDB /// /// Implemented for: UNIX, MS-Windows #include #include #include #include #include #include #include BEGIN_NCBI_SCOPE /// Include definitions from the objects namespace. USING_SCOPE(objects); /// Forward definition for PIMPL idiom. class CWriteDB_Impl; /// This represents a set of masks for a given sequence. It is represented as a /// vector because there can be multiple types of filtering applied to a single /// sequence (e.g.: DUST, WINDOWMASKER, REPEATS, etc). /// The type of masking data produced in IMaskDataSource class NCBI_XOBJWRITE_EXPORT CMaskedRangesVector: public vector { public: /// Our parent class typedef vector TParent; /// Redefine empty to mean no elements or none of its elements being empty bool empty() const { ITERATE(TParent, itr, *this) { if ( !itr->empty() ) { return false; } } return true; } }; /// CWriteDB /// /// User interface class for blast databases. /// /// This class provides the top-level interface class for BLAST /// database users. It defines access to the database component by /// calling methods on objects which represent the various database /// files, such as the index, header, sequence, and alias files. class NCBI_XOBJWRITE_EXPORT CWriteDB : public CObject { public: /// Sequence types. enum ESeqType { /// Protein database. eProtein = 0, /// Nucleotide database. eNucleotide = 1 }; /// Whether and what kind of indices to build. enum EIndexType { /// Build a database without any indices. eNoIndex = 0, /// Use only simple accessions in the string index. eSparseIndex = 0x1, /// Use several forms of each Seq-id in the string index. eFullIndex = 0x2, /// OR this in to add an index for trace IDs. eAddTrace = 0x4, /// Like eFullIndex but also build a numeric Trace ID index. eFullWithTrace = eFullIndex | eAddTrace, /// Like eFullIndex but also build a numeric Trace ID index. eDefault = eFullIndex | eAddTrace, // Specialized ISAMs; these can be ORred into the above. /// Add an index from sequence hash to OID. eAddHash = 0x100 }; typedef int TIndexType; ///< Bitwise OR of "EIndexType" // // Setup // /// Constructor /// /// Starts construction of a blast database. /// /// @param dbname /// A list of database or alias names, seperated by spaces. [in] /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. [in] /// @param title /// The database title. [in] /// @param itype /// Indicates the type of indices to build if specified. [in] /// @param parse_ids /// If true, generate ISAM files [in] /// @param use_gi_mask /// If true, generate GI-based mask files [in] CWriteDB(const string & dbname, ESeqType seqtype, const string & title, int itype = eDefault, bool parse_ids = true, bool use_gi_mask = false, /* *********** START ************* */ bool sort_sequences = false); /* ********** FINISH ************* */ /// Destructor. /// /// This will return resources acquired by this object, and call Close() /// if it has not already been called. ~CWriteDB(); // // Adding data // // Each new sequence is started when the client calls one of the // AddSequence() methods. This can optionally be followed by one // or more calls to Set...() methods or AddDefline(), to add or // change other data. The accumulated data for the sequence is // combined and written when the sequence after it is started // (with another AddSequence() call), or when Close() is called. /// Add a sequence as a CBioseq. /// /// This adds the sequence data in the specified CBioseq to the /// database. If the CBioseq contains deflines, they will also be /// used unless there is a call to SetDeflines() or AddDefline(). /// Note that the CBioseq will be held by CWriteDB at least until /// the next sequence is provided. If this method is used, the /// CBioseq is expected to contain sequence data accessible via /// GetInst().GetSeq_data(). If this might not be true, it may be /// better to use the version of this function that also takes a /// CSeqVector. /// /// @param bs The sequence and related data as a CBioseq. [in] void AddSequence(const CBioseq & bs); /// Add a sequence as a CBioseq. /// /// This adds the sequence data in the specified CSeqVector, and /// the meta data in the specified CBioseq, to the database. If /// the CBioseq contains deflines, they will also be used unless /// there is a call to SetDeflines() or AddDefline(). Note that /// the CBioseq will be held by CWriteDB at least until the next /// sequence is provided. This version will use the CSeqVector if /// the sequence data is not found in the CBioseq. /// /// @param bs A CBioseq containing meta data for the sequence. [in] /// @param sv The sequence data for the sequence. [in] void AddSequence(const CBioseq & bs, CSeqVector & sv); /// Add a sequence as a CBioseq. /// /// This adds the sequence found in the given CBioseq_Handle to /// the database. /// /// @param bsh The sequence and related data as a CBioseq_Handle. [in] void AddSequence(const CBioseq_Handle & bsh); /// Add a sequence as raw data. /// /// This adds a sequence provided as raw sequence data. The raw /// data must be (and is assumed to be) encoded correctly for the /// format of database being produced. For protein databases, the /// ambiguities string should be empty (and is thus optional). If /// this version of AddSequence() is used, the user must also /// provide one or more deflines with SetDeflines() or /// AddDefline() calls. /// /// @param sequence The sequence data as a string of bytes. [in] /// @param ambiguities The ambiguity data as a string of bytes. [in] void AddSequence(const CTempString & sequence, const CTempString & ambiguities = ""); /// Set the PIG to be used for the sequence. /// /// For proteins, this sets the PIG of the protein sequence. /// /// @param pig PIG identifier as an integer. [in] void SetPig(int pig); /// Set the deflines to be used for the sequence. /// /// This method sets all the deflines at once as a complete set, /// overriding any deflines provided by AddSequence(). If this /// method is used with the CBioseq version of AddSequence, it /// replaces the deflines found in the CBioseq. /// /// @param deflines Deflines to use for this sequence. [in] void SetDeflines(const CBlast_def_line_set & deflines); /// Register a type of filtering data found in this database. /// /// @return algorithm ID for the filtering data. /// @param program Program used to produce this masking data. [in] /// @param options Algorithm options provided to the program. [in] /// @param name Name of the GI-based mask. [in] int RegisterMaskAlgorithm(EBlast_filter_program program, const string & options = string(), const string & name = string()); /// Set filtering data for a sequence. /// /// This method specifies filtered regions for this sequence. A /// sequence may have filtering data from one or more algorithms. /// For each algorithm_id value specified in ranges, a description /// should be added to the database using RegisterMaskAlgorithm(). /// This must be done before the first call to SetMaskData() that /// uses the algorithm id for a non-empty offset range list. /// /// @param ranges Filtered ranges for this sequence and algorithm. /// @param gis GIs associated with this sequence. void SetMaskData(const CMaskedRangesVector & ranges, const vector & gis); // // Output // /// List Volumes /// /// Returns the base names of all volumes constructed by this /// class; the returned list may not be complete until Close() has /// been called. /// /// @param vols The set of volumes produced by this class. [out] void ListVolumes(vector & vols); /// List Filenames /// /// Returns a list of the files constructed by this class; the /// returned list may not be complete until Close() has been /// called. /// /// @param files The set of resolved database path names. [out] void ListFiles(vector & files); /// Close the Database. /// /// Flush all data to disk and close any open files. void Close(); // // Controls // // The blast volume format has internal limits for these fields; // these are called 'hard limits' here. If the value specified // here exceeds that limit, it will be silently reduced. Limits // are applied simultaneously; creation of a new volume is // triggered as soon as any of the limits is reached (unless the // current volume is empty). /// Set maximum size for output files. /// /// The provided size is applied as a limit on the size of output /// files. If adding a sequence would cause any output file to /// exceed this size, the volume is closed and a new volume is /// started (unless the current volume is empty, in which case the /// size limit is ignored and a one-sequence volume is created). /// The default value is 2^30-1. There is also a hard limit /// required by the database format. /// /// @param sz Maximum size in bytes of any volume component file. [in] void SetMaxFileSize(Uint8 sz); /// Set maximum letters for output volumes. /// /// The provided size is applied as a limit on the size of output /// volumes. If adding a sequence would cause a volume to exceed /// this many protein or nucleotide letters (*not* bytes), the /// volume is closed and a new volume is started (unless the /// volume is currently empty). There is no default, but there is /// a hard limit required by the format definition. Ambiguity /// encoding is not counted toward this limit. /// /// @param letters Maximum letters to pack in one volume. [in] void SetMaxVolumeLetters(Uint8 letters); /// Extract Deflines From Bioseq. /// /// Deflines are extracted from the CBioseq and returned to the /// user. The caller can then modify or inspect the deflines, and /// apply them to a sequence with SetDeflines(). /// /// @param bs The bioseq from which to extract a defline set. [in] /// @param parse_ids If seqid should be parsed [in] /// @return A set of deflines for this CBioseq. static CRef ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids=true); /// Set letters that should not be used in sequences. /// /// This method specifies letters that should not be used in the /// resulting database. The masked letters are expected to be /// specified in an IUPAC (alphabetic) encoding, and will be /// replaced by 'X' (for protein) when the sequences are packed. /// This method should be called before any sequences are added. /// This method only works with protein (the motivating case /// cannot happen with nucleotide). /// /// @param masked Letters to disinclude. [in] void SetMaskedLetters(const string & masked); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Find an existing column. /// /// This looks for an existing column with the specified title and /// returns the column ID if found. /// /// @param title The column title to look for. /// @return The column ID if this title is defined, otherwise -1. int FindColumn(const string & title) const; /// Set up a user-defined CWriteDB column. /// /// This method creates a user-defined column associated with this /// database. The column is indexed by OID and contains arbitrary /// binary data, which is applied using the SetBlobData method /// below. The `title' parameter identifies the column and must /// be unique within this database. Because tables are accessed /// by title, it is not necessary to permanently associate file /// extensions with specific purposes or data types. The return /// value of this method is an integer that identifies this column /// for the purpose of inserting blob data. (The number of columns /// allowed is currently limited due to the file naming scheme, /// but some columns are used for built-in purposes.) /// /// @param title Name identifying this column. /// @return Column identifier (a positive integer). int CreateUserColumn(const string & title); /// Add meta data to a user-defined column. /// /// In addition to normal blob data, database columns can store a /// `dictionary' of user-defined metadata in key/value form. This /// method adds one such key/value pair to the column. Specifying /// a key a second time causes replacement of the previous value. /// Using this mechanism to store large amounts of data may have a /// negative impact on performance. /// /// @param col_id Specifies the column to add this metadata to. /// @param key A unique key string. /// @param value A value string. void AddColumnMetaData(int col_id, const string & key, const string & value); /// Add blob data to a user-defined column. /// /// To add data to a user-defined blob column, call this method, /// providing the column handle. A blob object will be returned; /// the user data should be stored in this object. The data can /// be stored any time up to the next call to an `AddSequence' /// method (just as with any other per-sequence data) but access /// to the returned object after that point results is incorrect /// and will have undefined consequences. /// /// @param column_id Identifier for a user-defined column. /// @return Blob data should be written to this object. CBlastDbBlob & SetBlobData(int column_id); #endif protected: /// Implementation object. CWriteDB_Impl * m_Impl; }; /// Binary GI or TI List Builder. /// /// This class assists in building binary GI or TI lists for use with /// BLAST databases and associated software. class NCBI_XOBJWRITE_EXPORT CBinaryListBuilder { public: /// Type definition of the container that stores the IDs for this class typedef vector TContainerType; /// Standard size_type definition typedef TContainerType::size_type size_type; /// Identifier types. enum EIdType { /// Genomic id. eGi, /// Trace id. eTi }; /// Construct a list of a given type. CBinaryListBuilder(EIdType id_type); /// Write the list to a file. /// @param fname Filename of the file to write the object to. void Write(const string & fname); /// Write the list to a stream /// @param stream Stream to write the object to. void Write(CNcbiOstream& stream); /// Add an identifier to the list. void AppendId(const Int8 & id) { m_Ids.push_back(id); } /// Add several 4 byte IDs to the list. /// /// This should take begin and end indicators, such as pointers to /// the beginning and end (past the last element) of an array of /// integers, or begin() and end() iterators to a compatible STL /// collection type such as vector or set. /// /// @param a Iterator to the first included element. /// @param b Iterator to element after the last included element. template void AppendIdList(const T & a, const T & b) { for(T c = a; c != b; ++c) { Int8 id = *c; AppendId(id); } } /// Returns the number of IDs stored in an instance of this class size_type Size() const { return m_Ids.size(); } private: /// List of identifiers to use. TContainerType m_Ids; /// Whether to use GIs or TIs. EIdType m_IdType; /// Prevent copy construction. CBinaryListBuilder(CBinaryListBuilder&); /// Prevent copy assignment. CBinaryListBuilder& operator=(CBinaryListBuilder &); }; /// Builder for BlastDb format column files. /// /// This class supports construction of BlastDb format column files /// outside of BlastDb volumes. To build column files as part of a /// volume, use CWriteDB's column related methods. This class is an /// interface to the column file construction functionality, but is /// intended for data not associated with specific BlastDb volumes. /// Columns built with CWriteDB::CreateColumn participate in WriteDB's /// other volume-oriented policies such as volume breaking to enforce /// file size limits, and compatibility with component file naming /// conventions for CWriteDB and CSeqDB. class NCBI_XOBJWRITE_EXPORT CWriteDB_ColumnBuilder : public CObject { public: /// Construct a BlastDb format column. /// /// The `title' string names this column, and can be used to /// uniquely identify it in cases where the file name must be /// chosen arbitrarily. This version chooses file extensions /// using a basic pattern (.x?[ab]) designed to not conflict /// with columns created by WriteDB as part of a volume. The /// file_id character must be alphanumeric. /// /// @param title Internal name of this column. /// @param basename Column filename (minus extension). /// @param file_id Identifier for this column. CWriteDB_ColumnBuilder(const string & title, const string & basename, char file_id = 'a'); /// Add meta data to the column. /// /// In addition to normal blob data, database columns can store a /// `dictionary' of user-defined metadata in key/value form. This /// method adds one such key/value pair to the column. Specifying /// a key a second time causes replacement of the previous value. /// Using this mechanism to store large amounts of data may have a /// negative impact on performance. /// /// @param key Key string. /// @param value Value string. void AddMetaData(const string & key, const string & value); /// Destructor. ~CWriteDB_ColumnBuilder(); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Add a blob to the column. /// /// The data described by `blob' is added to the column. If the /// blob is empty, no data is stored but the OID is incremented. /// /// @param blob The blob to add to the column. void AddBlob(const CBlastDbBlob & blob); #endif /// Complete and close the column files. void Close(); /// List Filenames /// /// Returns a list of the files constructed by this class; the /// returned list may not be complete until Close() has been /// called. /// /// @param files The list of files created for this column. void ListFiles(vector & files) const; private: /// Prevent the copy constructor. CWriteDB_ColumnBuilder(const CWriteDB_ColumnBuilder&); /// Prevent copy assignment. CWriteDB_ColumnBuilder & operator= (CWriteDB_ColumnBuilder&); /// Implementation object. class CWriteDB_Column * m_Impl; }; /** * @brief Writes an alias file that restricts a database with a gi list. * * @param file_name alias file name to create, it will overwrite any existing * files of that name [in] * @param db_name database name to restrict [in] * @param seq_type type of sequences stored in the database [in] * @param gi_file_name name of the file containing gis [in] * @param title title to use in this alias file [in] */ NCBI_XOBJWRITE_EXPORT void CWriteDB_CreateAliasFile(const string& file_name, const string& db_name, CWriteDB::ESeqType seq_type, const string& gi_file_name, const string& title = string()); /** * @brief Writes an alias file that aggregates multiple existing BLAST * databases. * * @param file_name alias file name to create, it will overwrite any existing * files of that name [in] * @param db_names database names to aggregate [in] * @param gi_file_name name of the file containing gis [in] * @param seq_type type of sequences stored in the database [in] * @param title title to use in this alias file [in] */ NCBI_XOBJWRITE_EXPORT void CWriteDB_CreateAliasFile(const string& file_name, const vector & db_names, CWriteDB::ESeqType seq_type, const string& gi_file_name, const string& title = string()); /** * @brief Writes an alias file that aggregates multiple existing BLAST * database volumes. For instance, it can be used to request a top level alias * file for a database called wgs composed of 3 volumes, creating wgs.nal, * which refers to wgs.00, wgs.01, and wgs.02 * * @param file_name alias file name to create, it will overwrite any existing * files of that name [in] * @param num_volumes Number of volumes that will be referred to in the alias * file [in] * @param seq_type type of sequences stored in the database [in] * @param title title to use in this alias file [in] */ NCBI_XOBJWRITE_EXPORT void CWriteDB_CreateAliasFile(const string& file_name, unsigned int num_volumes, CWriteDB::ESeqType seq_type, const string& title = string()); END_NCBI_SCOPE #endif // OBJTOOLS_BLAST_SEQDB_WRITER___WRITEDB__HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/writedb.cpp0000644000175000017500000003403412001215336022727 0ustar ykeyke/* $Id: writedb.cpp 204621 2010-09-09 14:55:38Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file writedb.cpp /// Implementation for the CWriteDB class, the top level class for WriteDB. #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: writedb.cpp 204621 2010-09-09 14:55:38Z camacho $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include #include #include "writedb_impl.hpp" #include #include BEGIN_NCBI_SCOPE using namespace std; // Impl // CWriteDB CWriteDB::CWriteDB(const string & dbname, CWriteDB::ESeqType seqtype, const string & title, int indices, bool parse_ids, bool use_gi_mask, /* *********** START ************* */ bool sort_sequences) /* ********** FINISH ************* */ : m_Impl(0) { m_Impl = new CWriteDB_Impl(dbname, seqtype == eProtein, title, (EIndexType)indices, parse_ids, use_gi_mask, /* *********** START ************* */ sort_sequences); /* ********** FINISH ************* */ } CWriteDB::~CWriteDB() { delete m_Impl; } void CWriteDB::AddSequence(const CBioseq & bs) { m_Impl->AddSequence(bs); } void CWriteDB::AddSequence(const CBioseq_Handle & bsh) { m_Impl->AddSequence(bsh); } void CWriteDB::AddSequence(const CBioseq & bs, CSeqVector & sv) { m_Impl->AddSequence(bs, sv); } void CWriteDB::SetDeflines(const CBlast_def_line_set & deflines) { m_Impl->SetDeflines(deflines); } void CWriteDB::SetPig(int pig) { m_Impl->SetPig(pig); } void CWriteDB::Close() { m_Impl->Close(); } void CWriteDB::AddSequence(const CTempString & sequence, const CTempString & ambig) { string s(sequence.data(), sequence.length()); string a(ambig.data(), ambig.length()); m_Impl->AddSequence(s, a); } void CWriteDB::SetMaxFileSize(Uint8 sz) { m_Impl->SetMaxFileSize(sz); } void CWriteDB::SetMaxVolumeLetters(Uint8 sz) { m_Impl->SetMaxVolumeLetters(sz); } CRef CWriteDB::ExtractBioseqDeflines(const CBioseq & bs, bool parse_ids) { return CWriteDB_Impl::ExtractBioseqDeflines(bs, parse_ids); } void CWriteDB::SetMaskedLetters(const string & masked) { m_Impl->SetMaskedLetters(masked); } void CWriteDB::ListVolumes(vector & vols) { m_Impl->ListVolumes(vols); } void CWriteDB::ListFiles(vector & files) { m_Impl->ListFiles(files); } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) int CWriteDB:: RegisterMaskAlgorithm(EBlast_filter_program program, const string & options, const string & name) { return m_Impl->RegisterMaskAlgorithm(program, options, name); } void CWriteDB::SetMaskData(const CMaskedRangesVector & ranges, const vector & gis) { m_Impl->SetMaskData(ranges, gis); } int CWriteDB::FindColumn(const string & title) const { return m_Impl->FindColumn(title); } int CWriteDB::CreateUserColumn(const string & title) { return m_Impl->CreateColumn(title); } void CWriteDB::AddColumnMetaData(int col_id, const string & key, const string & value) { m_Impl->AddColumnMetaData(col_id, key, value); } CBlastDbBlob & CWriteDB::SetBlobData(int col_id) { return m_Impl->SetBlobData(col_id); } #endif CBinaryListBuilder::CBinaryListBuilder(EIdType id_type) : m_IdType(id_type) { } void CBinaryListBuilder::Write(const string & fname) { // Create a binary stream. ofstream outp(fname.c_str(), ios::binary); Write(outp); } void CBinaryListBuilder::Write(CNcbiOstream& outp) { // Header; first check for 8 byte ids. bool eight = false; ITERATE(vector, iter, m_Ids) { Int8 id = *iter; _ASSERT(id > 0); if ((id >> 32) != 0) { eight = true; break; } } Int4 magic = 0; switch(m_IdType) { case eGi: magic = eight ? -2 : -1; break; case eTi: magic = eight ? -4 : -3; break; default: NCBI_THROW(CWriteDBException, eArgErr, "Error: Unsupported ID type specified."); } s_WriteInt4(outp, magic); s_WriteInt4(outp, (int)m_Ids.size()); sort(m_Ids.begin(), m_Ids.end()); if (eight) { ITERATE(vector, iter, m_Ids) { s_WriteInt8BE(outp, *iter); } } else { ITERATE(vector, iter, m_Ids) { s_WriteInt4(outp, (int)*iter); } } } /// Returns true if the BLAST DB exists, otherwise throws a CSeqDBException /// @param dbname name of BLAST DB [in] /// @param is_prot is the BLAST DB protein? [in] static bool s_DoesBlastDbExist(const string& dbname, bool is_protein) { char dbtype(is_protein ? 'p' : 'n'); string path = SeqDB_ResolveDbPathNoExtension(dbname, dbtype); if (path.empty()) { string msg("Failed to find "); msg += (is_protein ? "protein " : "nucleotide "); msg += dbname + " BLAST database"; NCBI_THROW(CSeqDBException, eFileErr, msg); } return true; } /// Computes the number of sequences and (alias) database length for alias /// files /// @param dbname Name of the BLAST database over which the alias file is being /// created [in] /// @param is_prot is the BLAST database protein? [in] /// @param gi_file_name File name of the GI file to apply as a filter to the /// BLAST database, if empty, it's ignored [in] /// @param dbsize (Approximate) number of letters in the BLAST DB [out] /// @param num_seqs_found Number of sequences found in the dbname, or the /// number of sequences in the intersection between the dbname and the GIs in /// the gi_file_name (if applicable) [out] /// @param num_seqs_in_gifile Number of sequences in the gi_file_name (if /// applicable [out] static void s_ComputeNumSequencesAndDbLength(const string& dbname, bool is_prot, Uint8* dbsize, int* num_seqs_found, const string& gi_file_name = kEmptyStr, int* num_seqs_in_gifile = NULL) { _ASSERT((dbsize != NULL)); _ASSERT(num_seqs_found != NULL); *dbsize = 0u; *num_seqs_found = 0u; CSeqDB::ESeqType dbtype(is_prot ? CSeqDB::eProtein : CSeqDB::eNucleotide); CRef gilist; if ( !gi_file_name.empty() ) { gilist.Reset(new CSeqDBFileGiList(gi_file_name)); if (num_seqs_in_gifile) { *num_seqs_in_gifile = gilist->Size(); } } CRef dbhandle(new CSeqDB(dbname, dbtype, gilist.GetPointer())); dbhandle->GetTotals(CSeqDB::eFilteredAll, num_seqs_found, dbsize, true); if (*num_seqs_found == 0) { string msg("No GIs in "); msg += gi_file_name + " were found in "; msg += (is_prot ? "protein " : "nucleotide "); msg += dbname + " BLAST database"; NCBI_THROW(CSeqDBException, eArgErr, msg); } } static void s_PrintAliasFileCreationLog(const string& dbname, bool is_protein, int num_seqs_found, const string& gi_file_name = kEmptyStr, int num_seqs_in_gifile = 0) { if ( !gi_file_name.empty() ) { LOG_POST("Created " << (is_protein ? "protein " : "nucleotide ") << dbname << " BLAST (alias) database with " << num_seqs_found << " sequences (out of " << num_seqs_in_gifile << " in " << gi_file_name << ", " << setprecision(0) << fixed << (num_seqs_found*100.0/num_seqs_in_gifile) << "% found)"); } else { LOG_POST("Created " << (is_protein ? "protein " : "nucleotide ") << "BLAST (alias) database over " << dbname << " with " << num_seqs_found << " sequences"); } } void CWriteDB_CreateAliasFile(const string& file_name, const string& db_name, CWriteDB::ESeqType seq_type, const string& gi_file_name, const string& title) { bool is_prot(seq_type == CWriteDB::eProtein ? true : false); s_DoesBlastDbExist(db_name, is_prot); Uint8 dbsize = 0; int num_seqs = 0; int num_gis = 0; s_ComputeNumSequencesAndDbLength(db_name, is_prot, &dbsize, &num_seqs, gi_file_name, &num_gis); CNcbiOstrstream fname; fname << file_name << (is_prot ? ".pal" : ".nal"); ofstream out(((string)CNcbiOstrstreamToString(fname)).c_str()); out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString() << "\n#\n"; if ( !title.empty() ) { out << "TITLE " << title << "\n"; } out << "DBLIST " << db_name << "\n"; if ( !gi_file_name.empty() ){ out << "GILIST " << gi_file_name << "\n"; } out << "NSEQ " << num_seqs << "\n"; out << "LENGTH " << dbsize << "\n"; out.close(); s_PrintAliasFileCreationLog(file_name, is_prot, num_seqs, gi_file_name, num_gis); } void CWriteDB_CreateAliasFile(const string& file_name, const vector& databases, CWriteDB::ESeqType seq_type, const string& gi_file_name, const string& title) { string concatenated_blastdb_name; bool is_prot(seq_type == CWriteDB::eProtein ? true : false); ITERATE(vector, itr, databases) { concatenated_blastdb_name += *itr + " "; s_DoesBlastDbExist(*itr, is_prot); } Uint8 dbsize = 0; int num_seqs = 0; int num_gis = 0; s_ComputeNumSequencesAndDbLength(concatenated_blastdb_name, is_prot, &dbsize, &num_seqs, gi_file_name, &num_gis); CNcbiOstrstream fname; fname << file_name << (is_prot ? ".pal" : ".nal"); ofstream out(((string)CNcbiOstrstreamToString(fname)).c_str()); out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString() << "\n#\n"; if ( !title.empty() ) { out << "TITLE " << title << "\n"; } out << "DBLIST "; ITERATE(vector< string >, iter, databases) { out << "\"" << *iter << "\" "; } out << "\n"; if ( !gi_file_name.empty() ) { out << "GILIST " << gi_file_name << "\n"; } out << "NSEQ " << num_seqs << "\n"; out << "LENGTH " << dbsize << "\n"; out.close(); s_PrintAliasFileCreationLog(file_name, is_prot, num_seqs, gi_file_name, num_gis); } void CWriteDB_CreateAliasFile(const string& file_name, unsigned int num_volumes, CWriteDB::ESeqType seq_type, const string& title) { bool is_prot(seq_type == CWriteDB::eProtein ? true : false); string concatenated_blastdb_name; if (num_volumes >= 101) { NCBI_THROW(CWriteDBException, eArgErr, "No more than 100 volumes are supported"); } vector volume_names(num_volumes, kEmptyStr); for (unsigned int i = 0; i < num_volumes; i++) { CNcbiOstrstream oss; oss << file_name << "." << setfill('0') << setw(2) << i; const string vol_name((string)CNcbiOstrstreamToString(oss)); s_DoesBlastDbExist(vol_name, is_prot); volume_names.push_back(vol_name); concatenated_blastdb_name += vol_name + " "; } Uint8 dbsize = 0; int num_seqs = 0; s_ComputeNumSequencesAndDbLength(concatenated_blastdb_name, is_prot, &dbsize, &num_seqs); CNcbiOstrstream fname; fname << file_name << (is_prot ? ".pal" : ".nal"); ofstream out(((string)CNcbiOstrstreamToString(fname)).c_str()); out << "#\n# Alias file created " << CTime(CTime::eCurrent).AsString() << "\n#\n"; if ( !title.empty() ) { out << "TITLE " << title << "\n"; } out << "DBLIST "; ITERATE(vector, itr, volume_names) { out << *itr << " "; } out << "\n"; out << "NSEQ " << num_seqs << "\n"; out << "LENGTH " << dbsize << "\n"; out.close(); s_PrintAliasFileCreationLog(concatenated_blastdb_name, is_prot, num_seqs); } END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/seqsrc_seqdb.cpp0000644000175000017500000006406612001215336023755 0ustar ykeyke/* $Id: seqsrc_seqdb.cpp 226045 2011-01-27 20:24:02Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Ilya Dondoshansky * */ /// @file seqsrc_seqdb.cpp /// Implementation of the BlastSeqSrc interface for a C++ BLAST databases API #include #include #include #include #include #include #include "blast_setup.hpp" /** @addtogroup AlgoBlast * * @{ */ #ifndef SKIP_DOXYGEN_PROCESSING USING_NCBI_SCOPE; USING_SCOPE(objects); USING_SCOPE(blast); #endif /* SKIP_DOXYGEN_PROCESSING */ /// Simple container to support SeqSrc-local data. struct SSeqDB_SeqSrc_Data { /// Constructor. SSeqDB_SeqSrc_Data() : copied(false) { } /// Constructor. SSeqDB_SeqSrc_Data(CSeqDB * ptr, int id, int type) : seqdb((CSeqDBExpert*) ptr), mask_algo_id(id), mask_type(type), copied(false) { } /// Make a copy of this object, sharing the same SeqDB object. SSeqDB_SeqSrc_Data * clone() { return new SSeqDB_SeqSrc_Data(&* seqdb, mask_algo_id, mask_type); } /// Convenience to allow datap->method to use SeqDB methods. CSeqDBExpert * operator->() { _ASSERT(! seqdb.Empty()); return &*seqdb; } /// Convenience to allow datap->method to use SeqDB methods. CSeqDBExpert & operator*() { _ASSERT(! seqdb.Empty()); return *seqdb; } /// SeqDB object. CRef seqdb; /// Algorithm ID and type for mask data fetching. int mask_algo_id; int mask_type; bool copied; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Ranges of the sequence to include (for masking). CSeqDB::TSequenceRanges seq_ranges; #endif }; typedef SSeqDB_SeqSrc_Data TSeqDBData; extern "C" { #ifdef KAPPA_PRINT_DIAGNOSTICS static Blast_GiList* s_SeqDbGetGiList(void* seqdb_handle, void* args) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; Int4* oid = (Int4*) args; if (!datap || !oid) return NULL; vector gis; datap->GetGis(*oid, gis); Blast_GiList* retval = Blast_GiListNewEx(gis.size()); copy(gis.begin(), gis.end(), retval->data); retval->num_used = gis.size(); return retval; } #endif /* KAPPA_PRINT_DIAGNOSTICS */ /// Retrieves the length of the longest sequence in the BlastSeqSrc. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static Int4 s_SeqDbGetMaxLength(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetMaxLength(); } /// Setting number of threads in MT mode /// @param n_threads number of threads [in] static void s_SeqDbSetNumberOfThreads(void* seqdb_handle, int n) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; seqdb.SetNumberOfThreads(n); } /// Retrieves the number of sequences in the BlastSeqSrc. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static Int4 s_SeqDbGetNumSeqs(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetNumSeqs(); } /// Retrieves the number of sequences from alias file to be used for // search-space calculations. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static Int4 s_SeqDbGetNumSeqsStats(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetNumSeqsStats(); } /// Retrieves the total length of all sequences in the BlastSeqSrc. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static Int8 s_SeqDbGetTotLen(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetTotalLength(); } /// Retrieves the total length of all sequences from alias file // to be used for search space calculations. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static Int8 s_SeqDbGetTotLenStats(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetTotalLengthStats(); } /// Retrieves the average length of sequences in the BlastSeqSrc. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] /// @param ignoreme Unused by this implementation [in] static Int4 s_SeqDbGetAvgLength(void* seqdb_handle, void* ignoreme) { Int8 total_length = s_SeqDbGetTotLen(seqdb_handle, ignoreme); Int4 num_seqs = MAX(1, s_SeqDbGetNumSeqs(seqdb_handle, ignoreme)); return (Int4) (total_length/num_seqs); } /// Retrieves the name of the BLAST database. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static const char* s_SeqDbGetName(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetDBNameList().c_str(); } /// Checks whether database is protein or nucleotide. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] /// @return TRUE if database is protein, FALSE if nucleotide. static Boolean s_SeqDbGetIsProt(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return (seqdb.GetSequenceType() == CSeqDB::eProtein); } /// Determine if partial fetching should be enabled /// @param seqdb_handle Pointer to initialized CSeqDB object [in] static Boolean s_SeqDbGetSupportsPartialFetching(void* seqdb_handle, void*) { CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; if (seqdb.GetSequenceType() != CSeqDB::eNucleotide) { // don't bother doing this for proteins as the sequences are // never long enough to cause performance degredation return false; } // If longest sequence is below this we quit static const int kMaxLengthCutoff = 5000; if (seqdb.GetMaxLength() < kMaxLengthCutoff) { return false; } // If average length is below this amount we quit static const int kAvgLengthCutoff = 2048; Int8 total_length = seqdb.GetTotalLength(); Int4 num_seqs = MAX(1, seqdb.GetNumSeqs()); if ((Int4)(total_length/num_seqs) < kAvgLengthCutoff) { return false; } return true; } /// Set sequence ranges for partial fetching /// @param seqdb_handle Pointer to initialized CSeqDB object [in] /// @param args Pointer to BlastSeqSrcSetRangesArg structure [in] static void s_SeqDbSetRanges(void* seqdb_handle, BlastSeqSrcSetRangesArg* args) { if (!seqdb_handle || !args) return; CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; CSeqDB::TRangeList ranges; for (int i=0; i< args->num_ranges; ++i) { ranges.insert(pair (args->ranges[i*2], args->ranges[i*2+1])); } seqdb.SetOffsetRanges(args->oid, ranges, false, false); } /// Retrieves the sequence meeting the criteria defined by its second argument. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] /// @param args Pointer to BlastSeqSrcGetSeqArg structure [in] /// @return return codes defined in blast_seqsrc.h static Int2 s_SeqDbGetSequence(void* seqdb_handle, BlastSeqSrcGetSeqArg* args) { Int4 oid = -1, len = 0; Boolean has_sentinel_byte; if (!seqdb_handle || !args) return BLAST_SEQSRC_ERROR; TSeqDBData * datap = (TSeqDBData *) seqdb_handle; CSeqDBExpert & seqdb = **datap; oid = args->oid; // If we are asked to check for OID exclusion, and if the database // has a GI list, then we check whether all the seqids have been // removed by filtering. If so we return an error. The traceback // code will exclude this HSP list. if (args->check_oid_exclusion) { if (! seqdb.GetIdSet().Blank()) { list< CRef > seqids = seqdb.GetSeqIDs(oid); if (seqids.empty()) { return BLAST_SEQSRC_ERROR; } } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) if (datap->mask_type) { ASSERT(datap->mask_algo_id != -1); seqdb.GetMaskData(oid, datap->mask_algo_id, datap->seq_ranges); } #endif datap->copied = false; if ( args->encoding == eBlastEncodingNucleotide || args->encoding == eBlastEncodingNcbi4na || (datap->mask_type == DB_MASK_HARD && !(datap->seq_ranges.empty()) && args->check_oid_exclusion)) datap->copied = true; has_sentinel_byte = (args->encoding == eBlastEncodingNucleotide); /* free buffers if necessary */ if (args->seq) BlastSequenceBlkClean(args->seq); /* This occurs if the pre-selected partial sequence in the traceback stage * was too small to perform the traceback. Only do this for nucleotide * sequences as proteins are not long enough to be of significance */ if (args->reset_ranges && seqdb.GetSequenceType() == CSeqDB::eNucleotide) { seqdb.RemoveOffsetRanges(oid); } const char *buf; len = (datap->copied) /* This will consume and clear datap->seq_ranges */ ? seqdb.GetAmbigSeqAlloc(oid, const_cast(&buf), has_sentinel_byte, eMalloc, ((datap->mask_type == DB_MASK_HARD) ? &(datap->seq_ranges) : NULL)) : seqdb.GetSequence(oid, &buf); if (len <= 0) return BLAST_SEQSRC_ERROR; BlastSetUp_SeqBlkNew((Uint1*)buf, len, &args->seq, datap->copied); /* If there is no sentinel byte, and buffer is allocated, i.e. this is the traceback stage of a translated search, set "sequence" to the same position as "sequence_start". */ if (datap->copied && !has_sentinel_byte) args->seq->sequence = args->seq->sequence_start; /* For preliminary stage, even though sequence buffer points to a memory mapped location, we still need to call ReleaseSequence. This can only be guaranteed by making the engine believe tat sequence is allocated. */ if (!datap->copied) args->seq->sequence_allocated = TRUE; args->seq->oid = oid; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /* If masks have not been consumed (scanning phase), pass on to engine */ if (datap->mask_type) { if (BlastSeqBlkSetSeqRanges(args->seq, (SSeqRange*) datap->seq_ranges.get_data(), datap->seq_ranges.size() + 1, false, datap->mask_type) != 0) { return BLAST_SEQSRC_ERROR; } } #endif return BLAST_SEQSRC_SUCCESS; } /// Returns the memory allocated for the sequence buffer to the CSeqDB /// interface. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] /// @param args Pointer to the BlastSeqSrcGetSeqArgs structure, /// containing sequence block with the buffer that needs to be deallocated. [in] static void s_SeqDbReleaseSequence(void* seqdb_handle, BlastSeqSrcGetSeqArg* args) { TSeqDBData * datap = (TSeqDBData *) seqdb_handle; CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; _ASSERT(seqdb_handle); _ASSERT(args); _ASSERT(args->seq); if (args->seq->sequence_start_allocated) { ASSERT (datap->copied); sfree(args->seq->sequence_start); args->seq->sequence_start_allocated = FALSE; args->seq->sequence_start = NULL; } if (args->seq->sequence_allocated) { if (datap->copied) sfree(args->seq->sequence); else seqdb.RetSequence((const char**)&args->seq->sequence); args->seq->sequence_allocated = FALSE; args->seq->sequence = NULL; } } /// Retrieve length of a given database sequence. /// @param seqdb_handle Pointer to initialized CSeqDB object [in] /// @param args Pointer to integer indicating ordinal id [in] /// @return Length of the database sequence or BLAST_SEQSRC_ERROR. static Int4 s_SeqDbGetSeqLen(void* seqdb_handle, void* args) { Int4* oid = (Int4*) args; if (!seqdb_handle || !oid) return BLAST_SEQSRC_ERROR; CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; return seqdb.GetSeqLength(*oid); } /// Assigns next chunk of the database to the sequence source iterator. /// @param seqdb_handle Reference to the database object, cast to void* to /// satisfy the signature requirement. [in] /// @param itr Iterator over the database sequence source. [in|out] static Int2 s_SeqDbGetNextChunk(void* seqdb_handle, BlastSeqSrcIterator* itr) { if (!seqdb_handle || !itr) return BLAST_SEQSRC_ERROR; CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; vector oid_list; CSeqDB::EOidListType chunk_type = seqdb.GetNextOIDChunk(itr->oid_range[0], itr->oid_range[1], itr->chunk_sz, oid_list); if (itr->oid_range[1] <= itr->oid_range[0]) return BLAST_SEQSRC_EOF; if (chunk_type == CSeqDB::eOidRange) { itr->itr_type = eOidRange; itr->current_pos = itr->oid_range[0]; } else if (chunk_type == CSeqDB::eOidList) { Uint4 new_sz = (Uint4) oid_list.size(); itr->itr_type = eOidList; if (new_sz > 0) { itr->current_pos = 0; Uint4 index; if (itr->chunk_sz < new_sz) { sfree(itr->oid_list); itr->oid_list = (int *) malloc (new_sz * sizeof(unsigned int)); } itr->chunk_sz = new_sz; for (index = 0; index < new_sz; ++index) itr->oid_list[index] = oid_list[index]; } else { return s_SeqDbGetNextChunk(seqdb_handle, itr); } } return BLAST_SEQSRC_SUCCESS; } /// Finds the next not searched ordinal id in the iteration over BLAST database. /// @param seqdb_handle Reference to the database object, cast to void* to /// satisfy the signature requirement. [in] /// @param itr Iterator of the BlastSeqSrc pointed by ptr. [in] /// @return Next ordinal id. static Int4 s_SeqDbIteratorNext(void* seqdb_handle, BlastSeqSrcIterator* itr) { Int4 retval = BLAST_SEQSRC_EOF; Int4 status = BLAST_SEQSRC_SUCCESS; _ASSERT(seqdb_handle); _ASSERT(itr); /* If internal iterator is uninitialized/invalid, retrieve the next chunk from the BlastSeqSrc */ if (itr->current_pos == UINT4_MAX) { status = s_SeqDbGetNextChunk(seqdb_handle, itr); if (status == BLAST_SEQSRC_ERROR || status == BLAST_SEQSRC_EOF) { return status; } } Uint4 last_pos = 0; if (itr->itr_type == eOidRange) { retval = itr->current_pos; last_pos = itr->oid_range[1]; } else if (itr->itr_type == eOidList) { retval = itr->oid_list[itr->current_pos]; last_pos = itr->chunk_sz; } else { /* Unsupported/invalid iterator type! */ fprintf(stderr, "Invalid iterator type: %d\n", itr->itr_type); abort(); } ++itr->current_pos; if (itr->current_pos >= last_pos) { itr->current_pos = UINT4_MAX; /* invalidate internal iteration */ } return retval; } /// Resets CSeqDB's internal chunk bookmark /// @param seqdb_handle Reference to the database object, cast to void* to /// satisfy the signature requirement. [in] static void s_SeqDbResetChunkIterator(void* seqdb_handle) { _ASSERT(seqdb_handle); CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; seqdb.ResetInternalChunkBookmark(); seqdb.FlushOffsetRangeCache(); } /* *********** START ************* */ /// Sets CSeqDB's internal chunk bookmark /// @param seqdb_handle Reference to the database object, cast to void* to /// satisfy the signature requirement. [in] static void s_SeqDbSetChunkIterator(void* seqdb_handle, int InternalChunkBookmark) { _ASSERT(seqdb_handle); CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; seqdb.SetInternalChunkBookmark(InternalChunkBookmark); } static void s_SeqDbSetMmapMemory(void* seqdb_handle, Boolean MmapMemory) { _ASSERT(seqdb_handle); CSeqDB & seqdb = **(TSeqDBData *) seqdb_handle; seqdb.SetMmapMemory(MmapMemory); } /* ********** FINISH ************* */ } BEGIN_NCBI_SCOPE USING_SCOPE(objects); BEGIN_SCOPE(blast) /// Encapsulates the arguments needed to initialize CSeqDB. class CSeqDbSrcNewArgs { public: /// Constructor CSeqDbSrcNewArgs(const string& db, bool is_prot, Uint4 first_oid = 0, Uint4 final_oid = 0, Int4 mask_algo_id = -1, Int4 mask_type = DB_MASK_NONE) : m_DbName(db), m_IsProtein(is_prot), m_FirstDbSeq(first_oid), m_FinalDbSeq(final_oid), m_MaskAlgoId(mask_algo_id), m_MaskType(mask_type) {} /// Getter functions for the private fields const string GetDbName() const { return m_DbName; } /// Returns database type: protein or nucleotide char GetDbType() const { return m_IsProtein ? 'p' : 'n'; } /// Returns first database ordinal id covered by this BlastSeqSrc Uint4 GetFirstOid() const { return m_FirstDbSeq; } /// Returns last database ordinal id covered by this BlastSeqSrc Uint4 GetFinalOid() const { return m_FinalDbSeq; } /// Returns the default filtering algorithm to use with sequence data /// extracted from this BlastSeqSrc Int4 GetMaskAlgoId() const { return m_MaskAlgoId; } Int4 GetMaskType() const { return m_MaskType; } private: string m_DbName; ///< Database name bool m_IsProtein; ///< Is this database protein? Uint4 m_FirstDbSeq; ///< Ordinal id of the first sequence to search Uint4 m_FinalDbSeq; ///< Ordinal id of the last sequence to search /// filtering algorithm ID to use when retrieving sequence data Int4 m_MaskAlgoId; Int4 m_MaskType; }; extern "C" { /// SeqDb sequence source destructor: frees its internal data structure /// @param seq_src BlastSeqSrc structure to free [in] /// @return NULL static BlastSeqSrc* s_SeqDbSrcFree(BlastSeqSrc* seq_src) { if (!seq_src) return NULL; TSeqDBData * datap = static_cast (_BlastSeqSrcImpl_GetDataStructure(seq_src)); delete datap; return NULL; } /// SeqDb sequence source copier: creates a new reference to the CSeqDB object /// and copies the rest of the BlastSeqSrc structure. /// @param seq_src BlastSeqSrc structure to copy [in] /// @return Pointer to the new BlastSeqSrc. static BlastSeqSrc* s_SeqDbSrcCopy(BlastSeqSrc* seq_src) { if (!seq_src) return NULL; TSeqDBData * datap = static_cast (_BlastSeqSrcImpl_GetDataStructure(seq_src)); _BlastSeqSrcImpl_SetDataStructure(seq_src, (void*) datap->clone()); return seq_src; } /// Initializes the data structure and function pointers in a SeqDb based /// BlastSeqSrc. /// @param retval Structure to populate [in] [out] /// @param seqdb Reference to a CSeqDB object [in] static void s_InitNewSeqDbSrc(BlastSeqSrc* retval, TSeqDBData * datap) { _ASSERT(retval); _ASSERT(datap); /* Initialize the BlastSeqSrc structure fields with user-defined function * pointers and seqdb */ _BlastSeqSrcImpl_SetDeleteFnPtr (retval, & s_SeqDbSrcFree); _BlastSeqSrcImpl_SetCopyFnPtr (retval, & s_SeqDbSrcCopy); _BlastSeqSrcImpl_SetDataStructure (retval, (void*) datap); _BlastSeqSrcImpl_SetGetNumSeqs (retval, & s_SeqDbGetNumSeqs); _BlastSeqSrcImpl_SetGetNumSeqsStats(retval, & s_SeqDbGetNumSeqsStats); _BlastSeqSrcImpl_SetGetMaxSeqLen (retval, & s_SeqDbGetMaxLength); _BlastSeqSrcImpl_SetGetAvgSeqLen (retval, & s_SeqDbGetAvgLength); _BlastSeqSrcImpl_SetGetTotLen (retval, & s_SeqDbGetTotLen); _BlastSeqSrcImpl_SetGetTotLenStats(retval, & s_SeqDbGetTotLenStats); _BlastSeqSrcImpl_SetGetName (retval, & s_SeqDbGetName); _BlastSeqSrcImpl_SetGetIsProt (retval, & s_SeqDbGetIsProt); _BlastSeqSrcImpl_SetGetSupportsPartialFetching (retval, & s_SeqDbGetSupportsPartialFetching); _BlastSeqSrcImpl_SetSetSeqRange (retval, & s_SeqDbSetRanges); _BlastSeqSrcImpl_SetGetSequence (retval, & s_SeqDbGetSequence); _BlastSeqSrcImpl_SetGetSeqLen (retval, & s_SeqDbGetSeqLen); _BlastSeqSrcImpl_SetIterNext (retval, & s_SeqDbIteratorNext); _BlastSeqSrcImpl_SetResetChunkIterator(retval, & s_SeqDbResetChunkIterator); /* *********** START ************* */ _BlastSeqSrcImpl_SetSetChunkIterator(retval, & s_SeqDbSetChunkIterator); _BlastSeqSrcImpl_SetSetMmapMemory(retval, & s_SeqDbSetMmapMemory); /* ********** FINISH ************* */ _BlastSeqSrcImpl_SetReleaseSequence (retval, & s_SeqDbReleaseSequence); _BlastSeqSrcImpl_SetSetNumberOfThreads (retval, & s_SeqDbSetNumberOfThreads); #ifdef KAPPA_PRINT_DIAGNOSTICS _BlastSeqSrcImpl_SetGetGis (retval, & s_SeqDbGetGiList); #endif /* KAPPA_PRINT_DIAGNOSTICS */ } /// Populates a BlastSeqSrc, creating a new reference to the already existing /// SeqDb object. /// @param retval Original BlastSeqSrc [in] /// @param args Pointer to a reference to CSeqDB object [in] /// @return retval static BlastSeqSrc* s_SeqDbSrcSharedNew(BlastSeqSrc* retval, void* args) { _ASSERT(retval); _ASSERT(args); TSeqDBData * datap = (TSeqDBData *) args; s_InitNewSeqDbSrc(retval, datap->clone()); return retval; } /// SeqDb sequence source constructor /// @param retval BlastSeqSrc structure (already allocated) to populate [in] /// @param args Pointer to internal CSeqDbSrcNewArgs structure (@sa /// CSeqDbSrcNewArgs) [in] /// @return Updated seq_src structure (with all function pointers initialized static BlastSeqSrc* s_SeqDbSrcNew(BlastSeqSrc* retval, void* args) { _ASSERT(retval); _ASSERT(args); CSeqDbSrcNewArgs* seqdb_args = (CSeqDbSrcNewArgs*) args; _ASSERT(seqdb_args); TSeqDBData * datap = new TSeqDBData; try { bool is_protein = (seqdb_args->GetDbType() == 'p'); datap->seqdb.Reset(new CSeqDBExpert(seqdb_args->GetDbName(), (is_protein ? CSeqDB::eProtein : CSeqDB::eNucleotide))); datap->seqdb->SetIterationRange(seqdb_args->GetFirstOid(), seqdb_args->GetFinalOid()); datap->mask_algo_id = seqdb_args->GetMaskAlgoId(); datap->mask_type = seqdb_args->GetMaskType(); // Validate that the masking algorithm is supported if (datap->mask_algo_id > 0) { vector supported_algorithms; datap->seqdb->GetAvailableMaskAlgorithms(supported_algorithms); if (find(supported_algorithms.begin(), supported_algorithms.end(), datap->mask_algo_id) == supported_algorithms.end()) { CNcbiOstrstream oss; oss << "Masking algorithm ID " << datap->mask_algo_id << " is " << "not supported in " << (is_protein ? "protein" : "nucleotide") << " '" << seqdb_args->GetDbName() << "' BLAST database"; string msg = CNcbiOstrstreamToString(oss); throw runtime_error(msg); } } } catch (const ncbi::CException& e) { _BlastSeqSrcImpl_SetInitErrorStr(retval, strdup(e.ReportThis(eDPF_ErrCodeExplanation).c_str())); } catch (const std::exception& e) { _BlastSeqSrcImpl_SetInitErrorStr(retval, strdup(e.what())); } catch (...) { _BlastSeqSrcImpl_SetInitErrorStr(retval, strdup("Caught unknown exception from CSeqDB constructor")); } /* Initialize the BlastSeqSrc structure fields with user-defined function * pointers and seqdb */ s_InitNewSeqDbSrc(retval, datap); return retval; } } BlastSeqSrc* SeqDbBlastSeqSrcInit(const string& dbname, bool is_prot, Uint4 first_seq, Uint4 last_seq, Int4 mask_algo_id, Int4 mask_type) { BlastSeqSrcNewInfo bssn_info; BlastSeqSrc* seq_src = NULL; CSeqDbSrcNewArgs seqdb_args(dbname, is_prot, first_seq, last_seq, mask_algo_id, mask_type); bssn_info.constructor = &s_SeqDbSrcNew; // FIXME: shouldn't this be s_SeqDbSrcSharedNew? bssn_info.ctor_argument = (void*) &seqdb_args; seq_src = BlastSeqSrcNew(&bssn_info); return seq_src; } BlastSeqSrc* SeqDbBlastSeqSrcInit(CSeqDB * seqdb, Int4 mask_algo_id, Int4 mask_type) { BlastSeqSrcNewInfo bssn_info; BlastSeqSrc * seq_src = NULL; TSeqDBData data(seqdb, mask_algo_id, mask_type); bssn_info.constructor = & s_SeqDbSrcSharedNew; bssn_info.ctor_argument = (void*) & data; seq_src = BlastSeqSrcNew(& bssn_info); return seq_src; } END_SCOPE(blast) END_NCBI_SCOPE /* @} */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/seqdbimpl.hpp0000644000175000017500000015556312001215336023267 0ustar ykeyke#ifndef OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP #define OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP /* $Id: seqdbimpl.hpp 205653 2010-09-21 12:39:00Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file seqdbimpl.hpp /// The top level of the private implementation layer for SeqDB. /// /// Defines classes: /// CSeqDBImplFlush /// CSeqDBImpl /// /// Implemented for: UNIX, MS-Windows #include "seqdbvolset.hpp" #include "seqdbalias.hpp" #include "seqdboidlist.hpp" #include "seqdbcol.hpp" #include "seqdbgimask.hpp" BEGIN_NCBI_SCOPE using namespace ncbi::objects; /// CSeqDBImplFlush class /// /// This functor like object provides a call back mechanism to return /// memory holds to the atlas, from lease objects in the other objects /// under CSeqDBImpl. Without this class, CSeqDBAtlas and CSeqDBImpl /// would be codependant, which is somewhat bad style, and creates /// annoying cyclical dependencies among the include files. class CSeqDBImplFlush : public CSeqDBFlushCB { public: /// Constructor CSeqDBImplFlush() : m_Impl(0) { } /// Destructor virtual ~CSeqDBImplFlush() { } /// Specify the implementation layer object. /// /// This method sets the SeqDB implementation layer object /// pointer. Until this pointer is set, this object will ignore /// attempts to flush unused data. This pointer should not bet /// set until object construction is complete enough to permit the /// memory lease flushing to happen safely. /// /// @param impl /// A pointer to the implementation layer object. virtual void SetImpl(class CSeqDBImpl * impl) { m_Impl = impl; } /// Flush any held memory leases. /// /// At the beginning of garbage collection, this method is called /// to tell the implementation layer to release any held memory /// leases. If the SetImpl() method has not been called, this /// method will do nothing. virtual void operator()(); private: /// A pointer to the SeqDB implementation layer. CSeqDBImpl * m_Impl; }; /// Map user algorithm IDs to volume algorithm IDs. /// /// Each volume has a mapping of algorithm IDs to descriptions. This /// class builds a global list of algorithm IDs for all algorithm /// descriptions in all volumes. class CSeqDB_IdRemapper { public: /// Constructor. CSeqDB_IdRemapper(); /// Register a volume's algorithm definition. void AddMapping(int vol_id, int id, const string & desc); /// Get a list of user (real) IDs available here. void GetIdList(vector & algorithms); /// Is this object populated? bool Empty() { return m_Empty && m_IdToDesc.empty(); } /// Is this object populated? bool GetDesc(int algorithm_id, string & desc); /// Is this object populated? void SetNotEmpty() { m_Empty = false; } /// Build a list of volume algorithm IDs. /// /// This method takes a list of algorithm IDs and translates them /// to volume IDs. The translation is cached. The Atlas lock /// should be held while calling this method and kept until the /// the returned data is no longer needed. /// /// @param vol_idx The index of the database volume. /// @param algo_id A list of (global) algorithms ID. /// @return The volume specific algorithm ID. int GetVolAlgo(int vol_idx, int algo_id); /// Translate a real algorithm ID to a volume algorithm ID. int RealToVol(int vol_idx, int algo_id); private: /// Next unassigned synthetic ID. int m_NextId; /// Map of real IDs to descriptions. map m_IdToDesc; /// Map of descriptions to real IDs. map m_DescToId; /// Map of volume# to map of real id to volume-based id. map > m_RealIdToVolumeId; /// Is this object initialized? bool m_Empty; /// Cached list of real algorithms for BuildVolAlgos. int m_CacheRealAlgo; /// Cached volume index for BuildVolAlgos. int m_CacheVolIndex; /// Cached list of volume algorithms for BuildVolAlgos. int m_CacheVolAlgo; }; /// CSeqDBImpl class /// /// This is the main implementation layer of the CSeqDB class. This /// is seperated from that class so that various implementation /// details of CSeqDB are kept from the public interface. class CSeqDBImpl { /// Import type to allow shorter name. typedef TSeqDBAliasFileValues TAliasFileValues; public: /// Defines types of database summary information. typedef CSeqDB::ESummaryType ESummaryType; /// Standard Constructor /// /// This builds a CSeqDBImpl object from the provided parameters, /// which correspond to those of the longer CSeqDB constructor. /// /// @param db_name_list /// A list of database or alias names, seperated by spaces. /// @param prot_nucl /// Either kSeqTypeProt for a protein database, or kSeqTypeNucl /// for nucleotide. These can also be specified as 'p' or 'n'. /// @param oid_begin /// Iterator will skip OIDs less than this value. Only OIDs /// found in the OID lists (if any) will be returned. /// @param oid_end /// Iterator will return up to (but not including) this OID. /// @param use_mmap /// If kSeqDBMMap is specified (the default), memory mapping is /// attempted. If kSeqDBNoMMap is specified, memory mapping /// fails, or this platform does not support it, the less /// efficient read and write calls are used instead. /// @param gi_list /// If not null, specifies included deflines and OIDs. /// @param neg_list /// If not null, specifies excluded deflines and OIDs. /// @param idset /// Specifies included or excluded deflines and OIDs. CSeqDBImpl(const string & db_name_list, char prot_nucl, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list, CSeqDBNegativeList * neg_list, CSeqDBIdSet idset); /// Default Constructor /// /// This builds a null version of the CSeqDBImpl object. It is in /// support of the default constructor for the CSeqDBExpert class. CSeqDBImpl(); /// Destructor ~CSeqDBImpl(); /// Get the sequence length. /// /// This computes and returns the exact sequence length for the /// indicated sequence. /// /// @param oid /// The ordinal id of the sequence. /// @return /// The length of the sequence in bases. int GetSeqLength(int oid) const; /// Get the approximate sequence length. /// /// This computes and returns the approximate sequence length for /// the indicated sequence. /// /// @param oid /// The ordinal id of the sequence. /// @return /// The approximate length of the sequence in bases. int GetSeqLengthApprox(int oid) const; /// Get the sequence header data. /// /// This builds and returns the header data corresponding to the /// indicated sequence as a Blast-def-line-set. /// /// @param oid /// The ordinal id of the sequence. /// @return /// The length of the sequence in bases. CRef GetHdr(int oid); /// Get the sequence type. /// /// Return an enumerated value indicating which type of sequence /// data this instance of SeqDB stores. /// /// @return /// The type of sequences stored here, either kSeqTypeProt or kSeqTypeNucl. char GetSeqType() const; /// Get gi to taxid map for an OID. /// /// This finds the TAXIDS associated with a given OID and computes /// a mapping from GI to taxid. This mapping is added to the /// map provided by the user. If the "persist" flag is /// set to true, the new associations will simply be added to the /// map. If it is false (the default), the map will be cleared /// first. /// /// @param oid /// The ordinal id of the sequence. /// @param gi_to_taxid /// A returned mapping from GI to taxid. /// @param persist /// If false, the map will be cleared before adding new entries. void GetTaxIDs(int oid, map & gi_to_taxid, bool persist); /// Get taxids for an OID. /// /// This finds the TAXIDS associated with a given OID and returns /// them in a vector. If the "persist" flag is set to true, the /// new taxids will simply be appended to the vector. If it is /// false (the default), the vector will be cleared first. One /// advantage of this interface over the map version is /// that the vector interface works with databases with local IDs /// but lacking GIs. /// /// @param oid /// The ordinal id of the sequence. /// @param taxids /// A returned list of taxids. /// @param persist /// If false, the map will be cleared before adding new entries. void GetTaxIDs(int oid, vector & taxids, bool persist); /// Get a CBioseq for a sequence. /// /// This builds and returns the header and sequence data /// corresponding to the indicated sequence as a CBioseq. If /// target_gi is non-null, the header information will be filtered /// to only include the defline associated with that gi. /// /// @param oid /// The ordinal id of the sequence. /// @param target_gi /// The target gi to filter the header information by. /// @param target_seq_id /// The target seq_id to filter the header information by. /// @param seqdata /// If true, sequence data will be provided. /// @return /// A CBioseq object corresponding to the sequence. CRef GetBioseq(int oid, int target_gi, const CSeq_id * target_seq_id, bool seqdata); /// Get the sequence data for a sequence. /// /// Get the raw sequence (strand data). When done, resources /// should be returned with RetSequence. This data pointed to /// by *buffer is in read-only memory (where supported). /// @param oid /// The ordinal id of the sequence. /// @param buffer /// A returned pointer to the data in the sequence. /// @return /// The return value is the sequence length (in base pairs or /// residues). In case of an error, an exception is thrown. int GetSequence(int oid, const char ** buffer) const; /// Get a pointer to a range of sequence data with ambiguities. /// /// This is like GetAmbigSeq(), but the allocated object should be /// deleted by the caller. This is intended for users who are /// going to modify the sequence data, or are going to mix the /// data into a container with other data, and who are mixing data /// from multiple sources and want to free the data in the same /// way. The fourth parameter should be given one of the values /// from EAllocStrategy; the corresponding method should be used /// to delete the object. Note that "delete[]" should be used /// instead of "delete" /// /// @param oid /// The ordinal id of the sequence. /// @param buffer /// A returned pointer to the data in the sequence. /// @param nucl_code /// The encoding to use for the returned sequence data. /// @param region /// If non-null, the offset range to get. /// @param strategy /// Selects which function is used to allocate the buffer. /// @return /// The return value is the sequence length (in base pairs or /// residues). In case of an error, an exception is thrown. int GetAmbigSeq(int oid, char ** buffer, int nucl_code, SSeqDBSlice * region, ESeqDBAllocType strategy, CSeqDB::TSequenceRanges * masks = NULL ) const; /// Returns any resources associated with the sequence. /// /// Calls to GetSequence (but not GetBioseq()) /// either increment a counter corresponding to a section of the /// database where the sequence data lives, or allocate a buffer /// to return to the user. This method decrements that counter or /// frees the allocated buffer, so that the memory can be used by /// other processes. Each allocating call should be paired with a /// returning call. Note that this does not apply to GetBioseq(), /// or GetHdr(), for example. /// /// @param buffer /// A pointer to the sequence data to release. void RetSequence(const char ** buffer) const; /// Returns any resources associated with the sequence. /// /// Calls to GetAmbigSeq (but not GetBioseq()) /// either increment a counter corresponding to a section of the /// database where the sequence data lives, or allocate a buffer /// to return to the user. This method decrements that counter or /// frees the allocated buffer, so that the memory can be used by /// other processes. Each allocating call should be paired with a /// returning call. Note that this does not apply to GetBioseq(), /// or GetHdr(), for example. /// /// @param buffer /// A pointer to the sequence data to release. void RetAmbigSeq(const char ** buffer) const; /// Gets a list of sequence identifiers. /// /// This returns the list of CSeq_id identifiers associated with /// the sequence specified by the given OID. /// /// @param oid /// The oid of the sequence. /// @return /// A list of Seq-id objects for this sequence. list< CRef > GetSeqIDs(int oid); /// Look up for the GI of a sequence /// /// This returns the first GI (if any) that identifies the sequence /// specified by the given OID, or -1 if no GI is found. /// /// @param oid /// The oid of the sequence. /// @return /// GI or -1. int GetSeqGI(int oid); /// Returns the database title. /// /// This is usually read from database volumes or alias files. If /// multiple databases were passed to the constructor, this will /// be a concatenation of those databases' titles. string GetTitle() const; /// Returns the construction date of the database. /// /// This is encoded in the database. If multiple databases or /// multiple volumes were accessed, the first available date will /// be used. string GetDate() const; /// Returns the number of sequences available. int GetNumSeqs() const; /// Returns the number of sequences available. /// /// This may be overridden by the STATS_NSEQ key. int GetNumSeqsStats() const; /// Returns the size of the (possibly sparse) OID range. int GetNumOIDs() const; /// Returns the sum of the lengths of all available sequences. /// /// This uses summary information stored in the database volumes /// or alias files. It provides an exact value, without iterating /// over individual sequences. Uint8 GetTotalLength() const; /// Returns the sum of the lengths of all available sequences. /// /// This uses summary information stored in the database volumes /// or alias files. It provides either an exact value or a value /// changed in the alias files by the STATS_TOTLEN key. Uint8 GetTotalLengthStats() const; /// Returns the sum of the lengths of all volumes. /// /// This uses summary information stored in the database volumes /// (but not the alias files). It provides an exact value, /// without iterating over individual sequences. It includes all /// OIDs regardless of inclusion by the filtering mechanisms of /// the alias files. Uint8 GetVolumeLength() const; /// Returns the length of the largest sequence in the database. /// /// This uses summary information stored in the database volumes /// or alias files. This might be used to chose buffer sizes. int GetMaxLength() const; /// Find an included OID, incrementing next_oid if necessary. /// /// If the specified OID is not included in the set (i.e. the OID /// mask), the input parameter is incremented until one is found /// that is. The user will probably want to increment between /// calls, if iterating over the db. /// /// @param next_oid The starting oid, the selected oid [in|out]. /// @return True if a valid OID was found, false otherwise. bool CheckOrFindOID(int & next_oid); /// Return a chunk of OIDs, and update the OID bookmark. /// /// This method allows the caller to iterate over the database by /// fetching batches of OIDs. It will either return a list of OIDs in /// a vector, or set a pair of integers to indicate a range of OIDs. /// The return value will indicate which technique was used. The /// caller sets the number of OIDs to get by setting the size of the /// vector. If eOidRange is returned, the first included oid is /// oid_begin and oid_end is the oid after the last included oid. If /// eOidList is returned, the vector contain the included OIDs, and may /// be resized to a smaller value if fewer entries are available (for /// the last chunk). In some cases it may be desireable to have /// several concurrent, independent iterations over the same database /// object. If this is required, the caller should specify the address /// of an int to the optional parameter oid_state. This should be /// initialized to zero (before the iteration begins) but should /// otherwise not be modified by the calling code (except that it can /// be reset to zero to restart the iteration). For the normal case of /// one iteration per program, this parameter can be omitted. /// @param begin_chunk /// First included oid (if eOidRange is returned). /// @param end_chunk /// OID after last included (if eOidRange is returned). /// @param oid_size /// Number of OID to retrieve (ignored in MT environment). /// @param oid_list /// Empty list to be filled if eOidList is returned. /// @param oid_state /// Optional address of a state variable (for concurrent iterations). /// @return /// eOidList in enumeration case, or eOidRange in begin/end range case. CSeqDB::EOidListType GetNextOIDChunk(int & begin_chunk, int & end_chunk, int oid_size, vector & oid_list, int * oid_state); /// Restart chunk iteration at the beginning of the database. void ResetInternalChunkBookmark(); /* *********** START ************* */ /// Restart chunk iteration at the beginning of the database. void SetInternalChunkBookmark(int InternalChunkBookmark); void SetMmapMemory(bool mmap_memory ); /* ********** FINISH ************* */ /// Get list of database names. /// /// This returns the database name list used at construction. /// @return /// List of database names. const string & GetDBNameList() const; /// Get GI list attached to this database. /// /// This returns the GI list attached to this database, or NULL, /// if no GI list was used. The effects of changing the contents /// of this GI list are undefined. This method only deals with /// the GI list passed to the top level CSeqDB constructor; it /// does not consider volume GI lists. /// /// @return A pointer to the attached GI list, or NULL. const CSeqDBGiList * GetGiList() const { return m_UserGiList.GetPointerOrNull(); } /// Get IdSet list attached to this database. /// /// This returns the ID set used to filter this database. If a /// CSeqDBGiList or CSeqDBNegativeList was used instead, then an /// ID set object will be constructed and returned (and cached /// here). This method only deals with filtering applied to the /// top level CSeqDB constructor; it does not consider GI or TI /// lists attached from alias files. If no filtering was used, a /// 'blank' list will be returned (an empty negative list). /// /// @return A pointer to the attached ID set, or NULL. CSeqDBIdSet GetIdSet(); /// Set upper limit on memory and mapping slice size. /// /// This sets an approximate upper limit on memory used by CSeqDB /// for file mappings and large arrays. This will not be exactly /// enforced; the library will prefer to exceed the bound rather /// than return an error. Setting this to a very low value will /// cause bad performance. If this is not set, SeqDB picks a /// large value and lowers it if an allocation fails. /// /// @param membound Maximum memory to use for file mappings. void SetMemoryBound(Uint8 membound) { CHECK_MARKER(); m_Atlas.SetMemoryBound(membound); } /// Flush unnecessarily held memory /// /// This is used by the atlas garbage collection callback - when /// gc is running, it should not count references held by the /// volset. Thus, the no-longer-in-action volumes can be flushed /// out (currently, idx files are still kept for all volumes). /// The atlas should be locked when calling this method. void FlushSeqMemory(); /// Translate a PIG to an OID. bool PigToOid(int pig, int & oid) const; /// Translate a PIG to an OID. bool OidToPig(int oid, int & pig) const; /// Translate a TI to an OID. bool TiToOid(Int8 ti, int & oid); /// Translate a GI to an OID. bool GiToOid(int gi, int & oid) const; /// Translate a GI to an OID. bool OidToGi(int oid, int & gi); /// Find OIDs matching the specified string. void AccessionToOids(const string & acc, vector & oids); /// Translate a CSeq-id to a list of OIDs. void SeqidToOids(const CSeq_id & seqid, vector & oids, bool multi); /// Find the OID corresponding to the offset given in residues, /// into the database as a whole. int GetOidAtOffset(int first_seq, Uint8 residue) const; /// Find volume paths /// /// Find the base names of volumes/aliases. This version of this /// method builds an alias hierarchy (which should be much faster /// than constructing an entire CSeqDBImpl object), and returns /// the resolved volume file base names from that hierarchy. /// /// @param dbname /// The input name of the database /// @param prot_nucl /// Indicates whether the database is protein or nucleotide /// @param paths /// The returned set of resolved database volume path names /// @param alias_paths /// The returned set of resolved database alias path names /// @param recursive /// If true, search will traverse the full alias node tree static void FindVolumePaths(const string & dbname, char prot_nucl, vector & paths, vector * alias_paths, bool recursive); /// Find volume paths /// /// Find the base names of all volumes. This method version of /// this method returns the existing internal versions of the /// resolved volume file base names from that hierarchy. /// /// @param paths /// The returned set of resolved database path names /// @param recursive /// If true the search will traverse the full alias node tree void FindVolumePaths(vector & paths, bool recursive) const; /// Set Iteration Range /// /// This method sets the iteration range as a pair of OIDs. /// Iteration proceeds from begin, up to but not including end. /// End will be adjusted to the number of OIDs in the case that it /// is 0, negative, or greater than the number of OIDs. /// /// @param oid_begin /// Iterator will skip OIDs less than this value. Only OIDs /// found in the OID lists (if any) will be returned. /// @param oid_end /// Iterator will return up to (but not including) this OID. void SetIterationRange(int oid_begin, int oid_end); /// Get Name/Value Data From Alias Files /// /// SeqDB treats each alias file as a map from a variable name to /// a value. This method will return a map from the basename of /// the filename of each alias file, to a mapping from variable /// name to value for each entry in that file. For example, the /// value of the "DBLIST" entry in the "wgs.nal" file would be /// values["wgs"]["DBLIST"]. The lines returned have been /// processed somewhat by SeqDB, including normalizing tabs to /// whitespace, trimming leading and trailing whitespace, and /// removal of comments and other non-value lines. Care should be /// taken when using the values returned by this method. SeqDB /// uses an internal "virtual" alias file entry to aggregate the /// values passed into SeqDB by the user. This mapping uses a /// filename of "-" and contains a single entry mapping "DBLIST" /// to SeqDB's database name input. This entry is the root of the /// alias file inclusion tree. Also note that alias files that /// appear in several places in the alias file inclusion tree only /// have one entry in the returned map (and are only parsed once /// by SeqDB). /// /// @param afv /// The alias file values will be returned here. void GetAliasFileValues(TAliasFileValues & afv); /// Verify consistency of the memory management (atlas) layer. void Verify() { m_Atlas.Verify(false); } /// Get taxonomy information /// /// This method returns the taxonomy information for a single /// given taxid. This information does not vary with sequence /// type (protein vs. nucleotide) and should be the same, /// regardless of which blast database is loaded. /// /// @param taxid /// An integer identifying the taxid to fetch. /// @param info /// A structure containing taxonomic description strings. void GetTaxInfo(int taxid, SSeqDBTaxInfo & info); /// Returns the sum of the sequence lengths. /// /// This uses summary information and iteration to compute the /// total length and number of sequences for some subset of the /// database. If eUnfilteredAll is specified, it uses information /// from the underlying database volumes, without filtering. If /// eFilteredAll is specified, all of the included sequences are /// used, for all possible OIDs. If eFilteredRange is specified, /// the returned values correspond to the sum over only those /// sequences that survive filtering, and are within the iteration /// range. In some cases, the results can be computed in constant /// time; other cases require iteration proportional to the length /// of the database or the included OID range (see /// SetIterationRange()). /// /// @param sumtype /// Specifies the subset of sequences to include. /// @param oid_count /// The returned number of included OIDs. /// @param total_length /// The returned sum of included sequence lengths. /// @param use_approx /// Whether to use approximate lengths for nucleotide. void GetTotals(ESummaryType sumtype, int * oid_count, Uint8 * total_length, bool use_approx); /// Fetch data as a CSeq_data object. /// /// All or part of the sequence is fetched in a CSeq_data object. /// The portion of the sequence returned is specified by begin and /// end. An exception will be thrown if begin is greater than or /// equal to end, or if end is greater than or equal to the length /// of the sequence. Begin and end should be specified in bases; /// a range like (0,1) specifies 1 base, not 2. Nucleotide data /// will always be returned in ncbi4na format. /// /// @param oid Specifies the sequence to fetch. /// @param begin Specifies the start of the data to get. [in] /// @param end Specifies the end of the data to get. [in] /// @return The sequence data as a Seq-data object. CRef GetSeqData(int oid, TSeqPos begin, TSeqPos end) const; /// Raw Sequence and Ambiguity Data /// /// Get a pointer to the raw sequence and ambiguity data, and the /// length of each. The encoding for these is not defined here /// and should not be relied on to be compatible between different /// database format versions. NULL can be supplied for parameters /// that are not needed (except oid). RetSequence() must be /// called with the pointer returned by 'buffer' if and only if /// that pointer is supplied as non-null by the user. Protein /// sequences will never have ambiguity data. Ambiguity data will /// be packed in the returned buffer at offset *seq_length. /// /// @param oid Ordinal id of the sequence. /// @param buffer Buffer of raw data. /// @param seq_length Returned length of the sequence data. /// @param ambig_length Returned length of the ambiguity data. void GetRawSeqAndAmbig(int oid, const char ** buffer, int * seq_length, int * ambig_length) const; /// Get GI Bounds. /// /// Fetch the lowest, highest, and total number of GIs. A value /// is returned for each non-null argument. If the operation /// fails, an exception will be thrown, which probably indicates a /// missing index file. /// /// @param low_id Lowest GI value in database. [out] /// @param high_id Highest GI value in database. [out] /// @param count Number of GI values in database. [out] void GetGiBounds(int * low_id, int * high_id, int * count); /// Get PIG Bounds. /// /// Fetch the lowest, highest, and total number of PIGs. A value /// is returned for each non-null argument. If the operation /// fails, an exception will be thrown, which probably indicates a /// missing index file. /// /// @param low_id Lowest PIG value in database. [out] /// @param high_id Highest PIG value in database. [out] /// @param count Number of PIG values in database. [out] void GetPigBounds(int * low_id, int * high_id, int * count); /// Get String Bounds. /// /// Fetch the lowest, highest, and total number of string keys in /// the database index. A value is returned for each non-null /// argument. If the operation fails, an exception will be /// thrown, which probably indicates a missing index file. Note /// that the number of string keys does not directly correspond to /// the number of deflines, Seq-ids, or accessions. /// /// @param low_id Lowest string value in database. [out] /// @param high_id Highest string value in database. [out] /// @param count Number of string values in database. [out] void GetStringBounds(string * low_id, string * high_id, int * count); /// List of sequence offset ranges. typedef set< pair > TRangeList; /// Apply a range of offsets to a database sequence. /// /// The GetAmbigSeq() method requires an amount of work (and I/O) /// which is proportional to the size of the sequence data (more /// if ambiguities are present). In some cases, only certain /// subranges of this data will be utilized. This method allows /// the user to specify which parts of a sequence are actually /// needed by the user. (Care should be taken if one SeqDB object /// is shared by several program components.) (Note that offsets /// above the length of the sequence will not generate an error, /// and are replaced by the sequence length.) /// /// If ranges are specified for a sequence, data areas in /// specified sequences will be accurate, but data outside the /// specified ranges should not be accessed, and no guarantees are /// made about what data they will contain. If the keep_current /// flag is true, the range will be added to existing ranges. If /// false, existing ranges will be flushed and replaced by new /// ranges. To remove ranges, call this method with an empty list /// of ranges; future calls will return the complete sequence. /// /// If the cache_data flag is provided, data for this sequence /// will be kept for the duration of SeqDB's lifetime. To disable /// caching (and flush cached data) for this sequence, call the /// method again, but specify cache_data to be false. /// /// @param oid OID of the sequence. /// @param offset_ranges Ranges of sequence data to return. /// @param append_ranges Append new ranges to existing list. /// @param cache_data Keep sequence data for future callers. void SetOffsetRanges(int oid, const TRangeList & offset_ranges, bool append_ranges, bool cache_data); /// Flush all offset ranges cached void FlushOffsetRangeCache(); /// Set global default memory bound for SeqDB. /// /// The memory bound for individual SeqDB objects can be adjusted /// with SetMemoryBound(), but this cannot be called until after /// the object is constructed. Until that time, the value used is /// set from a global default. This method allows that global /// default value to be changed. Any SeqDB object constructed /// after this method is called will use this value as the initial /// memory bound. If zero is specified, an appropriate default /// will be selected based on system information. static void SetDefaultMemoryBound(Uint8 bytes); /// Get the sequence hash for a given OID. /// /// The sequence data is fetched and the sequence hash is /// computed and returned. /// /// @param oid The sequence to compute the hash of. [in] /// @return The sequence hash. unsigned GetSequenceHash(int oid); /// Get the OIDs for a given sequence hash. /// /// The OIDs corresponding to a hash value are found and returned. /// /// @param hash The sequence hash to look up. [in] /// @param oids OIDs of sequences with this hash. [out] void HashToOids(unsigned hash, vector & oids); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// List columns titles found in this database. /// /// This returns a list of the column titles of all user created /// (and system generated) columns found in any of this database's /// volumes. Column titles appearing in more than one volume are /// only listed here once. /// /// @param titles Column titles are returned here. [out] void ListColumns(vector & titles); /// Get an ID number for a given column title. /// /// For a given column title, this returns an ID that can be used /// to access that column in the future. The returned ID number /// is specific to this instance of SeqDB. If the database does /// not have a column with this name, -1 will be returned. /// /// @param title Column title to search for. [in] /// @return Column ID number for this column, or -1. [in] int GetColumnId(const string & title); /// Get all metadata for the specified column. /// /// Columns may contain user-defined metadata as a list of /// key-value pairs. For the specified column, this returns that /// column's metadata in the provided map. If multiple volumes /// are present, and they define contradictory meta data (this is /// more common when multiple databases are opened at once), this /// method returns the first value it finds for each metadata key. /// If this is unsatisfactory, the two-argument version of this /// method may be used to get more precise values for specific /// volumes. /// /// @param column_id The column id from GetColumnId. [in] /// @return The map of metadata for this column. [out] const map & GetColumnMetaData(int column_id); /// Get all metadata for the specified column. /// /// Columns may contain user-defined metadata as a list of /// key-value pairs. For the specified database volume and column /// id, this returns that column's metadata (as defined for that /// volume) in the provided map. The volume name should match /// the string returned by FindVolumePaths(vector&). /// /// @param column_id The column id from GetColumnId. [in] /// @param volname The volume to get metadata for. [in] /// @return The map of metadata for this column + volume. [out] const map & GetColumnMetaData(int column_id, const string & volname); /// Get all metadata for the specified column. /// /// Columns can contain user-defined metadata as a list of /// key-value pairs. For the specified column, this returns all /// of that column's metadata in the provided map. If there are /// multiple volumes, and those volumes define contradictory meta /// data (this is more common if multiple databases are opened at /// once), this method will return the first value it finds for /// each metadata key. In these cases, GetVolumeColumnProperties /// may be used instead. /// /// @param column_id The column id from GetColumnId. [in] /// @return The value corresponding to the specified key. [out] string GetColumnValue(int column_id, const string & key); /// Fetch the data blob for the given column and oid. /// @param col_id The column to fetch data from. [in] /// @param oid The OID of the blob. [in] /// @param keep Whether to add a hold on this blob's memory. [in] /// @param blob The data will be returned here. [out] void GetColumnBlob(int col_id, int oid, bool keep, CBlastDbBlob & blob); // Mask data support. /// Get a list of algorithm IDs for which mask data exists. /// /// Multiple sources of masking data may be used when building /// blast databases. This method retrieves a list of the IDs used /// to identify those types of filtering data to SeqDB. If the /// blast database volumes used by this instance of SeqDB were /// built with conflicting algorithm ID definitions, SeqDB will /// resolve the conflicts by renumbering some of the conflicting /// descriptions. For this reason, the IDs reported here may not /// match what was given to WriteDB when the database was created. /// /// @param algorithms List of algorithm ids. [out] void GetAvailableMaskAlgorithms(vector & algorithms); /// Get the numeric ID for a algorithm name int GetMaskAlgorithmId(const string &algo_name) const; /// Returns a formatted string with the list of available masking /// algorithms in this database for display purposes (i.e.: help) string GetAvailableMaskAlgorithmDescriptions(); /// Get information about one type of masking available here. /// /// For a given algorithm_id, this method fetches information /// describing the basic algorithm used, as well as options passed /// to that algorithm to generate the data stored here. Each /// sequence in the database can provide sequence masking data /// from one or more sources. There can also be multiple types of /// masking data from the same algorithm (such as DUST), but /// generated with different sets of input parameters. /// /// @param algorithm_id The ID as from GetAvailableMaskAlgorithms. [in] /// @param program Program used to produce this masking data (SEG, DUST, /// etc) [out] /// @param program_name string representation of program argument [out] /// @param algo_opts Describes options passed to `program'. [out] void GetMaskAlgorithmDetails(int algorithm_id, EBlast_filter_program & program, string & program_name, string & algo_opts); /// Get masked ranges of a sequence. /// /// For the provided OID and list of algorithm IDs, this method /// gets a list of masked areas of those sequences. The list of /// masked areas is returned via the ranges parameter. If the /// `inverted' parameter is true, the list of ranges returned is /// actually the list of non-maksed (rather than masked) ranges. /// /// @param oid The ordinal ID of the sequence. [in] /// @param algo_id The algorithm ID to get data for. [in] /// @param inverted If true, return a list of included ranges. [in] /// @param ranges The list of sequence offset ranges. [out] void GetMaskData(int oid, int algo_id, CSeqDB::TSequenceRanges & ranges); #endif /// Invoke the garbage collector to free up memory void GarbageCollect(void); /// Set number of threads void SetNumberOfThreads(int num_threads); private: CLASS_MARKER_FIELD("IMPL") /// Adjust string length to offset of first embedded NUL byte. /// /// This is a work-around for bad data in the database; probably /// the fault of formatdb. The problem is that the database date /// field has an incorrect length - possibly a general problem /// with string handling in formatdb? In any case, this method /// trims a string to the minimum of its length and the position /// of the first NULL. This technique will not work if the date /// field is not null terminated, but apparently it usually or /// always is, in spite of the length bug. /// /// @param s /// A string which may contain a NUL byte. /// @return /// The non-NUL-containing prefix of the input string. string x_FixString(const string & s) const; /// Returns the number of sequences available. int x_GetNumSeqs() const; /// Returns the number of sequences available. int x_GetNumSeqsStats() const; /// Returns the size of the (possibly sparse) OID range. int x_GetNumOIDs() const; /// Returns the sum of the lengths of all available sequences. /// /// This uses summary information stored in the database volumes /// or alias files. It provides an exact value, without iterating /// over individual sequences. This private version uses the /// alias files, and is used to populate a field that caches the /// value; the corresponding public method uses that cached value. Uint8 x_GetTotalLength() const; /// Returns the sum of the lengths of all available sequences. /// /// This uses summary information stored in the database volumes /// or alias files. It provides an exact value, without iterating /// over individual sequences. This private version uses the /// alias files, and is used to populate a field that caches the /// value; the corresponding public method uses that cached value. /// It works just like x_GetTotalLengthStats() except that it uses /// the STATS_TOTLEN alias key. Uint8 x_GetTotalLengthStats() const; /// Returns the sum of the lengths of all volumes. /// /// This uses summary information stored in the database volumes /// (but not the alias files). It provides an exact value, /// without iterating over individual sequences. It includes all /// OIDs regardless of inclusion by the filtering mechanisms of /// the alias files. This private version uses the alias files, /// and is used to populate a field that caches the value; the /// corresponding public method uses that cached value. Uint8 x_GetVolumeLength() const; /// Returns the longest sequence lengths of all volumes. int x_GetMaxLength() const; /// Build the OID list /// /// OID list setup is done once, but not until needed. /// /// @param locked /// The lock hold object for this thread. void x_GetOidList(CSeqDBLockHold & locked); /// Get the next included oid /// /// This method checks if the OID list has the specified OID, and /// if not, finds the next one it does have, if any. /// /// @param next_oid /// The next oid to check and to return to the user. /// @param locked /// The lock hold object for this thread. /// @return /// true if an OID was found, false otherwise. bool x_CheckOrFindOID(int & next_oid, CSeqDBLockHold & locked); /// Get the sequence header data. /// /// This builds and returns the header data corresponding to the /// indicated sequence as a Blast-def-line-set. /// /// @param oid /// The ordinal id of the sequence. /// @param locked /// The lock hold object for this thread. /// @return /// The length of the sequence in bases. CRef x_GetHdr(int oid, CSeqDBLockHold & locked); /// Look up for the GI of a sequence /// /// This returns the first GI (if any) that identifies the sequence /// specified by the given OID, or -1 if no GI is found. /// /// @param oid /// The oid of the sequence. /// @param locked /// The lock hold object for this thread. /// @return /// GI or -1. int x_GetSeqGI(int oid, CSeqDBLockHold & locked); /// Compute totals via iteration /// /// This method loops over the database, computing the total /// number of (included) sequences and bases from the OID mask and /// sequence lengths. It stores the computed values in m_NumSeqs /// and m_TotalLength. /// /// @param approx /// Specify true if approximate lengths are okay. /// @param seq_count /// Returned count of included OIDs in this range. /// @param base_count /// Returned sum of lengths of included sequences. /// @param max_count /// Returned longest of included sequences. /// @param locked /// The lock hold object for this thread. void x_ScanTotals(bool approx, int * seq_count, Uint8 * base_count, int * max_count, CSeqDBLockHold & locked); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Get the Column ID for the column with the specified title. /// @param title The column title. /// @param locked The lock hold object for this thread. [in] /// @return A positive ID (if found), a negative code otherwise. int x_GetColumnId(const string & title, CSeqDBLockHold & locked); /// Open the mask data column (if necessary) and return its id. /// @param locked The lock hold object for this thread. [in] /// @return The column id of the mask data column. int x_GetMaskDataColumn(CSeqDBLockHold & locked); /// Get a list of algorithm IDs for which mask data exists. /// /// Multiple sources of masking data may be used when building /// blast databases. This method retrieves a list of the IDs used /// to identify those types of filtering data to SeqDB. If the /// blast database volumes used by this instance of SeqDB were /// built with conflicting algorithm ID definitions, SeqDB will /// resolve the conflicts by renumbering some of the conflicting /// descriptions. For this reason, the IDs reported here may not /// match what was given to WriteDB when the database was created. /// /// @param locked The lock hold object for this thread. [in] void x_BuildMaskAlgorithmList(CSeqDBLockHold & locked); #endif /// Get the sequence length. /// /// This computes and returns the exact sequence length for the /// indicated sequence. /// /// @param oid The ordinal id of the sequence. [in] /// @param locked The lock holder object for this thread. [in] /// @return The length of the sequence in bases. int x_GetSeqLength(int oid, CSeqDBLockHold & locked) const; /// Get local cache ID for current thread. /// /// @param locked /// The lock hold object for this thread. /// @return /// The mapped local cache ID int x_GetCacheID(CSeqDBLockHold &locked) const { int threadID = CThread::GetSelf(); if (m_NextCacheID < 0) return m_CacheID[threadID]; int retval; m_Atlas.Lock(locked); if (m_CacheID.find(threadID) == m_CacheID.end()) { m_CacheID[threadID] = m_NextCacheID++; } retval = m_CacheID[threadID]; if (m_NextCacheID == m_NumThreads) { m_NextCacheID = -1; } m_Atlas.Unlock(locked); return retval; } /// This callback functor allows the atlas code flush any cached /// region holds prior to garbage collection. CSeqDBImplFlush m_FlushCB; /// Memory management layer guard (RIIA) object. CSeqDBAtlasHolder m_AtlasHolder; /// Reference to memory management layer. mutable CSeqDBAtlas & m_Atlas; /// The list of database names provided to the constructor. string m_DBNames; /// Alias node hierarchy management object. CSeqDBAliasFile m_Aliases; /// Set of volumes used by this database instance. CSeqDBVolSet m_VolSet; /// The list of included OIDs (construction is deferred). mutable CRef m_OIDList; /// Taxonomic information. CRef m_TaxInfo; /// Starting OID as provided to the constructor. int m_RestrictBegin; /// Ending OID as provided to the constructor. int m_RestrictEnd; /// Mutex which synchronizes access to the OID list. CFastMutex m_OIDLock; /// "Bookmark" for multithreaded chunk-type OID iteration. int m_NextChunkOID; /// Number of sequences in the overall database. int m_NumSeqs; /// Number of sequences in the overall database. int m_NumSeqsStats; /// Size of databases OID range. int m_NumOIDs; /// Total length of database (in bases). Uint8 m_TotalLength; /// Total length of database (in bases). Uint8 m_TotalLengthStats; /// Total length of all database volumes combined (in bases). Uint8 m_VolumeLength; /// Longest database sequence int m_MaxLength; /// Type of sequences used by this instance. char m_SeqType; /// True if OID list setup is done (or was not required). mutable bool m_OidListSetup; /// The User GI list for the entire CSeqDB object. mutable CRef m_UserGiList; /// The Negative ID list for the entire CSeqDB object. mutable CRef m_NegativeList; /// The positive or negative ID list for the entire CSeqDB object. CSeqDBIdSet m_IdSet; /// True if this configuration cannot deduce totals without a scan. bool m_NeedTotalsScan; /// Cached most recent date string for GetDate(). mutable string m_Date; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Map assigned global column IDs to column information. vector< CRef > m_ColumnInfo; #endif /// Map string column titles to global column IDs. map m_ColumnTitleMap; /// Status of a database column title. enum EColumnStatus { /// This column is not heard of yet. kUnknownTitle = -1, /// This column does not exist (we checked). kColumnNotFound = -2 }; /// Which type of masks are we using? bool m_UseGiMask; /// Gi-based mask. CRef m_GiMask; /// Column ID for mask data column. int m_MaskDataColumn; /// Algorithm ID mapping. CSeqDB_IdRemapper m_AlgorithmIds; /// number of thread clients int m_NumThreads; /// mapping thread ID to storage ID mutable std::map m_CacheID; mutable int m_NextCacheID; /// Structure to keep sequence retrieval results struct SSeqRes { int length; // length of the sequence const char* address;// mapped memory start }; /// Structure to buffer multiple TSeqRes struct SSeqResBuffer { int oid_start; // starting oid for this buffer int checked_out; // number of sequences checked out vector results; SSeqResBuffer() : oid_start(0), checked_out(0) { results.reserve(2 << 20); } }; /// Cached sequences. mutable vector m_CachedSeqs; /// Fill up the buffer void x_FillSeqBuffer(SSeqResBuffer * buffer, int oid, CSeqDBLockHold &locked) const; /// Get sequence from buffer int x_GetSeqBuffer(SSeqResBuffer * buffer, int oid, const char ** seq) const; /// Return sequence to buffer void x_RetSeqBuffer(SSeqResBuffer * buffer, CSeqDBLockHold & locked) const; /* *********** START ************* */ bool m_MmapMemory; /* ********** FINISH ************* */ }; END_NCBI_SCOPE #endif // OBJTOOLS_READERS_SEQDB__SEQDBIMPL_HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/seqdbimpl.cpp0000644000175000017500000017465212001215336023262 0ustar ykeyke/* $Id: seqdbimpl.cpp 258326 2011-03-18 18:45:30Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file seqdbimpl.cpp /// Implementation for the CSeqDBImpl class, the top implementation /// layer for SeqDB. #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: seqdbimpl.cpp 258326 2011-03-18 18:45:30Z rafanovi $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include "seqdbimpl.hpp" #include #include #include #include BEGIN_NCBI_SCOPE CSeqDBImpl::CSeqDBImpl(const string & db_name_list, char prot_nucl, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list, CSeqDBNegativeList * neg_list, CSeqDBIdSet idset) : m_AtlasHolder (use_mmap, & m_FlushCB, NULL), m_Atlas (m_AtlasHolder.Get()), m_DBNames (db_name_list), m_Aliases (m_Atlas, db_name_list, prot_nucl), m_VolSet (m_Atlas, m_Aliases.GetVolumeNames(), prot_nucl, gi_list, neg_list), m_RestrictBegin (oid_begin), m_RestrictEnd (oid_end), m_NextChunkOID (0), m_NumSeqs (0), m_NumSeqsStats (0), m_NumOIDs (0), m_TotalLength (0), m_TotalLengthStats(0), m_VolumeLength (0), m_MaxLength (0), m_SeqType (prot_nucl), m_OidListSetup (false), m_UserGiList (gi_list), m_NegativeList (neg_list), m_IdSet (idset), m_NeedTotalsScan (false), m_UseGiMask (m_Aliases.HasGiMask()), m_MaskDataColumn (kUnknownTitle), m_NumThreads (0), /* *********** START ************* */ m_MmapMemory (true) /* ********** FINISH ************* */ { INIT_CLASS_MARK(); if (m_UseGiMask) { vector mask_list; m_Aliases.GetMaskList(mask_list); m_GiMask.Reset(new CSeqDBGiMask(m_Atlas, mask_list)); } _ASSERT((! gi_list) || (! neg_list)); m_VolSet.OptimizeGiLists(); m_OidListSetup = ! (m_Aliases.HasFilters() || gi_list || neg_list); m_VolumeLength = x_GetVolumeLength(); m_NumOIDs = x_GetNumOIDs(); SetIterationRange(0, m_NumOIDs); try { m_Atlas.Verify(false); m_TaxInfo = new CSeqDBTaxInfo(m_Atlas); m_Atlas.Verify(false); } catch(CSeqDBException &) { } // Don't setup the flush callback until the implementation data // structures are fully populated (otherwise flushing may try to // flush unconstructed memory leases). m_FlushCB.SetImpl(this); // If the alias files seem to provide correct data for the totals, // use it; otherwise scan the OID list and use approximate lengths // to compute the totals. Presence of a user GI list implies that // the alias file cannot have correct values. try { if (gi_list || neg_list || m_Aliases.NeedTotalsScan(m_VolSet)) { m_NeedTotalsScan = true; } if ((! m_OidListSetup) && (oid_begin || oid_end)) { m_NeedTotalsScan = true; } if (m_NeedTotalsScan) { CSeqDBLockHold locked(m_Atlas); // This is a whole-database scan; it's always done in // approximate length mode. x_ScanTotals(true, & m_NumSeqs, & m_TotalLength, & m_MaxLength, locked); m_Atlas.Verify(locked); } else { m_NumSeqs = x_GetNumSeqs(); m_TotalLength = x_GetTotalLength(); m_MaxLength = x_GetMaxLength(); } m_NumSeqsStats = x_GetNumSeqsStats(); m_TotalLengthStats = x_GetTotalLengthStats(); } catch(CSeqDBException & e) { m_UserGiList.Reset(); m_NegativeList.Reset(); m_VolSet.UnLease(); m_FlushCB.SetImpl(0); throw e; } SetIterationRange(oid_begin, oid_end); CHECK_MARKER(); } CSeqDBImpl::CSeqDBImpl() : m_AtlasHolder (false, & m_FlushCB, NULL), m_Atlas (m_AtlasHolder.Get()), m_Aliases (m_Atlas, "", '-'), m_RestrictBegin (0), m_RestrictEnd (0), m_NextChunkOID (0), m_NumSeqs (0), m_NumOIDs (0), m_TotalLength (0), m_VolumeLength (0), m_SeqType ('-'), m_OidListSetup (true), m_NeedTotalsScan (false), m_UseGiMask (false), m_MaskDataColumn (kUnknownTitle), m_NumThreads (0), /* *********** START ************* */ m_MmapMemory (true) /* ********** FINISH ************* */ { INIT_CLASS_MARK(); try { m_TaxInfo = new CSeqDBTaxInfo(m_Atlas); } catch(CSeqDBException &) { } // Don't setup the flush callback until the implementation data // structures are fully populated (otherwise flushing may try to // flush unconstructed memory leases). m_FlushCB.SetImpl(this); CHECK_MARKER(); } void CSeqDBImpl::SetIterationRange(int oid_begin, int oid_end) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_RestrictBegin = (oid_begin < 0) ? 0 : oid_begin; m_RestrictEnd = (oid_end < 0) ? 0 : oid_end; if ((oid_begin == 0) && (oid_end == 0)) { m_RestrictEnd = m_VolSet.GetNumOIDs(); } else { if ((oid_end == 0) || (m_RestrictEnd > m_VolSet.GetNumOIDs())) { m_RestrictEnd = m_VolSet.GetNumOIDs(); } if (m_RestrictBegin > m_RestrictEnd) { m_RestrictBegin = m_RestrictEnd; } } } CSeqDBImpl::~CSeqDBImpl() { CHECK_MARKER(); SetNumberOfThreads(0); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); // Prevent GC from flushing volumes after they are torn down. m_FlushCB.SetImpl(0); m_TaxInfo.Reset(); m_VolSet.UnLease(); if (m_OIDList.NotEmpty()) { m_OIDList->UnLease(); } BREAK_MARKER(); } void CSeqDBImpl::x_GetOidList(CSeqDBLockHold & locked) { CHECK_MARKER(); if (! m_OidListSetup) { m_Atlas.Lock(locked); if (m_OIDList.Empty()) { m_OIDList.Reset( new CSeqDBOIDList(m_Atlas, m_VolSet, *m_Aliases.GetFilterTree(), m_UserGiList, m_NegativeList, locked) ); } m_OidListSetup = true; } } bool CSeqDBImpl::CheckOrFindOID(int & next_oid) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); return x_CheckOrFindOID(next_oid, locked); } bool CSeqDBImpl::x_CheckOrFindOID(int & next_oid, CSeqDBLockHold & locked) { CHECK_MARKER(); bool success = true; if (next_oid < m_RestrictBegin) { next_oid = m_RestrictBegin; } if (next_oid >= m_RestrictEnd) { success = false; } if (! m_OidListSetup) { x_GetOidList(locked); } if (success && m_OIDList.NotEmpty()) { success = m_OIDList->CheckOrFindOID(next_oid); if (next_oid > m_RestrictEnd) { success = false; } } return success; } CSeqDB::EOidListType CSeqDBImpl::GetNextOIDChunk(int & begin_chunk, // out int & end_chunk, // out int oid_size, // in vector & oid_list, // out int * state_obj) // in+out { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); int cacheID = (m_NumThreads) ? x_GetCacheID(locked) : 0; m_Atlas.Lock(locked); if (! state_obj) { state_obj = & m_NextChunkOID; } // This has to be done before ">=end" check, to insure correctness // in empty-range cases. if (*state_obj < m_RestrictBegin) { *state_obj = m_RestrictBegin; } // Case 1: Iteration's End. if (*state_obj >= m_RestrictEnd) { begin_chunk = 0; end_chunk = 0; return CSeqDB::eOidRange; } begin_chunk = * state_obj; // fill the cache for all sequence in mmaped slice /* *********** START ************* */ if (m_NumThreads && m_MmapMemory) { /* ********** FINISH ************* */ SSeqResBuffer * buffer = m_CachedSeqs[cacheID]; x_FillSeqBuffer(buffer, begin_chunk, locked); end_chunk = begin_chunk + buffer->results.size(); } else { end_chunk = begin_chunk + oid_size; } if (end_chunk > m_RestrictEnd) { end_chunk = m_RestrictEnd; } *state_obj = end_chunk; if (! m_OidListSetup) { x_GetOidList(locked); } // Case 2: Return a range if (m_OIDList.Empty()) { return CSeqDB::eOidRange; } // Case 3: Ones and Zeros - The bitmap provides OIDs. int next_oid = begin_chunk; if (m_NumThreads) { oid_list.clear(); while(next_oid < end_chunk) { // Find next ordinal id, and save it if it falls within iteration range. if (m_OIDList->CheckOrFindOID(next_oid) && next_oid < end_chunk) { oid_list.push_back(next_oid++); } else { next_oid = end_chunk; break; } } } else { int iter = 0; oid_list.resize(oid_size); while (iter < oid_size) { if (next_oid >= m_RestrictEnd) break; // Find next ordinal id, and save it if it falls within iteration range. if (m_OIDList->CheckOrFindOID(next_oid) && next_oid < m_RestrictEnd) { oid_list[iter++] = next_oid++; } else { next_oid = m_RestrictEnd; break; } } if (iter < oid_size) { oid_list.resize(iter); } *state_obj = next_oid; } return CSeqDB::eOidList; } void CSeqDBImpl::ResetInternalChunkBookmark() { CHECK_MARKER(); CFastMutexGuard guard(m_OIDLock); m_NextChunkOID = 0; } /* *********** START ************* */ void CSeqDBImpl::SetInternalChunkBookmark(int NextChunkOID){ CHECK_MARKER(); CFastMutexGuard guard(m_OIDLock); m_NextChunkOID = NextChunkOID; } void CSeqDBImpl::SetMmapMemory(bool mmap_memory){ m_MmapMemory = mmap_memory; } /* ********** FINISH ************* */ int CSeqDBImpl::GetSeqLength(int oid) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.MentionOid(oid, m_NumOIDs, locked); return x_GetSeqLength(oid, locked); } int CSeqDBImpl::x_GetSeqLength(int oid, CSeqDBLockHold & locked) const { m_Atlas.Lock(locked); int vol_oid = 0; if ('p' == m_SeqType) { if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSeqLengthProt(vol_oid, locked); } } else { if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSeqLengthExact(vol_oid, locked); } } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } int CSeqDBImpl::GetSeqLengthApprox(int oid) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.MentionOid(oid, m_NumOIDs, locked); int vol_oid = 0; if ('p' == m_SeqType) { if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSeqLengthProt(vol_oid, locked); } } else { if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSeqLengthApprox(vol_oid, locked); } } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } void CSeqDBImpl::GetTaxIDs(int oid, map & gi_to_taxid, bool persist) { CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); if (! persist) { gi_to_taxid.clear(); } CRef defline_set = x_GetHdr(oid, locked); if ((! defline_set.Empty()) && defline_set->CanGet()) { ITERATE(list< CRef >, defline, defline_set->Get()) { if (! (*defline)->CanGetSeqid()) { continue; } if (! (*defline)->IsSetTaxid()) { continue; } ITERATE(list< CRef >, seqid, (*defline)->GetSeqid()) { if (! (**seqid).IsGi()) { continue; } gi_to_taxid[(**seqid).GetGi()] = (*defline)->GetTaxid(); } } } } void CSeqDBImpl::GetTaxIDs(int oid, vector & taxids, bool persist) { CSeqDBLockHold locked(m_Atlas); m_Atlas.MentionOid(oid, m_NumOIDs, locked); if (! persist) { taxids.clear(); } CRef defline_set = x_GetHdr(oid, locked); if ((! defline_set.Empty()) && defline_set->CanGet()) { ITERATE(list< CRef >, defline, defline_set->Get()) { if (! (*defline)->IsSetTaxid()) { continue; } taxids.push_back((*defline)->GetTaxid()); } } } CRef CSeqDBImpl::GetBioseq(int oid, int target_gi, const CSeq_id * target_seq_id, bool seqdata) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); int vol_oid = 0; if (! m_OidListSetup) { x_GetOidList(locked); } if (CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetBioseq(vol_oid, target_gi, target_seq_id, m_TaxInfo, seqdata, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } void CSeqDBImpl::RetSequence(const char ** buffer) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (m_NumThreads) { int cacheID = x_GetCacheID(locked); (m_CachedSeqs[cacheID]->checked_out)--; *buffer = 0; return; } // This returns a reference to part of a memory mapped region. m_Atlas.Lock(locked); m_Atlas.RetRegion(*buffer); *buffer = 0; } void CSeqDBImpl::RetAmbigSeq(const char ** buffer) const { // This returns an allocated object. CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Atlas.RetRegion(*buffer); *buffer = 0; } void CSeqDBImpl::x_RetSeqBuffer(SSeqResBuffer * buffer, CSeqDBLockHold & locked ) const { // client must return sequence before getting a new one if (buffer->checked_out > 0) { NCBI_THROW(CSeqDBException, eArgErr, "Sequence not returned."); } buffer->checked_out = 0; m_Atlas.Lock(locked); for(Uint4 index = 0; index < buffer->results.size(); ++index) { m_Atlas.RetRegion(buffer->results[index].address); } buffer->results.clear(); } int CSeqDBImpl::x_GetSeqBuffer(SSeqResBuffer * buffer, int oid, const char ** seq) const { // Search local cache for oid Uint4 index = oid - buffer->oid_start; if (index < buffer->results.size()) { (buffer->checked_out)++; *seq = buffer->results[index].address; return buffer->results[index].length; } // Not in cache, fill the cache CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); x_FillSeqBuffer(buffer, oid, locked); (buffer->checked_out)++; *seq = buffer->results[0].address; return buffer->results[0].length; } void CSeqDBImpl::x_FillSeqBuffer(SSeqResBuffer *buffer, int oid, CSeqDBLockHold &locked) const { // Must lock the atlas m_Atlas.Lock(locked); // clear the buffer first x_RetSeqBuffer(buffer, locked); buffer->oid_start = oid; Int4 vol_oid = 0; // Get all sequences within the lease if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { SSeqRes res; const char * seq; Int8 tot_length = m_Atlas.GetSliceSize(); res.length = vol->GetSequence(vol_oid++, &seq, locked); if (res.length < 0) return; // must return at least one sequence do { tot_length -= res.length; res.address = seq; buffer->results.push_back(res); res.length = vol->GetSequence(vol_oid++, &seq, locked); } while (res.length >= 0 && tot_length >= res.length); if (res.length >= 0) m_Atlas.RetRegion(seq); return; } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } int CSeqDBImpl::GetSequence(int oid, const char ** buffer) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (m_NumThreads) { int cacheID = x_GetCacheID(locked); return x_GetSeqBuffer(m_CachedSeqs[cacheID], oid, buffer); } int vol_oid = 0; m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSequence(vol_oid, buffer, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } CRef CSeqDBImpl::GetSeqData(int oid, TSeqPos begin, TSeqPos end) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); int vol_oid = 0; m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSeqData(vol_oid, begin, end, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } int CSeqDBImpl::GetAmbigSeq(int oid, char ** buffer, int nucl_code, SSeqDBSlice * region, ESeqDBAllocType alloc_type, CSeqDB::TSequenceRanges * masks) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); int vol_oid = 0; if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetAmbigSeq(vol_oid, buffer, nucl_code, alloc_type, region, masks, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } list< CRef > CSeqDBImpl::GetSeqIDs(int oid) { CHECK_MARKER(); int vol_oid = 0; CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); if (! m_OidListSetup) { x_GetOidList(locked); } if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetSeqIDs(vol_oid, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } int CSeqDBImpl::GetSeqGI(int oid) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); return x_GetSeqGI(oid, locked); } int CSeqDBImpl::GetNumSeqs() const { CHECK_MARKER(); return m_NumSeqs; } int CSeqDBImpl::GetNumSeqsStats() const { CHECK_MARKER(); return m_NumSeqsStats; } int CSeqDBImpl::GetNumOIDs() const { CHECK_MARKER(); return m_NumOIDs; } Uint8 CSeqDBImpl::GetTotalLength() const { CHECK_MARKER(); return m_TotalLength; } Uint8 CSeqDBImpl::GetTotalLengthStats() const { CHECK_MARKER(); return m_TotalLengthStats; } Uint8 CSeqDBImpl::GetVolumeLength() const { CHECK_MARKER(); return m_VolumeLength; } int CSeqDBImpl::x_GetNumSeqs() const { CHECK_MARKER(); // GetNumSeqs should not overflow, even for alias files. Int8 rv = m_Aliases.GetNumSeqs(m_VolSet); _ASSERT((rv & 0x7FFFFFFF) == rv); return (int) rv; } int CSeqDBImpl::x_GetSeqGI(int oid, CSeqDBLockHold & locked) { CHECK_MARKER(); m_Atlas.Lock(locked); if (! m_OidListSetup) { x_GetOidList(locked); } int vol_oid = 0; if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { // Try lookup *.nxg first int gi = vol->GetSeqGI(vol_oid, locked); if (gi>=0) return gi; // Fall back to parsing deflines list< CRef > ids = vol->GetSeqIDs(vol_oid, locked); ITERATE(list< CRef >, id, ids) { if ((**id).IsGi()) { return (**id).GetGi(); } } // No GI found return -1; } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } int CSeqDBImpl::x_GetNumSeqsStats() const { CHECK_MARKER(); // GetNumSeqs should not overflow, even for alias files. Int8 rv = m_Aliases.GetNumSeqsStats(m_VolSet); _ASSERT((rv & 0x7FFFFFFF) == rv); return (int) rv; } int CSeqDBImpl::x_GetNumOIDs() const { CHECK_MARKER(); Int8 num_oids = m_VolSet.GetNumOIDs(); // The aliases file may have more of these, because walking the // alias tree will count volumes each time they appear in the // volume set. The volset number is the "good" one, because it // corresponds to the range of OIDs we accept in methods like // "GetSequence()". If you give SeqDB an OID, the volset number // is the range for that oid. // However, at this layer, we need to use Int8, because the alias // number can overestimate so much that it wraps a signed int. _ASSERT(num_oids <= m_Aliases.GetNumOIDs(m_VolSet)); _ASSERT((num_oids & 0x7FFFFFFF) == num_oids); return (int) num_oids; } Uint8 CSeqDBImpl::x_GetTotalLength() const { CHECK_MARKER(); return m_Aliases.GetTotalLength(m_VolSet); } Uint8 CSeqDBImpl::x_GetTotalLengthStats() const { CHECK_MARKER(); return m_Aliases.GetTotalLengthStats(m_VolSet); } Uint8 CSeqDBImpl::x_GetVolumeLength() const { CHECK_MARKER(); return m_VolSet.GetVolumeSetLength(); } int CSeqDBImpl::x_GetMaxLength() const { CHECK_MARKER(); return m_VolSet.GetMaxLength(); } string CSeqDBImpl::GetTitle() const { CHECK_MARKER(); return x_FixString( m_Aliases.GetTitle(m_VolSet) ); } char CSeqDBImpl::GetSeqType() const { CHECK_MARKER(); if (const CSeqDBVol * vol = m_VolSet.GetVol(0)) { return vol->GetSeqType(); } return '-'; } string CSeqDBImpl::GetDate() const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); if (! m_Date.empty()) { return m_Date; } // This is close enough to allow parsing but does not precisely // describe the format normally used for generated dates. string fmt = "b d, Y H:m P"; string date; for(int i = 0; i < m_VolSet.GetNumVols(); i++) { string d = x_FixString( m_VolSet.GetVol(i)->GetDate() ); if (date.empty()) { date = d; } else if (d != date) { try { CTime t1(date, fmt); CTime t2(d, fmt); if (t2 > t1) { date.swap(d); } } catch(CStringException &) { // Here I think it is better to pick any valid date // than to propagate a string exception. } } } m_Date = date; return date; } CRef CSeqDBImpl::GetHdr(int oid) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); return x_GetHdr(oid, locked); } CRef CSeqDBImpl::x_GetHdr(int oid, CSeqDBLockHold & locked) { CHECK_MARKER(); m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); if (! m_OidListSetup) { x_GetOidList(locked); } int vol_oid = 0; if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetFilteredHeader(vol_oid, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } int CSeqDBImpl::GetMaxLength() const { CHECK_MARKER(); return m_MaxLength; } const string & CSeqDBImpl::GetDBNameList() const { CHECK_MARKER(); return m_DBNames; } // This is a work-around for bad data in the database; probably the // fault of formatdb. The problem is that the database date field has // an incorrect length - possibly a general problem with string // handling in formatdb? In any case, this method trims a string to // the minimum of its length and the position of the first NULL. This // technique will not work if the date field is not null terminated, // but apparently it usually or always is, in spite of the length bug. string CSeqDBImpl::x_FixString(const string & s) const { CHECK_MARKER(); for(int i = 0; i < (int) s.size(); i++) { if (s[i] == char(0)) { return string(s,0,i); } } return s; } void CSeqDBImplFlush::operator()() { if (m_Impl) { m_Impl->FlushSeqMemory(); } } // Assumes atlas is locked void CSeqDBImpl::FlushSeqMemory() { m_VolSet.UnLease(); } bool CSeqDBImpl::PigToOid(int pig, int & oid) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); for(int i = 0; i < m_VolSet.GetNumVols(); i++) { if (m_VolSet.GetVol(i)->PigToOid(pig, oid, locked)) { oid += m_VolSet.GetVolOIDStart(i); return true; } } return false; } bool CSeqDBImpl::OidToPig(int oid, int & pig) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); int vol_oid(0); if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetPig(vol_oid, pig, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } bool CSeqDBImpl::TiToOid(Int8 ti, int & oid) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (! m_OidListSetup) { x_GetOidList(locked); } for(int i = 0; i < m_VolSet.GetNumVols(); i++) { if (m_VolSet.GetVol(i)->TiToOid(ti, oid, locked)) { oid += m_VolSet.GetVolOIDStart(i); return true; } } return false; } bool CSeqDBImpl::GiToOid(int gi, int & oid) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); // This could be accellerated (a little) if a GI list is used. // However, this should be done (if at all) at the volume layer, // not in *Impl. This volume may mask a particular GI that the // user gi list DOES NOT mask. Or, the user GI list may assign // this GI an OID that belongs to a different volume, for example, // if the same GI appears in more than one volume. In such cases, // the volume GI list (if one exists) is probably a better filter, // because it represents the restrictions of both the volume GI // list and the User GI list. It's also smaller, and therefore // should be easier to binary search. // (The hypothetical optimization described above changes if there // are Seq-ids in the user provided list, because you can no // longer assume that the GI list is all-inclusive -- you would // also need to fall back on regular lookups.) for(int i = 0; i < m_VolSet.GetNumVols(); i++) { if (m_VolSet.GetVol(i)->GiToOid(gi, oid, locked)) { oid += m_VolSet.GetVolOIDStart(i); return true; } } return false; } bool CSeqDBImpl::OidToGi(int oid, int & gi) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (! m_OidListSetup) { x_GetOidList(locked); } int vol_oid(0); if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { return vol->GetGi(vol_oid, gi, locked); } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } void CSeqDBImpl::AccessionToOids(const string & acc, vector & oids) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (! m_OidListSetup) { x_GetOidList(locked); } oids.clear(); vector vol_oids; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { // Append any additional OIDs from this volume's indices. m_VolSet.GetVol(vol_idx)->AccessionToOids(acc, vol_oids, locked); if (vol_oids.empty()) { continue; } int vol_start = m_VolSet.GetVolOIDStart(vol_idx); ITERATE(vector, iter, vol_oids) { int oid1 = ((*iter) + vol_start); int oid2 = oid1; // Remove OIDs already found in OIDs. if (find(oids.begin(), oids.end(), oid1) != oids.end()) { continue; } // Filter out any oids not in the virtual oid bitmaps. if (x_CheckOrFindOID(oid2, locked) && (oid1 == oid2)) { oids.push_back(oid1); } } vol_oids.clear(); } } void CSeqDBImpl::SeqidToOids(const CSeq_id & seqid_in, vector & oids, bool multi) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (! m_OidListSetup) { x_GetOidList(locked); } // The lower level functions modify the seqid - namely, changing // or clearing certain fields before printing it to a string. // Further analysis of data and exception flow might reveal that // the Seq_id will always be returned to the original state by // this operation... At the moment, safest route is to clone it. CSeq_id seqid; seqid.Assign(seqid_in); oids.clear(); vector vol_oids; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { // Append any additional OIDs from this volume's indices. m_VolSet.GetVol(vol_idx)->SeqidToOids(seqid, vol_oids, locked); if (vol_oids.empty()) { continue; } int vol_start = m_VolSet.GetVolOIDStart(vol_idx); ITERATE(vector, iter, vol_oids) { int oid1 = ((*iter) + vol_start); int oid2 = oid1; // Filter out any oids not in the virtual oid bitmaps. if (x_CheckOrFindOID(oid2, locked) && (oid1 == oid2)) { oids.push_back(oid1); if (! multi) { return; } } } vol_oids.clear(); } } int CSeqDBImpl::GetOidAtOffset(int first_seq, Uint8 residue) const { CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); CHECK_MARKER(); if (first_seq >= m_NumOIDs) { NCBI_THROW(CSeqDBException, eArgErr, "OID not in valid range."); } if (residue >= m_VolumeLength) { NCBI_THROW(CSeqDBException, eArgErr, "Residue offset not in valid range."); } int vol_start(0); for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { const CSeqDBVol * volp = m_VolSet.GetVol(vol_idx); int vol_cnt = volp->GetNumOIDs(); Uint8 vol_len = volp->GetVolumeLength(); // Both limits fit this volume, delegate to volume code. if ((first_seq < vol_cnt) && (residue < vol_len)) { return vol_start + volp->GetOidAtOffset(first_seq, residue, locked); } // Adjust each limit. vol_start += vol_cnt; if (first_seq > vol_cnt) { first_seq -= vol_cnt; } else { first_seq = 0; } if (residue > vol_len) { residue -= vol_len; } else { residue = 0; } } NCBI_THROW(CSeqDBException, eArgErr, "Could not find valid split point oid."); } void CSeqDBImpl::FindVolumePaths(const string & dbname, char prot_nucl, vector & paths, vector * alias_paths, bool recursive) { CSeqDBAtlasHolder AH(true, NULL, NULL); CSeqDBAtlas & atlas(AH.Get()); // This constructor handles its own locking. CSeqDBAliasFile aliases(atlas, dbname, prot_nucl); aliases.FindVolumePaths(paths, alias_paths, recursive); } void CSeqDBImpl::FindVolumePaths(vector & paths, bool recursive) const { CHECK_MARKER(); m_Aliases.FindVolumePaths(paths, NULL, recursive); } void CSeqDBImpl::GetAliasFileValues(TAliasFileValues & afv) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Aliases.GetAliasFileValues(afv, m_VolSet); } void CSeqDBImpl::x_ScanTotals(bool approx, int * numseq, Uint8 * totlen, int * maxlen, CSeqDBLockHold & locked) { int oid_count(0); Uint8 base_count(0); int max_count(0); const CSeqDBVol * volp = 0; m_Atlas.Lock(locked); for(int oid = 0; x_CheckOrFindOID(oid, locked); oid++) { ++ oid_count; int vol_oid = 0; volp = m_VolSet.FindVol(oid, vol_oid); _ASSERT(volp); if (totlen || maxlen ) { int len; if ('p' == m_SeqType) { len = volp->GetSeqLengthProt(vol_oid, locked); } else { if (approx) { len = volp->GetSeqLengthApprox(vol_oid, locked); } else { len = volp->GetSeqLengthExact(vol_oid, locked); } } max_count = max(len, max_count); base_count += len; } } if (numseq) { *numseq = oid_count; } if (totlen) { *totlen = base_count; } if (maxlen) { *maxlen = max_count; } } void CSeqDBImpl::GetTaxInfo(int taxid, SSeqDBTaxInfo & info) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); if (m_TaxInfo.Empty()) { NCBI_THROW(CSeqDBException, eFileErr, "Taxonomic database was not found."); } if (! m_TaxInfo->GetTaxNames(taxid, info, locked)) { NCBI_THROW(CSeqDBException, eArgErr, "Specified taxid was not found."); } } void CSeqDBImpl::GetTotals(ESummaryType sumtype, int * oid_count, Uint8 * total_length, bool use_approx) { CSeqDBLockHold locked(m_Atlas); if (oid_count) { *oid_count = 0; } if (total_length) { *total_length = 0; } switch(sumtype) { case CSeqDB::eUnfilteredAll: if (oid_count) { *oid_count = GetNumOIDs(); } if (total_length) { *total_length = GetVolumeLength(); } break; case CSeqDB::eFilteredAll: if (oid_count) { *oid_count = GetNumSeqs(); } if (total_length) { *total_length = GetTotalLength(); } break; case CSeqDB::eFilteredRange: x_ScanTotals(use_approx, oid_count, total_length, NULL, locked); break; } } void CSeqDBImpl::GetRawSeqAndAmbig(int oid, const char ** buffer, int * seq_length, int * ambig_length) const { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); m_Atlas.MentionOid(oid, m_NumOIDs, locked); int vol_oid = 0; if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { vol->GetRawSeqAndAmbig(vol_oid, buffer, seq_length, ambig_length, locked); return; } NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } /// Accumulate optional min, max, and count. /// /// This generic template describes the accumulation of low, high, and /// count values over any ordered type. The low_in, high_in, and /// count_in values are compared to the current values of low_out, /// high_out, and count_out. If the new value is lower than low_out, /// it will replace the value in low_out, and similarly for high_out. /// The count_out value just accumulates counts. If any of the *_out /// fields is NULL, that field will not be processed. If the set_all /// flag is true, the values in *_in are simply copied unchanged to /// the corresponding *_out fields. /// /// @param low_in The low value for one volume. [in] /// @param high_in The high value for one volume. [in] /// @param count_in The ID count for one volume. [in] /// @param low_out If non-null, the low output value. [out] /// @param high_out If non-null, the high output value. [out] /// @param count_out If non-null, the ID output value. [out] /// @param set_all If true, adopt values without testing. [in] template inline void s_AccumulateMinMaxCount(TId low_in, TId high_in, int count_in, TId * low_out, TId * high_out, int * count_out, bool set_all) { if (set_all) { if (low_out) *low_out = low_in; if (high_out) *high_out = high_in; if (count_out) *count_out = count_in; } else { if (low_out && (*low_out > low_in)) { *low_out = low_in; } if (high_out && (*high_out < high_in)) { *high_out = high_in; } if (count_out) { *count_out += count_in; } } } void CSeqDBImpl::GetGiBounds(int * low_id, int * high_id, int * count) { CSeqDBLockHold locked(m_Atlas); bool found = false; for(int i = 0; i < m_VolSet.GetNumVols(); i++) { int vlow(0), vhigh(0), vcount(0); m_VolSet.GetVol(i)->GetGiBounds(vlow, vhigh, vcount, locked); if (vcount) { s_AccumulateMinMaxCount(vlow, vhigh, vcount, low_id, high_id, count, ! found); found = true; } } if (! found) { NCBI_THROW(CSeqDBException, eArgErr, "No GIs found."); } } void CSeqDBImpl::GetPigBounds(int * low_id, int * high_id, int * count) { CSeqDBLockHold locked(m_Atlas); bool found = false; for(int i = 0; i < m_VolSet.GetNumVols(); i++) { int vlow(0), vhigh(0), vcount(0); m_VolSet.GetVol(i)->GetPigBounds(vlow, vhigh, vcount, locked); if (vcount) { s_AccumulateMinMaxCount(vlow, vhigh, vcount, low_id, high_id, count, ! found); found = true; } } if (! found) { NCBI_THROW(CSeqDBException, eArgErr, "No PIGs found."); } } void CSeqDBImpl::GetStringBounds(string * low_id, string * high_id, int * count) { CSeqDBLockHold locked(m_Atlas); bool found = false; for(int i = 0; i < m_VolSet.GetNumVols(); i++) { string vlow, vhigh; int vcount(0); m_VolSet.GetVol(i)->GetStringBounds(vlow, vhigh, vcount, locked); if (vcount) { s_AccumulateMinMaxCount(vlow, vhigh, vcount, low_id, high_id, count, ! found); found = true; } } if (! found) { NCBI_THROW(CSeqDBException, eArgErr, "No strings found."); } } void CSeqDBImpl::SetOffsetRanges(int oid, const TRangeList & offset_ranges, bool append_ranges, bool cache_data) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); int vol_oid = 0; m_Atlas.Lock(locked); if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid)) { vol->SetOffsetRanges(vol_oid, offset_ranges, append_ranges, cache_data, locked); } else { NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } } void CSeqDBImpl::FlushOffsetRangeCache() { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { CSeqDBVol* volp = m_VolSet.GetVolNonConst(vol_idx); volp->FlushOffsetRangeCache(locked); } } void CSeqDBImpl::SetDefaultMemoryBound(Uint8 bytes) { CSeqDBAtlas::SetDefaultMemoryBound(bytes); } unsigned CSeqDBImpl::GetSequenceHash(int oid) { char * datap(0); int base_len = GetAmbigSeq(oid, & datap, kSeqDBNuclNcbiNA8, 0, (ESeqDBAllocType) 0); unsigned h = SeqDB_SequenceHash(datap, base_len); RetAmbigSeq(const_cast(& datap)); return h; } void CSeqDBImpl::HashToOids(unsigned hash, vector & oids) { // Find all OIDs in all volumes that match this hash. CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); oids.clear(); vector vol_oids; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { // Append any additional OIDs from this volume's indices. m_VolSet.GetVol(vol_idx)->HashToOids(hash, vol_oids, locked); if (vol_oids.empty()) { continue; } int vol_start = m_VolSet.GetVolOIDStart(vol_idx); ITERATE(vector, iter, vol_oids) { int oid1 = (*iter) + vol_start; int oid2 = oid1; // Filter out any oids not in the virtual oid bitmaps. if (x_CheckOrFindOID(oid2, locked) && (oid1 == oid2)) { oids.push_back(oid1); } } vol_oids.clear(); } } CSeqDBIdSet CSeqDBImpl::GetIdSet() { if (m_IdSet.Blank()) { if (! m_UserGiList.Empty()) { // Note: this returns a 'blank' IdSet list for positive // lists that specify filtering using CSeq-id objects. if (m_UserGiList->GetNumGis()) { vector gis; m_UserGiList->GetGiList(gis); CSeqDBIdSet new_ids(gis, CSeqDBIdSet::eGi); m_IdSet = new_ids; } else if (m_UserGiList->GetNumTis()) { vector tis; m_UserGiList->GetTiList(tis); CSeqDBIdSet new_ids(tis, CSeqDBIdSet::eTi); m_IdSet = new_ids; } } else if (! m_NegativeList.Empty()) { const vector & ngis = m_NegativeList->GetGiList(); const vector & ntis = m_NegativeList->GetTiList(); if (! ngis.empty()) { CSeqDBIdSet new_ids(ngis, CSeqDBIdSet::eGi, false); m_IdSet = new_ids; } else if (! ntis.empty()) { CSeqDBIdSet new_ids(ntis, CSeqDBIdSet::eTi, false); m_IdSet = new_ids; } } } return m_IdSet; } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) void CSeqDBImpl::ListColumns(vector & titles) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); set all; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { m_VolSet.GetVolNonConst(vol_idx)->ListColumns(all, locked); } titles.resize(SeqDB_VectorAssign(all, titles)); } int CSeqDBImpl::GetColumnId(const string & title) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); return x_GetColumnId(title, locked); } int CSeqDBImpl::x_GetColumnId(const string & title, CSeqDBLockHold & locked) { m_Atlas.Lock(locked); int col_id = SeqDB_MapFind(m_ColumnTitleMap, title, (int) kUnknownTitle); if (col_id == kUnknownTitle) { vector vol_ids; bool found = false; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { CSeqDBVol * volp = m_VolSet.GetVolNonConst(vol_idx); int id = volp->GetColumnId(title, locked); vol_ids.push_back(id); if (id >= 0) { found = true; } } if (found) { CRef obj(new CSeqDB_ColumnEntry(vol_ids)); col_id = m_ColumnInfo.size(); m_ColumnInfo.push_back(obj); } else { col_id = kColumnNotFound; } // Cache this lookup even if it failed (-1). m_ColumnTitleMap[title] = col_id; } return col_id; } const map & CSeqDBImpl::GetColumnMetaData(int column_id) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); _ASSERT(column_id >= 0); _ASSERT(column_id < (int)m_ColumnInfo.size()); CSeqDB_ColumnEntry & entry = *m_ColumnInfo[column_id]; if (! entry.HaveMap()) { typedef map TStringMap; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { int vol_col_id = entry.GetVolumeIndex(vol_idx); if (vol_col_id < 0) continue; CSeqDBVol * volp = m_VolSet.GetVolNonConst(vol_idx); const TStringMap & volmap = volp->GetColumnMetaData(vol_col_id, locked); ITERATE(TStringMap, iter, volmap) { entry.SetMapValue(iter->first, iter->second); } } entry.SetHaveMap(); } return entry.GetMap(); } const map & CSeqDBImpl::GetColumnMetaData(int column_id, const string & volname) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); _ASSERT(column_id >= 0); _ASSERT(column_id < (int)m_ColumnInfo.size()); CSeqDB_ColumnEntry & entry = *m_ColumnInfo[column_id]; for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { CSeqDBVol * volp = m_VolSet.GetVolNonConst(vol_idx); if (volname != volp->GetVolName()) { continue; } // Found it. int vol_col_id = entry.GetVolumeIndex(vol_idx); return volp->GetColumnMetaData(vol_col_id, locked); } NCBI_THROW(CSeqDBException, eArgErr, "This column ID was not found."); } void CSeqDBImpl::GetColumnBlob(int col_id, int oid, bool keep, CBlastDbBlob & blob) { CHECK_MARKER(); // This Clear() must be done outside of the Lock()ed section below // to avoid possible self-deadlock. In general, do not clear or // allow the destruction of a blob that may have an attached // 'lifetime' object while the atlas lock is held. blob.Clear(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); _ASSERT(col_id >= 0); _ASSERT(col_id < (int)m_ColumnInfo.size()); CSeqDB_ColumnEntry & entry = *m_ColumnInfo[col_id]; // Find the volume for this OID. int vol_idx = -1, vol_oid = -1; if (const CSeqDBVol * vol = m_VolSet.FindVol(oid, vol_oid, vol_idx)) { int vol_col_id = entry.GetVolumeIndex(vol_idx); if (vol_col_id >= 0) { const_cast(vol)-> GetColumnBlob(vol_col_id, vol_oid, blob, keep, locked); } } } int CSeqDBImpl::x_GetMaskDataColumn(CSeqDBLockHold & locked) { m_Atlas.Lock(locked); if (m_MaskDataColumn == kUnknownTitle) { m_MaskDataColumn = x_GetColumnId("BlastDb/MaskData", locked); } _ASSERT(m_MaskDataColumn != kUnknownTitle); return m_MaskDataColumn; } #endif template bool s_Contains(const C & c, const K & k) { return c.find(k) != c.end(); } static const string* s_CheckUniqueValues(const map & m) { typedef map TStringMap; set seen; ITERATE(TStringMap, iter, m) { const string & v = iter->second; if (s_Contains(seen, v)) { return & iter->second; } seen.insert(v); } return NULL; } CSeqDB_IdRemapper::CSeqDB_IdRemapper() : m_NextId(100), m_Empty(true), m_CacheRealAlgo(-1) { } void CSeqDB_IdRemapper::GetIdList(vector & algorithms) { typedef map TIdMap; ITERATE(TIdMap, iter, m_IdToDesc) { algorithms.push_back(iter->first); } } void CSeqDB_IdRemapper::AddMapping(int vol_id, int id, const string & desc) { bool found_desc = s_Contains(m_DescToId, desc); bool found_id = s_Contains(m_IdToDesc, id); int real_id = id; if (found_desc) { if ((! found_id) || (m_DescToId[desc] != id)) { // This description is mapped to a different ID. real_id = m_DescToId[desc]; } } else { // New description. if (found_id) { // Pick a 'synthetic' ID for this description, // i.e. one that is not actually used by any of // the existing volumes so far. while(s_Contains(m_IdToDesc, m_NextId)) { m_NextId++; } real_id = m_NextId; } // Add the new description. m_IdToDesc[real_id] = desc; m_DescToId[desc] = real_id; } m_RealIdToVolumeId[vol_id][real_id] = id; } bool CSeqDB_IdRemapper::GetDesc(int algorithm_id, string & desc) { typedef map TIdMap; if (! s_Contains(m_IdToDesc, algorithm_id)) { return false; } desc = m_IdToDesc[algorithm_id]; return true; } int CSeqDB_IdRemapper::GetVolAlgo(int vol_idx, int algo_id) { if (algo_id != m_CacheRealAlgo || vol_idx != m_CacheVolIndex) { m_CacheVolIndex = vol_idx; m_CacheRealAlgo = algo_id; m_CacheVolAlgo = RealToVol(vol_idx, algo_id); } return m_CacheVolAlgo; } int CSeqDB_IdRemapper::RealToVol(int vol_idx, int algo_id) { if (! s_Contains(m_RealIdToVolumeId, vol_idx)) { NCBI_THROW(CSeqDBException, eArgErr, "Cannot find volume in algorithm map."); } map & trans = m_RealIdToVolumeId[vol_idx]; if (! s_Contains(trans, algo_id)) { NCBI_THROW(CSeqDBException, eArgErr, "Cannot find volume algorithm in algorithm map."); } return trans[algo_id]; } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) void CSeqDBImpl::GetAvailableMaskAlgorithms(vector & algorithms) { if (m_UseGiMask) { m_GiMask->GetAvailableMaskAlgorithms(algorithms); return; } CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); if (m_AlgorithmIds.Empty()) { x_BuildMaskAlgorithmList(locked); } algorithms.resize(0); m_AlgorithmIds.GetIdList(algorithms); } int CSeqDBImpl::GetMaskAlgorithmId(const string & algo) const { if (m_UseGiMask) { return m_GiMask->GetAlgorithmId(algo); } NCBI_THROW(CSeqDBException, eArgErr, "String algorithm ID is not supported for volumn masks."); } string CSeqDBImpl::GetAvailableMaskAlgorithmDescriptions() { vector algorithms; GetAvailableMaskAlgorithms(algorithms); if (algorithms.empty()) { return kEmptyStr; } CNcbiOstrstream retval; retval << endl << "Available filtering algorithms applied to database sequences:" << endl << endl; retval << setw(14) << left << "Algorithm ID" << setw(20) << left << "Algorithm name" << setw(40) << left << "Algorithm options" << endl; ITERATE(vector, algo_id, algorithms) { objects::EBlast_filter_program algo; string algo_opts, algo_name; GetMaskAlgorithmDetails(*algo_id, algo, algo_name, algo_opts); if (algo_opts.empty()) { algo_opts.assign("default options used"); } retval << " " << setw(10) << left << (*algo_id) << setw(20) << left << algo_name << setw(40) << left << algo_opts << endl; } return CNcbiOstrstreamToString(retval); } static void s_GetDetails(const string & desc, EBlast_filter_program & program, string & program_name, string & algo_opts) { static const CEnumeratedTypeValues* enum_type_vals = NULL; if (enum_type_vals == NULL) { enum_type_vals = GetTypeInfo_enum_EBlast_filter_program(); } _ASSERT(enum_type_vals); size_t p = desc.find(':'); if (p == string::npos) { NCBI_THROW(CSeqDBException, eArgErr, "Error in stored mask algorithm description data."); } program = (EBlast_filter_program) NStr::StringToInt(string(desc, 0, p)); program_name.assign(enum_type_vals->FindName(program, false)); algo_opts.assign(desc, p + 1, desc.size() - (p + 1)); } void CSeqDBImpl::GetMaskAlgorithmDetails(int algorithm_id, EBlast_filter_program & program, string & program_name, string & algo_opts) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); string s; bool found; if (m_UseGiMask) { // TODO: to get description s s = m_GiMask->GetDesc(algorithm_id, locked); found = true; } else { if (m_AlgorithmIds.Empty()) { x_BuildMaskAlgorithmList(locked); } found = m_AlgorithmIds.GetDesc(algorithm_id, s); } if (found == false) { CNcbiOstrstream oss; oss << "Filtering algorithm ID " << algorithm_id << " is not supported." << endl; oss << GetAvailableMaskAlgorithmDescriptions(); NCBI_THROW(CSeqDBException, eArgErr, CNcbiOstrstreamToString(oss)); } s_GetDetails(s, program, program_name, algo_opts); } void CSeqDBImpl::x_BuildMaskAlgorithmList(CSeqDBLockHold & locked) { m_Atlas.Lock(locked); if (! m_AlgorithmIds.Empty()) { return; } int col_id = x_GetMaskDataColumn(locked); if (col_id < 0) { // No mask data column exists, therefore, the algorithms list // is empty, and we are done. return; } CSeqDB_ColumnEntry & entry = *m_ColumnInfo[col_id]; typedef map TStringMap; // Results needed: // 1. Map global ids to desc. // 2. Map local id+vol -> global id for(int vol_idx = 0; vol_idx < m_VolSet.GetNumVols(); vol_idx++) { // Get volume column #. int vol_col_id = entry.GetVolumeIndex(vol_idx); if (vol_col_id < 0) { continue; } CSeqDBVol * volp = m_VolSet.GetVolNonConst(vol_idx); const TStringMap & volmap = volp->GetColumnMetaData(vol_col_id, locked); // Check for identical algorithm descriptions (should not happen.) const string * dup = s_CheckUniqueValues(volmap); if (dup != NULL) { ostringstream oss; oss << "Error: volume (" << volp->GetVolName() << ") mask data has duplicates value (" << *dup << ")"; NCBI_THROW(CSeqDBException, eArgErr, oss.str()); } ITERATE(TStringMap, iter, volmap) { int id1 = NStr::StringToInt(iter->first); const string & desc1 = iter->second; m_AlgorithmIds.AddMapping(vol_idx, id1, desc1); } } m_AlgorithmIds.SetNotEmpty(); } struct SReadInt4 { enum { numeric_size = 4 }; static int Read(CBlastDbBlob & blob) { return blob.ReadInt4(); } static void Read(CBlastDbBlob & blob, int n, CSeqDB::TSequenceRanges & ranges) { const void * src = (const void *) blob.ReadRaw(n*8); ranges.append(src, n); } }; template void s_ReadRanges(int vol_algo, CSeqDB::TSequenceRanges & ranges, CBlastDbBlob & blob) { int num_ranges = TRead::Read(blob); for(int rng = 0; rng < num_ranges; rng++) { int algo = TRead::Read(blob); int num_pairs = TRead::Read(blob); if (algo == vol_algo) { TRead::Read(blob, num_pairs, ranges); break; } int skip_amt = num_pairs * 2 * TRead::numeric_size; blob.SeekRead(blob.GetReadOffset() + skip_amt); } } void CSeqDBImpl::GetMaskData(int oid, int algo_id, CSeqDB::TSequenceRanges & ranges) { CHECK_MARKER(); // This reads the data written by CWriteDB_Impl::SetMaskData ranges.clear(); CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); if (m_UseGiMask) { m_GiMask->GetMaskData(algo_id, x_GetSeqGI(oid, locked), ranges, locked); return; } if (m_AlgorithmIds.Empty()) { x_BuildMaskAlgorithmList(locked); } int vol_oid = 0, vol_idx = -1; CSeqDBVol * vol = const_cast (m_VolSet.FindVol(oid, vol_oid, vol_idx)); if (! vol) { NCBI_THROW(CSeqDBException, eArgErr, CSeqDB::kOidNotFound); } // Get the data. CBlastDbBlob blob; vol->GetColumnBlob(x_GetMaskDataColumn(locked), vol_oid, blob, false, locked); if (blob.Size() != 0) { // If there actually is mask data, then we need to do the // algorithm translation. int vol_algo_id = m_AlgorithmIds.GetVolAlgo(vol_idx, algo_id); s_ReadRanges(vol_algo_id, ranges, blob); } //int seq_length = 0; } #endif void CSeqDBImpl::GarbageCollect(void) { CHECK_MARKER(); CSeqDBLockHold locked(m_Atlas); m_Atlas.GarbageCollect(locked); } void CSeqDBImpl::SetNumberOfThreads(int num_threads) { CSeqDBLockHold locked(m_Atlas); m_Atlas.Lock(locked); if (num_threads <= 1) num_threads = 0; if (num_threads > m_NumThreads ) { for (int thread = m_NumThreads; thread < num_threads; ++thread) { m_CachedSeqs.push_back(new SSeqResBuffer()); } } else if (num_threads < m_NumThreads) { for (int thread = num_threads; thread < m_NumThreads; ++thread) { SSeqResBuffer * buffer = m_CachedSeqs.back(); x_RetSeqBuffer(buffer, locked); m_CachedSeqs.pop_back(); delete buffer; } } m_CacheID.clear(); m_NextCacheID = 0; m_NumThreads = num_threads; m_Atlas.SetMTSliceSize(num_threads); } END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/seqdb.hpp0000644000175000017500000016355312001215336022403 0ustar ykeyke#ifndef OBJTOOLS_BLAST_SEQDB_READER___SEQDB__HPP #define OBJTOOLS_BLAST_SEQDB_READER___SEQDB__HPP /* $Id: seqdb.hpp 205653 2010-09-21 12:39:00Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file seqdb.hpp /// Defines BLAST database access classes. /// /// Defines classes: /// CSeqDB /// CSeqDBSequence /// /// Implemented for: UNIX, MS-Windows #include #include #include #include #include #include #include #include #include #include #include #include #include BEGIN_NCBI_SCOPE /// Include definitions from the objects namespace. USING_SCOPE(objects); /// Forward declaration of CSeqDB class class CSeqDB; /// CSeqDBIter /// /// Small class to iterate over a seqdb database. /// /// This serves something of the same role for a CSeqDB object that a /// vector iterator might serve in the standard template library. class NCBI_XOBJREAD_EXPORT CSeqDBIter { public: /// Destructor virtual ~CSeqDBIter() { x_RetSeq(); } /// Increment operator /// /// Returns the currently held sequence and gets pointers to the /// next sequence. CSeqDBIter & operator++(); /// Get the OID of the currently held sequence. int GetOID() { return m_OID; } /// Get the sequence data for the currently held sequence. const char * GetData() { return m_Data; } /// Get the length (in base pairs) of the currently held sequence. int GetLength() { return m_Length; } /// Returns true if the iterator points to a valid sequence. DECLARE_OPERATOR_BOOL(m_Length != -1); /// Construct one iterator from another. CSeqDBIter(const CSeqDBIter &); /// Copy one iterator to another. CSeqDBIter & operator =(const CSeqDBIter &); private: /// Get data pointer and length for the current sequence. inline void x_GetSeq(); /// Release hold on current sequence. inline void x_RetSeq(); /// CSeqDB is a friend so it alone can create objects of this type. friend class CSeqDB; /// Build an iterator (called only from CSeqDB). CSeqDBIter(const CSeqDB *, int oid); /// The CSeqDB object which this object iterates over. const CSeqDB * m_DB; /// The OID this iterator is currently accessing. int m_OID; /// The sequence data for this OID. const char * m_Data; /// The length of this OID. int m_Length; }; /// Forward declaration of CSeqDBGiList base class. class CSeqDBGiList; /// Forward declaration of CSeqDBIdSet class. class CSeqDBIdSet; /// CSeqDB /// /// User interface class for blast databases. /// /// This class provides the top-level interface class for BLAST /// database users. It defines access to the database component by /// calling methods on objects which represent the various database /// files, such as the index, header, sequence, and alias files. class NCBI_XOBJREAD_EXPORT CSeqDB : public CObject { public: /// Import type to allow shorter name. typedef TSeqDBAliasFileValues TAliasFileValues; /// Indicates how block of OIDs was returned. enum EOidListType { eOidList, eOidRange }; /// Sequence types (eUnknown tries protein, then nucleotide). enum ESeqType { eProtein, eNucleotide, eUnknown }; /// Converts a CSeqDB sequence type into a human readable string static string ESeqType2String(ESeqType type); /// Types of summary information available. enum ESummaryType { /// Sum of all sequences, ignoring GI and OID lists and alias files. eUnfilteredAll, /// Values from alias files, or summation over all included sequences. eFilteredAll, /// Sum of included sequences with OIDs within the iteration range. eFilteredRange }; /// Sequence type accepted and returned for OID indices. typedef int TOID; /// Sequence type accepted and returned for PIG indices. typedef int TPIG; /// Sequence type accepted and returned for GI indices. typedef int TGI; /// Structure to represent a range struct TOffsetPair { TSeqPos first; TSeqPos second; /// Default constructor TOffsetPair() : first(0), second(0) {} /// Convenient operator to convert to TSeqRange operator TSeqRange() const { return TSeqRange(first, second-1); } }; /// List of sequence offset ranges. struct TSequenceRanges { typedef size_t size_type; typedef TOffsetPair value_type; typedef const value_type* const_iterator; private: size_type _size; size_type _capacity; TSeqPos* _data; void x_reset_all() { _size = 0; _capacity = 0; _data = NULL; } void x_reallocate_if_necessary() { static size_t kResizeFactor = 2; if (_size + 1 > _capacity) { reserve((_capacity + 1) * kResizeFactor -1); } } public: TSequenceRanges() { x_reset_all(); reserve(7); // must reserve at least 1 element } ~TSequenceRanges() { free(_data); x_reset_all(); } void clear() { _size = 0; } bool empty() const { return _size == 0; } size_type size() const { return _size; } const_iterator begin() const { return const_iterator(&_data[1]); } const_iterator end() const { return const_iterator(&_data[1+ 2*_size]); } value_type& operator[](size_type i) { return (value_type &)_data[1+ 2*i]; } value_type * get_data() const { return (value_type *) _data; } /// Reserves capacity for at least num_elements elements /// @throw CSeqDBException in case of memory allocation failure void reserve(size_t num_elements) { if (num_elements > _capacity) { value_type* reallocation = (value_type*) realloc(_data, (num_elements + 1) * sizeof(value_type)); if ( !reallocation ) { string msg("Failed to allocate "); msg += NStr::IntToString(num_elements + 1) + " elements"; NCBI_THROW(CSeqDBException, eMemErr, msg); } _data = (TSeqPos*) reallocation; _capacity = num_elements; } } /// Append extra elements at the end void append(const void *src, size_type num_elements) { reserve(_size + num_elements); memcpy(&_data[1+ 2*_size], src, num_elements * sizeof(value_type)); _size += num_elements; } /// Append extra element at the end void push_back(const value_type& element) { x_reallocate_if_necessary(); append(&element, 1); } }; /// String containing the error message in exceptions thrown when a given /// OID cannot be found static const string kOidNotFound; /// Short Constructor /// /// This version of the constructor assumes memory mapping and /// that the entire possible OID range will be included. Please /// use quotes ("") around database names that contains space /// characters. /// /// @param dbname /// A list of database or alias names, seperated by spaces /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param gilist /// The database will be filtered by this GI list if non-null. CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBGiList * gilist = 0); /// Short Constructor with Negative ID list. /// /// This version of the constructor assumes the entire OID range /// will be included, and applies filtering by a negative ID list. /// Please use quotes ("") around database names that contains /// space characters. /// /// @param dbname /// A list of database or alias names, seperated by spaces /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param nlist /// The database will be filtered to not include these GIs or TIs. CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBNegativeList * nlist); /// Short Constructor with Computed ID list. /// /// This version of the constructor takes a computed CSeqDBIdSet /// list which can be positive or negative. This is equivalent to /// building a positive or negative list from the IdSet object and /// and passing it into one of the previous constructors. /// /// @param dbname /// A list of database or alias names, seperated by spaces /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param ids /// The database will be filtered by this set of IDs. CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBIdSet ids); /// Short Constructor /// /// This version of the constructor assumes memory mapping and /// that the entire possible OID range will be included. /// /// @param dbs /// A list of database or alias names. /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param gilist /// The database will be filtered by this GI list if non-null. CSeqDB(const vector & dbs, ESeqType seqtype, CSeqDBGiList * gilist = 0); /// Constructor with MMap Flag and OID Range. /// /// If the oid_end value is specified as zero, or as a value /// larger than the number of OIDs, it will be adjusted to the /// number of OIDs in the database. Specifying 0,0 for the start /// and end will cause inclusion of the entire database. This /// version of the constructor is obsolete because the sequence /// type is specified as a character (eventually only the ESeqType /// version will exist). Please use quotes ("") around database /// names that contains space characters. /// /// @param dbname /// A list of database or alias names, seperated by spaces. /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param oid_begin /// Iterator will skip OIDs less than this value. Only OIDs /// found in the OID lists (if any) will be returned. /// @param oid_end /// Iterator will return up to (but not including) this OID. /// @param use_mmap /// If kSeqDBMMap is specified (the default), memory mapping is /// attempted. If kSeqDBNoMMap is specified, or memory mapping /// fails, this platform does not support it, the less efficient /// read and write calls are used instead. /// @param gi_list /// The database will be filtered by this GI list if non-null. CSeqDB(const string & dbname, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list = 0); /// Constructor with MMap Flag and OID Range. /// /// If the oid_end value is specified as zero, or as a value /// larger than the number of OIDs, it will be adjusted to the /// number of OIDs in the database. Specifying 0,0 for the start /// and end will cause inclusion of the entire database. This /// version of the constructor is obsolete because the sequence /// type is specified as a character (eventually only the ESeqType /// version will exist). /// /// @param dbname /// A list of database or alias names. /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param oid_begin /// Iterator will skip OIDs less than this value. Only OIDs /// found in the OID lists (if any) will be returned. /// @param oid_end /// Iterator will return up to (but not including) this OID. /// @param use_mmap /// If kSeqDBMMap is specified (the default), memory mapping is /// attempted. If kSeqDBNoMMap is specified, or memory mapping /// fails, this platform does not support it, the less efficient /// read and write calls are used instead. /// @param gi_list /// The database will be filtered by this GI list if non-null. CSeqDB(const vector & dbname, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list = 0); /// Destructor. /// /// This will return resources acquired by this object, including /// any gotten by the GetSequence() call, whether or not they have /// been returned by RetSequence(). ~CSeqDB(); /// Returns the default BLAST database search path /// configured for this local installation of BLAST static string GenerateSearchPath(); /// Returns the sequence length in base pairs or residues. int GetSeqLength(int oid) const; /// Returns the first Gi (if any) of the sequence int GetSeqGI(int oid) const; /// Returns an unbiased, approximate sequence length. /// /// For protein DBs, this method is identical to GetSeqLength(). /// In the nucleotide case, computing the exact length requires /// examination of the sequence data. This method avoids doing /// that, returning an approximation ranging from L-3 to L+3 /// (where L indicates the exact length), and unbiased on average. int GetSeqLengthApprox(int oid) const; /// Get the ASN.1 header for the sequence. /// /// Do not modify the object returned here (e.g. by removing some /// of the deflines), as the object is cached internally and /// future operations on this OID may be affected. /// /// @param oid The ordinal ID of the sequence. /// @return The blast deflines for this sequence. CRef GetHdr(int oid) const; /// Get taxid for an OID. /// /// This finds the TAXIDS associated with a given OID and computes /// a mapping from GI to taxid. This mapping is added to the /// map provided by the user. If the "persist" flag is /// set to true, the new associations will simply be added to the /// map. If it is false (the default), the map will be cleared /// first. /// /// @param oid /// The ordinal id of the sequence. /// @param gi_to_taxid /// A returned mapping from GI to taxid. /// @param persist /// If false, the map will be cleared before adding new entries. void GetTaxIDs(int oid, map & gi_to_taxid, bool persist = false) const; /// Get taxids for an OID. /// /// This finds the TAXIDS associated with a given OID and returns /// them in a vector. If the "persist" flag is set to true, the /// new taxids will simply be appended to the vector. If it is /// false (the default), the vector will be cleared first. One /// advantage of this interface over the map version is /// that the vector interface works with databases with local IDs /// but lacking GIs. /// /// @param oid /// The ordinal id of the sequence. /// @param taxids /// A returned list of taxids. /// @param persist /// If false, the map will be cleared before adding new entries. void GetTaxIDs(int oid, vector & taxids, bool persist = false) const; /// Get a CBioseq for a sequence. /// /// This builds and returns the header and sequence data /// corresponding to the indicated sequence as a CBioseq. If /// target_gi is non-zero or target_seq_id is non-null, the header /// information will be filtered to only include the defline associated /// with that gi/seq_id. /// /// @param oid /// The ordinal id of the sequence. /// @param target_gi /// If nonzero, the target gi to filter the header information by. /// @param target_seq_id /// The target seq_id to filter the header information by. /// @return /// A CBioseq object corresponding to the sequence. CRef GetBioseq(int oid, int target_gi = 0, const CSeq_id * target_seq_id = NULL) const; /// Get a CBioseq for a sequence without sequence data. /// /// This builds and returns the data corresponding to the /// indicated sequence as a CBioseq, but without the sequence /// data. It is used when processing large sequences, to avoid /// accessing unused parts of the sequence. /// /// @param oid /// The ordinal id of the sequence. /// @param target_gi /// If nonzero, the target gi to filter the header information by. /// @param target_seq_id /// The target seq_id to filter the header information by. /// @return /// A CBioseq object corresponding to the sequence, but without /// sequence data. CRef GetBioseqNoData(int oid, int target_gi = 0, const CSeq_id * target_seq_id = NULL) const; /// Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB /// @param bioseq Bioseq retrieved from CSeqDB [in] static CRef ExtractBlastDefline(const CBioseq & bioseq); /// Get a pointer to raw sequence data. /// /// Get the raw sequence (strand data). When done, resources /// should be returned with RetSequence. This data pointed to /// by *buffer is in read-only memory (where supported). /// /// @param oid /// The ordinal id of the sequence. /// @param buffer /// A returned pointer to the data in the sequence. /// @return /// The return value is the sequence length (in base pairs or /// residues). In case of an error, an exception is thrown. int GetSequence(int oid, const char ** buffer) const; /// Get a pointer to sequence data with ambiguities. /// /// In the protein case, this is identical to GetSequence(). In /// the nucleotide case, it stores 2 bases per byte instead of 4. /// The third parameter indicates the encoding for nucleotide /// data, either kSeqDBNuclNcbiNA8 or kSeqDBNuclBlastNA8, ignored /// if the sequence is a protein sequence. When done, resources /// should be returned with RetSequence. /// /// @param oid /// The ordinal id of the sequence. /// @param buffer /// A returned pointer to the data in the sequence. /// @param nucl_code /// The encoding to use for the returned sequence data. /// @return /// The return value is the sequence length (in base pairs or /// residues). In case of an error, an exception is thrown. int GetAmbigSeq(int oid, const char ** buffer, int nucl_code) const; /// Get a pointer to a range of sequence data with ambiguities. /// /// This is like GetAmbigSeq(), but only a range of the sequence /// data is computed and returned. When done, resources should be /// returned with RetSequence. /// /// @param oid /// The ordinal id of the sequence. /// @param buffer /// A returned pointer to the data in the sequence. /// @param nucl_code /// The encoding to use for the returned sequence data. /// @param begin_offset /// The zero-based offset at which to start translating. /// @param end_offset /// The zero-based offset at which to end translation. /// @return /// The return value is the subsequence length (in base pairs or /// residues). In case of an error, an exception is thrown. int GetAmbigSeq(int oid, const char ** buffer, int nucl_code, int begin_offset, int end_offset) const; /// Get a pointer to sequence data with ambiguities. /// /// This is like GetAmbigSeq(), but the allocated object should be /// deleted by the caller. This is intended for users who are /// going to modify the sequence data, or are going to mix the /// data into a container with other data, and who are mixing data /// from multiple sources and want to free the data in the same /// way. The fourth parameter should be given one of the values /// from EAllocStrategy; the corresponding method should be used /// to delete the object. Note that "delete[]" should be used /// instead of "delete" /// /// @param oid /// Ordinal ID. /// @param buffer /// Address of a char pointer to access the sequence data. /// @param nucl_code /// The NA encoding, kSeqDBNuclNcbiNA8 or kSeqDBNuclBlastNA8. /// @param strategy /// Indicate which allocation strategy to use. /// @param masks /// If not empty, the return sequence will be (hard) masked. /// Masks are cleared on return. /// @return /// The return value is the sequence length (in base pairs or /// residues). In case of an error, an exception is thrown. int GetAmbigSeqAlloc(int oid, char ** buffer, int nucl_code, ESeqDBAllocType strategy, TSequenceRanges * masks = NULL) const; /// Returns any resources associated with the sequence. /// /// Calls to GetSequence (but not GetBioseq()) /// either increment a counter corresponding to a section of the /// database where the sequence data lives, or allocate a buffer /// to return to the user. This method decrements that counter or /// frees the allocated buffer, so that the memory can be used by /// other processes. Each allocating call should be paired with a /// returning call. Note that this does not apply to GetBioseq(), /// or GetHdr(), for example. /// /// @param buffer /// A pointer to the sequence data to release. void RetSequence(const char ** buffer) const; /// Returns any resources associated with the sequence. /// /// Calls to GetAmbigSeq (but not GetBioseq()) /// either increment a counter corresponding to a section of the /// database where the sequence data lives, or allocate a buffer /// to return to the user. This method decrements that counter or /// frees the allocated buffer, so that the memory can be used by /// other processes. Each allocating call should be paired with a /// returning call. Note that this does not apply to GetBioseq(), /// or GetHdr(), for example. /// /// @param buffer /// A pointer to the sequence data to release. void RetAmbigSeq(const char ** buffer) const; /// Gets a list of sequence identifiers. /// /// This returns the list of CSeq_id identifiers associated with /// the sequence specified by the given OID. /// /// @param oid /// The oid of the sequence. /// @return /// A list of Seq-id objects for this sequence. list< CRef > GetSeqIDs(int oid) const; /// Gets a list of GIs for an OID. /// /// This returns the GIs associated with the sequence specified by /// the given OID. If append is true, gis will be appended to the /// end of the provided vector; otherwise the vector will be /// emptied first. /// /// @param oid /// The oid of the sequence. /// @param gis /// The returned list of gis. /// @param append /// Specify true to append to gis, keeping existing elements. void GetGis(int oid, vector & gis, bool append = false) const; /// Returns the type of database opened - protein or nucleotide. /// /// This uses the same constants as the constructor. ESeqType GetSequenceType() const; /// Returns the database title. /// /// This is usually read from database volumes or alias files. If /// multiple databases were passed to the constructor, this will /// be a concatenation of those databases' titles. string GetTitle() const; /// Returns the construction date of the database. /// /// This is encoded in the database. If multiple databases or /// multiple volumes were accessed, the first available date will /// be used. string GetDate() const; /// Returns the number of sequences available. int GetNumSeqs() const; /// Returns the number of sequences available. /// /// This may be overridden by the STATS_NSEQ key. int GetNumSeqsStats() const; /// Returns the size of the (possibly sparse) OID range. int GetNumOIDs() const; /// Returns the sum of the lengths of all available sequences. /// /// This uses summary information stored in the database volumes /// or alias files. It provides an exact value, without iterating /// over individual sequences. Uint8 GetTotalLength() const; /// Returns the sum of the lengths of all available sequences. /// /// This uses summary information stored in the database volumes /// or alias files. It provides either an exact value or a value /// changed in the alias files by the STATS_TOTLEN key. Uint8 GetTotalLengthStats() const; /// Returns the sum of the lengths of all volumes. /// /// This uses summary information stored in the database volumes /// (but not the alias files). It provides an exact value, /// without iterating over individual sequences. It includes all /// OIDs regardless of inclusion by the filtering mechanisms of /// the alias files. Uint8 GetVolumeLength() const; /// Returns the sum of the sequence lengths. /// /// This uses summary information and iteration to compute the /// total length and number of sequences for some subset of the /// database. If eUnfilteredAll is specified, it uses information /// from the underlying database volumes, without filtering. If /// eFilteredAll is specified, all of the included sequences are /// used, for all possible OIDs. If eFilteredRange is specified, /// the returned values correspond to the sum over only those /// sequences that survive filtering, and are within the iteration /// range. If either of oid_count or total_length is passed NULL, /// that result is not returned. In some cases, the results can /// be computed in constant time; other cases require iteration /// proportional to the length of the database or the included OID /// range (see SetIterationRange()). /// /// @param sumtype /// Specifies the subset of sequences to include. /// @param oid_count /// The returned number of included OIDs. /// @param total_length /// The returned sum of included sequence lengths. /// @param use_approx /// Whether to use approximate lengths for nucleotide. void GetTotals(ESummaryType sumtype, int * oid_count, Uint8 * total_length, bool use_approx = true) const; /// Returns the length of the largest sequence in the database. /// /// This uses summary information stored in the database volumes /// or alias files. This might be used to chose buffer sizes. int GetMaxLength() const; /// Returns a sequence iterator. /// /// This gets an iterator designed to allow traversal of the /// database from beginning to end. CSeqDBIter Begin() const; /// Find an included OID, incrementing next_oid if necessary. /// /// If the specified OID is not included in the set (i.e. the OID /// mask), the input parameter is incremented until one is found /// that is. The user will probably want to increment between /// calls, if iterating over the db. /// /// @return /// True if a valid OID was found, false otherwise. bool CheckOrFindOID(int & next_oid) const; /// Return a chunk of OIDs, and update the OID bookmark. /// /// This method allows the caller to iterate over the database by /// fetching batches of OIDs. It will either return a list of OIDs in /// a vector, or set a pair of integers to indicate a range of OIDs. /// The return value will indicate which technique was used. The /// caller sets the number of OIDs to get by setting the size of the /// vector. If eOidRange is returned, the first included oid is /// oid_begin and oid_end is the oid after the last included oid. If /// eOidList is returned, the vector contain the included OIDs, and may /// be resized to a smaller value if fewer entries are available (for /// the last chunk). In some cases it may be desireable to have /// several concurrent, independent iterations over the same database /// object. If this is required, the caller should specify the address /// of an int to the optional parameter oid_state. This should be /// initialized to zero (before the iteration begins) but should /// otherwise not be modified by the calling code (except that it can /// be reset to zero to restart the iteration). For the normal case of /// one iteration per program, this parameter can be omitted. /// /// @param begin_chunk /// First included oid (if eOidRange is returned). /// @param end_chunk /// OID after last included (if eOidRange is returned). /// @param oid_size /// Number of OID to retrieve (ignored in MT environment) /// @param oid_list /// An empty list. Will contain oid list if eOidList is returned. /// @param oid_state /// Optional address of a state variable (for concurrent iterations). /// @return /// eOidList in enumeration case, or eOidRange in begin/end range case. EOidListType GetNextOIDChunk(int & begin_chunk, // out int & end_chunk, // out int oid_size, // in vector & oid_list, // out int * oid_state = NULL); // in+out /// Resets this object's internal chunk bookmark, which is used when the /// oid_state argument to GetNextOIDChunk is NULL. This allows for several /// iterations to be performed over the same CSeqDB object void ResetInternalChunkBookmark(); /* *********** START ************* */ /// Sets this object's internal chunk bookmark. void SetInternalChunkBookmark(int InternalChunkBoomark); void SetMmapMemory(bool MmapMemory); /* ********** FINISH ************* */ /// Get list of database names. /// /// This returns the database name list used at construction. /// @return /// List of database names. const string & GetDBNameList() const; /// Get GI list attached to this database. /// /// This returns the GI list attached to this database, or NULL, /// if no GI list was used. The effects of changing the contents /// of this GI list are undefined. This method only deals with /// the GI list passed to the top level CSeqDB constructor; it /// does not consider volume GI lists. /// /// @return A pointer to the attached GI list, or NULL. const CSeqDBGiList * GetGiList() const; /// Get IdSet list attached to this database. /// /// This returns the ID set used to filter this database. If a /// CSeqDBGiList or CSeqDBNegativeList was used instead, then an /// ID set object will be constructed and returned (and cached /// here). This method only deals with filtering applied to the /// top level CSeqDB constructor; it does not consider GI or TI /// lists attached from alias files. If no filtering was used, a /// 'blank' list will be returned (an empty negative list). /// /// @return A pointer to the attached ID set, or NULL. CSeqDBIdSet GetIdSet() const; /// Set upper limit on memory and mapping slice size. /// /// This sets a (not precisely enforced) upper limit on memory /// used by CSeqDB to memory map disk files (and for some large /// arrays). Setting this to a low value may degrade performance. /// Setting it to too high a value may cause address space /// exhaustion. Normally, SeqDB will start with a large bound and /// reduces it if memory exhaustion is detected. Applications /// that use a lot of memory outside of SeqDB may want to call /// this method to scale back SeqDB's demands. Note that slice /// size is no longer externally adjustable and may be removed in /// the future. Also note that if SeqDB detects a map failure, it /// will reduce the memory bound. /// /// @param membound Maximum memory for SeqDB. /// @param slice_size No longer used. void SetMemoryBound(Uint8 membound, Uint8 slice_size = 0); /// Translate a PIG to an OID. bool PigToOid(int pig, int & oid) const; /// Translate an OID to a PIG. bool OidToPig(int oid, int & pig) const; /// Translate a TI to an OID. bool TiToOid(Int8 ti, int & oid) const; /// Translate an OID to a GI. bool OidToGi(int oid, int & gi) const; /// Translate a GI to an OID. bool GiToOid(int gi, int & oid) const; /// Translate a GI to a PIG. bool GiToPig(int gi, int & pig) const; /// Translate a PIG to a GI. bool PigToGi(int pig, int & gi) const; /// Translate an Accession to a list of OIDs. void AccessionToOids(const string & acc, vector & oids) const; /// Translate a Seq-id to a list of OIDs. void SeqidToOids(const CSeq_id & seqid, vector & oids) const; /// Translate a Seq-id to any matching OID. bool SeqidToOid(const CSeq_id & seqid, int & oid) const; /// Find the sequence closest to the given offset into the database. /// /// The database volumes can be viewed as a single array of /// residues, partitioned into sequences by OID order. The length /// of this array is given by GetTotalLength(). Given an offset /// between 0 and this length, this method returns the OID of the /// sequence at the given offset into the array. It is normally /// used to split the database into sections with approximately /// equal numbers of residues. /// @param first_seq /// First oid to consider (will always return this or higher). /// @param residue /// The approximate number residues offset to search for. /// @return /// An OID near the specified residue offset. int GetOidAtOffset(int first_seq, Uint8 residue) const; /// Get a CBioseq for a given GI /// /// This builds and returns the header and sequence data /// corresponding to the indicated GI as a CBioseq. /// /// @param gi /// The GI of the sequence. /// @return /// A CBioseq object corresponding to the sequence. CRef GiToBioseq(int gi) const; /// Get a CBioseq for a given PIG /// /// This builds and returns the header and sequence data /// corresponding to the indicated PIG (a numeric identifier used /// for proteins) as a CBioseq. /// /// @param pig /// The protein identifier group id of the sequence. /// @return /// A CBioseq object corresponding to the sequence. CRef PigToBioseq(int pig) const; /// Get a CBioseq for a given Seq-id /// /// This builds and returns the header and sequence data /// corresponding to the indicated Seq-id as a CBioseq. Note that /// certain forms of Seq-id map to more than one OID. If this is /// the case for the provided Seq-id, the first matching OID will /// be used. /// /// @param seqid /// The Seq-id identifier of the sequence. /// @return /// A CBioseq object corresponding to the sequence. CRef SeqidToBioseq(const CSeq_id & seqid) const; /// Find volume paths /// /// Find the base names of all volumes (and alias nodes). This /// method builds an alias hierarchy (which should be much faster /// than constructing an entire CSeqDB object), and returns the /// resolved volume/alias file base names from that hierarchy. /// /// @param dbname /// The input name of the database /// @param seqtype /// Specify eProtein, eNucleotide, or eUnknown. /// @param paths /// The set of resolved database volume file names /// @param alias_paths /// The set of resolved database alias file names /// @param recursive /// If true, the search will traverse the full alias node tree static void FindVolumePaths(const string & dbname, ESeqType seqtype, vector & paths, vector * alias_paths = NULL, bool recursive = true); /// Find volume paths /// /// Find the base names of all volumes. This method returns the /// resolved base names of all referenced blast database volumes. /// /// @param paths /// The returned set of resolved database path names /// @param recursive /// If true, the search will traverse the full alias node tree void FindVolumePaths(vector & paths, bool recursive=true) const; /// Set Iteration Range /// /// This method sets the iteration range as a pair of OIDs. /// Iteration proceeds from begin, up to but not including end. /// End will be adjusted to the number of OIDs in the case that it /// is 0, negative, or greater than the number of OIDs. /// /// @param oid_begin /// Iterator will skip OIDs less than this value. Only OIDs /// found in the OID lists (if any) will be returned. /// @param oid_end /// Iterator will return up to (but not including) this OID. void SetIterationRange(int oid_begin, int oid_end); /// Get Name/Value Data From Alias Files /// /// SeqDB treats each alias file as a map from a variable name to /// a value. This method will return a map from the basename of /// the filename of each alias file, to a vector of maps from /// variable name to value for each entry in that file. For /// example, the value of the "DBLIST" entry in the "wgs.nal" file /// would be values["wgs"][0]["DBLIST"]. The lines returned have /// been processed somewhat by SeqDB, including normalizing tabs /// to whitespace, trimming leading and trailing whitespace, and /// removal of comments and other non-value lines. Care should be /// taken when using the values returned by this method. SeqDB /// uses an internal "virtual" alias file entry, which maps from a /// filename of "-" and contains a single entry mapping "DBLIST" /// to SeqDB's database name input. This entry is the root of the /// alias file inclusion tree. Also note that alias files that /// appear in several places in the alias file inclusion tree may /// be different -- SeqDB's internal editing distributes GI lists /// over sub-alias files, which is why the value type of the /// returned data is a vector. /// /// @param afv /// The alias file contents will be returned here. void GetAliasFileValues(TAliasFileValues & afv); /// Get taxonomy information /// /// This method returns taxonomy information for a single taxid. /// This information does not vary with sequence type (protein /// vs. nucleotide) and is the same for all blast databases. If /// the taxonomy database is not available or the taxid is not /// found, this method will throw an exception. /// /// @param taxid /// An integer identifying the taxid to fetch. /// @param info /// A structure containing taxonomic description strings. void GetTaxInfo(int taxid, SSeqDBTaxInfo & info) const; /// Fetch data as a CSeq_data object. /// /// All or part of the sequence is fetched in a CSeq_data object. /// The portion of the sequence returned is specified by begin and /// end. An exception will be thrown if begin is greater than or /// equal to end, or if end is greater than or equal to the length /// of the sequence. Begin and end should be specified in bases; /// a range like (0,1) specifies 1 base, not 2. Nucleotide data /// will always be returned in ncbi4na format. /// /// @param oid Specifies the sequence to fetch. /// @param begin Specifies the start of the data to get. [in] /// @param end Specifies the end of the data to get. [in] /// @return The sequence data as a Seq-data object. CRef GetSeqData(int oid, TSeqPos begin, TSeqPos end) const; /// Set global default memory bound for SeqDB. /// /// The memory bound for individual SeqDB objects can be adjusted /// with SetMemoryBound(), but this cannot be called until after /// the object is constructed. Until that time, the value used is /// set from a global default. This method allows that global /// default value to be changed. Any SeqDB object constructed /// after this method is called will use this value as the initial /// memory bound. If zero is specified, an appropriate default /// will be selected based on system information. static void SetDefaultMemoryBound(Uint8 bytes); /// Get a sequence in a given encoding. /// /// This method gets the sequence data for the given OID, converts /// it to the specified encoding, and returns it in a string. It /// supports all values of the CSeqUtil::ECoding enumeration (but /// the type must match the database type). This method returns the /// same data as GetAmbigSeq() (or GetSequence() for protein), but /// may be less efficient due to the cost of translation and string /// allocation. /// /// @param oid The OID of the sequence to fetch. /// @param coding The encoding to use for the data. /// @param output The returned sequence data as a string. /// @param range The range of the sequence to retrieve, if empty, the /// entire sequence will be retrived [in] void GetSequenceAsString(int oid, CSeqUtil::ECoding coding, string & output, TSeqRange range = TSeqRange()) const; /// Get a sequence in a readable text encoding. /// /// This method gets the sequence data for an OID, converts it to a /// human-readable encoding (either Iupacaa for protein, or Iupacna /// for nucleotide), and returns it in a string. This is equivalent /// to calling the three-argument versions of this method with those /// encodings. /// /// @param oid The OID of the sequence to fetch. /// @param output The returned sequence data as a string. /// @param range The range of the sequence to retrieve, if empty, the /// entire sequence will be retrived [in] void GetSequenceAsString(int oid, string & output, TSeqRange range = TSeqRange()) const; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// List columns titles found in this database. /// /// This returns a list of the column titles of all user created /// (and system generated) columns found in any of this database's /// volumes. Column titles appearing in more than one volume are /// only listed here once. /// /// @param titles Column titles are returned here. [out] void ListColumns(vector & titles); /// Get an ID number for a given column title. /// /// For a given column title, this returns an ID that can be used /// to access that column in the future. The returned ID number /// is specific to this instance of SeqDB. If the database does /// not have a column with this name, -1 will be returned. /// /// @param title Column title to search for. [in] /// @return Column ID number for this column, or -1. [in] int GetColumnId(const string & title); /// Get all metadata for the specified column. /// /// Columns may contain user-defined metadata as a list of /// key-value pairs. For the specified column, this returns that /// column's metadata in the provided map. If multiple volumes /// are present, and they define contradictory meta data (this is /// more common when multiple databases are opened at once), this /// method returns the first value it finds for each metadata key. /// If this is unsatisfactory, the two-argument version of this /// method may be used to get more precise values for specific /// volumes. /// /// @param column_id The column id from GetColumnId. [in] /// @return The map of metadata for this column. [out] const map & GetColumnMetaData(int column_id); /// Look up the value for a specific column metadata key. /// /// Columns can contain user-defined metadata as a list of /// key-value pairs. For the specified column, this returns the /// value associated with one particular key. /// /// @param column_id The column id from GetColumnId. [in] /// @return The value corresponding to the specified key. [out] const string & GetColumnValue(int column_id, const string & key); /// Get all metadata for the specified column. /// /// Columns may contain user-defined metadata as a list of /// key-value pairs. For the specified database volume and column /// id, this returns that column's metadata (as defined for that /// volume) in the provided map. The volume name should match /// the string returned by FindVolumePaths(vector&). /// /// @param column_id The column id from GetColumnId. [in] /// @param volname The volume to get metadata for. [in] /// @return The map of metadata for this column + volume. [out] const map & GetColumnMetaData(int column_id, const string & volname); /// Fetch the data blob for the given column and oid. /// @param col_id The column to fetch data from. [in] /// @param oid The OID of the blob. [in] /// @param blob The data will be returned here. [out] void GetColumnBlob(int col_id, int oid, CBlastDbBlob & blob); // Mask data support. /// Get a list of algorithm IDs for which mask data exists. /// /// Multiple sources of masking data may be used when building /// blast databases. This method retrieves a list of the IDs used /// to identify those types of filtering data to SeqDB. If the /// blast database volumes used by this instance of SeqDB were /// built with conflicting algorithm ID definitions, SeqDB will /// resolve the conflicts by renumbering some of the conflicting /// descriptions. For this reason, the IDs reported here may not /// match what was given to WriteDB when the database was created. /// /// @param algorithms List of algorithm ids. [out] void GetAvailableMaskAlgorithms(vector & algorithms); /// Get the numeric algorithm ID for a string. /// @param algo_name The name of the filtering algorithm int GetMaskAlgorithmId(const string &algo_name) const; /// Returns a formatted string with the list of available masking /// algorithms in this database for display purposes (i.e.: help) string GetAvailableMaskAlgorithmDescriptions(); /// Validates the algorithm IDs passed to this function, returning a vector /// of those algorithm IDs not present in this object vector ValidateMaskAlgorithms(const vector& algorithm_ids); /// Get information about one type of masking available here. /// /// For a given algorithm_id, this method fetches information /// describing the basic algorithm used, as well as options passed /// to that algorithm to generate the data stored here. Each /// sequence in the database can provide sequence masking data /// from one or more sources. There can also be multiple types of /// masking data from the same algorithm (such as DUST), but /// generated with different sets of input parameters. /// /// @param algorithm_id The ID as from GetAvailableMaskAlgorithms [in] /// @param program The filtering program used (DUST, SEG, etc.) [out] /// @param program_name string representation of program [out] /// @param algo_opts Describes options passed to `program'. [out] void GetMaskAlgorithmDetails(int algorithm_id, objects::EBlast_filter_program & program, string & program_name, string & algo_opts); /// Get masked ranges of a sequence. /// /// For the provided OID and list of algorithm IDs, this method /// gets a list of masked areas of those sequences for the first /// algorithm ID. The list of masked areas is returned via the /// ranges parameter. /// /// @param oid The ordinal ID of the sequence. [in] /// @param algo_id The algorithm ID to get data for. [in] /// @param ranges The list of sequence offset ranges. [out] NCBI_DEPRECATED void GetMaskData(int oid, const vector & algo_ids, TSequenceRanges & ranges) { GetMaskData(oid, algo_ids[0], ranges); } /// Get masked ranges of a sequence. /// /// For the provided OID and algorithm ID, this method /// gets a list of masked areas of those sequences. The list of /// masked areas is returned via the ranges parameter. /// /// @param oid The ordinal ID of the sequence. [in] /// @param algo_id The algorithm ID to get data for. [in] /// @param ranges The list of sequence offset ranges. [out] void GetMaskData(int oid, int algo_id, TSequenceRanges &ranges); #endif /// Invoke the garbage collector to free up memory void GarbageCollect(void); /***********************************************************************/ /* BEGIN: support for partial sequence fetching */ /// List of sequence offset ranges. typedef set< pair > TRangeList; /// Apply a range of offsets to a database sequence. /// /// The GetAmbigSeq() method requires an amount of work (and I/O) /// which is proportional to the size of the sequence data (more /// if ambiguities are present). In some cases, only certain /// subranges of this data will be utilized. This method allows /// the user to specify which parts of a sequence are actually /// needed by the user. (Care should be taken if one SeqDB object /// is shared by several program components.) (Note that offsets /// above the length of the sequence will not generate an error, /// and are replaced by the sequence length.) /// /// If ranges are specified for a sequence, data areas in /// specified sequences will be accurate, but data outside the /// specified ranges should not be accessed, and no guarantees are /// made about what data they will contain. If the append_ranges /// flag is true, the range will be added to existing ranges. If /// false, existing ranges will be flushed and replaced by new /// ranges. To remove ranges, call this method with an empty list /// of ranges (and append_ranges == false); future calls will then /// return the complete sequence. /// /// If the cache_data flag is set, data for this sequence will be /// kept for the duration of SeqDB's lifetime. To disable caching /// (and flush cached data) for this sequence, call the method /// again, but specify cache_data to be false. /// /// @param oid OID of the sequence. /// @param offset_ranges Ranges of sequence data to return. /// @param append_ranges Append new ranges to existing list. /// @param cache_data Keep sequence data for future callers. void SetOffsetRanges(int oid, const TRangeList & offset_ranges, bool append_ranges, bool cache_data); /// Remove any offset ranges for the given OID /// @param oid OID of the sequence. void RemoveOffsetRanges(int oid); /// Flush all offset ranges cached void FlushOffsetRangeCache(); /* END: support for partial sequence fetching */ /***********************************************************************/ /// Setting the number of threads /// /// This should be called by the master thread, before and after /// multiple threads run. /// /// @param num_threads Number of threads void SetNumberOfThreads(int num_threads); /// Retrieve the disk usage in bytes for this BLAST database Int8 GetDiskUsage() const; protected: /// Implementation details are hidden. (See seqdbimpl.hpp). class CSeqDBImpl * m_Impl; /// No-argument Constructor /// /// This version of the constructor is used as an extension by the /// 'expert' interface in seqdbexpert.hpp. CSeqDB(); }; /// Structure to define basic information to initialize a BLAST DB struct NCBI_XOBJREAD_EXPORT SSeqDBInitInfo : public CObject { /// The BLAST DB name string m_BlastDbName; /// The molecule type CSeqDB::ESeqType m_MoleculeType; /// Default constructor SSeqDBInitInfo() { m_MoleculeType = CSeqDB::eUnknown; } /// operator less to support sorting inline bool operator<(const SSeqDBInitInfo& rhs) const { if (m_BlastDbName < rhs.m_BlastDbName) { return true; } else if (m_BlastDbName > rhs.m_BlastDbName) { return false; } else { return ((int)m_MoleculeType < (int)rhs.m_MoleculeType); } } /// Create a new CSeqDB instance from this object CRef InitSeqDb() const { return CRef(new CSeqDB(m_BlastDbName, m_MoleculeType)); } }; /// Find BLAST DBs in the directory specified /// @param path directory to search BLAST DBs [in] /// @param dbtype BLAST DB molecule type, allowed values are 'prot', 'nucl', /// and 'guess' (which means any) [in] /// @param recurse whether BLAST DBs should be found recursively or not [in] /// @param include_alias_files Should alias files be included also? [in] NCBI_XOBJREAD_EXPORT vector FindBlastDBs(const string& path, const string& dbtype, bool recurse, bool include_alias_files = false); /// CSeqDBSequence -- /// /// Small class to implement RIAA for sequences. /// /// The CSeqDB class requires that sequences be returned at some point /// after they are gotten. This class provides that service via the /// destructor. It also insures that the database itself stays around /// for at least the duration of its lifetime, by holding a CRef<> to /// that object. CSeqDB::GetSequence may be used directly to avoid /// the small overhead of this class, provided care is taken to call /// CSeqDB::RetSequence. The data referred to by this object is not /// modifyable, and is memory mapped (read only) where supported. class NCBI_XOBJREAD_EXPORT CSeqDBSequence { public: /// Defines the type used to select which sequence to get. typedef CSeqDB::TOID TOID; /// Get a hold a database sequence. CSeqDBSequence(CSeqDB * db, int oid) : m_DB (db), m_Data (0), m_Length(0) { m_Length = m_DB->GetSequence(oid, & m_Data); } /// Destructor, returns the sequence. ~CSeqDBSequence() { if (m_Data) { m_DB->RetSequence(& m_Data); } } /// Get pointer to sequence data. const char * GetData() { return m_Data; } /// Get sequence length. int GetLength() { return m_Length; } private: /// Prevent copy construct. CSeqDBSequence(const CSeqDBSequence &); /// Prevent copy. CSeqDBSequence & operator=(const CSeqDBSequence &); /// The CSeqDB object this sequence is from. CRef m_DB; /// The sequence data for this sequence. const char * m_Data; /// The length of this sequence. int m_Length; }; // Inline methods for CSeqDBIter void CSeqDBIter::x_GetSeq() { m_Length = m_DB->GetSequence(m_OID, & m_Data); } void CSeqDBIter::x_RetSeq() { if (m_Data) m_DB->RetSequence(& m_Data); } END_NCBI_SCOPE #endif // OBJTOOLS_BLAST_SEQDB_READER___SEQDB__HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/seqdb.cpp0000644000175000017500000007513212001215336022371 0ustar ykeyke/* $Id: seqdb.cpp 205653 2010-09-21 12:39:00Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /// @file seqdb.cpp /// Implementation for the CSeqDB class, the top level class for SeqDB. #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: seqdb.cpp 205653 2010-09-21 12:39:00Z maning $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include #include #include "seqdbimpl.hpp" #include "seqdbgeneral.hpp" #include #include BEGIN_NCBI_SCOPE const string CSeqDB::kOidNotFound("OID not found"); /// Helper function to translate enumerated type to character. /// /// @param seqtype /// The sequence type (eProtein, eNucleotide, or eUnknown). /// @return /// The sequence type as a char ('p', 'n', or '-'). static char s_GetSeqTypeChar(CSeqDB::ESeqType seqtype) { switch(seqtype) { case CSeqDB::eProtein: return 'p'; case CSeqDB::eNucleotide: return 'n'; case CSeqDB::eUnknown: return '-'; } NCBI_THROW(CSeqDBException, eArgErr, "Invalid sequence type specified."); } /// Helper function to build private implementation object. /// /// This method builds and returns the object which implements the /// functionality for the CSeqDB API. If this method is called with /// '-' for the sequence data type, protein will be tried first, then /// nucleotide. The created object will be returned. Either /// kSeqTypeProt for a protein database, kSeqTypeNucl for nucleotide, /// or kSeqTypeUnkn to less this function try one then the other. /// /// @param dbname /// A list of database or alias names, seperated by spaces. /// @param prot_nucl /// Specify whether to use protein, nucleotide, or either. /// @param oid_begin /// Iterator will skip OIDs less than this value. Only OIDs /// found in the OID lists (if any) will be returned. /// @param oid_end /// Iterator will return up to (but not including) this OID. /// @param use_mmap /// If kSeqDBMMap is specified (the default), memory mapping is /// attempted. If kSeqDBNoMMap is specified, or memory mapping /// fails, this platform does not support it, the less efficient /// read and write calls are used instead. /// @param gi_list /// This ID list specifies OIDs and deflines to include. /// @param neg_list /// This negative ID list specifies deflines and OIDs to exclude. /// @param idset /// If set, this specifies IDs to either include or exclude. /// @return /// The CSeqDBImpl object that was created. static CSeqDBImpl * s_SeqDBInit(const string & dbname, char prot_nucl, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list = NULL, CSeqDBNegativeList * neg_list = NULL, CSeqDBIdSet idset = CSeqDBIdSet()) { CSeqDBImpl * impl = 0; if (prot_nucl == '-') { try { prot_nucl = 'p'; impl = new CSeqDBImpl(dbname, prot_nucl, oid_begin, oid_end, use_mmap, gi_list, neg_list, idset); } catch(CSeqDBException &) { prot_nucl = 'n'; } } if (! impl) { impl = new CSeqDBImpl(dbname, prot_nucl, oid_begin, oid_end, use_mmap, gi_list, neg_list, idset); } _ASSERT(impl); return impl; } CSeqDB::CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBGiList * gi_list) { if (dbname.size() == 0) { NCBI_THROW(CSeqDBException, eArgErr, "Database name is required."); } char seq_type = s_GetSeqTypeChar(seqtype); m_Impl = s_SeqDBInit(dbname, seq_type, 0, 0, true, gi_list); m_Impl->Verify(); } CSeqDB::CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBNegativeList * nlist) { if (dbname.size() == 0) { NCBI_THROW(CSeqDBException, eArgErr, "Database name is required."); } m_Impl = s_SeqDBInit(dbname, s_GetSeqTypeChar(seqtype), 0, 0, true, NULL, nlist); m_Impl->Verify(); } // This could become the primary constructor for SeqDB, and those // taking positive and negative lists could be deprecated. This // implies refactoring of code using SeqDB, addition of the third // (string/Seq-id) type IDs to the IdSet, and changes to client code. // Some non-SeqDB code uses FindOID and other methods of the GI list, // comparable functionality would need to be added to IdSet(). // // Before any of that is done, all the SeqDB classes should be made to // use CSeqDBIdSet instead of using positive and negative lists. This // implies widespread changes to CSeqDBIdSet and SeqDB internal code. // // I'll leave those changes for another time -- for now I'll just add // the pieces of framework that seem useful and are implied by the // current design. CSeqDB::CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBIdSet ids) { if (dbname.size() == 0) { NCBI_THROW(CSeqDBException, eArgErr, "Database name is required."); } CRef neg; CRef pos; if (! ids.Blank()) { if (ids.IsPositive()) { pos = ids.GetPositiveList(); } else { neg = ids.GetNegativeList(); } } m_Impl = s_SeqDBInit(dbname, s_GetSeqTypeChar(seqtype), 0, 0, true, pos.GetPointerOrNull(), neg.GetPointerOrNull(), ids); m_Impl->Verify(); } CSeqDB::CSeqDB(const vector & dbs, ESeqType seqtype, CSeqDBGiList * gi_list) { string dbname; SeqDB_CombineAndQuote(dbs, dbname); if (dbname.size() == 0) { NCBI_THROW(CSeqDBException, eArgErr, "Database name is required."); } m_Impl = s_SeqDBInit(dbname, s_GetSeqTypeChar(seqtype), 0, 0, true, gi_list); m_Impl->Verify(); } CSeqDB::CSeqDB(const string & dbname, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list) { if (dbname.size() == 0) { NCBI_THROW(CSeqDBException, eArgErr, "Database name is required."); } m_Impl = s_SeqDBInit(dbname, s_GetSeqTypeChar(seqtype), oid_begin, oid_end, use_mmap, gi_list); m_Impl->Verify(); } CSeqDB::CSeqDB(const vector & dbs, ESeqType seqtype, int oid_begin, int oid_end, bool use_mmap, CSeqDBGiList * gi_list) { string dbname; SeqDB_CombineAndQuote(dbs, dbname); if (dbname.size() == 0) { NCBI_THROW(CSeqDBException, eArgErr, "Database name is required."); } m_Impl = s_SeqDBInit(dbname, s_GetSeqTypeChar(seqtype), oid_begin, oid_end, use_mmap, gi_list); m_Impl->Verify(); } CSeqDB::CSeqDB() { m_Impl = new CSeqDBImpl; m_Impl->Verify(); } int CSeqDB::GetSeqLength(int oid) const { m_Impl->Verify(); int length = m_Impl->GetSeqLength(oid); m_Impl->Verify(); return length; } int CSeqDB::GetSeqLengthApprox(int oid) const { m_Impl->Verify(); int length = m_Impl->GetSeqLengthApprox(oid); m_Impl->Verify(); return length; } CRef CSeqDB::GetHdr(int oid) const { m_Impl->Verify(); CRef rv = m_Impl->GetHdr(oid); m_Impl->Verify(); return rv; } CSeqDB::ESeqType CSeqDB::GetSequenceType() const { switch(m_Impl->GetSeqType()) { case 'p': return eProtein; case 'n': return eNucleotide; } NCBI_THROW(CSeqDBException, eArgErr, "Internal sequence type is not valid."); } void CSeqDB::GetTaxIDs(int oid, map & gi_to_taxid, bool persist) const { m_Impl->Verify(); m_Impl->GetTaxIDs(oid, gi_to_taxid, persist); m_Impl->Verify(); } void CSeqDB::GetTaxIDs(int oid, vector & taxids, bool persist) const { m_Impl->Verify(); m_Impl->GetTaxIDs(oid, taxids, persist); m_Impl->Verify(); } CRef CSeqDB::GetBioseq(int oid, int target_gi, const CSeq_id * target_id) const { m_Impl->Verify(); CRef rv = m_Impl->GetBioseq(oid, target_gi, target_id, true); m_Impl->Verify(); return rv; } CRef CSeqDB::GetBioseqNoData(int oid, int target_gi, const CSeq_id * target_id) const { m_Impl->Verify(); CRef rv = m_Impl->GetBioseq(oid, target_gi, target_id, false); m_Impl->Verify(); return rv; } void CSeqDB::RetSequence(const char ** buffer) const { m_Impl->Verify(); m_Impl->RetSequence(buffer); m_Impl->Verify(); } int CSeqDB::GetSequence(int oid, const char ** buffer) const { m_Impl->Verify(); int rv = m_Impl->GetSequence(oid, buffer); m_Impl->Verify(); return rv; } CRef CSeqDB::GetSeqData(int oid, TSeqPos begin, TSeqPos end) const { m_Impl->Verify(); CRef rv = m_Impl->GetSeqData(oid, begin, end); m_Impl->Verify(); return rv; } int CSeqDB::GetAmbigSeq(int oid, const char ** buffer, int nucl_code) const { m_Impl->Verify(); int rv = m_Impl->GetAmbigSeq(oid, (char **)buffer, nucl_code, 0, (ESeqDBAllocType) 0); m_Impl->Verify(); return rv; } void CSeqDB::RetAmbigSeq(const char ** buffer) const { m_Impl->Verify(); m_Impl->RetAmbigSeq(buffer); m_Impl->Verify(); } int CSeqDB::GetAmbigSeq(int oid, const char ** buffer, int nucl_code, int begin_offset, int end_offset) const { m_Impl->Verify(); SSeqDBSlice region(begin_offset, end_offset); int rv = m_Impl->GetAmbigSeq(oid, (char **)buffer, nucl_code, & region, (ESeqDBAllocType) 0); m_Impl->Verify(); return rv; } int CSeqDB::GetAmbigSeqAlloc(int oid, char ** buffer, int nucl_code, ESeqDBAllocType strategy, TSequenceRanges *masks) const { m_Impl->Verify(); if ((strategy != eMalloc) && (strategy != eNew)) { NCBI_THROW(CSeqDBException, eArgErr, "Invalid allocation strategy specified."); } int rv = m_Impl->GetAmbigSeq(oid, buffer, nucl_code, 0, strategy, masks); m_Impl->Verify(); return rv; } string CSeqDB::GetTitle() const { return m_Impl->GetTitle(); } string CSeqDB::GetDate() const { return m_Impl->GetDate(); } int CSeqDB::GetNumSeqs() const { return m_Impl->GetNumSeqs(); } int CSeqDB::GetNumSeqsStats() const { return m_Impl->GetNumSeqsStats(); } int CSeqDB::GetNumOIDs() const { return m_Impl->GetNumOIDs(); } Uint8 CSeqDB::GetTotalLength() const { return m_Impl->GetTotalLength(); } Uint8 CSeqDB::GetTotalLengthStats() const { return m_Impl->GetTotalLengthStats(); } Uint8 CSeqDB::GetVolumeLength() const { return m_Impl->GetVolumeLength(); } int CSeqDB::GetMaxLength() const { return m_Impl->GetMaxLength(); } CSeqDB::~CSeqDB() { m_Impl->Verify(); if (m_Impl) delete m_Impl; } CSeqDBIter CSeqDB::Begin() const { return CSeqDBIter(this, 0); } bool CSeqDB::CheckOrFindOID(int & oid) const { m_Impl->Verify(); bool rv = m_Impl->CheckOrFindOID(oid); m_Impl->Verify(); return rv; } CSeqDB::EOidListType CSeqDB::GetNextOIDChunk(int & begin, int & end, int size, vector & lst, int * state) { m_Impl->Verify(); CSeqDB::EOidListType rv = m_Impl->GetNextOIDChunk(begin, end, size, lst, state); m_Impl->Verify(); return rv; } void CSeqDB::ResetInternalChunkBookmark() { m_Impl->ResetInternalChunkBookmark(); } /* *********** START ************* */ void CSeqDB::SetInternalChunkBookmark(int InternalChunkBookmark ) { m_Impl->SetInternalChunkBookmark(InternalChunkBookmark); } void CSeqDB::SetMmapMemory(bool MmapMemory ) { m_Impl->SetMmapMemory(MmapMemory); } /* ********** FINISH ************* */ const string & CSeqDB::GetDBNameList() const { return m_Impl->GetDBNameList(); } list< CRef > CSeqDB::GetSeqIDs(int oid) const { m_Impl->Verify(); list< CRef > rv = m_Impl->GetSeqIDs(oid); m_Impl->Verify(); return rv; } int CSeqDB::GetSeqGI(int oid) const { return m_Impl->GetSeqGI(oid); } bool CSeqDB::PigToOid(int pig, int & oid) const { m_Impl->Verify(); bool rv = m_Impl->PigToOid(pig, oid); m_Impl->Verify(); return rv; } bool CSeqDB::OidToPig(int oid, int & pig) const { m_Impl->Verify(); bool rv = m_Impl->OidToPig(oid, pig); m_Impl->Verify(); return rv; } bool CSeqDB::TiToOid(Int8 ti, int & oid) const { m_Impl->Verify(); bool rv = m_Impl->TiToOid(ti, oid); m_Impl->Verify(); return rv; } bool CSeqDB::GiToOid(int gi, int & oid) const { m_Impl->Verify(); bool rv = m_Impl->GiToOid(gi, oid); m_Impl->Verify(); return rv; } bool CSeqDB::OidToGi(int oid, int & gi) const { m_Impl->Verify(); bool rv = m_Impl->OidToGi(oid, gi); m_Impl->Verify(); return rv; } bool CSeqDB::PigToGi(int pig, int & gi) const { m_Impl->Verify(); bool rv = false; int oid(0); if (m_Impl->PigToOid(pig, oid)) { rv = m_Impl->OidToGi(oid, gi); } m_Impl->Verify(); return rv; } bool CSeqDB::GiToPig(int gi, int & pig) const { m_Impl->Verify(); bool rv = false; int oid(0); if (m_Impl->GiToOid(gi, oid)) { rv = m_Impl->OidToPig(oid, pig); } m_Impl->Verify(); return rv; } void CSeqDB::AccessionToOids(const string & acc, vector & oids) const { m_Impl->Verify(); m_Impl->AccessionToOids(acc, oids); // If we have a numeric ID and the search failed, try to look it // up as a GI (but not as a PIG or TI). Due to the presence of // PDB ids like "pdb|1914|a", the faster GitToOid is not done // first (unless the caller does so.) if (oids.empty()) { try { int gi = NStr::StringToInt(acc, NStr::fConvErr_NoThrow); int oid(-1); if (gi > 0 && GiToOid(gi, oid)) { oids.push_back(oid); } } catch(...) { } } m_Impl->Verify(); } void CSeqDB::SeqidToOids(const CSeq_id & seqid, vector & oids) const { m_Impl->Verify(); m_Impl->SeqidToOids(seqid, oids, true); m_Impl->Verify(); } bool CSeqDB::SeqidToOid(const CSeq_id & seqid, int & oid) const { m_Impl->Verify(); bool rv = false; oid = -1; vector oids; m_Impl->SeqidToOids(seqid, oids, false); if (! oids.empty()) { rv = true; oid = oids[0]; } m_Impl->Verify(); return rv; } void CSeqDB::SetMemoryBound(Uint8 membound, Uint8 slice_size) { m_Impl->SetMemoryBound(membound); } int CSeqDB::GetOidAtOffset(int first_seq, Uint8 residue) const { m_Impl->Verify(); int rv = m_Impl->GetOidAtOffset(first_seq, residue); m_Impl->Verify(); return rv; } CSeqDBIter::CSeqDBIter(const CSeqDB * db, int oid) : m_DB (db), m_OID (oid), m_Data (0), m_Length((int) -1) { if (m_DB->CheckOrFindOID(m_OID)) { x_GetSeq(); } } CSeqDBIter::CSeqDBIter(const CSeqDBIter & other) : m_DB (other.m_DB), m_OID (other.m_OID), m_Data (0), m_Length((int) -1) { if (m_DB->CheckOrFindOID(m_OID)) { x_GetSeq(); } } /// Copy one iterator to another. CSeqDBIter & CSeqDBIter::operator =(const CSeqDBIter & other) { x_RetSeq(); m_DB = other.m_DB; m_OID = other.m_OID; m_Data = 0; m_Length = -1; if (m_DB->CheckOrFindOID(m_OID)) { x_GetSeq(); } return *this; } CSeqDBIter & CSeqDBIter::operator++() { x_RetSeq(); ++m_OID; if (m_DB->CheckOrFindOID(m_OID)) { x_GetSeq(); } else { m_Length = -1; } return *this; } CRef CSeqDB::GiToBioseq(int gi) const { m_Impl->Verify(); CRef bs; int oid(0); if (m_Impl->GiToOid(gi, oid)) { bs = m_Impl->GetBioseq(oid, gi, NULL, true); } m_Impl->Verify(); return bs; } CRef CSeqDB::PigToBioseq(int pig) const { m_Impl->Verify(); int oid(0); CRef bs; if (m_Impl->PigToOid(pig, oid)) { bs = m_Impl->GetBioseq(oid, 0, NULL, true); } m_Impl->Verify(); return bs; } CRef CSeqDB::SeqidToBioseq(const CSeq_id & seqid) const { m_Impl->Verify(); vector oids; CRef bs; m_Impl->SeqidToOids(seqid, oids, false); if (! oids.empty()) { bs = m_Impl->GetBioseq(oids[0], 0, &seqid, true); } m_Impl->Verify(); return bs; } void CSeqDB::FindVolumePaths(const string & dbname, ESeqType seqtype, vector & paths, vector * alias_paths, bool recursive) { bool done = false; if (seqtype == CSeqDB::eProtein) { CSeqDBImpl::FindVolumePaths(dbname, 'p', paths, alias_paths, recursive); } else if (seqtype == CSeqDB::eNucleotide) { CSeqDBImpl::FindVolumePaths(dbname, 'n', paths, alias_paths, recursive); } else { try { CSeqDBImpl::FindVolumePaths(dbname, 'p', paths, alias_paths, recursive); done = true; } catch(...) { done = false; } if (! done) { CSeqDBImpl::FindVolumePaths(dbname, 'n', paths, alias_paths, recursive); } } } void CSeqDB::FindVolumePaths(vector & paths, bool recursive) const { m_Impl->Verify(); m_Impl->FindVolumePaths(paths, recursive); m_Impl->Verify(); } void CSeqDB::GetGis(int oid, vector & gis, bool append) const { m_Impl->Verify(); // This could be done a little faster at a lower level, but not // necessarily by too much. If this operation is important to // performance, that decision can be revisited. list< CRef > seqids = GetSeqIDs(oid); if (! append) { gis.clear(); } ITERATE(list< CRef >, seqid, seqids) { if ((**seqid).IsGi()) { gis.push_back((**seqid).GetGi()); } } m_Impl->Verify(); } void CSeqDB::SetIterationRange(int oid_begin, int oid_end) { m_Impl->SetIterationRange(oid_begin, oid_end); } void CSeqDB::GetAliasFileValues(TAliasFileValues & afv) { m_Impl->Verify(); m_Impl->GetAliasFileValues(afv); m_Impl->Verify(); } void CSeqDB::GetTaxInfo(int taxid, SSeqDBTaxInfo & info) const { m_Impl->Verify(); m_Impl->GetTaxInfo(taxid, info); m_Impl->Verify(); } void CSeqDB::GetTotals(ESummaryType sumtype, int * oid_count, Uint8 * total_length, bool use_approx) const { m_Impl->Verify(); m_Impl->GetTotals(sumtype, oid_count, total_length, use_approx); m_Impl->Verify(); } const CSeqDBGiList * CSeqDB::GetGiList() const { return m_Impl->GetGiList(); } CSeqDBIdSet CSeqDB::GetIdSet() const { return m_Impl->GetIdSet(); } void CSeqDB::SetDefaultMemoryBound(Uint8 bytes) { CSeqDBImpl::SetDefaultMemoryBound(bytes); } void CSeqDB::GetSequenceAsString(int oid, string & output, TSeqRange range /* = TSeqRange() */) const { CSeqUtil::ECoding code_to = ((GetSequenceType() == CSeqDB::eProtein) ? CSeqUtil::e_Iupacaa : CSeqUtil::e_Iupacna); GetSequenceAsString(oid, code_to, output, range); } void CSeqDB::GetSequenceAsString(int oid, CSeqUtil::ECoding coding, string & output, TSeqRange range /* = TSeqRange() */) const { output.erase(); string raw; const char * buffer = 0; int length = 0; // Protein dbs ignore encodings, always returning ncbistdaa. if (range.NotEmpty()) { length = GetAmbigSeq(oid, & buffer, kSeqDBNuclNcbiNA8, range.GetFrom(), range.GetToOpen()); } else { length = GetAmbigSeq(oid, & buffer, kSeqDBNuclNcbiNA8); } try { raw.assign(buffer, length); } catch(...) { RetAmbigSeq(& buffer); throw; } RetAmbigSeq(& buffer); CSeqUtil::ECoding code_from = ((GetSequenceType() == CSeqDB::eProtein) ? CSeqUtil::e_Ncbistdaa : CSeqUtil::e_Ncbi8na); string result; if (code_from == coding) { result.swap(raw); } else { CSeqConvert::Convert(raw, code_from, 0, length, result, coding); } output.swap(result); } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) void CSeqDB::ListColumns(vector & titles) { m_Impl->ListColumns(titles); } int CSeqDB::GetColumnId(const string & title) { return m_Impl->GetColumnId(title); } const map & CSeqDB::GetColumnMetaData(int column_id) { return m_Impl->GetColumnMetaData(column_id); } const string & CSeqDB::GetColumnValue(int column_id, const string & key) { static string mt; return SeqDB_MapFind(GetColumnMetaData(column_id), key, mt); } const map & CSeqDB::GetColumnMetaData(int column_id, const string & volname) { return m_Impl->GetColumnMetaData(column_id, volname); } void CSeqDB::GetColumnBlob(int col_id, int oid, CBlastDbBlob & blob) { m_Impl->GetColumnBlob(col_id, oid, true, blob); } void CSeqDB::GetAvailableMaskAlgorithms(vector & algorithms) { m_Impl->GetAvailableMaskAlgorithms(algorithms); } int CSeqDB::GetMaskAlgorithmId(const string &algo_name) const { return m_Impl->GetMaskAlgorithmId(algo_name); } string CSeqDB::GetAvailableMaskAlgorithmDescriptions() { return m_Impl->GetAvailableMaskAlgorithmDescriptions(); } vector CSeqDB::ValidateMaskAlgorithms(const vector& algorithm_ids) { vector invalid_algo_ids, available_algo_ids; GetAvailableMaskAlgorithms(available_algo_ids); invalid_algo_ids.reserve(algorithm_ids.size()); if (available_algo_ids.empty()) { copy(algorithm_ids.begin(), algorithm_ids.end(), back_inserter(invalid_algo_ids)); return invalid_algo_ids; } ITERATE(vector, itr, algorithm_ids) { vector::const_iterator pos = find(available_algo_ids.begin(), available_algo_ids.end(), *itr); if (pos == available_algo_ids.end()) { invalid_algo_ids.push_back(*itr); } } return invalid_algo_ids; } void CSeqDB::GetMaskAlgorithmDetails(int algorithm_id, objects::EBlast_filter_program & program, string & program_name, string & algo_opts) { m_Impl->GetMaskAlgorithmDetails(algorithm_id, program, program_name, algo_opts); } void CSeqDB::GetMaskData(int oid, int algo_id, TSequenceRanges & ranges) { m_Impl->GetMaskData(oid, algo_id, ranges); } #endif void CSeqDB::GarbageCollect(void) { m_Impl->GarbageCollect(); } void CSeqDB::SetOffsetRanges(int oid, const CSeqDB::TRangeList & offset_ranges, bool append_ranges, bool cache_data) { m_Impl->Verify(); m_Impl->SetOffsetRanges(oid, offset_ranges, append_ranges, cache_data); m_Impl->Verify(); } void CSeqDB::RemoveOffsetRanges(int oid) { static TRangeList empty; SetOffsetRanges(oid, empty, false, false); } void CSeqDB::FlushOffsetRangeCache() { m_Impl->FlushOffsetRangeCache(); } void CSeqDB::SetNumberOfThreads(int num_threads) { m_Impl->Verify(); m_Impl->SetNumberOfThreads(num_threads); } string CSeqDB::ESeqType2String(ESeqType type) { string retval("Unknown"); switch (type) { case eProtein: retval.assign("Protein"); break; case eNucleotide: retval.assign("Nucleotide"); break; case eUnknown: default: break; } return retval; } string CSeqDB::GenerateSearchPath() { return CSeqDBAtlas::GenerateSearchPath(); } /// Functor class for FindFilesInDir class CBlastDbFinder { public: void operator() (CDirEntry& de) { const string& extn = de.GetPath().substr(de.GetPath().length() - 3, 1); SSeqDBInitInfo value; // rm extension value.m_BlastDbName = de.GetPath().substr(0, de.GetPath().length() - 4); value.m_MoleculeType = (extn == "n" ? CSeqDB::eNucleotide : CSeqDB::eProtein); m_DBs.push_back(value); } vector m_DBs; }; vector FindBlastDBs(const string& path, const string& dbtype, bool recurse, bool include_alias_files /* = false */) { // 1. Find every database volume (but not alias files etc). vector fmasks, dmasks; // If the type is 'guess' we do both types of databases. if (dbtype != "nucl") { fmasks.push_back("*.pin"); if (include_alias_files) { fmasks.push_back("*.pal"); } } if (dbtype != "prot") { fmasks.push_back("*.nin"); if (include_alias_files) { fmasks.push_back("*.nal"); } } dmasks.push_back("*"); EFindFiles flags = (EFindFiles) (fFF_File | (recurse ? fFF_Recursive : 0)); CBlastDbFinder dbfinder; FindFilesInDir(CDir(path), fmasks, dmasks, dbfinder, flags); sort(dbfinder.m_DBs.begin(), dbfinder.m_DBs.end()); return dbfinder.m_DBs; } Int8 CSeqDB::GetDiskUsage() const { vector paths; FindVolumePaths(paths); _ASSERT( !paths.empty() ); Int8 retval = 0; vector extn; const bool is_protein(GetSequenceType() == CSeqDB::eProtein); SeqDB_GetFileExtensions(is_protein, extn); ITERATE(vector, path, paths) { ITERATE(vector, ext, extn) { CFile file(*path + "." + *ext); if (file.Exists()) { Int8 length = file.GetLength(); if (length != -1) { retval += length; } else { ERR_POST(Error << "Error retrieving file size for " << file.GetPath()); } } } } return retval; } END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/prelim_search_runner.hpp0000644000175000017500000001213412001215336025477 0ustar ykeyke/* $Id: prelim_search_runner.hpp 134303 2008-07-17 17:42:49Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file prelim_search_runner.hpp * Defines internal auxiliary functor object to run the preliminary stage of * the BLAST search. */ #ifndef ALGO_BLAST_API___PRELIM_SEARCH_RUNNER__HPP #define ALGO_BLAST_API___PRELIM_SEARCH_RUNNER__HPP /** @addtogroup AlgoBlast * * @{ */ #include // for CThread #include #include "blast_memento_priv.hpp" // CORE BLAST includes #include BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) /// Functor to run the preliminary stage of the BLAST search class CPrelimSearchRunner : public CObject { public: CPrelimSearchRunner(SInternalData& internal_data, const CBlastOptionsMemento* opts_memento) : m_InternalData(internal_data), m_OptsMemento(opts_memento) {} ~CPrelimSearchRunner() {} int operator()() { _ASSERT(m_OptsMemento); _ASSERT(m_InternalData.m_Queries); _ASSERT(m_InternalData.m_QueryInfo); _ASSERT(m_InternalData.m_SeqSrc); _ASSERT(m_InternalData.m_ScoreBlk); _ASSERT(m_InternalData.m_LookupTable); _ASSERT(m_InternalData.m_HspStream); Int2 retval = Blast_RunPreliminarySearch(m_OptsMemento->m_ProgramType, m_InternalData.m_Queries, m_InternalData.m_QueryInfo, m_InternalData.m_SeqSrc->GetPointer(), m_OptsMemento->m_ScoringOpts, m_InternalData.m_ScoreBlk->GetPointer(), m_InternalData.m_LookupTable->GetPointer(), m_OptsMemento->m_InitWordOpts, m_OptsMemento->m_ExtnOpts, m_OptsMemento->m_HitSaveOpts, m_OptsMemento->m_EffLenOpts, m_OptsMemento->m_PSIBlastOpts, m_OptsMemento->m_DbOpts, /* *********** START ************* */ m_OptsMemento->m_GpuOpts, /* ********** FINISH ************* */ m_InternalData.m_HspStream->GetPointer(), m_InternalData.m_Diagnostics->GetPointer()); return static_cast(retval); } private: /// Data structure containing all the needed C structures for the /// preliminary stage of the BLAST search SInternalData& m_InternalData; /// Pointer to memento which this class doesn't own const CBlastOptionsMemento* m_OptsMemento; /// Prohibit copy constructor CPrelimSearchRunner(const CPrelimSearchRunner& rhs); /// Prohibit assignment operator CPrelimSearchRunner& operator=(const CPrelimSearchRunner& rhs); }; /// Thread class to run the preliminary stage of the BLAST search class CPrelimSearchThread : public CThread { public: CPrelimSearchThread(SInternalData& internal_data, const CBlastOptionsMemento* opts_memento) : m_InternalData(internal_data), m_OptsMemento(opts_memento) { // The following fields need to be copied to ensure MT-safety BlastSeqSrc* seqsrc = BlastSeqSrcCopy(m_InternalData.m_SeqSrc->GetPointer()); m_InternalData.m_SeqSrc.Reset(new TBlastSeqSrc(seqsrc, BlastSeqSrcFree)); } protected: virtual ~CPrelimSearchThread(void) {} virtual void* Main(void) { return (void*) ((intptr_t) CPrelimSearchRunner(m_InternalData, m_OptsMemento)()); } private: SInternalData m_InternalData; const CBlastOptionsMemento* m_OptsMemento; }; END_SCOPE(blast) END_NCBI_SCOPE /* @} */ #endif /* ALGO_BLAST_API___PRELIM_SEARCH_RUNNER__HPP */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/makeblastdb.cpp0000644000175000017500000010220512001215336023534 0ustar ykeyke/* $Id: makeblastdb.cpp 256439 2011-03-04 16:49:18Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file makeblastdb.cpp * Command line tool to create BLAST databases. This is the successor to * formatdb from the C toolkit */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: makeblastdb.cpp 256439 2011-03-04 16:49:18Z rafanovi $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "../blast/blast_app_util.hpp" #include "masked_range_set.hpp" #include #include #include #ifndef SKIP_DOXYGEN_PROCESSING USING_NCBI_SCOPE; USING_SCOPE(blast); USING_SCOPE(objects); #endif /* SKIP_DOXYGEN_PROCESSING */ /// The main application class class CMakeBlastDBApp : public CNcbiApplication { public: /// Convenience typedef typedef CFormatGuess::EFormat TFormat; enum ESupportedInputFormats { eFasta, eXml, eBinaryASN, eTextASN, eBlastDb, eUnsupported = 256 }; /** @inheritDoc */ CMakeBlastDBApp() : m_LogFile(NULL), m_IsModifyMode(false) { CRef version(new CVersion()); version->SetVersionInfo(new CBlastVersion()); SetFullVersion(version); } private: /** @inheritDoc */ virtual void Init(); /** @inheritDoc */ virtual int Run(); void x_AddSequenceData(CNcbiIstream & input, TFormat fmt); vector x_GuessInputType(const vector& filenames, vector& blastdbs); ESupportedInputFormats x_GetUserInputTypeHint(void); TFormat x_ConvertToCFormatGuessType(ESupportedInputFormats fmt); ESupportedInputFormats x_ConvertToSupportedType(TFormat fmt); TFormat x_GuessFileType(CNcbiIstream & input); void x_BuildDatabase(); void x_AddFasta(CNcbiIstream & data); void x_AddSeqEntries(CNcbiIstream & data, TFormat fmt); void x_ProcessMaskData(); void x_ProcessInputData(const string & paths, bool is_protein); // Data CNcbiOstream * m_LogFile; CRef m_DB; CRef m_Ranges; bool m_IsModifyMode; }; /// Reads an object defined in a NCBI ASN.1 spec from a stream in multiple /// formats: binary and text ASN.1 and XML /// @param file stream to read the object from [in] /// @param fmt specifies the format in which the object is encoded [in] /// @param obj on input is an empty CRef<> object, on output it's populated /// with the object read [in|out] /// @param msg error message to display if reading fails [in] template void s_ReadObject(CNcbiIstream & file, CFormatGuess::EFormat fmt, CRef & obj, const string & msg) { obj.Reset(new TObj); switch (fmt) { case CFormatGuess::eBinaryASN: file >> MSerial_AsnBinary >> *obj; break; case CFormatGuess::eTextASN: file >> MSerial_AsnText >> *obj; break; case CFormatGuess::eXml: file >> MSerial_Xml >> *obj; break; default: NCBI_THROW(CInvalidDataException, eInvalidInput, string("Unknown encoding for ") + msg); } } /// Overloaded version of s_ReadObject which uses CFormatGuess to determine /// the encoding of the object in the file /// @param file stream to read the object from [in] /// @param obj on input is an empty CRef<> object, on output it's populated /// with the object read [in|out] /// @param msg error message to display if reading fails [in] template void s_ReadObject(CNcbiIstream & file, CRef & obj, const string & msg) { CFormatGuess fg; fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eBinaryASN); fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eTextASN); fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eXml); fg.GetFormatHints().DisableAllNonpreferred(); s_ReadObject(file, fg.Format(file), obj, msg); } /// Command line flag to represent the input static const string kInput("in"); /// Defines token separators when multiple inputs are present static const string kInputSeparators(" "); /// Command line flag to represent the output static const string kOutput("out"); void CMakeBlastDBApp::Init() { HideStdArgs(fHideConffile | fHideFullVersion | fHideXmlHelp | fHideDryRun); auto_ptr arg_desc(new CArgDescriptions); // Specify USAGE context arg_desc->SetUsageContext(GetArguments().GetProgramBasename(), "Application to create BLAST databases, version " + CBlastVersion().Print()); string dflt("Default = input file name provided to -"); dflt += kInput + " argument"; arg_desc->SetCurrentGroup("Input options"); arg_desc->AddDefaultKey(kInput, "input_file", "Input file/database name; the data type is " "automatically detected, it may be " "any of the following:\n" "\tFASTA file(s) and/or \n" "\tBLAST database(s)\n", CArgDescriptions::eInputFile, "-"); arg_desc->AddDefaultKey("dbtype", "molecule_type", "Molecule type of input", CArgDescriptions::eString, "prot"); arg_desc->SetConstraint("dbtype", &(*new CArgAllow_Strings, "nucl", "prot")); arg_desc->SetCurrentGroup("Configuration options"); arg_desc->AddOptionalKey("title", "database_title", "Title for BLAST database\n" + dflt, CArgDescriptions::eString); arg_desc->AddFlag("parse_seqids", "Parse Seq-ids in FASTA input", true); arg_desc->AddOptionalKey("input_type", "type", "Type of the data specified in input_file " "(if not specified it will be guessed)", CArgDescriptions::eString); arg_desc->SetConstraint("input_type", &(*new CArgAllow_Strings, "fasta", "blastdb", "xml", "asn1_bin", "asn1_txt")); arg_desc->AddFlag("hash_index", "Create index of sequence hash values.", true); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) arg_desc->SetCurrentGroup("Sequence masking options"); arg_desc->AddOptionalKey("mask_data", "mask_data_files", "Comma-separated list of input files containing " "masking data as produced by NCBI masking " "applications (e.g. dustmasker, segmasker, " "windowmasker)", CArgDescriptions::eString); arg_desc->AddFlag("gi_mask", "Create GI indexed masking data.", true); arg_desc->SetDependency("gi_mask", CArgDescriptions::eRequires, "parse_seqids"); arg_desc->AddOptionalKey("gi_mask_name", "gi_based_mask_names", "Comma-separated list of masking data output files.", CArgDescriptions::eString); arg_desc->SetDependency("gi_mask_name", CArgDescriptions::eRequires, "mask_data"); arg_desc->SetDependency("gi_mask_name", CArgDescriptions::eRequires, "gi_mask"); #endif arg_desc->SetCurrentGroup("Output options"); arg_desc->AddOptionalKey(kOutput, "database_name", "Name of BLAST database to be created\n" + dflt + "Required if multiple file(s)/database(s) are " "provided as input", CArgDescriptions::eString); arg_desc->AddDefaultKey("max_file_sz", "number_of_bytes", "Maximum file size for BLAST database files", CArgDescriptions::eString, "1GB"); #if _BLAST_DEBUG arg_desc->AddFlag("verbose", "Produce verbose output", true); #endif /* _BLAST_DEBUG */ arg_desc->SetCurrentGroup("Taxonomy options"); arg_desc->AddOptionalKey("taxid", "TaxID", "Taxonomy ID to assign to all sequences", CArgDescriptions::eInteger); arg_desc->SetConstraint("taxid", new CArgAllowValuesGreaterThanOrEqual(0)); arg_desc->SetDependency("taxid", CArgDescriptions::eExcludes, "taxid_map"); arg_desc->AddOptionalKey("taxid_map", "TaxIDMapFile", "Text file mapping sequence IDs to taxonomy IDs.\n" "Format: ", CArgDescriptions::eInputFile); /* *********** START ************* */ arg_desc->SetCurrentGroup("Miscellaneous options"); arg_desc->AddFlag("sort_volumes", "Sort the sequences according to length in each volume", true); /* ********** FINISH ************* */ SetupArgDescriptions(arg_desc.release()); } /// Converts a Uint8 into a string which contains a data size (converse to /// NStr::StringToUInt8_DataSize) /// @param v value to convert [in] /// @param minprec minimum precision [in] static string Uint8ToString_DataSize(Uint8 v, unsigned minprec = 10) { static string kMods = "KMGTPEZY"; size_t i(0); for(i = 0; i < kMods.size(); i++) { if (v < Uint8(minprec)*1024) { v /= 1024; } } string rv = NStr::UInt8ToString(v); if (i) { rv.append(kMods, i, 1); rv.append("B"); } return rv; } void CMakeBlastDBApp::x_AddFasta(CNcbiIstream & data) { m_DB->AddFasta(data); } class CSeqEntrySource : public IBioseqSource { public: /// Convenience typedef typedef CFormatGuess::EFormat TFormat; CSeqEntrySource(CNcbiIstream & is, TFormat fmt) :m_objmgr(CObjectManager::GetInstance()), m_scope(new CScope(*m_objmgr)), m_entry(new CSeq_entry) { char ch=is.peek(); // Get rid of white spaces while(!is.eof() && (ch==' ' || ch=='\t' || ch=='\n' || ch=='\r')) { is.read(&ch, 1); ch=is.peek(); } // If input is a Bioseq_set if(ch == 'B' || ch == '0') { CRef obj(new CBioseq_set); s_ReadObject(is, fmt, obj, "bioseq"); m_entry->SetSet(*obj); } else { s_ReadObject(is, fmt, m_entry, "bioseq"); } m_bio = Begin(*m_entry); m_scope->AddTopLevelSeqEntry(*m_entry); } virtual CConstRef GetNext() { CConstRef rv; if (m_bio ) { if (! m_bio ->CanGetDescr()) { sequence::CDeflineGenerator gen; const string & title = gen.GenerateDefline(*m_bio , *m_scope); CRef des(new CSeqdesc); des->SetTitle(title); CSeq_descr& desr(m_bio ->SetDescr()); desr.Set().push_back(des); } rv.Reset(&(*m_bio )); ++m_bio ; } return rv; } private: CRef m_objmgr; CRef m_scope; CRef m_entry; CTypeIterator m_bio; }; void CMakeBlastDBApp::x_AddSeqEntries(CNcbiIstream & data, TFormat fmt) { CSeqEntrySource src(data, fmt); m_DB->AddSequences(src); } class CRawSeqDBSource : public IRawSequenceSource { public: CRawSeqDBSource(const string & name, bool protein, CBuildDatabase * outdb); virtual ~CRawSeqDBSource() { if (m_Sequence) { m_Source->RetSequence(& m_Sequence); m_Sequence = NULL; } } virtual bool GetNext(CTempString & sequence, CTempString & ambiguities, CRef & deflines, vector & mask_range, vector & column_ids, vector & column_blobs); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) virtual void GetColumnNames(vector & names) { names = m_ColumnNames; } virtual int GetColumnId(const string & name) { return m_Source->GetColumnId(name); } virtual const map & GetColumnMetaData(int id) { return m_Source->GetColumnMetaData(id); } #endif void ClearSequence() { if (m_Sequence) { _ASSERT(m_Source.NotEmpty()); m_Source->RetSequence(& m_Sequence); } } private: CRef m_Source; const char * m_Sequence; int m_Oid; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) vector m_Blobs; vector m_ColumnIds; vector m_ColumnNames; vector m_MaskIds; map m_MaskIdMap; #endif }; CRawSeqDBSource::CRawSeqDBSource(const string & name, bool protein, CBuildDatabase * outdb) : m_Sequence(NULL), m_Oid(0) { CSeqDB::ESeqType seqtype = protein ? CSeqDB::eProtein : CSeqDB::eNucleotide; m_Source.Reset(new CSeqDBExpert(name, seqtype)); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) // Process mask meta data m_Source->GetAvailableMaskAlgorithms(m_MaskIds); ITERATE(vector, algo_id, m_MaskIds) { objects::EBlast_filter_program algo; string algo_opts, algo_name; m_Source->GetMaskAlgorithmDetails(*algo_id, algo, algo_name, algo_opts); algo_name += NStr::IntToString(*algo_id); m_MaskIdMap[*algo_id] = outdb->RegisterMaskingAlgorithm(algo, algo_opts, algo_name); } // Process columns m_Source->ListColumns(m_ColumnNames); for(int i = 0; i < (int)m_ColumnNames.size(); i++) { m_ColumnIds.push_back(m_Source->GetColumnId(m_ColumnNames[i])); } #endif } bool CRawSeqDBSource::GetNext(CTempString & sequence, CTempString & ambiguities, CRef & deflines, vector & mask_range, vector & column_ids, vector & column_blobs) { if (! m_Source->CheckOrFindOID(m_Oid)) return false; if (m_Sequence) { m_Source->RetSequence(& m_Sequence); m_Sequence = NULL; } int slength(0), alength(0); m_Source->GetRawSeqAndAmbig(m_Oid, & m_Sequence, & slength, & alength); sequence = CTempString(m_Sequence, slength); ambiguities = CTempString(m_Sequence + slength, alength); deflines = m_Source->GetHdr(m_Oid); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) // process masks ITERATE(vector, algo_id, m_MaskIds) { CSeqDB::TSequenceRanges ranges; m_Source->GetMaskData(m_Oid, *algo_id, ranges); SBlastDbMaskData mask_data; mask_data.algorithm_id = m_MaskIdMap[*algo_id]; ITERATE(CSeqDB::TSequenceRanges, range, ranges) { mask_data.offsets.push_back(pair(range->first, range->second)); } mask_range.push_back(mask_data); } // The column IDs will be the same each time; another approach is // to only send back the IDs for those columns that are non-empty. column_ids = m_ColumnIds; column_blobs.resize(column_ids.size()); m_Blobs.resize(column_ids.size()); for(int i = 0; i < (int)column_ids.size(); i++) { m_Source->GetColumnBlob(column_ids[i], m_Oid, m_Blobs[i]); column_blobs[i] = m_Blobs[i].Str(); } #endif m_Oid ++; return true; } CMakeBlastDBApp::TFormat CMakeBlastDBApp::x_ConvertToCFormatGuessType(CMakeBlastDBApp::ESupportedInputFormats fmt) { TFormat retval = CFormatGuess::eUnknown; switch (fmt) { case eFasta: retval = CFormatGuess::eFasta; break; case eXml: retval = CFormatGuess::eXml; break; case eBinaryASN: retval = CFormatGuess::eBinaryASN; break; case eTextASN: retval = CFormatGuess::eTextASN; break; default: break; } return retval; } CMakeBlastDBApp::ESupportedInputFormats CMakeBlastDBApp::x_ConvertToSupportedType(CMakeBlastDBApp::TFormat fmt) { ESupportedInputFormats retval = eUnsupported; switch (fmt) { case CFormatGuess::eFasta: retval = eFasta; break; case CFormatGuess::eXml: retval = eXml; break; case CFormatGuess::eBinaryASN: retval = eBinaryASN; break; case CFormatGuess::eTextASN: retval = eTextASN; break; default: break; } return retval; } CMakeBlastDBApp::ESupportedInputFormats CMakeBlastDBApp::x_GetUserInputTypeHint(void) { ESupportedInputFormats retval = eUnsupported; const CArgs& args = GetArgs(); if (args["input_type"].HasValue()) { const string& input_type = args["input_type"].AsString(); if (input_type == "fasta") { retval = eFasta; } else if (input_type == "xml") { retval = eXml; } else if (input_type == "asn1_bin") { retval = eBinaryASN; } else if (input_type == "asn1_txt") { retval = eTextASN; } else if (input_type == "blastdb") { retval = eBlastDb; } else { // need to add supported type to list of constraints! _ASSERT(false); } } return retval; } vector CMakeBlastDBApp::x_GuessInputType(const vector& filenames, vector& blastdbs) { vector retval(filenames.size(), eUnsupported); // Guess the input data type for (size_t i = 0; i < filenames.size(); i++) { // input_file could be FASTA, ASN.1 or XML, or if it doesn't match // exactly, a BLAST database const string & seq_file = filenames[i]; if (seq_file == "-") { retval[i] = x_ConvertToSupportedType(x_GuessFileType(cin)); } else { CFile input_file(seq_file); if ( !input_file.Exists() ) { blastdbs.push_back(seq_file); retval[i] = eBlastDb; continue; } if (input_file.GetLength() == 0) { ERR_POST(Error << "Ignoring sequence input file '" << seq_file << "' as it is empty."); continue; } CNcbiIfstream f(seq_file.c_str(), ios::binary); retval[i] = x_ConvertToSupportedType(x_GuessFileType(f)); } } return retval; } CMakeBlastDBApp::TFormat CMakeBlastDBApp::x_GuessFileType(CNcbiIstream & input) { CFormatGuess fg(input); fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eBinaryASN); fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eTextASN); fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eXml); fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eFasta); fg.GetFormatHints().DisableAllNonpreferred(); return fg.GuessFormat(); } void CMakeBlastDBApp::x_AddSequenceData(CNcbiIstream & input, CMakeBlastDBApp::TFormat fmt) { switch(fmt) { case CFormatGuess::eFasta: x_AddFasta(input); break; case CFormatGuess::eTextASN: case CFormatGuess::eBinaryASN: case CFormatGuess::eXml: x_AddSeqEntries(input, fmt); break; default: string msg("Input format not supported ("); msg += string(CFormatGuess::GetFormatName(fmt)) + " format). "; msg += "Use -input_type to specify the input type being used."; NCBI_THROW(CInvalidDataException, eInvalidInput, msg); } } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) void CMakeBlastDBApp::x_ProcessMaskData() { const CArgs & args = GetArgs(); const CArgValue & files = args["mask_data"]; if (! files.HasValue()) { return; } vector mask_list; NStr::Tokenize(NStr::TruncateSpaces(files.AsString()), ",", mask_list, NStr::eNoMergeDelims); if (! mask_list.size()) { NCBI_THROW(CInvalidDataException, eInvalidInput, "mask_data option found, but no files were specified."); } vector gi_mask_names; const CArgValue & gi_names = args["gi_mask_name"]; if (gi_names.HasValue()) { NStr::Tokenize(NStr::TruncateSpaces(gi_names.AsString()), ",", gi_mask_names, NStr::eNoMergeDelims); if (mask_list.size() != gi_mask_names.size()) { NCBI_THROW(CInvalidDataException, eInvalidInput, "gi_mask list does not correspond to mask_data list."); } // TODO optionally we need check to make sure the names are unique... } for (unsigned int i = 0; i < mask_list.size(); ++i) { if ( !CFile(mask_list[i]).Exists() ) { ERR_POST(Error << "Ignoring mask file '" << mask_list[i] << "' as it does not exist."); continue; } CNcbiIfstream mask_file(mask_list[i].c_str(), ios::binary); int algo_id = -1; while (true) { CRef first_obj; try { s_ReadObject(mask_file, first_obj, "mask data in '" + mask_list[i] + "'"); } catch(...) { // must be end of file break; } if (algo_id < 0) { *m_LogFile << "Mask file: " << mask_list[i] << endl; EBlast_filter_program prog_id = static_cast(first_obj->GetAlgo_program()); string opts = first_obj->GetAlgo_options(); string name = gi_mask_names.size() ? gi_mask_names[i] : mask_list[i]; algo_id = m_DB->RegisterMaskingAlgorithm(prog_id, opts, name); } CRef masks(& first_obj->SetMasks()); first_obj.Reset(); while(1) { if (m_Ranges.Empty() && ! masks->GetMasks().empty()) { m_Ranges.Reset(new CMaskedRangeSet); m_DB->SetMaskDataSource(*m_Ranges); } ITERATE(CBlast_mask_list::TMasks, iter, masks->GetMasks()) { CConstRef seqid((**iter).GetId()); if (seqid.Empty()) { NCBI_THROW(CInvalidDataException, eInvalidInput, "Cannot get masked range Seq-id"); } m_Ranges->Insert(algo_id, *seqid, **iter); } if (! masks->GetMore()) break; s_ReadObject(mask_file, masks, "mask data (continuation)"); } } } } #endif void CMakeBlastDBApp::x_ProcessInputData(const string & paths, bool is_protein) { bool has_fasta_data = false; vector names; SeqDB_SplitQuoted(paths, names); vector blastdb; vector input_types; ESupportedInputFormats hint = eUnsupported; if ( (hint = x_GetUserInputTypeHint()) != eUnsupported) { input_types.assign(names.size(), hint); } else { input_types = x_GuessInputType(names, blastdb); } _ASSERT(input_types.size() == names.size()); for (size_t i = 0; i < names.size(); i++) { // input_file could be FASTA, ASN.1 or XML. const string & seq_file = names[i]; if (seq_file == "-") { _ASSERT(input_types[i] != eBlastDb); x_AddSequenceData(cin, x_ConvertToCFormatGuessType(input_types[i])); has_fasta_data = TRUE; } else { CFile input_file(seq_file); if ( !input_file.Exists() ) { // this is a BLAST database _ASSERT(find(blastdb.begin(), blastdb.end(), seq_file) != blastdb.end()); continue; } if (input_file.GetLength() == 0) { ERR_POST(Error << "Ignoring sequence input file '" << seq_file << "' as it is empty."); continue; } CNcbiIfstream f(seq_file.c_str(), ios::binary); _ASSERT(input_types[i] != eBlastDb); x_AddSequenceData(f, x_ConvertToCFormatGuessType(input_types[i])); has_fasta_data = TRUE; } } if (blastdb.size() > 0) { CSeqDB::ESeqType seqtype = (is_protein ? CSeqDB::eProtein : CSeqDB::eNucleotide); vector final_blastdb; if (m_IsModifyMode) { ASSERT(blastdb.size()==1); CSeqDB db(blastdb[0], seqtype); vector paths; db.FindVolumePaths(paths); // if paths.size() == 1, we will happily take it to be the same // case as a single volume database and recreate a new db if (paths.size() > 1) { NCBI_THROW(CInvalidDataException, eInvalidInput, "Modifying an alias BLAST db is currently not supported."); } final_blastdb.push_back(blastdb[0]); } else { ITERATE(vector, iter, blastdb) { const string & s = *iter; try { CSeqDB db(s, seqtype); } catch(const CSeqDBException &) { ERR_POST(Error << "Unable to open input " << s << " as either FASTA file or BLAST db"); continue; } final_blastdb.push_back(s); } } if (final_blastdb.size()) { string quoted; SeqDB_CombineAndQuote(final_blastdb, quoted); if (has_fasta_data) { ERR_POST(Error << "Ignoring sequence input file '" << quoted << "' as it mixes with FASTA files."); } else { CRef raw(new CRawSeqDBSource(quoted, is_protein, m_DB)); m_DB->AddSequences(*raw); } } } } void CMakeBlastDBApp::x_BuildDatabase() { const CArgs & args = GetArgs(); // Get arguments to the CBuildDatabase constructor. bool is_protein = (args["dbtype"].AsString() == "prot"); // 1. title option if present // 2. otherwise, kInput string title = (args["title"].HasValue() ? args["title"] : args[kInput]).AsString(); // 1. database name option if present // 2. else, kInput string dbname = (args[kOutput].HasValue() ? args[kOutput] : args[kInput]).AsString(); vector input_files; NStr::Tokenize(dbname, kInputSeparators, input_files); if (dbname == "-" || input_files.size() > 1) { NCBI_THROW(CInvalidDataException, eInvalidInput, "Please provide a database name using -" + kOutput); } if (args[kInput].AsString() == dbname) { m_IsModifyMode = true; } // N.B.: Source database(s) in the current working directory will // be overwritten (as in formatdb) if (title == "-") { NCBI_THROW(CInvalidDataException, eInvalidInput, "Please provide a title using -title"); } m_LogFile = & (args["logfile"].HasValue() ? args["logfile"].AsOutputFile() : cout); bool parse_seqids = args["parse_seqids"]; bool hash_index = args["hash_index"]; bool use_gi_mask = args["gi_mask"]; CWriteDB::TIndexType indexing = CWriteDB::eNoIndex; indexing |= (hash_index ? CWriteDB::eAddHash : 0); indexing |= (parse_seqids ? CWriteDB::eFullIndex : 0); /* *********** START ************* */ bool sort_sequences = false; if( args["sort_volumes"].HasValue() ) { if( is_protein ) sort_sequences = true; else { cout << "Error: sorting supports only protein databases. Exiting..." << endl; exit(0); } } /* ********** FINISH ************* */ m_DB.Reset(new CBuildDatabase(dbname, title, is_protein, indexing, use_gi_mask, m_LogFile, /* *********** START ************* */ sort_sequences) /* ********** FINISH ************* */ ); #if _BLAST_DEBUG if (args["verbose"]) { m_DB->SetVerbosity(true); } #endif /* _BLAST_DEBUG */ // Should we keep the linkout and membership bits? Sure. // Create empty linkout bit table in order to call these methods; // however, in the future it would probably be good to populate // this from a user provided option as multisource does. Also, it // might be wasteful to copy membership bits, as the resulting // database will most likely not have corresponding mask files; // but until there is a way to configure membership bits with this // tool, I think it is better to keep, than to toss. TLinkoutMap no_bits; m_DB->SetLinkouts(no_bits, true); m_DB->SetMembBits(no_bits, true); // Max file size Uint8 bytes = NStr::StringToUInt8_DataSize(args["max_file_sz"].AsString()); *m_LogFile << "Maximum file size: " << Uint8ToString_DataSize(bytes) << endl; m_DB->SetMaxFileSize(bytes); if (args["taxid"].HasValue()) { _ASSERT( !args["taxid_map"].HasValue() ); CRef taxids(new CTaxIdSet(args["taxid"].AsInteger())); m_DB->SetTaxids(*taxids); } else if (args["taxid_map"].HasValue()) { _ASSERT( !args["taxid"].HasValue() ); CRef taxids(new CTaxIdSet()); taxids->SetMappingFromFile(args["taxid_map"].AsInputFile()); m_DB->SetTaxids(*taxids); } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) x_ProcessMaskData(); #endif x_ProcessInputData(args[kInput].AsString(), is_protein); } int CMakeBlastDBApp::Run(void) { int status = 0; try { x_BuildDatabase(); } CATCH_ALL(status) return status; } #ifndef SKIP_DOXYGEN_PROCESSING int main(int argc, const char* argv[] /*, const char* envp[]*/) { return CMakeBlastDBApp().AppMain(argc, argv, 0, eDS_Default, 0); } #endif /* SKIP_DOXYGEN_PROCESSING */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/functions_faster.cpp0000644000175000017500000021552312001215336024647 0ustar ykeyke// 1k, 4 threads : 3'10'' // 5k, 4 threads : 5'26'' ///////============= new code segment start =============== #define CURRENT(a) ((a)&0x1) #define NEXT(a) CURRENT(a+1) void get_GPU_result( Int4** _h_Hits, const Int4 _h_Hits_bytes, GPUBlastInitHitList** _h_GPUBlastInitHitList, const Int4 _h_GPUBlastInitHitList_bytes, const Int4 _num_sequences, double * _elapsed_time) { Int4* h_Hits_temp=NULL; GPUBlastInitHitList* h_GPUBlastInitHitList_temp=NULL; struct timespec CPU_start, CPU_end; ///**************** The following code is modified by YKE ************************** h_Hits_temp = (Int4*) realloc(*_h_Hits, _h_Hits_bytes); ///**************** The code segment ends ************************** if( NULL != h_Hits_temp ) *_h_Hits = h_Hits_temp; else { puts("Error (re)allocating memory for the GPU\n"); gpu_abnormally_exit(1); } h_GPUBlastInitHitList_temp = (GPUBlastInitHitList*) realloc(*_h_GPUBlastInitHitList, _h_GPUBlastInitHitList_bytes); if( NULL != h_GPUBlastInitHitList_temp ) *_h_GPUBlastInitHitList = h_GPUBlastInitHitList_temp; else { printf("Error (re)allocating memory for the GPU\n"); gpu_abnormally_exit(1); } clock_gettime(CLOCK_MONOTONIC, &CPU_start); //writing h_Hits and h_GPUBlastInitHitList doesn't require a mutex because because it is accessed by only one thread GPU_BLASTP_get_data(*_h_Hits, _h_Hits_bytes, *_h_GPUBlastInitHitList, _h_GPUBlastInitHitList_bytes, _num_sequences); clock_gettime(CLOCK_MONOTONIC, &CPU_end); if(_elapsed_time ==NULL) { fprintf(stderr, "get_GPU_result: Error, \"_elapsed_time\" is invaild!\n"); gpu_abnormally_exit(1); } *_elapsed_time = (CPU_end.tv_sec - CPU_start.tv_sec) + (double)(CPU_end.tv_nsec - CPU_start.tv_nsec) / BILLION; ///============================= printf("Get data elapses %lg sec\n", *_elapsed_time); ///============================= return; } ///////============= new code segment end=============== void Write_GPU_information_file_preliminary(FILE* GPU_information_file, const Int4 num_blocksx, const Int4 num_threadsx, const char percentage, const Int4 num_volumes) { fprintf(GPU_information_file,"#Number of blocksx\n"); fprintf(GPU_information_file,"%d\n", num_blocksx ); fprintf(GPU_information_file,"#Number of threadsx\n"); fprintf(GPU_information_file,"%d\n", num_threadsx); fprintf(GPU_information_file,"#Percentage\n"); fprintf(GPU_information_file,"%d\n", percentage); fprintf(GPU_information_file,"#Number of volumes\n"); fprintf(GPU_information_file,"%d\n", num_volumes ); } void Write_GPU_information_file(FILE* GPU_information_file, const char* GPU_Database_name, const unsigned long GPU_BLASTP_database_bytes, const Int4 volume_length, const Int4 num_sequences_to, const Int4 store_limit, const Int4 break_limit, const Int4 Group_number, const Int4* Sequence_length_vector) { fprintf(GPU_information_file,"#Volume name\n"); fprintf(GPU_information_file,"%s\n", GPU_Database_name); fprintf(GPU_information_file,"#Volume size in bytes\n"); fprintf(GPU_information_file,"%ld\n", GPU_BLASTP_database_bytes ); fprintf(GPU_information_file,"#Volume sequences\n"); fprintf(GPU_information_file,"%d\n", volume_length ); fprintf(GPU_information_file,"#Number of sequences in GPU volume\n"); fprintf(GPU_information_file,"%d\n", num_sequences_to ); fprintf(GPU_information_file,"#Store limit\n"); fprintf(GPU_information_file,"%d\n", store_limit ); fprintf(GPU_information_file,"#Break limit\n"); fprintf(GPU_information_file,"%d\n", break_limit ); fprintf(GPU_information_file,"#Group number\n"); fprintf(GPU_information_file,"%d\n", Group_number ); fprintf(GPU_information_file,"#Length of each group\n"); Int4 i = 0; for(i = 0; i < Group_number; ++i) fprintf(GPU_information_file,"%d\n", Sequence_length_vector[i] ); } void Read_GPU_information_file_preliminary(FILE** GPU_information_file, const BlastSeqSrc* seq_src, Int4* num_blocksx, Int4* num_threadsx, Int4* percentage, Int4* num_volumes) { char* Database_name = BlastSeqSrcGetName(seq_src); char* GPU_information_name = (char*) calloc(strlen(Database_name) + strlen(".gpuinfo") + 1,sizeof(char)); strcat(GPU_information_name, Database_name); strcat(GPU_information_name, ".gpuinfo"); *GPU_information_file = fopen( GPU_information_name, "rb"); if( NULL == (*GPU_information_file) ) { printf("GPU information file cannot be opened for reading. Exiting...\n"); exit(1); } char *line_read = (char *) malloc( sizeof(char) ); size_t nbytes = 1; Int4 bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read first line which is a comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read number of blocksx *num_blocksx = atoi(line_read); bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read number of threads *num_threadsx = atoi(line_read); bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read percentage *percentage = atoi(line_read); bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read number of volumes *num_volumes = atoi(line_read); free(line_read); free(GPU_information_name); } void Read_GPU_information_file(const FILE* GPU_information_file, char** GPU_volume_name, unsigned long* GPU_BLASTP_database_bytes, Int4* volume_length, Int4* num_sequences_to, Int4* store_limit, Int4* break_limit, Int4* Group_number, Int4** Sequence_length_vector, const Int4 cpu_threads) { char *line_read = (char *) malloc( sizeof(char) ); size_t nbytes = 1; Int4 bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read first line which is a comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the volume name char* GPU_volume_name_temp = (char*)realloc(*GPU_volume_name, bytes_read*sizeof(char) ); if( NULL != GPU_volume_name_temp ) { *GPU_volume_name = GPU_volume_name_temp; memset(*GPU_volume_name, 0, bytes_read*sizeof(char)); memcpy(*GPU_volume_name, line_read, bytes_read - 1); } else { printf("Error (re)allocating memory for the GPU information file\n"); exit(1); } bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the size of the volume in bytes *GPU_BLASTP_database_bytes = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of sequences in this volume *volume_length = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of sequences processed by the GPU in this volume *num_sequences_to = atoi(line_read); switch ( cpu_threads ) { case 1: *num_sequences_to = ((*volume_length) * 95) / 100; break; case 2: *num_sequences_to = ((*volume_length) * 85) / 100; // *num_sequences_to = ((*volume_length) * 88) / 100; break; case 3: *num_sequences_to = ((*volume_length) * 80) / 100; // *num_sequences_to = ((*volume_length) * 83) / 100; break; case 4: *num_sequences_to = ((*volume_length) * 76) / 100; // *num_sequences_to = ((*volume_length) * 80) / 100; break; case 5: *num_sequences_to = ((*volume_length) * 73) / 100; break; case 6: *num_sequences_to = ((*volume_length) * 70) / 100; break; default: *num_sequences_to = ((*volume_length) * 70) / 100; break; } bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the ID of the last sequences processed by the GPU in this volume *store_limit = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the ID of the last sequences of this volume *break_limit = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of groups in this volume *Group_number = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment Int4* Sequence_length_vector_temp = (Int4*) realloc(*Sequence_length_vector, (*Group_number)*sizeof(Int4)); if( NULL != Sequence_length_vector_temp ) *Sequence_length_vector = Sequence_length_vector_temp; else { printf("Error (re)allocating memory for the GPU information file\n"); exit(1); } Int4 i = 0; for( i = 0; i < *Group_number; ++i) { bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the length of each group of this volume (*Sequence_length_vector)[i] = atoi(line_read); } free(line_read); } int ExtractVolumeSequences(unsigned char * buffer) { //Extracting information from the index file (see index_file.txt for the format information) int version = buffer[0 + 0]*(1<<24) + buffer[0 + 1]*(1<<16) + buffer[0 + 2]*(1<<8) + buffer[0 + 2]; int type = buffer[4 + 0]*(1<<24) + buffer[4 + 1]*(1<<16) + buffer[4 + 2]*(1<<8) + buffer[4 + 3]; if( type != 1 ) { fprintf(stderr,"Error index file is not a protein index file\n"); exit(1); } int title_bytes = buffer[8 + 0]*(1<<24) + buffer[8 + 1]*(1<<16) + buffer[8 + 2]*(1<<8) + buffer[8 + 3]; int date_bytes = buffer[8 + 4 + title_bytes + 0 ]*(1<<24) + buffer[8 + 4 + title_bytes + 1 ]*(1<<16) + buffer[8 + 4 + title_bytes + 2 ]*(1<<8) + buffer[8 + 4 + title_bytes + 3 ]; int sequences = buffer[8 + 4 + 4 + title_bytes + date_bytes + 0 ]*(1<<24) + buffer[8 + 4 + 4 + title_bytes + date_bytes + 1 ]*(1<<16) + buffer[8 + 4 + 4 + title_bytes + date_bytes + 2 ]*(1<<8) + buffer[8 + 4 + 4 + title_bytes + date_bytes + 3 ]; return sequences; } void ReadGPU_BLASTP_volinfo(const BlastSeqSrc* seq_src, Int4 *num_volumes, Int4** volume_lengths) { if( GPU_VERBOSE ) printf("Reading volume information\n"); Int4* volume_lengths_temp; *volume_lengths = NULL; //deep copy the database path to a temporary string because "dirname()" might modify the database path char* Database_name = BlastSeqSrcGetName(seq_src); int Database_name_bytes = strlen( Database_name ) + 1; char* Database_copy = (char*) calloc( Database_name_bytes, sizeof(char) ); memcpy( Database_copy, Database_name, Database_name_bytes ); char *aliasfile_name = (char*)calloc(strlen(Database_copy) + strlen(".pal") + 1, sizeof(char)); strcat(aliasfile_name, Database_copy); strcat(aliasfile_name, ".pal"); FILE* aliasfile = fopen(aliasfile_name, "r" ); if( NULL == aliasfile ) //if the the protein alias file (.pal) file doesn't exist then { *num_volumes = 1; //there is only one volume char *indexfile_name = (char*)calloc(strlen(Database_copy) + strlen(".pin") + 1, sizeof(char)); strcat(indexfile_name, Database_copy); strcat(indexfile_name, ".pin"); FILE* indexfile = fopen(indexfile_name, "r" );//read index file if( NULL == indexfile) { fprintf(stderr, "Cannot open index file %s\n", indexfile_name); exit(1); } else { size_t result = 0; unsigned char* buffer = (char*)malloc(10000*sizeof(char)); result = fread(buffer, sizeof(char), 10000, indexfile);//read the first 10000 bytes of the index file volume_lengths_temp = (Int4*) realloc( *volume_lengths, 1*sizeof(Int4) ); if( NULL != volume_lengths_temp ) *volume_lengths = volume_lengths_temp; else { printf("Error (re)allocating during index file reading\n"); exit(1); } (*volume_lengths)[0] = ExtractVolumeSequences(buffer); free(buffer); } free(indexfile_name); fclose(indexfile); } else //else read the lines line by line to find the "DBLIST" line { char* line_read = (char *) malloc( sizeof(char) ); size_t nbytes = 1; Int4 bytes_read = getline(&line_read, &nbytes, aliasfile);//Read firs line char * pch; *num_volumes = 0; int k = 0; for(k = 0; k < 1000; ++k) //read the first 1000 lines of the alias file { if( feof(aliasfile) ) //at end of file break break; pch = strtok (line_read," "); //extract the first word of the line int diff = strncmp(pch, "DBLIST", 6); //compare the word with "DBLIST" if(diff) //if it is not "DBLIST" read the next line and continue { bytes_read = getline(&line_read, &nbytes, aliasfile);//Read firs line which is a comment continue; } else //if it is "DBLIST" read the rest of the volume names { pch = strtok (NULL, " "); //extract the first volume name while (pch != NULL) { //check if the last character of pch is '\n' which means this is the last index file if( pch[strlen(pch) - 1 ] == '\n') pch[strlen(pch) - 1 ] = '\0'; //replace with the null character char *indexfile_name = (char*)calloc(strlen(pch) + strlen(".pin") + 1, sizeof(char)); strcat(indexfile_name, pch); strcat(indexfile_name, ".pin"); FILE* indexfile = fopen(indexfile_name, "r" );//read index file if( NULL == indexfile) { fprintf(stderr, "Cannot open the index file %s\n", indexfile_name); exit(1); } else { size_t result = 0; unsigned char* buffer = (char*)malloc(10000*sizeof(char)); result = fread(buffer, sizeof(char), 1000, indexfile);//read the first 1000 bytes of the index file volume_lengths_temp = (Int4*) realloc( *volume_lengths, ((*num_volumes)+1)*sizeof(Int4) ); if( NULL != volume_lengths_temp ) *volume_lengths = volume_lengths_temp; else { printf("Error (re)allocating during index file reading\n"); exit(1); } (*volume_lengths)[*num_volumes] = ExtractVolumeSequences(buffer); printf("%s: %d\n",indexfile_name, (*volume_lengths)[*num_volumes]); free(buffer); } (*num_volumes)++; free(indexfile_name); fclose(indexfile); pch = strtok (NULL, " "); //extract the next volume name } break; //after done with reading all volume names break } } free(line_read); } if( NULL != aliasfile ) fclose(aliasfile); free(aliasfile_name); free(Database_copy); } /** Creates the database used by the GPU_BLASTP @param Sequence_length_vector vector that holds the length of each sequence group [in] @param Group_number the number of groups that the sequence database is split [in] @param Group_size size of each group of sequences [in] @param stride that is used in createing the GPU database [in] @param seq_arc data structure that holds information about the sequence database [in] @param num_sequence_to last sequence of the database that is stored in the GPU database [in] */ void CreateGPU_BLASTP_database(BlastSeqSrc* seq_src, const BlastGPUOptions* gpu_options) { Int4 i = 0, j = 0; Int4 stride = 4; Int4 Group_size = (gpu_options->num_blocksx) * (gpu_options->num_threadsx); char percentage = PERCENTAGE; BlastSeqSrcIterator* itr = BlastSeqSrcIteratorNewEx(MAX(BlastSeqSrcGetNumSeqs(seq_src)/100,1)); BlastSeqSrcGetSeqArg seq_arg; memset((void*) &seq_arg, 0, sizeof(seq_arg)); /* Encoding is set so there are no sentinel bytes, and protein/nucleotide sequences are retrieved in ncbistdaa/ncbi2na encodings respectively. */ seq_arg.encoding = eBlastEncodingProtein; char* Database_name = BlastSeqSrcGetName(seq_src); char* GPU_Database_name = NULL; char* GPU_Database_name_temp; char* GPU_BLASTP_database = NULL; char* GPU_BLASTP_database_temp; Int4* Sequence_length_vector = NULL; Int4* Sequence_length_vector_temp; char* digits = (char*) calloc(10, sizeof(char));//10 digits are enough to cover up to 999999999 volumes char* GPU_information_name = (char*) calloc(strlen(Database_name) + strlen(".gpuinfo") + 1,sizeof(char)); strcat(GPU_information_name, Database_name); strcat(GPU_information_name, ".gpuinfo"); FILE* GPU_information_file = fopen( GPU_information_name, "wb"); if ( NULL == GPU_information_file ) printf("GPU information file cannot be opened for writing\n"); Int4* volume_lengths = NULL; Int4 num_volumes = 0; ReadGPU_BLASTP_volinfo(seq_src, &num_volumes, &volume_lengths); printf("num_volumes = %d\n",num_volumes); Write_GPU_information_file_preliminary(GPU_information_file, gpu_options->num_blocksx, gpu_options->num_threadsx, percentage, num_volumes); Int4 volume = 0, break_limit = 0; for(volume = 0; volume < num_volumes; ++volume) { Int4 num_sequences_to = (percentage * volume_lengths[volume]) / 100; Int4 store_limit = break_limit + num_sequences_to; Int4 Group_number = (num_sequences_to / Group_size ) + (( (num_sequences_to % Group_size ) == 0)?0:1); Sequence_length_vector_temp = (Int4*) realloc( Sequence_length_vector, Group_number*sizeof(Int4) ); if( NULL != Sequence_length_vector_temp ) Sequence_length_vector = Sequence_length_vector_temp; else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } Int4 vector_counter = 0; unsigned long GPU_BLASTP_database_bytes = 0; Int4 oid = break_limit + Group_size - 1; //initialized oid to the last sequence of the first group if( oid >= store_limit ) oid = store_limit - 1; //Initializes the Sequence_length_vector with the length of the longest sequence in each group //The length is converted to a multiple of WIDTH_MULTIPLE (defined in gpu_cpu_common.h) int previous_sequence_length = 0; do { Int4 sequence_length = BlastSeqSrcGetSeqLen( seq_src, (void*) &oid ); if( previous_sequence_length > sequence_length ) { fprintf(stderr,"ERROR: the input database is not sorted\n"); fprintf(stderr,"Sort the database by using the option \"-sort_volumes\" with \"makeblastdb.\"\n"); fprintf(stderr,"Exiting...\n"); exit(1); } previous_sequence_length = sequence_length; Round2Multiple( &sequence_length ); Sequence_length_vector[ vector_counter ] = sequence_length; if( GPU_VERBOSE ) printf("Group %d starts at sequence %d and has length = %d\n", vector_counter, oid, Sequence_length_vector[vector_counter]); ++vector_counter; if( oid == store_limit - 1 ) break; oid += Group_size; } while( oid < store_limit - 1 ); //If the last iteration of the previous do-while didn't cover all sequences (i.e. the Group_size is not a multiple of num_sequences) //the remaining sequences form the last group, and the last element of Sequence_length_vector is initialized if( oid != store_limit - 1 ) { oid = store_limit - 1; Int4 sequence_length = BlastSeqSrcGetSeqLen( seq_src, (void*) &oid ); /* check if the volume is sorted */ if( previous_sequence_length > sequence_length ) { fprintf(stderr,"ERROR: the input database is not sorted\n"); fprintf(stderr,"Sort the database by using the option \"-sort_volumes\" with \"makeblastdb.\"\n"); fprintf(stderr,"Exiting...\n"); exit(1); } Round2Multiple( &sequence_length ); Sequence_length_vector[ vector_counter ] = sequence_length; if( GPU_VERBOSE ) printf("Group %d starts at sequence %d and has length = %d\n", vector_counter, oid, Sequence_length_vector[vector_counter]); } //Calculate the total size of the GPU database for(i = 0; i < Group_number; ++i) GPU_BLASTP_database_bytes += Sequence_length_vector[i]*Group_size*sizeof(char); //This helps to check if there is a very large sequence that can cause the GPU memory to explode if( GPU_BLASTP_database_bytes > UINT4_MAX ) { printf("Memory requirements for GPU database larger than 4 GB. Exiting...\n"); exit(0); } GPU_BLASTP_database_temp = (char*) realloc( GPU_BLASTP_database, GPU_BLASTP_database_bytes*sizeof(char) ); if( NULL != GPU_BLASTP_database_temp ) GPU_BLASTP_database = GPU_BLASTP_database_temp; else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } memset(GPU_BLASTP_database, 0, GPU_BLASTP_database_bytes*sizeof(char)); int length = 0; int group_member = 0; int counter = 0, sequence = 0, AminoAcids = 0, base = 0; break_limit += volume_lengths[volume]; /* iterate over all subject sequences of this volume */ previous_sequence_length = 0; while ( ( (seq_arg.oid = BlastSeqSrcIteratorNext(seq_src, itr)) != BLAST_SEQSRC_EOF) ) { if (seq_arg.oid == BLAST_SEQSRC_ERROR) break; if (BlastSeqSrcGetSequence(seq_src, &seq_arg) < 0) continue; if( seq_arg.oid < store_limit ) { if( (counter % Group_size) == 0 ) { base += length*Group_size; length = Sequence_length_vector[ group_member ]; group_member++; sequence = 0; } AminoAcids = 0; int sequence_length = BlastSeqSrcGetSeqLen( seq_src, (void*) &seq_arg.oid ); if( previous_sequence_length > sequence_length ) { fprintf(stderr,"ERROR: the input database is not sorted\n"); fprintf(stderr,"Sort the database by using the option \"-sort_volumes\" with \"makeblastdb.\"\n"); fprintf(stderr,"Exiting...\n"); exit(1); } previous_sequence_length = sequence_length; for(i = 0; i < sequence_length/stride + 1; ++i) { for(j = 0; j < stride; ++j) { (GPU_BLASTP_database)[ base + (sequence + i*Group_size)*stride + j] = (seq_arg.seq->sequence)[AminoAcids]; AminoAcids++; if( AminoAcids >= sequence_length ) goto done; } } done: counter++; sequence++; } /* if ( seq_arg.oid < num_sequences_to ) */ BlastSeqSrcReleaseSequence(seq_src, &seq_arg); if( seq_arg.oid == (break_limit-1) ) break; } /* while loop */ //Create the name of the gpu database if( 1 == num_volumes ) { int GPU_Database_name_bytes = strlen(Database_name) + strlen(".gpu") + 1; GPU_Database_name_temp = (char*) realloc(GPU_Database_name, GPU_Database_name_bytes*sizeof(char)); if( NULL != GPU_Database_name_temp ) { GPU_Database_name = GPU_Database_name_temp; memset(GPU_Database_name, 0, GPU_Database_name_bytes); } else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } strcat(GPU_Database_name, Database_name); } else //if there are more than one volumes then extra characters are needed for the volume number { sprintf(digits,".%02d",volume); Int4 GPU_Database_name_bytes = strlen(Database_name) + strlen(digits) + strlen(".gpu") + 1; GPU_Database_name_temp = (char*) realloc(GPU_Database_name, GPU_Database_name_bytes*sizeof(char)); if( NULL != GPU_Database_name_temp ) { GPU_Database_name = GPU_Database_name_temp; memset(GPU_Database_name, 0, GPU_Database_name_bytes); } else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } strcat(GPU_Database_name, Database_name); strcat(GPU_Database_name, digits); } strcat(GPU_Database_name, ".gpu"); FILE* Database_file = fopen( GPU_Database_name,"wb"); if ( NULL == Database_file ) printf("GPU Database file cannot be opened for writing\n"); if( GPU_VERBOSE ) printf("GPU BLASTP database size = %ld bytes\n", GPU_BLASTP_database_bytes); fwrite(GPU_BLASTP_database, sizeof(char), GPU_BLASTP_database_bytes, Database_file); fclose(Database_file); Write_GPU_information_file(GPU_information_file, GPU_Database_name, GPU_BLASTP_database_bytes, volume_lengths[volume], num_sequences_to, store_limit, break_limit, Group_number, Sequence_length_vector); printf("Done with creating the GPU Database file (%s)\n", GPU_Database_name); }//for(volume = 0; volume < num_volumes; ++volume) fclose(GPU_information_file); free(GPU_Database_name); free(GPU_BLASTP_database); free(Sequence_length_vector); free(digits); } ///**************** The following code is modified by YKE ************************** /*void GPU_BLASTP_Execute(const int cuda_device_id, ///**************** The code segment ends ************************** const BlastSeqSrc* seq_src, const LookupTableWrap* lookup_wrap, const BlastCoreAuxStruct* aux_struct, const BLAST_SequenceBlk* query, const BlastQueryInfo* query_info, const BlastInitialWordParameters* word_params, const BlastGPUOptions* gpu_options, const Int4 h_Hits_bytes, const Int4 h_GPUBlastInitHitList_bytes, const char* GPU_volume_name, const unsigned long h_GPU_BLASTP_database_bytes, const Int4* h_Sequence_length_vector, const Int4 Group_number, Int4** d_Hits, GPUBlastInitHitList** d_GPUBlastInitHitList, Int4** d_Database2Dpadded, Int4** d_RepeatedSubstitutionMatrix, Int4** d_RepeatedSequence_length_vector, PV_ARRAY_TYPE** d_RepeatedPV, AaLookupSmallboneCell** d_ThickBackbone, Uint2** d_overflow , Int4** d_RepeatedDiag_array, double *GPU_elapsed, double *FillDatabase_elapsed) */ void GPU_BLASTP_Execute(const int cuda_device_id, const BlastSeqSrc* seq_src, const LookupTableWrap* lookup_wrap, const BlastCoreAuxStruct* aux_struct, const BLAST_SequenceBlk* query, const BlastQueryInfo* query_info, const BlastInitialWordParameters* word_params, const BlastGPUOptions* gpu_options, const Int4 h_Hits_bytes, const Int4 h_GPUBlastInitHitList_bytes, const char* GPU_volume_name, const unsigned long h_GPU_BLASTP_database_bytes, const Int4* h_Sequence_length_vector, const Int4 Group_number, double *GPU_elapsed, double *FillDatabase_elapsed) { //const char* h_GPU_BLASTP_database = (char*) calloc( h_GPU_BLASTP_database_bytes, sizeof(char) ); struct timespec GPU_start, GPU_end, CPU_start, CPU_end; clock_gettime(CLOCK_MONOTONIC, &CPU_start); if(GPU_VERBOSE) fprintf(stderr,"threadId = 0: Reading the GPU database...\n"); ReadGPU_BLASTP_database(//h_GPU_BLASTP_database, GPU_volume_name, h_GPU_BLASTP_database_bytes); if(GPU_VERBOSE) fprintf(stderr,"threadId = 0: Done reading the GPU database\n"); clock_gettime(CLOCK_MONOTONIC, &CPU_end); *FillDatabase_elapsed = (CPU_end.tv_sec - CPU_start.tv_sec) + (double)(CPU_end.tv_nsec - CPU_start.tv_nsec)/ BILLION; clock_gettime(CLOCK_MONOTONIC, &GPU_start); /* if( sufficient_memory ) GPU_BLASTP_pre(cuda_device_id, query, query_info, lookup_wrap, aux_struct->ewp, word_params, gpu_options, h_Sequence_length_vector, h_GPU_BLASTP_database_bytes, //h_GPU_BLASTP_database, d_Hits, h_Hits_bytes, d_GPUBlastInitHitList, h_GPUBlastInitHitList_bytes, d_Database2Dpadded, d_RepeatedSubstitutionMatrix, d_RepeatedSequence_length_vector, d_RepeatedPV, d_ThickBackbone, d_overflow, d_RepeatedDiag_array ); */ if( sufficient_memory ) GPU_BLASTP_pre(cuda_device_id, query, query_info, lookup_wrap, aux_struct->ewp, word_params, gpu_options, h_Sequence_length_vector, h_GPU_BLASTP_database_bytes, //h_GPU_BLASTP_database, h_Hits_bytes, h_GPUBlastInitHitList_bytes ); clock_gettime(CLOCK_MONOTONIC, &GPU_end); *GPU_elapsed = (double) (GPU_end.tv_sec - GPU_start.tv_sec) + (double)(GPU_end.tv_nsec - GPU_start.tv_nsec) / BILLION; //free(h_GPU_BLASTP_database); } /** Perform the gapped alignment of the hits returned by the GPU * @param program_number Type of BLAST program [in] * @param query The query sequence [in] * @param query_info Additional query information [in] * @param seq_src Structure containing BLAST database [in] * @param gap_align Structure containing scoring block and memory allocated * for gapped alignment. [in] * @param score_params Hit scoring parameters [in] * @param lookup_wrap The lookup table, constructed earlier [in] * @param word_options Options for processing initial word hits [in] * @param ext_params Parameters for the gapped extension [in] * @param hit_params Parameters for saving the HSPs [in] * @param eff_len_params Parameters for setting effective lengths [in] * @param psi_options Options specific to PSI-BLAST [in] * @param db_options Options for handling BLAST database [in] * @param gpu_options Options for handling the GPU execution [in] * @param hsp_stream Placeholder for saving HSP lists [in] * @param diagnostics Return statistics containing numbers of hits on * different stages of the search. Statistics saved only * for the allocated parts of the structure. [in] [out] * @param interrupt_search function callback to allow interruption of BLAST * search [in, optional] * @param progress_info contains information about the progress of the current * BLAST search [in|out] * @param h_Hits vector holding the hits, successful hits, and extensions returned by the GPU [in] * @param h_GPUBlastInitHitList vector holding the info of the successful hits returnedby the GPU [in] */ Int4 BLASTP_GetGPUHits(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, BlastGPUOptions* gpu_options, BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info, Int4* h_Hits, GPUBlastInitHitList* h_GPUBlastInitHitList, BlastHSPList** hsp_list, BlastCoreAuxStruct* aux_struct, BlastInitialWordParameters* word_params, Int4 gpu_limit, Int4 break_limit, BlastSeqSrcIterator* itr, BlastSeqSrcGetSeqArg seq_arg, Int4 volume_base, Int4 threadId) { Int2 status = 0; Int8 db_length = 0; const BlastScoringOptions* score_options = score_params->options; Boolean gapped_calculation = score_options->gapped_calculation; BlastScoreBlk* sbp = gap_align->sbp; const Boolean kNucleotide = (program_number == eBlastTypeBlastn || program_number == eBlastTypePhiBlastn); /* remember the current search state */ if (progress_info) progress_info->stage = ePrelimSearch; /* For RPS BLAST, there is no loop over subject sequences, so the preliminary search engine is done in a separate function. */ /* Update the parameters for linking HSPs, if necessary. */ /* Encoding is set so there are no sentinel bytes, and protein/nucleotide sequences are retieved in ncbistdaa/ncbi2na encodings respectively. */ seq_arg.encoding = eBlastEncodingProtein; db_length = BlastSeqSrcGetTotLen(seq_src); ///**************** The following code is modified by YKE ************************** Int4 print_point = BlastSeqSrcGetNumSeqs(seq_src) / 50 + 1; ///**************** The code segment ends ************************** /* iterate over all subject sequences */ while ( ( (seq_arg.oid = BlastSeqSrcIteratorNext(seq_src, itr)) != BLAST_SEQSRC_EOF) ) { if (seq_arg.oid == BLAST_SEQSRC_ERROR) break; if (BlastSeqSrcGetSequence(seq_src, (void*) &seq_arg) < 0) continue; if (db_length == 0) { /* This is not a database search, hence need to recalculate and save the effective search spaces and length adjustments for all queries based on the length of the current single subject sequence. */ if ((status = BLAST_OneSubjectUpdateParameters(program_number, seq_arg.seq->length, score_options, query_info, sbp, hit_params, word_params, eff_len_params)) != 0) return status; } /* Calculate cutoff scores for linking HSPs. Do this only for ungapped protein searches and ungapped translated searches. */ if (hit_params->link_hsp_params && !kNucleotide && !gapped_calculation) { CalculateLinkHSPCutoffs(program_number, query_info, sbp, hit_params->link_hsp_params, word_params, db_length, seq_arg.seq->length); } /* If the subject is translated and the BlastSeqSrc implementation * doesn't provide a genetic code string, use the default genetic * code for all subjects (as in the C toolkit) */ if( seq_arg.oid < gpu_limit ) { if( GPU_VERBOSE ) if( !(seq_arg.oid % print_point ) ) fprintf(stderr,"threadId = %d, seq_arg.oid = %6d, ranges:[%6d, %6d)\n", threadId, seq_arg.oid, itr->oid_range[0], itr->oid_range[1]); status = s_BlastSearchEngineCore(program_number, query, query_info, seq_arg.seq, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, db_options, diagnostics, aux_struct, &(*hsp_list), interrupt_search, progress_info, gpu_options, h_Hits, h_GPUBlastInitHitList, volume_base); } if (status) { break; } if (*hsp_list && (*hsp_list)->hspcnt > 0) { if (!gapped_calculation) { /* The following must be performed for any ungapped search with a nucleotide database. */ status = Blast_HSPListReevaluateUngapped( program_number, *hsp_list, query, seq_arg.seq, word_params, hit_params, query_info, sbp, score_params, seq_src, seq_arg.seq->gen_code_string); if (status) { BlastSeqSrcReleaseSequence(seq_src, (void*) &seq_arg); return status; } /* Relink HSPs if sum statistics is used, because scores might * have changed after reevaluation with ambiguities, and there * will be no traceback stage where relinking is done normally. * If sum statistics are not used, just recalculate e-values. */ if (hit_params->link_hsp_params) { status = BLAST_LinkHsps(program_number, *hsp_list, query_info, seq_arg.seq->length, sbp, hit_params->link_hsp_params, gapped_calculation); } else { Blast_HSPListGetEvalues(query_info, *hsp_list, gapped_calculation, sbp, 0, 1.0); } status = Blast_HSPListReapByEvalue(*hsp_list, hit_params->options); /* Calculate and fill the bit scores, since there will be no traceback stage where this can be done. */ Blast_HSPListGetBitScores(*hsp_list, gapped_calculation, sbp); } /* if (!gapped_calculation) */ /* Save the results. */ status = BlastHSPStreamWrite(hsp_stream, hsp_list); if (status != 0) break; } /* if (hsp_list && hsp_list->hspcnt > 0) */ BlastSeqSrcReleaseSequence(seq_src, (void*) &seq_arg); /* check for interrupt */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { status = BLASTERR_INTERRUPTED; break; } if( seq_arg.oid >= (break_limit-1) ) break; }//while loop /* Fill the cutoff values in the diagnostics structure */ if (diagnostics && diagnostics->cutoffs) { s_FillReturnCutoffsInfo(diagnostics->cutoffs, score_params, word_params, ext_params, hit_params); } return status; } Int4 GPU_BLAST_PreliminarySearchEngine(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, const BlastGPUOptions* gpu_options, BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info) { BlastCoreAuxStruct* aux_struct = NULL; BlastHSPList* hsp_list = NULL; BlastSeqSrcGetSeqArg seq_arg; BlastSeqSrcGetSeqArg gpu_seq_arg; Int2 status = 0; Int8 db_length = 0; const BlastScoringOptions* score_options = score_params->options; const BlastHitSavingOptions* hit_options = hit_params->options; const BlastExtensionOptions* ext_options = ext_params->options; BlastInitialWordParameters* word_params = NULL; Boolean gapped_calculation = score_options->gapped_calculation; BlastScoreBlk* sbp = gap_align->sbp; BlastSeqSrcIterator* itr; BlastSeqSrcIterator* gpu_itr; itr = BlastSeqSrcIteratorNewEx(MAX(BlastSeqSrcGetNumSeqs(seq_src)/2000,1)); gpu_itr = BlastSeqSrcIteratorNewEx(MAX(BlastSeqSrcGetNumSeqs(seq_src)/2000,1)); memset((void*) &seq_arg, 0, sizeof(seq_arg)); memset((void*) &gpu_seq_arg, 0, sizeof(gpu_seq_arg)); const Boolean kNucleotide = (program_number == eBlastTypeBlastn || program_number == eBlastTypePhiBlastn); BlastInitialWordParametersNew(program_number, word_options, hit_params, lookup_wrap, sbp, query_info, BlastSeqSrcGetAvgSeqLen(seq_src), &word_params); if ((status = s_BlastSetUpAuxStructures(seq_src, lookup_wrap, word_params, ext_options, hit_options, query, &aux_struct)) != 0) return status; pthread_mutex_lock(&thread_counter_mutex); Int4 threadId = thread_counter++; if( 0 == threadId ) { int init_return = pthread_barrier_init(&barr, NULL, gpu_options->cpu_threads); } pthread_mutex_unlock(&thread_counter_mutex); if ( (2 == gpu_options->method) ) { if( 0 == threadId ) //only one threads creates the database { CreateGPU_BLASTP_database(seq_src, gpu_options); } exit(0); } struct timespec CPU_start, CPU_end, Total_start, Total_end; double GPU_elapsed = 0, CPU_elapsed = 0, Total_elapsed = 0, FillDatabase_elapsed = 0; Int4 num_blocksx, num_threadsx, num_volumes = 0, percentage = 0; FILE* GPU_information_file = NULL; Read_GPU_information_file_preliminary(&GPU_information_file, seq_src, &num_blocksx, &num_threadsx, &percentage, &num_volumes); //By using gpu_options_local there is no need for a mutex and synchronization for writing "gpu_options_local->use_gpu = FALSE" later on, BlastGPUOptions* gpu_options_local = (BlastGPUOptions *) calloc(2, sizeof(BlastGPUOptions)); gpu_options_local[0].use_gpu = gpu_options->use_gpu; gpu_options_local[1].use_gpu = gpu_options->use_gpu; gpu_options_local[0].num_blocksx = num_blocksx; gpu_options_local[1].num_blocksx = num_blocksx; gpu_options_local[0].num_threadsx = num_threadsx; gpu_options_local[1].num_threadsx = num_threadsx; gpu_options_local[0].num_sequences_to = percentage; gpu_options_local[1].num_sequences_to = percentage; gpu_options_local[0].method = gpu_options->method; gpu_options_local[1].method = gpu_options->method; char* GPU_volume_name = NULL; Int4* Sequence_length_vector = NULL; // Int4* h_Hits_temp = NULL; // GPUBlastInitHitList* h_GPUBlastInitHitList_temp = NULL; //Initialize global variables if( 0 == threadId ) { h_Hits = NULL; h_GPUBlastInitHitList = NULL; sufficient_memory[0] = FALSE; sufficient_memory[1] = FALSE; } Int4 volume = 0; /// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! unsigned long h_GPU_BLASTP_database_bytes[2]; Int4 gpu_limit[2]= {0,0}, gpu_limit_temp; Int4 num_sequences_to[2]= {0,0}; Int4 Group_number[2]= {0,0}; Int4 gpu_NextChunkOID[2]= {0,0}; Int4 volume_length[2]= {0,0}; Int4 break_limit[2]= {0,0}; int SubjectIsTranslated_flag = Blast_SubjectIsTranslated(program_number); for(volume = -1; volume < num_volumes; ++volume) { Int4 h_Hits_bytes; Int4 h_GPUBlastInitHitList_bytes; Int4 break_limit_temp = 0; double GPU_BLASTP_get_data_elapsed, freeing_memory, waiting_time1; clock_gettime(CLOCK_MONOTONIC, &Total_start); /// If @volume is greater than -1, and the last volume DB used GPU, /// then get the result of last volume first and free the gpu memory. if(volume >-1 && sufficient_memory[CURRENT(volume)] ) { clock_gettime(CLOCK_MONOTONIC, &CPU_start); //wait for both threads before global memory free since one thread might using @h_Hits and @h_GPUBlastInitHitList while the //other one might free them. pthread_barrier_wait(&barr); clock_gettime(CLOCK_MONOTONIC, &CPU_end ); waiting_time1 = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; if( 0 == threadId ) { get_GPU_result( &h_Hits, h_Hits_bytes, &h_GPUBlastInitHitList, h_GPUBlastInitHitList_bytes, num_sequences_to[CURRENT(volume)], &GPU_BLASTP_get_data_elapsed); clock_gettime(CLOCK_MONOTONIC, &CPU_start); GPU_BLASTP_free_memory( ); clock_gettime(CLOCK_MONOTONIC, &CPU_end ); freeing_memory = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; } } /// If @volume is less than @num_volumes-1, /// send GPU command. if(volume<(num_volumes-1)) { h_GPU_BLASTP_database_bytes[NEXT(volume)] = 0; num_sequences_to[NEXT(volume)] = 0; gpu_limit[NEXT(volume)] = 0, gpu_limit_temp = 0; Group_number[NEXT(volume)] = 0; gpu_NextChunkOID[NEXT(volume)] = gpu_NextChunkOID[CURRENT(volume)] + volume_length[CURRENT(volume)]; /// Read the next volume DB info Read_GPU_information_file(GPU_information_file, &GPU_volume_name, &(h_GPU_BLASTP_database_bytes[NEXT(volume)]), &(volume_length[NEXT(volume)]), &(num_sequences_to[NEXT(volume)]), &gpu_limit_temp, &break_limit_temp, &(Group_number[NEXT(volume)]), &Sequence_length_vector, gpu_options->cpu_threads); gpu_options_local[NEXT(volume)].num_sequences_to = num_sequences_to[NEXT(volume)]; gpu_limit[NEXT(volume)] = break_limit[CURRENT(volume)] + num_sequences_to[NEXT(volume)]; break_limit[NEXT(volume)] = break_limit_temp; /*num_sequences_to[CURRENT(volume)] is multiplied by 3 because for each sequence we store hits, successful_extensions, hits_extended */ h_Hits_bytes = num_sequences_to[NEXT(volume)] * 3 * sizeof(Int4); h_GPUBlastInitHitList_bytes = num_sequences_to[NEXT(volume)] * MAX_SUCCESSFUL_HITS_PER_SEQUENCE * sizeof(GPUBlastInitHitList); //The GPU arrays are declared here because we want to be able to deallocate them in this function. If we deallocated them in //GPU_BLASTP() then that would act as an thread synchronizer, and wouldn't allow asynchronous execution sufficient_memory[NEXT(volume)] = GPU_BLASTP_check_memory(lookup_wrap, aux_struct->ewp, &(gpu_options_local[NEXT(volume)]), h_GPU_BLASTP_database_bytes[NEXT(volume)], h_Hits_bytes, h_GPUBlastInitHitList_bytes, Group_number[NEXT(volume)], query_info->num_queries, query->length); if( (0 == threadId) && !sufficient_memory[NEXT(volume)] ) { fprintf(stderr,"WARNING: Not enough GPU global memory to process volume No. %02d of the database. Continuing without the CPU...\n",volume); fprintf(stderr," Consider splitting the input database in volumes with smaller size by using the option \"-max_file_size \" (e.g. -max_file_sz 500MB).\n"); fprintf(stderr," Consider using fewer GPU blocks and then fewer GPU thread when formating the database with (e.g. \"-gpu_blocks 256\" and/or \"-gpu_threads 32\") to reduce the GPU global memory requiremenets.\n"); } // if( (0 == threadId) && sufficient_memory[NEXT(volume)] && (gpu_options->cpu_threads > 1) ) // BlastSeqSrcSetMmapMemory(seq_src, FALSE); // else if ( (0 == threadId) && sufficient_memory[NEXT(volume)] ) // BlastSeqSrcSetMmapMemory(seq_src, TRUE); // // //wait until GPU_BLASTP_check_memory() is finished in order to have global variable // //"sufficient_memory[CURRENT(volume)]" updated for all threads. And, until MmapMemory is set // pthread_barrier_wait(&barr); if( sufficient_memory[NEXT(volume)] && (0 == threadId) ) { ///**************** The following code is modified by YKE ************************** GPU_BLASTP_Execute(0, seq_src, lookup_wrap, aux_struct, query, query_info, word_params, &(gpu_options_local[NEXT(volume)]), h_Hits_bytes, h_GPUBlastInitHitList_bytes, GPU_volume_name, h_GPU_BLASTP_database_bytes[NEXT(volume)], Sequence_length_vector, Group_number[NEXT(volume)], &GPU_elapsed, &FillDatabase_elapsed); } } /// If @volume is greater than -1, /// process the GPU result and other unprocessed /// DB. if(volume>-1) { if( (0 == threadId) && sufficient_memory[CURRENT(volume)] && (gpu_options->cpu_threads > 1) ) { BlastSeqSrcSetMmapMemory(seq_src, FALSE); } else if ( (0 == threadId) && sufficient_memory[CURRENT(volume)] ) { BlastSeqSrcSetMmapMemory(seq_src, TRUE); } //wait until GPU_BLASTP_check_memory() is finished in order to have global variable //"sufficient_memory[CURRENT(volume)]" updated for all threads. And, until MmapMemory is set pthread_barrier_wait(&barr); /// RPS processing /* remember the current search state */ if (progress_info) progress_info->stage = ePrelimSearch; /* For RPS BLAST, there is no loop over subject sequences, so the preliminary search engine is done in a separate function. */ if (Blast_ProgramIsRpsBlast(program_number)) { status = s_RPSPreliminarySearchEngine(program_number, query, query_info, seq_src, score_params, lookup_wrap, aux_struct, word_params, ext_params, gap_align, hit_params, hsp_stream, diagnostics, interrupt_search, progress_info, &(gpu_options_local[CURRENT(volume)]), h_Hits, h_GPUBlastInitHitList ); word_params = BlastInitialWordParametersFree(word_params); s_BlastCoreAuxStructFree(aux_struct); return status; } /// CPU post-processing preperation /* Update the parameters for linking HSPs, if necessary. */ BlastLinkHSPParametersUpdate(word_params, hit_params, gapped_calculation); /* Encoding is set so there are no sentinel bytes, and protein/nucleotide sequences are retieved in ncbistdaa/ncbi2na encodings respectively. */ seq_arg.encoding = eBlastEncodingProtein; db_length = BlastSeqSrcGetTotLen(seq_src); //if there is not enough GPU memory use only the CPU and start alignment from the first database sequence num_sequences_to[CURRENT(volume)] = sufficient_memory[CURRENT(volume)] ? num_sequences_to[CURRENT(volume)] : 0; gpu_limit[CURRENT(volume)] = sufficient_memory[CURRENT(volume)] ? gpu_limit[CURRENT(volume)] : (break_limit[CURRENT(volume)] - volume_length[CURRENT(volume)]); Int4 print_point = 0; if(GPU_VERBOSE) { fprintf(stderr,"threadID = %d: CPU execution...\n", threadId); ///**************** The following code is modified by YKE ************************** print_point = BlastSeqSrcGetNumSeqs(seq_src) / 50 +1; ///**************** The code segment ends ************************** } /// CPU post-processing // clock_gettime(CLOCK_MONOTONIC, &CPU_start); // //// if( sufficient_memory[CURRENT(volume)] && (0 == threadId) ) //// BlastSeqSrcSetChunkIterator(seq_src, gpu_NextChunkOID[CURRENT(volume)]); // // clock_gettime(CLOCK_MONOTONIC, &CPU_start); // //wait for both threads after BlastSeqSrcResetChunkIterator() since one thread might start working on the database // //in BLASTP_GetGPUHits() and it can find seq_src pointing at the end of the database, and thus won't work on it. // pthread_barrier_wait(&barr); // clock_gettime(CLOCK_MONOTONIC, &CPU_end ); // double waiting_time2 = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; // // double BLAST_GetGPUHits_elapsed = 0; // if( sufficient_memory[CURRENT(volume)] ) // { // clock_gettime(CLOCK_MONOTONIC, &CPU_start ); // // if(GPU_VERBOSE) // fprintf(stderr,"threadID = %d: CPU processing GPU output...\n",threadId); // // // if( sufficient_memory[CURRENT(volume)] ) // gpu_options_local[CURRENT(volume)].use_gpu = TRUE; // gpu_itr->current_pos = UINT4_MAX;//make this UINT4_MAX to get a new chunk // // //When processing the GPU outputs use mmap since all sequences are processed by the CPU // if( 0 == threadId ) // BlastSeqSrcSetMmapMemory(seq_src, FALSE ); // // status = BLASTP_GetGPUHits(program_number, query, query_info, seq_src, gap_align, // score_params, lookup_wrap, word_options, ext_params, // hit_params, eff_len_params, psi_options, db_options, // &(gpu_options_local[CURRENT(volume)]), hsp_stream, diagnostics, interrupt_search, // progress_info, h_Hits, h_GPUBlastInitHitList, // &hsp_list, aux_struct, word_params, gpu_limit[CURRENT(volume)], break_limit[CURRENT(volume)], // gpu_itr, gpu_seq_arg, gpu_NextChunkOID[CURRENT(volume)], // threadId); // // clock_gettime(CLOCK_MONOTONIC, &CPU_end ); // BLAST_GetGPUHits_elapsed = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; // // if(GPU_VERBOSE) // fprintf(stderr,"threadId = %d: Done with CPU processing GPU output (%.2f sec)\n",threadId, BLAST_GetGPUHits_elapsed); // // pthread_barrier_wait(&barr); // // } /// CPU DB procedure // if( sufficient_memory[CURRENT(volume)] && (0 == threadId) ) // BlastSeqSrcSetChunkIterator(seq_src, gpu_limit[CURRENT(volume)]); // pthread_barrier_wait(&barr); //gpu_options_local->use_gpu is set to FALSE in order the CPU to carry out the rest of alignments // gpu_options_local[CURRENT(volume)].use_gpu = FALSE; /* iterate over all subject sequences */ // gpu_options_local[CURRENT(volume)].use_gpu = TRUE; // printf("current limit is :%ld\n", gpu_limit[CURRENT(volume)]); clock_gettime(CLOCK_MONOTONIC, &CPU_start); while ( (seq_arg.oid = BlastSeqSrcIteratorNext(seq_src, itr)) != BLAST_SEQSRC_EOF) { if (seq_arg.oid == BLAST_SEQSRC_ERROR) break; if (BlastSeqSrcGetSequence(seq_src, &seq_arg) < 0) continue; //if( seq_arg.oid >= gpu_limit[CURRENT(volume)] ) //{ // if( sufficient_memory[CURRENT(volume)] && seq_arg.oid < gpu_limit[CURRENT(volume)]) // gpu_options_local[CURRENT(volume)].use_gpu = TRUE; // else // gpu_options_local[CURRENT(volume)].use_gpu = FALSE; if(GPU_VERBOSE) if( !(seq_arg.oid % print_point ) ) fprintf(stderr,"threadId = %d, seq_arg.oid = %6d, ranges:[%6d, %6d)\n", threadId, seq_arg.oid, itr->oid_range[0], itr->oid_range[1]); if (db_length == 0) { /* This is not a database search, hence need to recalculate and save the effective search spaces and length adjustments for all queries based on the length of the current single subject sequence. */ if ((status = BLAST_OneSubjectUpdateParameters(program_number, seq_arg.seq->length, score_options, query_info, sbp, hit_params, word_params, eff_len_params)) != 0) return status; } /* Calculate cutoff scores for linking HSPs. Do this only for ungapped protein searches and ungapped translated searches. */ if (hit_params->link_hsp_params && !kNucleotide && !gapped_calculation) { CalculateLinkHSPCutoffs(program_number, query_info, sbp, hit_params->link_hsp_params, word_params, db_length, seq_arg.seq->length); } //if (Blast_SubjectIsTranslated(program_number)) if (seq_arg.oid >= gpu_limit[CURRENT(volume)] && ( SubjectIsTranslated_flag >0 ) ) { /* Convert the subject sequence ranges to protein coordinates */ Uint4 i; for (i = 0; i < seq_arg.seq->num_seq_ranges; i++) { seq_arg.seq->seq_ranges[i].left = CONV_NUCL2PROT_COORDINATES(seq_arg.seq->seq_ranges[i].left); seq_arg.seq->seq_ranges[i].right = CONV_NUCL2PROT_COORDINATES(seq_arg.seq->seq_ranges[i].right); } /* If the subject is translated and the BlastSeqSrc implementation * doesn't provide a genetic code string, use the default genetic * code for all subjects (as in the C toolkit) */ if (seq_arg.seq->gen_code_string == NULL) { seq_arg.seq->gen_code_string = GenCodeSingletonFind(db_options->genetic_code); } ASSERT(seq_arg.seq->gen_code_string); } if( sufficient_memory[CURRENT(volume)] && seq_arg.oid < gpu_limit[CURRENT(volume)]) { gpu_options_local[CURRENT(volume)].use_gpu = TRUE; status = s_BlastSearchEngineCore(program_number, query, query_info, seq_arg.seq, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, db_options, diagnostics, aux_struct, &hsp_list, interrupt_search, progress_info, &(gpu_options_local[CURRENT(volume)]), h_Hits, h_GPUBlastInitHitList, gpu_NextChunkOID[CURRENT(volume)]); } else if(seq_arg.oid >= gpu_limit[CURRENT(volume)]) { gpu_options_local[CURRENT(volume)].use_gpu = FALSE; status = s_BlastSearchEngineCore(program_number, query, query_info, seq_arg.seq, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, db_options, diagnostics, aux_struct, &hsp_list, interrupt_search, progress_info, &(gpu_options_local[CURRENT(volume)]), h_Hits, h_GPUBlastInitHitList, 0); } if (status) { break; } if (hsp_list && hsp_list->hspcnt > 0) { if (!gapped_calculation) { /* The following must be performed for any ungapped search with a nucleotide database. */ status = Blast_HSPListReevaluateUngapped( program_number, hsp_list, query, seq_arg.seq, word_params, hit_params, query_info, sbp, score_params, seq_src, seq_arg.seq->gen_code_string); if (status) { BlastSeqSrcReleaseSequence(seq_src, &seq_arg); return status; } /* Relink HSPs if sum statistics is used, because scores might * have changed after reevaluation with ambiguities, and there * will be no traceback stage where relinking is done normally. * If sum statistics are not used, just recalculate e-values. */ if (hit_params->link_hsp_params) { status = BLAST_LinkHsps(program_number, hsp_list, query_info, seq_arg.seq->length, sbp, hit_params->link_hsp_params, gapped_calculation); } else { Blast_HSPListGetEvalues(query_info, hsp_list, gapped_calculation, sbp, 0, 1.0); } status = Blast_HSPListReapByEvalue(hsp_list, hit_params->options); /* Calculate and fill the bit scores, since there will be no traceback stage where this can be done. */ Blast_HSPListGetBitScores(hsp_list, gapped_calculation, sbp); } /* Save the results. */ status = BlastHSPStreamWrite(hsp_stream, &hsp_list); if (status != 0) break; } //} //if( seq_arg.oid >= gpu_limit[CURRENT(volume)] ) BlastSeqSrcReleaseSequence(seq_src, &seq_arg); /* check for interrupt */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { status = BLASTERR_INTERRUPTED; break; } if( seq_arg.oid >= (break_limit[CURRENT(volume)]-1) ) break; } clock_gettime(CLOCK_MONOTONIC, &CPU_end); CPU_elapsed = (CPU_end.tv_sec - CPU_start.tv_sec) + (double)(CPU_end.tv_nsec - CPU_start.tv_nsec) / BILLION; if(GPU_VERBOSE) fprintf(stderr,"threadID = %d: Done with CPU processing (%.2f sec)\n", threadId, CPU_elapsed); /// Record walltime clock_gettime(CLOCK_MONOTONIC, &CPU_start); //wait until both threads are done with BLASTP_GetGPUHits() before deallocating h_Hits and h_GPUBlastInitHitList since //if one threadId=0 deallocates these arrays while other threads are still working on them a segmentation fault will occur if( sufficient_memory[CURRENT(volume)] ) pthread_barrier_wait(&barr); clock_gettime(CLOCK_MONOTONIC, &CPU_end ); double waiting_time3 = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; clock_gettime(CLOCK_MONOTONIC, &Total_end); Total_elapsed = (Total_end.tv_sec - Total_start.tv_sec) + (double)(Total_end.tv_nsec - Total_start.tv_nsec)/ BILLION; if(GPU_VERBOSE) { pthread_mutex_lock(&thread_print_mutex); fprintf(stderr,"\nthreadId = %d: Fill GPU database = %.2f sec",threadId, FillDatabase_elapsed); fprintf(stderr,"\nthreadId = %d: GPU processing = %.2f sec",threadId,GPU_elapsed); fprintf(stderr,"\nthreadId = %d: CPU processing = %.2f sec",threadId,CPU_elapsed); fprintf(stderr,"\nthreadId = %d: Get GPU data = %.2f sec",threadId,GPU_BLASTP_get_data_elapsed); fprintf(stderr,"\nthreadId = %d: Waiting before iterator reset = %.2f sec",threadId,waiting_time1); // fprintf(stderr,"\nthreadId = %d: Waiting after iterator reset = %.2f sec",threadId,waiting_time2); // fprintf(stderr,"\nthreadId = %d: GPU output processing = %.2f sec",threadId,BLAST_GetGPUHits_elapsed); fprintf(stderr,"\nthreadId = %d: Waiting after GPU output processing = %.2f sec",threadId,waiting_time3); fprintf(stderr,"\nthreadId = %d: Freeing GPU memory = %.2f sec",threadId,freeing_memory); fprintf(stderr,"\nthreadId = %d: Total = %.2f sec\n\n",threadId,Total_elapsed); pthread_mutex_unlock(&thread_print_mutex); } } } /// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! if( sufficient_memory[NEXT(volume)] && (0 == threadId) ) { free(h_Hits); free(h_GPUBlastInitHitList); } pthread_mutex_lock(&thread_counter_mutex); thread_counter--; pthread_mutex_unlock(&thread_counter_mutex); free(Sequence_length_vector); free(GPU_volume_name); free(gpu_options_local); fclose(GPU_information_file); ///**************** The following code is modified by YKE ************************** gpu_quit(); ///**************** The code segment ends ************************** hsp_list = Blast_HSPListFree(hsp_list); /* in case we were interrupted */ BlastSequenceBlkFree(seq_arg.seq); itr = BlastSeqSrcIteratorFree(itr); gpu_itr = BlastSeqSrcIteratorFree(gpu_itr); /* Fill the cutoff values in the diagnostics structure */ if (diagnostics && diagnostics->cutoffs) { s_FillReturnCutoffsInfo(diagnostics->cutoffs, score_params, word_params, ext_params, hit_params); } word_params = BlastInitialWordParametersFree(word_params); s_BlastCoreAuxStructFree(aux_struct); return status; } h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/cmdline_flags.hpp0000644000175000017500000003245412001215336024067 0ustar ykeyke/* $Id: cmdline_flags.hpp 222376 2011-01-25 22:52:57Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file cmdline_flags.hpp * Constant declarations for command line arguments for BLAST programs */ #ifndef ALGO_BLAST_BLASTINPUT__CMDLINE_FLAGS__HPP #define ALGO_BLAST_BLASTINPUT__CMDLINE_FLAGS__HPP #include #include #include #include BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) /// Query sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kArgQuery; /// Default value for query sequence input NCBI_BLASTINPUT_EXPORT extern const string kDfltArgQuery; /// Output file name NCBI_BLASTINPUT_EXPORT extern const string kArgOutput; /// BLAST database name NCBI_BLASTINPUT_EXPORT extern const string kArgDb; /// Effective length of BLAST database NCBI_BLASTINPUT_EXPORT extern const string kArgDbSize; /// Subject input file to search NCBI_BLASTINPUT_EXPORT extern const string kArgSubject; /// BLAST database molecule type NCBI_BLASTINPUT_EXPORT extern const string kArgDbType; /// gi list file name to restrict BLAST database NCBI_BLASTINPUT_EXPORT extern const string kArgGiList; /// seqid list file name to restrict BLAST database NCBI_BLASTINPUT_EXPORT extern const string kArgSeqIdList; /// argument for gi list to exclude from a BLAST database search NCBI_BLASTINPUT_EXPORT extern const string kArgNegativeGiList; /// List of filtering algorithms to apply to subjects as soft masking extern const string kArgDbSoftMask; // List of filtering algorithms to apply to subjects as hard masking extern const string kArgDbHardMask; /// Task to perform NCBI_BLASTINPUT_EXPORT extern const string kTask; /// Query genetic code NCBI_BLASTINPUT_EXPORT extern const string kArgQueryGeneticCode; /// Database genetic code NCBI_BLASTINPUT_EXPORT extern const string kArgDbGeneticCode; /// Argument to determine whether searches should be run locally or remotely NCBI_BLASTINPUT_EXPORT extern const string kArgRemote; /// Argument to determine the number of threads to use when running BLAST NCBI_BLASTINPUT_EXPORT extern const string kArgNumThreads; /// Argument for scoring matrix NCBI_BLASTINPUT_EXPORT extern const string kArgMatrixName; /// Argument for expectation value cutoff NCBI_BLASTINPUT_EXPORT extern const string kArgEvalue; /// Argument for minimum raw gapped score for preliminary gapped and traceback /// stages NCBI_BLASTINPUT_EXPORT extern const string kArgMinRawGappedScore; /// Argument to specify the maximum number of target sequences to keep (a.k.a.: /// hitlist size) /// If not set in the command line, this value is the maximum of the number of /// alignments/descriptions to show in the traditional BLAST report NCBI_BLASTINPUT_EXPORT extern const string kArgMaxTargetSequences; /// Default maximum number of target sequences, to be used only on the web NCBI_BLASTINPUT_EXPORT extern const TSeqPos kDfltArgMaxTargetSequences; /// Argument to select the gap opening penalty NCBI_BLASTINPUT_EXPORT extern const string kArgGapOpen; /// Argument to select the gap extending penalty NCBI_BLASTINPUT_EXPORT extern const string kArgGapExtend; /// Argument to select the nucleotide mismatch penalty NCBI_BLASTINPUT_EXPORT extern const string kArgMismatch; /// Argument to select the nucleotide match reward NCBI_BLASTINPUT_EXPORT extern const string kArgMatch; /// Argument to select the ungapped X dropoff value NCBI_BLASTINPUT_EXPORT extern const string kArgUngappedXDropoff; /// Argument to select the gapped X dropoff value NCBI_BLASTINPUT_EXPORT extern const string kArgGappedXDropoff; /// Argument to select the final gapped X dropoff value NCBI_BLASTINPUT_EXPORT extern const string kArgFinalGappedXDropoff; /// Argument to select the window size in the 2-hit wordfinder algorithm NCBI_BLASTINPUT_EXPORT extern const string kArgWindowSize; /// Argument to select the off-diagonal scan range in the 2-hit wordfinder algorithm NCBI_BLASTINPUT_EXPORT extern const string kArgOffDiagonalRange; NCBI_BLASTINPUT_EXPORT extern const int kDfltOffDiagonalRange; /// Argument to select the wordfinder's word size NCBI_BLASTINPUT_EXPORT extern const string kArgWordSize; /// Argument to specify the minimum word score such that the word is added to /// the lookup table NCBI_BLASTINPUT_EXPORT extern const string kArgWordScoreThreshold; /// Argument to specify the effective length of the search space NCBI_BLASTINPUT_EXPORT extern const string kArgEffSearchSpace; /// Argument to specify that Smith-Waterman algorithm should be used to compute /// locally optimal alignments NCBI_BLASTINPUT_EXPORT extern const string kArgUseSWTraceback; /// Argument to specify whether lowercase masking in the query sequence(s) /// should be interpreted as masking NCBI_BLASTINPUT_EXPORT extern const string kArgUseLCaseMasking; /// Default argument to specify whether lowercase masking should be used NCBI_BLASTINPUT_EXPORT extern const bool kDfltArgUseLCaseMasking; /// Argument to select the query strand(s) to search NCBI_BLASTINPUT_EXPORT extern const string kArgStrand; /// Default value for strand selection NCBI_BLASTINPUT_EXPORT extern const string kDfltArgStrand; /// Argument to specify a location to restrict the query sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kArgQueryLocation; /// Argument to specify a location to restrict the subject sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kArgSubjectLocation; /// Argument to specify if the query and subject sequences defline should be /// parsed NCBI_BLASTINPUT_EXPORT extern const string kArgParseDeflines; /// Default argument to specify whether sequences deflines should be parsed NCBI_BLASTINPUT_EXPORT extern const bool kDfltArgParseDeflines; /// Argument to specify the maximum length of an intron when linking multiple /// distinct alignments (applicable to translated queries only) NCBI_BLASTINPUT_EXPORT extern const string kArgMaxIntronLength; /// Default value for maximum intron length NCBI_BLASTINPUT_EXPORT extern const int kDfltArgMaxIntronLength; /// Argument to specify the culling limit NCBI_BLASTINPUT_EXPORT extern const string kArgCullingLimit; /// Default argument to specify the culling limit NCBI_BLASTINPUT_EXPORT extern const int kDfltArgCullingLimit; /// Argument to specify the overhang parameter to the best hit algorithm NCBI_BLASTINPUT_EXPORT extern const string kArgBestHitOverhang; /// Default argument for the overhang parameter to the best hit algorithm NCBI_BLASTINPUT_EXPORT extern const double kDfltArgBestHitOverhang; /// Argument to specify the score edge parameter to the best hit algorithm NCBI_BLASTINPUT_EXPORT extern const string kArgBestHitScoreEdge; /// Default argument for the score edge parameter to the best hit algorithm NCBI_BLASTINPUT_EXPORT extern const double kDfltArgBestHitScoreEdge; /// Argument to specify the frame shift penality NCBI_BLASTINPUT_EXPORT extern const string kArgFrameShiftPenalty; /// Argument to specify number of bits to initiate gapping NCBI_BLASTINPUT_EXPORT extern const string kArgGapTrigger; /// Argument to specify whether the search should be ungapped only NCBI_BLASTINPUT_EXPORT extern const string kArgUngapped; /// Argument to specify the composition based statistics mode to sue NCBI_BLASTINPUT_EXPORT extern const string kArgCompBasedStats; /// Default argument to specify no filtering NCBI_BLASTINPUT_EXPORT extern const string kDfltArgNoFiltering; /// Default argument to specify filtering NCBI_BLASTINPUT_EXPORT extern const string kDfltArgApplyFiltering; /// Argument to specify SEG filtering on query sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kArgSegFiltering; /// Default arguments to apply SEG filtering on query sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kDfltArgSegFiltering; /// Argument to specify DUST filtering on query sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kArgDustFiltering; /// Default arguments to apply DUST filtering on query sequence(s) NCBI_BLASTINPUT_EXPORT extern const string kDfltArgDustFiltering; /// Argument to specify a filtering database (i.e.: one containing repetitive /// elements) NCBI_BLASTINPUT_EXPORT extern const string kArgFilteringDb; /// Argument to specify a taxid for Window Masker. NCBI_BLASTINPUT_EXPORT extern const string kArgWindowMaskerTaxId; /// Argument to specify a path to a Window Masker database. NCBI_BLASTINPUT_EXPORT extern const string kArgWindowMaskerDatabase; /// Argument to specify to mask query during lookup table creation NCBI_BLASTINPUT_EXPORT extern const string kArgLookupTableMaskingOnly; /* PSI-BLAST options */ /// Argument to select the number of iterations to perform in PSI-BLAST NCBI_BLASTINPUT_EXPORT extern const string kArgPSINumIterations; /// Argument to specify a 'checkpoint' file to recover the PSSM from NCBI_BLASTINPUT_EXPORT extern const string kArgPSIInputChkPntFile; /// Argument to specify a multiple sequence alignment file to create a PSSM from NCBI_BLASTINPUT_EXPORT extern const string kArgMSAInputFile; /// Argument to specify the index (1-based) of the sequence in the multiple /// sequence alignment to use as a master sequence NCBI_BLASTINPUT_EXPORT extern const string kArgMSAMasterIndex; /// Argument to specify a 'checkpoint' file to write the PSSM NCBI_BLASTINPUT_EXPORT extern const string kArgPSIOutputChkPntFile; /// Argument to specify the file name for saving the ASCII representation of /// the PSSM NCBI_BLASTINPUT_EXPORT extern const string kArgAsciiPssmOutputFile; /// Argument to specify a PHI-BLAST pattern file NCBI_BLASTINPUT_EXPORT extern const string kArgPHIPatternFile; /// Argument to specify the pseudo-count value used when constructing PSSM NCBI_BLASTINPUT_EXPORT extern const string kArgPSIPseudocount; /// Argument to specify the evalue inclusion threshold for considering /// aligned sequences for PSSM constructions NCBI_BLASTINPUT_EXPORT extern const string kArgPSIInclusionEThreshold; /// Argument to specify non-greedy dynamic programming extension NCBI_BLASTINPUT_EXPORT extern const string kArgNoGreedyExtension; /// Argument to specify the discontinuous megablast template type NCBI_BLASTINPUT_EXPORT extern const string kArgDMBTemplateType; /// Argument to specify the discontinuous megablast template length NCBI_BLASTINPUT_EXPORT extern const string kArgDMBTemplateLength; #if 0 /// Argument to specify the maximum number of HPSs to save per subject NCBI_BLASTINPUT_EXPORT extern const string kArgMaxHSPsPerSubject; /// Default value for specifying the maximum number of HPSs to save per subject NCBI_BLASTINPUT_EXPORT extern const int kDfltArgMaxHSPsPerSubject; #endif /// Argument to specify the target percent identity NCBI_BLASTINPUT_EXPORT extern const string kArgPercentIdentity; /// Argument to specify the search strategy file to read and use for a BLAST /// search NCBI_BLASTINPUT_EXPORT extern const string kArgInputSearchStrategy; /// Argument to specify the file name to save the search strategy used for a /// BLAST search NCBI_BLASTINPUT_EXPORT extern const string kArgOutputSearchStrategy; /// Flag to force using or not using megablast database index. NCBI_BLASTINPUT_EXPORT extern const string kArgUseIndex; /// Megablast database index name. NCBI_BLASTINPUT_EXPORT extern const string kArgIndexName; /// Entrez query. NCBI_BLASTINPUT_EXPORT extern const string kArgEntrezQuery; /* *********** START ************* */ /// GPU arguments NCBI_BLASTINPUT_EXPORT extern const string kArgUseGpu; NCBI_BLASTINPUT_EXPORT extern const string kDfltArgUseGpu; NCBI_BLASTINPUT_EXPORT extern const string kArgNumGpuThreads; NCBI_BLASTINPUT_EXPORT extern const string kDfltArgNumGpuThreads; NCBI_BLASTINPUT_EXPORT extern const string kArgNumGpuBlocks; NCBI_BLASTINPUT_EXPORT extern const string kDfltArgNumGpuBlocks; NCBI_BLASTINPUT_EXPORT extern const string kArgNumGpuSequences; NCBI_BLASTINPUT_EXPORT extern const string kDfltArgNumGpuSequences; NCBI_BLASTINPUT_EXPORT extern const string kArgGpuMethod; NCBI_BLASTINPUT_EXPORT extern const string kDfltArgGpuMethod; NCBI_BLASTINPUT_EXPORT extern const string kArgNumCpuThreads; /* ********** FINISH ************* */ END_SCOPE(blast) END_NCBI_SCOPE #endif /* ALGO_BLAST_BLASTINPUT__CMDLINE_FLAGS__HPP */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/cmdline_flags.cpp0000644000175000017500000001516412001215337024062 0ustar ykeyke/* $Id: cmdline_flags.cpp 222376 2011-01-25 22:52:57Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file cmdline_flags.cpp * Constant definitions for command line arguments for BLAST programs */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: cmdline_flags.cpp 222376 2011-01-25 22:52:57Z rafanovi $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #ifndef SKIP_DOXYGEN_PROCESSING #include #include #include #include BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) USING_SCOPE(align_format); const string kArgQuery("query"); const string kDfltArgQuery("-"); const string kArgOutput("out"); const string kArgDb("db"); const string kArgSubject("subject"); const string kArgDbSize("dbsize"); const string kArgDbType("dbtype"); const string kArgGiList("gilist"); const string kArgSeqIdList("seqidlist"); const string kArgNegativeGiList("negative_gilist"); const string kArgDbSoftMask("db_soft_mask"); const string kArgDbHardMask("db_hard_mask"); const string kTask("task"); const string kArgQueryGeneticCode("query_gencode"); const string kArgDbGeneticCode("db_gencode"); const string kArgRemote("remote"); const string kArgNumThreads("num_threads"); const string kArgMatrixName("matrix"); const string kArgEvalue("evalue"); const string kArgMinRawGappedScore("min_raw_gapped_score"); const string kArgMaxTargetSequences("max_target_seqs"); const TSeqPos kDfltArgMaxTargetSequences = 100; const string kArgGapOpen("gapopen"); const string kArgGapExtend("gapextend"); const string kArgMismatch("penalty"); const string kArgMatch("reward"); const string kArgUngappedXDropoff("xdrop_ungap"); const string kArgGappedXDropoff("xdrop_gap"); const string kArgFinalGappedXDropoff("xdrop_gap_final"); const string kArgWindowSize("window_size"); const string kArgOffDiagonalRange("off_diagonal_range"); const int kDfltOffDiagonalRange = 0; const string kArgWordSize("word_size"); const string kArgWordScoreThreshold("threshold"); const string kArgEffSearchSpace("searchsp"); const string kArgUseSWTraceback("use_sw_tback"); const string kArgUseLCaseMasking("lcase_masking"); const bool kDfltArgUseLCaseMasking = false; const string kArgStrand("strand"); const string kDfltArgStrand("both"); const string kArgQueryLocation("query_loc"); const string kArgSubjectLocation("subject_loc"); const string kArgParseDeflines("parse_deflines"); const bool kDfltArgParseDeflines = false; const string kArgMaxIntronLength("max_intron_length"); const int kDfltArgMaxIntronLength = 0; const string kArgCullingLimit("culling_limit"); const int kDfltArgCullingLimit = 0; const string kArgBestHitOverhang("best_hit_overhang"); const double kDfltArgBestHitOverhang = kBestHit_OverhangDflt; const string kArgBestHitScoreEdge("best_hit_score_edge"); const double kDfltArgBestHitScoreEdge = kBestHit_ScoreEdgeDflt; const string kArgFrameShiftPenalty("frame_shift_penalty"); const string kArgGapTrigger("gap_trigger"); const string kArgUngapped("ungapped"); const string kArgCompBasedStats("comp_based_stats"); const string kDfltArgNoFiltering("no"); const string kDfltArgApplyFiltering("yes"); const string kArgSegFiltering("seg"); const string kDfltArgSegFiltering = NStr::IntToString(kSegWindow) + string(" ") + NStr::DoubleToString(kSegLocut) + string(" ") + NStr::DoubleToString(kSegHicut); const string kArgDustFiltering("dust"); const string kDfltArgDustFiltering = NStr::IntToString(kDustLevel) + string(" ") + NStr::DoubleToString(kDustWindow) + string(" ") + NStr::DoubleToString(kDustLinker); const string kArgFilteringDb("filtering_db"); const string kArgWindowMaskerTaxId("window_masker_taxid"); const string kArgWindowMaskerDatabase("window_masker_db"); const string kArgLookupTableMaskingOnly("soft_masking"); const string kArgPSINumIterations("num_iterations"); const string kArgPSIInputChkPntFile("in_pssm"); const string kArgPSIOutputChkPntFile("out_pssm"); const string kArgAsciiPssmOutputFile("out_ascii_pssm"); const string kArgMSAInputFile("in_msa"); const string kArgMSAMasterIndex("msa_master_idx"); const string kArgPSIPseudocount("pseudocount"); const string kArgPSIInclusionEThreshold("inclusion_ethresh"); const string kArgPHIPatternFile("phi_pattern"); #if 0 const string kArgMaxHSPsPerSubject("max_hsps_per_subject"); const int kDfltArgMaxHSPsPerSubject = 0; #endif const string kArgPercentIdentity("perc_identity"); const string kArgNoGreedyExtension("no_greedy"); const string kArgDMBTemplateType("template_type"); const string kArgDMBTemplateLength("template_length"); const string kArgInputSearchStrategy("import_search_strategy"); const string kArgOutputSearchStrategy("export_search_strategy"); const string kArgUseIndex("use_index"); const string kArgIndexName("index_name"); const string kArgEntrezQuery("entrez_query"); /* *********** START ************* */ const string kArgUseGpu("gpu"); const string kDfltArgUseGpu("F"); const string kArgNumGpuThreads("gpu_threads"); const string kDfltArgNumGpuThreads("64"); const string kArgNumGpuBlocks("gpu_blocks"); const string kDfltArgNumGpuBlocks("512"); const string kArgNumGpuSequences("num_sequences"); const string kDfltArgNumGpuSequences("97"); const string kArgGpuMethod("method"); const string kDfltArgGpuMethod("1"); /* ********** FINISH ************* */ END_SCOPE(blast) END_NCBI_SCOPE #endif /* SKIP_DOXYGEN_PROCESSING */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/build_db.hpp0000644000175000017500000006145612001215337023051 0ustar ykeyke/* $Id: build_db.hpp 176293 2009-11-17 15:41:30Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /** @file * Code to build a database given various sources of sequence data. */ #ifndef OBJTOOLS_BLAST_SEQDB_WRITER___BUILD_DB__HPP #define OBJTOOLS_BLAST_SEQDB_WRITER___BUILD_DB__HPP #include // Blast databases #include #include // ObjMgr #include #include // Local #include #include BEGIN_NCBI_SCOPE /// Interface to a source of Bioseq objects. class NCBI_XOBJWRITE_EXPORT IBioseqSource : public CObject { public: /// Get a Bioseq object if there are any more to get. /// /// This method should return Bioseq objects one at a time until /// there are no more to get, then it should return NULL. /// /// @return A Bioseq object, or NULL if there are no more. virtual CConstRef GetNext() = 0; }; /// Interface to a source of raw sequence data. /// /// This interface provides raw data, including column data, from a /// BlastDB-like data source. class NCBI_XOBJWRITE_EXPORT IRawSequenceSource : public CObject { public: /// Get a raw sequence. /// /// This method provides information about a sequence, including /// the header, zero or more columns, and (raw) sequence data. /// /// The sequence data is split into the sequence + ambiguities /// strings, which should be in the format used by BlastDB /// databases. (If the database type is protein, "ambiguities" /// should be an empty string.) /// /// For each column of the database for which this OID has blob /// data, the column index should be found in column_ids, and a /// reference to the blob data should be stored at the same index /// in the column_blob vector. If this OID does not have a data /// object for this column, either the column may be missing from /// the list, or the blob data string should be empty. /// /// @param sequence Sequence data packed in BlastDB disk format. [out] /// @param ambiguities Ambiguities packed in BlastDB disk format. [out] /// @param deflines This OID's headers as a Blast-def-line-set. [out] /// @param column_ids Column IDs of this OID's nonempty blobs. [out] /// @param column_blobs All non-empty blobs for this OID. [out] virtual bool GetNext(CTempString & sequence, CTempString & ambiguities, CRef & deflines, vector & mask_ranges, vector & column_ids, vector & column_blobs) = 0; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) /// Get the names of all columns defined by this sequence source. /// @param names A list of column names. [out] virtual void GetColumnNames(vector & names) = 0; /// Get the column ID for a column mentioned by name. /// @param name The name (column title) of the column. [in] /// @return The corresponding Column-ID. virtual int GetColumnId(const string & name) = 0; /// Get metadata for the column with the specified Column ID. /// @param id The column-id for which to get meta-data. [in] /// @return All meta-data for this column-id. virtual const map & GetColumnMetaData(int id) = 0; #endif }; /// An interface providing lookups of mask-data by Seq-id. class NCBI_XOBJWRITE_EXPORT IMaskDataSource : public CObject { public: /// Get ranges of masking data for the given Seq-ids. /// @param id Seq-ids for which to get masking data. /// @return Masking data for these Seq-ids. virtual CMaskedRangesVector & GetRanges(const list< CRef > & id) = 0; }; /// Build BlastDB format databases from various data sources. /// /// This class provides an API for building BlastDB format databases. /// The WriteDB library is used internally to produce the actual /// database; the functionality provided by this class helps to bridge /// the gap between the WriteDB API and the needs of a command line /// database construction tool. class NCBI_XOBJWRITE_EXPORT CBuildDatabase : public CObject { public: /// Constructor. /// /// Create a database with the specified name, type, and other /// characteristics. The database will use the specified dbname /// as the base name for database volumes. Note that the indexing /// argument will be combined with either eSparseIndex or eDefault, /// depending on the "sparse" flag. /// /// @param dbname Name of the database to create. [in] /// @param title Title to use for newly created database. [in] /// @param is_protein Use true for protein, false for nucleotide. [in] /// @param sparse Specify true to use sparse Seq-id indexing. [in] /// @param Logging will be done to this stream. [in] /// @param use_gi_mask if true will generate GI-based mask files [in] /// @param logfile file to write the log to [in] CBuildDatabase(const string & dbname, const string & title, bool is_protein, CWriteDB::TIndexType indexing, bool use_gi_mask, ostream * logfile, /* *********** START ************* */ bool sort_sequences); /* ********** FINISH ************* */ // Note -- should deprecate (or just remove) the following one: // - sparse does nothing // - parse_seqids is always true /// Constructor. /// /// Create a database with the specified name, type, and other /// characteristics. The database will use the specified dbname /// as the base name for database volumes. Note that the indexing /// argument will be combined with either eSparseIndex or eDefault, /// depending on the "sparse" flag. /// /// @param dbname Name of the database to create. [in] /// @param title Title to use for newly created database. [in] /// @param is_protein Use true for protein, false for nucleotide. [in] /// @param sparse Specify true to use sparse Seq-id indexing. [in] /// @param parse_seqids specify true to parse the sequence IDs [in] /// @param use_gi_mask if true will generate GI-based mask files [in] /// @param indexing index fields to add to database. [in] CBuildDatabase(const string & dbname, const string & title, bool is_protein, bool sparse, bool parse_seqids, bool use_gi_mask, ostream * logfile); ~CBuildDatabase(); /// Specify a mapping of sequence ids to taxonomic ids. /// /// When adding sequences CBuildDatabase will use the object /// provided here to find TaxIDs for sequences it adds to the /// newly created database. /// /// @param taxids An object providing defline-to-TaxID lookups. [in] void SetTaxids(CTaxIdSet & taxids); /// Specify letters to mask out of protein sequence data. /// /// Protein sequences sometimes contain rare (or recently defined) /// letters that cause trouble for some algorithms. This method /// specifies a list of protein letters that might be found in the /// input sequences, but which should be replaced by "X" before /// adding those sequences to the database. /// /// @param taxids An object providing defline-to-TaxID lookups. [in] void SetMaskLetters(const string & mask_letters); /// Specify source database(s) via the database name(s). /// /// The provided name will be used to find a source database (or /// several) to look up sequence information for the list of /// sequences specified by AddIds(). /// /// @param src_db_name Database name of the source database. [in] void SetSourceDb(const string & src_db_name); /// Specify source database. /// /// The provided source database will be used to look up sequence /// information for the list of sequences specified by AddIds(). /// /// @param src_db The source database. [in] void SetSourceDb(CRef src_db); /// Specify a linkout bit lookup object. /// /// The provided mapping will be used to look up linkout bits for /// sequences added to the database. /// /// @param src_db The source database. [in] void SetLinkouts(const TLinkoutMap & linkouts, bool keep_links); /// Specify a membership bit lookup object. /// /// The provided mapping will be used to look up membership bit /// data for sequences added to the database. /// /// @param src_db The source database. [in] void SetMembBits(const TLinkoutMap & membbits, bool keep_mbits); /// Build the database. /// /// This method builds a database from the given list of Sequence /// IDs and the provided file, which should contain FASTA format /// data. It is equivalent to calling StartBuild(), AddIds(), /// AddFasta(), and EndBuild() in that order (except that a little /// additional logging is done with summary information.). /// /// @param ids List of identifiers to add to the database. /// @param fasta_file FASTA format data for bool Build(const vector & ids, CNcbiIstream * fasta_file); /// Start building a new database. /// /// This method sets up a new database to begin receiving /// sequences. It should be called before AddIds, AddFasta, /// AddSequences, or AddRawSequences is called. void StartBuild(); /// Add the specified sequences from the source database. /// /// The list of strings are interpreted as GIs if they're composed /// only of numeric digits, or as Seq-ids otherwise. The sequence /// IDs will be resolved, and a sequence corresponding to each ID /// will be added to the output database. If remote resolution is /// enabled, it will be used to find up-to-date versions for any /// ambiguously versioned IDs (i.e. unversioned IDs of versioned /// Seq-id types). Then local fetching will be used to process /// IDs using the source database if one was specified. If any /// sequences have not be found, and remote services are enabled, /// remote fetching will be used for IDs not resolved locally. If /// any IDs are not found at all, they will be reported as part of /// the logging output. /// /// @param ids List of sequence IDs as strings. /// @return true if all sequences were found locally or remotely. bool AddIds(const vector & ids); /// Add sequences from a file containing FASTA data. /// /// The provided file is expected to contain FASTA data for one or /// more sequences. The data should be suitable input as required /// by CFastaReader. /// /// @param fasta_file A file containing FASTA data. /// @return True if at least one sequence was added. bool AddFasta(CNcbiIstream & fasta_file); /// Add sequences from an IBioseqSource object. /// /// The provided `src' object is queried using GetNext() to get a /// Bioseq object. The Bioseq is added to the output database /// (with appropriate modifications of taxid, membership bits, and /// linkout bits, as configured here). This process repeats until /// the GetNext() method returns NULL. /// /// @param src An object providing one or more Bioseq objects. /// @return True if at least one sequence was added. bool AddSequences(IBioseqSource & src); /// Add sequences from an IRawSequenceSource object. /// /// The provided `src' object is queried using GetNext() to get /// various "raw format" sequence data and metadata components. /// These pieces of data are added to the output database (with /// appropriate modifications of taxid, membership bits, and /// linkout bits, as configured here). This process repeats until /// the GetNext() method returns false. /// /// @param src An object providing one or more "raw" sequences. /// @return True if at least one sequence was added. bool AddSequences(IRawSequenceSource & src); /// Finish building a new database. /// /// This method closes the newly constructed database, flushing /// any unflushed volumes, creating an alias file to tie the /// volumes together, and so on. /// @param erase Will erase all files created if true. bool EndBuild(bool erase = false); /// Specify whether to use remote fetching for locally absent IDs. /// /// If identifiers in the list provided to Build or to AddIds is /// not found in the source database (if any), remote sequence /// fetching APIs can be used to fetch those sequences. Normally /// this happens in two cases. First, sequences listed in the /// list of IDs are sometimes too new to be found in the source /// database. Secondly, sequences may be found in the source /// database, but newer versions might be available in the remote /// database. /// /// If the use_remote flag is set to true, this class finds the /// latest version number for unversioned IDs (but only of types /// that can have versions in the first place), and will attempt /// to remotely fetch any sequences for which the source database /// does not have the latest version. If the flag is specified as /// false, no remote lookups will be done, and sequences found in /// ids but not found in the source database will not be added to /// the output database. /// /// Note: This does not affect the AddSequences, AddRawSequences, /// or AddFasta methods; in those cases, all provided sequences /// are added in the form they are provided in. /// /// The default value for this flag is "true". /// /// @param use_remote Specify true for remote checking & fetching. void SetUseRemote(bool use_remote) { m_UseRemote = use_remote; } /// Specify level of output verbosity. /// @param v Specify true if output should be more detailed. void SetVerbosity(bool v) { m_Verbose = v; } /// Set the maximum size of database component files. /// /// This will specify the maximum size of file that will be /// made as a component of a database volume manufactured by the /// WriteDB library. The default value is 10^9 (one billion /// bytes.) /// /// @param max_file_size Maximum file size in bytes. void SetMaxFileSize(Uint8 max_file_size); /// Define a masking algorithm. /// /// The returned integer ID will be defined as corresponding to the /// provided program enumeration (e.g. DUST, SEG, etc) and options /// string, for subject masking. Each program enumeration (such /// as DUST) may be used several times with different options /// strings, however, the combination of program and options /// should be unique for each algorithm ID. The options string is /// a free-form string (at least from this class's point of view). /// /// @param program One of the predefined masking types (dust etc). [in] /// @param options A free-form string describing this type of data. /// The empty string should be used to indicate default parameters. [in] /// @param name Name of the GI-base mask file [in] int RegisterMaskingAlgorithm(EBlast_filter_program program, const string & options, const string & name = ""); /// Specify an object mapping Seq-id to subject masking data. /// /// Masking data is provided to CBuildDatabase by implementing an /// interface that can produce masking data given the Seq-ids for /// the sequence that is to be masked. This object could wrap a /// simple lookup table, an algorithm that produces the data on /// the fly, or a wrapper around an existing database that fetches /// the masking data from that database. /// /// @param ranges An object mapping Seq-ids to their masking data. void SetMaskDataSource(IMaskDataSource & ranges); private: /// Get a scope for remote loading of objects. objects::CScope & x_GetScope(); /// Duplicate IDs from local databases. /// /// This method iterates over the list of IDs, copying sequences /// found in the source databases to the output database. void x_DupLocal(); /// Resolve an ID remotely. /// /// This method looks up the given ID via remote services in order /// to find an ID for the most up-to-date version of the sequence. /// The remote service will return a list of Seq-ids; if at least /// one of these is a GI, that will be returned in `gi'. If no GI /// is found, but at least one of the returned IDs is of the same /// type as the input Seq-id, the version number of the input /// Seq-id will be updated. /// /// @param seqid Sequence identifier to look up remotely. [in|out] /// @param gi Genomic ID if one is found, otherwise 0. [out] void x_ResolveRemoteId(CRef & seqid, int & gi); /// Resolve various input IDs (as strings) to GIs. /// /// The input IDs are examined, the type of each is determined as /// a GIs or some other kind of Seq-id, and each ID is resolved to /// a GI where possible. The list of GIs and other Seq-ids found /// is returned in a GI list. /// /// @param ids List of strings representing IDs to resolve. /// @return GI list produced from the input ids. CRef x_ResolveGis(const vector & ids); /// Modify deflines with linkout and membership bits and taxids. /// /// The provided deflines are modified: the taxid is set (0 is /// used if no taxid is known), and linkout and membership bits /// are set. The input object is modified. /// /// @param headers Headers to modify. void x_EditHeaders(CRef headers); /// Modify a Bioseq as needed and add it to the database. /// /// The provided Bioseq is added to the database. Modifications /// are made to the data as needed (but the input object is not /// affected). In particular, the taxid is set (0 is used if no /// taxid is known), and linkout and membership bits are set. /// /// @param bs Bioseq to add to the database. /// @param bs Sequence data to add to the database. void x_EditAndAddBioseq(CConstRef bs, objects::CSeqVector * sv); /// Add the masks for the Seq-id(s) (usually just one) to the database /// being created /// @param ids Seq-id(s) of the sequence to which masks should be added [in] void x_AddMasksForSeqId(const list< CRef >& ids); /// Duplicate IDs from local databases. /// /// This method iterates over the list of IDs; any IDs that were /// not found in the source database are added by fetching the /// sequence from remote services. (Whether an ID was found /// locally can be determined by whether the OID found in the GI /// list is valid.) /// /// @param gi_list A list of GIs and Seq-ids. /// @return True if all IDs could be added. bool x_AddRemoteSequences(CInputGiList & gi_list); /// Write log messages for any unresolved IDs. /// @param gi_list List of GIs and Seq-ids. /// @return True if all sequences were resolved. bool x_ReportUnresolvedIds(const CInputGiList & gi_list) const; /// Store linkout and membership bits in provided headers. /// /// Each Seq-id found in each defline in the provided headers will /// be looked up in the set of linkout and membership bits /// provided for building this database, and the appropriate bits /// will be set for each defline. /// /// @param headers These deflines will be modified. [in|out] void x_SetLinkAndMbit(CRef headers); /// Fetch a sequence from the remote service and add it to the db. /// /// The provided Seq-id will be used to fetch a Bioseq remotely, /// and this Bioseq will be added to this database. If /// /// @param seqid Identifies the sequence to fetch. [in] /// @param found Will be set to true if a sequence was found. [out] /// @param error Will be set to true if an error occurred. [out] void x_AddOneRemoteSequence(const objects::CSeq_id & seqid, bool & found, bool & error); /// Determine if this string ID can be found in the source database. /// /// The provided string will be looked up as an accession in the /// source database. If a corresponding sequence is found, it /// will be returned in the `id' field. The resolution is only /// considered a match if the provided string is a substring of /// the FASTA representation of the provided Seq-id, and if that /// substring seems to represent whole components (so that it's /// surrounded by delimeters such as `|' and `.' rather than by /// alphanumeric characters, which may be part of another ID). /// /// @param acc The accession or ID to look up. [in] /// @param id The returned Seq-id if one is found. [out] /// @return true if the resolution was successful. bool x_ResolveFromSource(const string & acc, CRef & id); /// True for a protein database, false for nucleotide. bool m_IsProtein; /// True to keep linkout bits from source dbs, false to discard. bool m_KeepLinks; /// Table of linkout bits to apply to sequences. TIdToBits m_Id2Links; /// True to keep membership bits from source dbs, false to discard. bool m_KeepMbits; /// Table of membership bits to apply to sequences. TIdToBits m_Id2Mbits; /// Object manager, used for remote fetching. CRef m_ObjMgr; /// Sequence scope, used for remote fetching. CRef m_Scope; /// Set of TaxIDs configured to apply to sequences. CRef m_Taxids; /// Database being produced here. CRef m_OutputDb; /// Database for duplicating sequences locally (-sourcedb option.) CRef m_SourceDb; /// Subject masking data. CRef m_MaskData; /// Logfile. ostream & m_LogFile; /// Whether to use remote resolution and sequence fetching. bool m_UseRemote; /// Define count. int m_DeflineCount; /// Number of OIDs stored in this database. int m_OIDCount; /// If true, more detailed log messages will be produced. bool m_Verbose; /// If true, string IDs found in FASTA input will be parsed as Seq-ids. bool m_ParseIDs; /// If true, there were sequences whose IDs matched those in the provided /// masking locations (via SetMaskDataSource). Used to display a warning in /// case this didn't happen bool m_FoundMatchingMasks; }; END_NCBI_SCOPE #endif // OBJTOOLS_BLAST_SEQDB_WRITER___BUILD_DB__HPP h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/build_db.cpp0000644000175000017500000012121412001215337023031 0ustar ykeyke/* $Id: build_db.cpp 208050 2010-10-13 15:48:11Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Kevin Bealer * */ /** @file build_db.cpp Code to build a database given various sources of sequence data. */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: build_db.cpp 208050 2010-10-13 15:48:11Z maning $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include // Blast databases #include #include #include // Object Manager #include #include #include #include // for CObjReaderParseException // Other utilities #include // Local #include #include #ifndef SKIP_DOXYGEN_PROCESSING BEGIN_NCBI_SCOPE USING_SCOPE(objects); #endif int debug_mode = 0; void CBuildDatabase::x_ResolveRemoteId(CRef & seqid, int & gi) { CScope::TIds ids = x_GetScope().GetIds(*seqid); bool have_seqid = false; bool have_gi = false; gi = 0; ITERATE(CScope::TIds, iter, ids) { CConstRef id = iter->GetSeqId(); if (debug_mode > 5) m_LogFile << "Seq-id " << seqid->AsFastaString() << " contains id " << id->AsFastaString() << endl; if (id->IsGi()) { if (gi > 0) { if (debug_mode > 5) m_LogFile << "WARNING: multiple GIs discovered; gi[0] = " << gi << endl; } else { if (debug_mode > 5) m_LogFile << "Seq-id " << seqid->AsFastaString() << " resolved to " << id->GetGi() << endl; gi = id->GetGi(); have_gi = true; } } else if ((! have_seqid) && (id->Which() == seqid->Which())) { m_LogFile << "Remote: Resolving <" << seqid->AsFastaString() << "> to <" << id->AsFastaString() << ">" << endl; if (id->GetTextseq_Id() == NULL || id->GetTextseq_Id()->IsSetVersion() == false) { m_LogFile << "Warning: Resolution still does not provide version." << endl; } else { seqid.Reset(const_cast(id.GetPointer())); have_seqid = true; } } if (have_gi) break; } } // Resolve all ids to GIs, storing them in a GI list. CRef CBuildDatabase::x_ResolveGis(const vector & ids) { CRef gi_list(new CInputGiList); ITERATE(vector, id, ids) { // There are three possibilities: // // 1. Numbers are added to the list as GIs. // 2. Remote services may be called to determine the most // recent version. // 3. Non-numerical types are added to the list as Seq-ids. // // For #2, the remote service call is only made if: // // A. Remote services are enabled. // B. The Seq-id can have a version (only CTextseq_id types.) // C. The version is not present. int gi(0); bool specific = false; CRef seqid; bool worked = CheckAccession(*id, gi, seqid, specific); // If a source database is specified, try that as a backup // resolution mechanism. if (! worked) { if (m_SourceDb.NotEmpty()) { worked = x_ResolveFromSource(*id, seqid); } } if (! worked) { m_LogFile << "Did not recognize id: \"" << *id << "\"" << endl; continue; } // 1. Numeric GI if (gi != 0) { if (debug_mode > 5) m_LogFile << "Found numerical GI:" << gi << endl; gi_list->AppendGi(gi); continue; } // 2. Possible remote resolution. We look for a GI and if // that is not found, try to find a Seq-id of the same type // (but with a version). if (m_UseRemote && (! specific)) { x_ResolveRemoteId(seqid, gi); if (gi != 0) { gi_list->AppendGi(gi); continue; } } // 3. Just add the Seq-id as a Seq-id. gi_list->AppendSi(*id); } return gi_list; } bool CBuildDatabase::x_ResolveFromSource(const string & acc, CRef & id) { if (m_SourceDb.Empty()) { return false; } vector oids; m_SourceDb->AccessionToOids(acc, oids); bool found(false), done(false); ITERATE(vector, oid, oids) { list< CRef > ids = m_SourceDb->GetSeqIDs(*oid); ITERATE(list< CRef >, seqid, ids) { CRef s = *seqid; string S = s->AsFastaString(); size_t pos = S.find(acc); if (pos != string::npos) { size_t endpos = pos + acc.size(); bool start_okay = (pos == 0 || S[pos-1] == '|'); bool end_okay = ((endpos == S.size()) || (S[endpos] == '.' || S[endpos] == '|')); if (start_okay && end_okay) { done = true; } if (done || (! found)) { found = true; id = s; } } if (done) break; } if (done) break; } return found; } void CBuildDatabase::x_DupLocal() { TIdToBits bitset; // Get sequence, deflines, ambiguities, and sometimes pigs. The // simplest route (for WriteDB) is raw data + asn deflines, so we // use that when possible. CStopWatch sw(CStopWatch::eStart); int count = 0; for(int oid = 0; m_SourceDb->CheckOrFindOID(oid); oid++) { // Raw data. const char * buffer (0); int slength(0); int alength(0); m_SourceDb->GetRawSeqAndAmbig(oid, & buffer, & slength, & alength); CSequenceReturn seqret(*m_SourceDb, buffer); CTempString sequence(buffer, slength); CTempString ambig(buffer + slength, alength); // Deflines CRef headers = m_SourceDb->GetHdr(oid); m_DeflineCount += headers->Get().size(); m_OIDCount ++; x_SetLinkAndMbit(headers); // Always include the taxid; although OPTIONAL, some programs // expect it, since the C ASN.1 loaders always emit integers. m_Taxids->FixTaxId(headers); // Now, add the sequence to the WriteDB database. m_OutputDb->AddSequence(sequence, ambig); m_OutputDb->SetDeflines(*headers); count ++; } if (count) { double t = sw.Elapsed(); m_LogFile << "Duplication from source DB; duplicated " << count << " sequences in " << t << " seconds." << endl; } } // This could be moved to writedb once it is tested and working. static CConstRef s_FixBioseqDeltas(CConstRef bs) { if ((! bs->CanGetInst()) || bs->GetInst().CanGetSeq_data()) { return bs; } if (bs->CanGetInst() && bs->GetInst().CanGetExt() && bs->GetInst().GetExt().IsDelta() && bs->GetInst().CanGetMol() && (bs->GetInst().GetMol() != CSeq_inst::eMol_na)) { NCBI_THROW(CMultisourceException, eArg, "Protein delta sequences are not supported."); } try { const CDelta_ext & dext = bs->GetInst().GetExt().GetDelta(); typedef list< CRef< CDelta_seq > > TItems; // Don't really want to use na4, because a half byte at the // end of a string would require that string to be manually // adjusted before appending. string seq8na; if (bs->GetInst().CanGetLength()) { seq8na.reserve(bs->GetInst().GetLength()); } string na8; ITERATE(TItems, item, dext.Get()) { const CSeq_literal & L = (**item).GetLiteral(); if (L.GetSeq_data().IsNcbi2na()) { CSeqConvert::Convert(L.GetSeq_data().GetNcbi2na(), CSeqUtil::e_Ncbi2na, 0, L.GetLength(), na8, CSeqUtil::e_Ncbi8na); } else if (L.GetSeq_data().IsNcbi4na()) { CSeqConvert::Convert(L.GetSeq_data().GetNcbi4na(), CSeqUtil::e_Ncbi4na, 0, L.GetLength(), na8, CSeqUtil::e_Ncbi8na); } else { NCBI_THROW(CMultisourceException, eArg, "Unhandled type of sequence data encountered."); } seq8na += na8; na8.resize(0); } // Now convert back to 4na, since WriteDB does not yet handle // 8na sequences. int length = seq8na.size(); vector seq4na; CSeqConvert::Convert(seq8na, CSeqUtil::e_Ncbi8na, 0, length, seq4na, CSeqUtil::e_Ncbi4na); // Copy the needed fields of the CBioseq (but remove the delta // sequence) and add a Seq-data. CRef bs2(new CBioseq); if (bs->IsSetId()) { bs2->SetId() = bs->GetId(); } if (bs->IsSetDescr()) { bs2->SetDescr(const_cast(bs->GetDescr())); } CRef inst(new CSeq_inst); inst->SetSeq_data().SetNcbi4na().Set().swap(seq4na); inst->SetMol(CSeq_inst::eMol_na); inst->SetLength(length); inst->SetRepr(CSeq_inst::eRepr_raw); bs2->SetInst(*inst); if (bs->IsSetAnnot()) { bs2->SetAnnot() = bs->GetAnnot(); } bs = bs2; } catch(CInvalidChoiceSelection &) { NCBI_THROW(CMultisourceException, eArg, "Bioseq must have Seq-data or " "Delta containing only literals."); } return bs; } void CBuildDatabase::x_EditHeaders(CRef headers) { // Always include the taxid; although OPTIONAL, some programs // expect it, since the C ASN.1 loaders always emit integers. m_Taxids->FixTaxId(headers); // Edit the linkouts x_SetLinkAndMbit(headers); } #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) void CBuildDatabase::x_AddMasksForSeqId(const list< CRef >& ids) { if (m_MaskData.Empty()) { return; } const CMaskedRangesVector& rng = m_MaskData->GetRanges(ids); if (rng.empty()) { return; } vector gis; ITERATE(list< CRef >, id, ids) { if ((*id)->IsGi()) { gis.push_back((*id)->GetGi()); } } m_OutputDb->SetMaskData(rng, gis); m_FoundMatchingMasks = true; } #endif void CBuildDatabase::x_EditAndAddBioseq(CConstRef bs, objects::CSeqVector * sv) { CRef headers = CWriteDB::ExtractBioseqDeflines(*bs, m_ParseIDs); m_DeflineCount += headers->Get().size(); m_OIDCount ++; x_EditHeaders(headers); // Add the sequence if (sv) { m_OutputDb->AddSequence(*bs, *sv); } else { bs = s_FixBioseqDeltas(bs); m_OutputDb->AddSequence(*bs); } m_OutputDb->SetDeflines(*headers); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) const list< CRef > & ids = bs->GetId(); x_AddMasksForSeqId(ids); #endif } void CBuildDatabase::x_AddOneRemoteSequence(const objects::CSeq_id & seqid, bool & found_all, bool & error) { // Get handle and bioseq CConstRef bs; CBioseq_Handle bsh; try { bsh = x_GetScope().GetBioseqHandle(seqid); bs = bsh.GetCompleteBioseq(); if (debug_mode > 5) m_LogFile << MSerial_AsnText << *bs << endl; } catch (const CException & e) { m_LogFile << "Caught exception for query: " << seqid.AsFastaString() << endl << e.what() << endl; found_all = false; error = true; } if (bsh.GetState() & CBioseq_Handle::fState_not_found) { error = true; } if (error) { if (debug_mode > 5) m_LogFile << "Could not find entry for: " << seqid.AsFastaString() << endl; found_all = false; return; } CSeqVector sv(bsh); x_EditAndAddBioseq(bs, & sv); if (debug_mode > 5) m_LogFile << "-- REMOTE: Found sequence " << seqid.AsFastaString() << endl; } bool CBuildDatabase::x_AddRemoteSequences(CInputGiList & gi_list) { CStopWatch sw(CStopWatch::eStart); int count = 0; bool found_all = true; int num_gis = gi_list.GetNumGis(); int i = 0; for(i = 0; i < num_gis; i++) { if (m_Verbose) m_LogFile << "GI " << gi_list.GetKey(i); // We only need to fetch here for those cases where the SeqDB // attempt could not translate the GI. if (gi_list.GetGiOid(i).oid == -1) { if (m_Verbose) m_LogFile << " not found locally; adding remotely." << endl; CRef id(new CSeq_id); id->SetGi(gi_list.GetKey(i)); bool error = false; x_AddOneRemoteSequence(*id, found_all, error); count++; } else { if (m_Verbose) m_LogFile << " found locally; not adding remotely." << endl; } } int num_seqids = gi_list.GetNumSis(); for(i = 0; i < num_seqids; i++) { if (m_Verbose) m_LogFile << "Seq-id " << gi_list.GetKey(i); // We only need to fetch here for those cases where the SeqDB // attempt could not translate the GI. if (gi_list.GetSiOid(i).oid == -1) { if (m_Verbose) m_LogFile << " not found locally; adding remotely." << endl; bool error = false; string acc = gi_list.GetKey(i); CRef id(new CSeq_id(acc)); x_AddOneRemoteSequence(*id, found_all, error); count++; } else { if (m_Verbose) m_LogFile << " found locally; not adding remotely." << endl; } } if (count) { double t = sw.Elapsed(); m_LogFile << "Adding sequences from remote source; added " << count << " sequences in " << t << " seconds." << endl; } return found_all; } bool CBuildDatabase::x_ReportUnresolvedIds(const CInputGiList & gi_list) const { bool success = true; int num_gis = gi_list.GetNumGis(); int unresolved = 0; int i; for(i = 0; i < num_gis; i++) { // We only need to fetch here for those cases where the SeqDB // attempt could not translate the GI. if (gi_list.GetGiOid(i).oid == -1) { if (m_Verbose) m_LogFile << "GI " << gi_list.GetKey(i) << " was not resolvable." << endl; success = false; unresolved ++; } else { if (m_Verbose) m_LogFile << "GI " << gi_list.GetKey(i) << " found locally." << endl; } } int num_seqids = gi_list.GetNumSis(); for(i = 0; i < num_seqids; i++) { // We only need to fetch here for those cases where the SeqDB // attempt could not translate the GI. if (gi_list.GetSiOid(i).oid == -1) { if (m_Verbose) m_LogFile << "Seq-id " << gi_list.GetKey(i) << " was not resolvable." << endl; unresolved ++; success = false; } else { if (m_Verbose) m_LogFile << "Seq-id " << gi_list.GetKey(i) << " found locally." << endl; } } if (unresolved) { m_LogFile << "Could not resolve " << unresolved << " IDs." << endl; } success = false; unresolved ++; return success; } class CFastaBioseqSource : public IBioseqSource { public: CFastaBioseqSource(CNcbiIstream & fasta_file, bool is_protein, bool parse_ids); ~CFastaBioseqSource(); virtual CConstRef GetNext(); private: CRef m_LineReader; CFastaReader* m_FastaReader; }; CFastaBioseqSource::CFastaBioseqSource(CNcbiIstream & fasta_file, bool is_protein, bool parse_ids) : m_FastaReader(NULL) { m_LineReader.Reset(new CBufferedLineReader(fasta_file)); typedef CFastaReader::EFlags TFlags; int iflags = CFastaReader::fAllSeqIds | CFastaReader::fForceType; if (is_protein) { iflags |= CFastaReader::fAssumeProt; } else { iflags |= CFastaReader::fAssumeNuc; } if (parse_ids) { iflags |= CFastaReader::fAllSeqIds; } else { iflags |= CFastaReader::fNoParseID; } TFlags flags = (TFlags) iflags; m_FastaReader = new CFastaReader(*m_LineReader, flags); } CFastaBioseqSource::~CFastaBioseqSource() { delete m_FastaReader; } CConstRef CFastaBioseqSource::GetNext() { CConstRef rv; if (m_LineReader.NotEmpty() && ! m_LineReader->AtEOF()) { CRef entry; try { entry = m_FastaReader->ReadOneSeq(); } catch (const CObjReaderParseException& e) { static const string kKeyword("m_Pos = "); SIZE_TYPE start = NStr::Find(e.what(), kKeyword); SIZE_TYPE end = NStr::Find(e.what(), ")", start); string pos("unknown"); if (start != NPOS && end != NPOS) { start += kKeyword.size(); pos = string(e.what()).substr(start, end-start); } ERR_POST(Error << "Error while reading input at position " << pos); ERR_POST(Error << "Aborting processing prematurely."); // additional handling needed throw(e); } if (entry.NotEmpty()) { _ASSERT(entry->IsSeq()); rv.Reset(& entry->GetSeq()); } } // Any failure to read a Bioseq is considered an EOF. if (rv.Empty()) { m_LineReader.Reset(); } return rv; } bool CBuildDatabase::AddSequences(IBioseqSource & src) { bool found = false; CStopWatch sw(CStopWatch::eStart); int count = 0; CConstRef bs = src.GetNext(); while(bs.NotEmpty()) { string bioseq_id("Unknown"); if (bs->CanGetId()) { const list< CRef > & ids = bs->GetId(); if (! ids.empty() && ids.front().NotEmpty()) { bioseq_id.assign(ids.front()->AsFastaString()); } } if (bs->GetLength() == 0) { m_LogFile << "Ignoring sequence '" << bioseq_id << "' as it has no sequence data" << endl; bs = src.GetNext(); continue; } if (m_Verbose) { m_LogFile << "Adding bioseq from fasta; first id is: '" << bioseq_id << "'" << endl; } // No linkouts or memberships here (yet). x_EditAndAddBioseq(bs, NULL); found = true; count++; if (debug_mode > 5) m_LogFile << "-- FASTA: Found sequence." << endl; bs = src.GetNext(); } if (count) { double t = sw.Elapsed(); m_LogFile << "Adding sequences from FASTA; added " << count << " sequences in " << t << " seconds." << endl; } return found; } bool CBuildDatabase::AddSequences(IRawSequenceSource & src) { CStopWatch sw(CStopWatch::eStart); bool done = false; bool rv = false; #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) // Get all column names. vector all_names; map in2out; int mask_id; src.GetColumnNames(all_names); for(int i = 0; i < (int) all_names.size(); i++) { string name = all_names[i]; int in_id = src.GetColumnId(name); // skip masking data column if (name == "BlastDb/MaskData") { mask_id = in_id; continue; } int out_id = m_OutputDb->FindColumn(name); if (out_id < 0) { out_id = m_OutputDb->CreateUserColumn(name); } typedef map StringPairMap; const StringPairMap & meta = src.GetColumnMetaData(in_id); ITERATE(StringPairMap, iter, meta) { m_OutputDb->AddColumnMetaData(out_id, iter->first, iter->second); } in2out[in_id] = out_id; } #endif // Copy all data. vector column_blobs; vector column_ids; int count = 0; while(! done) { CTempString sequence, ambiguities; CRef deflines; CMaskedRangesVector mask_data; if (src.GetNext(sequence, ambiguities, deflines, mask_data, column_ids, column_blobs)) { // Copy data _ASSERT(column_blobs.size() == column_ids.size()); if (sequence.empty()) { NCBI_THROW(CMultisourceException, eArg, "Error in raw data: no sequence"); } if ((! ambiguities.empty()) && m_IsProtein) { NCBI_THROW(CMultisourceException, eArg, "Error in raw data: " "protein db cannot with ambiguities"); } if (deflines.Empty()) { NCBI_THROW(CMultisourceException, eArg, "Error in raw data: no headers provided"); } x_EditHeaders(deflines); m_OutputDb->AddSequence(sequence, ambiguities); m_OutputDb->SetDeflines(*deflines); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) for(int i = 0; i < (int)column_ids.size(); i++) { int in_id = column_ids[i]; if (in_id == mask_id) continue; if (column_blobs[i].size() == 0) continue; _ASSERT(in2out.find(in_id) != in2out.end()); int out_id = in2out[in_id]; CTempString blob_in = column_blobs[i]; CBlastDbBlob & blob_out = m_OutputDb->SetBlobData(out_id); blob_out.Clear(); blob_out.WriteRaw(& blob_in.data()[0], blob_in.size()); } // Don't forget about the IMaskDataSource! vector gis; // GIs associated with this sequence if (!mask_data.empty() || !m_MaskData.Empty()) { ITERATE(CBlast_def_line_set::Tdata, defline, deflines->Get()) { const list< CRef > & ids = (*defline)->GetSeqid(); ITERATE(list< CRef >, id, ids) { if ((*id)->IsGi()) { gis.push_back((*id)->GetGi()); } } if (!m_MaskData.Empty()) { const CMaskedRangesVector rng = m_MaskData->GetRanges(ids); if (!rng.empty()) { mask_data.insert(mask_data.end(), rng.begin(), rng.end()); m_FoundMatchingMasks = true; } } } } if (!mask_data.empty()) { m_OutputDb->SetMaskData(mask_data, gis); } #endif rv = true; count ++; } else { done = true; } } if (count) { double t = sw.Elapsed(); m_LogFile << "Adding sequences from raw db source; added " << count << " sequences in " << t << " seconds." << endl; } return rv; } static void s_CreateDirectories(const string& dbname) { CDirEntry dir_entry(dbname); string dir_name = dir_entry.GetDir(CDirEntry::eIfEmptyPath_Empty); if (dir_name.empty()) { return; } CDir d(dir_name); if ( !d.Exists() ) { if ( !d.CreatePath() ) { string msg("Failed to create directory '" + d.GetName() + "'"); NCBI_THROW(CMultisourceException, eOutputFileError, msg); } } if (!d.CheckAccess(CDirEntry::fWrite)) { string msg("You do not have write permissions on '" + d.GetName() + "'"); NCBI_THROW(CMultisourceException, eOutputFileError, msg); } } CBuildDatabase::CBuildDatabase(const string & dbname, const string & title, bool is_protein, CWriteDB::TIndexType indexing, bool use_gi_mask, ostream * logfile, /* *********** START ************* */ bool sort_sequences) /* ********** FINISH ************* */ : m_IsProtein (is_protein), m_KeepLinks (false), m_KeepMbits (false), m_Taxids (new CTaxIdSet()), m_LogFile (*logfile), m_UseRemote (true), m_DeflineCount (0), m_OIDCount (0), m_Verbose (false), m_ParseIDs (((indexing & CWriteDB::eFullIndex) != 0 ? true : false)), m_FoundMatchingMasks(false) { s_CreateDirectories(dbname); m_LogFile << "\n\nBuilding a new DB, current time: " << CTime(CTime::eCurrent).AsString() << endl; m_LogFile << "New DB name: " << dbname << endl; m_LogFile << "New DB title: " << title << endl; m_LogFile << "Sequence type: " << (is_protein ? "Protein" : "Nucleotide") << endl; CWriteDB::ESeqType seqtype = (is_protein ? CWriteDB::eProtein : CWriteDB::eNucleotide); m_OutputDb.Reset(new CWriteDB(dbname, seqtype, title, indexing, m_ParseIDs, use_gi_mask, /* *********** START ************* */ sort_sequences)); /* ********** FINISH ************* */ // Standard 1 GB limit m_OutputDb->SetMaxFileSize(1000*1000*1000); } CBuildDatabase::CBuildDatabase(const string & dbname, const string & title, bool is_protein, bool sparse, bool parse_seqids, bool use_gi_mask, ostream * logfile) : m_IsProtein (is_protein), m_KeepLinks (false), m_KeepMbits (false), m_Taxids (new CTaxIdSet()), m_LogFile (*logfile), m_UseRemote (true), m_DeflineCount (0), m_OIDCount (0), m_Verbose (false), m_ParseIDs (parse_seqids), m_FoundMatchingMasks(false) { s_CreateDirectories(dbname); m_LogFile << "\n\nBuilding a new DB, current time: " << CTime(CTime::eCurrent).AsString() << endl; m_LogFile << "New DB name: " << dbname << endl; m_LogFile << "New DB title: " << title << endl; m_LogFile << "Sequence type: " << (is_protein ? "Protein" : "Nucleotide") << endl; CWriteDB::ESeqType seqtype = (is_protein ? CWriteDB::eProtein : CWriteDB::eNucleotide); CWriteDB::EIndexType ix = (sparse ? CWriteDB::eSparseIndex : CWriteDB::eDefault); m_OutputDb.Reset(new CWriteDB(dbname, seqtype, title, ix, m_ParseIDs, use_gi_mask)); // Standard 1 GB limit m_OutputDb->SetMaxFileSize(1000*1000*1000); } CBuildDatabase::~CBuildDatabase() { if (m_MaskData.NotEmpty() && !m_FoundMatchingMasks) { ERR_POST(Error << "No sequences matched any of the masks provided.\n" << "Please ensure that the -parse_seqids option is used " << "in the\nfiltering program as well as makeblastdb."); } if (!m_Taxids->HasEverFixedId()) { ERR_POST(Error << "No sequences matched any of the taxids provided."); } } void CBuildDatabase::SetTaxids(CTaxIdSet & taxids) { m_Taxids.Reset(& taxids); } void CBuildDatabase::SetMaskLetters(const string & letters) { m_OutputDb->SetMaskedLetters(letters); } CScope & CBuildDatabase::x_GetScope() { if (m_Scope.Empty()) { if (m_ObjMgr.Empty()) { m_ObjMgr.Reset(CObjectManager::GetInstance()); } m_Scope.Reset(new CScope(*m_ObjMgr)); // Add default loaders (GB loader in this demo) to the scope. m_Scope->AddDefaults(); } return *m_Scope; } void CBuildDatabase::SetSourceDb(CRef seqdb) { m_LogFile << "Configured source DB: " << seqdb->GetDBNameList() << endl; m_LogFile << "Source DB has title: " << seqdb->GetTitle() << endl; m_LogFile << "Source DB time stamp: " << seqdb->GetDate() << endl; m_SourceDb = seqdb; } void CBuildDatabase::SetSourceDb(const string & src_db_name) { _ASSERT(src_db_name.size()); CRef src_db(new CSeqDBExpert(src_db_name, m_IsProtein ? CSeqDB::eProtein : CSeqDB::eNucleotide)); SetSourceDb(src_db); } void CBuildDatabase::SetLinkouts(const TLinkoutMap & linkouts, bool keep_links) { m_LogFile << "Keep Linkouts: " << (keep_links ? "T" : "F") << endl; MapToLMBits(linkouts, m_Id2Links); m_KeepLinks = keep_links; } void CBuildDatabase::SetMembBits(const TLinkoutMap & membbits, bool keep_mbits) { m_LogFile << "Keep MBits: " << (keep_mbits ? "T" : "F") << endl; MapToLMBits(membbits, m_Id2Mbits); m_KeepMbits = keep_mbits; } bool CBuildDatabase::Build(const vector & ids, CNcbiIstream * fasta_file) { CStopWatch sw(CStopWatch::eStart); StartBuild(); bool success = AddIds(ids); if (success) { success = AddFasta(*fasta_file); } bool success2 = EndBuild(); success = success || success2; double t = sw.Elapsed(); m_LogFile << "Total sequences stored: " << m_OIDCount << endl; m_LogFile << "Total deflines stored: " << m_DeflineCount << endl; m_LogFile << "Total time to build database: " << t << " seconds.\n" << endl; return success; } void CBuildDatabase::StartBuild() { } bool CBuildDatabase::AddIds(const vector & ids) { bool success = true; // Resolve all ids to GIs, storing them in a GI list. CRef gi_list; if (m_SourceDb.NotEmpty() && ! ids.empty()) { gi_list = x_ResolveGis(ids); } // Translate the GI list. if (gi_list.NotEmpty() && (gi_list->GetNumGis() || gi_list->GetNumSis())) { // The process of constructing a SeqDB object with a user GI // list causes translation of the User GI list, and is the // fastest way of performing such a translation in bulk. It // is possible to iterate the list afterwards to determine // what subset of it that has been translated; non-translated // GIs will need to be fetched using a data loader. // // It is not necessary, however, to iterate the GI list to // find OIDs that correspond to the filtered DB; these can be // found using OID iteration over SeqDB, which produces a // better ordering inasmuch as the reads from the source // sequence data will be sequential on disk. _ASSERT(m_SourceDb.NotEmpty()); CRef filtered (new CSeqDBExpert(m_SourceDb->GetDBNameList(), m_SourceDb->GetSequenceType(), &* gi_list)); m_SourceDb = filtered; // Add all local database sequences to the output DB. x_DupLocal(); if (m_Verbose) { // Map oid to gi. map seen_it; for(int i = 0; i < gi_list->GetNumGis(); i++) { int this_oid = gi_list->GetGiOid(i).oid; int this_gi = gi_list->GetGiOid(i).gi; if (this_oid != -1) { if (seen_it.find(this_oid) == seen_it.end()) { seen_it[this_oid] = this_gi; } else { m_LogFile << "GI " << this_gi << " is duplicate of GI " << seen_it[this_oid] << endl; } } } } } if (gi_list.NotEmpty()) { if (m_UseRemote) { success = x_AddRemoteSequences(*gi_list); } else { success = x_ReportUnresolvedIds(*gi_list); } } return success; } bool CBuildDatabase::AddFasta(CNcbiIstream & fasta_file) { // Add any fasta sequences as well. bool success = true; if (fasta_file) { CFastaBioseqSource fbs(fasta_file, m_IsProtein, m_ParseIDs); try { success = AddSequences(fbs); } catch (...) { EndBuild(true); throw; } } return success; } bool CBuildDatabase::EndBuild(bool erase) { bool success = false; bool can_not_close = false; try { m_OutputDb->Close(); } catch (...) { if (!erase) { erase = true; can_not_close = true; } } vector vols; vector files; m_OutputDb->ListVolumes(vols); m_OutputDb->ListFiles(files); m_LogFile << endl; _ASSERT(vols.empty() == files.empty()); if (vols.empty()) { m_LogFile << "No volumes were created because no sequences were found." << endl; success = false; } else { ITERATE(vector, iterv, vols) { m_LogFile << "volume: " << *iterv << endl; } m_LogFile << endl; ITERATE(vector, iterf, files) { m_LogFile << "file: " << *iterf << endl; if (erase) { CFile(*iterf).Remove(); } } } m_LogFile << endl; if (can_not_close) { NCBI_THROW(CWriteDBException, eArgErr, "Can not close files."); } return success; } static void s_SetDeflineBits(objects::CBlast_def_line & defline, TIdToBits & bitmap, bool keep_old, bool is_memb, vector & keys) { bool found = false; int value = 0; ITERATE(vector, key, keys) { if (! key->size()) continue; TIdToBits::iterator item = bitmap.find(*key); if (item != bitmap.end()) { found = true; value |= item->second; } } if (found) { list & linkv = (is_memb ? defline.SetMemberships() : defline.SetLinks()); if (! keep_old) { linkv.clear(); } if (linkv.empty()) { linkv.push_back(value); } else { linkv.front() |= value; } } else { if (! keep_old) { if (is_memb) { defline.ResetMemberships(); } else { defline.ResetLinks(); } } } } void CBuildDatabase::x_SetLinkAndMbit(CRef headers) { vector keys; NON_CONST_ITERATE(CBlast_def_line_set::Tdata, iter, headers->Set()) { CBlast_def_line & defline = **iter; GetDeflineKeys(defline, keys); s_SetDeflineBits(defline, m_Id2Links, m_KeepLinks, false, keys); s_SetDeflineBits(defline, m_Id2Mbits, m_KeepMbits, true, keys); } } void CBuildDatabase::SetMaxFileSize(Uint8 max_file_size) { m_OutputDb->SetMaxFileSize(max_file_size); } int CBuildDatabase::RegisterMaskingAlgorithm(EBlast_filter_program program, const string & options, const string & name) { #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) return m_OutputDb->RegisterMaskAlgorithm(program, options, name); #else return 0; #endif } void CBuildDatabase::SetMaskDataSource(IMaskDataSource & ranges) { m_MaskData.Reset(& ranges); } END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blastp_args.cpp0000644000175000017500000001077012001215337023572 0ustar ykeyke/* $Id: blastp_args.cpp 174882 2009-11-02 16:46:46Z madden $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file blastp_args.cpp * Implementation of the BLASTP command line arguments */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: blastp_args.cpp 174882 2009-11-02 16:46:46Z madden $"; #endif #include #include #include #include #include #include BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) USING_SCOPE(objects); CBlastpAppArgs::CBlastpAppArgs() { CRef arg; static const string kProgram("blastp"); arg.Reset(new CProgramDescriptionArgs(kProgram, "Protein-Protein BLAST")); const bool kQueryIsProtein = true; bool const kFilterByDefault = false; m_Args.push_back(arg); m_ClientId = kProgram + " " + CBlastVersion().Print(); static const string kDefaultTask = "blastp"; SetTask(kDefaultTask); set tasks (CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eProtProt)); arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask)); m_Args.push_back(arg); m_BlastDbArgs.Reset(new CBlastDatabaseArgs); m_BlastDbArgs->SetDatabaseMaskingSupport(true); arg.Reset(m_BlastDbArgs); m_Args.push_back(arg); m_StdCmdLineArgs.Reset(new CStdCmdLineArgs); arg.Reset(m_StdCmdLineArgs); m_Args.push_back(arg); arg.Reset(new CGenericSearchArgs(kQueryIsProtein)); m_Args.push_back(arg); arg.Reset(new CFilteringArgs(kQueryIsProtein, kFilterByDefault)); m_Args.push_back(arg); arg.Reset(new CMatrixNameArg); m_Args.push_back(arg); arg.Reset(new CWordThresholdArg); m_Args.push_back(arg); m_HspFilteringArgs.Reset(new CHspFilteringArgs); arg.Reset(m_HspFilteringArgs); m_Args.push_back(arg); arg.Reset(new CWindowSizeArg); m_Args.push_back(arg); m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein)); arg.Reset(m_QueryOptsArgs); m_Args.push_back(arg); m_FormattingArgs.Reset(new CFormattingArgs); arg.Reset(m_FormattingArgs); m_Args.push_back(arg); m_MTArgs.Reset(new CMTArgs); arg.Reset(m_MTArgs); m_Args.push_back(arg); arg.Reset(new CGappedArgs); m_Args.push_back(arg); m_RemoteArgs.Reset(new CRemoteArgs); arg.Reset(m_RemoteArgs); m_Args.push_back(arg); arg.Reset(new CCompositionBasedStatsArgs); m_Args.push_back(arg); m_DebugArgs.Reset(new CDebugArgs); arg.Reset(m_DebugArgs); m_Args.push_back(arg); /* *********** START ************* */ m_GpuArgs.Reset(new CGpuArgs); arg.Reset(m_GpuArgs); m_Args.push_back(arg); /* ********** FINISH ************* */ } CRef CBlastpAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& args) { CRef retval; SetTask(args[kTask].AsString()); retval.Reset(CBlastOptionsFactory::CreateTask(GetTask(), locality)); _ASSERT(retval.NotEmpty()); return retval; } int CBlastpAppArgs::GetQueryBatchSize() const { return blast::GetQueryBatchSize(eBlastp, m_IsUngapped); } END_SCOPE(blast) END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/functions.cpp0000644000175000017500000017757112137172260023325 0ustar ykeyke#define CURRENT(a) ((a)&0x1) #define NEXT(a) CURRENT(a+1) ///============= OCT. 16, 2012 ============================ #define MAX_CPU_CORE_NO 100 static double max_cpu_walltime[3]; static double current_cpu_walltime[MAX_CPU_CORE_NO]; /// @gpu_cpu_capability_rate shows /// the comp. capability between one /// gpu card and a cpu core static double gpu_cpu_capability_rate=2; static float Gpu_db_used_ratio_in_byte=0.8; /// the flag shows gpu_db_used_ratio is fixed or not, /// '1' for fixed, others for changed by program itself static char flag_fixed_gpu_db_used_ratio=1; void init_max_and_current_cpu_walltime() { int i; for(i=0; i0) adjust_ratio *= no_of_gpu_cards/equivalent_no_of_gpu_cards; else adjust_ratio *= 1.0 - no_of_gpu_cards/equivalent_no_of_gpu_cards; new_rate = old_gpudb_ratio + adjust_ratio; new_rate = (new_rate>1)?1:new_rate; new_rate = (new_rate<0)?0:new_rate; return new_rate; } int Read_Gpu_db_aux_file() { FILE * pFile; char* gpu_db_used_ratio_file_name = "./gpu_db_used_ratioq"; pFile = fopen ( gpu_db_used_ratio_file_name, "rb" ); if (pFile==NULL) { printf ("Warning: There is no user defined Gpu db used ratio! Use the default one!\n"); return; } char *line_read = (char *) malloc( sizeof(char) ); size_t nbytes = 1; int bytes_read, max_storage_tmp = 0; /// Read Gpu_db_used_ratio_in_byte to determind the gpu work load in whole bytes_read = getline(&line_read, &nbytes, pFile);//Read comment bytes_read = getline(&line_read, &nbytes, pFile);//Read the size of the Gpu_db_used_ratio_in_byte Gpu_db_used_ratio_in_byte = ( (atof(line_read) < 0 ) || (atof(line_read) >1 ) ) ? 0.0 :(double)atof(line_read); /// Read Gpu_db_used_ratio_in_byte to determind the gpu work load in whole bytes_read = getline(&line_read, &nbytes, pFile);//Read comment bytes_read = getline(&line_read, &nbytes, pFile);//Read the flag flag_fixed_gpu_db_used_ratio flag_fixed_gpu_db_used_ratio = ( 1 == atoi(line_read) ) ? 1:0; /// Read Gpu_db_used_ratio_in_byte to determind the gpu work load in whole bytes_read = getline(&line_read, &nbytes, pFile);//Read comment bytes_read = getline(&line_read, &nbytes, pFile);//Read the size of the gpu_cpu_capability_rate gpu_cpu_capability_rate = ( atof(line_read) <= 0 ) ? 2 :(double)atof(line_read); /// Read Gpu_db_used_ratio_in_byte to determind the gpu work load in whole bytes_read = getline(&line_read, &nbytes, pFile);//Read comment bytes_read = getline(&line_read, &nbytes, pFile);//Read the size of the MAX_SUCCESSFUL_HITS_PER_SEQUENCE max_storage_tmp = ( atoi(line_read) > 0 ) ? atoi(line_read) : 19 ; set_MAX_SUCCESSFUL_HITS_PER_SEQUENCE(max_storage_tmp); free(line_read); fclose(pFile); } void get_GPU_result( Int4** _h_Hits, const Int4 _h_Hits_bytes, GPUBlastInitHitList** _h_GPUBlastInitHitList, const Int4 _h_GPUBlastInitHitList_bytes, const Int4 _num_sequences, double * _elapsed_time) { Int4* h_Hits_temp=NULL; GPUBlastInitHitList* h_GPUBlastInitHitList_temp=NULL; struct timespec CPU_start, CPU_end; h_Hits_temp = (Int4*) realloc(*_h_Hits, _h_Hits_bytes); if( NULL != h_Hits_temp ) *_h_Hits = h_Hits_temp; else { puts("Error (re)allocating memory for the GPU\n"); all_gpu_abnormally_exit(1); } h_GPUBlastInitHitList_temp = (GPUBlastInitHitList*) realloc(*_h_GPUBlastInitHitList, _h_GPUBlastInitHitList_bytes); if( NULL != h_GPUBlastInitHitList_temp ) *_h_GPUBlastInitHitList = h_GPUBlastInitHitList_temp; else { printf("Error (re)allocating memory for the GPU\n"); all_gpu_abnormally_exit(1); } clock_gettime(CLOCK_MONOTONIC, &CPU_start); //writing h_Hits and h_GPUBlastInitHitList doesn't require a mutex because because it is accessed by only one thread GPU_BLASTP_get_data(*_h_Hits, _h_Hits_bytes, *_h_GPUBlastInitHitList, _h_GPUBlastInitHitList_bytes, _num_sequences); if(BRIEF_INFO) GPU_BLASTP_check_rehit_ratio(*_h_Hits, _num_sequences); clock_gettime(CLOCK_MONOTONIC, &CPU_end); if(_elapsed_time ==NULL) { fprintf(stderr, "get_GPU_result: Error, \"_elapsed_time\" is invaild!\n"); all_gpu_abnormally_exit(1); } *_elapsed_time = (CPU_end.tv_sec - CPU_start.tv_sec) + (double)(CPU_end.tv_nsec - CPU_start.tv_nsec) / BILLION; if(BRIEF_INFO) { printf("\n============================================\n"); printf("Get data elapses %lg sec\n", *_elapsed_time); } return; } void Write_GPU_information_file_preliminary(FILE* GPU_information_file, const Int4 num_blocksx, const Int4 num_threadsx, const char percentage, const Int4 num_volumes) { fprintf(GPU_information_file,"#Number of blocksx\n"); fprintf(GPU_information_file,"%d\n", num_blocksx ); fprintf(GPU_information_file,"#Number of threadsx\n"); fprintf(GPU_information_file,"%d\n", num_threadsx); fprintf(GPU_information_file,"#Percentage\n"); fprintf(GPU_information_file,"%d\n", percentage); fprintf(GPU_information_file,"#Number of volumes\n"); fprintf(GPU_information_file,"%d\n", num_volumes ); } void Write_GPU_information_file(FILE* GPU_information_file, const char* GPU_Database_name, const unsigned long GPU_BLASTP_database_bytes, const Int4 volume_length, const Int4 num_sequences_to, const Int4 store_limit, const Int4 break_limit, const Int4 Group_number, const Int4* Sequence_length_vector, //+ CPU_rest_bytes const unsigned long CPU_rest_bytes) { fprintf(GPU_information_file,"#Volume name\n"); fprintf(GPU_information_file,"%s\n", GPU_Database_name); fprintf(GPU_information_file,"#Volume size in bytes\n"); fprintf(GPU_information_file,"%ld\n", GPU_BLASTP_database_bytes ); fprintf(GPU_information_file,"#Volume sequences\n"); fprintf(GPU_information_file,"%d\n", volume_length ); fprintf(GPU_information_file,"#Number of sequences in GPU volume\n"); fprintf(GPU_information_file,"%d\n", num_sequences_to ); fprintf(GPU_information_file,"#Store limit\n"); fprintf(GPU_information_file,"%d\n", store_limit ); fprintf(GPU_information_file,"#Break limit\n"); fprintf(GPU_information_file,"%d\n", break_limit ); fprintf(GPU_information_file,"#Group number\n"); fprintf(GPU_information_file,"%d\n", Group_number ); fprintf(GPU_information_file,"#Length of each group\n"); Int4 i = 0; for(i = 0; i < Group_number; ++i) fprintf(GPU_information_file,"%d\n", Sequence_length_vector[i] ); fprintf(GPU_information_file,"#Length of the rest sequences in CPU database\n"); fprintf(GPU_information_file,"%ld\n",CPU_rest_bytes); } void Read_GPU_information_file_preliminary(FILE** GPU_information_file, const BlastSeqSrc* seq_src, Int4* num_blocksx, Int4* num_threadsx, Int4* percentage, Int4* num_volumes) { char* Database_name = BlastSeqSrcGetName(seq_src); char* GPU_information_name = (char*) calloc(strlen(Database_name) + strlen(".gpuinfox") + 1,sizeof(char)); strcat(GPU_information_name, Database_name); strcat(GPU_information_name, ".gpuinfox"); *GPU_information_file = fopen( GPU_information_name, "rb"); if( NULL == (*GPU_information_file) ) { printf("GPU information file cannot be opened for reading. Exiting...\n"); exit(1); } char *line_read = (char *) malloc( sizeof(char) ); size_t nbytes = 1; Int4 bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read first line which is a comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read number of blocksx *num_blocksx = atoi(line_read); bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read number of threads *num_threadsx = atoi(line_read); bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read percentage *percentage = atoi(line_read); bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, *GPU_information_file);//Read number of volumes *num_volumes = atoi(line_read); free(line_read); free(GPU_information_name); } void Read_GPU_information_file(const FILE* GPU_information_file, char** GPU_volume_name, unsigned long* GPU_BLASTP_database_bytes, Int4* volume_length, Int4* num_sequences_to, Int4* store_limit, Int4* break_limit, Int4* Group_number, Int4** Sequence_length_vector, const Int4 cpu_threads, const int thread_count_per_block, const int gpu_db_group_size, float* gpu_db_ratio_ptr ) { char *line_read = (char *) malloc( sizeof(char) ); size_t nbytes = 1; Int4 bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read first line which is a comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the volume name char* GPU_volume_name_temp = (char*)realloc(*GPU_volume_name, bytes_read*sizeof(char) ); if( NULL != GPU_volume_name_temp ) { *GPU_volume_name = GPU_volume_name_temp; memset(*GPU_volume_name, 0, bytes_read*sizeof(char)); memcpy(*GPU_volume_name, line_read, bytes_read - 1); } else { printf("Error (re)allocating memory for the GPU information file\n"); exit(1); } bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the size of the volume in bytes *GPU_BLASTP_database_bytes = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of sequences in this volume *volume_length = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of sequences processed by the GPU in this volume *num_sequences_to = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the ID of the last sequences processed by the GPU in this volume *store_limit = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the ID of the last sequences of this volume *break_limit = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of groups in this volume *Group_number = atoi(line_read); bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment Int4* Sequence_length_vector_temp = (Int4*) realloc(*Sequence_length_vector, (*Group_number)*sizeof(Int4)); if( NULL != Sequence_length_vector_temp ) *Sequence_length_vector = Sequence_length_vector_temp; else { printf("Error (re)allocating memory for the GPU information file\n"); exit(1); } Int4 i = 0; for( i = 0; i < *Group_number; ++i) { bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the length of each group of this volume (*Sequence_length_vector)[i] = atoi(line_read); } //Read CPU_rest_bytes unsigned long CPU_rest_bytes = 0; bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read comment bytes_read = getline(&line_read, &nbytes, GPU_information_file);//Read the number of groups in this volume CPU_rest_bytes = atoi(line_read); ///------------ Oct. 16. 2012 ----------- if(NULL==gpu_db_ratio_ptr) { printf("Error: gpu ratio is unaccessable!\n"); exit(-1); } ///------------ Oct. 16. 2012 ----------- /// determind the size of GPU DB to be processed double ratio = 0; if(0==(*gpu_db_ratio_ptr) ) { switch ( cpu_threads ) { case 1: ratio = 1; break; case 2: ratio = 1; break; case 3: ratio = 0.8; break; case 4: ratio = 0.76; break; case 5: ratio = 0.7; break; case 6: ratio = 0.6; break; default: ratio = 0.6; break; } } else ratio = (*gpu_db_ratio_ptr); /// Compute the total workload by the sum of length^2 Int4 l=0; double total_workload_cost=0, actual_workload_cost=0; for(l=0; l<(*Group_number-1); l++) total_workload_cost += (*Sequence_length_vector)[l] * (*Sequence_length_vector)[l]; total_workload_cost*=gpu_db_group_size; total_workload_cost += ((double)(*Sequence_length_vector)[*Group_number-1]) * (*Sequence_length_vector)[*Group_number-1] * (*num_sequences_to - (*Group_number-1)*gpu_db_group_size); actual_workload_cost = total_workload_cost * ratio; //recalculate num_sequences_to Int4 k = (*Group_number); double tmp_workload_cost = total_workload_cost; if(ratio<1) { tmp_workload_cost -= ((double)(*Sequence_length_vector)[*Group_number-1]) * (*Sequence_length_vector)[*Group_number-1] * (*num_sequences_to - (*Group_number-1)*gpu_db_group_size); k--; do { if(tmp_workload_cost<= actual_workload_cost ) break; else { tmp_workload_cost -= (double)(*Sequence_length_vector)[k-1]*(*Sequence_length_vector)[k-1]*gpu_db_group_size; k--; } } while(k>0); } if(k!=*Group_number) { double rest_workload_from_expected = actual_workload_cost - tmp_workload_cost; int no_threads_added = (0!=(*Sequence_length_vector)[k])? (rest_workload_from_expected / ( (*Sequence_length_vector)[k] *(*Sequence_length_vector)[k] *thread_count_per_block) )*thread_count_per_block : 0; tmp_workload_cost += (double)(*Sequence_length_vector)[k] *(*Sequence_length_vector)[k] *no_threads_added; if(flag_fixed_gpu_db_used_ratio!=1) { *gpu_db_ratio_ptr = tmp_workload_cost / total_workload_cost; *gpu_db_ratio_ptr = ((*gpu_db_ratio_ptr)>1)?1:(*gpu_db_ratio_ptr); *gpu_db_ratio_ptr = ((*gpu_db_ratio_ptr)<0)?0:(*gpu_db_ratio_ptr); } /// To determind the no. of sequences that the gpu processes on, we /// first determind how many group of sequences to be processed, and /// then get the no. of blocks sequences to be processed on (each block /// of sequences has @thread_count_per_block sequences). if( (k* gpu_db_group_size + no_threads_added) < *num_sequences_to) { *num_sequences_to = k* gpu_db_group_size + no_threads_added; *Group_number = k; *Group_number+= (0==no_threads_added)?0:1; unsigned long GPU_db_bytes_count = 0; for(l=0; lnum_blocksx) * (gpu_options->num_threadsx); char percentage = PERCENTAGE; BlastSeqSrcIterator* itr = BlastSeqSrcIteratorNewEx(MAX(BlastSeqSrcGetNumSeqs(seq_src)/100,1)); BlastSeqSrcGetSeqArg seq_arg; memset((void*) &seq_arg, 0, sizeof(seq_arg)); /* Encoding is set so there are no sentinel bytes, and protein/nucleotide sequences are retrieved in ncbistdaa/ncbi2na encodings respectively. */ seq_arg.encoding = eBlastEncodingProtein; char* Database_name = BlastSeqSrcGetName(seq_src); char* GPU_Database_name = NULL; char* GPU_Database_name_temp; char* GPU_BLASTP_database = NULL; char* GPU_BLASTP_database_temp; Int4* Sequence_length_vector = NULL; Int4* Sequence_length_vector1 = NULL; Int4* Sequence_length_vector_temp; char* digits = (char*) calloc(10, sizeof(char));//10 digits are enough to cover up to 999999999 volumes // ".gpuinfo" changed to ".gpuinfox" char* GPU_information_name = (char*) calloc(strlen(Database_name) + strlen(".gpuinfox") + 1,sizeof(char)); strcat(GPU_information_name, Database_name); strcat(GPU_information_name, ".gpuinfox"); FILE* GPU_information_file = fopen( GPU_information_name, "wb"); if ( NULL == GPU_information_file ) printf("GPU information file cannot be opened for writing\n"); Int4* volume_lengths = NULL; Int4 num_volumes = 0; ReadGPU_BLASTP_volinfo(seq_src, &num_volumes, &volume_lengths); printf("num_volumes = %d\n",num_volumes); Write_GPU_information_file_preliminary(GPU_information_file, gpu_options->num_blocksx, gpu_options->num_threadsx, percentage, num_volumes); //Calculate the total size of the rest of the CPU database unsigned long CPU_rest_bytes = 0; Int4 volume = 0, break_limit = 0; for(volume = 0; volume < num_volumes; ++volume) { CPU_rest_bytes = 0; Int4 num_sequences_to = (percentage * volume_lengths[volume]) / 100; Int4 store_limit = break_limit + num_sequences_to; Int4 Group_number = (num_sequences_to / Group_size ) + (( (num_sequences_to % Group_size ) == 0)?0:1); Sequence_length_vector_temp = (Int4*) realloc( Sequence_length_vector, Group_number*sizeof(Int4) ); if( NULL != Sequence_length_vector_temp ) Sequence_length_vector = Sequence_length_vector_temp; else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } Int4 vector_counter = 0; unsigned long GPU_BLASTP_database_bytes = 0; Int4 oid = break_limit + Group_size - 1; //initialized oid to the last sequence of the first group if( oid >= store_limit ) oid = store_limit - 1; //Initializes the Sequence_length_vector with the length of the longest sequence in each group //The length is converted to a multiple of WIDTH_MULTIPLE (defined in gpu_cpu_common.h) int previous_sequence_length = 0; do { Int4 sequence_length = BlastSeqSrcGetSeqLen( seq_src, (void*) &oid ); if( previous_sequence_length > sequence_length ) { fprintf(stderr,"ERROR: the input database is not sorted\n"); fprintf(stderr,"Sort the database by using the option \"-sort_volumes\" with \"makeblastdb.\"\n"); fprintf(stderr,"Exiting...\n"); exit(1); } previous_sequence_length = sequence_length; Round2Multiple( &sequence_length ); Sequence_length_vector[ vector_counter ] = sequence_length; if( GPU_VERBOSE ) printf("Group %d starts at sequence %d and has length = %d\n", vector_counter, oid, Sequence_length_vector[vector_counter]); ++vector_counter; if( oid == store_limit - 1 ) break; oid += Group_size; } while( oid < store_limit - 1 ); //If the last iteration of the previous do-while didn't cover all sequences (i.e. the Group_size is not a multiple of num_sequences) //the remaining sequences form the last group, and the last element of Sequence_length_vector is initialized if( oid != store_limit - 1 ) { oid = store_limit - 1; Int4 sequence_length = BlastSeqSrcGetSeqLen( seq_src, (void*) &oid ); /* check if the volume is sorted */ if( previous_sequence_length > sequence_length ) { fprintf(stderr,"ERROR: the input database is not sorted\n"); fprintf(stderr,"Sort the database by using the option \"-sort_volumes\" with \"makeblastdb.\"\n"); fprintf(stderr,"Exiting...\n"); exit(1); } Round2Multiple( &sequence_length ); Sequence_length_vector[ vector_counter ] = sequence_length; if( GPU_VERBOSE ) printf("Group %d starts at sequence %d and has length = %d\n", vector_counter, oid, Sequence_length_vector[vector_counter]); } //Calculate the total size of the GPU database for(i = 0; i < Group_number; ++i) GPU_BLASTP_database_bytes += Sequence_length_vector[i]*Group_size*sizeof(char); //This helps to check if there is a very large sequence that can cause the GPU memory to explode if( GPU_BLASTP_database_bytes > UINT4_MAX ) { printf("Memory requirements for GPU database larger than 4 GB. Exiting...\n"); exit(0); } GPU_BLASTP_database_temp = (char*) realloc( GPU_BLASTP_database, GPU_BLASTP_database_bytes*sizeof(char) ); if( NULL != GPU_BLASTP_database_temp ) GPU_BLASTP_database = GPU_BLASTP_database_temp; else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } memset(GPU_BLASTP_database, 0, GPU_BLASTP_database_bytes*sizeof(char)); int length = 0; int group_member = 0; int counter = 0, sequence = 0, AminoAcids = 0, base = 0; break_limit += volume_lengths[volume]; /* iterate over all subject sequences of this volume */ previous_sequence_length = 0; while ( ( (seq_arg.oid = BlastSeqSrcIteratorNext(seq_src, itr)) != BLAST_SEQSRC_EOF) ) { if (seq_arg.oid == BLAST_SEQSRC_ERROR) break; if (BlastSeqSrcGetSequence(seq_src, &seq_arg) < 0) continue; if( seq_arg.oid < store_limit ) { if( (counter % Group_size) == 0 ) { base += length*Group_size; length = Sequence_length_vector[ group_member ]; group_member++; sequence = 0; } AminoAcids = 0; int sequence_length = BlastSeqSrcGetSeqLen( seq_src, (void*) &seq_arg.oid ); if( previous_sequence_length > sequence_length ) { fprintf(stderr,"ERROR: the input database is not sorted\n"); fprintf(stderr,"Sort the database by using the option \"-sort_volumes\" with \"makeblastdb.\"\n"); fprintf(stderr,"Exiting...\n"); exit(1); } previous_sequence_length = sequence_length; for(i = 0; i < sequence_length/stride + 1; ++i) { for(j = 0; j < stride; ++j) { (GPU_BLASTP_database)[ base + (sequence + i*Group_size)*stride + j] = (seq_arg.seq->sequence)[AminoAcids]; AminoAcids++; if( AminoAcids >= sequence_length ) goto done; } } done: counter++; sequence++; } /* if ( seq_arg.oid < num_sequences_to ) */ BlastSeqSrcReleaseSequence(seq_src, &seq_arg); if( seq_arg.oid == (break_limit-1) ) break; } /* while loop */ //Create the name of the gpu database if( 1 == num_volumes ) { int GPU_Database_name_bytes = strlen(Database_name) + strlen(".gpu") + 1; GPU_Database_name_temp = (char*) realloc(GPU_Database_name, GPU_Database_name_bytes*sizeof(char)); if( NULL != GPU_Database_name_temp ) { GPU_Database_name = GPU_Database_name_temp; memset(GPU_Database_name, 0, GPU_Database_name_bytes); } else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } strcat(GPU_Database_name, Database_name); } else //if there are more than one volumes then extra characters are needed for the volume number { sprintf(digits,".%02d",volume); Int4 GPU_Database_name_bytes = strlen(Database_name) + strlen(digits) + strlen(".gpu") + 1; GPU_Database_name_temp = (char*) realloc(GPU_Database_name, GPU_Database_name_bytes*sizeof(char)); if( NULL != GPU_Database_name_temp ) { GPU_Database_name = GPU_Database_name_temp; memset(GPU_Database_name, 0, GPU_Database_name_bytes); } else { printf("Error (re)allocating memory for the GPU database creation\n"); exit(1); } strcat(GPU_Database_name, Database_name); strcat(GPU_Database_name, digits); } strcat(GPU_Database_name, ".gpu"); FILE* Database_file = fopen( GPU_Database_name,"wb"); if ( NULL == Database_file ) printf("GPU Database file cannot be opened for writing\n"); if( GPU_VERBOSE ) printf("GPU BLASTP database size = %ld bytes\n", GPU_BLASTP_database_bytes); fwrite(GPU_BLASTP_database, sizeof(char), GPU_BLASTP_database_bytes, Database_file); fclose(Database_file); // + CPU_rest_bytes Write_GPU_information_file(GPU_information_file, GPU_Database_name, GPU_BLASTP_database_bytes, volume_lengths[volume], num_sequences_to, store_limit, break_limit, Group_number, Sequence_length_vector, CPU_rest_bytes); printf("Done with creating the GPU Database file (%s)\n", GPU_Database_name); }//for(volume = 0; volume < num_volumes; ++volume) fclose(GPU_information_file); free(GPU_Database_name); free(GPU_BLASTP_database); free(Sequence_length_vector); free(digits); } void GPU_BLASTP_Execute(//const int cuda_device_id, const BlastSeqSrc* seq_src, const LookupTableWrap* lookup_wrap, const BlastCoreAuxStruct* aux_struct, const BLAST_SequenceBlk* query, const BlastQueryInfo* query_info, const BlastInitialWordParameters* word_params, const BlastGPUOptions* gpu_options, const Int4 h_Hits_bytes, const Int4 h_GPUBlastInitHitList_bytes, const char* GPU_volume_name, const unsigned long h_GPU_BLASTP_database_bytes, Int4* h_Sequence_length_vector, const Int4 Group_number, double *GPU_elapsed, double *FillDatabase_elapsed) { struct timespec GPU_start, GPU_end, CPU_start, CPU_end; clock_gettime(CLOCK_MONOTONIC, &CPU_start); if(GPU_VERBOSE) fprintf(stderr,"threadId = 0: Reading the GPU database...\n"); ReadGPU_BLASTP_database( GPU_volume_name, h_GPU_BLASTP_database_bytes); if(GPU_VERBOSE) fprintf(stderr,"threadId = 0: Done reading the GPU database\n"); clock_gettime(CLOCK_MONOTONIC, &CPU_end); *FillDatabase_elapsed = (CPU_end.tv_sec - CPU_start.tv_sec) + (double)(CPU_end.tv_nsec - CPU_start.tv_nsec)/ BILLION; clock_gettime(CLOCK_MONOTONIC, &GPU_start); GPU_BLASTP_pre( query, query_info, lookup_wrap, aux_struct->ewp, word_params, gpu_options, h_Sequence_length_vector, h_GPU_BLASTP_database_bytes, Group_number, h_Hits_bytes, h_GPUBlastInitHitList_bytes ); clock_gettime(CLOCK_MONOTONIC, &GPU_end); *GPU_elapsed = (double) (GPU_end.tv_sec - GPU_start.tv_sec) + (double)(GPU_end.tv_nsec - GPU_start.tv_nsec) / BILLION; } Int4 GPU_BLAST_PreliminarySearchEngine(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, const BlastGPUOptions* gpu_options, BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info) { BlastCoreAuxStruct* aux_struct = NULL; BlastHSPList* hsp_list = NULL; BlastSeqSrcGetSeqArg seq_arg; BlastSeqSrcGetSeqArg gpu_seq_arg; Int2 status = 0; Int8 db_length = 0; const BlastScoringOptions* score_options = score_params->options; const BlastHitSavingOptions* hit_options = hit_params->options; const BlastExtensionOptions* ext_options = ext_params->options; BlastInitialWordParameters* word_params = NULL; Boolean gapped_calculation = score_options->gapped_calculation; BlastScoreBlk* sbp = gap_align->sbp; BlastSeqSrcIterator* itr; BlastSeqSrcIterator* gpu_itr; itr = BlastSeqSrcIteratorNewEx(300); gpu_itr = BlastSeqSrcIteratorNewEx(MAX(BlastSeqSrcGetNumSeqs(seq_src)/4500,1)); memset((void*) &seq_arg, 0, sizeof(seq_arg)); memset((void*) &gpu_seq_arg, 0, sizeof(gpu_seq_arg)); const Boolean kNucleotide = (program_number == eBlastTypeBlastn || program_number == eBlastTypePhiBlastn); BlastInitialWordParametersNew(program_number, word_options, hit_params, lookup_wrap, sbp, query_info, BlastSeqSrcGetAvgSeqLen(seq_src), &word_params); if ((status = s_BlastSetUpAuxStructures(seq_src, lookup_wrap, word_params, ext_options, hit_options, query, &aux_struct)) != 0) return status; pthread_mutex_lock(&thread_counter_mutex); Int4 threadId = thread_counter++; if( 0 == threadId ) { int init_return = pthread_barrier_init(&barr, NULL, gpu_options->cpu_threads); Read_Gpu_db_aux_file(); init_max_and_current_gpu_walltime(); lut_sorting((BlastAaLookupTable*) lookup_wrap->lut); } pthread_mutex_unlock(&thread_counter_mutex); if ( (-1 == gpu_options->method) ) { if( 0 == threadId ) //only one threads creates the database { CreateGPU_BLASTP_database(seq_src, gpu_options); } exit(0); } else { /// Set no. of gpu cards if( 0 == threadId ) //only one threads creates the database { SetNumOfGpuCards( gpu_options->method); } } unsigned long mask = 1<use_gpu = FALSE" later on, BlastGPUOptions* gpu_options_local = (BlastGPUOptions *) calloc(2, sizeof(BlastGPUOptions)); gpu_options_local[0].use_gpu = gpu_options->use_gpu; gpu_options_local[1].use_gpu = gpu_options->use_gpu; gpu_options_local[0].num_blocksx = num_blocksx; gpu_options_local[1].num_blocksx = num_blocksx; gpu_options_local[0].num_threadsx = num_threadsx; gpu_options_local[1].num_threadsx = num_threadsx; gpu_options_local[0].num_sequences_to = percentage; gpu_options_local[1].num_sequences_to = percentage; gpu_options_local[0].method = gpu_options->method; gpu_options_local[1].method = gpu_options->method; char* GPU_volume_name = NULL; Int4* Sequence_length_vector = NULL; //Initialize global variables if( 0 == threadId ) { h_Hits = NULL; h_GPUBlastInitHitList = NULL; sufficient_memory[0] = FALSE; sufficient_memory[1] = FALSE; } Int4 volume = 0; unsigned long h_GPU_BLASTP_database_bytes[2]; Int4 gpu_limit[2]= {0,0}, gpu_limit_temp; Int4 num_sequences_to[2]= {0,0}; Int4 Group_number[2]= {0,0}; Int4 gpu_NextChunkOID[2]= {0,0}; Int4 volume_length[2]= {0,0}; Int4 break_limit[2]= {0,0}; Int4 first_oid[4] = {0,0,0,0}; int SubjectIsTranslated_flag = Blast_SubjectIsTranslated(program_number); /// Set MmapMemory if( (0 == threadId) && (gpu_options->cpu_threads > 1) ) { BlastSeqSrcSetMmapMemory(seq_src, FALSE); } else if ( (0 == threadId) ) { BlastSeqSrcSetMmapMemory(seq_src, TRUE); } //wait until GPU_BLASTP_check_memory() is finished in order to have global variable //"sufficient_memory[CURRENT(volume)]" updated for all threads. And, until MmapMemory is set pthread_barrier_wait(&barr); for(volume = -1; volume < num_volumes; ++volume) { Int4 h_Hits_bytes; Int4 h_GPUBlastInitHitList_bytes; Int4 break_limit_temp = 0; double GPU_BLASTP_get_data_elapsed, freeing_memory, waiting_time1; clock_gettime(CLOCK_MONOTONIC, &Total_start); /// If @volume is greater than -1, and the last volume DB used GPU, /// then get the result of last volume first and free the gpu memory. if(volume >-1 && sufficient_memory[CURRENT(volume)] ) { clock_gettime(CLOCK_MONOTONIC, &CPU_start); //wait for both threads before global memory free since one thread might using @h_Hits and @h_GPUBlastInitHitList while the //other one might free them. pthread_barrier_wait(&barr); if ( (volume>0) && (0==threadId ) ) { int q=0; double max_cpu_wall_time_in_previous_round = 0; for(q=0; qcpu_threads; q++) { if(current_cpu_walltime[q]>max_cpu_wall_time_in_previous_round) max_cpu_wall_time_in_previous_round = current_cpu_walltime[q]; } max_cpu_walltime[(volume-1)%3] = max_cpu_wall_time_in_previous_round; } clock_gettime(CLOCK_MONOTONIC, &CPU_end ); waiting_time1 = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; if( 0 == threadId ) { pthread_mutex_lock(&thread_counter_mutex); get_GPU_result( &h_Hits, h_Hits_bytes, &h_GPUBlastInitHitList, h_GPUBlastInitHitList_bytes, num_sequences_to[CURRENT(volume)], &GPU_BLASTP_get_data_elapsed); clock_gettime(CLOCK_MONOTONIC, &CPU_start); GPU_BLASTP_free_memory( ); clock_gettime(CLOCK_MONOTONIC, &CPU_end ); freeing_memory = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; pthread_mutex_unlock(&thread_counter_mutex); } } /// for new ratio caculation pthread_barrier_wait(&barr); if ( (volume>0) && (flag_fixed_gpu_db_used_ratio!=1) ) { local_gpu_db_used_ratio=get_new_gpudb_ratio(volume-1, local_gpu_db_used_ratio, gpu_options->cpu_threads, get_num_of_gpu_cards_used()); } /// If @volume is less than @num_volumes-1, /// send GPU command. int gpu_db_group_size = gpu_options_local[0].num_blocksx * gpu_options_local[0].num_threadsx; if(volume<(num_volumes-1)) { h_GPU_BLASTP_database_bytes[NEXT(volume)] = 0; num_sequences_to[NEXT(volume)] = 0; gpu_limit[NEXT(volume)] = 0, gpu_limit_temp = 0; Group_number[NEXT(volume)] = 0; gpu_NextChunkOID[NEXT(volume)] = gpu_NextChunkOID[CURRENT(volume)] + volume_length[CURRENT(volume)]; /// Read the next volume DB info Read_GPU_information_file(GPU_information_file, &GPU_volume_name, &(h_GPU_BLASTP_database_bytes[NEXT(volume)]), &(volume_length[NEXT(volume)]), &(num_sequences_to[NEXT(volume)]), &gpu_limit_temp, &break_limit_temp, &(Group_number[NEXT(volume)]), &Sequence_length_vector, gpu_options->cpu_threads, gpu_options_local[0].num_threadsx, gpu_db_group_size, &local_gpu_db_used_ratio); if( (0 == threadId) && (volume>0) ) printf("vol = %d, mnew ratio = %lg\n", volume, local_gpu_db_used_ratio); gpu_options_local[NEXT(volume)].num_sequences_to = num_sequences_to[NEXT(volume)]; gpu_limit[NEXT(volume)] = break_limit[CURRENT(volume)] + num_sequences_to[NEXT(volume)]; break_limit[NEXT(volume)] = break_limit_temp; if(volume<(num_volumes-2)) first_oid[(volume+2)&0x3] = break_limit[NEXT(volume)]; /*num_sequences_to[CURRENT(volume)] is multiplied by H_HITS_SIZE_BYTE because for each sequence we store hits, successful_extensions, hits_extended */ h_Hits_bytes = num_sequences_to[NEXT(volume)] * H_HITS_SIZE_BYTE * sizeof(Int4); h_GPUBlastInitHitList_bytes = num_sequences_to[NEXT(volume)] * get_MAX_SUCCESSFUL_HITS_PER_SEQUENCE() * sizeof(GPUBlastInitHitList); if ( get_num_of_gpu_cards_used() > 1 ) h_GPUBlastInitHitList_bytes *= 1.5; //The GPU arrays are declared here because we want to be able to deallocate them in this function. If we deallocated them in //GPU_BLASTP() then that would act as an thread synchronizer, and wouldn't allow asynchronous execution sufficient_memory[NEXT(volume)] = GPU_BLASTP_check_memory(lookup_wrap, aux_struct->ewp, &(gpu_options_local[NEXT(volume)]), h_GPU_BLASTP_database_bytes[NEXT(volume)], h_Hits_bytes, h_GPUBlastInitHitList_bytes, Group_number[NEXT(volume)], query_info->num_queries, query->length); if( (0 == threadId) && !sufficient_memory[NEXT(volume)] ) { fprintf(stderr,"WARNING: Not enough GPU global memory to process volume No. %02d of the database. Continuing without the CPU...\n",volume); fprintf(stderr," Consider splitting the input database in volumes with smaller size by using the option \"-max_file_size \" (e.g. -max_file_sz 500MB).\n"); fprintf(stderr," Consider using fewer GPU blocks and then fewer GPU thread when formating the database with (e.g. \"-gpu_blocks 256\" and/or \"-gpu_threads 32\") to reduce the GPU global memory requiremenets.\n"); } if( sufficient_memory[NEXT(volume)] && (0 == threadId) ) { if(BRIEF_INFO) printf("Checking %d volume gpuDB\n", volume+1); GPU_BLASTP_Execute(seq_src, lookup_wrap, aux_struct, query, query_info, word_params, &(gpu_options_local[NEXT(volume)]), h_Hits_bytes, h_GPUBlastInitHitList_bytes, GPU_volume_name, h_GPU_BLASTP_database_bytes[NEXT(volume)], Sequence_length_vector, Group_number[NEXT(volume)], &GPU_elapsed, &FillDatabase_elapsed); if(BRIEF_INFO) { printf("launch gpu kernel is %lg sec\n", GPU_elapsed); printf("copy data is %lg sec\n", FillDatabase_elapsed); } } } /// If @volume is greater than -1, /// process the GPU result and other unprocessed /// DB. if(volume>-1) { pthread_barrier_wait(&barr); /// RPS processing /* remember the current search state */ if (progress_info) progress_info->stage = ePrelimSearch; /* For RPS BLAST, there is no loop over subject sequences, so the preliminary search engine is done in a separate function. */ if (Blast_ProgramIsRpsBlast(program_number)) { status = s_RPSPreliminarySearchEngine(program_number, query, query_info, seq_src, score_params, lookup_wrap, aux_struct, word_params, ext_params, gap_align, hit_params, hsp_stream, diagnostics, interrupt_search, progress_info, &(gpu_options_local[CURRENT(volume)]), h_Hits, h_GPUBlastInitHitList ); word_params = BlastInitialWordParametersFree(word_params); s_BlastCoreAuxStructFree(aux_struct); return status; } /// CPU post-processing preperation /* Update the parameters for linking HSPs, if necessary. */ BlastLinkHSPParametersUpdate(word_params, hit_params, gapped_calculation); /* Encoding is set so there are no sentinel bytes, and protein/nucleotide sequences are retieved in ncbistdaa/ncbi2na encodings respectively. */ seq_arg.encoding = eBlastEncodingProtein; db_length = BlastSeqSrcGetTotLen(seq_src); //if there is not enough GPU memory use only the CPU and start alignment from the first database sequence num_sequences_to[CURRENT(volume)] = sufficient_memory[CURRENT(volume)] ? num_sequences_to[CURRENT(volume)] : 0; gpu_limit[CURRENT(volume)] = sufficient_memory[CURRENT(volume)] ? gpu_limit[CURRENT(volume)] : (break_limit[CURRENT(volume)] - volume_length[CURRENT(volume)]); Int4 print_point = 0; if(GPU_VERBOSE) { fprintf(stderr,"threadID = %d: CPU execution...\n", threadId); print_point = BlastSeqSrcGetNumSeqs(seq_src) / 50 +1; } clock_gettime(CLOCK_MONOTONIC, &CPU_start); while ( (seq_arg.oid = BlastSeqSrcIteratorNext(seq_src, itr)) != BLAST_SEQSRC_EOF) { if (seq_arg.oid == BLAST_SEQSRC_ERROR) break; if( sufficient_memory[CURRENT(volume)] && ( seq_arg.oid < gpu_limit[CURRENT(volume)] ) && (h_Hits[(seq_arg.oid - first_oid[volume&0x3])*4+1] == 0) ) continue; if (BlastSeqSrcGetSequence(seq_src, &seq_arg) < 0) continue; if(GPU_VERBOSE) if( !(seq_arg.oid % print_point ) ) fprintf(stderr,"threadId = %d, seq_arg.oid = %6d, ranges:[%6d, %6d)\n", threadId, seq_arg.oid, itr->oid_range[0], itr->oid_range[1]); if (db_length == 0) { /* This is not a database search, hence need to recalculate and save the effective search spaces and length adjustments for all queries based on the length of the current single subject sequence. */ if ((status = BLAST_OneSubjectUpdateParameters(program_number, seq_arg.seq->length, score_options, query_info, sbp, hit_params, word_params, eff_len_params)) != 0) return status; } /* Calculate cutoff scores for linking HSPs. Do this only for ungapped protein searches and ungapped translated searches. */ if (hit_params->link_hsp_params && !kNucleotide && !gapped_calculation) { CalculateLinkHSPCutoffs(program_number, query_info, sbp, hit_params->link_hsp_params, word_params, db_length, seq_arg.seq->length); } /// For CPU DB processing //if (Blast_SubjectIsTranslated(program_number)) if (seq_arg.oid >= gpu_limit[CURRENT(volume)] && ( SubjectIsTranslated_flag >0 ) ) { /* Convert the subject sequence ranges to protein coordinates */ Uint4 i; for (i = 0; i < seq_arg.seq->num_seq_ranges; i++) { seq_arg.seq->seq_ranges[i].left = CONV_NUCL2PROT_COORDINATES(seq_arg.seq->seq_ranges[i].left); seq_arg.seq->seq_ranges[i].right = CONV_NUCL2PROT_COORDINATES(seq_arg.seq->seq_ranges[i].right); } /* If the subject is translated and the BlastSeqSrc implementation * doesn't provide a genetic code string, use the default genetic * code for all subjects (as in the C toolkit) */ if (seq_arg.seq->gen_code_string == NULL) { seq_arg.seq->gen_code_string = GenCodeSingletonFind(db_options->genetic_code); } ASSERT(seq_arg.seq->gen_code_string); } /// CPU post-processing //if( sufficient_memory[CURRENT(volume)] && ( seq_arg.oid < gpu_limit[CURRENT(volume)] ) && (h_Hits[(seq_arg.oid - first_oid[volume&0x3])*4+1]>0) ) if( sufficient_memory[CURRENT(volume)] && ( seq_arg.oid < gpu_limit[CURRENT(volume)] ) ) { gpu_options_local[CURRENT(volume)].use_gpu = TRUE; status = s_BlastSearchEngineCore(program_number, query, query_info, seq_arg.seq, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, db_options, diagnostics, aux_struct, &hsp_list, interrupt_search, progress_info, &(gpu_options_local[CURRENT(volume)]), h_Hits, h_GPUBlastInitHitList, gpu_NextChunkOID[CURRENT(volume)]); } /// CPU DB processing else if(seq_arg.oid >= gpu_limit[CURRENT(volume)]) { gpu_options_local[CURRENT(volume)].use_gpu = FALSE; status = s_BlastSearchEngineCore(program_number, query, query_info, seq_arg.seq, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, db_options, diagnostics, aux_struct, &hsp_list, interrupt_search, progress_info, &(gpu_options_local[CURRENT(volume)]), h_Hits, h_GPUBlastInitHitList, 0); } if (status) { break; } if (hsp_list && hsp_list->hspcnt > 0) { if (!gapped_calculation) { /* The following must be performed for any ungapped search with a nucleotide database. */ status = Blast_HSPListReevaluateUngapped( program_number, hsp_list, query, seq_arg.seq, word_params, hit_params, query_info, sbp, score_params, seq_src, seq_arg.seq->gen_code_string); if (status) { BlastSeqSrcReleaseSequence(seq_src, &seq_arg); return status; } /* Relink HSPs if sum statistics is used, because scores might * have changed after reevaluation with ambiguities, and there * will be no traceback stage where relinking is done normally. * If sum statistics are not used, just recalculate e-values. */ if (hit_params->link_hsp_params) { status = BLAST_LinkHsps(program_number, hsp_list, query_info, seq_arg.seq->length, sbp, hit_params->link_hsp_params, gapped_calculation); } else { Blast_HSPListGetEvalues(query_info, hsp_list, gapped_calculation, sbp, 0, 1.0); } status = Blast_HSPListReapByEvalue(hsp_list, hit_params->options); /* Calculate and fill the bit scores, since there will be no traceback stage where this can be done. */ Blast_HSPListGetBitScores(hsp_list, gapped_calculation, sbp); } /* Save the results. */ status = BlastHSPStreamWrite(hsp_stream, &hsp_list); if (status != 0) break; } //} //if( seq_arg.oid >= gpu_limit[CURRENT(volume)] ) BlastSeqSrcReleaseSequence(seq_src, &seq_arg); /* check for interrupt */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { status = BLASTERR_INTERRUPTED; break; } if( seq_arg.oid >= (break_limit[CURRENT(volume)]-1) ) break; } clock_gettime(CLOCK_MONOTONIC, &CPU_end); CPU_elapsed = (CPU_end.tv_sec - CPU_start.tv_sec) + (double)(CPU_end.tv_nsec - CPU_start.tv_nsec) / BILLION; if(GPU_VERBOSE) fprintf(stderr,"threadID = %d: Done with CPU processing (%.2f sec)\n", threadId, CPU_elapsed); /// Record walltime clock_gettime(CLOCK_MONOTONIC, &CPU_start); //wait until both threads are done with BLASTP_GetGPUHits() before deallocating h_Hits and h_GPUBlastInitHitList since //if one threadId=0 deallocates these arrays while other threads are still working on them a segmentation fault will occur if( sufficient_memory[CURRENT(volume)] ) pthread_barrier_wait(&barr); clock_gettime(CLOCK_MONOTONIC, &CPU_end ); double waiting_time3 = ( CPU_end.tv_sec - CPU_start.tv_sec ) + (double)( CPU_end.tv_nsec - CPU_start.tv_nsec ) / BILLION; clock_gettime(CLOCK_MONOTONIC, &Total_end); Total_elapsed = (Total_end.tv_sec - Total_start.tv_sec) + (double)(Total_end.tv_nsec - Total_start.tv_nsec)/ BILLION; current_cpu_walltime[threadId] = CPU_elapsed; if(GPU_VERBOSE) { pthread_mutex_lock(&thread_print_mutex); fprintf(stderr,"\nthreadId = %d: Fill GPU database = %.2f sec",threadId, FillDatabase_elapsed); fprintf(stderr,"\nthreadId = %d: GPU processing = %.2f sec",threadId,GPU_elapsed); fprintf(stderr,"\nthreadId = %d: CPU processing = %.2f sec",threadId,CPU_elapsed); fprintf(stderr,"\nthreadId = %d: Get GPU data = %.2f sec",threadId,GPU_BLASTP_get_data_elapsed); fprintf(stderr,"\nthreadId = %d: Waiting before iterator reset = %.2f sec",threadId,waiting_time1); fprintf(stderr,"\nthreadId = %d: Waiting after GPU output processing = %.2f sec",threadId,waiting_time3); fprintf(stderr,"\nthreadId = %d: Freeing GPU memory = %.2f sec",threadId,freeing_memory); fprintf(stderr,"\nthreadId = %d: Total = %.2f sec\n\n",threadId,Total_elapsed); pthread_mutex_unlock(&thread_print_mutex); } if(BRIEF_INFO) { printf("\nthreadId = %d: CPU processing = %lg sec\n", threadId, CPU_elapsed); if(0 == threadId) { printf("\nTotal processing = %lg sec\n", threadId, Total_elapsed); } } } } if( sufficient_memory[NEXT(volume)] && (0 == threadId) ) { free(h_Hits); free(h_GPUBlastInitHitList); } pthread_mutex_lock(&thread_counter_mutex); thread_counter--; pthread_mutex_unlock(&thread_counter_mutex); free(Sequence_length_vector); free(GPU_volume_name); free(gpu_options_local); fclose(GPU_information_file); all_gpu_quit(); hsp_list = Blast_HSPListFree(hsp_list); /* in case we were interrupted */ BlastSequenceBlkFree(seq_arg.seq); itr = BlastSeqSrcIteratorFree(itr); gpu_itr = BlastSeqSrcIteratorFree(gpu_itr); /* Fill the cutoff values in the diagnostics structure */ if (diagnostics && diagnostics->cutoffs) { s_FillReturnCutoffsInfo(diagnostics->cutoffs, score_params, word_params, ext_params, hit_params); } word_params = BlastInitialWordParametersFree(word_params); s_BlastCoreAuxStructFree(aux_struct); return status; } h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_seqsrc_impl.h0000644000175000017500000004062512001215337024446 0ustar ykeyke/* $Id: blast_seqsrc_impl.h 219801 2011-01-13 16:10:57Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file blast_seqsrc_impl.h * Definitions needed for implementing the BlastSeqSrc interface and low level * details of the implementation of the BlastSeqSrc framework */ #ifndef ALGO_BLAST_CORE__BLAST_SEQSRC_IMPL__H #define ALGO_BLAST_CORE__BLAST_SEQSRC_IMPL__H #include #include #ifdef __cplusplus extern "C" { #endif /** Function pointer typedef to create a new BlastSeqSrc structure. * BlastSeqSrcNew uses this function pointer and the ctor_argument (both * obtained from the BlastSeqSrcNewInfo structure) after allocating the * BlastSeqSrc structure. * Client implementations MUST return a non-NULL BlastSeqSrc (the one that is * actually passed in) even if initialization of the BlastSeqSrc * implementation fails, case in which only the functionality to retrieve an * initialization error message and to deallocate the BlastSeqSrc structure * must be defined (C++ implementations must NOT throw exceptions!). * If initialization of the BlastSeqSrc implementation succeeds, then this * function should initialize all the function pointers and appropriate data * fields for the BlastSeqSrc using the _BlastSeqSrcImpl_* functions * defined by the macros at the end of this file. */ typedef BlastSeqSrc* (*BlastSeqSrcConstructor) (BlastSeqSrc* seqsrc, /**< pointer to an already allocated structure to be populated with implementation's function pointers and data structures */ void* arg /**< place holder argument to pass arguments to the client-defined BlastSeqSrc implementation */ ); /** Complete type definition of the structure used to create a new * BlastSeqSrc */ struct BlastSeqSrcNewInfo { BlastSeqSrcConstructor constructor; /**< User-defined function to initialize a BlastSeqSrc structure */ void* ctor_argument; /**< Argument to the above function */ }; /** Function pointer typedef to deallocate a BlastSeqSrc structure, always * returns NULL. This function's implementation should free resources allocated * in the BlastSeqSrcConstructor, the BlastSeqSrc structure itself is free'd by * BlastSeqSrcFree */ typedef BlastSeqSrc* (*BlastSeqSrcDestructor) (BlastSeqSrc* seqrc /**< BlastSeqSrc structure to free */ ); /** Function pointer typedef to modify the contents of a BlastSeqSrc * structure, copied by BlastSeqSrcCopy, to achieve multi-thread safety. * Argument is a pointer to the BlastSeqSrc structure to be modified. * Returns the same structure, with modified contents. */ typedef BlastSeqSrc* (*BlastSeqSrcCopier) (BlastSeqSrc*); /** Function pointer typedef to set a 4-byte integer. */ typedef void (*SetInt4FnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ int arg); /** Function pointer typedef to return a 4-byte integer. */ typedef Int4 (*GetInt4FnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ void* arg /**< place holder argument to pass arguments to the client-defined BlastSeqSrc implementation */ ); /* *********** START ************* */ /** Function pointer typedef to set a Boolean. */ typedef void (*SetBoolFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ Boolean arg); /* ********** FINISH ************* */ /** Function pointer typedef to return a 8-byte integer. */ typedef Int8 (*GetInt8FnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ void* arg /**< place holder argument to pass arguments to the client-defined BlastSeqSrc implementation */ ); /** Function pointer typedef to return a null terminated string, used to return * the name of a BlastSeqSrc implementation (e.g.: BLAST database name). */ typedef const char* (*GetStrFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ void* arg /**< place holder argument to pass arguments to the client-defined BlastSeqSrc implementation */ ); /** Function pointer typedef to return a boolean value, used to return whether * a given BlastSeqSrc implementation contains protein or nucleotide sequences * (e.g.: BlastSeqSrcGetIsProt). */ typedef Boolean (*GetBoolFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ void* arg /**< place holder argument to pass arguments to the client-defined BlastSeqSrc implementation */ ); /** Function pointer typedef to set partial fetching range */ typedef void (*SetSeqRangeFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ BlastSeqSrcSetRangesArg* arg /**< arguments to set partial fetching ranges */ ); /** Function pointer typedef to retrieve sequences from data structure embedded * in the BlastSeqSrc structure. Return value is one of the BLAST_SEQSRC_* * defines @sa BlastSeqSrcGetSeqArg */ typedef Int2 (*GetSeqBlkFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ BlastSeqSrcGetSeqArg* arg /**< arguments to fetch sequence data from a client-defined BlastSeqSrc implementation */ ); /** Function pointer typedef to release sequences obtained from the data * structure embedded in the BlastSeqSrc structure. * @sa BlastSeqSrcGetSeqArg */ typedef void (*ReleaseSeqBlkFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ BlastSeqSrcGetSeqArg* arg /**< arguments to fetch sequence data from a client-defined BlastSeqSrc implementation */ ); #ifdef KAPPA_PRINT_DIAGNOSTICS /** Function pointer typedef to retrieve gis for a given ordinal id */ typedef Blast_GiList* (*GetGisFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ void* arg /**< place holder argument to pass arguments to the client-defined BlastSeqSrc implementation */ ); #endif /* KAPPA_PRINT_DIAGNOSTICS */ /******************** BlastSeqSrcIterator API *******************************/ /** Defines the type of data contained in the BlastSeqSrcIterator structure */ typedef enum BlastSeqSrcItrType { eOidList, /**< Data is a list of discontiguous ordinal ids (indices) */ eOidRange /**< Data is a range of contiguous ordinal ids (indices) */ } BlastSeqSrcItrType; /** Complete type definition of Blast Sequence Source Iterator */ struct BlastSeqSrcIterator { /** Indicates which member to access: oid_list or oid_range */ BlastSeqSrcItrType itr_type; /** Array of ordinal ids used when itr_type is eOidList */ int* oid_list; /** This is a half-closed interval [a,b) */ int oid_range[2]; /** Keep track of this iterator's current position, implementations use * UINT4_MAX to indicate this is uninitialized/invalid */ unsigned int current_pos; /** Size of the chunks to advance over the BlastSeqSrc, also size of * oid_list member, this is provided to reduce mutex contention when * implementing MT-safe iteration */ unsigned int chunk_sz; }; /** Function pointer typedef to obtain the next ordinal id to fetch from the * BlastSeqSrc structure. * Return value is the next ordinal id, or BLAST_SEQSRC_EOF if no more * sequences are available. This is to be used in the oid field of the * BlastSeqSrcGetSeqArg structure to indicate an index into the BlastSeqSrc * from which the next sequence should be retrieved using * BlastSeqSrcGetSequence */ typedef Int4 (*AdvanceIteratorFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ BlastSeqSrcIterator* itr /**< iterator which contains the state of the iteration being performed */ ); /** Function pointer typedef to obtain the next chunk of ordinal ids for the * BLAST engine to search. By calling this function with a give chunk size * (stored in the iterator structure), one reduces the number of calls which * have to be guarded by a mutex in a multi-threaded environment by examining * the BlastSeqSrc structure infrequently, i.e.: not every implementation of * the BlastSeqSrc needs to provide this if this does not help in satisfying * the MT-safe iteration requirement of the BlastSeqSrc interface. * Return value is one of the BLAST_SEQSRC_* defines */ typedef Int2 (*GetNextChunkFnPtr) (void* seqsrc_impl, /**< BlastSeqSrc implementation's data structure */ BlastSeqSrcIterator* itr /**< iterator which contains the state of the iteration being performed */ ); /** Function pointer typedef to reset the internal "bookmark" of the last chunk * provided for iteration by the data structure embedded in the BlastSeqSrc * structure. */ typedef void (*ResetChunkIteratorFnPtr) (void* seqsrc_impl); /**< BlastSeqSrc implementation's data structure */ /*****************************************************************************/ #ifndef SKIP_DOXYGEN_PROCESSING /* The following macros provide access to the BlastSeqSrc structure's data This is provided to allow some basic error checking (no NULL pointer dereferencing or assignment). These "member functions" of the BlastSeqSrc should be called by implementations of the interface to set the appropriate function pointers and data structures. */ #define DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(member_type, member) \ DECLARE_BLAST_SEQ_SRC_ACCESSOR(member_type, member); \ DECLARE_BLAST_SEQ_SRC_MUTATOR(member_type, member) #define DECLARE_BLAST_SEQ_SRC_ACCESSOR(member_type, member) \ NCBI_XBLAST_EXPORT \ member_type _BlastSeqSrcImpl_Get##member(const BlastSeqSrc* var) #define DECLARE_BLAST_SEQ_SRC_MUTATOR(member_type, member) \ NCBI_XBLAST_EXPORT \ void _BlastSeqSrcImpl_Set##member(BlastSeqSrc* var, member_type arg) \ DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(BlastSeqSrcConstructor, NewFnPtr); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(BlastSeqSrcDestructor, DeleteFnPtr); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(BlastSeqSrcCopier, CopyFnPtr); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetInt4FnPtr, SetNumberOfThreads); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetNumSeqs); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetNumSeqsStats); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetMaxSeqLen); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetAvgSeqLen); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt8FnPtr, GetTotLen); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt8FnPtr, GetTotLenStats); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetStrFnPtr, GetName); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetBoolFnPtr, GetIsProt); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetBoolFnPtr, GetSupportsPartialFetching); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetSeqRangeFnPtr, SetSeqRange); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetSeqBlkFnPtr, GetSequence); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetSeqLen); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(ReleaseSeqBlkFnPtr, ReleaseSequence); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(AdvanceIteratorFnPtr, IterNext); #ifdef KAPPA_PRINT_DIAGNOSTICS DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetGisFnPtr, GetGis); #endif /* KAPPA_PRINT_DIAGNOSTICS */ DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(ResetChunkIteratorFnPtr, ResetChunkIterator); /* *********** START ************* */ DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetInt4FnPtr, SetChunkIterator); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetBoolFnPtr, SetMmapMemory); /* ********** FINISH ************* */ /* Not really a member functions, but fields */ DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(void*, DataStructure); DECLARE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(char*, InitErrorStr); #endif /** * @page _impl_blast_seqsrc_howto Implementing the BlastSeqSrc interface * * Implementations of this interface should provide life-cycle functions as * well as functions which satisfy the BlastSeqSrc interface. These functions * must have C linkage, as these functions are invoked by the BlastSeqSrc * framework. * An initialization function must also be provided, this is intended to be * invoked by client code which wants to use a specific BlastSeqSrc * implementation through the BlastSeqSrc interface. * For example, MyDatabaseFormat implementation would define the following * functions: * * - Initialization function * @code * // Calls BlastSeqSrcNew in behalf of client code, client should free using * // BlastSeqSrcFree * BlastSeqSrc* MyDatabaseFormatBlastSeqSrcInit(...); * @endcode * * - Life-cycle functions * @code * extern "C" { * // required signature: BlastSeqSrcConstructor * BlastSeqSrc* MyDatabaseFormatNew(BlastSeqSrc*, void*); * // required signature: BlastSeqSrcDestructor * BlastSeqSrc* MyDatabaseFormatFree(BlastSeqSrc*); * // required signature: BlastSeqSrcCopier * BlastSeqSrc* MyDatabaseFormatCopy(BlastSeqSrc*); * } * @endcode * * - BlastSeqSrc interface * @code * extern "C" { * // required signature: SetInt4FnPtr * void MyDatabaseFormatSetNumberOfThreads(int); * // required signature: GetInt4FnPtr * Int4 MyDatabaseFormatGetNumSeqs(void*, void*); * // required signature: GetInt4FnPtr * Int4 MyDatabaseFormatGetNumSeqsStats(void*, void*); * // required signature: GetInt4FnPtr * Int4 MyDatabaseFormatGetMaxSeqLen(void*, void*); * // required signature: GetInt4FnPtr * Int4 MyDatabaseFormatGetAvgSeqLen(void*, void*); * // required signature: GetInt8FnPtr * Int8 MyDatabaseFormatGetTotLen(void*, void*); * // required signature: GetInt8FnPtr * Int8 MyDatabaseFormatGetTotLenStats(void*, void*); * // required signature: GetStrFnPtr * const char* MyDatabaseFormatGetName(void*, void*); * // required signature: GetBoolFnPtr * Boolean MyDatabaseFormatGetIsProt(void*, void*); * // required signature: GetSeqBlkFnPtr * Int2 MyDatabaseFormatGetSequence(void*, BlastSeqSrcGetSeqArg*); * // required signature: GetInt4FnPtr * Int4 MyDatabaseFormatGetSeqLen(void*, void*); * // required signature: ReleaseSeqBlkFnPtr * void MyDatabaseFormatReleaseSequence(void*, BlastSeqSrcGetSeqArg*); * // required signature: AdvanceIteratorFnPtr * Int4 MyDatabaseFormatItrNext(void*, BlastSeqSrcIterator* itr); * // required signature: ResetChunkIteratorFnPtr * Int4 MyDatabaseFormatResetChunkIterator(void*); * } * @endcode * * Since the life-cycle and BlastSeqSrc interface functions above are * called by the BlastSeqSrc framework (BlastSeqSrc* functions declared in * blast_seqsrc.h), no exceptions should be thrown in C++ implementations. * When not obvious, please see the required signature's documentation for * determining what to implement (see blast_seqsrc_impl.h). * * For ease of maintenance, please follow the following conventions: * - Client implementations' initialization function should be called * \c XBlastSeqSrcInit, where \c X is the name of the implementation * - Client implementations should reside in a file named \c seqsrc_X.[hc] or * \c seqsrc_X.[ch]pp, where \c X is the name of the implementation. */ #ifdef __cplusplus } #endif #endif /* !ALGO_BLAST_CORE__BLAST_SEQSRC__H */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_seqsrc.c0000644000175000017500000004371512001215337023423 0ustar ykeyke/* $Id: blast_seqsrc.c 219802 2011-01-13 16:11:17Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * * */ /** @file blast_seqsrc.c * Definition of ADT to retrieve sequences for the BLAST engine and * low level details of the implementation of the BlastSeqSrc framework. */ #ifndef SKIP_DOXYGEN_PROCESSING #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: blast_seqsrc.c 219802 2011-01-13 16:11:17Z rafanovi $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #endif #include #include /** Complete type definition of Blast Sequence Source ADT. * The members of this structure should only be accessed by BlastSeqSrc * implementations using the _BlastSeqSrcImpl_* functions. */ struct BlastSeqSrc { BlastSeqSrcConstructor NewFnPtr; /**< Constructor */ BlastSeqSrcDestructor DeleteFnPtr; /**< Destructor */ BlastSeqSrcCopier CopyFnPtr; /**< Copier */ /* Functions to set the number of threads in MT mode */ SetInt4FnPtr SetNumberOfThreads; /**< Set number of threads */ /* Functions to get information about database as a whole */ GetInt4FnPtr GetNumSeqs; /**< Get number of sequences in set */ GetInt4FnPtr GetNumSeqsStats; /**< Number of sequences for statistical purposes. */ GetInt4FnPtr GetMaxSeqLen; /**< Get length of longest seq in set */ GetInt4FnPtr GetAvgSeqLen; /**< Get average length of sequences in the set */ GetInt8FnPtr GetTotLen; /**< Get tot length of all seqs in set */ GetInt8FnPtr GetTotLenStats; /**< Total length of all seqs for statistical purposes. */ GetStrFnPtr GetName; /**< Get the name of the database */ GetBoolFnPtr GetIsProt; /**< Find if database is a protein or nucleotide */ /* Functions that supports partial sequence fetching */ GetBoolFnPtr GetSupportsPartialFetching; /**< Find if database supports partial fetching */ SetSeqRangeFnPtr SetSeqRange; /**< Setting ranges for partial fetching */ /* Functions that deal with individual sequences */ GetSeqBlkFnPtr GetSequence; /**< Retrieve individual sequence */ GetInt4FnPtr GetSeqLen; /**< Retrieve given sequence length */ ReleaseSeqBlkFnPtr ReleaseSequence; /**< Deallocate individual sequence (if applicable) */ /* Functions to iterate over sequences in the database */ AdvanceIteratorFnPtr IterNext; /**< Gets next oid from the iterator */ ResetChunkIteratorFnPtr ResetChunkIterator; /**< Reset the implementation's chunk "bookmark" */ /* *********** START ************* */ SetInt4FnPtr SetChunkIterator; /**< Set the implementation's chunk "bookmark" */ SetBoolFnPtr SetMmapMemory; /**< Set the implementation's chunk "bookmark" */ /* ********** FINISH ************* */ void* DataStructure; /**< ADT holding the sequence data */ char* InitErrorStr; /**< initialization error string */ #ifdef KAPPA_PRINT_DIAGNOSTICS GetGisFnPtr GetGis; /**< Retrieve a sequence's gi(s) */ #endif /* KAPPA_PRINT_DIAGNOSTICS */ }; BlastSeqSrc* BlastSeqSrcNew(const BlastSeqSrcNewInfo* bssn_info) { BlastSeqSrc* retval = NULL; if (!bssn_info) { return (BlastSeqSrc*) NULL; } if ( !(retval = (BlastSeqSrc*) calloc(1, sizeof(BlastSeqSrc)))) { return (BlastSeqSrc*) NULL; } /* Save the constructor and invoke it */ if ((retval->NewFnPtr = bssn_info->constructor)) { retval = (*retval->NewFnPtr)(retval, bssn_info->ctor_argument); } else { sfree(retval); } return retval; } BlastSeqSrc* BlastSeqSrcFree(BlastSeqSrc* seq_src) { BlastSeqSrcDestructor destructor_fnptr = NULL; BlastSeqSrc* retval; if (!seq_src) { return (BlastSeqSrc*) NULL; } if (seq_src->InitErrorStr) { sfree(seq_src->InitErrorStr); } /* This could leave a memory leak if destructor function pointer is not * initialized! It is the implementation's resposibility to provide this */ if ( !(destructor_fnptr = (*seq_src->DeleteFnPtr))) { sfree(seq_src); return (BlastSeqSrc*) NULL; } retval = (BlastSeqSrc*) (*destructor_fnptr)(seq_src); ASSERT(retval == NULL); sfree(seq_src); return retval; } BlastSeqSrc* BlastSeqSrcCopy(const BlastSeqSrc* seq_src) { BlastSeqSrcCopier copy_fnptr = NULL; BlastSeqSrc* retval = NULL; if (!seq_src) { return (BlastSeqSrc*) NULL; } if ( !(retval = (BlastSeqSrc*) BlastMemDup(seq_src, sizeof(BlastSeqSrc)))) { return (BlastSeqSrc*) NULL; } /* If copy function is not provided, just return a copy of the structure */ if ( !(copy_fnptr = (*seq_src->CopyFnPtr))) { return retval; } return (BlastSeqSrc*) (*copy_fnptr)(retval); } char* BlastSeqSrcGetInitError(const BlastSeqSrc* seq_src) { if ( !seq_src || !seq_src->InitErrorStr ) { return NULL; } return strdup(seq_src->InitErrorStr); } void BlastSeqSrcSetNumberOfThreads(BlastSeqSrc* seq_src, int n_threads) { if (!seq_src || !seq_src->SetNumberOfThreads) { return; } (*seq_src->SetNumberOfThreads)(seq_src->DataStructure, n_threads); } Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetNumSeqs); return (*seq_src->GetNumSeqs)(seq_src->DataStructure, NULL); } Int4 BlastSeqSrcGetNumSeqsStats(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetNumSeqsStats); return (*seq_src->GetNumSeqsStats)(seq_src->DataStructure, NULL); } Int4 BlastSeqSrcGetMaxSeqLen(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetMaxSeqLen); return (*seq_src->GetMaxSeqLen)(seq_src->DataStructure, NULL); } Int4 BlastSeqSrcGetAvgSeqLen(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetAvgSeqLen); return (*seq_src->GetAvgSeqLen)(seq_src->DataStructure, NULL); } Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetTotLen); return (*seq_src->GetTotLen)(seq_src->DataStructure, NULL); } Int8 BlastSeqSrcGetTotLenStats(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetTotLenStats); return (*seq_src->GetTotLenStats)(seq_src->DataStructure, NULL); } const char* BlastSeqSrcGetName(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetName); return (*seq_src->GetName)(seq_src->DataStructure, NULL); } Boolean BlastSeqSrcGetIsProt(const BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->GetIsProt); return (*seq_src->GetIsProt)(seq_src->DataStructure, NULL); } Boolean BlastSeqSrcGetSupportsPartialFetching(const BlastSeqSrc* seq_src) { ASSERT(seq_src); if (seq_src->GetSupportsPartialFetching) { return (*seq_src->GetSupportsPartialFetching)(seq_src->DataStructure, NULL); } return FALSE; } void BlastSeqSrcSetSeqRanges(const BlastSeqSrc* seq_src, BlastSeqSrcSetRangesArg* arg) { ASSERT(seq_src); if (seq_src->SetSeqRange) { (*seq_src->SetSeqRange)(seq_src->DataStructure, arg); } } Int2 BlastSeqSrcGetSequence(const BlastSeqSrc* seq_src, BlastSeqSrcGetSeqArg* getseq_arg) { ASSERT(seq_src); ASSERT(seq_src->GetSequence); ASSERT(getseq_arg); return (*seq_src->GetSequence)(seq_src->DataStructure, getseq_arg); } Int4 BlastSeqSrcGetSeqLen(const BlastSeqSrc* seq_src, void* oid) { ASSERT(seq_src); ASSERT(seq_src->GetSeqLen); return (*seq_src->GetSeqLen)(seq_src->DataStructure, oid); } void BlastSeqSrcReleaseSequence(const BlastSeqSrc* seq_src, BlastSeqSrcGetSeqArg* getseq_arg) { ASSERT(seq_src); ASSERT(seq_src->ReleaseSequence); ASSERT(getseq_arg); (*seq_src->ReleaseSequence)(seq_src->DataStructure, getseq_arg); } #ifdef KAPPA_PRINT_DIAGNOSTICS static const size_t kInitialGiListSize = 10; Blast_GiList* Blast_GiListNew(void) { return Blast_GiListNewEx(kInitialGiListSize); } Blast_GiList* Blast_GiListNewEx(size_t list_size) { Blast_GiList* retval = (Blast_GiList*) calloc(1, sizeof(Blast_GiList)); if ( !retval ) { return NULL; } retval->data = (Int4*) calloc(list_size, sizeof(Int4)); if ( !retval->data ) { return Blast_GiListFree(retval); } retval->num_allocated = list_size; return retval; } Blast_GiList* Blast_GiListFree(Blast_GiList* gilist) { if ( !gilist ) { return NULL; } if (gilist->data) { sfree(gilist->data); } sfree(gilist); return NULL; } Int2 Blast_GiList_ReallocIfNecessary(Blast_GiList* gilist) { ASSERT(gilist); if (gilist->num_used+1 > gilist->num_allocated) { /* we need more room for elements */ gilist->num_allocated *= 2; gilist->data = (Int4*) realloc(gilist->data, gilist->num_allocated * sizeof(Int4)); if ( !gilist->data ) { return kOutOfMemory; } } return 0; } Int2 Blast_GiList_Append(Blast_GiList* gilist, Int4 gi) { Int2 retval = 0; ASSERT(gilist); if ( (retval = Blast_GiList_ReallocIfNecessary(gilist)) != 0) { return retval; } gilist->data[gilist->num_used++] = gi; return retval; } Blast_GiList* BlastSeqSrcGetGis(const BlastSeqSrc* seq_src, void* oid) { ASSERT(seq_src); ASSERT(seq_src->GetSeqLen); return (*seq_src->GetGis)(seq_src->DataStructure, oid); } #endif /* KAPPA_PRINT_DIAGNOSTICS */ /******************** BlastSeqSrcIterator API *******************************/ BlastSeqSrcIterator* BlastSeqSrcIteratorNew() { return BlastSeqSrcIteratorNewEx(0); } const unsigned int kBlastSeqSrcDefaultChunkSize = 1024; BlastSeqSrcIterator* BlastSeqSrcIteratorNewEx(unsigned int chunk_sz) { BlastSeqSrcIterator* itr = NULL; if (chunk_sz == 0) chunk_sz = kBlastSeqSrcDefaultChunkSize; itr = (BlastSeqSrcIterator*) calloc(1, sizeof(BlastSeqSrcIterator)); if (!itr) { return NULL; } /* Should employ lazy initialization? */ itr->oid_list = (int*)malloc(chunk_sz * sizeof(unsigned int)); if (!itr->oid_list) { sfree(itr); return NULL; } itr->chunk_sz = chunk_sz; itr->current_pos = UINT4_MAX; /* mark iterator as uninitialized */ return itr; } BlastSeqSrcIterator* BlastSeqSrcIteratorFree(BlastSeqSrcIterator* itr) { if (!itr) { return NULL; } if (itr->oid_list) { sfree(itr->oid_list); } sfree(itr); return NULL; } Int4 BlastSeqSrcIteratorNext(const BlastSeqSrc* seq_src, BlastSeqSrcIterator* itr) { ASSERT(seq_src); ASSERT(itr); ASSERT(seq_src->IterNext); return (*seq_src->IterNext)(seq_src->DataStructure, itr); } void BlastSeqSrcResetChunkIterator(BlastSeqSrc* seq_src) { ASSERT(seq_src); ASSERT(seq_src->ResetChunkIterator); (*seq_src->ResetChunkIterator)(seq_src->DataStructure); } BlastSeqSrcSetRangesArg * BlastSeqSrcSetRangesArgNew(Int4 num_ranges) { BlastSeqSrcSetRangesArg * retv = (BlastSeqSrcSetRangesArg *) malloc(sizeof(BlastSeqSrcSetRangesArg)); retv->num_ranges = num_ranges; retv->ranges = (Int4 *) malloc(2*num_ranges*sizeof(Int4)); return retv; } void BlastSeqSrcSetRangesArgFree(BlastSeqSrcSetRangesArg *arg) { sfree(arg->ranges); sfree(arg); } BlastHSPRangeList * BlastHSPRangeListNew(Int4 begin, Int4 end, BlastHSPRangeList *next) { BlastHSPRangeList *retv = (BlastHSPRangeList *) malloc(sizeof(BlastHSPRangeList)); retv->begin = begin; retv->end = end; retv->next = next; return retv; } BlastHSPRangeList * BlastHSPRangeListAddRange(BlastHSPRangeList *list, Int4 begin, Int4 end) { BlastHSPRangeList *q, *p; begin = MAX(0, begin - BLAST_SEQSRC_OVERHANG); end += BLAST_SEQSRC_OVERHANG; /* special case: an empty list, or insert from front */ if (!list || begin <= list->begin) { return BlastHSPRangeListNew(begin, end, list); } p = list; q = p; /* sorting in begin order */ while (p && begin > p->begin) { q = p; p = p->next; } q->next = BlastHSPRangeListNew(begin, end, p); return list; } void BlastHSPRangeBuildSetRangesArg(BlastHSPRangeList *list, BlastSeqSrcSetRangesArg *arg) { BlastHSPRangeList *p = list->next; Int4 i=0; ASSERT(arg); arg->ranges[0] = list->begin; arg->ranges[1] = list->end; while (p) { ASSERT(p->begin >= arg->ranges[2*i]); if (p->begin > arg->ranges[2*i+1] + BLAST_SEQSRC_MINGAP) { /* insert as a new range */ ++i; arg->ranges[i*2] = p->begin; arg->ranges[i*2+1] = p->end; } else if (p->end > arg->ranges[2*i+1]) { /* merge into the previous range */ arg->ranges[i*2+1] = p->end; } p = p->next; } arg->num_ranges = i+1; } void BlastHSPRangeListFree(BlastHSPRangeList *list) { BlastHSPRangeList *p = list; while(p) { list = p->next; sfree(p); p = list; } } /* *********** START ************* */ void BlastSeqSrcSetChunkIterator(BlastSeqSrc* seq_src, int ChunkIterator) { ASSERT(seq_src); ASSERT(seq_src->SetChunkIterator); (*seq_src->SetChunkIterator)(seq_src->DataStructure, ChunkIterator); } void BlastSeqSrcSetMmapMemory(BlastSeqSrc* seq_src, Boolean MmapMemory) { ASSERT(seq_src); ASSERT(seq_src->SetMmapMemory); (*seq_src->SetMmapMemory)(seq_src->DataStructure, MmapMemory); } /* ********** FINISH ************* */ /*****************************************************************************/ /* The following macros implement the "member functions" of the BlastSeqSrc * structure so that its various fields can be accessed by the implementors of * the BlastSeqSrc interface */ #ifndef SKIP_DOXYGEN_PROCESSING #define DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(member_type, member) \ DEFINE_BLAST_SEQ_SRC_ACCESSOR(member_type, member) \ DEFINE_BLAST_SEQ_SRC_MUTATOR(member_type, member) #define DEFINE_BLAST_SEQ_SRC_ACCESSOR(member_type, member) \ member_type \ _BlastSeqSrcImpl_Get##member(const BlastSeqSrc* var) \ { \ if (var) \ return var->member; \ else \ return (member_type) NULL; \ } #define DEFINE_BLAST_SEQ_SRC_MUTATOR(member_type, member) \ void \ _BlastSeqSrcImpl_Set##member(BlastSeqSrc* var, member_type arg) \ { if (var) var->member = arg; } #endif /* Note there's no ; after these macros! */ DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(BlastSeqSrcConstructor, NewFnPtr) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(BlastSeqSrcDestructor, DeleteFnPtr) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(BlastSeqSrcCopier, CopyFnPtr) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(void*, DataStructure) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(char*, InitErrorStr) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetInt4FnPtr, SetNumberOfThreads) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetNumSeqs) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetNumSeqsStats) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetMaxSeqLen) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetAvgSeqLen) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt8FnPtr, GetTotLen) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt8FnPtr, GetTotLenStats) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetStrFnPtr, GetName) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetBoolFnPtr, GetIsProt) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetBoolFnPtr, GetSupportsPartialFetching) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetSeqRangeFnPtr, SetSeqRange) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetSeqBlkFnPtr, GetSequence) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetInt4FnPtr, GetSeqLen) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(ReleaseSeqBlkFnPtr, ReleaseSequence) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(AdvanceIteratorFnPtr, IterNext) #ifdef KAPPA_PRINT_DIAGNOSTICS DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(GetGisFnPtr, GetGis) #endif /* KAPPA_PRINT_DIAGNOSTICS */ DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(ResetChunkIteratorFnPtr, ResetChunkIterator) /* *********** START ************* */ DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetInt4FnPtr, SetChunkIterator) DEFINE_BLAST_SEQ_SRC_MEMBER_FUNCTIONS(SetBoolFnPtr, SetMmapMemory) /* ********** FINISH ************* */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_options_local_priv.hpp0000644000175000017500000011737412001215337026400 0ustar ykeyke/* $Id: blast_options_local_priv.hpp 168287 2009-08-13 19:08:07Z maning $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file blast_options_local_priv.hpp * Private header for local representation of BLAST options. */ #ifndef ALGO_BLAST_API___BLAST_OPTIONS_LOCAL_PRIV__HPP #define ALGO_BLAST_API___BLAST_OPTIONS_LOCAL_PRIV__HPP #include #include #include #include #include /** @addtogroup AlgoBlast * * @{ */ BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) #ifndef SKIP_DOXYGEN_PROCESSING static const int kInvalidFilterValue = -1; // Forward declarations class CBlastOptionsMemento; /// Encapsulates all blast input parameters class NCBI_XBLAST_EXPORT CBlastOptionsLocal : public CObject { public: CBlastOptionsLocal(); ~CBlastOptionsLocal(); /// Copy constructor CBlastOptionsLocal(const CBlastOptionsLocal& optsLocal); /// Assignment operator CBlastOptionsLocal& operator=(const CBlastOptionsLocal& optsLocal); /// Validate the options bool Validate() const; /// Accessors/Mutators for individual options EProgram GetProgram() const; EBlastProgramType GetProgramType() const; void SetProgram(EProgram p); /******************* Lookup table options ***********************/ double GetWordThreshold() const; void SetWordThreshold(double w); ELookupTableType GetLookupTableType() const; void SetLookupTableType(ELookupTableType type); int GetWordSize() const; void SetWordSize(int ws); /// Megablast only lookup table options unsigned char GetMBTemplateLength() const; void SetMBTemplateLength(unsigned char len); unsigned char GetMBTemplateType() const; void SetMBTemplateType(unsigned char type); /******************* Query setup options ************************/ char* GetFilterString() const; void SetFilterString(const char* f); bool GetMaskAtHash() const; void SetMaskAtHash(bool val = true); bool GetDustFiltering() const; void SetDustFiltering(bool val = true); int GetDustFilteringLevel() const; void SetDustFilteringLevel(int m); int GetDustFilteringWindow() const; void SetDustFilteringWindow(int m); int GetDustFilteringLinker() const; void SetDustFilteringLinker(int m); bool GetSegFiltering() const; void SetSegFiltering(bool val = true); int GetSegFilteringWindow() const; void SetSegFilteringWindow(int m); double GetSegFilteringLocut() const; void SetSegFilteringLocut(double m); double GetSegFilteringHicut() const; void SetSegFilteringHicut(double m); bool GetRepeatFiltering() const; void SetRepeatFiltering(bool val = true); const char* GetRepeatFilteringDB() const; void SetRepeatFilteringDB(const char* db); int GetWindowMaskerTaxId() const; void SetWindowMaskerTaxId(int taxid); const char* GetWindowMaskerDatabase() const; void SetWindowMaskerDatabase(const char* db); objects::ENa_strand GetStrandOption() const; void SetStrandOption(objects::ENa_strand s); int GetQueryGeneticCode() const; void SetQueryGeneticCode(int gc); /******************* Initial word options ***********************/ int GetWindowSize() const; void SetWindowSize(int w); int GetOffDiagonalRange() const; void SetOffDiagonalRange(int r); double GetXDropoff() const; void SetXDropoff(double x); /******************* Gapped extension options *******************/ double GetGapXDropoff() const; void SetGapXDropoff(double x); double GetGapXDropoffFinal() const; void SetGapXDropoffFinal(double x); EBlastPrelimGapExt GetGapExtnAlgorithm() const; void SetGapExtnAlgorithm(EBlastPrelimGapExt a); EBlastTbackExt GetGapTracebackAlgorithm() const; void SetGapTracebackAlgorithm(EBlastTbackExt a); ECompoAdjustModes GetCompositionBasedStats() const; void SetCompositionBasedStats(ECompoAdjustModes mode); bool GetSmithWatermanMode() const; void SetSmithWatermanMode(bool m = true); int GetUnifiedP() const; void SetUnifiedP(int u = 0); /******************* Hit saving options *************************/ int GetHitlistSize() const; void SetHitlistSize(int s); int GetMaxNumHspPerSequence() const; void SetMaxNumHspPerSequence(int m); int GetCullingLimit() const; void SetCullingLimit(int s); double GetBestHitOverhang() const; void SetBestHitOverhang(double s); void SetBestHitScoreEdge(double score_edge); double GetBestHitScoreEdge() const; // Expect value cut-off threshold for an HSP, or a combined hit if sum // statistics is used double GetEvalueThreshold() const; void SetEvalueThreshold(double eval); // Raw score cutoff threshold int GetCutoffScore() const; void SetCutoffScore(int s); double GetPercentIdentity() const; void SetPercentIdentity(double p); int GetMinDiagSeparation() const; void SetMinDiagSeparation(int d); /// Sum statistics options bool GetSumStatisticsMode() const; void SetSumStatisticsMode(bool m = true); int GetLongestIntronLength() const; // for linking HSPs with uneven gaps void SetLongestIntronLength(int l); // for linking HSPs with uneven gaps /// Returns true if gapped BLAST is set, false otherwise bool GetGappedMode() const; void SetGappedMode(bool m = true); double GetGapTrigger() const; void SetGapTrigger(double g); /************************ Scoring options ************************/ const char* GetMatrixName() const; void SetMatrixName(const char* matrix); int GetMatchReward() const; void SetMatchReward(int r); // r should be a positive integer int GetMismatchPenalty() const; void SetMismatchPenalty(int p); // p should be a negative integer int GetGapOpeningCost() const; void SetGapOpeningCost(int g); // g should be a positive integer int GetGapExtensionCost() const; void SetGapExtensionCost(int e); // e should be a positive integer int GetFrameShiftPenalty() const; void SetFrameShiftPenalty(int p); bool GetOutOfFrameMode() const; void SetOutOfFrameMode(bool m = true); /******************** Effective Length options *******************/ Int8 GetDbLength() const; void SetDbLength(Int8 l); unsigned int GetDbSeqNum() const; void SetDbSeqNum(unsigned int n); Int8 GetEffectiveSearchSpace() const; void SetEffectiveSearchSpace(Int8 eff); void SetEffectiveSearchSpace(const vector& eff); int GetDbGeneticCode() const; // Set genetic code id void SetDbGeneticCode(int gc); /// @todo PSI-Blast options could go on their own subclass? const char* GetPHIPattern() const; void SetPHIPattern(const char* pattern, bool is_dna); /// Allows to dump a snapshot of the object void DebugDump(CDebugDumpContext ddc, unsigned int depth) const; /******************** PSIBlast options *******************/ double GetInclusionThreshold() const; void SetInclusionThreshold(double incthr); int GetPseudoCount() const; void SetPseudoCount(int ps); /******************** Megablast Database Index *******************/ bool GetUseIndex() const; bool GetForceIndex() const; const string GetIndexName() const; void SetUseIndex( bool use_index = true, const string & index_name = "", bool force_index = false ); bool GetMBIndexLoaded() const; void SetMBIndexLoaded( bool index_loaded = true ); bool operator==(const CBlastOptionsLocal& rhs) const; bool operator!=(const CBlastOptionsLocal& rhs) const; /* *********** START ************* */ /******************** GPU options *******************/ bool GetUseGpu() const; int GetNumGpuThreads() const; int GetNumGpuBlocks() const; int GetNumGpuSequences() const; int GetGpuMethod() const; int GetNumCpuThreads() const; void SetUseGpu( bool use_gpu ); void SetNumGpuThreads( int gpu_threads); void SetNumGpuBlocks( int gpu_blocks ); void SetNumGpuSequences( int gpu_num_sequences ); void SetGpuMethod( int gpu_method ); void SetNumCpuThreads( int cpu_threads ); /* ********** FINISH ************* */ private: /// Query sequence settings CQuerySetUpOptions m_QueryOpts; /// Lookup table settings CLookupTableOptions m_LutOpts; /// Word settings CBlastInitialWordOptions m_InitWordOpts; /// Hit extension settings CBlastExtensionOptions m_ExtnOpts; /// Hit saving settings CBlastHitSavingOptions m_HitSaveOpts; /// PSI-Blast settings CPSIBlastOptions m_PSIBlastOpts; /// Blast database settings CBlastDatabaseOptions m_DbOpts; /// Scoring options CBlastScoringOptions m_ScoringOpts; /// Effective lengths options CBlastEffectiveLengthsOptions m_EffLenOpts; /// Blast program EProgram m_Program; /// Use megablast database index. bool m_UseMBIndex; bool m_ForceMBIndex; /// Database index has been loaded. bool m_MBIndexLoaded; /// Megablast database index name. string m_MBIndexName; /* *********** START ************* */ /// GPU options bool m_UseGpu; int m_NumGpuThreads; int m_NumGpuBlocks; int m_NumGpuSequences; int m_GpuMethod; int m_NumCpuThreads; /* ********** FINISH ************* */ friend class CBlastOptions; /// Friend class which allows extraction of this class' data members for /// internal use in the C++ API APIs friend class CBlastOptionsMemento; friend class CEffectiveSearchSpacesMemento; /// @internal QuerySetUpOptions * GetQueryOpts() const { return m_QueryOpts; } /// @internal LookupTableOptions * GetLutOpts() const { return m_LutOpts; } /// @internal BlastInitialWordOptions * GetInitWordOpts() const { return m_InitWordOpts; } /// @internal BlastExtensionOptions * GetExtnOpts() const { return m_ExtnOpts; } /// @internal BlastHitSavingOptions * GetHitSaveOpts() const { return m_HitSaveOpts; } /// @internal PSIBlastOptions * GetPSIBlastOpts() const { return m_PSIBlastOpts; } /// @internal BlastDatabaseOptions * GetDbOpts() const { return m_DbOpts; } /// @internal BlastScoringOptions * GetScoringOpts() const { return m_ScoringOpts; } /// @internal BlastEffectiveLengthsOptions * GetEffLenOpts() const { return m_EffLenOpts; } /// Perform a "deep copy" of local Blast options /// @param optsLocal local Blast options object to copy from. void x_DoDeepCopy(const CBlastOptionsLocal& optsLocal); /// Get a copy of CQuerySetUpOptions /// @param queryOptsDst options structure to copy to. /// @param queryOptsSrc options structure to copy from. static void x_Copy_CQuerySetUpOptions( CQuerySetUpOptions& queryOptsDst, const CQuerySetUpOptions& queryOptsSrc); /// Get a copy of CLookupTableOptions /// @param lutOptsDst options structure to copy to. /// @param lutOptsSrc options structure to copy from. static void x_Copy_CLookupTableOptions( CLookupTableOptions& lutOptsDst, const CLookupTableOptions& lutOptsSrc); /// Get a copy of CBlastInitialWordOptions /// @param initWordOptsDst options structure to copy to. /// @param initWordOptsSrc options structure to copy from. static void x_Copy_CBlastInitialWordOptions( CBlastInitialWordOptions& initWordOptsDst, const CBlastInitialWordOptions& initWordOptsSrc); /// Get a copy of CBlastExtensionOptions /// @param extnOptsDst options structure to copy to. /// @param extnOptsSrc options structure to copy from. static void x_Copy_CBlastExtensionOptions( CBlastExtensionOptions& extnOptsDst, const CBlastExtensionOptions& extnOptsSrc); /// Get a copy of CBlastHitSavingOptions /// @param hitSaveOptsDst options structure to copy to. /// @param hitSaveOptsSrc options structure to copy from. static void x_Copy_CBlastHitSavingOptions( CBlastHitSavingOptions& hitSaveOptsDst, const CBlastHitSavingOptions& hitSaveOptsSrc); /// Get a copy of CPSIBlastOptions /// @param psiBlastOptsDst options structure to copy to. /// @param psiBlastOptsSrc options structure to copy from. static void x_Copy_CPSIBlastOptions( CPSIBlastOptions& psiBlastOptsDst, const CPSIBlastOptions& psiBlastOptsSrc); /// Get a copy of CBlastDatabaseOptions /// @param dbOptsDst options structure to copy to. /// @param dbOptsSrc options structure to copy from. static void x_Copy_CBlastDatabaseOptions( CBlastDatabaseOptions& dbOptsDst, const CBlastDatabaseOptions& dbOptsSrc); /// Get a copy of CBlastScoringOptions /// @param scoringOptsDst options structure to copy to. /// @param scoringOptsSrc options structure to copy from. static void x_Copy_CBlastScoringOptions( CBlastScoringOptions& scoringOptsDst, const CBlastScoringOptions& scoringOptsSrc); /// Get a copy of CBlastEffectiveLengthsOptions /// @param effLenOptsDst options structure to copy to. /// @param effLenOptsSrc options structure to copy from. static void x_Copy_CBlastEffectiveLengthsOptions( CBlastEffectiveLengthsOptions& effLenOptsDst, const CBlastEffectiveLengthsOptions& effLenOptsSrc); }; inline EProgram CBlastOptionsLocal::GetProgram() const { return m_Program; } inline void CBlastOptionsLocal::SetProgram(EProgram p) { _ASSERT(p >= eBlastn && p < eBlastProgramMax); m_Program = p; const EBlastProgramType prog_type = EProgramToEBlastProgramType(p); if (prog_type == eBlastTypeUndefined) { return; } GetScoringOpts()->program_number = prog_type; GetLutOpts()->program_number = prog_type; GetInitWordOpts()->program_number = prog_type; GetExtnOpts()->program_number = prog_type; GetHitSaveOpts()->program_number = prog_type; if ( !Blast_SubjectIsTranslated(prog_type) ) { // not needed for non-translated databases/subjects GetDbOpts()->genetic_code = 0; } } inline const char* CBlastOptionsLocal::GetMatrixName() const { return m_ScoringOpts->matrix; } inline void CBlastOptionsLocal::SetMatrixName(const char* matrix) { if (!matrix) return; sfree(m_ScoringOpts->matrix); m_ScoringOpts->matrix = strdup(matrix); } inline double CBlastOptionsLocal::GetWordThreshold() const { return m_LutOpts->threshold; } inline void CBlastOptionsLocal::SetWordThreshold(double w) { m_LutOpts->threshold = w; } inline ELookupTableType CBlastOptionsLocal::GetLookupTableType() const { return m_LutOpts->lut_type; } inline void CBlastOptionsLocal::SetLookupTableType(ELookupTableType type) { m_LutOpts->lut_type = type; if (type == eMBLookupTable) { m_LutOpts->word_size = BLAST_WORDSIZE_MEGABLAST; } } inline int CBlastOptionsLocal::GetWordSize() const { return m_LutOpts->word_size; } inline void CBlastOptionsLocal::SetWordSize(int ws) { m_LutOpts->word_size = ws; } inline unsigned char CBlastOptionsLocal::GetMBTemplateLength() const { return m_LutOpts->mb_template_length; } inline void CBlastOptionsLocal::SetMBTemplateLength(unsigned char len) { m_LutOpts->mb_template_length = len; } inline unsigned char CBlastOptionsLocal::GetMBTemplateType() const { return m_LutOpts->mb_template_type; } inline void CBlastOptionsLocal::SetMBTemplateType(unsigned char type) { m_LutOpts->mb_template_type = type; } /******************* Query setup options ************************/ inline char* CBlastOptionsLocal::GetFilterString() const { if (m_QueryOpts->filter_string == NULL) { // Don't cache this in case the filtering options are changed return BlastFilteringOptionsToString(m_QueryOpts->filtering_options); } _ASSERT(m_QueryOpts->filter_string != NULL); return strdup(m_QueryOpts->filter_string); } inline void CBlastOptionsLocal::SetFilterString(const char* f) { if (!f) return; sfree(m_QueryOpts->filter_string); m_QueryOpts->filter_string = strdup(f); SBlastFilterOptions* new_opts = NULL; BlastFilteringOptionsFromString(GetProgramType(), f, &(new_opts), NULL); if (m_QueryOpts->filtering_options) { SBlastFilterOptions* old_opts = m_QueryOpts->filtering_options; m_QueryOpts->filtering_options = NULL; SBlastFilterOptionsMerge(&(m_QueryOpts->filtering_options), old_opts, new_opts); old_opts = SBlastFilterOptionsFree(old_opts); new_opts = SBlastFilterOptionsFree(new_opts); } else { if (m_QueryOpts->filtering_options) m_QueryOpts->filtering_options = SBlastFilterOptionsFree(m_QueryOpts->filtering_options); m_QueryOpts->filtering_options = new_opts; new_opts = NULL; } // Repeat filtering is only allowed for blastn. if (GetProgramType() != eBlastTypeBlastn && m_QueryOpts->filtering_options->repeatFilterOptions) m_QueryOpts->filtering_options->repeatFilterOptions = SRepeatFilterOptionsFree(m_QueryOpts->filtering_options->repeatFilterOptions); return; } inline bool CBlastOptionsLocal::GetMaskAtHash() const { if (m_QueryOpts->filtering_options->mask_at_hash) return true; else return false; } inline void CBlastOptionsLocal::SetMaskAtHash(bool val) { m_QueryOpts->filtering_options->mask_at_hash = val; return; } inline bool CBlastOptionsLocal::GetDustFiltering() const { if (m_QueryOpts->filtering_options->dustOptions) return true; else return false; } inline void CBlastOptionsLocal::SetDustFiltering(bool val) { if (m_QueryOpts->filtering_options->dustOptions) // free previous structure so we provide defaults. m_QueryOpts->filtering_options->dustOptions = SDustOptionsFree(m_QueryOpts->filtering_options->dustOptions); if (val == false) // filtering should be turned off return; SDustOptionsNew(&(m_QueryOpts->filtering_options->dustOptions)); return; } inline int CBlastOptionsLocal::GetDustFilteringLevel() const { if (m_QueryOpts->filtering_options->dustOptions == NULL) return kInvalidFilterValue; return m_QueryOpts->filtering_options->dustOptions->level; } inline void CBlastOptionsLocal::SetDustFilteringLevel(int level) { if (m_QueryOpts->filtering_options->dustOptions == NULL) SDustOptionsNew(&(m_QueryOpts->filtering_options->dustOptions)); m_QueryOpts->filtering_options->dustOptions->level = level; return; } inline int CBlastOptionsLocal::GetDustFilteringWindow() const { if (m_QueryOpts->filtering_options->dustOptions == NULL) return kInvalidFilterValue; return m_QueryOpts->filtering_options->dustOptions->window; } inline void CBlastOptionsLocal::SetDustFilteringWindow(int window) { if (m_QueryOpts->filtering_options->dustOptions == NULL) SDustOptionsNew(&(m_QueryOpts->filtering_options->dustOptions)); m_QueryOpts->filtering_options->dustOptions->window = window; return; } inline int CBlastOptionsLocal::GetDustFilteringLinker() const { if (m_QueryOpts->filtering_options->dustOptions == NULL) return kInvalidFilterValue; return m_QueryOpts->filtering_options->dustOptions->linker; } inline void CBlastOptionsLocal::SetDustFilteringLinker(int linker) { if (m_QueryOpts->filtering_options->dustOptions == NULL) SDustOptionsNew(&(m_QueryOpts->filtering_options->dustOptions)); m_QueryOpts->filtering_options->dustOptions->linker = linker; return; } inline bool CBlastOptionsLocal::GetSegFiltering() const { if (m_QueryOpts->filtering_options->segOptions) return true; else return false; } inline void CBlastOptionsLocal::SetSegFiltering(bool val) { if (m_QueryOpts->filtering_options->segOptions) // free previous structure so we provide defaults. m_QueryOpts->filtering_options->segOptions = SSegOptionsFree(m_QueryOpts->filtering_options->segOptions); if (val == false) // filtering should be turned off return; SSegOptionsNew(&(m_QueryOpts->filtering_options->segOptions)); return; } inline int CBlastOptionsLocal::GetSegFilteringWindow() const { if (m_QueryOpts->filtering_options->segOptions == NULL) return kInvalidFilterValue; return m_QueryOpts->filtering_options->segOptions->window; } inline void CBlastOptionsLocal::SetSegFilteringWindow(int window) { if (m_QueryOpts->filtering_options->segOptions == NULL) SSegOptionsNew(&(m_QueryOpts->filtering_options->segOptions)); m_QueryOpts->filtering_options->segOptions->window = window; return; } inline double CBlastOptionsLocal::GetSegFilteringLocut() const { if (m_QueryOpts->filtering_options->segOptions == NULL) return kInvalidFilterValue; return m_QueryOpts->filtering_options->segOptions->locut; } inline void CBlastOptionsLocal::SetSegFilteringLocut(double locut) { if (m_QueryOpts->filtering_options->segOptions == NULL) SSegOptionsNew(&(m_QueryOpts->filtering_options->segOptions)); m_QueryOpts->filtering_options->segOptions->locut = locut; return; } inline double CBlastOptionsLocal::GetSegFilteringHicut() const { if (m_QueryOpts->filtering_options->segOptions == NULL) return kInvalidFilterValue; return m_QueryOpts->filtering_options->segOptions->hicut; } inline void CBlastOptionsLocal::SetSegFilteringHicut(double hicut) { if (m_QueryOpts->filtering_options->segOptions == NULL) SSegOptionsNew(&(m_QueryOpts->filtering_options->segOptions)); m_QueryOpts->filtering_options->segOptions->hicut = hicut; return; } inline bool CBlastOptionsLocal::GetRepeatFiltering() const { if (m_QueryOpts->filtering_options->repeatFilterOptions) return true; else return false; } inline void CBlastOptionsLocal::SetRepeatFiltering(bool val) { if (m_QueryOpts->filtering_options->repeatFilterOptions) // free previous structure so we provide defaults. m_QueryOpts->filtering_options->repeatFilterOptions = SRepeatFilterOptionsFree(m_QueryOpts->filtering_options->repeatFilterOptions); if (val == false) // filtering should be turned off return; SRepeatFilterOptionsNew(&(m_QueryOpts->filtering_options->repeatFilterOptions)); return; } inline const char* CBlastOptionsLocal::GetRepeatFilteringDB() const { if (m_QueryOpts->filtering_options->repeatFilterOptions == NULL) return NULL; return m_QueryOpts->filtering_options->repeatFilterOptions->database; } inline void CBlastOptionsLocal::SetRepeatFilteringDB(const char* db) { if (!db) return; SRepeatFilterOptionsResetDB(&(m_QueryOpts->filtering_options->repeatFilterOptions), db); return; } inline int CBlastOptionsLocal::GetWindowMaskerTaxId() const { if (m_QueryOpts->filtering_options->windowMaskerOptions == NULL) return 0; return m_QueryOpts->filtering_options->windowMaskerOptions->taxid; } inline void CBlastOptionsLocal::SetWindowMaskerTaxId(int taxid) { if (m_QueryOpts->filtering_options->windowMaskerOptions == NULL) SWindowMaskerOptionsNew (&(m_QueryOpts->filtering_options->windowMaskerOptions)); m_QueryOpts->filtering_options->windowMaskerOptions->taxid = taxid; } inline const char* CBlastOptionsLocal::GetWindowMaskerDatabase() const { if (! m_QueryOpts->filtering_options->windowMaskerOptions) return NULL; return m_QueryOpts->filtering_options->windowMaskerOptions->database; } inline void CBlastOptionsLocal::SetWindowMaskerDatabase(const char* db) { if (m_QueryOpts->filtering_options->windowMaskerOptions == NULL) SWindowMaskerOptionsNew (&(m_QueryOpts->filtering_options->windowMaskerOptions)); SWindowMaskerOptionsResetDB (&(m_QueryOpts->filtering_options->windowMaskerOptions), db); } inline objects::ENa_strand CBlastOptionsLocal::GetStrandOption() const { return (objects::ENa_strand) m_QueryOpts->strand_option; } inline void CBlastOptionsLocal::SetStrandOption(objects::ENa_strand s) { m_QueryOpts->strand_option = (unsigned char) s; } inline int CBlastOptionsLocal::GetQueryGeneticCode() const { return m_QueryOpts->genetic_code; } inline void CBlastOptionsLocal::SetQueryGeneticCode(int gc) { m_QueryOpts->genetic_code = gc; } /******************* Initial word options ***********************/ inline int CBlastOptionsLocal::GetWindowSize() const { return m_InitWordOpts->window_size; } inline void CBlastOptionsLocal::SetWindowSize(int s) { m_InitWordOpts->window_size = s; } inline int CBlastOptionsLocal::GetOffDiagonalRange() const { return m_InitWordOpts->scan_range; } inline void CBlastOptionsLocal::SetOffDiagonalRange(int r) { m_InitWordOpts->scan_range = r; } inline double CBlastOptionsLocal::GetXDropoff() const { return m_InitWordOpts->x_dropoff; } inline void CBlastOptionsLocal::SetXDropoff(double x) { m_InitWordOpts->x_dropoff = x; } inline double CBlastOptionsLocal::GetGapTrigger() const { return m_InitWordOpts->gap_trigger; } inline void CBlastOptionsLocal::SetGapTrigger(double g) { m_InitWordOpts->gap_trigger = g; } /******************* Gapped extension options *******************/ inline double CBlastOptionsLocal::GetGapXDropoff() const { return m_ExtnOpts->gap_x_dropoff; } inline void CBlastOptionsLocal::SetGapXDropoff(double x) { m_ExtnOpts->gap_x_dropoff = x; } inline double CBlastOptionsLocal::GetGapXDropoffFinal() const { return m_ExtnOpts->gap_x_dropoff_final; } inline void CBlastOptionsLocal::SetGapXDropoffFinal(double x) { m_ExtnOpts->gap_x_dropoff_final = x; } inline EBlastPrelimGapExt CBlastOptionsLocal::GetGapExtnAlgorithm() const { return m_ExtnOpts->ePrelimGapExt; } inline void CBlastOptionsLocal::SetGapExtnAlgorithm(EBlastPrelimGapExt a) { m_ExtnOpts->ePrelimGapExt = a; } inline EBlastTbackExt CBlastOptionsLocal::GetGapTracebackAlgorithm() const { return m_ExtnOpts->eTbackExt; } inline void CBlastOptionsLocal::SetGapTracebackAlgorithm(EBlastTbackExt a) { m_ExtnOpts->eTbackExt = a; } inline ECompoAdjustModes CBlastOptionsLocal::GetCompositionBasedStats() const { return static_cast(m_ExtnOpts->compositionBasedStats); } inline void CBlastOptionsLocal::SetCompositionBasedStats(ECompoAdjustModes mode) { m_ExtnOpts->compositionBasedStats = static_cast(mode); } inline bool CBlastOptionsLocal::GetSmithWatermanMode() const { if (m_ExtnOpts->eTbackExt == eSmithWatermanTbck) return true; else return false; } inline void CBlastOptionsLocal::SetSmithWatermanMode(bool m) { if (m == true) m_ExtnOpts->eTbackExt = eSmithWatermanTbck; else m_ExtnOpts->eTbackExt = eDynProgTbck; } inline int CBlastOptionsLocal::GetUnifiedP() const { return m_ExtnOpts->unifiedP; } inline void CBlastOptionsLocal::SetUnifiedP(int u) { m_ExtnOpts->unifiedP = u; } /******************* Hit saving options *************************/ inline int CBlastOptionsLocal::GetHitlistSize() const { return m_HitSaveOpts->hitlist_size; } inline void CBlastOptionsLocal::SetHitlistSize(int s) { m_HitSaveOpts->hitlist_size = s; } inline int CBlastOptionsLocal::GetMaxNumHspPerSequence() const { return m_HitSaveOpts->hsp_num_max; } inline void CBlastOptionsLocal::SetMaxNumHspPerSequence(int m) { m_HitSaveOpts->hsp_num_max = m; } inline int CBlastOptionsLocal::GetCullingLimit() const { _ASSERT( (m_HitSaveOpts->culling_limit && m_HitSaveOpts->hsp_filt_opt->culling_opts->max_hits == m_HitSaveOpts->culling_limit) || (m_HitSaveOpts->culling_limit == 0 && ( (m_HitSaveOpts->hsp_filt_opt == NULL) || (m_HitSaveOpts->hsp_filt_opt->culling_opts == NULL) ) ) ); return m_HitSaveOpts->culling_limit; } inline void CBlastOptionsLocal::SetCullingLimit(int s) { if (s <= 0) { return; } if ( !m_HitSaveOpts->hsp_filt_opt ) { m_HitSaveOpts->hsp_filt_opt = BlastHSPFilteringOptionsNew(); } // N.B.: ePrelimSearch is the default culling implemetation if (m_HitSaveOpts->hsp_filt_opt->culling_opts == NULL) { BlastHSPCullingOptions* culling = BlastHSPCullingOptionsNew(s); BlastHSPFilteringOptions_AddCulling(m_HitSaveOpts->hsp_filt_opt, &culling, ePrelimSearch); _ASSERT(culling == NULL); } else { m_HitSaveOpts->hsp_filt_opt->culling_opts->max_hits = s; } // for backwards compatibility reasons m_HitSaveOpts->culling_limit = s; } inline double CBlastOptionsLocal::GetBestHitScoreEdge() const { if (m_HitSaveOpts->hsp_filt_opt && m_HitSaveOpts->hsp_filt_opt->best_hit) { return m_HitSaveOpts->hsp_filt_opt->best_hit->score_edge; } else { return kBestHit_ScoreEdgeMin; } } inline void CBlastOptionsLocal::SetBestHitScoreEdge(double score_edge) { if ( !m_HitSaveOpts->hsp_filt_opt ) { m_HitSaveOpts->hsp_filt_opt = BlastHSPFilteringOptionsNew(); } // per this object's assumption, just set the value if (m_HitSaveOpts->hsp_filt_opt->best_hit) { m_HitSaveOpts->hsp_filt_opt->best_hit->score_edge = score_edge; } else { BlastHSPBestHitOptions* best_hit_opts = BlastHSPBestHitOptionsNew(kBestHit_OverhangDflt, score_edge); BlastHSPFilteringOptions_AddBestHit(m_HitSaveOpts->hsp_filt_opt, &best_hit_opts, eBoth); _ASSERT(best_hit_opts == NULL); } } inline double CBlastOptionsLocal::GetBestHitOverhang() const { if (m_HitSaveOpts->hsp_filt_opt && m_HitSaveOpts->hsp_filt_opt->best_hit) { return m_HitSaveOpts->hsp_filt_opt->best_hit->overhang; } else { return kBestHit_OverhangMin; } } inline void CBlastOptionsLocal::SetBestHitOverhang(double overhang) { if ( !m_HitSaveOpts->hsp_filt_opt ) { m_HitSaveOpts->hsp_filt_opt = BlastHSPFilteringOptionsNew(); } // per this object's assumption, just set the value if (m_HitSaveOpts->hsp_filt_opt->best_hit) { m_HitSaveOpts->hsp_filt_opt->best_hit->overhang = overhang; } else { BlastHSPBestHitOptions* best_hit_opts = BlastHSPBestHitOptionsNew(overhang, kBestHit_ScoreEdgeDflt); BlastHSPFilteringOptions_AddBestHit(m_HitSaveOpts->hsp_filt_opt, &best_hit_opts, eBoth); _ASSERT(best_hit_opts == NULL); } } inline double CBlastOptionsLocal::GetEvalueThreshold() const { return m_HitSaveOpts->expect_value; } inline void CBlastOptionsLocal::SetEvalueThreshold(double eval) { m_HitSaveOpts->expect_value = eval; } inline int CBlastOptionsLocal::GetCutoffScore() const { return m_HitSaveOpts->cutoff_score; } inline void CBlastOptionsLocal::SetCutoffScore(int s) { m_HitSaveOpts->cutoff_score = s; } inline double CBlastOptionsLocal::GetPercentIdentity() const { return m_HitSaveOpts->percent_identity; } inline void CBlastOptionsLocal::SetPercentIdentity(double p) { m_HitSaveOpts->percent_identity = p; } inline int CBlastOptionsLocal::GetMinDiagSeparation() const { return m_HitSaveOpts->min_diag_separation; } inline void CBlastOptionsLocal::SetMinDiagSeparation(int d) { m_HitSaveOpts->min_diag_separation = d; } inline bool CBlastOptionsLocal::GetSumStatisticsMode() const { return m_HitSaveOpts->do_sum_stats ? true : false; } inline void CBlastOptionsLocal::SetSumStatisticsMode(bool m) { m_HitSaveOpts->do_sum_stats = m; } inline int CBlastOptionsLocal::GetLongestIntronLength() const { return m_HitSaveOpts->longest_intron; } inline void CBlastOptionsLocal::SetLongestIntronLength(int l) { m_HitSaveOpts->longest_intron = l; } inline bool CBlastOptionsLocal::GetGappedMode() const { return m_ScoringOpts->gapped_calculation ? true : false; } inline void CBlastOptionsLocal::SetGappedMode(bool m) { m_ScoringOpts->gapped_calculation = m; } /************************ Scoring options ************************/ inline int CBlastOptionsLocal::GetMatchReward() const { return m_ScoringOpts->reward; } inline void CBlastOptionsLocal::SetMatchReward(int r) { m_ScoringOpts->reward = r; } inline int CBlastOptionsLocal::GetMismatchPenalty() const { return m_ScoringOpts->penalty; } inline void CBlastOptionsLocal::SetMismatchPenalty(int p) { m_ScoringOpts->penalty = p; } inline int CBlastOptionsLocal::GetGapOpeningCost() const { return m_ScoringOpts->gap_open; } inline void CBlastOptionsLocal::SetGapOpeningCost(int g) { m_ScoringOpts->gap_open = g; } inline int CBlastOptionsLocal::GetGapExtensionCost() const { return m_ScoringOpts->gap_extend; } inline void CBlastOptionsLocal::SetGapExtensionCost(int e) { m_ScoringOpts->gap_extend = e; } inline int CBlastOptionsLocal::GetFrameShiftPenalty() const { return m_ScoringOpts->shift_pen; } inline void CBlastOptionsLocal::SetFrameShiftPenalty(int p) { m_ScoringOpts->shift_pen = p; } inline bool CBlastOptionsLocal::GetOutOfFrameMode() const { return m_ScoringOpts->is_ooframe ? true : false; } inline void CBlastOptionsLocal::SetOutOfFrameMode(bool m) { m_ScoringOpts->is_ooframe = m; } /******************** Effective Length options *******************/ inline Int8 CBlastOptionsLocal::GetDbLength() const { return m_EffLenOpts->db_length; } inline void CBlastOptionsLocal::SetDbLength(Int8 l) { m_EffLenOpts->db_length = l; } inline unsigned int CBlastOptionsLocal::GetDbSeqNum() const { return (unsigned int) m_EffLenOpts->dbseq_num; } inline void CBlastOptionsLocal::SetDbSeqNum(unsigned int n) { m_EffLenOpts->dbseq_num = (Int4) n; } inline Int8 CBlastOptionsLocal::GetEffectiveSearchSpace() const { if (m_EffLenOpts->num_searchspaces == 0) return 0; return m_EffLenOpts->searchsp_eff[0]; } inline void CBlastOptionsLocal::SetEffectiveSearchSpace(Int8 eff) { if (m_EffLenOpts->num_searchspaces < 1) { m_EffLenOpts->num_searchspaces = 1; if (m_EffLenOpts->searchsp_eff) sfree(m_EffLenOpts->searchsp_eff); m_EffLenOpts->searchsp_eff = (Int8 *)malloc(sizeof(Int8)); } fill(m_EffLenOpts->searchsp_eff, m_EffLenOpts->searchsp_eff+m_EffLenOpts->num_searchspaces, eff); } inline void CBlastOptionsLocal::SetEffectiveSearchSpace(const vector& eff) { if (m_EffLenOpts->num_searchspaces < static_cast(eff.size())) { m_EffLenOpts->num_searchspaces = static_cast(eff.size()); if (m_EffLenOpts->searchsp_eff) sfree(m_EffLenOpts->searchsp_eff); m_EffLenOpts->searchsp_eff = (Int8 *)malloc(eff.size() * sizeof(Int8)); } copy(eff.begin(), eff.end(), m_EffLenOpts->searchsp_eff); } inline int CBlastOptionsLocal::GetDbGeneticCode() const { return m_DbOpts->genetic_code; } inline const char* CBlastOptionsLocal::GetPHIPattern() const { return m_LutOpts->phi_pattern; } inline double CBlastOptionsLocal::GetInclusionThreshold() const { return m_PSIBlastOpts->inclusion_ethresh; } inline void CBlastOptionsLocal::SetInclusionThreshold(double incthr) { m_PSIBlastOpts->inclusion_ethresh = incthr; } inline int CBlastOptionsLocal::GetPseudoCount() const { return m_PSIBlastOpts->pseudo_count; } inline void CBlastOptionsLocal::SetPseudoCount(int pc) { m_PSIBlastOpts->pseudo_count = pc; } inline void CBlastOptionsLocal::SetPHIPattern(const char* pattern, bool is_dna) { if (is_dna) m_LutOpts->lut_type = ePhiNaLookupTable; else m_LutOpts->lut_type = ePhiLookupTable; if (pattern) m_LutOpts->phi_pattern = strdup(pattern); else if (m_LutOpts->phi_pattern) sfree(m_LutOpts->phi_pattern); } /******************** Megablast Database Index *******************/ inline bool CBlastOptionsLocal::GetUseIndex() const { return m_UseMBIndex; } inline bool CBlastOptionsLocal::GetForceIndex() const { return m_ForceMBIndex; } inline bool CBlastOptionsLocal::GetMBIndexLoaded() const { return m_MBIndexLoaded; } inline const string CBlastOptionsLocal::GetIndexName() const { return m_MBIndexName; } inline void CBlastOptionsLocal::SetMBIndexLoaded( bool index_loaded ) { m_MBIndexLoaded = index_loaded; } inline void CBlastOptionsLocal::SetUseIndex( bool use_index, const string & index_name, bool force_index ) { m_UseMBIndex = use_index; if( m_UseMBIndex ) { m_ForceMBIndex = force_index; m_MBIndexName = index_name; } } /* *********** START ************* */ /******************** GPU Options *******************/ inline bool CBlastOptionsLocal::GetUseGpu() const { return m_UseGpu; } inline int CBlastOptionsLocal::GetNumGpuThreads() const { return m_NumGpuThreads; } inline int CBlastOptionsLocal::GetNumGpuBlocks() const { return m_NumGpuBlocks; } inline int CBlastOptionsLocal::GetNumGpuSequences() const { return m_NumGpuSequences; } inline int CBlastOptionsLocal::GetGpuMethod() const { return m_GpuMethod; } inline int CBlastOptionsLocal::GetNumCpuThreads() const { return m_NumCpuThreads; } inline void CBlastOptionsLocal::SetUseGpu( bool use_gpu ) { m_UseGpu = use_gpu; } inline void CBlastOptionsLocal::SetNumGpuThreads( int num_gpu_threads ) { m_NumGpuThreads = num_gpu_threads; } inline void CBlastOptionsLocal::SetNumGpuBlocks( int num_gpu_blocks ) { m_NumGpuBlocks = num_gpu_blocks; } inline void CBlastOptionsLocal::SetNumGpuSequences( int num_sequences ) { m_NumGpuSequences = num_sequences; } inline void CBlastOptionsLocal::SetGpuMethod( int method ) { m_GpuMethod = method; } inline void CBlastOptionsLocal::SetNumCpuThreads( int num_cpu_threads ) { m_NumCpuThreads = num_cpu_threads; } /* ********** FINISH ************* */ #endif /* SKIP_DOXYGEN_PROCESSING */ END_SCOPE(blast) END_NCBI_SCOPE /* @} */ #endif /* ALGO_BLAST_API___BLAST_OPTIONS_LOCAL_PRIV__HPP */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_options_cxx.cpp0000644000175000017500000016157112001215337025041 0ustar ykeyke#ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: blast_options_cxx.cpp 192787 2010-05-27 13:52:50Z madden $"; #endif /* SKIP_DOXYGEN_PROCESSING */ /* =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /// @file blast_options_cxx.cpp /// Implements the CBlastOptions class, which encapsulates options structures /// from algo/blast/core #include #include #include "blast_setup.hpp" #include "blast_options_local_priv.hpp" #include "blast_memento_priv.hpp" #include #include #include #include /** @addtogroup AlgoBlast * * @{ */ BEGIN_NCBI_SCOPE USING_SCOPE(objects); BEGIN_SCOPE(blast) #ifndef SKIP_DOXYGEN_PROCESSING /// Index of remote BLAST options. enum EBlastOptIdx { eBlastOpt_Program = 100, eBlastOpt_WordThreshold, eBlastOpt_LookupTableType, eBlastOpt_WordSize, eBlastOpt_AlphabetSize, eBlastOpt_MBTemplateLength, eBlastOpt_MBTemplateType, eBlastOpt_FilterString, eBlastOpt_MaskAtHash, eBlastOpt_DustFiltering, eBlastOpt_DustFilteringLevel, eBlastOpt_DustFilteringWindow, eBlastOpt_DustFilteringLinker, eBlastOpt_SegFiltering, eBlastOpt_SegFilteringWindow, eBlastOpt_SegFilteringLocut, eBlastOpt_SegFilteringHicut, eBlastOpt_RepeatFiltering, eBlastOpt_RepeatFilteringDB, eBlastOpt_StrandOption, eBlastOpt_QueryGeneticCode, eBlastOpt_WindowSize, eBlastOpt_SeedContainerType, eBlastOpt_SeedExtensionMethod, eBlastOpt_XDropoff, eBlastOpt_GapXDropoff, eBlastOpt_GapXDropoffFinal, eBlastOpt_GapTrigger, eBlastOpt_GapExtnAlgorithm, eBlastOpt_HitlistSize, eBlastOpt_MaxNumHspPerSequence, eBlastOpt_CullingLimit, eBlastOpt_EvalueThreshold, eBlastOpt_CutoffScore, eBlastOpt_PercentIdentity, eBlastOpt_SumStatisticsMode, eBlastOpt_LongestIntronLength, eBlastOpt_GappedMode, eBlastOpt_MatrixName, eBlastOpt_MatrixPath, eBlastOpt_MatchReward, eBlastOpt_MismatchPenalty, eBlastOpt_GapOpeningCost, eBlastOpt_GapExtensionCost, eBlastOpt_FrameShiftPenalty, eBlastOpt_OutOfFrameMode, eBlastOpt_DbLength, eBlastOpt_DbSeqNum, eBlastOpt_EffectiveSearchSpace, eBlastOpt_DbGeneticCode, eBlastOpt_PHIPattern, eBlastOpt_InclusionThreshold, eBlastOpt_PseudoCount, eBlastOpt_GapTracebackAlgorithm, eBlastOpt_CompositionBasedStats, eBlastOpt_SmithWatermanMode, eBlastOpt_UnifiedP, eBlastOpt_WindowMaskerDatabase, eBlastOpt_WindowMaskerTaxId, eBlastOpt_ForceMbIndex, // corresponds to -use_index flag eBlastOpt_MbIndexName, // corresponds to -index_name flag eBlastOpt_BestHitScoreEdge, eBlastOpt_BestHitOverhang }; /// Encapsulates all blast input parameters class NCBI_XBLAST_EXPORT CBlastOptionsRemote : public CObject { public: CBlastOptionsRemote(void) : m_DefaultsMode(false) { m_ReqOpts.Reset(new objects::CBlast4_parameters); } ~CBlastOptionsRemote() { } /// Copy constructor CBlastOptionsRemote(const CBlastOptionsRemote& optsRemote) : m_DefaultsMode(false) { x_DoDeepCopy(optsRemote); } /// Assignment operator CBlastOptionsRemote& operator=(const CBlastOptionsRemote& optsRemote) { x_DoDeepCopy(optsRemote); return *this; } // the "new paradigm" typedef ncbi::objects::CBlast4_parameters TBlast4Opts; TBlast4Opts * GetBlast4AlgoOpts() { return m_ReqOpts; } typedef vector< CConstRef > TSeqLocVector; // SetValue(x,y) with different types: void SetValue(EBlastOptIdx opt, const EProgram & x); void SetValue(EBlastOptIdx opt, const int & x); void SetValue(EBlastOptIdx opt, const double & x); void SetValue(EBlastOptIdx opt, const char * x); void SetValue(EBlastOptIdx opt, const TSeqLocVector & x); void SetValue(EBlastOptIdx opt, const ESeedContainerType & x); void SetValue(EBlastOptIdx opt, const bool & x); void SetValue(EBlastOptIdx opt, const Int8 & x); // Pseudo-types: void SetValue(EBlastOptIdx opt, const short & x) { int x2 = x; SetValue(opt, x2); } void SetValue(EBlastOptIdx opt, const unsigned int & x) { int x2 = x; SetValue(opt, x2); } void SetValue(EBlastOptIdx opt, const unsigned char & x) { int x2 = x; SetValue(opt, x2); } void SetValue(EBlastOptIdx opt, const objects::ENa_strand & x) { int x2 = x; SetValue(opt, x2); } /// Remove any objects matching this Blast4 field object. /// /// The given field object represents a Blast4 field to remove /// from the list of remote options. /// /// @param opt Field object representing option to remove. void ResetValue(CBlast4Field & opt) { x_ResetValue(opt); } void SetDefaultsMode(bool dmode) { m_DefaultsMode = dmode; } bool GetDefaultsMode() { return m_DefaultsMode; } private: //CRef m_Req; CRef m_ReqOpts; bool m_DefaultsMode; /// Perform a "deep copy" of remote Blast options /// @param optsRemote remote Blast options object to copy from. void x_DoDeepCopy(const CBlastOptionsRemote& optsRemote) { if (&optsRemote != this) { m_ReqOpts.Reset(new objects::CBlast4_parameters); m_ReqOpts->Assign(*optsRemote.m_ReqOpts); m_DefaultsMode = optsRemote.m_DefaultsMode; } } template void x_SetParam(CBlast4Field & name, T & value) { x_SetOneParam(name, & value); } void x_SetOneParam(CBlast4Field & field, const int * x) { CRef v(new objects::CBlast4_value); v->SetInteger(*x); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_SetOneParam(CBlast4Field & field, const char ** x) { CRef v(new objects::CBlast4_value); v->SetString().assign((x && (*x)) ? (*x) : ""); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_SetOneParam(CBlast4Field & field, const bool * x) { CRef v(new objects::CBlast4_value); v->SetBoolean(*x); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_SetOneParam(CBlast4Field & field, CRef * x) { CRef v(new objects::CBlast4_value); v->SetCutoff(**x); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_SetOneParam(CBlast4Field & field, const double * x) { CRef v(new objects::CBlast4_value); v->SetReal(*x); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_SetOneParam(CBlast4Field & field, const Int8 * x) { CRef v(new objects::CBlast4_value); v->SetBig_integer(*x); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_SetOneParam(CBlast4Field & field, objects::EBlast4_strand_type * x) { CRef v(new objects::CBlast4_value); v->SetStrand_type(*x); CRef p(new objects::CBlast4_parameter); p->SetName(field.GetName()); p->SetValue(*v); x_AttachValue(p); } void x_AttachValue(CRef p) { typedef objects::CBlast4_parameter TParam; NON_CONST_ITERATE(list< CRef >, iter, m_ReqOpts->Set()) { if ((**iter).GetName() == p->GetName()) { (*iter) = p; return; } } m_ReqOpts->Set().push_back(p); } /// Remove values for a given Blast4 field. /// @param f Field to search for and remove. void x_ResetValue(CBlast4Field & f) { typedef list< CRef > TParamList; typedef TParamList::iterator TParamIter; const string & nm = f.GetName(); TParamList & lst = m_ReqOpts->Set(); TParamIter pos = lst.begin(), end = lst.end(); while(pos != end) { TParamIter current = pos; pos++; if ((**current).GetName() == nm) { lst.erase(current); } } } void x_Throwx(const string& msg) const { NCBI_THROW(CBlastException, eInvalidOptions, msg); } }; CBlastOptions::CBlastOptions(EAPILocality locality) : m_Local (0), m_Remote(0), m_DefaultsMode(false) { if (locality == eRemote) locality = eBoth; if (locality != eRemote) { m_Local = new CBlastOptionsLocal(); } if (locality != eLocal) { m_Remote = new CBlastOptionsRemote(); } } CBlastOptions::~CBlastOptions() { if (m_Local) { delete m_Local; } if (m_Remote) { delete m_Remote; } } CRef CBlastOptions::Clone() const { CRef optsRef; optsRef.Reset(new CBlastOptions(GetLocality())); optsRef->x_DoDeepCopy(*this); return optsRef; } CBlastOptions::EAPILocality CBlastOptions::GetLocality(void) const { if (! m_Remote) { return eLocal; } if (! m_Local) { return eRemote; } return eBoth; } // Note: only some of the options are supported for the remote case; // An exception is thrown if the option is not available. void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const EProgram & v) { if (m_DefaultsMode) { return; } switch(opt) { case eBlastOpt_Program: return; default: break; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%d), line (%d).", int(opt), v, __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const int & v) { if (m_DefaultsMode) { return; } switch(opt) { case eBlastOpt_WordSize: x_SetParam(B4Param_WordSize, v); return; case eBlastOpt_LookupTableType: // do nothing, should be specified by the task return; case eBlastOpt_StrandOption: { typedef objects::EBlast4_strand_type TSType; TSType strand; bool set_strand = true; switch(v) { case 1: strand = eBlast4_strand_type_forward_strand; break; case 2: strand = eBlast4_strand_type_reverse_strand; break; case 3: strand = eBlast4_strand_type_both_strands; break; default: set_strand = false; } if (set_strand) { x_SetParam(B4Param_StrandOption, strand); return; } } case eBlastOpt_WindowSize: x_SetParam(B4Param_WindowSize, v); return; case eBlastOpt_GapOpeningCost: x_SetParam(B4Param_GapOpeningCost, v); return; case eBlastOpt_GapExtensionCost: x_SetParam(B4Param_GapExtensionCost, v); return; case eBlastOpt_HitlistSize: x_SetParam(B4Param_HitlistSize, v); return; case eBlastOpt_CutoffScore: if (0) { typedef objects::CBlast4_cutoff TCutoff; CRef cutoff(new TCutoff); cutoff->SetRaw_score(v); x_SetParam(B4Param_CutoffScore, cutoff); } return; case eBlastOpt_MatchReward: x_SetParam(B4Param_MatchReward, v); return; case eBlastOpt_MismatchPenalty: x_SetParam(B4Param_MismatchPenalty, v); return; case eBlastOpt_WordThreshold: x_SetParam(B4Param_WordThreshold, v); return; case eBlastOpt_PseudoCount: x_SetParam(B4Param_PseudoCountWeight, v); return; case eBlastOpt_CompositionBasedStats: if (v < eNumCompoAdjustModes) { x_SetParam(B4Param_CompositionBasedStats, v); return; } case eBlastOpt_MBTemplateLength: x_SetParam(B4Param_MBTemplateLength, v); return; case eBlastOpt_MBTemplateType: x_SetParam(B4Param_MBTemplateType, v); return; case eBlastOpt_GapExtnAlgorithm: x_SetParam(B4Param_GapExtnAlgorithm, v); return; case eBlastOpt_GapTracebackAlgorithm: x_SetParam(B4Param_GapTracebackAlgorithm, v); return; case eBlastOpt_SegFilteringWindow: x_SetParam(B4Param_SegFilteringWindow, v); return; case eBlastOpt_DustFilteringLevel: x_SetParam(B4Param_DustFilteringLevel, v); return; case eBlastOpt_DustFilteringWindow: x_SetParam(B4Param_DustFilteringWindow, v); return; case eBlastOpt_DustFilteringLinker: x_SetParam(B4Param_DustFilteringLinker, v); return; case eBlastOpt_CullingLimit: x_SetParam(B4Param_CullingLimit, v); return; case eBlastOpt_LongestIntronLength: x_SetParam(B4Param_LongestIntronLength, v); return; case eBlastOpt_QueryGeneticCode: x_SetParam(B4Param_QueryGeneticCode, v); return; case eBlastOpt_DbGeneticCode: x_SetParam(B4Param_DbGeneticCode, v); return; case eBlastOpt_UnifiedP: x_SetParam(B4Param_UnifiedP, v); return; case eBlastOpt_WindowMaskerTaxId: x_SetParam(B4Param_WindowMaskerTaxId, v); return; default: break; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%d), line (%d).", int(opt), v, __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const double & v) { if (m_DefaultsMode) { return; } switch(opt) { case eBlastOpt_EvalueThreshold: { typedef objects::CBlast4_cutoff TCutoff; CRef cutoff(new TCutoff); cutoff->SetE_value(v); x_SetParam(B4Param_EvalueThreshold, cutoff); } return; case eBlastOpt_PercentIdentity: x_SetParam(B4Param_PercentIdentity, v); return; case eBlastOpt_InclusionThreshold: x_SetParam(B4Param_InclusionThreshold, v); return; case eBlastOpt_GapXDropoff: x_SetParam(B4Param_GapXDropoff, v); return; case eBlastOpt_GapXDropoffFinal: x_SetParam(B4Param_GapXDropoffFinal, v); return; case eBlastOpt_XDropoff: //x_SetParam(B4Param_XDropoff, v); return; case eBlastOpt_SegFilteringLocut: x_SetParam(B4Param_SegFilteringLocut, v); return; case eBlastOpt_SegFilteringHicut: x_SetParam(B4Param_SegFilteringHicut, v); return; case eBlastOpt_GapTrigger: x_SetParam(B4Param_GapTrigger, v); return; case eBlastOpt_BestHitScoreEdge: x_SetParam(B4Param_BestHitScoreEdge, v); return; case eBlastOpt_BestHitOverhang: x_SetParam(B4Param_BestHitOverhang, v); return; default: break; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%f), line (%d).", int(opt), v, __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const char * v) { if (m_DefaultsMode) { return; } switch(opt) { case eBlastOpt_FilterString: x_SetParam(B4Param_FilterString, v); return; case eBlastOpt_RepeatFilteringDB: x_SetParam(B4Param_RepeatFilteringDB, v); return; case eBlastOpt_MatrixName: x_SetParam(B4Param_MatrixName, v); return; case eBlastOpt_WindowMaskerDatabase: x_SetParam(B4Param_WindowMaskerDatabase, v); return; case eBlastOpt_PHIPattern: x_SetParam(B4Param_PHIPattern, v); return; case eBlastOpt_MbIndexName: x_SetParam(B4Param_MbIndexName, v); return; default: break; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%.20s), line (%d).", int(opt), v, __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const TSeqLocVector & v) { if (m_DefaultsMode) { return; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and TSeqLocVector (size %zd), line (%d).", int(opt), v.size(), __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const ESeedContainerType & v) { if (m_DefaultsMode) { return; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%d), line (%d).", int(opt), v, __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const bool & v) { if (m_DefaultsMode) { return; } switch(opt) { case eBlastOpt_GappedMode: { bool ungapped = ! v; x_SetParam(B4Param_UngappedMode, ungapped); // inverted return; } case eBlastOpt_OutOfFrameMode: x_SetParam(B4Param_OutOfFrameMode, v); return; case eBlastOpt_SegFiltering: x_SetParam(B4Param_SegFiltering, v); return; case eBlastOpt_DustFiltering: x_SetParam(B4Param_DustFiltering, v); return; case eBlastOpt_RepeatFiltering: x_SetParam(B4Param_RepeatFiltering, v); return; case eBlastOpt_MaskAtHash: x_SetParam(B4Param_MaskAtHash, v); return; case eBlastOpt_SumStatisticsMode: x_SetParam(B4Param_SumStatistics, v); return; case eBlastOpt_SmithWatermanMode: x_SetParam(B4Param_SmithWatermanMode, v); return; case eBlastOpt_ForceMbIndex: x_SetParam(B4Param_ForceMbIndex, v); return; default: break; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%s), line (%d).", int(opt), (v ? "true" : "false"), __LINE__); x_Throwx(string("err:") + errbuf); } void CBlastOptionsRemote::SetValue(EBlastOptIdx opt, const Int8 & v) { if (m_DefaultsMode) { return; } switch(opt) { case eBlastOpt_EffectiveSearchSpace: x_SetParam(B4Param_EffectiveSearchSpace, v); return; case eBlastOpt_DbLength: x_SetParam(B4Param_DbLength, v); return; default: break; } char errbuf[1024]; sprintf(errbuf, "tried to set option (%d) and value (%f), line (%d).", int(opt), double(v), __LINE__); x_Throwx(string("err:") + errbuf); } const CBlastOptionsMemento* CBlastOptions::CreateSnapshot() const { if ( !m_Local ) { NCBI_THROW(CBlastException, eInvalidArgument, "Cannot create CBlastOptionsMemento without a local " "CBlastOptions object"); } return new CBlastOptionsMemento(m_Local); } bool CBlastOptions::operator==(const CBlastOptions& rhs) const { if (m_Local && rhs.m_Local) { return (*m_Local == *rhs.m_Local); } else { NCBI_THROW(CBlastException, eNotSupported, "Equality operator unsupported for arguments"); } } bool CBlastOptions::operator!=(const CBlastOptions& rhs) const { return !(*this == rhs); } bool CBlastOptions::Validate() const { bool local_okay = m_Local ? (m_Local ->Validate()) : true; return local_okay; } EProgram CBlastOptions::GetProgram() const { if (! m_Local) { x_Throwx("Error: GetProgram() not available."); } return m_Local->GetProgram(); } EBlastProgramType CBlastOptions::GetProgramType() const { if (! m_Local) { x_Throwx("Error: GetProgramType() not available."); } return m_Local->GetProgramType(); } void CBlastOptions::SetProgram(EProgram p) { if (m_Local) { m_Local->SetProgram(p); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_Program, p); } } /******************* Lookup table options ***********************/ double CBlastOptions::GetWordThreshold() const { if (! m_Local) { x_Throwx("Error: GetWordThreshold() not available."); } return m_Local->GetWordThreshold(); } void CBlastOptions::SetWordThreshold(double w) { if (m_Local) { m_Local->SetWordThreshold(w); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_WordThreshold, static_cast(w)); } } ELookupTableType CBlastOptions::GetLookupTableType() const { if (! m_Local) { x_Throwx("Error: GetLookupTableType() not available."); } return m_Local->GetLookupTableType(); } void CBlastOptions::SetLookupTableType(ELookupTableType type) { if (m_Local) { m_Local->SetLookupTableType(type); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_LookupTableType, type); } } int CBlastOptions::GetWordSize() const { if (! m_Local) { x_Throwx("Error: GetWordSize() not available."); } return m_Local->GetWordSize(); } void CBlastOptions::SetWordSize(int ws) { if (m_Local) { m_Local->SetWordSize(ws); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_WordSize, ws); } } /// Megablast only lookup table options unsigned char CBlastOptions::GetMBTemplateLength() const { if (! m_Local) { x_Throwx("Error: GetMBTemplateLength() not available."); } return m_Local->GetMBTemplateLength(); } void CBlastOptions::SetMBTemplateLength(unsigned char len) { if (m_Local) { m_Local->SetMBTemplateLength(len); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MBTemplateLength, len); } } unsigned char CBlastOptions::GetMBTemplateType() const { if (! m_Local) { x_Throwx("Error: GetMBTemplateType() not available."); } return m_Local->GetMBTemplateType(); } void CBlastOptions::SetMBTemplateType(unsigned char type) { if (m_Local) { m_Local->SetMBTemplateType(type); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MBTemplateType, type); } } /******************* Query setup options ************************/ void CBlastOptions::ClearFilterOptions() { SetDustFiltering(false); SetSegFiltering(false); SetRepeatFiltering(false); SetMaskAtHash(false); SetWindowMaskerTaxId(0); SetWindowMaskerDatabase(NULL); return; } char* CBlastOptions::GetFilterString() const { if (! m_Local) { x_Throwx("Error: GetFilterString() not available."); } return m_Local->GetFilterString();/* NCBI_FAKE_WARNING */ } void CBlastOptions::SetFilterString(const char* f, bool clear) { // Clear if clear is true or filtering set to FALSE. if (clear == true || NStr::CompareNocase("F", f) == 0) { ClearFilterOptions(); } if (m_Local) { m_Local->SetFilterString(f);/* NCBI_FAKE_WARNING */ } if (m_Remote) { // When maintaining this code, please insure the following: // // 1. This list of items is parallel to the list found // below, in the "set" block. // // 2. Both lists should also correspond to the list of // options in names.hpp and names.cpp that are related // to filtering options. // // 3. Blast4's code in CCollectFilterOptions should also // handle the set of options handled here. // // 4. CRemoteBlast and CRemoteBlastService's handling of // filtering options (CBlastOptionsBuilder) should // include all of these elements. // // 5. Libnet2blast should deal with all of these filtering // options when it builds CBlastOptionsHandle objects. // // 6. Probably at least one or two other places that I forgot. m_Remote->SetValue(eBlastOpt_MaskAtHash, m_Local->GetMaskAtHash()); bool do_dust(false), do_seg(false), do_rep(false); if (Blast_QueryIsProtein(GetProgramType()) || Blast_QueryIsTranslated(GetProgramType())) { do_seg = m_Local->GetSegFiltering(); m_Remote->SetValue(eBlastOpt_SegFiltering, do_seg); } else { m_Remote->ResetValue(B4Param_SegFiltering); m_Remote->ResetValue(B4Param_SegFilteringWindow); m_Remote->ResetValue(B4Param_SegFilteringLocut); m_Remote->ResetValue(B4Param_SegFilteringHicut); } if (Blast_QueryIsNucleotide(GetProgramType()) && !Blast_QueryIsTranslated(GetProgramType())) { do_dust = m_Local->GetDustFiltering(); do_rep = m_Local->GetRepeatFiltering(); m_Remote->SetValue(eBlastOpt_DustFiltering, do_dust); m_Remote->SetValue(eBlastOpt_RepeatFiltering, do_rep); } else { m_Remote->ResetValue(B4Param_DustFiltering); m_Remote->ResetValue(B4Param_DustFilteringLevel); m_Remote->ResetValue(B4Param_DustFilteringWindow); m_Remote->ResetValue(B4Param_DustFilteringLinker); m_Remote->ResetValue(B4Param_RepeatFiltering); m_Remote->ResetValue(B4Param_RepeatFilteringDB); } if (do_dust) { m_Remote->SetValue(eBlastOpt_DustFilteringLevel, m_Local->GetDustFilteringLevel()); m_Remote->SetValue(eBlastOpt_DustFilteringWindow, m_Local->GetDustFilteringWindow()); m_Remote->SetValue(eBlastOpt_DustFilteringLinker, m_Local->GetDustFilteringLinker()); } if (do_rep) { m_Remote->SetValue(eBlastOpt_RepeatFilteringDB, m_Local->GetRepeatFilteringDB()); } if (do_seg) { m_Remote->SetValue(eBlastOpt_SegFilteringWindow, m_Local->GetSegFilteringWindow()); m_Remote->SetValue(eBlastOpt_SegFilteringLocut, m_Local->GetSegFilteringLocut()); m_Remote->SetValue(eBlastOpt_SegFilteringHicut, m_Local->GetSegFilteringHicut()); } } } bool CBlastOptions::GetMaskAtHash() const { if (! m_Local) { x_Throwx("Error: GetMaskAtHash() not available."); } return m_Local->GetMaskAtHash(); } void CBlastOptions::SetMaskAtHash(bool val) { if (m_Local) { m_Local->SetMaskAtHash(val); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MaskAtHash, val); } } bool CBlastOptions::GetDustFiltering() const { if (! m_Local) { x_Throwx("Error: GetDustFiltering() not available."); } return m_Local->GetDustFiltering(); } void CBlastOptions::SetDustFiltering(bool val) { if (m_Local) { m_Local->SetDustFiltering(val); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DustFiltering, val); } } int CBlastOptions::GetDustFilteringLevel() const { if (! m_Local) { x_Throwx("Error: GetDustFilteringLevel() not available."); } return m_Local->GetDustFilteringLevel(); } void CBlastOptions::SetDustFilteringLevel(int m) { if (m_Local) { m_Local->SetDustFilteringLevel(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DustFilteringLevel, m); } } int CBlastOptions::GetDustFilteringWindow() const { if (! m_Local) { x_Throwx("Error: GetDustFilteringWindow() not available."); } return m_Local->GetDustFilteringWindow(); } void CBlastOptions::SetDustFilteringWindow(int m) { if (m_Local) { m_Local->SetDustFilteringWindow(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DustFilteringWindow, m); } } int CBlastOptions::GetDustFilteringLinker() const { if (! m_Local) { x_Throwx("Error: GetDustFilteringLinker() not available."); } return m_Local->GetDustFilteringLinker(); } void CBlastOptions::SetDustFilteringLinker(int m) { if (m_Local) { m_Local->SetDustFilteringLinker(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DustFilteringLinker, m); } } bool CBlastOptions::GetSegFiltering() const { if (! m_Local) { x_Throwx("Error: GetSegFiltering() not available."); } return m_Local->GetSegFiltering(); } void CBlastOptions::SetSegFiltering(bool val) { if (m_Local) { m_Local->SetSegFiltering(val); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_SegFiltering, val); } } int CBlastOptions::GetSegFilteringWindow() const { if (! m_Local) { x_Throwx("Error: GetSegFilteringWindow() not available."); } return m_Local->GetSegFilteringWindow(); } void CBlastOptions::SetSegFilteringWindow(int m) { if (m_Local) { m_Local->SetSegFilteringWindow(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_SegFilteringWindow, m); } } double CBlastOptions::GetSegFilteringLocut() const { if (! m_Local) { x_Throwx("Error: GetSegFilteringLocut() not available."); } return m_Local->GetSegFilteringLocut(); } void CBlastOptions::SetSegFilteringLocut(double m) { if (m_Local) { m_Local->SetSegFilteringLocut(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_SegFilteringLocut, m); } } double CBlastOptions::GetSegFilteringHicut() const { if (! m_Local) { x_Throwx("Error: GetSegFilteringHicut() not available."); } return m_Local->GetSegFilteringHicut(); } void CBlastOptions::SetSegFilteringHicut(double m) { if (m_Local) { m_Local->SetSegFilteringHicut(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_SegFilteringHicut, m); } } bool CBlastOptions::GetRepeatFiltering() const { if (! m_Local) { x_Throwx("Error: GetRepeatFiltering() not available."); } return m_Local->GetRepeatFiltering(); } void CBlastOptions::SetRepeatFiltering(bool val) { if (m_Local) { m_Local->SetRepeatFiltering(val); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_RepeatFiltering, val); } } const char* CBlastOptions::GetRepeatFilteringDB() const { if (! m_Local) { x_Throwx("Error: GetRepeatFilteringDB() not available."); } return m_Local->GetRepeatFilteringDB(); } void CBlastOptions::SetRepeatFilteringDB(const char* db) { if (m_Local) { m_Local->SetRepeatFilteringDB(db); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_RepeatFilteringDB, db); } } int CBlastOptions::GetWindowMaskerTaxId() const { if (! m_Local) { x_Throwx("Error: GetWindowMaskerTaxId() not available."); } return m_Local->GetWindowMaskerTaxId(); } void CBlastOptions::SetWindowMaskerTaxId(int value) { if (m_Local) { m_Local->SetWindowMaskerTaxId(value); } if (m_Remote) { if (value) { m_Remote->SetValue(eBlastOpt_WindowMaskerTaxId, value); } else { m_Remote->ResetValue(B4Param_WindowMaskerTaxId); } } } const char * CBlastOptions::GetWindowMaskerDatabase() const { if (! m_Local) { x_Throwx("Error: GetWindowMaskerDatabase() not available."); } return m_Local->GetWindowMaskerDatabase(); } void CBlastOptions::SetWindowMaskerDatabase(const char * value) { if (m_Local) { m_Local->SetWindowMaskerDatabase(value); } if (m_Remote) { if (value) { m_Remote->SetValue(eBlastOpt_WindowMaskerDatabase, value); } else { m_Remote->ResetValue(B4Param_WindowMaskerDatabase); } } } objects::ENa_strand CBlastOptions::GetStrandOption() const { if (! m_Local) { x_Throwx("Error: GetStrandOption() not available."); } return m_Local->GetStrandOption(); } void CBlastOptions::SetStrandOption(objects::ENa_strand s) { if (m_Local) { m_Local->SetStrandOption(s); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_StrandOption, s); } } int CBlastOptions::GetQueryGeneticCode() const { if (! m_Local) { x_Throwx("Error: GetQueryGeneticCode() not available."); } return m_Local->GetQueryGeneticCode(); } void CBlastOptions::SetQueryGeneticCode(int gc) { if (m_Local) { m_Local->SetQueryGeneticCode(gc); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_QueryGeneticCode, gc); } } /******************* Initial word options ***********************/ int CBlastOptions::GetWindowSize() const { if (! m_Local) { x_Throwx("Error: GetWindowSize() not available."); } return m_Local->GetWindowSize(); } void CBlastOptions::SetWindowSize(int w) { if (m_Local) { m_Local->SetWindowSize(w); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_WindowSize, w); } } int CBlastOptions::GetOffDiagonalRange() const { if (! m_Local) { x_Throwx("Error: GetOffDiagonalRange() not available."); } return m_Local->GetOffDiagonalRange(); } void CBlastOptions::SetOffDiagonalRange(int w) { if (m_Local) { m_Local->SetOffDiagonalRange(w); } // N/A for the time being //if (m_Remote) { // m_Remote->SetValue(eBlastOpt_OffDiagonalRange, w); //} } double CBlastOptions::GetXDropoff() const { if (! m_Local) { x_Throwx("Error: GetXDropoff() not available."); } return m_Local->GetXDropoff(); } void CBlastOptions::SetXDropoff(double x) { if (m_Local) { m_Local->SetXDropoff(x); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_XDropoff, x); } } /******************* Gapped extension options *******************/ double CBlastOptions::GetGapXDropoff() const { if (! m_Local) { x_Throwx("Error: GetGapXDropoff() not available."); } return m_Local->GetGapXDropoff(); } void CBlastOptions::SetGapXDropoff(double x) { if (m_Local) { m_Local->SetGapXDropoff(x); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapXDropoff, x); } } double CBlastOptions::GetGapXDropoffFinal() const { if (! m_Local) { x_Throwx("Error: GetGapXDropoffFinal() not available."); } return m_Local->GetGapXDropoffFinal(); } void CBlastOptions::SetGapXDropoffFinal(double x) { if (m_Local) { m_Local->SetGapXDropoffFinal(x); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapXDropoffFinal, x); } } double CBlastOptions::GetGapTrigger() const { if (! m_Local) { x_Throwx("Error: GetGapTrigger() not available."); } return m_Local->GetGapTrigger(); } void CBlastOptions::SetGapTrigger(double g) { if (m_Local) { m_Local->SetGapTrigger(g); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapTrigger, g); } } EBlastPrelimGapExt CBlastOptions::GetGapExtnAlgorithm() const { if (! m_Local) { x_Throwx("Error: GetGapExtnAlgorithm() not available."); } return m_Local->GetGapExtnAlgorithm(); } void CBlastOptions::SetGapExtnAlgorithm(EBlastPrelimGapExt a) { if (m_Local) { m_Local->SetGapExtnAlgorithm(a); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapExtnAlgorithm, a); } } EBlastTbackExt CBlastOptions::GetGapTracebackAlgorithm() const { if (! m_Local) { x_Throwx("Error: GetGapTracebackAlgorithm() not available."); } return m_Local->GetGapTracebackAlgorithm(); } void CBlastOptions::SetGapTracebackAlgorithm(EBlastTbackExt a) { if (m_Local) { m_Local->SetGapTracebackAlgorithm(a); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapTracebackAlgorithm, a); } } ECompoAdjustModes CBlastOptions::GetCompositionBasedStats() const { if (! m_Local) { x_Throwx("Error: GetCompositionBasedStats() not available."); } return m_Local->GetCompositionBasedStats(); } void CBlastOptions::SetCompositionBasedStats(ECompoAdjustModes mode) { if (m_Local) { m_Local->SetCompositionBasedStats(mode); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_CompositionBasedStats, mode); } } bool CBlastOptions::GetSmithWatermanMode() const { if (! m_Local) { x_Throwx("Error: GetSmithWatermanMode() not available."); } return m_Local->GetSmithWatermanMode(); } void CBlastOptions::SetSmithWatermanMode(bool m) { if (m_Local) { m_Local->SetSmithWatermanMode(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_SmithWatermanMode, m); } } int CBlastOptions::GetUnifiedP() const { if (! m_Local) { x_Throwx("Error: GetUnifiedP() not available."); } return m_Local->GetUnifiedP(); } void CBlastOptions::SetUnifiedP(int u) { if (m_Local) { m_Local->SetUnifiedP(u); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_UnifiedP, u); } } /******************* Hit saving options *************************/ int CBlastOptions::GetHitlistSize() const { if (! m_Local) { x_Throwx("Error: GetHitlistSize() not available."); } return m_Local->GetHitlistSize(); } void CBlastOptions::SetHitlistSize(int s) { if (m_Local) { m_Local->SetHitlistSize(s); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_HitlistSize, s); } } int CBlastOptions::GetMaxNumHspPerSequence() const { if (! m_Local) { x_Throwx("Error: GetMaxNumHspPerSequence() not available."); } return m_Local->GetMaxNumHspPerSequence(); } void CBlastOptions::SetMaxNumHspPerSequence(int m) { if (m_Local) { m_Local->SetMaxNumHspPerSequence(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MaxNumHspPerSequence, m); } } int CBlastOptions::GetCullingLimit() const { if (! m_Local) { x_Throwx("Error: GetCullingMode() not available."); } return m_Local->GetCullingLimit(); } void CBlastOptions::SetCullingLimit(int s) { if (m_Local) { m_Local->SetCullingLimit(s); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_CullingLimit, s); } } double CBlastOptions::GetBestHitOverhang() const { if (! m_Local) { x_Throwx("Error: GetBestHitOverhangMode() not available."); } return m_Local->GetBestHitOverhang(); } void CBlastOptions::SetBestHitOverhang(double overhang) { if (m_Local) { m_Local->SetBestHitOverhang(overhang); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_BestHitOverhang, overhang); } } double CBlastOptions::GetBestHitScoreEdge() const { if (! m_Local) { x_Throwx("Error: GetBestHitScoreEdgeMode() not available."); } return m_Local->GetBestHitScoreEdge(); } void CBlastOptions::SetBestHitScoreEdge(double score_edge) { if (m_Local) { m_Local->SetBestHitScoreEdge(score_edge); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_BestHitScoreEdge, score_edge); } } double CBlastOptions::GetEvalueThreshold() const { if (! m_Local) { x_Throwx("Error: GetEvalueThreshold() not available."); } return m_Local->GetEvalueThreshold(); } void CBlastOptions::SetEvalueThreshold(double eval) { if (m_Local) { m_Local->SetEvalueThreshold(eval); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_EvalueThreshold, eval); } } int CBlastOptions::GetCutoffScore() const { if (! m_Local) { x_Throwx("Error: GetCutoffScore() not available."); } return m_Local->GetCutoffScore(); } void CBlastOptions::SetCutoffScore(int s) { if (m_Local) { m_Local->SetCutoffScore(s); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_CutoffScore, s); } } double CBlastOptions::GetPercentIdentity() const { if (! m_Local) { x_Throwx("Error: GetPercentIdentity() not available."); } return m_Local->GetPercentIdentity(); } void CBlastOptions::SetPercentIdentity(double p) { if (m_Local) { m_Local->SetPercentIdentity(p); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_PercentIdentity, p); } } int CBlastOptions::GetMinDiagSeparation() const { if (! m_Local) { x_Throwx("Error: GetMinDiagSeparation() not available."); } return m_Local->GetMinDiagSeparation(); } void CBlastOptions::SetMinDiagSeparation(int d) { if (! m_Local) { x_Throwx("Error: SetMinDiagSeparation() not available."); } m_Local->SetMinDiagSeparation(d); } bool CBlastOptions::GetSumStatisticsMode() const { if (! m_Local) { x_Throwx("Error: GetSumStatisticsMode() not available."); } return m_Local->GetSumStatisticsMode(); } void CBlastOptions::SetSumStatisticsMode(bool m) { if (m_Local) { m_Local->SetSumStatisticsMode(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_SumStatisticsMode, m); } } int CBlastOptions::GetLongestIntronLength() const { if (! m_Local) { x_Throwx("Error: GetLongestIntronLength() not available."); } return m_Local->GetLongestIntronLength(); } void CBlastOptions::SetLongestIntronLength(int l) { if (m_Local) { m_Local->SetLongestIntronLength(l); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_LongestIntronLength, l); } } bool CBlastOptions::GetGappedMode() const { if (! m_Local) { x_Throwx("Error: GetGappedMode() not available."); } return m_Local->GetGappedMode(); } void CBlastOptions::SetGappedMode(bool m) { if (m_Local) { m_Local->SetGappedMode(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GappedMode, m); } } /************************ Scoring options ************************/ const char* CBlastOptions::GetMatrixName() const { if (! m_Local) { x_Throwx("Error: GetMatrixName() not available."); } return m_Local->GetMatrixName(); } void CBlastOptions::SetMatrixName(const char* matrix) { if (m_Local) { m_Local->SetMatrixName(matrix); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MatrixName, matrix); } } int CBlastOptions::GetMatchReward() const { if (! m_Local) { x_Throwx("Error: GetMatchReward() not available."); } return m_Local->GetMatchReward(); } void CBlastOptions::SetMatchReward(int r) { if (m_Local) { m_Local->SetMatchReward(r); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MatchReward, r); } } int CBlastOptions::GetMismatchPenalty() const { if (! m_Local) { x_Throwx("Error: GetMismatchPenalty() not available."); } return m_Local->GetMismatchPenalty(); } void CBlastOptions::SetMismatchPenalty(int p) { if (m_Local) { m_Local->SetMismatchPenalty(p); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_MismatchPenalty, p); } } int CBlastOptions::GetGapOpeningCost() const { if (! m_Local) { x_Throwx("Error: GetGapOpeningCost() not available."); } return m_Local->GetGapOpeningCost(); } void CBlastOptions::SetGapOpeningCost(int g) { if (m_Local) { m_Local->SetGapOpeningCost(g); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapOpeningCost, g); } } int CBlastOptions::GetGapExtensionCost() const { if (! m_Local) { x_Throwx("Error: GetGapExtensionCost() not available."); } return m_Local->GetGapExtensionCost(); } void CBlastOptions::SetGapExtensionCost(int e) { if (m_Local) { m_Local->SetGapExtensionCost(e); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_GapExtensionCost, e); } } int CBlastOptions::GetFrameShiftPenalty() const { if (! m_Local) { x_Throwx("Error: GetFrameShiftPenalty() not available."); } return m_Local->GetFrameShiftPenalty(); } void CBlastOptions::SetFrameShiftPenalty(int p) { if (m_Local) { m_Local->SetFrameShiftPenalty(p); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_FrameShiftPenalty, p); } } bool CBlastOptions::GetOutOfFrameMode() const { if (! m_Local) { x_Throwx("Error: GetOutOfFrameMode() not available."); } return m_Local->GetOutOfFrameMode(); } void CBlastOptions::SetOutOfFrameMode(bool m) { if (m_Local) { m_Local->SetOutOfFrameMode(m); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_OutOfFrameMode, m); } } /******************** Effective Length options *******************/ Int8 CBlastOptions::GetDbLength() const { if (! m_Local) { x_Throwx("Error: GetDbLength() not available."); } return m_Local->GetDbLength(); } void CBlastOptions::SetDbLength(Int8 l) { if (m_Local) { m_Local->SetDbLength(l); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DbLength, l); } } unsigned int CBlastOptions::GetDbSeqNum() const { if (! m_Local) { x_Throwx("Error: GetDbSeqNum() not available."); } return m_Local->GetDbSeqNum(); } void CBlastOptions::SetDbSeqNum(unsigned int n) { if (m_Local) { m_Local->SetDbSeqNum(n); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DbSeqNum, n); } } Int8 CBlastOptions::GetEffectiveSearchSpace() const { if (! m_Local) { x_Throwx("Error: GetEffectiveSearchSpace() not available."); } return m_Local->GetEffectiveSearchSpace(); } void CBlastOptions::SetEffectiveSearchSpace(Int8 eff) { if (m_Local) { m_Local->SetEffectiveSearchSpace(eff); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_EffectiveSearchSpace, eff); } } void CBlastOptions::SetEffectiveSearchSpace(const vector& eff) { if (m_Local) { m_Local->SetEffectiveSearchSpace(eff); } if (m_Remote) { _ASSERT( !eff.empty() ); // This is the best we can do because remote BLAST only accepts one // value for the effective search space m_Remote->SetValue(eBlastOpt_EffectiveSearchSpace, eff.front()); } } int CBlastOptions::GetDbGeneticCode() const { if (! m_Local) { x_Throwx("Error: GetDbGeneticCode() not available."); } return m_Local->GetDbGeneticCode(); } void CBlastOptions::SetDbGeneticCode(int gc) { if (m_Local) { m_Local->SetDbGeneticCode(gc); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_DbGeneticCode, gc); } } const char* CBlastOptions::GetPHIPattern() const { if (! m_Local) { x_Throwx("Error: GetPHIPattern() not available."); } return m_Local->GetPHIPattern(); } void CBlastOptions::SetPHIPattern(const char* pattern, bool is_dna) { if (m_Local) { m_Local->SetPHIPattern(pattern, is_dna); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_PHIPattern, pattern); // For now I will assume this is handled when the data is passed to the // code in blast4_options - i.e. that code will discriminate on the basis // of the type of *OptionHandle that is passed in. // // if (is_dna) { // m_Remote->SetProgram("blastn"); // } else { // m_Remote->SetProgram("blastp"); // } // // m_Remote->SetService("phi"); } } /******************** PSIBlast options *******************/ double CBlastOptions::GetInclusionThreshold() const { if (! m_Local) { x_Throwx("Error: GetInclusionThreshold() not available."); } return m_Local->GetInclusionThreshold(); } void CBlastOptions::SetInclusionThreshold(double u) { if (m_Local) { m_Local->SetInclusionThreshold(u); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_InclusionThreshold, u); } } int CBlastOptions::GetPseudoCount() const { if (! m_Local) { x_Throwx("Error: GetPseudoCount() not available."); } return m_Local->GetPseudoCount(); } void CBlastOptions::SetPseudoCount(int u) { if (m_Local) { m_Local->SetPseudoCount(u); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_PseudoCount, u); } } /// Allows to dump a snapshot of the object void CBlastOptions::DebugDump(CDebugDumpContext ddc, unsigned int depth) const { if (m_Local) { m_Local->DebugDump(ddc, depth); } } void CBlastOptions::DoneDefaults() const { if (m_Remote) { m_Remote->SetDefaultsMode(false); } } // typedef ncbi::objects::CBlast4_queue_search_request TBlast4Req; // CRef GetBlast4Request() const // { // CRef result; // if (m_Remote) { // result = m_Remote->GetBlast4Request(); // } // return result; // } // the "new paradigm" CBlastOptions::TBlast4Opts * CBlastOptions::GetBlast4AlgoOpts() { TBlast4Opts * result = 0; if (m_Remote) { result = m_Remote->GetBlast4AlgoOpts(); } return result; } bool CBlastOptions::GetUseIndex() const { if (! m_Local) { x_Throwx("Error: GetUseIndex() not available."); } return m_Local->GetUseIndex(); } bool CBlastOptions::GetForceIndex() const { if (! m_Local) { x_Throwx("Error: GetForceIndex() not available."); } return m_Local->GetForceIndex(); } bool CBlastOptions::GetMBIndexLoaded() const { if (! m_Local) { x_Throwx("Error: GetMBIndexLoaded() not available."); } return m_Local->GetMBIndexLoaded(); } const string CBlastOptions::GetIndexName() const { if (! m_Local) { x_Throwx("Error: GetIndexName() not available."); } return m_Local->GetIndexName(); } void CBlastOptions::SetUseIndex( bool use_index, const string & index_name, bool force_index ) { if (m_Local) { m_Local->SetUseIndex( use_index, index_name, force_index ); } if (m_Remote) { m_Remote->SetValue(eBlastOpt_ForceMbIndex, force_index); if ( !index_name.empty() ) { m_Remote->SetValue(eBlastOpt_MbIndexName, index_name.c_str()); } } } void CBlastOptions::SetMBIndexLoaded( bool index_loaded ) { if (! m_Local) { x_Throwx("Error: SetMBIndexLoaded() not available."); } m_Local->SetMBIndexLoaded( index_loaded ); } QuerySetUpOptions * CBlastOptions::GetQueryOpts() const { return m_Local ? m_Local->GetQueryOpts() : 0; } LookupTableOptions * CBlastOptions::GetLutOpts() const { return m_Local ? m_Local->GetLutOpts() : 0; } BlastInitialWordOptions * CBlastOptions::GetInitWordOpts() const { return m_Local ? m_Local->GetInitWordOpts() : 0; } BlastExtensionOptions * CBlastOptions::GetExtnOpts() const { return m_Local ? m_Local->GetExtnOpts() : 0; } BlastHitSavingOptions * CBlastOptions::GetHitSaveOpts() const { return m_Local ? m_Local->GetHitSaveOpts() : 0; } PSIBlastOptions * CBlastOptions::GetPSIBlastOpts() const { return m_Local ? m_Local->GetPSIBlastOpts() : 0; } BlastDatabaseOptions * CBlastOptions::GetDbOpts() const { return m_Local ? m_Local->GetDbOpts() : 0; } BlastScoringOptions * CBlastOptions::GetScoringOpts() const { return m_Local ? m_Local->GetScoringOpts() : 0; } BlastEffectiveLengthsOptions * CBlastOptions::GetEffLenOpts() const { return m_Local ? m_Local->GetEffLenOpts() : 0; } void CBlastOptions::x_Throwx(const string& msg) const { NCBI_THROW(CBlastException, eInvalidOptions, msg); } void CBlastOptions::SetDefaultsMode(bool dmode) { if (m_Remote) { m_Remote->SetDefaultsMode(dmode); } } bool CBlastOptions::GetDefaultsMode() const { if (m_Remote) { return m_Remote->GetDefaultsMode(); } else return false; } void CBlastOptions::x_DoDeepCopy(const CBlastOptions& opts) { if (&opts != this) { // Clean up the old object if (m_Local) { delete m_Local; m_Local = 0; } if (m_Remote) { delete m_Remote; m_Remote = 0; } // Copy the contents of the new object if (opts.m_Remote) { m_Remote = new CBlastOptionsRemote(*opts.m_Remote); } if (opts.m_Local) { m_Local = new CBlastOptionsLocal(*opts.m_Local); } m_ProgramName = opts.m_ProgramName; m_ServiceName = opts.m_ServiceName; m_DefaultsMode = opts.m_DefaultsMode; } } /* *********** START ************* */ bool CBlastOptions::GetUseGpu() const { if (! m_Local) { x_Throwx("Error: GetUseGPU() not available."); } return m_Local->GetUseGpu(); } int CBlastOptions::GetNumGpuThreads() const { if (! m_Local) { x_Throwx("Error: GetNumGpuThreads() not available."); } return m_Local->GetNumGpuThreads(); } int CBlastOptions::GetNumGpuBlocks() const { if (! m_Local) { x_Throwx("Error: GetNumGpuBlocks() not available."); } return m_Local->GetNumGpuBlocks(); } int CBlastOptions::GetNumGpuSequences() const { if (! m_Local) { x_Throwx("Error: GetNumGpuSequences() not available."); } return m_Local->GetNumGpuSequences(); } int CBlastOptions::GetGpuMethod() const { if (! m_Local) { x_Throwx("Error: GetGpuMethod() not available."); } return m_Local->GetGpuMethod(); } int CBlastOptions::GetNumCpuThreads() const { if (! m_Local) { x_Throwx("Error: GetNumCpuThreads() not available."); } return m_Local->GetNumCpuThreads(); } void CBlastOptions::SetUseGpu( bool use_gpu ) { if (m_Local) { m_Local->SetUseGpu( use_gpu ); } if (m_Remote) { // } } void CBlastOptions::SetNumGpuThreads( int gpu_num_threads ) { if (m_Local) { m_Local->SetNumGpuThreads( gpu_num_threads ); } if (m_Remote) { // } } void CBlastOptions::SetNumGpuBlocks( int gpu_num_blocks ) { if (m_Local) { m_Local->SetNumGpuBlocks( gpu_num_blocks ); } if (m_Remote) { // } } void CBlastOptions::SetNumGpuSequences( int gpu_num_sequences ) { if (m_Local) { m_Local->SetNumGpuSequences( gpu_num_sequences ); } if (m_Remote) { // } } void CBlastOptions::SetGpuMethod( int gpu_method ) { if (m_Local) { m_Local->SetGpuMethod( gpu_method ); } if (m_Remote) { // } } void CBlastOptions::SetNumCpuThreads( int cpu_num_threads ) { if (m_Local) { m_Local->SetNumCpuThreads( cpu_num_threads ); } if (m_Remote) { // } } /* ********** FINISH ************* */ #endif /* SKIP_DOXYGEN_PROCESSING */ END_SCOPE(blast) END_NCBI_SCOPE /* @} */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_options.hpp0000644000175000017500000006122012001215337024152 0ustar ykeyke/* $Id: blast_options.hpp 171208 2009-09-22 17:46:01Z avagyanv $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file blast_options.hpp * Declares class to encapsulate all BLAST options */ #ifndef ALGO_BLAST_API___BLAST_OPTION__HPP #define ALGO_BLAST_API___BLAST_OPTION__HPP #include #include #include #include #include #include #include #include #include // Forward declarations of classes that need to be declared friend // (mostly unit test classes) class CTracebackTestFixture; class CBlastSetupTestFixture; class CUniformSearchTest; class CTracebackSearchTestFixture; class CBlastTabularFormatThread; BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) class CSeq_loc; END_SCOPE(objects) /** @addtogroup AlgoBlast * * @{ */ BEGIN_SCOPE(blast) //#ifndef SKIP_DOXYGEN_PROCESSING // Forward declarations class CBlastOptionsLocal; class CBlastOptionsRemote; class CBlastOptionsMemento; /// Encapsulates ALL the BLAST algorithm's options. To ensure that the default /// options are set properly, it is recommended that this object is not created /// directly by the calling code, instead, it should be obtained from calling /// CBlastOptionsHandle::[GS]etOptions(). /// @note This class provides accessors and mutators for all BLAST options /// without preventing the caller from setting inconsistent options. /// @sa @ref blast_opts_cookbook class NCBI_XBLAST_EXPORT CBlastOptions : public CObject { public: /// Enumerates the possible contexts in which objects of this type can be /// used enum EAPILocality { /// To be used for running BLAST locally. /// @sa CBl2Seq, CLocalBlast eLocal, /// To be used when running BLAST remotely. /// @sa CRemoteBlast eRemote, eBoth }; /// Constructor which allows specification of local or remote version of /// the options (might change in the future) /// @param locality specification of whether this type will be used with a /// remote or local BLAST search database class CBlastOptions(EAPILocality locality = eLocal); /// Destructor ~CBlastOptions(); /// Explicit deep copy of the Blast options object. /// @return Copy of this Blast options object. CRef Clone() const; /// Return the locality used when the object was created EAPILocality GetLocality() const; /// Validate the options bool Validate() const; /// Accessors/Mutators for individual options /// Returns the task this object is best suited for EProgram GetProgram() const; /// Sets the task this object is best suited for void SetProgram(EProgram p); /// Returns the CORE BLAST notion of program type EBlastProgramType GetProgramType() const; /******************* Lookup table options ***********************/ /// Returns WordThreshold double GetWordThreshold() const; /// Sets WordThreshold /// @param w WordThreshold [in] void SetWordThreshold(double w); #ifndef SKIP_DOXYGEN_PROCESSING ELookupTableType GetLookupTableType() const; void SetLookupTableType(ELookupTableType type); int GetWordSize() const; void SetWordSize(int ws); /// Megablast only lookup table options unsigned char GetMBTemplateLength() const; void SetMBTemplateLength(unsigned char len); unsigned char GetMBTemplateType() const; void SetMBTemplateType(unsigned char type); /******************* Query setup options ************************/ void ClearFilterOptions(); #endif /* SKIP_DOXYGEN_PROCESSING */ /// Return the filtering string used /// @return copy of the filtering options string, caller must free() the /// return value /// @deprecated Do not use this method, instead use the various methods to /// retrieve filtering options /// @sa GetMaskAtHash, GetDustFiltering, GetDustFilteringLevel, /// GetDustFilteringWindow, GetDustFilteringWindow, GetSegFiltering, /// GetSegFilteringWindow, GetSegFilteringLocut, GetSegFilteringHicut /// GetRepeatFiltering, GetRepeatFilteringDB NCBI_DEPRECATED char* GetFilterString() const; #ifndef SKIP_DOXYGEN_PROCESSING NCBI_DEPRECATED void SetFilterString(const char* f, bool clear = true); bool GetMaskAtHash() const; void SetMaskAtHash(bool val = true); bool GetDustFiltering() const; void SetDustFiltering(bool val = true); int GetDustFilteringLevel() const; void SetDustFilteringLevel(int m); int GetDustFilteringWindow() const; void SetDustFilteringWindow(int m); int GetDustFilteringLinker() const; void SetDustFilteringLinker(int m); bool GetSegFiltering() const; void SetSegFiltering(bool val = true); int GetSegFilteringWindow() const; void SetSegFilteringWindow(int m); double GetSegFilteringLocut() const; void SetSegFilteringLocut(double m); double GetSegFilteringHicut() const; void SetSegFilteringHicut(double m); #endif /* SKIP_DOXYGEN_PROCESSING */ /// Returns true if repeat filtering is on bool GetRepeatFiltering() const; /// Turns on repeat filtering using the default repeat database, namely /// kDefaultRepeatFilterDb /// @note Either SetRepeatFiltering or SetRepeatFilteringDB should be /// called, if both are called, only the last one called will take effect void SetRepeatFiltering(bool val = true); /// Returns the name of the repeat filtering database to use const char* GetRepeatFilteringDB() const; /// Sets the repeat filtering database to use /// @note Either SetRepeatFiltering or SetRepeatFilteringDB should be /// called, if both are called, only the last one called will take effect void SetRepeatFilteringDB(const char* db); /// Returns the tax id used for the windowmasker database to use, if set /// via SetWindowMaskerTaxId (otherwise, returns 0) int GetWindowMaskerTaxId() const; /// Sets the tax id to select an appropriate windowmasker database /// Conversion algorithm from tax id to database name is specific to NCBI, /// will not work outside NCBI. /// @note this only runs on machines that have the WINDOW_MASKER_PATH /// configuration value set and have the the correct endianness. If /// windowmasker databases are not available, the filtering will fail /// silently void SetWindowMaskerTaxId(int taxid); /// Return the name of the windowmasker database to use const char* GetWindowMaskerDatabase() const; /// Sets the windowmasker database to use. This must be the name of a /// subdirectory of WINDOW_MASKER_PATH /// @note this only runs on machines that have the WINDOW_MASKER_PATH /// configuration value set and have the the correct endianness. If /// windowmasker databases are not available, the filtering will fail /// silently void SetWindowMaskerDatabase(const char* db); #ifndef SKIP_DOXYGEN_PROCESSING objects::ENa_strand GetStrandOption() const; void SetStrandOption(objects::ENa_strand s); int GetQueryGeneticCode() const; void SetQueryGeneticCode(int gc); /******************* Initial word options ***********************/ int GetWindowSize() const; void SetWindowSize(int w); int GetOffDiagonalRange() const; void SetOffDiagonalRange(int r); double GetXDropoff() const; void SetXDropoff(double x); /******************* Gapped extension options *******************/ double GetGapXDropoff() const; void SetGapXDropoff(double x); double GetGapXDropoffFinal() const; void SetGapXDropoffFinal(double x); double GetGapTrigger() const; void SetGapTrigger(double g); EBlastPrelimGapExt GetGapExtnAlgorithm() const; void SetGapExtnAlgorithm(EBlastPrelimGapExt a); EBlastTbackExt GetGapTracebackAlgorithm() const; void SetGapTracebackAlgorithm(EBlastTbackExt a); ECompoAdjustModes GetCompositionBasedStats() const; void SetCompositionBasedStats(ECompoAdjustModes mode); bool GetSmithWatermanMode() const; void SetSmithWatermanMode(bool m = true); int GetUnifiedP() const; void SetUnifiedP(int u = 0); /******************* Hit saving options *************************/ int GetHitlistSize() const; void SetHitlistSize(int s); int GetMaxNumHspPerSequence() const; void SetMaxNumHspPerSequence(int m); int GetCullingLimit() const; void SetCullingLimit(int s); double GetBestHitOverhang() const; void SetBestHitOverhang(double overhang); double GetBestHitScoreEdge() const; void SetBestHitScoreEdge(double score_edge); // Expect value cut-off threshold for an HSP, or a combined hit if sum // statistics is used double GetEvalueThreshold() const; void SetEvalueThreshold(double eval); // Raw score cutoff threshold int GetCutoffScore() const; void SetCutoffScore(int s); double GetPercentIdentity() const; void SetPercentIdentity(double p); int GetMinDiagSeparation() const; void SetMinDiagSeparation(int d); /// Sum statistics options bool GetSumStatisticsMode() const; void SetSumStatisticsMode(bool m = true); /// for linking HSPs with uneven gaps /// @todo fix this description int GetLongestIntronLength() const; /// for linking HSPs with uneven gaps /// @todo fix this description void SetLongestIntronLength(int l); /// Returns true if gapped BLAST is set, false otherwise bool GetGappedMode() const; void SetGappedMode(bool m = true); /************************ Scoring options ************************/ const char* GetMatrixName() const; void SetMatrixName(const char* matrix); int GetMatchReward() const; void SetMatchReward(int r); int GetMismatchPenalty() const; void SetMismatchPenalty(int p); int GetGapOpeningCost() const; void SetGapOpeningCost(int g); int GetGapExtensionCost() const; void SetGapExtensionCost(int e); int GetFrameShiftPenalty() const; void SetFrameShiftPenalty(int p); bool GetOutOfFrameMode() const; void SetOutOfFrameMode(bool m = true); /******************** Effective Length options *******************/ Int8 GetDbLength() const; void SetDbLength(Int8 l); unsigned int GetDbSeqNum() const; void SetDbSeqNum(unsigned int n); Int8 GetEffectiveSearchSpace() const; void SetEffectiveSearchSpace(Int8 eff); void SetEffectiveSearchSpace(const vector& eff); int GetDbGeneticCode() const; // Set both integer and string genetic code in one call void SetDbGeneticCode(int gc); /// @todo PSI-Blast options could go on their own subclass? const char* GetPHIPattern() const; void SetPHIPattern(const char* pattern, bool is_dna); /******************** PSIBlast options *******************/ double GetInclusionThreshold() const; void SetInclusionThreshold(double u); int GetPseudoCount() const; void SetPseudoCount(int u); /******************** Megablast Database Index *******************/ bool GetUseIndex() const; bool GetForceIndex() const; bool GetMBIndexLoaded() const; const string GetIndexName() const; void SetMBIndexLoaded( bool index_loaded = true ); void SetUseIndex( bool use_index = true, const string & index_name = "", bool force_index = false ); /* *********** START ************* */ /******************** GPU Options *******************/ bool GetUseGpu() const; int GetNumGpuThreads() const; int GetNumGpuBlocks() const; int GetNumGpuSequences() const; int GetGpuMethod() const; int GetNumCpuThreads() const; void SetUseGpu( bool use_gpu ); void SetNumGpuThreads( int gpu_threads ); void SetNumGpuBlocks( int gpu_blocks ); void SetNumGpuSequences( int gpu_num_sequences ); void SetGpuMethod( int gpu_method ); void SetNumCpuThreads( int cpu_threads ); /* ********** FINISH ************* */ /// Allows to dump a snapshot of the object /// @todo this doesn't do anything for locality eRemote void DebugDump(CDebugDumpContext ddc, unsigned int depth) const; void DoneDefaults() const; /// This returns a list of parameters for remote searches. typedef ncbi::objects::CBlast4_parameters TBlast4Opts; TBlast4Opts * GetBlast4AlgoOpts(); bool operator==(const CBlastOptions& rhs) const; bool operator!=(const CBlastOptions& rhs) const; #endif /* SKIP_DOXYGEN_PROCESSING */ /// Set the program and service name for remote blast. void SetRemoteProgramAndService_Blast3(const string & p, const string & s) { m_ProgramName = p; m_ServiceName = s; } /// Get the program and service name for remote blast. virtual void GetRemoteProgramAndService_Blast3(string & p, string & s) const { _ASSERT(m_Remote); p = m_ProgramName; s = m_ServiceName; } /// Create a snapshot of the state of this object for internal use of its /// data structures (BLAST C++ APIs only) const CBlastOptionsMemento* CreateSnapshot() const; /// If this is true, remote options will ignore "Set" calls. void SetDefaultsMode(bool dmode); bool GetDefaultsMode() const; private: /// Prohibit copy c-tor CBlastOptions(const CBlastOptions& bo); /// Prohibit assignment operator CBlastOptions& operator=(const CBlastOptions& bo); // Pointers to local and remote objects CBlastOptionsLocal * m_Local; CBlastOptionsRemote * m_Remote; /// Program Name for Blast3 string m_ProgramName; /// Service Name for Blast3 string m_ServiceName; /// Defaults mode (remote options will ignore Set ops). bool m_DefaultsMode; /// Auxiliary to throw CBlastExceptions /// @param msg message to pass in the exception [in] void x_Throwx(const string& msg) const; /// Returns QuerySetUpOptions for eLocal objects, NULL for eRemote /// @internal QuerySetUpOptions * GetQueryOpts() const; /// Returns LookupTableOptions for eLocal objects, NULL for eRemote LookupTableOptions * GetLutOpts() const; /// Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote BlastInitialWordOptions * GetInitWordOpts() const; /// Returns BlastExtensionOptions for eLocal objects, NULL for eRemote BlastExtensionOptions * GetExtnOpts() const; /// Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote BlastHitSavingOptions * GetHitSaveOpts() const; /// Returns PSIBlastOptions for eLocal objects, NULL for eRemote PSIBlastOptions * GetPSIBlastOpts() const; /// Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote BlastDatabaseOptions * GetDbOpts() const; /// Returns BlastScoringOptions for eLocal objects, NULL for eRemote BlastScoringOptions * GetScoringOpts() const; /// Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for /// eRemote BlastEffectiveLengthsOptions * GetEffLenOpts() const; /// Perform a "deep copy" of Blast options /// @param opts Blast options object to copy from. void x_DoDeepCopy(const CBlastOptions& opts); /// This field is add CAutomaticGenCodeSingleton m_GenCodeSingletonVar; friend class CBl2Seq; friend class CDbBlast; friend class CDbBlastTraceback; friend class CDbBlastPrelim; friend class CEffectiveSearchSpacesMemento; // Tabular formatting thread needs to calculate parameters structures // and hence needs access to individual options structures. friend class ::CBlastTabularFormatThread; /// @todo Strive to remove these classes friend class ::CTracebackTestFixture; // unit test class friend class ::CBlastSetupTestFixture; // unit test class friend class ::CUniformSearchTest; // unit test class friend class ::CTracebackSearchTestFixture; // unit test class }; //#endif /* SKIP_DOXYGEN_PROCESSING */ END_SCOPE(blast) END_NCBI_SCOPE /* @} */ /** @page blast_opts_cookbook C++ BLAST Options Cookbook The purpose of the C++ BLAST options APIs is to provide convenient access to the various algorithm options for a variety of users of BLAST as well as a means to validating the options, while isolating them from the details of the CORE BLAST implementation. Please note that these objects are instantiated with the default options set and these defaults can be queried via the corresponding accessor method(s). @section _basic_opts_usage Basic usage For users who only want to perform a single BLAST searches using default options for a specific task (EProgram) \em without modifying the options, one can let the BLAST search classes create and validate the appropriate BLAST options object internally: @code using ncbi::blast; try { // Task is specified by the eBlastp argument CBl2Seq bl2seq(query, subject, eBlastp); TSeqAlignVector results = bl2seq.Run(); } catch (const CBlastException& e) { // Handle exception ... } @endcode Using the approach above guarantees that the BLAST options will be valid. An alternative to this approach is to use the CBlastOptionsFactory to create a CBlastOptionsHandle object, which allows the caller to set options which are applicable to all variants of BLAST (e.g.: E-value threshold, effective search space, window size). Furthermore, this approach allows the caller to reuse the CBlastOptionsHandle object with multiple BLAST search objects: @code using ncbi::blast; CRef opts_handle(CBlastOptionsFactory::Create(eBlastn)); ... opts_handle.SetEvalueThreshold(1e-20); CBl2Seq bl2seq(query, subjects, opts_handle); ... opts_handle.SetEvalueThreshold(1e-10); CLocalBlast blast(query_factory, opts_handle, seq_src); @endcode @section _validating_opts Options validation The CBlastOptionsHandle classes offers a Validate method in its interface which is called by the BLAST search classes prior to performing the actual search, but users of the C++ BLAST options APIs might also want to invoke this method so that any exceptions thrown by the BLAST search classes can be guaranteed not originate from an incorrect setting of BLAST options. Please note that the Validate method throws a CBlastException in case of failure. @section _intermediate_opts_usage Intermediate options usage For users who want to obtain default options, yet modify the most popular options, one should create instances of derived classes of the CBlastOptionsHandle, because these should expose an interface that is relevant to the task at hand (although not an exhaustive interface, for that see @ref _advanced_opts_usage): @code using ncbi::blast; CBlastNucleotideOptionsHandle opts_handle; opts_handle.SetTraditionalBlastnDefaults(); opts_handle.SetStrandOption(objects::eNa_strand_plus); CBl2Seq bl2seq(query, subject, opts_handle); TSeqAlignVector results = bl2seq.Run(); @endcode By using this interface, the likelihood of setting invalid options is reduced, but the validity of the options cannot be fully guaranteed. @note BLAST help desk and developers reserve the right to determine which options are popular. @section _advanced_opts_usage Advanced options usage For users who want to have full control over setting the algorithm's options, or whose options of interest are not available in any of the classes in the CBlastOptionsHandle hierarchy, the GetOptions and SetOptions methods of the CBlastOptionsHandle hierarchy allow access to the CBlastOptions class, the lowest level class in the C++ BLAST options API which contains all options available to all variants of the BLAST algorithm. No guarantees about the validity of the options are made if this interface is used, therefore invoking Validate is \em strongly recommended. @code using ncbi::blast; try { CBlastProteinOptionsHandle opts_handle; opts_handle.SetMatrixName("PAM30"); opts_handle.SetGapOpeningCost(9); opts_handle.SetGapExtensionCost(1); opts_handle.SetOptions().SetCompositionBasedStats(eCompositionBasedStats); opts_handle.Validate(); CBl2Seq bl2seq(query, subject, opts_handle); TSeqAlignVector results = bl2seq.Run(); } catch (const CBlastException& e) { // Handle exception ... } @endcode @sa @ref blast_opts_cpp_design. @author Christiam Camacho */ /** @page blast_opts_cpp_design C++ BLAST Options Design @section _blast_opts_cpp_goals Design goals - Isolate C++ toolkit users from details of CORE BLAST - Allow easy setting of default options for common tasks for which BLAST is used - Expose in an interface only those options that are relevant to the task at hand - Provide a means of validating BLAST options - Allow 'power' users to have unrestricted access to all BLAST options - Design should be flexible to accomodate introduction/removal of options @section Components - CBlastOptionsFactory: This class offers a single static method to create CBlastOptionsHandle subclasses so that options that are applicable to all variants of BLAST can be inspected or modified. The actual type of the CBlastOptionsHandle returned by Create is determined by its EProgram argument. The return value of this function is guaranteed to have reasonable defaults set for the selected task. - CBlastOptionsHandle hierarchy: The intent of this class is to encapsulate options that are common to all variants of BLAST, from which more specific tasks can inherit the common options. The subclasses of CBlastOptionsHandle should present an interface that is more specific, i.e.: only contain options relevant to the task at hand, although it might not be an exhaustive interface for all options available for the task. Please note that the initialization of this class' data members follows the template method design pattern, and this should be followed by subclasses also. - CBlastOptions: This class contains all available BLAST options and it is provided to satisfy the design goal of allowing qualified users unrestricted access to all BLAST options. Because of this, it is very easy to set incorrect options, and hence it should be use sparingly. The use of its Validate method is strongly recommended. @section _blast_opts_cpp_deficiencies Known deficiencies The current design in noticeably weak in fulfilling the last design goal, in that it uses an inheritance hierarchy of CBlastOptionsHandle classes to provide specific interfaces for tasks, but this approach is breaks when an option is applicable to a parent class and not its child. Furthermore, the EProgram enumeration is misnamed, as it should convey the notion of a task, similar to those exposed in the BLAST web page. @section _blast_opts_cpp_future Future plans A redesign of the C++ BLAST options API might be available in the future to overcome the deficiencies of the current APIs. Additional design goals include: - Consistent local/remote behavior - Provide distinction between algorithm options and application options - Provide well defined guarantees about the validity of BLAST options - Easy to use correctly, difficult to use incorrectly @author Christiam Camacho */ #endif /* ALGO_BLAST_API___BLAST_OPTION__HPP */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_options.h0000644000175000017500000013333312001215337023617 0ustar ykeyke/* $Id: blast_options.h 217124 2010-12-14 16:46:24Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Tom Madden * */ /** @file blast_options.h * The structures and functions in blast_options.[ch] should be used to specify * user preferences. The options structures should not be changed by the BLAST code * but rather be read to determine user preferences. When possible these structures * should be passed in as "const". */ #ifndef __BLASTOPTIONS__ #define __BLASTOPTIONS__ #include #include #include #include #include #ifdef __cplusplus extern "C" { #endif /** Some default values (used when creating blast options block and for * command-line program defaults. When changing these defaults, please * remember to update the defaults in the command-line programs */ /** "window" between hits to trigger an extension. */ #define BLAST_WINDOW_SIZE_PROT 40 /**< default window (all protein searches) */ #define BLAST_WINDOW_SIZE_NUCL 0 /**< default window size (blastn) */ #define BLAST_WINDOW_SIZE_MEGABLAST 0 /**< default window size (contiguous megablast) */ #define BLAST_WINDOW_SIZE_DISC 40 /**< default window size (discontiguous megablast) */ #define BLAST_SCAN_RANGE_NUCL 0 /**< default scan range (blastn) */ /** length of word to trigger an extension. */ #define BLAST_WORDSIZE_PROT 3 /**< default word size (all protein searches) */ #define BLAST_WORDSIZE_NUCL 11 /**< default word size (blastn) */ #define BLAST_WORDSIZE_MEGABLAST 28 /**< default word size (contiguous megablast; for discontig megablast the word size is explicitly overridden) */ /** Default matrix name: BLOSUM62 */ #define BLAST_DEFAULT_MATRIX "BLOSUM62" /** Protein gap costs are the defaults for the BLOSUM62 scoring matrix. * More gap costs are listed in BLASTOptionSetGapParams */ /** cost for the existence of a gap.*/ #define BLAST_GAP_OPEN_PROT 11 /**< default gap open penalty (all protein searches) */ #define BLAST_GAP_OPEN_NUCL 5 /**< default gap open penalty (blastn) */ #define BLAST_GAP_OPEN_MEGABLAST 0 /**< default gap open penalty (megablast with greedy gapped alignment) */ /** cost to extend a gap. */ #define BLAST_GAP_EXTN_PROT 1 /**< default gap open penalty (all protein searches) */ #define BLAST_GAP_EXTN_NUCL 2 /**< default gap open penalty (blastn) */ #define BLAST_GAP_EXTN_MEGABLAST 0 /**< default gap open penalty (megablast) with greedy gapped alignment) */ /** neighboring word score thresholds; a threshold of zero * means that only query and subject words that match exactly * will go into the BLAST lookup table when it is generated */ #define BLAST_WORD_THRESHOLD_BLASTP 11 /**< default neighboring threshold (blastp and for rpsblast at RPS-BLAST database creation time) */ #define BLAST_WORD_THRESHOLD_BLASTN 0 /**< default threshold (blastn) */ #define BLAST_WORD_THRESHOLD_BLASTX 12 /**< default threshold (blastx) */ #define BLAST_WORD_THRESHOLD_TBLASTN 13 /**< default neighboring threshold (tblastn/rpstblastn) */ #define BLAST_WORD_THRESHOLD_TBLASTX 13 /**< default threshold (tblastx) */ #define BLAST_WORD_THRESHOLD_MEGABLAST 0 /**< default threshold (megablast) */ /** default dropoff for ungapped extension; ungapped extensions * will stop when the score for the extension has dropped from * the current best score by at least this much */ #define BLAST_UNGAPPED_X_DROPOFF_PROT 7 /**< ungapped dropoff score for all searches except blastn */ #define BLAST_UNGAPPED_X_DROPOFF_NUCL 20 /**< ungapped dropoff score for blastn (and megablast) */ /** default dropoff for preliminary gapped extensions */ #define BLAST_GAP_X_DROPOFF_PROT 15 /**< default dropoff (all protein- based gapped extensions) */ #define BLAST_GAP_X_DROPOFF_NUCL 30 /**< default dropoff for non-greedy nucleotide gapped extensions */ #define BLAST_GAP_X_DROPOFF_GREEDY 25 /**< default dropoff for greedy nucleotide gapped extensions */ #define BLAST_GAP_X_DROPOFF_TBLASTX 0 /**< default dropoff for tblastx */ /** default bit score that will trigger gapped extension */ #define BLAST_GAP_TRIGGER_PROT 22.0 /**< default bit score that will trigger a gapped extension for all protein- based searches */ #define BLAST_GAP_TRIGGER_NUCL 25.0 /**< default bit score that will trigger a gapped extension for blastn */ /** default dropoff for the final gapped extension with traceback */ #define BLAST_GAP_X_DROPOFF_FINAL_PROT 25 /**< default dropoff (all protein- based gapped extensions) */ #define BLAST_GAP_X_DROPOFF_FINAL_NUCL 100 /**< default dropoff for nucleotide gapped extensions) */ #define BLAST_GAP_X_DROPOFF_FINAL_TBLASTX 0 /**< default dropoff for tblastx */ /** default reward and penalty (only applies to blastn/megablast) */ #define BLAST_PENALTY -3 /**< default nucleotide mismatch score */ #define BLAST_REWARD 1 /**< default nucleotide match score */ /** Default parameters for saving hits */ #define BLAST_EXPECT_VALUE 10.0 /**< by default, alignments whose expect value exceeds this number are discarded */ #define BLAST_HITLIST_SIZE 500 /**< Number of database sequences to save hits for */ /** Defaults for PSI-BLAST options */ #define PSI_INCLUSION_ETHRESH 0.002 /**< Inclusion threshold for PSI BLAST */ #define PSI_PSEUDO_COUNT_CONST 0 /**< Pseudo-count constant for PSI-BLAST */ /** Default genetic code for query and/or database */ #define BLAST_GENETIC_CODE 1 /**< Use the standard genetic code for converting groups of three nucleotide bases to protein letters */ /** Value used to indicate that no IMPALA-style scaling should be performed * when scaling a PSSM */ extern const double kPSSM_NoImpalaScaling; /** Types of the lookup table */ typedef enum { eMBLookupTable, /**< megablast lookup table (includes both contiguous and discontiguous megablast) */ eSmallNaLookupTable, /**< lookup table for blastn with small query*/ eNaLookupTable, /**< blastn lookup table */ eAaLookupTable, /**< standard protein (blastp) lookup table */ eCompressedAaLookupTable, /**< compressed alphabet (blastp) lookup table */ ePhiLookupTable, /**< protein lookup table specialized for phi-blast */ ePhiNaLookupTable, /**< nucleotide lookup table for phi-blast */ eRPSLookupTable, /**< RPS lookup table (rpsblast and rpstblastn) */ eIndexedMBLookupTable /**< use database index as a lookup structure */ } ELookupTableType; /** Options needed to construct a lookup table * Also needed: query sequence and query length. */ typedef struct LookupTableOptions { double threshold; /**< Score threshold for putting words in a lookup table (fractional values are allowed, and could be important if there is scaling involved) */ ELookupTableType lut_type; /**< What kind of lookup table to construct? */ Int4 word_size; /**< Determines the size of the lookup table */ Int4 mb_template_length; /**< Length of the discontiguous words */ Int4 mb_template_type; /**< Type of a discontiguous word template */ char* phi_pattern; /**< PHI-BLAST pattern */ EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */ } LookupTableOptions; /** Options for dust algorithm, applies only to nucl.-nucl. comparisons. * value of less than zero means default value will be applied. */ typedef struct SDustOptions { int level; int window; int linker; /**< min distance to link segments. */ } SDustOptions; /** Options for SEG algorithm, applies only to protein-protein comparisons. * value of less than zero means default value will be applied. */ typedef struct SSegOptions { int window; /**< initial window to trigger further work. */ double locut; double hicut; } SSegOptions; /// Default value for repeats database filtering #define kDefaultRepeatFilterDb "repeat/repeat_9606" /** Filtering options for organsim specific repeats filtering. Currently this consist of only the db name but could be expanded in the future to include other types of filtering or other options. */ typedef struct SRepeatFilterOptions { char* database; /**< Nucleotide database for mini BLAST search. */ } SRepeatFilterOptions; /** Filtering options for organism-specific filtering with Window Masker. The taxid and filename are alternative means of choosing which Window Masker database to use. */ typedef struct SWindowMaskerOptions { int taxid; /**< Select masking database for this TaxID. */ const char * database; /**< Use winmasker database at this location. */ } SWindowMaskerOptions; /** All filtering options */ typedef struct SBlastFilterOptions { Boolean mask_at_hash; /**< mask query only for lookup table creation */ SDustOptions* dustOptions; /**< low-complexity filtering for nucleotides. */ SSegOptions* segOptions; /**< low-complexity filtering for proteins sequences (includes translated nucleotides). */ SRepeatFilterOptions* repeatFilterOptions; /**< for organism specific repeat filtering. */ SWindowMaskerOptions* windowMaskerOptions; /**< organism specific filtering with window masker. */ } SBlastFilterOptions; /** Options required for setting up the query sequence */ typedef struct QuerySetUpOptions { SBlastFilterOptions* filtering_options; /**< structured options for all filtering offered from algo/blast/core for BLAST. */ char* filter_string; /**< DEPRECATED, filtering options above. */ Uint1 strand_option; /**< In blastn: which strand to search: 1 = forward; 2 = reverse; 3 = both */ Int4 genetic_code; /**< Genetic code to use for translation, [t]blastx only */ } QuerySetUpOptions; /** Options needed for initial word finding and processing */ typedef struct BlastInitialWordOptions { double gap_trigger; /**< Score in bits for starting gapped extension */ Int4 window_size; /**< Maximal allowed distance between 2 hits in case 2 hits are required to trigger the extension */ Int4 scan_range; /**< Maximal number of gaps allowed between 2 hits */ double x_dropoff; /**< X-dropoff value (in bits) for the ungapped extension */ EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */ } BlastInitialWordOptions; /** The algorithm to be used for preliminary * gapped extensions */ typedef enum EBlastPrelimGapExt { eDynProgScoreOnly, /**< standard affine gapping */ eGreedyScoreOnly, /**< Greedy extension (megaBlast) */ eSmithWatermanScoreOnly /**< Score-only smith-waterman */ } EBlastPrelimGapExt; /** The algorithm to be used for final gapped * extensions with traceback */ typedef enum EBlastTbackExt { eDynProgTbck, /**< standard affine gapping */ eGreedyTbck, /**< Greedy extension (megaBlast) */ eSmithWatermanTbck, /**< Smith-waterman finds optimal scores, then ALIGN_EX to find alignment. */ eSmithWatermanTbckFull /**< Smith-waterman to find all alignments */ } EBlastTbackExt; /** Options used for gapped extension * These include: * a. Penalties for various types of gapping; * b. Drop-off values for the extension algorithms tree exploration; * c. Parameters identifying what kind of extension algorithm(s) should * be used. */ typedef struct BlastExtensionOptions { double gap_x_dropoff; /**< X-dropoff value for gapped extension (in bits) */ double gap_x_dropoff_final;/**< X-dropoff value for the final gapped extension (in bits) */ EBlastPrelimGapExt ePrelimGapExt; /**< type of preliminary gapped extension (normally) for calculating score. */ EBlastTbackExt eTbackExt; /**< type of traceback extension. */ Int4 compositionBasedStats; /**< mode of compositional adjustment to use; if zero then compositional adjustment is not used */ Int4 unifiedP; /**< Indicates unified P values to be used in blastp or tblastn */ EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */ } BlastExtensionOptions; /** Options for the Best Hit HSP collection algorithm */ typedef struct BlastHSPBestHitOptions { double overhang; double score_edge; } BlastHSPBestHitOptions; /** Options for the HSP culling algorithm */ typedef struct BlastHSPCullingOptions { int max_hits; /**< Maximum number of hits per area of query. */ } BlastHSPCullingOptions; /** Structure containing the HSP filtering/writing options */ typedef struct BlastHSPFilteringOptions { /** Best Hit algorithm */ BlastHSPBestHitOptions* best_hit; EBlastStage best_hit_stage; /*<< when to apply the best hit algorithm */ /** culling algorithm */ BlastHSPCullingOptions* culling_opts; EBlastStage culling_stage; /*<< when to apply the culling algorithm */ } BlastHSPFilteringOptions; /** Options used when evaluating and saving hits * These include: * a. Restrictions on the number of hits to be saved; * b. Restrictions on the quality and positions of hits to be saved; * c. Parameters used to evaluate the quality of hits. */ typedef struct BlastHitSavingOptions { double expect_value; /**< The expect value cut-off threshold for an HSP, or a combined hit if sum statistics is used */ Int4 cutoff_score; /**< The (raw) score cut-off threshold */ double percent_identity; /**< The percent identity cut-off threshold */ Int4 hitlist_size;/**< Maximal number of database sequences to return results for */ Int4 hsp_num_max; /**< Maximal number of HSPs to save for one database sequence */ Int4 total_hsp_limit; /**< Maximal total number of HSPs to keep */ Int4 culling_limit; /**< If the query range of an HSP is contained in at least this many higher-scoring HSPs, throw away the HSP as redundant (turned off if zero) */ /********************************************************************/ /* Merge all these in a structure for clarity? */ Boolean do_sum_stats; /**< Force sum statistics to be used to combine HSPs, TRUE by default for all ungapped searches and translated gapped searches (except RPS-BLAST) */ Int4 longest_intron; /**< The longest distance between HSPs allowed for combining via sum statistics with uneven gaps */ /********************************************************************/ Int4 min_hit_length; /**< optional minimum alignment length; alignments not at least this long are discarded */ Int4 min_diag_separation; /**< How many diagonals separate a hit from a substantial alignment before it's not blocked out. Must be > 0 to be used. */ EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */ /** Contains options to configure the HSP filtering/writering structures * If not set, the default HSP filtering strategy is used. */ BlastHSPFilteringOptions* hsp_filt_opt; } BlastHitSavingOptions; /** Scoring options block * Used to produce the BlastScoreBlk structure * This structure may be needed for lookup table construction (proteins only), * and for evaluating alignments. */ typedef struct BlastScoringOptions { char* matrix; /**< Name of the matrix containing all scores: needed for finding neighboring words */ char* matrix_path; /**< Directory path to where matrices are stored. */ Int2 reward; /**< Reward for a match */ Int2 penalty; /**< Penalty for a mismatch */ Boolean gapped_calculation; /**< gap-free search if FALSE */ Int4 gap_open; /**< Extra penalty for starting a gap */ Int4 gap_extend; /**< Penalty for each gap residue */ /* only blastx and tblastn (When query & subj are diff) */ Boolean is_ooframe; /**< Should out-of-frame gapping be used in a translated search? */ Int4 shift_pen; /**< Penalty for shifting a frame in out-of-frame gapping */ EBlastProgramType program_number; /**< indicates blastn, blastp, etc. */ } BlastScoringOptions; /** Options for setting up effective lengths and search spaces. * The values are those the user has specified to override the real sizes. */ typedef struct BlastEffectiveLengthsOptions { Int8 db_length; /**< Database length to be used for statistical calculations */ Int4 dbseq_num; /**< Number of database sequences to be used for statistical calculations */ Int4 num_searchspaces; /**< Number of elements in searchsp_eff, this must be equal to the number of contexts in the search */ Int8 *searchsp_eff; /**< Search space to be used for statistical calculations (one such per query context) */ } BlastEffectiveLengthsOptions; /** Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) * Some of these possibly should be transfered elsewhere */ typedef struct PSIBlastOptions { /** Pseudocount constant. Needed for the computing the PSSM residue * frequencies */ Int4 pseudo_count; /*** The following options are used at the API layer to specify how the * multiple sequence alignment is built from pairwise alignments. These * could go in their own structure in the future. */ /** Minimum evalue for inclusion in PSSM calculation. Needed for the * conversion of Seq-align into a multiple sequence alignment and for * composition based statistics */ double inclusion_ethresh; /** If set to TRUE, use the best alignment when multiple HSPs are found * in a query-subject alignment (i.e.: HSP with the lowest e-value), else * use all HSPs in a query-subject alignment. This option does not apply to * the PSSM engine, it applies to the processing of pairwise sequence * alignments to build a multiple sequence alignment structure * @sa CPsiBlastInputData (to be implemented) */ Boolean use_best_alignment; /** Compatibility option for the NCBI's structure group (note * nsg_ prefix, stands for NCBI's structure group). When set to true, the * PSSM engine will function in the same way the C toolkit PSSM engine did * in the structure group's cddumper application. This option should be * set to FALSE by default as it enables the following behavior in the * PSSM engine: * 
     * 1) Ignores the query sequence (on certain stages of PSSM creation only)
     * 2) Skips validation of multiple sequence alignment data
     * 3) Disables assertions and validation in _PSICheckSequenceWeights
     * 4) If no aligned sequences are provided in the multiple sequence
     * alignment, NULL PSSM frequency ratios are returned and the PSSM is built
     * based on the underlying substitution matrix.
     *
* Do not set this to TRUE unless you know what you are doing. */ Boolean nsg_compatibility_mode; /** Scaling factor as used in IMPALA to do the matrix rescaling. Default * value of 1.0 means not to use it. Makemat/formatrpsdb set this value to * 100 by default, Kappa_RedoAlignmentCore uses 32. Provided so that the * NCBI structure group can create scaled PSSMs as the output of the PSSM * engine. Do not change this unless you know what you are doing. */ double impala_scaling_factor; /** This turns off a validation for the multiple sequence alignment in the * PSSM engine for unaligned positions. Needed when a multiple sequence * alignment is provided on the command line (e.g.: -in_msa option). */ Boolean ignore_unaligned_positions; } PSIBlastOptions; /* *********** START ************* */ /** Options used by GPU BLAST */ typedef struct BlastGPUOptions { char use_gpu; int num_blocksx; int num_threadsx; int num_sequences_to; int method; int cpu_threads; } BlastGPUOptions; /* ********** FINISH ************* */ /** Options used to create the ReadDBFILE structure * Include database name and various information for restricting the database * to a subset. */ typedef struct BlastDatabaseOptions { Int4 genetic_code; /**< Genetic code to use for translation, tblast[nx] only */ } BlastDatabaseOptions; /******************************************************************************** Functions to create options blocks with default values and free them after use. *********************************************************************************/ /** Frees SDustOptions. * @param dust_options object to free * @return NULL pointer */ NCBI_XBLAST_EXPORT SDustOptions* SDustOptionsFree(SDustOptions* dust_options); /** Allocates memory for SDustOptions, fills in defaults. * @param dust_options options that are being returned [in|out] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SDustOptionsNew(SDustOptions* *dust_options); /** Frees SSegOptions. * @param seg_options object to free [in] * @return NULL pointer */ NCBI_XBLAST_EXPORT SSegOptions* SSegOptionsFree(SSegOptions* seg_options); /** Allocates memory for SSegOptions, fills in defaults. [in|out] * @param seg_options options that are being returned [in|out] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SSegOptionsNew(SSegOptions* *seg_options); /** Resets name of db for repeat filtering. * @param repeat_options already allocated options constaining field to be reset [in|out] * @param dbname name of the database(s) [in] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SRepeatFilterOptionsResetDB(SRepeatFilterOptions* *repeat_options, const char* dbname); /** Resets name of db for window masker filtering. * @param winmask_options options block constaining field to be reset [in|out] * @param dbname name of the database(s) [in] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SWindowMaskerOptionsResetDB(SWindowMaskerOptions ** winmask_options, const char * dbname); /** Frees SRepeatFilterOptions. * @param repeat_options object to free [in] * @return NULL pointer */ NCBI_XBLAST_EXPORT SRepeatFilterOptions* SRepeatFilterOptionsFree(SRepeatFilterOptions* repeat_options); /** Frees SWindowMaskerOptions. * @param winmask_options object to free [in] * @return NULL pointer */ NCBI_XBLAST_EXPORT SWindowMaskerOptions* SWindowMaskerOptionsFree(SWindowMaskerOptions * winmask_options); /** Allocates memory for SRepeatFilterOptions, fills in defaults. * @param repeat_options options that are being returned [in|out] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SRepeatFilterOptionsNew(SRepeatFilterOptions ** repeat_options); /** Allocates memory for SWindowMaskerOptions, fills in defaults. * @param winmask_options options that are being returned [in|out] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SWindowMaskerOptionsNew(SWindowMaskerOptions ** winmask_options); /** Frees SBlastFilterOptions and all subservient structures. * @param filter_options object to free * @return NULL pointer */ NCBI_XBLAST_EXPORT SBlastFilterOptions* SBlastFilterOptionsFree(SBlastFilterOptions* filter_options); /** Merges two sets of options together, taking the non-default one as preferred. if * both are non-default then one or the other is taken. * @param combined object that is returned [in|out] * @param opt1 first set of options [in] * @param opt2 second set of options [in] * @return zero on success. */ NCBI_XBLAST_EXPORT Int2 SBlastFilterOptionsMerge(SBlastFilterOptions** combined, const SBlastFilterOptions* opt1, const SBlastFilterOptions* opt2); /** Types of filtering options. */ typedef enum EFilterOptions { eSeg, /**< low-complexity for proteins. */ eDust, /**< low-complexity for nucleotides. */ eRepeats, /**< Repeat filtering for nucleotides. */ eDustRepeats, /**< Repeat and dust filtering for nucleotides. */ eEmpty /**< no filtering at all. */ } EFilterOptions; /** Allocates memory for SBlastFilterOptions and * @param filter_options options that are being returned [in|out] * @param type specify either dust or seg (now) with EFilterOptions [in] * @return zero on sucess */ NCBI_XBLAST_EXPORT Int2 SBlastFilterOptionsNew(SBlastFilterOptions* *filter_options, EFilterOptions type); /** Queries whether no masking is required * @param filter_options the object to be queried [in] * @return TRUE if no filtering is required or argument is NULL, FALSE * otherwise */ NCBI_XBLAST_EXPORT Boolean SBlastFilterOptionsNoFiltering(const SBlastFilterOptions* filter_options); /** Queries whether masking should be done only for the lookup table or for the entire search. * @param filter_options the object to be queried [in] * @return TRUE or FALSE, FALSE if filter_options is NULL. */ NCBI_XBLAST_EXPORT Boolean SBlastFilterOptionsMaskAtHash(const SBlastFilterOptions* filter_options); /** Validates filter options to ensure that program and options are consistent * and that options have valid values. * @param program_number Program number (blastn, blastp, etc.) [in] * @param filter_options options to add to [in] * @param blast_message error or warning (optional) [out] * @return zero on success */ NCBI_XBLAST_EXPORT Int2 SBlastFilterOptionsValidate(EBlastProgramType program_number, const SBlastFilterOptions* filter_options, Blast_Message* *blast_message); /** Deallocate memory for QuerySetUpOptions. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT QuerySetUpOptions* BlastQuerySetUpOptionsFree(QuerySetUpOptions* options); /** Allocate memory for QuerySetUpOptions and fill with default values. * @param options The options that have are being returned [out] */ NCBI_XBLAST_EXPORT Int2 BlastQuerySetUpOptionsNew(QuerySetUpOptions* *options); /** Fill non-default contents of the QuerySetUpOptions. * @param options The options structure [in] [out] * @param program Program number (blastn, blastp, etc.) [in] * @param filter_string Parsable string of filtering options [in] * @param strand_option which strand to search [in] */ NCBI_XBLAST_EXPORT Int2 BLAST_FillQuerySetUpOptions(QuerySetUpOptions* options, EBlastProgramType program, const char *filter_string, Uint1 strand_option); /** Deallocate memory for BlastInitialWordOptions. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT BlastInitialWordOptions* BlastInitialWordOptionsFree(BlastInitialWordOptions* options); /** Allocate memory for BlastInitialWordOptions and fill with default values. * @param program Program number (blastn, blastp, etc.) [in] * @param options The options that have are being returned [out] */ NCBI_XBLAST_EXPORT Int2 BlastInitialWordOptionsNew(EBlastProgramType program, BlastInitialWordOptions* *options); /** Validate correctness of the initial word options. * @param program_number Type of BLAST program [in] * @param options Initial word options [in] * @param blast_msg Describes any validation problems found [out] * @return Validation status */ NCBI_XBLAST_EXPORT Int2 BlastInitialWordOptionsValidate(EBlastProgramType program_number, const BlastInitialWordOptions* options, Blast_Message* *blast_msg); /** Fill non-default values in the BlastInitialWordOptions structure. * @param options The options structure [in] [out] * @param program Program number (blastn, blastp, etc.) [in] * @param window_size Size of a largest window between 2 words for the two-hit * version [in] * @param xdrop_ungapped The value of the X-dropoff for ungapped extensions [in] */ NCBI_XBLAST_EXPORT Int2 BLAST_FillInitialWordOptions(BlastInitialWordOptions* options, EBlastProgramType program, Int4 window_size, double xdrop_ungapped); /** Deallocate memory for BlastExtensionOptions. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT BlastExtensionOptions* BlastExtensionOptionsFree(BlastExtensionOptions* options); /** Allocate memory for BlastExtensionOptions and fill with default values. * @param program Program number (blastn, blastp, etc.) [in] * @param options The options that are being returned [out] * @param gapped The search is gapped [in] */ NCBI_XBLAST_EXPORT Int2 BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions* *options, Boolean gapped); /** Fill non-default values in the BlastExtensionOptions structure. * @param options The options structure [in] [out] * @param program Program number (blastn, blastp, etc.) [in] * @param greedy In how many stages of the search greedy alignment is * used (values 0, 1, 2)? FIXME [in] * @param x_dropoff X-dropoff parameter value for preliminary gapped * extensions [in] * @param x_dropoff_final X-dropoff parameter value for final gapped * extensions with traceback [in] * @todo the greedy parameter to this function is tied to the blast_driver's * command line argument for greedy... couldn't this be EBlastPrelimGapExt? */ NCBI_XBLAST_EXPORT Int2 BLAST_FillExtensionOptions(BlastExtensionOptions* options, EBlastProgramType program, Int4 greedy, double x_dropoff, double x_dropoff_final); /** Validate contents of BlastExtensionOptions. * @param program_number Type of BLAST program [in] * @param options Options to be validated [in] * @param blast_msg Describes any validation problems found [out] */ NCBI_XBLAST_EXPORT Int2 BlastExtensionOptionsValidate(EBlastProgramType program_number, const BlastExtensionOptions* options, Blast_Message* *blast_msg); /** Deallocate memory for BlastScoringOptions. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT BlastScoringOptions* BlastScoringOptionsFree(BlastScoringOptions* options); /** Allocate memory for BlastScoringOptions and fill with default values. * @param program Program number (blastn, blastp, etc.) [in] * @param options The options that are being returned [out] */ NCBI_XBLAST_EXPORT Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions* *options); /** Fill non-default values in the BlastScoringOptions structure. * @param options The options structure [in] [out] * @param program Program number (blastn, blastp, etc.) [in] * @param greedy_extension Is greedy extension algorithm used? [in] * @param penalty Mismatch penalty score (blastn only) [in] * @param reward Match reward score (blastn only) [in] * @param matrix Name of the BLAST matrix (all except blastn) [in] * @param gap_open Extra cost for opening a gap [in] * @param gap_extend Cost of a gap [in] */ NCBI_XBLAST_EXPORT Int2 BLAST_FillScoringOptions(BlastScoringOptions* options, EBlastProgramType program, Boolean greedy_extension, Int4 penalty, Int4 reward, const char *matrix, Int4 gap_open, Int4 gap_extend); /** Validate contents of BlastScoringOptions. * @param program_number Type of BLAST program [in] * @param options Options to be validated [in] * @param blast_msg Describes any validation problems found [out] */ NCBI_XBLAST_EXPORT Int2 BlastScoringOptionsValidate(EBlastProgramType program_number, const BlastScoringOptions* options, Blast_Message* *blast_msg); /** Produces copy of "old" options, with new memory allocated. * @param new_opt Contains copied BlastScoringOptions upon return [out] * @param old_opt BlastScoringOptions to be copied [in] */ NCBI_XBLAST_EXPORT Int2 BlastScoringOptionsDup(BlastScoringOptions* *new_opt, const BlastScoringOptions* old_opt); /** Resets matrix name option. Automatically converts the name to upper case. * @param opts Options structure to update. [in] [out] * @param matrix_name New matrix name. If NULL, old matrix name is left * as is. [in] */ NCBI_XBLAST_EXPORT Int2 BlastScoringOptionsSetMatrix(BlastScoringOptions* opts, const char* matrix_name); /** Deallocate memory for BlastEffectiveLengthsOptions*. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT BlastEffectiveLengthsOptions* BlastEffectiveLengthsOptionsFree(BlastEffectiveLengthsOptions* options); /** Allocate memory for BlastEffectiveLengthsOptions* and fill with * default values. * @param options The options that are being returned [out] */ NCBI_XBLAST_EXPORT Int2 BlastEffectiveLengthsOptionsNew(BlastEffectiveLengthsOptions* *options); /** Return true if the search spaces is set for any of the queries in the * search * @param options The options to examine [in] */ NCBI_XBLAST_EXPORT Boolean BlastEffectiveLengthsOptions_IsSearchSpaceSet(const BlastEffectiveLengthsOptions* options); /** Fill the non-default values in the BlastEffectiveLengthsOptions structure. * @param options The options [in] [out] * @param dbseq_num Number of sequences in the database (if zero real value will be used) [in] * @param db_length Total length of the database (if zero real value will be used) [in] * @param *searchsp_eff Array of effective search spaces (the real value * will be used for elements that are 0). If array * contains one element, all contexts use this value. * If array has multiple elements, the number must match * the number of contexts in the search [in] * @param num_searchsp The number of elements in searchsp_eff [in] */ NCBI_XBLAST_EXPORT Int2 BLAST_FillEffectiveLengthsOptions(BlastEffectiveLengthsOptions* options, Int4 dbseq_num, Int8 db_length, Int8 *searchsp_eff, Int4 num_searchsp); /** Allocate memory for lookup table options and fill with default values. * @param program Program number (blastn, blastp, etc.) [in] * @param options The options that are being returned [out] */ NCBI_XBLAST_EXPORT Int2 LookupTableOptionsNew(EBlastProgramType program, LookupTableOptions* *options); /** Allocate memory for lookup table options and fill with default values. * @param options The options [in] [out] * @param program Program number (blastn, blastp, etc.) [in] * @param is_megablast Megablast (instead of blastn) if TRUE [in] * @param threshold Threshold value for finding neighboring words (fractional values are allowed, though unless the engine scales up alignment scores a fractional threshold will be rounded down) [in] * @param word_size Number of matched residues in an initial word [in] */ NCBI_XBLAST_EXPORT Int2 BLAST_FillLookupTableOptions(LookupTableOptions* options, EBlastProgramType program, Boolean is_megablast, double threshold, Int4 word_size); /** Deallocates memory for LookupTableOptions*. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT LookupTableOptions* LookupTableOptionsFree(LookupTableOptions* options); /** Validate LookupTableOptions. * @param program_number BLAST program [in] * @param options The options that have are being returned [in] * @param blast_msg Describes any validation problems found [out] */ NCBI_XBLAST_EXPORT Int2 LookupTableOptionsValidate(EBlastProgramType program_number, const LookupTableOptions* options, Blast_Message* *blast_msg); /** Deallocate memory for BlastHitSavingOptions. * @param options Structure to free [in] */ NCBI_XBLAST_EXPORT BlastHitSavingOptions* BlastHitSavingOptionsFree(BlastHitSavingOptions* options); /** Validate BlastHitSavingOptions * @param program_number BLAST program [in] * @param options The options that have are being returned [in] * @param blast_msg Describes any validation problems found [out] */ NCBI_XBLAST_EXPORT Int2 BlastHitSavingOptionsValidate(EBlastProgramType program_number, const BlastHitSavingOptions* options, Blast_Message* *blast_msg); /** Allocate memory for BlastHitSavingOptions. * @param program Program number (blastn, blastp, etc.) [in] * @param options The options that are being returned [out] * @param gapped_calculation is this search gapped? [in] */ NCBI_XBLAST_EXPORT Int2 BlastHitSavingOptionsNew(EBlastProgramType program, BlastHitSavingOptions** options, Boolean gapped_calculation); /** Allocate memory for BlastHitSavingOptions. * @param options The options [in] [out] * @param evalue The expected value threshold [in] * @param hitlist_size How many database sequences to save per query? [in] * @param is_gapped is this a gapped alignment? [in] * @param culling_limit Number of higher-scoring HSPs that must contain * the query range of an HSP before that HSP is declared * to be redundant (ignored if zero) [in] * @param min_diag_separation Delete HSPs whose endpoints are at most this * many diagonals from a higher-scoring HSP. If zero, * delete HSPs whose query and subject ranges are * enveloped by those of a higher-scoring HSP [in] */ NCBI_XBLAST_EXPORT Int2 BLAST_FillHitSavingOptions(BlastHitSavingOptions* options, double evalue, Int4 hitlist_size, Boolean is_gapped, Int4 culling_limit, Int4 min_diag_separation); /** Initialize default options for PSI BLAST * @param psi_options pointer to pointer where structure will be allocated [in] * @return 1 in case of memory allocation failure or if psi_options is NULL, 0 * in case of success */ NCBI_XBLAST_EXPORT Int2 PSIBlastOptionsNew(PSIBlastOptions** psi_options); /** Validates the PSI BLAST options so that they have sane values. * @param psi_options structure to validate [in] * @param blast_msg Describes any validation problems found [out] * @return 0 on success 1 on failure */ Int2 PSIBlastOptionsValidate(const PSIBlastOptions* psi_options, Blast_Message** blast_msg); /** Deallocate PSI BLAST options */ NCBI_XBLAST_EXPORT PSIBlastOptions* PSIBlastOptionsFree(PSIBlastOptions* psi_options); /** Allocate and initialize a BlastHSPBestHitOptions structure */ NCBI_XBLAST_EXPORT BlastHSPBestHitOptions* BlastHSPBestHitOptionsNew(double overhang, double score_edge); /** Validate the best hit algorithm parameters (if any) in the * @param opts BlastHSPFilteringOptions structure * @return 0 on success, else non-zero */ NCBI_XBLAST_EXPORT Int2 BlastHSPBestHitOptionsValidate(const BlastHSPFilteringOptions* opts); /** Deallocate a BlastHSPBestHitOptions structure * @param opt object to be deallocated. [in] */ NCBI_XBLAST_EXPORT BlastHSPBestHitOptions* BlastHSPBestHitOptionsFree(BlastHSPBestHitOptions* opt); /** Allocate a new object for culling options. * @param max number of HSPs that may be aligned to one part of query [in] */ NCBI_XBLAST_EXPORT BlastHSPCullingOptions* BlastHSPCullingOptionsNew(int max); /** Validate culling options. * @param opts BlastHSPFilteringOptions structure * @return 0 on success, else non-zero */ NCBI_XBLAST_EXPORT Int2 BlastHSPCullingOptionsValidate(const BlastHSPFilteringOptions* opts); /** Deallocates culling options structure. * @param culling_opts object to be deallocated. [in] */ NCBI_XBLAST_EXPORT BlastHSPCullingOptions* BlastHSPCullingOptionsFree(BlastHSPCullingOptions* culling_opts); /** Allocate and initialize a BlastHSPFilteringOptions structure */ NCBI_XBLAST_EXPORT BlastHSPFilteringOptions* BlastHSPFilteringOptionsNew(); /** Add the best hit options. Responsibility for best_hit is taken over by the * BlastHSPFilteringOptions * @param filt_opts HSP filtering options [in] * @param best_hit Best Hit algorithm options. Ownership of this is taken by * the BlastHSPFilteringOptions structure [in|out] */ NCBI_XBLAST_EXPORT Int2 BlastHSPFilteringOptions_AddBestHit(BlastHSPFilteringOptions* filt_opts, BlastHSPBestHitOptions** opts, EBlastStage stage); /** Validates the BlastHSPFilteringOptions structure */ NCBI_XBLAST_EXPORT Int2 BlastHSPFilteringOptions_AddCulling(BlastHSPFilteringOptions* filt_opts, BlastHSPCullingOptions** opts, EBlastStage stage); /** Validates the BlastHSPFilteringOptions structure */ NCBI_XBLAST_EXPORT Int2 BlastHSPFilteringOptionsValidate(const BlastHSPFilteringOptions* opts); /** Deallocate a BlastHSPFilteringOptions structure */ NCBI_XBLAST_EXPORT BlastHSPFilteringOptions* BlastHSPFilteringOptionsFree(BlastHSPFilteringOptions* opts); /** Allocates the BlastDatabase options structure and sets the default * database genetic code value (BLAST_GENETIC_CODE). Genetic code string in * ncbistdaa must be populated by client code */ NCBI_XBLAST_EXPORT Int2 BlastDatabaseOptionsNew(BlastDatabaseOptions** db_options); /** Deallocate database options */ NCBI_XBLAST_EXPORT BlastDatabaseOptions* BlastDatabaseOptionsFree(BlastDatabaseOptions* db_options); /** Initialize all the BLAST search options structures with the default * values. * @param blast_program Type of blast program: blastn, blastp, blastx, * tblastn, tblastx) [in] * @param lookup_options Lookup table options [out] * @param query_setup_options Query options [out] * @param word_options Initial word processing options [out] * @param ext_options Extension options [out] * @param hit_options Hit saving options [out] * @param score_options Scoring options [out] * @param eff_len_options Effective length options [out] * @param protein_options Protein BLAST options [out] * @param db_options BLAST database options [out] */ NCBI_XBLAST_EXPORT Int2 BLAST_InitDefaultOptions(EBlastProgramType blast_program, LookupTableOptions** lookup_options, QuerySetUpOptions** query_setup_options, BlastInitialWordOptions** word_options, BlastExtensionOptions** ext_options, BlastHitSavingOptions** hit_options, BlastScoringOptions** score_options, BlastEffectiveLengthsOptions** eff_len_options, PSIBlastOptions** protein_options, BlastDatabaseOptions** db_options); /** Validate all options */ NCBI_XBLAST_EXPORT Int2 BLAST_ValidateOptions(EBlastProgramType program_number, const BlastExtensionOptions* ext_options, const BlastScoringOptions* score_options, const LookupTableOptions* lookup_options, const BlastInitialWordOptions* word_options, const BlastHitSavingOptions* hit_options, Blast_Message* *blast_msg); /** Get thresholds for word-finding suggested by Stephen Altschul. * * @param program_number Type of blast program: blastn, blastp, blastx, * tblastn, tblastx) [in] * @param matrixName matrix, e.g., BLOSUM62 [in] * @param threshold returns suggested value [in|out] * @return zero on success */ NCBI_XBLAST_EXPORT Int2 BLAST_GetSuggestedThreshold(EBlastProgramType program_number, const char* matrixName, double* threshold); /** Get window sizes for two hit algorithm suggested by Stephen Altschul. * * @param program_number Type of blast program: blastn, blastp, blastx, * tblastn, tblastx) [in] * @param matrixName matrix, e.g., BLOSUM62 [in] * @param window_size returns suggested value [in|out] * @return zero on success */ NCBI_XBLAST_EXPORT Int2 BLAST_GetSuggestedWindowSize(EBlastProgramType program_number, const char* matrixName, Int4* window_size); #ifdef __cplusplus } #endif #endif /* !__BLASTOPTIONS__ */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_memento_priv.hpp0000644000175000017500000001461612001215337025172 0ustar ykeyke/* $Id: blast_memento_priv.hpp 113776 2007-11-08 22:38:18Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho, Kevin Bealer * */ /// @file blast_memento_priv.hpp /// Classes that capture the state of the BLAST options (or subsets of options) /// and restore them later (usually upon destruction) using the RAII idiom. #ifndef ALGO_BLAST_API__BLAST_MEMENTO_PRIV__HPP #define ALGO_BLAST_API__BLAST_MEMENTO_PRIV__HPP #include #include #include "blast_options_local_priv.hpp" /** @addtogroup AlgoBlast * * @{ */ BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) /// Class that allows the transfer of data structures from the /// CBlastOptionsLocal class to either the BLAST preliminary or /// traceback search classes. /// /// It is a modification of the memento design pattern in which the object is /// not to restore state but rather to control access to private data /// structures of classes enclosing BLAST CORE C-structures. class CBlastOptionsMemento : public CObject { public: /// Note the no-op destructor, this class does not own any of its data /// members! ~CBlastOptionsMemento() {} private: CBlastOptionsMemento(CBlastOptionsLocal* local_opts) { m_ProgramType = local_opts->GetProgramType(); m_QueryOpts = local_opts->m_QueryOpts.Get(); m_LutOpts = local_opts->m_LutOpts.Get(); m_InitWordOpts = local_opts->m_InitWordOpts.Get(); m_ExtnOpts = local_opts->m_ExtnOpts.Get(); m_HitSaveOpts = local_opts->m_HitSaveOpts.Get(); m_PSIBlastOpts = local_opts->m_PSIBlastOpts.Get(); m_DbOpts = local_opts->m_DbOpts.Get(); m_ScoringOpts = local_opts->m_ScoringOpts.Get(); m_EffLenOpts = local_opts->m_EffLenOpts.Get(); /* *********** START ************* */ m_GpuOpts = (BlastGPUOptions*)malloc(sizeof(BlastGPUOptions)); m_GpuOpts->use_gpu = (char)local_opts->GetUseGpu(); m_GpuOpts->num_threadsx = local_opts->GetNumGpuThreads(); m_GpuOpts->num_blocksx = local_opts->GetNumGpuBlocks(); m_GpuOpts->num_sequences_to = local_opts->GetNumGpuSequences(); m_GpuOpts->method = local_opts->GetGpuMethod(); m_GpuOpts->cpu_threads = local_opts->GetNumCpuThreads(); /* ********** FINISH ************* */ } // The originator friend class CBlastOptions; // Recipients of data friend class CSetupFactory; friend class CPrelimSearchRunner; friend class CBlastPrelimSearch; friend class CBlastTracebackSearch; friend class CFilteringMemento; friend class CEffectiveSearchSpaceCalculator; // The data that is being shared (not that this object doesn't own these) EBlastProgramType m_ProgramType; QuerySetUpOptions* m_QueryOpts; LookupTableOptions* m_LutOpts; BlastInitialWordOptions* m_InitWordOpts; BlastExtensionOptions* m_ExtnOpts; BlastHitSavingOptions* m_HitSaveOpts; PSIBlastOptions* m_PSIBlastOpts; BlastDatabaseOptions* m_DbOpts; BlastScoringOptions* m_ScoringOpts; BlastEffectiveLengthsOptions* m_EffLenOpts; /* *********** START ************* */ BlastGPUOptions* m_GpuOpts; /* ********** FINISH ************* */ }; /// Memento class to save, replace out, and restore the effective search space /// options of the CBlastOptions object passed to its constructor. /// This is done because the SplitQuery_SetEffectiveSearchSpace function /// modifies the search spaces in the CBlastOptions object, but this shouldn't /// be modified, so a temporary object is created and the destroyed. class CEffectiveSearchSpacesMemento { public: /// Parametrized constructor /// @param options the BLAST options [in] CEffectiveSearchSpacesMemento(CBlastOptions* options) : m_Options(options), m_EffLenOrig(0), m_EffLenReplace(0) { _ASSERT(options); if (options->m_Local) { m_EffLenOrig = options->m_Local->m_EffLenOpts.Release(); BlastEffectiveLengthsOptionsNew(&m_EffLenReplace); memcpy((void*) m_EffLenReplace, (void*) m_EffLenOrig, sizeof(*m_EffLenOrig)); m_EffLenReplace->searchsp_eff = (Int8*)malloc(sizeof(Int8) * m_EffLenOrig->num_searchspaces); memcpy((void*) m_EffLenReplace->searchsp_eff, (void*) m_EffLenOrig->searchsp_eff, sizeof(Int8) * m_EffLenOrig->num_searchspaces); options->m_Local->m_EffLenOpts.Reset(m_EffLenReplace); } } /// Destructor ~CEffectiveSearchSpacesMemento() { _ASSERT(m_Options->m_Local); m_Options->m_Local->m_EffLenOpts.Reset(m_EffLenOrig); m_Options = NULL; m_EffLenOrig = m_EffLenReplace = NULL; } private: /** Snapshopt of BLAST options */ CBlastOptions* m_Options; /** Original effective length options */ BlastEffectiveLengthsOptions* m_EffLenOrig; /** Effective length that will be replaced in the BLAST options object */ BlastEffectiveLengthsOptions* m_EffLenReplace; }; END_SCOPE(blast) END_NCBI_SCOPE /* @} */ #endif /* ALGO_BLAST_API__BLAST_MEMENTO_PRIV__HPP */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_engine.h0000644000175000017500000002422712001215340023364 0ustar ykeyke/* $Id: blast_engine.h 103491 2007-05-04 17:18:18Z kazimird $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Ilya Dondoshansky * */ /** @file blast_engine.h * Function calls to actually perform a BLAST search (high level). */ #ifndef ALGO_BLAST_CORE__BLAST_ENGINE__H #define ALGO_BLAST_CORE__BLAST_ENGINE__H #include #include #include #include #include #include #include #include #include #include #include #include #ifdef __cplusplus extern "C" { #endif NCBI_XBLAST_EXPORT extern const int kBlastMajorVersion; /**< Major version */ NCBI_XBLAST_EXPORT extern const int kBlastMinorVersion; /**< Minor version */ NCBI_XBLAST_EXPORT extern const int kBlastPatchVersion; /**< Patch version */ /** Date of the most recent BLAST release (kept for historical reasons) */ NCBI_XBLAST_EXPORT extern const char* kBlastReleaseDate; /** The high level function performing the BLAST search against a BLAST * database after all the setup has been done. * @param program_number Type of BLAST program [in] * @param query The query sequence [in] * @param query_info Additional query information [in] * @param seq_src Structure containing BLAST database [in] * @param sbp Scoring and statistical parameters [in] * @param score_options Hit scoring options [in] * @param lookup_wrap The lookup table, constructed earlier [in] * @param word_options Options for processing initial word hits [in] * @param ext_options Options and parameters for the gapped extension [in] * @param hit_options Options for saving the HSPs [in] * @param eff_len_options Options for setting effective lengths [in] * @param psi_options Options specific to PSI-BLAST [in] * @param db_options Options for handling BLAST database [in] * @param hsp_stream Structure for streaming results [in] [out] * @param rps_info RPS BLAST auxiliary data structure [in] * @param diagnostics Return statistics containing numbers of hits on * different stages of the search [out] * @param results Results of the BLAST search [out] * @param interrupt_search function callback to allow interruption of BLAST * search [in, optional] * @param progress_info contains information about the progress of the current * BLAST search [in|out] */ Int4 Blast_RunFullSearch(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastScoreBlk* sbp, const BlastScoringOptions* score_options, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, const BlastExtensionOptions* ext_options, const BlastHitSavingOptions* hit_options, const BlastEffectiveLengthsOptions* eff_len_options, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, /* *********** START ************* */ const BlastGPUOptions* gpu_options, /* ********** FINISH ************* */ BlastHSPStream* hsp_stream, const BlastRPSInfo* rps_info, BlastDiagnostics* diagnostics, BlastHSPResults** results, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info); /** Perform the preliminary stage of the BLAST search. * @param program_number Type of BLAST program [in] * @param query The query sequence [in] * @param query_info Additional query information [in] * @param seq_src Structure containing BLAST database [in] * @param gap_align Structure containing scoring block and memory allocated * for gapped alignment. [in] * @param score_params Hit scoring parameters [in] * @param lookup_wrap The lookup table, constructed earlier [in] * @param word_options Options for processing initial word hits [in] * @param ext_params Parameters for the gapped extension [in] * @param hit_params Parameters for saving the HSPs [in] * @param eff_len_params Parameters for setting effective lengths [in] * @param psi_options Options specific to PSI-BLAST [in] * @param db_options Options for handling BLAST database [in] * @param hsp_stream Placeholder for saving HSP lists [in] * @param diagnostics Return statistics containing numbers of hits on * different stages of the search. Statistics saved only * for the allocated parts of the structure. [in] [out] * @param interrupt_search function callback to allow interruption of BLAST * search [in, optional] * @param progress_info contains information about the progress of the current * BLAST search [in|out] */ Int4 BLAST_PreliminarySearchEngine(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, /* *********** START ************* */ const BlastGPUOptions* gpu_options, /* ********** FINISH ************* */ BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info); /* *********** START ************* */ Int4 GPU_BLAST_PreliminarySearchEngine(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, const BlastGPUOptions* gpu_options, BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info); /* ********** FINISH ************* */ /** The high level function performing the BLAST search against a BLAST * database after all the setup has been done. * @param program_number Type of BLAST program [in] * @param query The query sequence [in] * @param query_info Additional query information [in] * @param seq_src Structure containing BLAST database [in] * @param score_options Hit scoring options [in] * @param sbp Scoring and statistical parameters [in] * @param lookup_wrap The lookup table, constructed earlier [in] * @param word_options Options for processing initial word hits [in] * @param ext_options Options and parameters for the gapped extension [in] * @param hit_options Options for saving the HSPs [in] * @param eff_len_options Options for setting effective lengths [in] * @param psi_options Options specific to PSI-BLAST [in] * @param db_options Options for handling BLAST database [in] * @param hsp_stream Structure for streaming results [in] [out] * @param diagnostics Return statistics containing numbers of hits on * different stages of the search [out] */ Int2 Blast_RunPreliminarySearch(EBlastProgramType program, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, const BlastScoringOptions* score_options, BlastScoreBlk* sbp, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, const BlastExtensionOptions* ext_options, const BlastHitSavingOptions* hit_options, const BlastEffectiveLengthsOptions* eff_len_options, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, /* *********** START ************* */ const BlastGPUOptions* gpu_options, /* ********** FINISH ************* */ BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics); /** Gapped extension function pointer type */ typedef Int2 (*BlastGetGappedScoreType) (EBlastProgramType, /**< @todo comment function pointer types */ BLAST_SequenceBlk*, BlastQueryInfo*, BLAST_SequenceBlk*, BlastGapAlignStruct*, const BlastScoringParameters*, const BlastExtensionParameters*, const BlastHitSavingParameters*, BlastInitHitList*, BlastHSPList**, BlastGappedStats*, Boolean * fence_hit); /** Word finder function pointer type */ typedef Int2 (*BlastWordFinderType) (BLAST_SequenceBlk*, /**< @todo comment function pointer types */ BLAST_SequenceBlk*, BlastQueryInfo*, LookupTableWrap*, Int4**, const BlastInitialWordParameters*, Blast_ExtendWord*, BlastOffsetPair*, Int4, BlastInitHitList*, BlastUngappedStats*); #ifdef __cplusplus } #endif #endif /* !ALGO_BLAST_CORE__BLAST_ENGINE__H */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_engine.c0000644000175000017500000021040012015067701023360 0ustar ykeyke/* $Id: blast_engine.c 240651 2011-02-09 16:57:10Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * */ /** @file blast_engine.c * Function calls to actually perform a BLAST search (high level). * The hierarchy of function calls, starting from * the top level in the BLAST core, is described below. * 
 * Preliminary stage of the BLAST search:
 *
 *    Blast_RunPreliminarySearch
 *        BLAST_GapAlignSetUp
 *        BLAST_PreliminarySearchEngine
 *            if (RPS BLAST) {
 *                s_RPSPreliminarySearchEngine
 *                    s_BlastSearchEngineCore
 *            } else {
 *                for (all sequences in the database)
 *                    s_BlastSearchEngineCore
 *            }
 *
 * Full BLAST search, including preliminary search and traceback:
 *
 *    Blast_RunFullSearch
 *        BLAST_GapAlignSetUp
 *        BLAST_PreliminarySearchEngine
 *        BLAST_ComputeTraceback
 *
 *
*/ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: blast_engine.c 240651 2011-02-09 16:57:10Z rafanovi $"; #endif /* SKIP_DOXYGEN_PROCESSING */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "blast_gapalign_priv.h" /* *********** START ************* */ #include #include #include #include #include #include //this is included for the itr->oid_range[] #define BILLION 1000000000 /* ********** FINISH ************* */ /** Converts nucleotide coordinates to protein */ #define CONV_NUCL2PROT_COORDINATES(length) (length) / CODON_LENGTH NCBI_XBLAST_EXPORT const int kBlastMajorVersion = 2; NCBI_XBLAST_EXPORT const int kBlastMinorVersion = 2; NCBI_XBLAST_EXPORT const int kBlastPatchVersion = 25; NCBI_XBLAST_EXPORT const char* kBlastReleaseDate = "Feb-01-2011"; /* *********** START ************* */ /* To enable incremental local thread id's */ static Uint4 thread_counter = 0; static Uint4 thread_counter2 = 0; /* Protective mutex for the counter */ //static TNlmMutex thread_counter_mutex = 0; pthread_mutex_t thread_counter_mutex = PTHREAD_MUTEX_INITIALIZER; pthread_mutex_t thread_counter2_mutex = PTHREAD_MUTEX_INITIALIZER; pthread_mutex_t thread_print_mutex = PTHREAD_MUTEX_INITIALIZER; //static int thread_counter_mutex = 0 pthread_barrier_t barr; static Int4* h_Hits = NULL; static GPUBlastInitHitList* h_GPUBlastInitHitList = NULL; static Boolean sufficient_memory[2]= {FALSE,FALSE}; /* ********** FINISH ************* */ /** Structure to be passed to s_BlastSearchEngineCore, containing pointers to various preallocated structures and arrays. */ typedef struct BlastCoreAuxStruct { Blast_ExtendWord* ewp; /**< Structure for keeping track of diagonal information for initial word matches */ BlastWordFinderType WordFinder; /**< Word finder function pointer */ BlastGetGappedScoreType GetGappedScore; /**< Gapped extension function pointer */ BlastInitHitList* init_hitlist; /**< Placeholder for HSPs after ungapped extension */ BlastOffsetPair* offset_pairs; /**< Array of offset pairs for initial seeds. */ Uint1* translation_buffer; /**< Placeholder for translated subject sequences */ Uint1* translation_table; /**< Translation table for forward strand */ Uint1* translation_table_rc; /**< Translation table for reverse strand */ } BlastCoreAuxStruct; /** Deallocates all memory in BlastCoreAuxStruct */ static BlastCoreAuxStruct* s_BlastCoreAuxStructFree(BlastCoreAuxStruct* aux_struct) { BlastExtendWordFree(aux_struct->ewp); BLAST_InitHitListFree(aux_struct->init_hitlist); sfree(aux_struct->offset_pairs); sfree(aux_struct); return NULL; } /** Structure used for subject sequence split */ typedef struct SubjectSplitStruct { Uint1* sequence; /**< backup of original sequence */ SSeqRange full_range; /**< full sequence range */ SSeqRange* seq_ranges; /**< backup of original sequence range */ Int4 num_seq_ranges; /**< backup of original number of items in seq_ranges */ Int4 allocated; /**< number of seq_range allocated for subject */ SSeqRange* hard_ranges; /**< sequence ranges for hard masking */ Int4 num_hard_ranges; /**< number of hard masking ranges */ Int4 hm_index; /**< the current hard masking range index*/ SSeqRange* soft_ranges; /**< sequence ranges for soft masking */ Int4 num_soft_ranges; /**< number of soft masking ranges */ Int4 sm_index; /**< the current soft masking range index*/ Int4 offset; /**< the offset of current chunk */ Int4 next; /**< the offset of next chunk */ } SubjectSplitStruct; static void s_BackupSubject(BLAST_SequenceBlk* subject, SubjectSplitStruct* backup) { if (backup->sequence) return; backup->sequence = subject->sequence; backup->full_range.left = 0; backup->full_range.right = subject->length; backup->seq_ranges = subject->seq_ranges; backup->num_seq_ranges = subject->num_seq_ranges; backup->allocated = 0; backup->hard_ranges = &(backup->full_range); backup->num_hard_ranges = 1; backup->hm_index = 0; backup->soft_ranges = &(backup->full_range); backup->num_soft_ranges = 1; backup->sm_index = 0; if (subject->mask_type == DB_MASK_SOFT) { ASSERT (backup->seq_ranges); ASSERT (backup->num_seq_ranges >= 1); backup->soft_ranges = backup->seq_ranges; backup->num_soft_ranges = backup->num_seq_ranges; } else if (subject->mask_type == DB_MASK_HARD) { ASSERT (backup->seq_ranges); ASSERT (backup->num_seq_ranges >= 1); backup->hard_ranges = backup->seq_ranges; backup->num_hard_ranges = backup->num_seq_ranges; } backup->offset = backup->hard_ranges[0].left; backup->next = backup->offset; subject->chunk = -1; } static void s_AllocateSeqRange(BLAST_SequenceBlk* subject, SubjectSplitStruct* backup, Int4 num_seq_ranges) { ASSERT(num_seq_ranges >= 1); subject->num_seq_ranges = num_seq_ranges; if (backup->allocated >= num_seq_ranges) return; if (backup->allocated) { sfree(subject->seq_ranges); } backup->allocated = num_seq_ranges; subject->seq_ranges = (SSeqRange *) calloc(backup->allocated, sizeof(SSeqRange)); } static void s_RestoreSubject(BLAST_SequenceBlk* subject, SubjectSplitStruct* backup) { if (! backup->sequence) return; subject->sequence = backup->sequence; subject->length = backup->full_range.right; if (backup->allocated) { sfree(subject->seq_ranges); } subject->seq_ranges = backup->seq_ranges; subject->num_seq_ranges = backup->num_seq_ranges; backup->sequence = NULL; } const Int2 SUBJECT_SPLIT_DONE = 0; /**< return value indicating hitting the end */ const Int2 SUBJECT_SPLIT_OK = 1; /**< return value indicating OK */ const Int2 SUBJECT_SPLIT_NO_RANGE = 2; /**< return value indicating all masked out */ static Int2 s_GetNextSubjectChunk(BLAST_SequenceBlk* subject, SubjectSplitStruct *backup, Boolean is_nucleotide) { int start, len, i, residual; ASSERT(subject); ASSERT(backup); if (backup->next >= backup->full_range.right) return SUBJECT_SPLIT_DONE; residual = is_nucleotide ? backup->next % COMPRESSION_RATIO : 0; backup->offset = backup->next - residual; subject->sequence = backup->sequence + ((is_nucleotide) ? backup->offset /COMPRESSION_RATIO : backup->offset); if (backup->offset + MAX_DBSEQ_LEN < backup->hard_ranges[backup->hm_index].right) { subject->length = MAX_DBSEQ_LEN; backup->next = backup->offset + MAX_DBSEQ_LEN - DBSEQ_CHUNK_OVERLAP; } else { subject->length = backup->hard_ranges[backup->hm_index].right - backup->offset; backup->hm_index++; backup->next = (backup->hm_index < backup->num_hard_ranges) ? backup->hard_ranges[backup->hm_index].left : backup->full_range.right; } (subject->chunk)++; /* if no chunking is performed */ if (backup->offset == 0 && backup->next == backup->full_range.right) { subject->seq_ranges = backup->soft_ranges; subject->num_seq_ranges = backup->num_soft_ranges; return SUBJECT_SPLIT_OK; } /* if soft masking is off */ if (subject->mask_type != DB_MASK_SOFT) { s_AllocateSeqRange(subject, backup, 1); subject->seq_ranges[0].left = residual; subject->seq_ranges[0].right = subject->length; return SUBJECT_SPLIT_OK; } /* soft masking is on, sequence is chunked, must re-allocate and adjust */ ASSERT (residual == 0); start = backup->offset; len = start + subject->length; i = backup->sm_index; while (backup->soft_ranges[i].right < start) ++i; start = i; while (i < backup->num_soft_ranges && backup->soft_ranges[i].left < len) ++i; len = i - start; backup->sm_index = i - 1; ASSERT(len >= 0); ASSERT(backup->sm_index >= 0); if (len == 0) return SUBJECT_SPLIT_NO_RANGE; s_AllocateSeqRange(subject, backup, len); for (i=0; iseq_ranges[i].left = backup->soft_ranges[i+start].left - backup->offset; subject->seq_ranges[i].right = backup->soft_ranges[i+start].right - backup->offset; } if (subject->seq_ranges[0].left < 0) subject->seq_ranges[0].left = 0; if (subject->seq_ranges[len-1].right > subject->length) subject->seq_ranges[len-1].right = subject->length; return SUBJECT_SPLIT_OK; } /** Adjust HSP coordinates for out-of-frame gapped extension. * @param program One of blastx or tblastn [in] * @param init_hitlist List of hits after ungapped extension [in] * @param query_info Query information containing context offsets; * needed for blastx only [in] * @param subject_frame Frame of the subject sequence; tblastn only [in] * @param subject_length Length of the original nucleotide subject sequence; * tblastn only [in] * @param offset Shift in the subject sequence protein coordinates [in] */ static void s_TranslateHSPsToDNAPCoord(EBlastProgramType program, BlastInitHitList* init_hitlist, const BlastQueryInfo* query_info, Int2 subject_frame, Int4 subject_length, Int4 offset) { BlastInitHSP * init_hsp = 0; Int4 index = 0; for(index = 0; index < init_hitlist->total; ++index) { BlastContextInfo * contexts = query_info->contexts; init_hsp = &init_hitlist->init_hsp_array[index]; if (program == eBlastTypeBlastx) { Int4 context_idx = 0; /* Index of this HSP's context */ Int4 frame_idx = 0; /* Index of this frame within set of frames with same query and sign */ Int4 init_frame_idx = 0; /* First frame of this query */ Int4 frame_pos = 0; /* Start of this frame in DNA */ /* Find context containing this HSP */ context_idx = BSearchContextInfo(init_hsp->offsets.qs_offsets.q_off, query_info); frame_idx = context_idx % CODON_LENGTH; init_frame_idx = context_idx - frame_idx; frame_pos = contexts[init_frame_idx].query_offset + frame_idx; init_hsp->offsets.qs_offsets.q_off = (init_hsp->offsets.qs_offsets.q_off - contexts[context_idx].query_offset) * CODON_LENGTH + frame_pos; init_hsp->ungapped_data->q_start = (init_hsp->ungapped_data->q_start - contexts[context_idx].query_offset) * CODON_LENGTH + frame_pos; } else { init_hsp->offsets.qs_offsets.s_off += offset; init_hsp->ungapped_data->s_start += offset; if (subject_frame > 0) { init_hsp->offsets.qs_offsets.s_off = (init_hsp->offsets.qs_offsets.s_off * CODON_LENGTH) + subject_frame - 1; init_hsp->ungapped_data->s_start = (init_hsp->ungapped_data->s_start * CODON_LENGTH) + subject_frame - 1; } else { init_hsp->offsets.qs_offsets.s_off = (init_hsp->offsets.qs_offsets.s_off * CODON_LENGTH) + subject_length - subject_frame; init_hsp->ungapped_data->s_start = (init_hsp->ungapped_data->s_start * CODON_LENGTH) + subject_length - subject_frame; } } } Blast_InitHitListSortByScore(init_hitlist); } /** Set up context offsets for the auxiliary BlastQueryInfo structure that is * created for the concatenated database in RPS BLAST search. Calls the public * function OffsetArrayToContextOffsets with a blastp program, because subjects * are protein sequences. This guarantees that all frames are set to 0. * @param info The preallocated structure [in] [out] * @param new_offsets The array context offsets to fill [in] */ static void s_RPSOffsetArrayToContextOffsets(BlastQueryInfo * info, Int4 * new_offsets) { const EBlastProgramType kProgram = eBlastTypeBlastp; OffsetArrayToContextOffsets(info, new_offsets, kProgram); } /** Searches only one context of a database sequence, but does all chunks if it is split. * @param program_number BLAST program type [in] * @param query Query sequence structure [in] * @param query_info Query information [in] * @param subject Subject sequence structure [in] * @param orig_length original length of query before translation [in] * @param lookup Lookup table [in] * @param gap_align Structure for gapped alignment information [in] * @param score_params Scoring parameters [in] * @param word_params Initial word finding and ungapped extension * parameters [in] * @param ext_params Gapped extension parameters [in] * @param hit_params Hit saving parameters [in] * @param diagnostics Hit counts and other diagnostics [in] [out] * @param aux_struct Structure containing different auxiliary data and memory * for the preliminary stage of the BLAST search [in] * @param hsp_list_out_ptr List of HSPs found for a given subject sequence [out] * @param interrupt_search function callback to allow interruption of BLAST * search [in, optional] * @param progress_info contains information about the progress of the current * BLAST search [in|out] */ /* *********** START ************* */ static Int2 s_BlastSearchEngineOneContext(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, BLAST_SequenceBlk* subject, Int4 orig_length, LookupTableWrap* lookup, BlastGapAlignStruct* gap_align, const BlastScoringParameters* score_params, const BlastInitialWordParameters* word_params, const BlastExtensionParameters* ext_params, const BlastHitSavingParameters* hit_params, BlastDiagnostics* diagnostics, BlastCoreAuxStruct* aux_struct, BlastHSPList** hsp_list_out_ptr, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info, /* *********** START ************* */ const BlastGPUOptions* gpu_options, Int4* h_Hits, GPUBlastInitHitList* h_GPUBlastInitHitList, Int4 volume_base) /* ********** FINISH ************* */ { Int2 status = 0; /* return value */ BlastHSPList* combined_hsp_list = NULL; BlastHSPList* hsp_list = NULL; BlastInitHitList* init_hitlist = aux_struct->init_hitlist; BlastScoringOptions* score_options = score_params->options; BlastUngappedStats* ungapped_stats = NULL; BlastGappedStats* gapped_stats = NULL; Int4 **matrix = (gap_align->positionBased) ? gap_align->sbp->psi_matrix->pssm->data : gap_align->sbp->matrix->data; const Boolean kTranslatedSubject = (Blast_SubjectIsTranslated(program_number) || program_number == eBlastTypeRpsTblastn); const Boolean kNucleotide = (program_number == eBlastTypeBlastn || program_number == eBlastTypePhiBlastn); const int kHspNumMax = BlastHspNumMax(score_options->gapped_calculation, hit_params->options); const int kScanSubjectOffsetArraySize = GetOffsetArraySize(lookup); Int4 overlap; SubjectSplitStruct backup; backup.sequence = NULL; if (diagnostics) { ungapped_stats = diagnostics->ungapped_stat; gapped_stats = diagnostics->gapped_stat; } s_BackupSubject(subject, &backup); while (TRUE) { status = s_GetNextSubjectChunk(subject, &backup, kNucleotide); if (status == SUBJECT_SPLIT_DONE) break; if (status == SUBJECT_SPLIT_NO_RANGE) continue; ASSERT(status == SUBJECT_SPLIT_OK); ASSERT(subject->num_seq_ranges >= 1); ASSERT(subject->seq_ranges); /* Delete if not done in last loop iteration to prevent memory leak. */ hsp_list = Blast_HSPListFree(hsp_list); BlastInitHitListReset(init_hitlist); /* *********** START ************* */ int GPUBlastInitHitList_base = 0; int hits = 0, successful_extensions = 0, hits_extended = 0; int subject_oid = subject->oid - volume_base; if(gpu_options->use_gpu) { hits=h_Hits[ (subject_oid)*4 ]; successful_extensions = h_Hits[ (subject_oid)*4 + 1]; hits_extended = h_Hits[ (subject_oid)*4 + 2]; GPUBlastInitHitList_base = h_Hits[ (subject_oid)*4 + 3]; } if (aux_struct->WordFinder) { /* if the GPU is not used, or if the GPU alignment found more hits that it could store in its datastructure carry out the alignment on the CPU */ /// the condition (GPUBlastInitHitList_base == -1) means the subject needs to be re-hit if( (!gpu_options->use_gpu) || (GPUBlastInitHitList_base == -1) ) { aux_struct->WordFinder(subject, query, query_info, lookup, matrix, word_params, aux_struct->ewp, aux_struct->offset_pairs, kScanSubjectOffsetArraySize, init_hitlist, ungapped_stats); } else { // for every successful extension save the results in the init_hitlist Int4 i = 0; for( i = 0; i < successful_extensions; ++i) BlastSaveInitHsp(init_hitlist, h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].hsp_q, h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].hsp_s, h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].hsp_q +h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].offset_from_first_position, h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].hsp_s +h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].offset_from_first_position, h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].hsp_len, h_GPUBlastInitHitList[GPUBlastInitHitList_base + i].score); Blast_UngappedStatsUpdate(ungapped_stats, hits, hits_extended, init_hitlist->total); Blast_InitHitListSortByScore(init_hitlist); } if (init_hitlist->total == 0) continue; } /* ********** FINISH ************* */ if (score_options->gapped_calculation) { Int4 prot_length = 0; if (score_options->is_ooframe) { /* Convert query offsets in all HSPs into the mixed-frame coordinates */ s_TranslateHSPsToDNAPCoord(program_number, init_hitlist, query_info, subject->frame, orig_length, backup.offset); if (kTranslatedSubject) { prot_length = subject->length; subject->length = orig_length; } } /** NB: If queries are concatenated, HSP offsets must be adjusted * inside the following function call, so coordinates are * relative to the individual contexts (i.e. queries, strands or * frames). Contexts should also be filled in HSPs when they * are saved. */ /* fence_hit is null, since this is only for prelim stage. */ status = aux_struct->GetGappedScore(program_number, query, query_info, subject, gap_align, score_params, ext_params, hit_params, init_hitlist, &hsp_list, gapped_stats, NULL); if (status) break; /* Removes redundant HSPs. */ Blast_HSPListPurgeHSPsWithCommonEndpoints(program_number, hsp_list); /* For nucleotide search, if match score is = 2, the odd scores are rounded down to the nearest even number. */ Blast_HSPListAdjustOddBlastnScores(hsp_list, score_options->gapped_calculation, gap_align->sbp); Blast_HSPListSortByScore(hsp_list); if (score_options->is_ooframe && kTranslatedSubject) subject->length = prot_length; } else { BLAST_GetUngappedHSPList(init_hitlist, query_info, subject, hit_params->options, &hsp_list); } if (hsp_list->hspcnt == 0) continue; /* The subject ordinal id is not yet filled in this HSP list */ hsp_list->oid = subject->oid; /* check for interrupt */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { combined_hsp_list = Blast_HSPListFree(combined_hsp_list); BlastInitHitListReset(init_hitlist); status = BLASTERR_INTERRUPTED; break; } Blast_HSPListAdjustOffsets(hsp_list, backup.offset); overlap = (backup.offset == backup.hard_ranges[backup.hm_index].left) ? 0 : DBSEQ_CHUNK_OVERLAP; status = Blast_HSPListsMerge(&hsp_list, &combined_hsp_list, kHspNumMax, &(backup.offset), INT4_MIN, overlap, score_options->gapped_calculation); } /* End loop on chunks of subject sequence */ s_RestoreSubject(subject, &backup); hsp_list = Blast_HSPListFree(hsp_list); /* In case this was not freed in above loop. */ *hsp_list_out_ptr = combined_hsp_list; return status; } /* ********** FINISH ************* */ /** Clean up function for s_BlastSearchEngineCore * @param program_number BLAST program type [in] * @param query_info Query information structure local to * s_BlastSearchEngineCore, which may or may not be deallocated [in] * @param query_info_in Query information [in] * @param translation_buffer buffer containing translated sequence data [in] * @param frame_offsets_a FIXME */ static void s_BlastSearchEngineCoreCleanUp(EBlastProgramType program_number, BlastQueryInfo* query_info, const BlastQueryInfo* query_info_in, Uint1* translation_buffer, Int4* frame_offsets_a) { /* Free the local query info structure when needed (in RPS BLAST). */ if (query_info != query_info_in) BlastQueryInfoFree(query_info); /* Free translation buffer and frame offsets, except for RPS tblastn, * where they are taken from different structures, and hence shouldn't * be freed here. */ if (program_number != eBlastTypeRpsTblastn) { if (translation_buffer) { sfree(translation_buffer); } } if (frame_offsets_a) { sfree(frame_offsets_a); } } /** The core of the BLAST search: comparison between the (concatenated) * query against one subject sequence. Translation of the subject sequence * into 6 frames is done inside, if necessary. If subject sequence is * too long, it can be split into several chunks. * @param program_number BLAST program type [in] * @param query Query sequence structure [in] * @param query_info_in Query information [in] * @param subject Subject sequence structure [in] * @param lookup Lookup table [in] * @param gap_align Structure for gapped alignment information [in] * @param score_params Scoring parameters [in] * @param word_params Initial word finding and ungapped extension * parameters [in] * @param ext_params Gapped extension parameters [in] * @param hit_params Hit saving parameters [in] * @param db_options Database options [in] * @param diagnostics Hit counts and other diagnostics [in] [out] * @param aux_struct Structure containing different auxiliary data and memory * for the preliminary stage of the BLAST search [in] * @param hsp_list_out_ptr List of HSPs found for a given subject sequence [in] * @param interrupt_search function callback to allow interruption of BLAST * search [in, optional] * @param progress_info contains information about the progress of the current * BLAST search [in|out] */ static Int2 s_BlastSearchEngineCore(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info_in, BLAST_SequenceBlk* subject, LookupTableWrap* lookup, BlastGapAlignStruct* gap_align, const BlastScoringParameters* score_params, const BlastInitialWordParameters* word_params, const BlastExtensionParameters* ext_params, const BlastHitSavingParameters* hit_params, const BlastDatabaseOptions* db_options, BlastDiagnostics* diagnostics, BlastCoreAuxStruct* aux_struct, BlastHSPList** hsp_list_out_ptr, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info, /* *********** START ************* */ BlastGPUOptions* gpu_options, Int4* h_Hits, GPUBlastInitHitList* h_GPUBlastInitHitList, Int4 volume_base) /* ********** FINISH ************* */ { BlastHSPList* hsp_list_out=NULL; Uint1* translation_buffer = NULL; Int4* frame_offsets = NULL; Int4* frame_offsets_a = NULL; /* Will be freed if non-null */ BlastHitSavingOptions* hit_options = hit_params->options; BlastScoringOptions* score_options = score_params->options; Int2 status = 0; Uint4 context, first_context, last_context; BlastQueryInfo* query_info = query_info_in; Int4 orig_length = subject->length; const Boolean kTranslatedSubject = (Blast_SubjectIsTranslated(program_number) || program_number == eBlastTypeRpsTblastn); const Boolean kNucleotide = (program_number == eBlastTypeBlastn || program_number == eBlastTypePhiBlastn); const int kHspNumMax = BlastHspNumMax(score_options->gapped_calculation, hit_options); SubjectSplitStruct backup; backup.sequence = NULL; *hsp_list_out_ptr = NULL; if (kTranslatedSubject) { s_BackupSubject(subject, &backup); if (subject->mask_type) { s_AllocateSeqRange(subject, &backup, backup.num_seq_ranges); } else { subject->num_seq_ranges = 0; subject->seq_ranges = NULL; } first_context = 0; last_context = 5; if (score_options->is_ooframe) { BLAST_GetAllTranslations(backup.sequence, eBlastEncodingNcbi2na, backup.full_range.right, subject->gen_code_string, &translation_buffer, &frame_offsets, &subject->oof_sequence); subject->oof_sequence_allocated = TRUE; frame_offsets_a = frame_offsets; } else if (program_number == eBlastTypeRpsTblastn ) { /* For RPS tblastn, subject is actually query, which has already been translated during the setup stage. */ translation_buffer = backup.sequence - 1; frame_offsets_a = frame_offsets = ContextOffsetsToOffsetArray(query_info_in); } else { BLAST_GetAllTranslations(backup.sequence, eBlastEncodingNcbi2na, backup.full_range.right, subject->gen_code_string, &translation_buffer, &frame_offsets, NULL); frame_offsets_a = frame_offsets; /* The following limits the search to plus or minus strand if desired. */ if (subject->subject_strand == 1) { first_context = 0; last_context = 2; } else if (subject->subject_strand == 2) { first_context = 3; last_context = 5; } } } else if (kNucleotide) { first_context = 1; last_context = 1; } else { first_context = 0; last_context = 0; } /* Substitute query info by concatenated database info for RPS BLAST search */ if (Blast_ProgramIsRpsBlast(program_number)) { BlastRPSLookupTable* lut = (BlastRPSLookupTable*) lookup->lut; query_info = BlastQueryInfoNew(eBlastTypeRpsBlast, lut->num_profiles); /* Since this will really be "subject info", not "query info", pass program argument such that all frames will be set to 0. */ s_RPSOffsetArrayToContextOffsets(query_info, lut->rps_seq_offsets); } /* Loop over frames of the subject sequence */ for (context=first_context; context<=last_context; context++) { BlastHSPList* hsp_list_for_chunks = NULL; if (kTranslatedSubject) { Uint4 i; subject->frame = BLAST_ContextToFrame(eBlastTypeBlastx, context); subject->sequence = translation_buffer + frame_offsets[context] + 1; subject->length = frame_offsets[context+1] - frame_offsets[context] - 1; /* perform per-context mask translation */ if (context == 0) /* first positive context */ { for (i = 0; i < subject->num_seq_ranges; i++) { subject->seq_ranges[i].left = CONV_NUCL2PROT_COORDINATES(backup.seq_ranges[i].left); subject->seq_ranges[i].right = CONV_NUCL2PROT_COORDINATES(backup.seq_ranges[i].right); } } else if (context == 3) /* first negative context */ { for (i = 0; i < subject->num_seq_ranges; i++) { subject->seq_ranges[subject->num_seq_ranges-i-1].left = subject->length - CONV_NUCL2PROT_COORDINATES(backup.seq_ranges[i].right); subject->seq_ranges[subject->num_seq_ranges-i-1].right = subject->length - CONV_NUCL2PROT_COORDINATES(backup.seq_ranges[i].left); } } } else { subject->frame = context; } status = s_BlastSearchEngineOneContext(program_number, query, query_info, subject, orig_length, lookup, gap_align, score_params, word_params, ext_params, hit_params, diagnostics, aux_struct, &hsp_list_for_chunks, interrupt_search, progress_info, /* *********** START ************* */ gpu_options, h_Hits, h_GPUBlastInitHitList, volume_base); /* ********** FINISH ************* */ if (status != 0) break; if (Blast_HSPListAppend(&hsp_list_for_chunks, &hsp_list_out, kHspNumMax)) { status = 1; break; } /* if searching was interrupted, delete accumulated results but continue execution so temporary structures get freed */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { status = BLASTERR_INTERRUPTED; break; } } /* End loop on frames */ /* restore mask ranges */ if (kTranslatedSubject) { s_RestoreSubject(subject, &backup); } if (status) { hsp_list_out = Blast_HSPListFree(hsp_list_out); s_BlastSearchEngineCoreCleanUp(program_number, query_info, query_info_in, translation_buffer, frame_offsets_a); return status; } if (hit_params->link_hsp_params) { status = BLAST_LinkHsps(program_number, hsp_list_out, query_info, subject->length, gap_align->sbp, hit_params->link_hsp_params, score_options->gapped_calculation); } else if (!Blast_ProgramIsPhiBlast(program_number) && !Blast_ProgramIsRpsBlast(program_number)) { /* Calculate e-values for all HSPs. Skip this step for PHI and RPS BLAST, since calculating the E values requires precomputation that has not been done yet */ status = Blast_HSPListGetEvalues(query_info, hsp_list_out, score_options->gapped_calculation, gap_align->sbp, 0, 1.0); } /* Discard HSPs that don't pass the e-value test. */ status = Blast_HSPListReapByEvalue(hsp_list_out, hit_options); /* If there are no HSPs left, destroy the HSP list too. */ if (hsp_list_out && hsp_list_out->hspcnt == 0) *hsp_list_out_ptr = hsp_list_out = Blast_HSPListFree(hsp_list_out); if (diagnostics && diagnostics->gapped_stat && hsp_list_out && hsp_list_out->hspcnt > 0) { BlastGappedStats* gapped_stats = diagnostics->gapped_stat; ++gapped_stats->num_seqs_passed; gapped_stats->good_extensions += hsp_list_out->hspcnt; } s_BlastSearchEngineCoreCleanUp(program_number, query_info, query_info_in, translation_buffer, frame_offsets_a); *hsp_list_out_ptr = hsp_list_out; return status; } /** Fills the output information about the cutoffs uses in a BLAST search. * @param return_cutoffs Structure for saving cutoffs information [in] [out] * @param score_params Scoring parameters, containing the scaling factor [in] * @param word_params Initial word parameters [in] * @param ext_params Gapped extension parameters [in] * @param hit_params Hit saving parameters [in] */ static Int2 s_FillReturnCutoffsInfo(BlastRawCutoffs* return_cutoffs, const BlastScoringParameters* score_params, const BlastInitialWordParameters* word_params, const BlastExtensionParameters* ext_params, const BlastHitSavingParameters* hit_params) { /* since the cutoff score here will be used for display purposes, strip out any internal scaling of the scores If this was a multi-query search, use the least stringent cutoff and most generous dropoff value among all the possible sequences */ Int4 scale_factor = (Int4)score_params->scale_factor; if (!return_cutoffs) return -1; return_cutoffs->x_drop_ungapped = word_params->x_dropoff_max / scale_factor; return_cutoffs->x_drop_gap = ext_params->gap_x_dropoff / scale_factor; return_cutoffs->x_drop_gap_final = ext_params->gap_x_dropoff_final / scale_factor; return_cutoffs->ungapped_cutoff = word_params->cutoff_score_min / scale_factor; return_cutoffs->cutoff_score = hit_params->cutoff_score_min / scale_factor; return 0; } /** Setup of the auxiliary BLAST structures; * also calculates internally used parameters from options. * @param seq_src Sequence source information, with callbacks to get * sequences, their lengths, etc. [in] * @param lookup_wrap Lookup table, already constructed. [in] * @param word_params Parameters for initial word finding and ungapped * extension. [in] * @param ext_options options for gapped extension. [in] * @param hit_options options for saving hits. [in] * @param query The query sequence block [in] * @param aux_struct_ptr Placeholder joining various auxiliary memory * structures [out] */ static Int2 s_BlastSetUpAuxStructures(const BlastSeqSrc* seq_src, LookupTableWrap* lookup_wrap, const BlastInitialWordParameters* word_params, const BlastExtensionOptions* ext_options, const BlastHitSavingOptions* hit_options, BLAST_SequenceBlk* query, BlastCoreAuxStruct** aux_struct_ptr) { Int2 status = 0; BlastCoreAuxStruct* aux_struct; Boolean blastp = (lookup_wrap->lut_type == eAaLookupTable || lookup_wrap->lut_type == eCompressedAaLookupTable); Boolean rpsblast = (lookup_wrap->lut_type == eRPSLookupTable); Boolean indexed_mb_lookup = (lookup_wrap->lut_type == eIndexedMBLookupTable); Boolean phi_lookup = (lookup_wrap->lut_type == ePhiLookupTable || lookup_wrap->lut_type == ePhiNaLookupTable); Boolean smith_waterman = (ext_options->ePrelimGapExt == eSmithWatermanScoreOnly); Int4 offset_array_size = GetOffsetArraySize(lookup_wrap); ASSERT(seq_src); *aux_struct_ptr = aux_struct = (BlastCoreAuxStruct*) calloc(1, sizeof(BlastCoreAuxStruct)); if ((status = BlastExtendWordNew(query->length, word_params, &aux_struct->ewp)) != 0) return status; if (smith_waterman) { aux_struct->WordFinder = NULL; } else if (indexed_mb_lookup) { aux_struct->WordFinder = MB_IndexedWordFinder; } else if (phi_lookup) { aux_struct->WordFinder = PHIBlastWordFinder; } else if (blastp) { BlastChooseProteinScanSubject(lookup_wrap); aux_struct->WordFinder = BlastAaWordFinder; } else if (rpsblast) { aux_struct->WordFinder = BlastRPSWordFinder; } else { BlastChooseNucleotideScanSubject(lookup_wrap); BlastChooseNaExtend(lookup_wrap); aux_struct->WordFinder = BlastNaWordFinder; } aux_struct->offset_pairs = (BlastOffsetPair*) malloc(offset_array_size * sizeof(BlastOffsetPair)); aux_struct->init_hitlist = BLAST_InitHitListNew(); /* Pick which gapped alignment algorithm to use. */ if (phi_lookup) aux_struct->GetGappedScore = PHIGetGappedScore; else if (smith_waterman) aux_struct->GetGappedScore = BLAST_SmithWatermanGetGappedScore; else aux_struct->GetGappedScore = BLAST_GetGappedScore; return status; } /** Performs the preliminary stage of an RPS BLAST search, after all set up has * already been done. * @param program_number Type of BLAST program [in] * @param query The query sequence [in] * @param query_info Additional query information [in] * @param seq_src Structure containing BLAST database [in] * @param score_params Hit scoring parameters [in] * @param lookup_wrap The lookup table, constructed earlier [in] * @param aux_struct Wrapper for auxiliary structures used in preliminary * search [in] * @param word_params Parameters for processing initial word hits [in] * @param ext_params Parameters for the gapped extension [in] * @param gap_align Structure containing scoring block and memory allocated * for gapped alignment. [in] * @param hit_params Parameters for saving the HSPs [in] * @param hsp_stream Placeholder for saving HSP lists [in] * @param diagnostics Return statistics containing numbers of hits on * different stages of the search. Statistics saved only * for the allocated parts of the structure. [in] [out] * @param interrupt_search function callback to allow interruption of BLAST * search [in, optional] * @param progress_info contains information about the progress of the current * BLAST search [in|out] */ static Int2 s_RPSPreliminarySearchEngine(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, const BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, BlastCoreAuxStruct* aux_struct, const BlastInitialWordParameters* word_params, const BlastExtensionParameters* ext_params, BlastGapAlignStruct* gap_align, const BlastHitSavingParameters* hit_params, BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info, /* *********** START ************* */ BlastGPUOptions* gpu_options, Int4* h_Hits, GPUBlastInitHitList* h_GPUBlastInitHitList) /* ********** FINISH ************* */ { BlastHSPList* hsp_list = NULL; Int2 status = 0; Int8 dbsize; Int4 num_db_seqs; BlastRPSLookupTable *lookup = (BlastRPSLookupTable *)lookup_wrap->lut; BLAST_SequenceBlk concat_db; BlastQueryInfo* one_query_info = NULL; BLAST_SequenceBlk* one_query = NULL; Int4 index; if ( !Blast_ProgramIsRpsBlast(program_number)) return -1; /* modify scoring and gap alignment structures for use with RPS blast. */ gap_align->positionBased = TRUE; RPSPsiMatrixAttach(gap_align->sbp, lookup->rps_pssm, lookup->alphabet_size); /* determine the total number of residues in the db. This figure must also include one trailing NULL for each DB sequence */ num_db_seqs = BlastSeqSrcGetNumSeqs(seq_src); dbsize = BlastSeqSrcGetTotLen(seq_src) + num_db_seqs; if (dbsize > INT4_MAX) return -3; /* Concatenate all of the DB sequences together, and pretend this is a large multiplexed sequence. Note that because the scoring is position-specific, the actual sequence data is not needed */ memset(&concat_db, 0, sizeof(concat_db)); /* fill in SequenceBlk */ concat_db.length = (Int4) dbsize; /* Change the table of diagonals that will be used for the search; we need a diag table that can fit the entire concatenated DB */ BlastExtendWordFree(aux_struct->ewp); BlastExtendWordNew(concat_db.length, word_params, &aux_struct->ewp); /* Run the search; the input query is what gets scanned and the concatenated DB is the sequence associated with the score matrix. This essentially means that 'query' and 'subject' have opposite conventions for the search. Note that while scores can be calculated for any alignment found, we have not set up any Karlin parameters or effective search space sizes for the concatenated DB. This means that E-values cannot be calculated after hits are found. */ for (index = 0; index < query_info->num_queries; ++index) { /* Separate one query from the set: create an auxiliary query_info structure which refers to this single query. */ if (Blast_GetOneQueryStructs(&one_query_info, &one_query, query_info, query, index) != 0) return -1; /* It is OK to pass NULL for the BlastDatabaseOptions argument, because it will not be checked for RPS BLAST program types. */ status = (Int4) s_BlastSearchEngineCore(program_number, &concat_db, one_query_info, one_query, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, NULL, diagnostics, aux_struct, &hsp_list, interrupt_search, progress_info, /* *********** START ************* */ gpu_options, h_Hits, h_GPUBlastInitHitList, 0); /* ********** FINISH ************* */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { hsp_list = Blast_HSPListFree(hsp_list); status = BLASTERR_INTERRUPTED; break; } /* Save the resulting list of HSPs. 'query' and 'subject' are still reversed */ if (hsp_list && hsp_list->hspcnt > 0) { hsp_list->query_index = index; /* Save the HSP list */ BlastHSPStreamWrite(hsp_stream, &hsp_list); } } BlastQueryInfoFree(one_query_info); BlastSequenceBlkFree(one_query); /* Restore original settings in the gapped alignment structure. */ RPSPsiMatrixDetach(gap_align->sbp); gap_align->positionBased = FALSE; /* Fill the cutoff values in the diagnostics structure */ if (diagnostics && diagnostics->cutoffs) { s_FillReturnCutoffsInfo(diagnostics->cutoffs, score_params, word_params, ext_params, hit_params); } return status; } /* *********** START ************* */ #include "functions.cpp" /* ********** FINISH ************* */ Int4 BLAST_PreliminarySearchEngine(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, /* *********** START ************* */ const BlastGPUOptions* gpu_options, /* ********** FINISH ************* */ BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info) { BlastCoreAuxStruct* aux_struct = NULL; BlastHSPList* hsp_list = NULL; BlastSeqSrcGetSeqArg seq_arg; Int2 status = 0; Int8 db_length = 0; const BlastScoringOptions* score_options = score_params->options; const BlastHitSavingOptions* hit_options = hit_params->options; const BlastExtensionOptions* ext_options = ext_params->options; BlastInitialWordParameters* word_params = NULL; Boolean gapped_calculation = score_options->gapped_calculation; BlastScoreBlk* sbp = gap_align->sbp; BlastSeqSrcIterator* itr; const Boolean kNucleotide = (program_number == eBlastTypeBlastn || program_number == eBlastTypePhiBlastn); BlastInitialWordParametersNew(program_number, word_options, hit_params, lookup_wrap, sbp, query_info, BlastSeqSrcGetAvgSeqLen(seq_src), &word_params); if ((status = s_BlastSetUpAuxStructures(seq_src, lookup_wrap, word_params, ext_options, hit_options, query, &aux_struct)) != 0) return status; /* *********** START ************* */ Int4 threadId = 0; Int4 print_point = 0; if (GPU_VERBOSE) { pthread_mutex_lock(&thread_counter_mutex); threadId = thread_counter++; pthread_mutex_unlock(&thread_counter_mutex); print_point = BlastSeqSrcGetNumSeqs(seq_src) / 50; } /* remember the current search state */ if (progress_info) progress_info->stage = ePrelimSearch; /* For RPS BLAST, there is no loop over subject sequences, so the preliminary search engine is done in a separate function. */ if (Blast_ProgramIsRpsBlast(program_number)) { status = s_RPSPreliminarySearchEngine(program_number, query, query_info, seq_src, score_params, lookup_wrap, aux_struct, word_params, ext_params, gap_align, hit_params, hsp_stream, diagnostics, interrupt_search, progress_info, /* *********** START ************* */ gpu_options, h_Hits, h_GPUBlastInitHitList); /* ********** FINISH ************* */ word_params = BlastInitialWordParametersFree(word_params); s_BlastCoreAuxStructFree(aux_struct); return status; } /* Update the parameters for linking HSPs, if necessary. */ BlastLinkHSPParametersUpdate(word_params, hit_params, gapped_calculation); memset((void*) &seq_arg, 0, sizeof(seq_arg)); /* Encoding is set so there are no sentinel bytes, and protein/nucleotide sequences are retieved in ncbistdaa/ncbi2na encodings respectively. */ seq_arg.encoding = eBlastEncodingProtein; db_length = BlastSeqSrcGetTotLen(seq_src); itr = BlastSeqSrcIteratorNewEx(MAX(BlastSeqSrcGetNumSeqs(seq_src)/100,1)); /* iterate over all subject sequences */ while ( (seq_arg.oid = BlastSeqSrcIteratorNext(seq_src, itr)) != BLAST_SEQSRC_EOF) { if (seq_arg.oid == BLAST_SEQSRC_ERROR) break; if (BlastSeqSrcGetSequence(seq_src, &seq_arg) < 0) continue; if (db_length == 0) { /* This is not a database search, hence need to recalculate and save the effective search spaces and length adjustments for all queries based on the length of the current single subject sequence. */ if ((status = BLAST_OneSubjectUpdateParameters(program_number, seq_arg.seq->length, score_options, query_info, sbp, hit_params, word_params, eff_len_params)) != 0) return status; } /* Calculate cutoff scores for linking HSPs. Do this only for ungapped protein searches and ungapped translated searches. */ if (hit_params->link_hsp_params && !kNucleotide && !gapped_calculation) { CalculateLinkHSPCutoffs(program_number, query_info, sbp, hit_params->link_hsp_params, word_params, db_length, seq_arg.seq->length); } if (Blast_SubjectIsTranslated(program_number)) { /* If the subject is translated and the BlastSeqSrc implementation * doesn't provide a genetic code string, use the default genetic * code for all subjects (as in the C toolkit) */ if (seq_arg.seq->gen_code_string == NULL) { seq_arg.seq->gen_code_string = GenCodeSingletonFind(db_options->genetic_code); } ASSERT(seq_arg.seq->gen_code_string); } status = s_BlastSearchEngineCore(program_number, query, query_info, seq_arg.seq, lookup_wrap, gap_align, score_params, word_params, ext_params, hit_params, db_options, diagnostics, aux_struct, &hsp_list, interrupt_search, progress_info, /* *********** START ************* */ gpu_options, h_Hits, h_GPUBlastInitHitList, 0); /* ********** FINISH ************* */ if (status) { break; } if (hsp_list && hsp_list->hspcnt > 0) { if (!gapped_calculation) { /* The following must be performed for any ungapped search with a nucleotide database. */ status = Blast_HSPListReevaluateUngapped( program_number, hsp_list, query, seq_arg.seq, word_params, hit_params, query_info, sbp, score_params, seq_src, seq_arg.seq->gen_code_string); if (status) { BlastSeqSrcReleaseSequence(seq_src, &seq_arg); return status; } /* Relink HSPs if sum statistics is used, because scores might * have changed after reevaluation with ambiguities, and there * will be no traceback stage where relinking is done normally. * If sum statistics are not used, just recalculate e-values. */ if (hit_params->link_hsp_params) { status = BLAST_LinkHsps(program_number, hsp_list, query_info, seq_arg.seq->length, sbp, hit_params->link_hsp_params, gapped_calculation); } else { Blast_HSPListGetEvalues(query_info, hsp_list, gapped_calculation, sbp, 0, 1.0); } status = Blast_HSPListReapByEvalue(hsp_list, hit_params->options); /* Calculate and fill the bit scores, since there will be no traceback stage where this can be done. */ Blast_HSPListGetBitScores(hsp_list, gapped_calculation, sbp); } /* Save the results. */ status = BlastHSPStreamWrite(hsp_stream, &hsp_list); if (status != 0) break; } BlastSeqSrcReleaseSequence(seq_src, &seq_arg); /* check for interrupt */ if (interrupt_search && (*interrupt_search)(progress_info) == TRUE) { status = BLASTERR_INTERRUPTED; break; } } hsp_list = Blast_HSPListFree(hsp_list); /* in case we were interrupted */ BlastSequenceBlkFree(seq_arg.seq); itr = BlastSeqSrcIteratorFree(itr); /* Fill the cutoff values in the diagnostics structure */ if (diagnostics && diagnostics->cutoffs) { s_FillReturnCutoffsInfo(diagnostics->cutoffs, score_params, word_params, ext_params, hit_params); } word_params = BlastInitialWordParametersFree(word_params); s_BlastCoreAuxStructFree(aux_struct); /* *********** START ************* */ if( GPU_VERBOSE ) { pthread_mutex_lock(&thread_counter_mutex); thread_counter--; pthread_mutex_unlock(&thread_counter_mutex); } /* ********** FINISH ************* */ return status; } Int2 Blast_RunPreliminarySearch(EBlastProgramType program, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, const BlastScoringOptions* score_options, BlastScoreBlk* sbp, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, const BlastExtensionOptions* ext_options, const BlastHitSavingOptions* hit_options, const BlastEffectiveLengthsOptions* eff_len_options, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, /* *********** START ************* */ const BlastGPUOptions* gpu_options, /* ********** FINISH ************* */ BlastHSPStream* hsp_stream, BlastDiagnostics* diagnostics) { Int2 status = 0; BlastScoringParameters* score_params = NULL;/**< Scoring parameters */ BlastExtensionParameters* ext_params = NULL;/**< Gapped extension parameters */ BlastHitSavingParameters* hit_params = NULL;/**< Hit saving parameters */ BlastEffectiveLengthsParameters* eff_len_params = NULL; /**< Parameters for effective lengths calculations */ BlastGapAlignStruct* gap_align = NULL; /**< Gapped alignment structure */ /* Use a local diagnostics structure, because the one passed in an input argument can be shared between multiple threads, so we don't want to pass it to the engine and have a lot of mutex contention. */ BlastDiagnostics* local_diagnostics = Blast_DiagnosticsInit(); if ((status = BLAST_GapAlignSetUp(program, seq_src, score_options, eff_len_options, ext_options, hit_options, query_info, sbp, &score_params, &ext_params, &hit_params, &eff_len_params, &gap_align)) != 0) return status; /* *********** START ************* */ Boolean available_gpu = FALSE; //If the user wants to use the GPU check if it is available if( gpu_options->use_gpu ) { available_gpu = GPU_BLAST_check_availability(); //If there is no availalbe GPU print the message only once if( !available_gpu ) { //Use threadId to make sure to print the message only once pthread_mutex_lock(&thread_counter2_mutex); Int4 threadId = thread_counter2++; pthread_mutex_unlock(&thread_counter2_mutex); if( 0 == threadId ) fprintf(stderr,"WARNING: There is no available device supporting CUDA. Continuing with the CPU only...\n"); } } if( (gpu_options->use_gpu) && available_gpu ) { if ((status= GPU_BLAST_PreliminarySearchEngine(program, query, query_info, seq_src, gap_align, score_params, lookup_wrap, word_options, ext_params, hit_params, eff_len_params, psi_options, db_options, gpu_options, hsp_stream, local_diagnostics, 0, 0)) != 0) return status; } else { if ((status= BLAST_PreliminarySearchEngine(program, query, query_info, seq_src, gap_align, score_params, lookup_wrap, word_options, ext_params, hit_params, eff_len_params, psi_options, /* *********** START ************* */ gpu_options, /* ********** FINISH ************* */ db_options, hsp_stream, local_diagnostics, 0, 0)) != 0) return status; } if( !available_gpu ) { pthread_mutex_lock(&thread_counter2_mutex); thread_counter2--; pthread_mutex_unlock(&thread_counter2_mutex); } /* ********** FINISH ************* */ /* Do not destruct score block here */ gap_align->sbp = NULL; gap_align = BLAST_GapAlignStructFree(gap_align); score_params = BlastScoringParametersFree(score_params); hit_params = BlastHitSavingParametersFree(hit_params); ext_params = BlastExtensionParametersFree(ext_params); eff_len_params = BlastEffectiveLengthsParametersFree(eff_len_params); /* Now update the input diagonistics structure. */ Blast_DiagnosticsUpdate(diagnostics, local_diagnostics); Blast_DiagnosticsFree(local_diagnostics); return status; } /** Function to deallocate data structures allocated in Blast_RunFullSearch */ static void s_BlastRunFullSearchCleanUp(BlastGapAlignStruct* gap_align, BlastScoringParameters* score_params, BlastExtensionParameters* ext_params, BlastHitSavingParameters* hit_params, BlastEffectiveLengthsParameters* eff_len_params) { /* Do not destruct score block here */ gap_align->sbp = NULL; BLAST_GapAlignStructFree(gap_align); BlastScoringParametersFree(score_params); BlastHitSavingParametersFree(hit_params); BlastExtensionParametersFree(ext_params); BlastEffectiveLengthsParametersFree(eff_len_params); } Int4 Blast_RunFullSearch(EBlastProgramType program_number, BLAST_SequenceBlk* query, BlastQueryInfo* query_info, const BlastSeqSrc* seq_src, BlastScoreBlk* sbp, const BlastScoringOptions* score_options, LookupTableWrap* lookup_wrap, const BlastInitialWordOptions* word_options, const BlastExtensionOptions* ext_options, const BlastHitSavingOptions* hit_options, const BlastEffectiveLengthsOptions* eff_len_options, const PSIBlastOptions* psi_options, const BlastDatabaseOptions* db_options, /* *********** START ************* */ const BlastGPUOptions* gpu_options, /* ********** FINISH ************* */ BlastHSPStream* hsp_stream, const BlastRPSInfo* rps_info, BlastDiagnostics* diagnostics, BlastHSPResults** results, TInterruptFnPtr interrupt_search, SBlastProgress* progress_info) { Int4 status = 0; BlastScoringParameters* score_params = NULL; BlastExtensionParameters* ext_params = NULL; BlastHitSavingParameters* hit_params = NULL; BlastEffectiveLengthsParameters* eff_len_params = NULL; BlastGapAlignStruct* gap_align = NULL; SPHIPatternSearchBlk* pattern_blk = NULL; if ((status = BLAST_GapAlignSetUp(program_number, seq_src, score_options, eff_len_options, ext_options, hit_options, query_info, sbp, &score_params, &ext_params, &hit_params, &eff_len_params, &gap_align)) != 0) { s_BlastRunFullSearchCleanUp(gap_align, score_params, ext_params, hit_params, eff_len_params); return status; } if ((status= BLAST_PreliminarySearchEngine(program_number, query, query_info, seq_src, gap_align, score_params, lookup_wrap, word_options, ext_params, hit_params, eff_len_params, psi_options, db_options, /* *********** START ************* */ gpu_options, /* ********** FINISH ************* */ hsp_stream, diagnostics, interrupt_search, progress_info)) != 0) { s_BlastRunFullSearchCleanUp(gap_align, score_params, ext_params, hit_params, eff_len_params); return status; } /* Prohibit any subsequent writing to the HSP stream. */ BlastHSPStreamClose(hsp_stream); if (Blast_ProgramIsPhiBlast(program_number)) { pattern_blk = ((SPHIPatternSearchBlk*) lookup_wrap->lut); pattern_blk->num_patterns_db = (Int4)diagnostics->ungapped_stat->lookup_hits; } if ((status = BLAST_ComputeTraceback(program_number, hsp_stream, query, query_info, seq_src, gap_align, score_params, ext_params, hit_params, eff_len_params, db_options, psi_options, rps_info, pattern_blk, results, interrupt_search, progress_info)) != 0) { s_BlastRunFullSearchCleanUp(gap_align, score_params, ext_params, hit_params, eff_len_params); return status; } s_BlastRunFullSearchCleanUp(gap_align, score_params, ext_params, hit_params, eff_len_params); return status; } h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_args.hpp0000644000175000017500000012403312001215340023407 0ustar ykeyke/* $Id: blast_args.hpp 222376 2011-01-25 22:52:57Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Jason Papadopoulos * */ /** @file blast_args.hpp * Interface for converting blast-related command line * arguments into blast options */ #ifndef ALGO_BLAST_BLASTINPUT___BLAST_ARGS__HPP #define ALGO_BLAST_BLASTINPUT___BLAST_ARGS__HPP #include #include #include #include #include #include // for CThreadable #include #include #include // for CScope #include #include BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) /** * BLAST Command line arguments design * The idea is to have several small objects (subclasses of IBlastCmdLineArgs) * which can do two things: * 1) On creation, add flags/options/etc to a CArgs object * 2) When passed in a CBlastOptions object, call the appropriate methods based * on the CArgs options set when the NCBI application framework parsed the * command line. If data collected by the small object (from the command line) * cannot be applied to the CBlastOptions object, then it's provided to the * application via some other interface methods. * * Each command line application will have its own argument class (e.g.: * CPsiBlastAppArgs), which will contain several of the aformentioned small * objects. It will create and hold a reference to a CArgs class as well as * a CBlastOptionsHandle object, which will pass to each of its small objects * aggregated as data members and then return it to the caller (application) * * Categories of data to extract from command line options * 1) BLAST algorithm options * 2) Input/Output files, and their modifiers (e.g.: believe query defline) * 3) BLAST database information (names, limitations, num db seqs) * 4) Formatting options (html, display formats, etc) */ /** Interface definition for a generic command line option for BLAST */ class NCBI_BLASTINPUT_EXPORT IBlastCmdLineArgs : public CObject { public: /** Our virtual destructor */ virtual ~IBlastCmdLineArgs() {} /** Sets the command line descriptions in the CArgDescriptions object * relevant to the subclass * @param arg_desc the argument descriptions object [in|out] */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc) = 0; /** Extracts BLAST algorithmic options from the command line arguments into * the CBlastOptions object. Default implementation does nothing. * @param cmd_line_args Command line arguments parsed by the NCBI * application framework [in] * @param options object to which the appropriate options will be set * [in|out] */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class to retrieve input and output streams for a command line * program. */ class NCBI_BLASTINPUT_EXPORT CStdCmdLineArgs : public IBlastCmdLineArgs { public: /** Default constructor */ CStdCmdLineArgs() : m_InputStream(0), m_OutputStream(0) {}; /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /** Get the input stream for a command line application */ CNcbiIstream& GetInputStream() const; /** Get the output stream for a command line application */ CNcbiOstream& GetOutputStream() const; /** Set the input stream if read from a saved search strategy */ void SetInputStream(CRef input_file); private: CNcbiIstream* m_InputStream; ///< Application's input stream CNcbiOstream* m_OutputStream; ///< Application's output stream /// ASN.1 specification of query sequences when read from a saved search /// strategy CRef m_QueryTmpInputFile; }; /** Argument class to populate an application's name and description */ class NCBI_BLASTINPUT_EXPORT CProgramDescriptionArgs : public IBlastCmdLineArgs { public: /** * @brief Constructor * * @param program_name application's name [in] * @param program_description application's description [in] */ CProgramDescriptionArgs(const string& program_name, const string& program_description); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); private: string m_ProgName; ///< Application's name string m_ProgDesc; ///< Application's description }; /// Argument class to specify the supported tasks a given program class NCBI_BLASTINPUT_EXPORT CTaskCmdLineArgs : public IBlastCmdLineArgs { public: /** Constructor * @param supported_tasks list of supported tasks [in] * @param default_task One of the tasks above, to be displayed as * default in the command line arguments (cannot be empty or absent from * the set above) [in] */ CTaskCmdLineArgs(const set& supported_tasks, const string& default_task); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); private: /// Set of supported tasks by this command line argument const set m_SupportedTasks; /// Default task for this command line argument string m_DefaultTask; }; /** Argument class to retrieve and set the window size BLAST algorithm * option */ class NCBI_BLASTINPUT_EXPORT CWindowSizeArg : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions * @note this depends on the matrix already being set... */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class to retrieve and set the off-diagonal range used in 2-hit algorithm */ class NCBI_BLASTINPUT_EXPORT COffDiagonalRangeArg : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions * @note this depends on the matrix already being set... */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class to retrieve and set the word threshold BLAST algorithm * option */ class NCBI_BLASTINPUT_EXPORT CWordThresholdArg : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions * @note this depends on the matrix already being set... */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class to retrieve and set the scoring matrix name BLAST algorithm * option */ class NCBI_BLASTINPUT_EXPORT CMatrixNameArg : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class for general search BLAST algorithm options: evalue, gap * penalties, query filter string, ungapped x-drop, initial and final gapped * x-drop, word size, percent identity, and effective search space. */ class NCBI_BLASTINPUT_EXPORT CGenericSearchArgs : public IBlastCmdLineArgs { public: /** * @brief Constructor * * @param query_is_protein is the query sequence(s) protein? [in] * @param is_rpsblast is it RPS-BLAST? [in] * @param show_perc_identity should the percent identity be shown? * Currently only supported for blastn [in] */ CGenericSearchArgs(bool query_is_protein = true, bool is_rpsblast = false, bool show_perc_identity = false, bool is_tblastx = false) : m_QueryIsProtein(query_is_protein), m_IsRpsBlast(is_rpsblast), m_ShowPercentIdentity(show_perc_identity), m_IsTblastx(is_tblastx) {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); private: bool m_QueryIsProtein; /**< true if the query is protein */ bool m_IsRpsBlast; /**< true if the search is RPS-BLAST */ bool m_ShowPercentIdentity; /**< true if the percent identity option should be shown */ bool m_IsTblastx; /**< true if the search is tblastx */ }; /** Argument class for collecting filtering options */ class NCBI_BLASTINPUT_EXPORT CFilteringArgs : public IBlastCmdLineArgs { public: /** * @brief Constructor * * @param query_is_protein is the query sequence(s) protein? [in] * @param filter_by_default should filtering be applied by default? [in] */ CFilteringArgs(bool query_is_protein = true, bool filter_by_default = true) : m_QueryIsProtein(query_is_protein), m_FilterByDefault(filter_by_default) {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); private: bool m_QueryIsProtein; /**< true if the query is protein */ bool m_FilterByDefault; /**< Should filtering be applied by default? */ /** * @brief Auxiliary method to tokenize the filtering string. * * @param filtering_args string to tokenize [in] * @param output vector with tokens [in|out] */ void x_TokenizeFilteringArgs(const string& filtering_args, vector& output) const; }; /// Defines values for match and mismatch in nucleotide comparisons as well as /// non-greedy extension class NCBI_BLASTINPUT_EXPORT CNuclArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /// Argument class to retrieve discontiguous megablast arguments class NCBI_BLASTINPUT_EXPORT CDiscontiguousMegablastArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Value to specify coding template type static const string kTemplType_Coding; /// Value to specify optimal template type static const string kTemplType_Optimal; /// Value to specify coding+optimal template type static const string kTemplType_CodingAndOptimal; }; /** Argument class for collecting composition based statistics options */ class NCBI_BLASTINPUT_EXPORT CCompositionBasedStatsArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class for collecting gapped options */ class NCBI_BLASTINPUT_EXPORT CGappedArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /** Argument class for collecting the largest intron size */ class NCBI_BLASTINPUT_EXPORT CLargestIntronSizeArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /// Argument class to collect the frame shift penalty for out-of-frame searches class NCBI_BLASTINPUT_EXPORT CFrameShiftArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /// Argument class to collect the genetic code for all queries/subjects class NCBI_BLASTINPUT_EXPORT CGeneticCodeArgs : public IBlastCmdLineArgs { public: /// Enumeration defining which sequences the genetic code applies to enum ETarget { eQuery, ///< Query genetic code eDatabase ///< Database genetic code }; /** * @brief Constructor * * @param t genetic code target (query or database) */ CGeneticCodeArgs(ETarget t) : m_Target(t) {}; /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); private: ETarget m_Target; ///< Genetic code target }; /// Argument class to retrieve the gap trigger option class NCBI_BLASTINPUT_EXPORT CGapTriggerArgs : public IBlastCmdLineArgs { public: /** * @brief Constructor * * @param query_is_protein is the query sequence(s) protein? */ CGapTriggerArgs(bool query_is_protein) : m_QueryIsProtein(query_is_protein) {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); private: bool m_QueryIsProtein; /**< true if the query is protein */ }; /// Argument class to collect PSSM engine options class NCBI_BLASTINPUT_EXPORT CPssmEngineArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /// Argument class to import/export the search strategy class NCBI_BLASTINPUT_EXPORT CSearchStrategyArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Get the input stream for the search strategy CNcbiIstream* GetImportStream(const CArgs& args) const; /// Get the output stream for the search strategy CNcbiOstream* GetExportStream(const CArgs& args) const; }; /// Argument class to collect options specific to PSI-BLAST class NCBI_BLASTINPUT_EXPORT CPsiBlastArgs : public IBlastCmdLineArgs { public: /// Enumeration to determine the molecule type of the database enum ETargetDatabase { eProteinDb, ///< Traditional, iterated PSI-BLAST eNucleotideDb ///< PSI-Tblastn, non-iterated }; /** * @brief Constructor * * @param db_target Molecule type of the database */ CPsiBlastArgs(ETargetDatabase db_target = eProteinDb) : m_DbTarget(db_target), m_NumIterations(1), m_CheckPointOutput(0), m_AsciiMatrixOutput(0) {}; /// Our virtual destructor virtual ~CPsiBlastArgs() {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Retrieve the number of iterations to perform size_t GetNumberOfIterations() const { return m_NumIterations; } /// Returns true if checkpoint PSSM is required to be printed bool RequiresCheckPointOutput() const { return m_CheckPointOutput != NULL; } /// Get the checkpoint file output stream /// @return pointer to output stream, not to be free'd by the caller CNcbiOstream* GetCheckPointOutputStream() { return m_CheckPointOutput ? m_CheckPointOutput->GetStream() : NULL; } /// Returns true if ASCII PSSM is required to be printed bool RequiresAsciiPssmOutput() const { return m_AsciiMatrixOutput != NULL; } /// Get the ASCII matrix output stream /// @return pointer to output stream, not to be free'd by the caller CNcbiOstream* GetAsciiMatrixOutputStream() { return m_AsciiMatrixOutput ? m_AsciiMatrixOutput->GetStream() : NULL; } /// Get the PSSM read from checkpoint file CRef GetInputPssm() const { return m_Pssm; } /// Set the PSSM read from saved search strategy void SetInputPssm(CRef pssm) { m_Pssm = pssm; } private: /// Molecule of the database ETargetDatabase m_DbTarget; /// number of iterations to perform size_t m_NumIterations; /// checkpoint output file CRef m_CheckPointOutput; /// ASCII matrix output file CRef m_AsciiMatrixOutput; /// PSSM CRef m_Pssm; /// Prohibit copy constructor CPsiBlastArgs(const CPsiBlastArgs& rhs); /// Prohibit assignment operator CPsiBlastArgs& operator=(const CPsiBlastArgs& rhs); /// Auxiliary function to create a PSSM from a multiple sequence alignment /// file CRef x_CreatePssmFromMsa(CNcbiIstream& input_stream, CBlastOptions& opt, bool save_ascii_pssm, unsigned int msa_master_idx); }; /// Argument class to collect options specific to PHI-BLAST class NCBI_BLASTINPUT_EXPORT CPhiBlastArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); }; /*****************************************************************************/ // Input options /// Argument class to collect query options class NCBI_BLASTINPUT_EXPORT CQueryOptionsArgs : public IBlastCmdLineArgs { public: /** * @brief Constructor * * @param query_cannot_be_nucl can the query not be nucleotide? */ CQueryOptionsArgs(bool query_cannot_be_nucl = false) : m_Strand(objects::eNa_strand_unknown), m_Range(), m_UseLCaseMask(kDfltArgUseLCaseMasking), m_ParseDeflines(kDfltArgParseDeflines), m_QueryCannotBeNucl(query_cannot_be_nucl) {}; /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Get query sequence range restriction TSeqRange GetRange() const { return m_Range; } /// Set query sequence range restriction void SetRange(const TSeqRange& range) { m_Range = range; } /// Get strand to search in query sequence(s) objects::ENa_strand GetStrand() const { return m_Strand; } /// Use lowercase masking in FASTA input? bool UseLowercaseMasks() const { return m_UseLCaseMask; } /// Should the defline be parsed? bool GetParseDeflines() const { return m_ParseDeflines; } /// Is the query sequence protein? bool QueryIsProtein() const { return m_QueryCannotBeNucl; } private: /// Strand(s) to search objects::ENa_strand m_Strand; /// range to restrict the query sequence(s) TSeqRange m_Range; /// use lowercase masking in FASTA input bool m_UseLCaseMask; /// Should the deflines be parsed? bool m_ParseDeflines; /// only false for blast[xn], and tblastx /// true in case of PSI-BLAST bool m_QueryCannotBeNucl; }; /// Argument class to collect database/subject arguments class NCBI_BLASTINPUT_EXPORT CBlastDatabaseArgs : public IBlastCmdLineArgs { public: /// The default priority for subjects, should be used for /// subjects/databases static const int kSubjectsDataLoaderPriority = 10; /// alias for the database molecule type typedef CSearchDatabase::EMoleculeType EMoleculeType; /// Auxiliary function to determine if the database/subject sequence has /// been set static bool HasBeenSet(const CArgs& args); /// Constructor /// @param request_mol_type If true, the command line arguments will /// include a mandatory option to disambiguate whether a protein or a /// nucleotide database is searched /// @param is_rpsblast is it RPS-BLAST? CBlastDatabaseArgs(bool request_mol_type = false, bool is_rpsblast = false); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts); /// Turns on/off database masking support void SetDatabaseMaskingSupport(bool val) { m_SupportsDatabaseMasking = val; } /// Is the database/subject protein? bool IsProtein() const { return m_IsProtein; } /// Get the BLAST database name /// @return empty string in the case of BLAST2Sequences, otherwise the /// BLAST database name string GetDatabaseName() const { return m_SearchDb.Empty() ? kEmptyStr : m_SearchDb->GetDatabaseName(); } /// Retrieve the search database information CRef GetSearchDatabase() const { return m_SearchDb; } /// Set the search database information. /// use case: recovering from search strategy void SetSearchDatabase(CRef search_db) { m_SearchDb = search_db; m_IsProtein = search_db->IsProtein(); } /// Sets the subject sequences. /// use case: recovering from search strategy void SetSubjects(CRef subjects, CRef scope, bool is_protein) { m_Subjects = subjects; m_Scope = scope; m_IsProtein = is_protein; } /// Retrieve subject sequences, if provided /// @param scope scope to which to sequence read will be added (if /// non-NULL) [in] /// @return empty CRef<> if no subjects were provided, otherwise a properly /// initialized IQueryFactory object CRef GetSubjects(objects::CScope* scope = NULL) { if (m_Subjects && scope) { // m_Scope contains the subject(s) read _ASSERT(m_Scope.NotEmpty()); // Add the scope with a lower priority to avoid conflicts scope->AddScope(*m_Scope, kSubjectsDataLoaderPriority); } return m_Subjects; } private: CRef m_SearchDb;/**< Description of the BLAST database */ bool m_RequestMoleculeType; /**< Determines whether the database's molecule type should be requested in the command line, true in case of PSI-BLAST */ bool m_IsRpsBlast; /**< true if the search is RPS-BLAST */ bool m_IsProtein; /**< Is the database/subject(s) protein? */ CRef m_Subjects; /**< The subject sequences */ CRef m_Scope; /**< CScope object in which all subject sequences read are kept */ bool m_SupportsDatabaseMasking; /**< true if it's supported */ }; /// Argument class to collect formatting options, use this to create a /// CBlastFormat object. /// @note This object is also needed to set the maximum number of target /// sequences to save (hitlist size) class NCBI_BLASTINPUT_EXPORT CFormattingArgs : public IBlastCmdLineArgs { public: /// Defines the output formats supported by our command line formatter enum EOutputFormat { /// Standard pairwise alignments ePairwise = 0, ///< Query anchored showing identities eQueryAnchoredIdentities, ///< Query anchored no identities eQueryAnchoredNoIdentities, ///< Flat query anchored showing identities eFlatQueryAnchoredIdentities, ///< Flat query anchored no identities eFlatQueryAnchoredNoIdentities, /// XML output eXml, /// Tabular output eTabular, /// Tabular output with comments eTabularWithComments, /// ASN.1 text output eAsnText, /// ASN.1 binary output eAsnBinary, /// Comma-separated values eCommaSeparatedValues, /// BLAST archive format eArchiveFormat, /// Sentinel value for error checking eEndValue }; /// Default constructor CFormattingArgs() : m_OutputFormat(ePairwise), m_ShowGis(false), m_NumDescriptions(align_format::kDfltArgNumDescriptions), m_NumAlignments(align_format::kDfltArgNumAlignments), m_Html(false) {}; /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts); /// Parses the output format command line option value, returns the /// requested output format type and any custom output formats (if /// any and applicable) /// @param args Command line arguments object [in] /// @param fmt_type Output format type requested in command line options /// [out] /// @param custom_fmt_spec Custom output format specification in command /// line options [out] static void ParseFormattingString(const CArgs& args, EOutputFormat& fmt_type, string& custom_fmt_spec); /// Get the choice of formatted output EOutputFormat GetFormattedOutputChoice() const { return m_OutputFormat; } /// Returns true if the desired output format is structured (needed to /// determine whether to print or not that a PSI-BLAST search has /// converged - this is not supported in structured formats) bool HasStructuredOutputFormat() const { return m_OutputFormat == eXml || m_OutputFormat == eAsnText || m_OutputFormat == eAsnBinary; } /// Display the NCBI GIs in formatted output? bool ShowGis() const { return m_ShowGis; } /// Number of one-line descriptions to show in traditional BLAST output TSeqPos GetNumDescriptions() const { return m_NumDescriptions; } /// Number of alignments to show in traditional BLAST output TSeqPos GetNumAlignments() const { return m_NumAlignments; } /// Display HTML output? bool DisplayHtmlOutput() const { return m_Html; } /// Retrieve for string that specifies the custom output format for tabular /// and comma-separated value string GetCustomOutputFormatSpec() const { return m_CustomOutputFormatSpec; } bool ArchiveFormatRequested(const CArgs& args) const; private: EOutputFormat m_OutputFormat; ///< Choice of formatting output bool m_ShowGis; ///< Display NCBI GIs? TSeqPos m_NumDescriptions; ///< Number of 1-line descr. to show TSeqPos m_NumAlignments; ///< Number of alignments to show bool m_Html; ///< Display HTML output? /// The format specification for custom output, e.g.: tabular or /// comma-separated value (populated if applicable) string m_CustomOutputFormatSpec; }; /// Argument class to collect multi-threaded arguments class NCBI_BLASTINPUT_EXPORT CMTArgs : public IBlastCmdLineArgs { public: /// Default Constructor CMTArgs() : m_NumThreads(CThreadable::kMinNumThreads) {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Get the number of threads to spawn size_t GetNumThreads() const { return m_NumThreads; } private: size_t m_NumThreads; ///< Number of threads to spawn }; /// Argument class to collect remote vs. local execution class NCBI_BLASTINPUT_EXPORT CRemoteArgs : public IBlastCmdLineArgs { public: /// Default constructor CRemoteArgs() : m_IsRemote(false) {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Return whether the search should be executed remotely or not bool ExecuteRemotely() const { return m_IsRemote; } private: /// Should the search be executed remotely? bool m_IsRemote; }; /// Argument class to collect debugging options. /// Only show in command line if compiled with _DEBUG class NCBI_BLASTINPUT_EXPORT CDebugArgs : public IBlastCmdLineArgs { public: /// Default constructor CDebugArgs() : m_DebugOutput(false), m_RmtDebugOutput(false) {} /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options); /// Return whether debug (verbose) output should be produced on remote /// searches (only available when compiled with _DEBUG) bool ProduceDebugRemoteOutput() const { return m_RmtDebugOutput; } /// Return whether debug (verbose) output should be produced /// (only available when compiled with _DEBUG) bool ProduceDebugOutput() const { return m_DebugOutput; } private: /// Should debugging (verbose) output be printed bool m_DebugOutput; /// Should debugging (verbose) output be printed for remote BLAST bool m_RmtDebugOutput; }; /// Argument class to retrieve options for filtering HSPs (e.g.: culling /// options, best hit algorithm options) class NCBI_BLASTINPUT_EXPORT CHspFilteringArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts); }; /// Argument class to retrieve megablast database indexing options class NCBI_BLASTINPUT_EXPORT CMbIndexArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts); /// Auxiliary function to determine if the megablast database indexing /// options have been set static bool HasBeenSet(const CArgs& args); }; /* *********** START ************* */ /// Argument class to retrieve GPU options class NCBI_BLASTINPUT_EXPORT CGpuArgs : public IBlastCmdLineArgs { public: /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void SetArgumentDescriptions(CArgDescriptions& arg_desc); /** Interface method, \sa IBlastCmdLineArgs::SetArgumentDescriptions */ virtual void ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts); }; /* ********** FINISH ************* */ /// Type definition of a container of IBlastCmdLineArgs typedef vector< CRef > TBlastCmdLineArgs; /// Base command line argument class for a generic BLAST command line binary class NCBI_BLASTINPUT_EXPORT CBlastAppArgs : public CObject { public: /// Default constructor CBlastAppArgs(); /// Our virtual destructor virtual ~CBlastAppArgs() {} /// Set the command line arguments CArgDescriptions* SetCommandLine(); /// Get the task for this object string GetTask() const { return m_Task; } /// Set the task for this object /// @param task task name to set [in] void SetTask(const string& task); /// Extract the command line arguments into a CBlastOptionsHandle object /// @param args Commad line arguments [in] CRef SetOptions(const CArgs& args); /// Setter for the BLAST options handle, this is used if the options are /// recovered from a saved BLAST search strategy void SetOptionsHandle(CRef opts_hndl) { m_OptsHandle = opts_hndl; } /// Get the BLAST database arguments CRef GetBlastDatabaseArgs() const { return m_BlastDbArgs; } /// Set the BLAST database arguments void SetBlastDatabaseArgs(CRef args) { m_BlastDbArgs = args; } /// Get the options for the query sequence(s) CRef GetQueryOptionsArgs() const { return m_QueryOptsArgs; } /// Get the formatting options CRef GetFormattingArgs() const { return m_FormattingArgs; } /// Get the number of threads to spawn size_t GetNumThreads() const { return m_MTArgs->GetNumThreads(); } /// Get the input stream CNcbiIstream& GetInputStream() const { return m_StdCmdLineArgs->GetInputStream(); } /// Get the output stream CNcbiOstream& GetOutputStream() const { return m_StdCmdLineArgs->GetOutputStream(); } /// Set the input stream to a temporary input file (needed when importing /// a search strategy) /// @param input_file temporary input file to read [in] void SetInputStream(CRef input_file) { m_StdCmdLineArgs->SetInputStream(input_file); } /// Get the input stream for the search strategy CNcbiIstream* GetImportSearchStrategyStream(const CArgs& args) { return m_SearchStrategyArgs->GetImportStream(args); } /// Get the output stream for the search strategy CNcbiOstream* GetExportSearchStrategyStream(const CArgs& args) { return m_SearchStrategyArgs->GetExportStream(args); } /// Determine whether the search should be executed remotely or not bool ExecuteRemotely() const { return m_RemoteArgs->ExecuteRemotely(); } /// Return whether debug (verbose) output should be produced on remote /// searches (only available when compiled with _DEBUG) bool ProduceDebugRemoteOutput() const { return m_DebugArgs->ProduceDebugRemoteOutput(); } /// Return whether debug (verbose) output should be produced on remote /// searches (only available when compiled with _DEBUG) bool ProduceDebugOutput() const { return m_DebugArgs->ProduceDebugOutput(); } /// Get the query batch size virtual int GetQueryBatchSize() const = 0; /// Retrieve the client ID for remote requests string GetClientId() const { _ASSERT( !m_ClientId.empty() ); return m_ClientId; } protected: /// Set of command line argument objects TBlastCmdLineArgs m_Args; /// query options object CRef m_QueryOptsArgs; /// database/subject object CRef m_BlastDbArgs; /// formatting options CRef m_FormattingArgs; /// multi-threaded options CRef m_MTArgs; /// remote vs. local execution options CRef m_RemoteArgs; /// standard command line arguments class CRef m_StdCmdLineArgs; /// arguments for dealing with search strategies CRef m_SearchStrategyArgs; /// Debugging arguments CRef m_DebugArgs; /* *********** START ************* */ /// GPU options CRef m_GpuArgs; /* ********** FINISH ************* */ /// HSP filtering arguments CRef m_HspFilteringArgs; /// The BLAST options handle, only non-NULL if assigned via /// SetOptionsHandle, i.e.: from a saved search strategy CRef m_OptsHandle; /// Task specified in the command line string m_Task; /// Client ID used for remote BLAST submissions, must be populated by /// subclasses string m_ClientId; /// Is this application being run ungapped bool m_IsUngapped; /// Create the options handle based on the command line arguments /// @param locality whether the search will be executed locally or remotely /// [in] /// @param args command line arguments [in] virtual CRef x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& args) = 0; }; /** * @brief Create a CArgDescriptions object and invoke SetArgumentDescriptions * for each of the TBlastCmdLineArgs in its argument list * * @param args arguments to configure the return value [in] * * @return a CArgDescriptions object with the command line options set */ NCBI_BLASTINPUT_EXPORT CArgDescriptions* SetUpCommandLineArguments(TBlastCmdLineArgs& args); END_SCOPE(blast) END_NCBI_SCOPE #endif /* ALGO_BLAST_BLASTINPUT___BLAST_ARGS__HPP */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/blast_args.cpp0000644000175000017500000022753212001215340023412 0ustar ykeyke/* $Id: blast_args.cpp 257681 2011-03-15 19:23:36Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's offical duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * ===========================================================================*/ /***************************************************************************** File name: blast_args.cpp Author: Jason Papadopoulos ******************************************************************************/ /** @file blast_args.cpp * convert blast-related command line * arguments into blast options */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: blast_args.cpp 257681 2011-03-15 19:23:36Z rafanovi $"; #endif #include #include #include #include #include #include /* for CObjMgrQueryFactory */ #include #include #include #include #include #include // for CInputException #include #include // for CPsiBlastInputClustalW #include // for CPssmEngine BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) USING_SCOPE(objects); USING_SCOPE(align_format); void IBlastCmdLineArgs::ExtractAlgorithmOptions(const CArgs& /* cmd_line_args */, CBlastOptions& /* options */) {} CProgramDescriptionArgs::CProgramDescriptionArgs(const string& program_name, const string& program_desc) : m_ProgName(program_name), m_ProgDesc(program_desc) {} void CProgramDescriptionArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { // program description arg_desc.SetUsageContext(m_ProgName, m_ProgDesc + " " + CBlastVersion().Print()); } CTaskCmdLineArgs::CTaskCmdLineArgs(const set& supported_tasks, const string& default_task) : m_SupportedTasks(supported_tasks), m_DefaultTask(default_task) { _ASSERT( !m_SupportedTasks.empty() ); if ( !m_DefaultTask.empty() ) { _ASSERT(m_SupportedTasks.find(m_DefaultTask) != m_SupportedTasks.end()); } } void CTaskCmdLineArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); if ( !m_DefaultTask.empty() ) { arg_desc.AddDefaultKey(kTask, "task_name", "Task to execute", CArgDescriptions::eString, m_DefaultTask); } else { arg_desc.AddKey(kTask, "task_name", "Task to execute", CArgDescriptions::eString); } arg_desc.SetConstraint(kTask, new CArgAllowStringSet(m_SupportedTasks)); arg_desc.SetCurrentGroup(""); } void CTaskCmdLineArgs::ExtractAlgorithmOptions(const CArgs& /* cmd_line_args */, CBlastOptions& /* options */) { // N.B.: handling of tasks occurs at the application level to ensure that // only relevant tasks are added (@sa CBlastnAppArgs) } void CGenericSearchArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); // evalue cutoff arg_desc.AddDefaultKey(kArgEvalue, "evalue", "Expectation value (E) threshold for saving hits ", CArgDescriptions::eDouble, NStr::DoubleToString(BLAST_EXPECT_VALUE)); // word size // Default values: blastn=11, megablast=28, others=3 const string description = m_QueryIsProtein ? "Word size for wordfinder algorithm" : "Word size for wordfinder algorithm (length of best perfect match)"; arg_desc.AddOptionalKey(kArgWordSize, "int_value", description, CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgWordSize, m_QueryIsProtein ? new CArgAllowValuesGreaterThanOrEqual(2) : new CArgAllowValuesGreaterThanOrEqual(4)); if ( !m_IsRpsBlast && !m_IsTblastx) { // gap open penalty arg_desc.AddOptionalKey(kArgGapOpen, "open_penalty", "Cost to open a gap", CArgDescriptions::eInteger); // gap extend penalty arg_desc.AddOptionalKey(kArgGapExtend, "extend_penalty", "Cost to extend a gap", CArgDescriptions::eInteger); } if (m_ShowPercentIdentity) { arg_desc.SetCurrentGroup("Restrict search or results"); arg_desc.AddOptionalKey(kArgPercentIdentity, "float_value", "Percent identity", CArgDescriptions::eDouble); arg_desc.SetConstraint(kArgPercentIdentity, new CArgAllow_Doubles(0.0, 100.0)); } arg_desc.SetCurrentGroup("Extension options"); // ungapped X-drop // Default values: blastn=20, megablast=10, others=7 arg_desc.AddOptionalKey(kArgUngappedXDropoff, "float_value", "X-dropoff value (in bits) for ungapped extensions", CArgDescriptions::eDouble); // Tblastx is ungapped only. if (!m_IsTblastx) { // initial gapped X-drop // Default values: blastn=30, megablast=20, tblastx=0, others=15 arg_desc.AddOptionalKey(kArgGappedXDropoff, "float_value", "X-dropoff value (in bits) for preliminary gapped extensions", CArgDescriptions::eDouble); // final gapped X-drop // Default values: blastn/megablast=50, tblastx=0, others=25 arg_desc.AddOptionalKey(kArgFinalGappedXDropoff, "float_value", "X-dropoff value (in bits) for final gapped alignment", CArgDescriptions::eDouble); } arg_desc.SetCurrentGroup("Statistical options"); // effective search space // Default value is the real size arg_desc.AddOptionalKey(kArgEffSearchSpace, "int_value", "Effective length of the search space", CArgDescriptions::eInt8); arg_desc.SetConstraint(kArgEffSearchSpace, new CArgAllowValuesGreaterThanOrEqual(0)); #if 0 arg_desc.AddDefaultKey(kArgMaxHSPsPerSubject, "int_value", "Maximum number of HPSs per subject to save " "( " + NStr::IntToString(kDfltArgMaxHSPsPerSubject) + " means infinite)", CArgDescriptions::eInteger, NStr::IntToString(kDfltArgMaxHSPsPerSubject)); arg_desc.SetConstraint(kArgMaxHSPsPerSubject, new CArgAllowValuesGreaterThanOrEqual(0)); #endif arg_desc.SetCurrentGroup(""); } void CGenericSearchArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgEvalue]) { opt.SetEvalueThreshold(args[kArgEvalue].AsDouble()); } int gap_open=0, gap_extend=0; if (args.Exist(kArgMatrixName) && args[kArgMatrixName]) BLAST_GetProteinGapExistenceExtendParams (args[kArgMatrixName].AsString().c_str(), &gap_open, &gap_extend); if (args.Exist(kArgGapOpen) && args[kArgGapOpen]) { opt.SetGapOpeningCost(args[kArgGapOpen].AsInteger()); } else if (args.Exist(kArgMatrixName) && args[kArgMatrixName]) { opt.SetGapOpeningCost(gap_open); } if (args.Exist(kArgGapExtend) && args[kArgGapExtend]) { opt.SetGapExtensionCost(args[kArgGapExtend].AsInteger()); } else if (args.Exist(kArgMatrixName) && args[kArgMatrixName]) { opt.SetGapExtensionCost(gap_extend); } if (args[kArgUngappedXDropoff]) { opt.SetXDropoff(args[kArgUngappedXDropoff].AsDouble()); } if (args.Exist(kArgGappedXDropoff) && args[kArgGappedXDropoff]) { opt.SetGapXDropoff(args[kArgGappedXDropoff].AsDouble()); } if (args.Exist(kArgFinalGappedXDropoff) && args[kArgFinalGappedXDropoff]) { opt.SetGapXDropoffFinal(args[kArgFinalGappedXDropoff].AsDouble()); } if (args[kArgWordSize]) { if (m_QueryIsProtein && args[kArgWordSize].AsInteger() > 5) opt.SetLookupTableType(eCompressedAaLookupTable); opt.SetWordSize(args[kArgWordSize].AsInteger()); } if (args[kArgEffSearchSpace]) { opt.SetEffectiveSearchSpace(args[kArgEffSearchSpace].AsInt8()); } if (args.Exist(kArgPercentIdentity) && args[kArgPercentIdentity]) { opt.SetPercentIdentity(args[kArgPercentIdentity].AsDouble()); } #if 0 if (args[kArgMaxHSPsPerSubject]) { const int value = args[kArgMaxHSPsPerSubject].AsInteger(); if (value != kDfltArgMaxHSPsPerSubject) { opt.SetMaxNumHspPerSequence(value); } } #endif } void CFilteringArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Query filtering options"); if (m_QueryIsProtein) { arg_desc.AddDefaultKey(kArgSegFiltering, "SEG_options", "Filter query sequence with SEG " "(Format: '" + kDfltArgApplyFiltering + "', " + "'window locut hicut', or '" + kDfltArgNoFiltering + "' to disable)", CArgDescriptions::eString, m_FilterByDefault ? kDfltArgSegFiltering : kDfltArgNoFiltering); arg_desc.AddDefaultKey(kArgLookupTableMaskingOnly, "soft_masking", "Apply filtering locations as soft masks", CArgDescriptions::eBoolean, "false"); } else { arg_desc.AddDefaultKey(kArgDustFiltering, "DUST_options", "Filter query sequence with DUST " "(Format: '" + kDfltArgApplyFiltering + "', " + "'level window linker', or '" + kDfltArgNoFiltering + "' to disable)", CArgDescriptions::eString, m_FilterByDefault ? kDfltArgDustFiltering : kDfltArgNoFiltering); arg_desc.AddOptionalKey(kArgFilteringDb, "filtering_database", "BLAST database containing filtering elements (i.e.: repeats)", CArgDescriptions::eString); arg_desc.AddOptionalKey(kArgWindowMaskerTaxId, "window_masker_taxid", "Enable WindowMasker filtering using a Taxonomic ID", CArgDescriptions::eInteger); arg_desc.AddOptionalKey(kArgWindowMaskerDatabase, "window_masker_db", "Enable WindowMasker filtering using this repeats database.", CArgDescriptions::eString); arg_desc.AddDefaultKey(kArgLookupTableMaskingOnly, "soft_masking", "Apply filtering locations as soft masks", CArgDescriptions::eBoolean, "true"); } arg_desc.SetCurrentGroup(""); } void CFilteringArgs::x_TokenizeFilteringArgs(const string& filtering_args, vector& output) const { output.clear(); NStr::Tokenize(filtering_args, " ", output); if (output.size() != 3) { NCBI_THROW(CInputException, eInvalidInput, "Invalid number of arguments to filtering option"); } } void CFilteringArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgLookupTableMaskingOnly]) { opt.SetMaskAtHash(args[kArgLookupTableMaskingOnly].AsBoolean()); } vector tokens; try { if (m_QueryIsProtein && args[kArgSegFiltering]) { const string& seg_opts = args[kArgSegFiltering].AsString(); if (seg_opts == kDfltArgNoFiltering) { opt.SetSegFiltering(false); } else if (seg_opts == kDfltArgApplyFiltering) { opt.SetSegFiltering(true); } else { x_TokenizeFilteringArgs(seg_opts, tokens); opt.SetSegFilteringWindow(NStr::StringToInt(tokens[0])); opt.SetSegFilteringLocut(NStr::StringToDouble(tokens[1])); opt.SetSegFilteringHicut(NStr::StringToDouble(tokens[2])); } } if ( !m_QueryIsProtein && args[kArgDustFiltering]) { const string& dust_opts = args[kArgDustFiltering].AsString(); if (dust_opts == kDfltArgNoFiltering) { opt.SetDustFiltering(false); } else if (dust_opts == kDfltArgApplyFiltering) { opt.SetDustFiltering(true); } else { x_TokenizeFilteringArgs(dust_opts, tokens); opt.SetDustFilteringLevel(NStr::StringToInt(tokens[0])); opt.SetDustFilteringWindow(NStr::StringToInt(tokens[1])); opt.SetDustFilteringLinker(NStr::StringToInt(tokens[2])); } } } catch (const CStringException& e) { if (e.GetErrCode() == CStringException::eConvert) { NCBI_THROW(CInputException, eInvalidInput, "Invalid input for filtering parameters"); } } int filter_dbs = 0; if (args.Exist(kArgFilteringDb) && args[kArgFilteringDb]) { opt.SetRepeatFilteringDB(args[kArgFilteringDb].AsString().c_str()); filter_dbs++; } if (args.Exist(kArgWindowMaskerTaxId) && args[kArgWindowMaskerTaxId]) { opt.SetWindowMaskerTaxId (args[kArgWindowMaskerTaxId].AsInteger()); filter_dbs++; } if (args.Exist(kArgWindowMaskerDatabase) && args[kArgWindowMaskerDatabase]) { opt.SetWindowMaskerDatabase (args[kArgWindowMaskerDatabase].AsString().c_str()); filter_dbs++; } if (filter_dbs > 1) { string msg = string("Please specify at most one of ") + kArgFilteringDb + ", " + kArgWindowMaskerTaxId + ", or " + kArgWindowMaskerDatabase + "."; NCBI_THROW(CInputException, eInvalidInput, msg); } } void CWindowSizeArg::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Extension options"); // 2-hit wordfinder window size arg_desc.AddOptionalKey(kArgWindowSize, "int_value", "Multiple hits window size, use 0 to specify " "1-hit algorithm", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgWindowSize, new CArgAllowValuesGreaterThanOrEqual(0)); arg_desc.SetCurrentGroup(""); } void CWindowSizeArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgWindowSize]) { opt.SetWindowSize(args[kArgWindowSize].AsInteger()); } else { int window = -1; BLAST_GetSuggestedWindowSize(opt.GetProgramType(), opt.GetMatrixName(), &window); if (window != -1) { opt.SetWindowSize(window); } } } void COffDiagonalRangeArg::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Extension options"); // 2-hit wordfinder off diagonal range arg_desc.AddDefaultKey(kArgOffDiagonalRange, "int_value", "Number of off-diagonals to search for the 2nd hit, " "use 0 to turn off", CArgDescriptions::eInteger, NStr::IntToString(kDfltOffDiagonalRange)); arg_desc.SetConstraint(kArgOffDiagonalRange, new CArgAllowValuesGreaterThanOrEqual(0)); arg_desc.SetCurrentGroup(""); } void COffDiagonalRangeArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgOffDiagonalRange]) { opt.SetOffDiagonalRange(args[kArgOffDiagonalRange].AsInteger()); } else { opt.SetOffDiagonalRange(0); } } void CWordThresholdArg::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); // lookup table word score threshold arg_desc.AddOptionalKey(kArgWordScoreThreshold, "float_value", "Minimum word score such that the word is added to the " "BLAST lookup table", CArgDescriptions::eDouble); arg_desc.SetConstraint(kArgWordScoreThreshold, new CArgAllowValuesGreaterThanOrEqual(0)); arg_desc.SetCurrentGroup(""); } void CWordThresholdArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgWordScoreThreshold]) { opt.SetWordThreshold(args[kArgWordScoreThreshold].AsDouble()); } else { double threshold = -1; BLAST_GetSuggestedThreshold(opt.GetProgramType(), opt.GetMatrixName(), &threshold); if (threshold != -1) { opt.SetWordThreshold(threshold); } } } void CMatrixNameArg::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); arg_desc.AddOptionalKey(kArgMatrixName, "matrix_name", "Scoring matrix name (normally BLOSUM62)", CArgDescriptions::eString); arg_desc.SetCurrentGroup(""); } void CMatrixNameArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgMatrixName]) { opt.SetMatrixName(args[kArgMatrixName].AsString().c_str()); } } void CNuclArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { // TLM arg_desc.SetCurrentGroup("Nucleotide scoring options"); arg_desc.SetCurrentGroup("General search options"); // blastn mismatch penalty arg_desc.AddOptionalKey(kArgMismatch, "penalty", "Penalty for a nucleotide mismatch", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgMismatch, new CArgAllowValuesLessThanOrEqual(0)); // blastn match reward arg_desc.AddOptionalKey(kArgMatch, "reward", "Reward for a nucleotide match", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgMatch, new CArgAllowValuesGreaterThanOrEqual(0)); arg_desc.SetCurrentGroup("Extension options"); arg_desc.AddFlag(kArgNoGreedyExtension, "Use non-greedy dynamic programming extension", true); arg_desc.SetCurrentGroup(""); } void CNuclArgs::ExtractAlgorithmOptions(const CArgs& cmd_line_args, CBlastOptions& options) { if (cmd_line_args[kArgMismatch]) { options.SetMismatchPenalty(cmd_line_args[kArgMismatch].AsInteger()); } if (cmd_line_args[kArgMatch]) { options.SetMatchReward(cmd_line_args[kArgMatch].AsInteger()); } if (cmd_line_args[kArgNoGreedyExtension]) { options.SetGapExtnAlgorithm(eDynProgScoreOnly); options.SetGapTracebackAlgorithm(eDynProgTbck); } } const string CDiscontiguousMegablastArgs::kTemplType_Coding("coding"); const string CDiscontiguousMegablastArgs::kTemplType_Optimal("optimal"); const string CDiscontiguousMegablastArgs::kTemplType_CodingAndOptimal("coding_and_optimal"); void CDiscontiguousMegablastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Extension options"); // FIXME: this can be applied to any program, but since it was only offered // in megablast, we're putting it here arg_desc.AddOptionalKey(kArgMinRawGappedScore, "int_value", "Minimum raw gapped score to keep an alignment " "in the preliminary gapped and traceback stages", CArgDescriptions::eInteger); arg_desc.SetCurrentGroup("Discontiguous MegaBLAST options"); arg_desc.AddOptionalKey(kArgDMBTemplateType, "type", "Discontiguous MegaBLAST template type", CArgDescriptions::eString); arg_desc.SetConstraint(kArgDMBTemplateType, &(*new CArgAllow_Strings, kTemplType_Coding, kTemplType_Optimal, kTemplType_CodingAndOptimal)); arg_desc.SetDependency(kArgDMBTemplateType, CArgDescriptions::eRequires, kArgDMBTemplateLength); arg_desc.AddOptionalKey(kArgDMBTemplateLength, "int_value", "Discontiguous MegaBLAST template length", CArgDescriptions::eInteger); set allowed_values; allowed_values.insert(16); allowed_values.insert(18); allowed_values.insert(21); arg_desc.SetConstraint(kArgDMBTemplateLength, new CArgAllowIntegerSet(allowed_values)); arg_desc.SetDependency(kArgDMBTemplateLength, CArgDescriptions::eRequires, kArgDMBTemplateType); arg_desc.SetCurrentGroup(""); } void CDiscontiguousMegablastArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& options) { if (args[kArgMinRawGappedScore]) { options.SetCutoffScore(args[kArgMinRawGappedScore].AsInteger()); } if (args[kArgDMBTemplateType]) { const string& type = args[kArgDMBTemplateType].AsString(); EDiscWordType temp_type = eMBWordCoding; if (type == kTemplType_Coding) { temp_type = eMBWordCoding; } else if (type == kTemplType_Optimal) { temp_type = eMBWordOptimal; } else if (type == kTemplType_CodingAndOptimal) { temp_type = eMBWordTwoTemplates; } else { abort(); } options.SetMBTemplateType(static_cast(temp_type)); } if (args[kArgDMBTemplateLength]) { unsigned char tlen = static_cast(args[kArgDMBTemplateLength].AsInteger()); options.SetMBTemplateLength(tlen); } // FIXME: should the window size be adjusted if this is set? } void CCompositionBasedStatsArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); // composition based statistics, keep in sync with ECompoAdjustModes // documentation in composition_constants.h arg_desc.AddDefaultKey(kArgCompBasedStats, "compo", "Use composition-based statistics for blastp / tblastn:\n" " D or d: default (equivalent to 2)\n" " 0 or F or f: no composition-based statistics\n" " 1: Composition-based statistics " "as in NAR 29:2994-3005, 2001\n" " 2 or T or t : Composition-based score adjustment as in " "Bioinformatics 21:902-911,\n" " 2005, conditioned on sequence properties\n" " 3: Composition-based score adjustment as in " "Bioinformatics 21:902-911,\n" " 2005, unconditionally\n" "For programs other than tblastn, must either be " "absent or be D, F or 0", CArgDescriptions::eString, "2"); arg_desc.SetCurrentGroup("Miscellaneous options"); // Use Smith-Waterman algorithm in traceback stage // FIXME: available only for gapped blastp/tblastn, and with // composition-based statistics arg_desc.AddFlag(kArgUseSWTraceback, "Compute locally optimal Smith-Waterman alignments?", true); arg_desc.SetCurrentGroup(""); } /** * @brief Auxiliary function to set the composition based statistics and smith * waterman options * * @param opt BLAST options object [in|out] * @param comp_stat_string command line value for composition based statistics * [in] * @param smith_waterman_value command line value for determining the use of * the smith-waterman algorithm [in] * @param ungapped pointer to the value which determines whether the search * should be ungapped or not. It is NULL if ungapped searches are not * applicable */ static void s_SetCompositionBasedStats(CBlastOptions& opt, const string& comp_stat_string, bool smith_waterman_value, bool* ungapped = NULL) { const EProgram program = opt.GetProgram(); if (program == eBlastp || program == eTblastn || program == ePSIBlast || program == ePSITblastn) { ECompoAdjustModes compo_mode = eNoCompositionBasedStats; switch (comp_stat_string[0]) { case '0': case 'F': case 'f': compo_mode = eNoCompositionBasedStats; break; case '1': compo_mode = eCompositionBasedStats; break; case 'D': case 'd': case '2': case 'T': case 't': compo_mode = eCompositionMatrixAdjust; break; case '3': compo_mode = eCompoForceFullMatrixAdjust; break; } if(program == ePSITblastn) { compo_mode = eNoCompositionBasedStats; } if (ungapped && *ungapped && compo_mode != eNoCompositionBasedStats) { NCBI_THROW(CInputException, eInvalidInput, "Composition-adjusted searched are not supported with " "an ungapped search, please add -comp_based_stats F or " "do a gapped search"); } opt.SetCompositionBasedStats(compo_mode); if (program == eBlastp && compo_mode != eNoCompositionBasedStats && tolower(comp_stat_string[1]) == 'u') { opt.SetUnifiedP(1); } opt.SetSmithWatermanMode(smith_waterman_value); } } void CCompositionBasedStatsArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgCompBasedStats]) { auto_ptr ungapped(args.Exist(kArgUngapped) ? new bool(args[kArgUngapped]) : 0); s_SetCompositionBasedStats(opt, args[kArgCompBasedStats].AsString(), args[kArgUseSWTraceback], ungapped.get()); } } void CGappedArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { // perform gapped search #if 0 arg_desc.AddOptionalKey(ARG_GAPPED, "gapped", "Perform gapped alignment (default T, but " "not available for tblastx)", CArgDescriptions::eBoolean, CArgDescriptions::fOptionalSeparator); arg_desc.AddAlias("-gapped", ARG_GAPPED); #endif arg_desc.SetCurrentGroup("Extension options"); arg_desc.AddFlag(kArgUngapped, "Perform ungapped alignment only?", true); arg_desc.SetCurrentGroup(""); } void CGappedArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& options) { #if 0 if (args[ARG_GAPPED] && options.GetProgram() != eTblastx) { options.SetGappedMode(args[ARG_GAPPED].AsBoolean()); } #endif options.SetGappedMode( !args[kArgUngapped] ); if (options.GetGappedMode() == false) options.SetSumStatisticsMode(true); } void CLargestIntronSizeArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); // largest intron length arg_desc.AddDefaultKey(kArgMaxIntronLength, "length", "Length of the largest intron allowed in a translated " "nucleotide sequence when linking multiple distinct " "alignments (a negative value disables linking)", CArgDescriptions::eInteger, NStr::IntToString(kDfltArgMaxIntronLength)); arg_desc.SetCurrentGroup(""); } void CLargestIntronSizeArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if ( !args[kArgMaxIntronLength] ) { return; } if (args[kArgMaxIntronLength].AsInteger() < 0) { opt.SetSumStatisticsMode(false); } else { opt.SetSumStatisticsMode(); opt.SetLongestIntronLength(args[kArgMaxIntronLength].AsInteger()); } } void CFrameShiftArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); // applicable in blastx/tblastn, off by default arg_desc.AddOptionalKey(kArgFrameShiftPenalty, "frameshift", "Frame shift penalty (for use with out-of-frame " "gapped alignment in blastx or tblastn, default " "ignored)", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgFrameShiftPenalty, new CArgAllowValuesGreaterThanOrEqual(1)); arg_desc.SetCurrentGroup(""); } void CFrameShiftArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgFrameShiftPenalty]) { opt.SetOutOfFrameMode(); opt.SetFrameShiftPenalty(args[kArgFrameShiftPenalty].AsInteger()); } } void CGeneticCodeArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { if (m_Target == eQuery) { arg_desc.SetCurrentGroup("Input query options"); // query genetic code arg_desc.AddDefaultKey(kArgQueryGeneticCode, "int_value", "Genetic code to use to translate query", CArgDescriptions::eInteger, NStr::IntToString(BLAST_GENETIC_CODE)); } else { arg_desc.SetCurrentGroup("General search options"); // DB genetic code arg_desc.AddDefaultKey(kArgDbGeneticCode, "int_value", "Genetic code to use to translate " "database/subjects", CArgDescriptions::eInteger, NStr::IntToString(BLAST_GENETIC_CODE)); } arg_desc.SetCurrentGroup(""); } void CGeneticCodeArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { const EProgram program = opt.GetProgram(); if (m_Target == eQuery && args[kArgQueryGeneticCode]) { opt.SetQueryGeneticCode(args[kArgQueryGeneticCode].AsInteger()); } if (m_Target == eDatabase && args[kArgDbGeneticCode] && (program == eTblastn || program == eTblastx) ) { opt.SetDbGeneticCode(args[kArgDbGeneticCode].AsInteger()); } } void CGapTriggerArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Extension options"); const double default_value = m_QueryIsProtein ? BLAST_GAP_TRIGGER_PROT : BLAST_GAP_TRIGGER_NUCL; arg_desc.AddDefaultKey(kArgGapTrigger, "float_value", "Number of bits to trigger gapping", CArgDescriptions::eDouble, NStr::DoubleToString(default_value)); arg_desc.SetCurrentGroup(""); } void CGapTriggerArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgGapTrigger]) { opt.SetGapTrigger(args[kArgGapTrigger].AsDouble()); } } void CPssmEngineArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("PSSM engine options"); // Pseudo count arg_desc.AddDefaultKey(kArgPSIPseudocount, "pseudocount", "Pseudo-count value used when constructing PSSM", CArgDescriptions::eInteger, NStr::IntToString(PSI_PSEUDO_COUNT_CONST)); // Evalue inclusion threshold arg_desc.AddDefaultKey(kArgPSIInclusionEThreshold, "ethresh", "E-value inclusion threshold for pairwise alignments", CArgDescriptions::eDouble, NStr::DoubleToString(PSI_INCLUSION_ETHRESH)); arg_desc.SetCurrentGroup(""); } void CPssmEngineArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args[kArgPSIPseudocount]) { opt.SetPseudoCount(args[kArgPSIPseudocount].AsInteger()); } if (args[kArgPSIInclusionEThreshold]) { opt.SetInclusionThreshold(args[kArgPSIInclusionEThreshold].AsDouble()); } } void CPsiBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { if (m_DbTarget == eNucleotideDb) { arg_desc.SetCurrentGroup("PSI-TBLASTN options"); // PSI-tblastn checkpoint arg_desc.AddOptionalKey(kArgPSIInputChkPntFile, "psi_chkpt_file", "PSI-TBLASTN checkpoint file", CArgDescriptions::eInputFile); arg_desc.SetDependency(kArgPSIInputChkPntFile, CArgDescriptions::eExcludes, kArgRemote); } else { arg_desc.SetCurrentGroup("PSI-BLAST options"); // Number of iterations arg_desc.AddDefaultKey(kArgPSINumIterations, "int_value", "Number of iterations to perform", CArgDescriptions::eInteger, NStr::IntToString(1)); arg_desc.SetConstraint(kArgPSINumIterations, new CArgAllowValuesGreaterThanOrEqual(1)); arg_desc.SetDependency(kArgPSINumIterations, CArgDescriptions::eExcludes, kArgRemote); // checkpoint file arg_desc.AddOptionalKey(kArgPSIOutputChkPntFile, "checkpoint_file", "File name to store checkpoint file", CArgDescriptions::eOutputFile); // ASCII matrix file arg_desc.AddOptionalKey(kArgAsciiPssmOutputFile, "ascii_mtx_file", "File name to store ASCII version of PSSM", CArgDescriptions::eOutputFile); vector msa_exclusions; msa_exclusions.push_back(kArgPSIInputChkPntFile); msa_exclusions.push_back(kArgQuery); msa_exclusions.push_back(kArgQueryLocation); // pattern and MSA is not supported msa_exclusions.push_back(kArgPHIPatternFile); // MSA restart file arg_desc.AddOptionalKey(kArgMSAInputFile, "align_restart", "File name of multiple sequence alignment to " "restart PSI-BLAST", CArgDescriptions::eInputFile); ITERATE(vector, exclusion, msa_exclusions) { arg_desc.SetDependency(kArgMSAInputFile, CArgDescriptions::eExcludes, *exclusion); } arg_desc.AddOptionalKey(kArgMSAMasterIndex, "index", "Index (1-based) of sequence to use as a master" " in the multiple sequence alignment. If not " "provided, the first sequence in the multiple " "sequence alignment will be used", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgMSAMasterIndex, new CArgAllowValuesGreaterThanOrEqual(1)); ITERATE(vector, exclusion, msa_exclusions) { arg_desc.SetDependency(kArgMSAInputFile, CArgDescriptions::eExcludes, *exclusion); } // PSI-BLAST checkpoint arg_desc.AddOptionalKey(kArgPSIInputChkPntFile, "psi_chkpt_file", "PSI-BLAST checkpoint file", CArgDescriptions::eInputFile); } arg_desc.SetDependency(kArgPSIInputChkPntFile, CArgDescriptions::eExcludes, kArgQuery); arg_desc.SetDependency(kArgPSIInputChkPntFile, CArgDescriptions::eExcludes, kArgQueryLocation); arg_desc.SetCurrentGroup(""); } CRef CPsiBlastArgs::x_CreatePssmFromMsa(CNcbiIstream& input_stream, CBlastOptions& opt, bool save_ascii_pssm, unsigned int msa_master_idx) { // FIXME get these from CBlastOptions CPSIBlastOptions psiblast_opts; PSIBlastOptionsNew(&psiblast_opts); CPSIDiagnosticsRequest diags(PSIDiagnosticsRequestNewEx(save_ascii_pssm)); CPsiBlastInputClustalW pssm_input(input_stream, *psiblast_opts, opt.GetMatrixName(), diags, NULL, 0, opt.GetGapOpeningCost(), opt.GetGapExtensionCost(), msa_master_idx); CPssmEngine pssm_engine(&pssm_input); return pssm_engine.Run(); } void CPsiBlastArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (m_DbTarget == eProteinDb) { if (args[kArgPSINumIterations]) { m_NumIterations = args[kArgPSINumIterations].AsInteger(); } if (args.Exist(kArgPSIOutputChkPntFile) && args[kArgPSIOutputChkPntFile]) { m_CheckPointOutput.Reset (new CAutoOutputFileReset (args[kArgPSIOutputChkPntFile].AsString())); } const bool kSaveAsciiPssm = args[kArgAsciiPssmOutputFile]; if (kSaveAsciiPssm) { m_AsciiMatrixOutput.Reset (new CAutoOutputFileReset (args[kArgAsciiPssmOutputFile].AsString())); } if (args[kArgMSAInputFile]) { CNcbiIstream& in = args[kArgMSAInputFile].AsInputFile(); unsigned int msa_master_idx = 0; if (args[kArgMSAMasterIndex]) { msa_master_idx = args[kArgMSAMasterIndex].AsInteger() - 1; } m_Pssm = x_CreatePssmFromMsa(in, opt, kSaveAsciiPssm, msa_master_idx); } } if (args.Exist(kArgPSIInputChkPntFile) && args[kArgPSIInputChkPntFile]) { CNcbiIstream& in = args[kArgPSIInputChkPntFile].AsInputFile(); _ASSERT(m_Pssm.Empty()); m_Pssm.Reset(new CPssmWithParameters); try { switch (CFormatGuess().Format(in)) { case CFormatGuess::eBinaryASN: in >> MSerial_AsnBinary >> *m_Pssm; break; case CFormatGuess::eTextASN: in >> MSerial_AsnText >> *m_Pssm; break; case CFormatGuess::eXml: in >> MSerial_Xml >> *m_Pssm; break; default: NCBI_THROW(CInputException, eInvalidInput, "Unsupported format for PSSM"); } } catch (const CSerialException&) { string msg("Unrecognized format for PSSM in "); msg += args[kArgPSIInputChkPntFile].AsString() + " (must be "; msg += "PssmWithParameters)"; NCBI_THROW(CInputException, eInvalidInput, msg); } _ASSERT(m_Pssm.NotEmpty()); } } void CPhiBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("PHI-BLAST options"); arg_desc.AddOptionalKey(kArgPHIPatternFile, "file", "File name containing pattern to search", CArgDescriptions::eInputFile); arg_desc.SetDependency(kArgPHIPatternFile, CArgDescriptions::eExcludes, kArgPSIInputChkPntFile); arg_desc.SetCurrentGroup(""); } void CPhiBlastArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { if (args.Exist(kArgPHIPatternFile) && args[kArgPHIPatternFile]) { CNcbiIstream& in = args[kArgPHIPatternFile].AsInputFile(); in.clear(); in.seekg(0); char buffer[4096]; string line; string pattern; string name; while (in.getline(buffer, 4096)) { line = buffer; string ltype = line.substr(0, 2); if (ltype == "ID") name = line.substr(5); else if (ltype == "PA") pattern = line.substr(5); } if (!pattern.empty()) opt.SetPHIPattern(pattern.c_str(), (Blast_QueryIsNucleotide(opt.GetProgramType()) ? true : false)); else NCBI_THROW(CInputException, eInvalidInput, "PHI pattern not read"); } } void CQueryOptionsArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Query filtering options"); // lowercase masking arg_desc.AddFlag(kArgUseLCaseMasking, "Use lower case filtering in query and subject sequence(s)?", true); arg_desc.SetCurrentGroup("Input query options"); // query location arg_desc.AddOptionalKey(kArgQueryLocation, "range", "Location on the query sequence in 1-based offsets " "(Format: start-stop)", CArgDescriptions::eString); if ( !m_QueryCannotBeNucl ) { // search strands arg_desc.AddDefaultKey(kArgStrand, "strand", "Query strand(s) to search against database/subject", CArgDescriptions::eString, kDfltArgStrand); arg_desc.SetConstraint(kArgStrand, &(*new CArgAllow_Strings, kDfltArgStrand, "plus", "minus")); } arg_desc.SetCurrentGroup("Miscellaneous options"); arg_desc.AddFlag(kArgParseDeflines, "Should the query and subject defline(s) be parsed?", true); arg_desc.SetCurrentGroup(""); } void CQueryOptionsArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { // Get the strand { m_Strand = eNa_strand_unknown; if (!Blast_QueryIsProtein(opt.GetProgramType()) && args[kArgStrand]) { const string& kStrand = args[kArgStrand].AsString(); if (kStrand == "both") { m_Strand = eNa_strand_both; } else if (kStrand == "plus") { m_Strand = eNa_strand_plus; } else if (kStrand == "minus") { m_Strand = eNa_strand_minus; } else { abort(); } } } // set the sequence range if (args[kArgQueryLocation]) { m_Range = ParseSequenceRange(args[kArgQueryLocation].AsString(), "Invalid specification of query location"); } m_UseLCaseMask = static_cast(args[kArgUseLCaseMasking]); m_ParseDeflines = static_cast(args[kArgParseDeflines]); } CBlastDatabaseArgs::CBlastDatabaseArgs(bool request_mol_type /* = false */, bool is_rpsblast /* = false */) : m_RequestMoleculeType(request_mol_type), m_IsRpsBlast(is_rpsblast), m_IsProtein(true), m_SupportsDatabaseMasking(false) {} bool CBlastDatabaseArgs::HasBeenSet(const CArgs& args) { if ( (args.Exist(kArgDb) && args[kArgDb].HasValue()) || (args.Exist(kArgSubject) && args[kArgSubject].HasValue()) ) { return true; } return false; } void CBlastDatabaseArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); // database filename arg_desc.AddOptionalKey(kArgDb, "database_name", "BLAST database name", CArgDescriptions::eString); arg_desc.SetCurrentGroup(""); if (m_RequestMoleculeType) { arg_desc.AddKey(kArgDbType, "database_type", "BLAST database molecule type", CArgDescriptions::eString); arg_desc.SetConstraint(kArgDbType, &(*new CArgAllow_Strings, "prot", "nucl")); } vector database_args; database_args.push_back(kArgDb); database_args.push_back(kArgGiList); database_args.push_back(kArgSeqIdList); database_args.push_back(kArgNegativeGiList); if (m_SupportsDatabaseMasking) { database_args.push_back(kArgDbSoftMask); database_args.push_back(kArgDbHardMask); } // DB size arg_desc.SetCurrentGroup("Statistical options"); arg_desc.AddOptionalKey(kArgDbSize, "num_letters", "Effective length of the database ", CArgDescriptions::eInt8); arg_desc.SetCurrentGroup("Restrict search or results"); // GI list arg_desc.AddOptionalKey(kArgGiList, "filename", "Restrict search of database to list of GI's", CArgDescriptions::eString); // SeqId list arg_desc.AddOptionalKey(kArgSeqIdList, "filename", "Restrict search of database to list of SeqId's", CArgDescriptions::eString); // Negative GI list arg_desc.AddOptionalKey(kArgNegativeGiList, "filename", "Restrict search of database to everything except the listed GIs", CArgDescriptions::eString); arg_desc.SetDependency(kArgGiList, CArgDescriptions::eExcludes, kArgNegativeGiList); arg_desc.SetDependency(kArgGiList, CArgDescriptions::eExcludes, kArgSeqIdList); arg_desc.SetDependency(kArgSeqIdList, CArgDescriptions::eExcludes, kArgNegativeGiList); // Entrez Query arg_desc.AddOptionalKey(kArgEntrezQuery, "entrez_query", "Restrict search with the given Entrez query", CArgDescriptions::eString); // For now, disable pairing -remote with either -gilist or // -negative_gilist as this is not implemented in the BLAST server arg_desc.SetDependency(kArgGiList, CArgDescriptions::eExcludes, kArgRemote); arg_desc.SetDependency(kArgSeqIdList, CArgDescriptions::eExcludes, kArgRemote); arg_desc.SetDependency(kArgNegativeGiList, CArgDescriptions::eExcludes, kArgRemote); // Entrez query currently requires the -remote option arg_desc.SetDependency(kArgEntrezQuery, CArgDescriptions::eRequires, kArgRemote); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) // Masking of database if (m_SupportsDatabaseMasking) { arg_desc.AddOptionalKey(kArgDbSoftMask, "filtering_algorithm", "Filtering algorithm ID to apply to the BLAST database as soft " "masking", CArgDescriptions::eString); arg_desc.SetDependency(kArgDbSoftMask, CArgDescriptions::eExcludes, kArgDbHardMask); arg_desc.AddOptionalKey(kArgDbHardMask, "filtering_algorithm", "Filtering algorithm ID to apply to the BLAST database as hard " "masking", CArgDescriptions::eString); } #endif // There is no RPS-BLAST 2 sequences if ( !m_IsRpsBlast ) { arg_desc.SetCurrentGroup("BLAST-2-Sequences options"); // subject sequence input (for bl2seq) arg_desc.AddOptionalKey(kArgSubject, "subject_input_file", "Subject sequence(s) to search", CArgDescriptions::eInputFile); ITERATE(vector, dbarg, database_args) { arg_desc.SetDependency(kArgSubject, CArgDescriptions::eExcludes, *dbarg); } // subject location arg_desc.AddOptionalKey(kArgSubjectLocation, "range", "Location on the subject sequence in 1-based offsets " "(Format: start-stop)", CArgDescriptions::eString); ITERATE(vector, dbarg, database_args) { arg_desc.SetDependency(kArgSubjectLocation, CArgDescriptions::eExcludes, *dbarg); } // Because Blast4-subject does not support Seq-locs, specifying a // subject range does not work for remote searches arg_desc.SetDependency(kArgSubjectLocation, CArgDescriptions::eExcludes, kArgRemote); } arg_desc.SetCurrentGroup(""); } void CBlastDatabaseArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts) { EMoleculeType mol_type = Blast_SubjectIsNucleotide(opts.GetProgramType()) ? CSearchDatabase::eBlastDbIsNucleotide : CSearchDatabase::eBlastDbIsProtein; m_IsProtein = (mol_type == CSearchDatabase::eBlastDbIsProtein); if (args.Exist(kArgDb) && args[kArgDb]) { m_SearchDb.Reset(new CSearchDatabase(args[kArgDb].AsString(), mol_type)); if (args.Exist(kArgGiList) && args[kArgGiList]) { string fn(SeqDB_ResolveDbPath(args[kArgGiList].AsString())); m_SearchDb->SetGiList(CRef (new CSeqDBFileGiList(fn))); } else if (args.Exist(kArgNegativeGiList) && args[kArgNegativeGiList]) { string fn(SeqDB_ResolveDbPath(args[kArgNegativeGiList].AsString())); m_SearchDb->SetNegativeGiList(CRef (new CSeqDBFileGiList(fn))); } else if (args.Exist(kArgSeqIdList) && args[kArgSeqIdList]) { string fn(SeqDB_ResolveDbPath(args[kArgSeqIdList].AsString())); m_SearchDb->SetGiList(CRef (new CSeqDBFileGiList(fn, CSeqDBFileGiList::eSiList))); } if (args.Exist(kArgEntrezQuery) && args[kArgEntrezQuery]) m_SearchDb->SetEntrezQueryLimitation(args[kArgEntrezQuery].AsString()); #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ (!defined(NCBI_COMPILER_MIPSPRO)) ) if (args.Exist(kArgDbSoftMask) && args[kArgDbSoftMask]) { m_SearchDb->SetFilteringAlgorithm(args[kArgDbSoftMask].AsString(), DB_MASK_SOFT); } else if (args.Exist(kArgDbHardMask) && args[kArgDbHardMask]) { m_SearchDb->SetFilteringAlgorithm(args[kArgDbHardMask].AsString(), DB_MASK_HARD); } #endif } else if (args.Exist(kArgSubject) && args[kArgSubject]) { CNcbiIstream& subj_input_stream = args[kArgSubject].AsInputFile(); TSeqRange subj_range; if (args.Exist(kArgSubjectLocation) && args[kArgSubjectLocation]) { subj_range = ParseSequenceRange(args[kArgSubjectLocation].AsString(), "Invalid specification of subject location"); } const bool parse_deflines = args.Exist(kArgParseDeflines) ? args[kArgParseDeflines] : kDfltArgParseDeflines; const bool use_lcase_masks = args.Exist(kArgUseLCaseMasking) ? args[kArgUseLCaseMasking] : kDfltArgUseLCaseMasking; CRef subjects; m_Scope = ReadSequencesToBlast(subj_input_stream, IsProtein(), subj_range, parse_deflines, use_lcase_masks, subjects); m_Subjects.Reset(new blast::CObjMgr_QueryFactory(*subjects)); } else { NCBI_THROW(CInputException, eInvalidInput, "Either a BLAST database or subject sequence(s) must be specified"); } if (opts.GetEffectiveSearchSpace() != 0) { // no need to set any other options, as this trumps them return; } if (args[kArgDbSize]) { opts.SetDbLength(args[kArgDbSize].AsInt8()); } } void CFormattingArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Formatting options"); const string kOutputFormatDescription = string( "alignment view options:\n" " 0 = pairwise,\n" " 1 = query-anchored showing identities,\n" " 2 = query-anchored no identities,\n" " 3 = flat query-anchored, show identities,\n" " 4 = flat query-anchored, no identities,\n" " 5 = XML Blast output,\n" " 6 = tabular,\n" " 7 = tabular with comment lines,\n" " 8 = Text ASN.1,\n" " 9 = Binary ASN.1,\n" " 10 = Comma-separated values,\n" " 11 = BLAST archive format (ASN.1) \n\n" "Options 6, 7, and 10 can be additionally configured to produce\n" "a custom format specified by space delimited format specifiers.\n" "The supported format specifiers are:\n") + DescribeTabularOutputFormatSpecifiers() + string("\n"); // alignment view arg_desc.AddDefaultKey(kArgOutputFormat, "format", kOutputFormatDescription, CArgDescriptions::eString, NStr::IntToString(kDfltArgOutputFormat)); // show GIs in deflines arg_desc.AddFlag(kArgShowGIs, "Show NCBI GIs in deflines?", true); // number of one-line descriptions to display arg_desc.AddDefaultKey(kArgNumDescriptions, "int_value", "Number of database sequences to show one-line " "descriptions for", CArgDescriptions::eInteger, NStr::IntToString(kDfltArgNumDescriptions)); arg_desc.SetConstraint(kArgNumDescriptions, new CArgAllowValuesGreaterThanOrEqual(0)); // number of alignments per DB sequence arg_desc.AddDefaultKey(kArgNumAlignments, "int_value", "Number of database sequences to show alignments for", CArgDescriptions::eInteger, NStr::IntToString(kDfltArgNumAlignments)); arg_desc.SetConstraint(kArgNumAlignments, new CArgAllowValuesGreaterThanOrEqual(0)); // Produce HTML? arg_desc.AddFlag(kArgProduceHtml, "Produce HTML output?", true); /// Hit list size, listed here for convenience only arg_desc.SetCurrentGroup("Restrict search or results"); arg_desc.AddOptionalKey(kArgMaxTargetSequences, "num_sequences", "Maximum number of aligned sequences to keep", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgMaxTargetSequences, new CArgAllowValuesGreaterThanOrEqual(1)); arg_desc.SetCurrentGroup(""); } bool CFormattingArgs::ArchiveFormatRequested(const CArgs& args) const { EOutputFormat output_fmt; string ignore; ParseFormattingString(args, output_fmt, ignore); return (output_fmt == eArchiveFormat ? true : false); } void CFormattingArgs::ParseFormattingString(const CArgs& args, EOutputFormat& fmt_type, string& custom_fmt_spec) { custom_fmt_spec.clear(); if (args[kArgOutputFormat]) { string fmt_choice = NStr::TruncateSpaces(args[kArgOutputFormat].AsString()); string::size_type pos; if ( (pos = fmt_choice.find_first_of(' ')) != string::npos) { custom_fmt_spec.assign(fmt_choice, pos+1, fmt_choice.size()-(pos+1)); fmt_choice.erase(pos); } int val = 0; try { val = NStr::StringToInt(fmt_choice); } catch (const CStringException&) { // probably a conversion error CNcbiOstrstream os; os << "'" << fmt_choice << "' is not a valid output format"; string msg = CNcbiOstrstreamToString(os); NCBI_THROW(CInputException, eInvalidInput, msg); } if (val < 0 || val >= static_cast(eEndValue)) { string msg("Formatting choice is out of range"); throw std::out_of_range(msg); } fmt_type = static_cast(val); if ( !(fmt_type == eTabular || fmt_type == eTabularWithComments || fmt_type == eCommaSeparatedValues) ) { custom_fmt_spec.clear(); } } } void CFormattingArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt) { ParseFormattingString(args, m_OutputFormat, m_CustomOutputFormatSpec); m_ShowGis = static_cast(args[kArgShowGIs]); if (args[kArgNumDescriptions]) { m_NumDescriptions = args[kArgNumDescriptions].AsInteger(); } if (args[kArgNumAlignments]) { m_NumAlignments = args[kArgNumAlignments].AsInteger(); } TSeqPos hitlist_size = 0; if (args[kArgMaxTargetSequences]) { hitlist_size = args[kArgMaxTargetSequences].AsInteger(); if (hitlist_size > 0 && m_OutputFormat == ePairwise) { /* Only non-default values will be overriden */ string warnings = CalculateFormattingParams(hitlist_size, m_NumDescriptions != kDfltArgNumDescriptions ? &m_NumDescriptions : 0, m_NumAlignments != kDfltArgNumAlignments ? &m_NumAlignments : 0); if ( !warnings.empty() ) { ERR_POST(Warning << warnings); } } } if (m_NumDescriptions == 0 && m_NumAlignments == 0 && hitlist_size == 0) { string msg("Either -"); msg += kArgMaxTargetSequences + ", -"; msg += kArgNumDescriptions + ", or -" + kArgNumAlignments + " must "; msg += "be non-zero"; NCBI_THROW(CInputException, eInvalidInput, msg); } else if (hitlist_size != 0) { opt.SetHitlistSize(hitlist_size); // alignments and descriptions are set here so that limiting is done // correctly for tabular output m_NumDescriptions = MIN(m_NumDescriptions, (TSeqPos)opt.GetHitlistSize()); m_NumAlignments = MIN(m_NumAlignments, (TSeqPos)opt.GetHitlistSize()); } else { if (m_OutputFormat <= eFlatQueryAnchoredNoIdentities) opt.SetHitlistSize(MAX(m_NumDescriptions, m_NumAlignments)); else { // These formats do not have sections just for descriptions or alignments. opt.SetHitlistSize(MIN(m_NumDescriptions, m_NumAlignments)); } } m_Html = static_cast(args[kArgProduceHtml]); } void CMTArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { const int kMinValue = static_cast(CThreadable::kMinNumThreads); // number of threads arg_desc.SetCurrentGroup("Miscellaneous options"); arg_desc.AddDefaultKey(kArgNumThreads, "int_value", "Number of threads (CPUs) to use in the BLAST search", CArgDescriptions::eInteger, NStr::IntToString(kMinValue)); arg_desc.SetConstraint(kArgNumThreads, new CArgAllowValuesGreaterThanOrEqual(kMinValue)); arg_desc.SetDependency(kArgNumThreads, CArgDescriptions::eExcludes, kArgRemote); /* arg_desc.SetDependency(kArgNumThreads, CArgDescriptions::eExcludes, kArgUseIndex); */ arg_desc.SetCurrentGroup(""); } void CMTArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */) { if (args.Exist(kArgNumThreads) && args[kArgNumThreads].HasValue()) { // could be cancelled by the exclusion in CRemoteArgs m_NumThreads = args[kArgNumThreads].AsInteger(); // This is temporarily ignored (per SB-635) if (args.Exist(kArgSubject) && args[kArgSubject].HasValue() && m_NumThreads != CThreadable::kMinNumThreads) { m_NumThreads = CThreadable::kMinNumThreads; LOG_POST(Warning << "'" << kArgNumThreads << "' is currently " << "ignored when '" << kArgSubject << "' is specified."); } } } void CRemoteArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Miscellaneous options"); arg_desc.AddFlag(kArgRemote, "Execute search remotely?", true); arg_desc.SetCurrentGroup(""); } void CRemoteArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */) { if (args.Exist(kArgRemote)) { m_IsRemote = static_cast(args[kArgRemote]); } } void CDebugArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { #if _BLAST_DEBUG arg_desc.SetCurrentGroup("Miscellaneous options"); arg_desc.AddFlag("verbose", "Produce verbose output (show BLAST options)", true); arg_desc.AddFlag("remote_verbose", "Produce verbose output for remote searches", true); arg_desc.AddFlag("use_test_remote_service", "Send remote requests to test servers", true); arg_desc.SetCurrentGroup(""); #endif /* _BLAST_DEBUG */ } void CDebugArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */) { #if _BLAST_DEBUG m_DebugOutput = static_cast(args["verbose"]); m_RmtDebugOutput = static_cast(args["remote_verbose"]); if (args["use_test_remote_service"]) { IRWRegistry& reg = CNcbiApplication::Instance()->GetConfig(); reg.Set("BLAST4", DEF_CONN_REG_SECTION "_" REG_CONN_SERVICE_NAME, "blast4_test"); } #endif /* _BLAST_DEBUG */ } void CHspFilteringArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { // culling limit arg_desc.SetCurrentGroup("Restrict search or results"); arg_desc.AddOptionalKey(kArgCullingLimit, "int_value", "If the query range of a hit is enveloped by that of at " "least this many higher-scoring hits, delete the hit", CArgDescriptions::eInteger); arg_desc.SetConstraint(kArgCullingLimit, // best hit algorithm arguments new CArgAllowValuesGreaterThanOrEqual(kDfltArgCullingLimit)); arg_desc.AddOptionalKey(kArgBestHitOverhang, "float_value", "Best Hit algorithm overhang value " "(recommended value: " + NStr::DoubleToString(kDfltArgBestHitOverhang) + ")", CArgDescriptions::eDouble); arg_desc.SetConstraint(kArgBestHitOverhang, new CArgAllowValuesBetween(kBestHit_OverhangMin, kBestHit_OverhangMax)); arg_desc.SetDependency(kArgBestHitOverhang, CArgDescriptions::eExcludes, kArgCullingLimit); arg_desc.AddOptionalKey(kArgBestHitScoreEdge, "float_value", "Best Hit algorithm score edge value " "(recommended value: " + NStr::DoubleToString(kDfltArgBestHitScoreEdge) + ")", CArgDescriptions::eDouble); arg_desc.SetConstraint(kArgBestHitScoreEdge, new CArgAllowValuesBetween(kBestHit_ScoreEdgeMin, kBestHit_ScoreEdgeMax)); arg_desc.SetDependency(kArgBestHitScoreEdge, CArgDescriptions::eExcludes, kArgCullingLimit); arg_desc.SetCurrentGroup(""); } void CHspFilteringArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts) { if (args[kArgCullingLimit]) { opts.SetCullingLimit(args[kArgCullingLimit].AsInteger()); } if (args[kArgBestHitOverhang]) { opts.SetBestHitOverhang(args[kArgBestHitOverhang].AsDouble()); } if (args[kArgBestHitScoreEdge]) { opts.SetBestHitScoreEdge(args[kArgBestHitScoreEdge].AsDouble()); } } void CMbIndexArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("General search options"); arg_desc.AddOptionalKey( kArgUseIndex, "boolean", "Use MegaBLAST database index", CArgDescriptions::eBoolean ); arg_desc.AddOptionalKey( kArgIndexName, "string", "MegaBLAST database index name", CArgDescriptions::eString ); arg_desc.SetCurrentGroup( "" ); } bool CMbIndexArgs::HasBeenSet(const CArgs& args) { if ( (args.Exist(kArgUseIndex) && args[kArgUseIndex].HasValue()) || (args.Exist(kArgIndexName) && args[kArgIndexName].HasValue()) ) { return true; } return false; } void CMbIndexArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts) { // MB Index does not apply to Blast2Sequences if( args.Exist( kArgUseIndex ) && !(args.Exist( kArgSubject ) && args[kArgSubject])) { bool use_index = true; bool force_index = false; if( args[kArgUseIndex] ) { if( args[kArgUseIndex].AsBoolean() ) force_index = true; else use_index = false; } if( args.Exist( kTask ) && args[kTask] && args[kTask].AsString() != "megablast" ) { use_index = false; } if( use_index ) { string index_name; if( args.Exist( kArgIndexName ) && args[kArgIndexName] ) { index_name = args[kArgIndexName].AsString(); } else if( args.Exist( kArgDb ) && args[kArgDb] ) { index_name = args[kArgDb].AsString(); } else { NCBI_THROW(CInputException, eInvalidInput, "Can not deduce database index name" ); } opts.SetUseIndex( true, index_name, force_index ); } } } void CStdCmdLineArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Input query options"); // query filename arg_desc.AddDefaultKey(kArgQuery, "input_file", "Input file name", CArgDescriptions::eInputFile, kDfltArgQuery); arg_desc.SetCurrentGroup("General search options"); // report output file arg_desc.AddDefaultKey(kArgOutput, "output_file", "Output file name", CArgDescriptions::eOutputFile, "-"); arg_desc.SetCurrentGroup(""); } void CStdCmdLineArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opt */) { if (args.Exist(kArgQuery) && args[kArgQuery].HasValue() && m_InputStream == NULL) { m_InputStream = &args[kArgQuery].AsInputFile(); } m_OutputStream = &args[kArgOutput].AsOutputFile(); } CNcbiIstream& CStdCmdLineArgs::GetInputStream() const { // programmer must ensure the ExtractAlgorithmOptions method is called // before this method is invoked if ( !m_InputStream ) { abort(); } return *m_InputStream; } CNcbiOstream& CStdCmdLineArgs::GetOutputStream() const { // programmer must ensure the ExtractAlgorithmOptions method is called // before this method is invoked _ASSERT(m_OutputStream); return *m_OutputStream; } void CStdCmdLineArgs::SetInputStream(CRef input_file) { m_QueryTmpInputFile = input_file; m_InputStream = &input_file->AsInputFile(CTmpFile::eIfExists_Throw); } void CSearchStrategyArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("Search strategy options"); arg_desc.AddOptionalKey(kArgInputSearchStrategy, "filename", "Search strategy to use", CArgDescriptions::eInputFile); arg_desc.AddOptionalKey(kArgOutputSearchStrategy, "filename", "File name to record the search strategy used", CArgDescriptions::eOutputFile); arg_desc.SetDependency(kArgInputSearchStrategy, CArgDescriptions::eExcludes, kArgOutputSearchStrategy); arg_desc.SetCurrentGroup(""); } void CSearchStrategyArgs::ExtractAlgorithmOptions(const CArgs& /* cmd_line_args */, CBlastOptions& /* options */) { } CNcbiIstream* CSearchStrategyArgs::GetImportStream(const CArgs& args) const { CNcbiIstream* retval = NULL; if (args[kArgInputSearchStrategy].HasValue()) { retval = &args[kArgInputSearchStrategy].AsInputFile(); } return retval; } CNcbiOstream* CSearchStrategyArgs::GetExportStream(const CArgs& args) const { CNcbiOstream* retval = NULL; if (args[kArgOutputSearchStrategy].HasValue()) { retval = &args[kArgOutputSearchStrategy].AsOutputFile(); } return retval; } CBlastAppArgs::CBlastAppArgs() { m_SearchStrategyArgs.Reset(new CSearchStrategyArgs); m_Args.push_back(CRef(&*m_SearchStrategyArgs)); m_IsUngapped = false; } CArgDescriptions* CBlastAppArgs::SetCommandLine() { return SetUpCommandLineArguments(m_Args); } CRef CBlastAppArgs::SetOptions(const CArgs& args) { // We're recovering from a saved strategy or combining // CBlastOptions/CBlastOptionsHandle with command line options (in GBench, // see GB-1116), so we need to still extract // certain options from the command line, include overriding query // and/or database if (m_OptsHandle.NotEmpty()) { CBlastOptions& opts = m_OptsHandle->SetOptions(); const bool mbidxargs_set = CMbIndexArgs::HasBeenSet(args); const bool dbargs_set = CBlastDatabaseArgs::HasBeenSet(args); NON_CONST_ITERATE(TBlastCmdLineArgs, arg, m_Args) { if (dynamic_cast(&**arg)) { if (mbidxargs_set) (*arg)->ExtractAlgorithmOptions(args, opts); } else if (dynamic_cast(&**arg)) { if (dbargs_set) m_BlastDbArgs->ExtractAlgorithmOptions(args, opts); } else { (*arg)->ExtractAlgorithmOptions(args, opts); } } m_IsUngapped = !opts.GetGappedMode(); try { m_OptsHandle->Validate(); } catch (const CBlastException& e) { NCBI_THROW(CInputException, eInvalidInput, e.GetMsg()); } return m_OptsHandle; } CBlastOptions::EAPILocality locality = (args.Exist(kArgRemote) && args[kArgRemote]) ? CBlastOptions::eRemote : CBlastOptions::eLocal; // This is needed as a CRemoteBlast object and its options are instantiated // to create the search strategy if (GetExportSearchStrategyStream(args) || m_FormattingArgs->ArchiveFormatRequested(args)) { locality = CBlastOptions::eBoth; } CRef retval(x_CreateOptionsHandle(locality, args)); CBlastOptions& opts = retval->SetOptions(); NON_CONST_ITERATE(TBlastCmdLineArgs, arg, m_Args) { (*arg)->ExtractAlgorithmOptions(args, opts); } m_IsUngapped = !opts.GetGappedMode(); try { retval->Validate(); } catch (const CBlastException& e) { NCBI_THROW(CInputException, eInvalidInput, e.GetMsg()); } return retval; } void CBlastAppArgs::SetTask(const string& task) { #if _BLAST_DEBUG ThrowIfInvalidTask(task); #endif m_Task.assign(task); } /* *********** START ************* */ void CGpuArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc) { arg_desc.SetCurrentGroup("GPU Options"); arg_desc.AddDefaultKey(kArgUseGpu, "boolean", "Use GPU for blastp", CArgDescriptions::eBoolean, kDfltArgUseGpu); arg_desc.AddDefaultKey(kArgNumGpuThreads, "int_value", "Number of GPU threads per block", CArgDescriptions::eInteger, kDfltArgNumGpuThreads); arg_desc.SetConstraint(kArgNumGpuThreads, new CArgAllow_Integers(1,1024) ); arg_desc.AddDefaultKey(kArgNumGpuBlocks, "int_value", "Number of GPU block per grid", CArgDescriptions::eInteger, kDfltArgNumGpuBlocks); arg_desc.SetConstraint(kArgNumGpuBlocks, new CArgAllow_Integers(1,65536) ); // arg_desc.AddDefaultKey(kArgNumGpuSequences, "int_value", // "Number of sequences in the GPU database", // CArgDescriptions::eInteger, // kDfltArgNumGpuSequences); // arg_desc.SetConstraint(kArgNumGpuSequences, new CArgAllow_Integers(1,97) ); arg_desc.AddDefaultKey(kArgGpuMethod, "int_value", "Method to be used\n" " 1 = for GPU-based sequence alignment with 1 gpu card (default),\n" " 0 = for GPU-based sequence alignment with all gpu cards in the machine,\n" " 2...6 = for GPU-based sequence alignment with num of gpu cards,\n" " -1 = for GPU database creation, \n", CArgDescriptions::eInteger, kDfltArgGpuMethod); /// Modified by Weicai Ye arg_desc.SetConstraint(kArgGpuMethod, new CArgAllow_Integers(-1, 6) ); } void CGpuArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opts) { if( args[kArgUseGpu] ){ opts.SetUseGpu(args[kArgUseGpu].AsBoolean()); } if( args[kArgNumGpuThreads] ){ opts.SetNumGpuThreads(args[kArgNumGpuThreads].AsInteger()); } if( args[kArgNumGpuBlocks] ){ opts.SetNumGpuBlocks(args[kArgNumGpuBlocks].AsInteger()); } // if( args[kArgNumGpuSequences] ){ // opts.SetNumGpuSequences(args[kArgNumGpuSequences].AsInteger()); // } if( args[kArgGpuMethod] ){ opts.SetGpuMethod(args[kArgGpuMethod].AsInteger()); } if (args.Exist(kArgNumThreads) && args[kArgNumThreads].HasValue()) { // could be cancelled by the exclusion in CRemoteArgs opts.SetNumCpuThreads(args[kArgNumThreads].AsInteger()); } } /* ********** FINISH ************* */ CArgDescriptions* SetUpCommandLineArguments(TBlastCmdLineArgs& args) { auto_ptr retval(new CArgDescriptions); // Create the groups so that the ordering is established retval->SetCurrentGroup("Input query options"); retval->SetCurrentGroup("General search options"); retval->SetCurrentGroup("BLAST database options"); retval->SetCurrentGroup("BLAST-2-Sequences options"); retval->SetCurrentGroup("Formatting options"); retval->SetCurrentGroup("Query filtering options"); retval->SetCurrentGroup("Restrict search or results"); retval->SetCurrentGroup("Discontiguous MegaBLAST options"); retval->SetCurrentGroup("Statistical options"); retval->SetCurrentGroup("Search strategy options"); retval->SetCurrentGroup("Extension options"); /* *********** START ************* */ retval->SetCurrentGroup("GPU options"); /* ********** FINISH ************* */ retval->SetCurrentGroup(""); NON_CONST_ITERATE(TBlastCmdLineArgs, arg, args) { (*arg)->SetArgumentDescriptions(*retval); } return retval.release(); } END_SCOPE(blast) END_NCBI_SCOPE h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/bl2seq.cpp0000644000175000017500000003402612001215340022453 0ustar ykeyke/* $Id: bl2seq.cpp 211150 2010-11-10 22:05:00Z rafanovi $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Christiam Camacho * * =========================================================================== */ /// @file bl2seq.cpp /// Implementation of CBl2Seq class. #include #include #include #include #include #include #include #include #include "dust_filter.hpp" #include #include "blast_seqalign.hpp" #include "blast_objmgr_priv.hpp" #include // NewBlast includes #include #include #include #include #include #include #include #include #include "blast_aux_priv.hpp" /** @addtogroup AlgoBlast * * @{ */ BEGIN_NCBI_SCOPE USING_SCOPE(objects); BEGIN_SCOPE(blast) CBl2Seq::CBl2Seq(const SSeqLoc& query, const SSeqLoc& subject, EProgram p) : mi_bQuerySetUpDone(false) { TSeqLocVector queries; TSeqLocVector subjects; queries.push_back(query); subjects.push_back(subject); x_Init(queries, subjects); m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); } CBl2Seq::CBl2Seq(const SSeqLoc& query, const SSeqLoc& subject, CBlastOptionsHandle& opts) : mi_bQuerySetUpDone(false) { TSeqLocVector queries; TSeqLocVector subjects; queries.push_back(query); subjects.push_back(subject); x_Init(queries, subjects); m_OptsHandle.Reset(&opts); } CBl2Seq::CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects, EProgram p) : mi_bQuerySetUpDone(false) { TSeqLocVector queries; queries.push_back(query); x_Init(queries, subjects); m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); } CBl2Seq::CBl2Seq(const SSeqLoc& query, const TSeqLocVector& subjects, CBlastOptionsHandle& opts) : mi_bQuerySetUpDone(false) { TSeqLocVector queries; queries.push_back(query); x_Init(queries, subjects); m_OptsHandle.Reset(&opts); } CBl2Seq::CBl2Seq(const TSeqLocVector& queries, const TSeqLocVector& subjects, EProgram p) : mi_bQuerySetUpDone(false) { x_Init(queries, subjects); m_OptsHandle.Reset(CBlastOptionsFactory::Create(p)); } CBl2Seq::CBl2Seq(const TSeqLocVector& queries, const TSeqLocVector& subjects, CBlastOptionsHandle& opts) : mi_bQuerySetUpDone(false) { x_Init(queries, subjects); m_OptsHandle.Reset(&opts); } void CBl2Seq::x_Init(const TSeqLocVector& queries, const TSeqLocVector& subjs) { m_tQueries = queries; m_tSubjects = subjs; mi_pScoreBlock = NULL; mi_pLookupTable = NULL; mi_pLookupSegments = NULL; mi_pResults = NULL; mi_pDiagnostics = NULL; mi_pSeqSrc = NULL; m_ipFilteredRegions = NULL; m_fnpInterrupt = NULL; m_ProgressMonitor = NULL; } CBl2Seq::~CBl2Seq() { x_ResetQueryDs(); x_ResetSubjectDs(); } void CBl2Seq::x_ResetQueryDs() { mi_bQuerySetUpDone = false; // should be changed if derived classes are created mi_clsQueries.Reset(); mi_clsQueryInfo.Reset(); m_Messages.clear(); mi_pScoreBlock = BlastScoreBlkFree(mi_pScoreBlock); mi_pLookupTable = LookupTableWrapFree(mi_pLookupTable); mi_pLookupSegments = BlastSeqLocFree(mi_pLookupSegments); m_ipFilteredRegions = BlastMaskLocFree(m_ipFilteredRegions); } void CBl2Seq::x_ResetSubjectDs() { // Clean up structures and results from any previous search mi_pSeqSrc = BlastSeqSrcFree(mi_pSeqSrc); mi_pResults = Blast_HSPResultsFree(mi_pResults); mi_pDiagnostics = Blast_DiagnosticsFree(mi_pDiagnostics); m_AncillaryData.clear(); m_SubjectMasks.clear(); } TSeqAlignVector CBl2Seq::Run() { //m_OptsHandle->GetOptions().DebugDumpText(cerr, "m_OptsHandle", 1); m_OptsHandle->GetOptions().Validate(); // throws an exception on failure SetupSearch(); RunFullSearch(); TSeqAlignVector retval = x_Results2SeqAlign(); x_BuildAncillaryData(retval); return retval; } void CBl2Seq::x_BuildAncillaryData(const TSeqAlignVector& alignments) { vector< CConstRef > query_ids; x_SimplifyTSeqLocVector(m_tQueries, query_ids); BuildBlastAncillaryData(m_OptsHandle->GetOptions().GetProgramType(), query_ids, mi_pScoreBlock, mi_clsQueryInfo, alignments, ncbi::blast::eSequenceComparison, m_AncillaryData); } void CBl2Seq::x_SimplifyTSeqLocVector(const TSeqLocVector& slv, vector< CConstRef >& query_ids) { query_ids.clear(); for (size_t i = 0; i < slv.size(); i++) { query_ids.push_back(CConstRef(slv[i].seqloc->GetId())); } } CRef CBl2Seq::RunEx() { TSeqAlignVector alignments = Run(); TSeqLocInfoVector query_masks = GetFilteredQueryRegions(); vector< CConstRef > query_ids; x_SimplifyTSeqLocVector(m_tQueries, query_ids); CRef retval = BlastBuildSearchResultSet(query_ids, mi_pScoreBlock, mi_clsQueryInfo, m_OptsHandle->GetOptions().GetProgramType(), alignments, m_Messages, m_SubjectMasks, &query_masks, ncbi::blast::eSequenceComparison); m_AncillaryData.reserve(retval->size()); ITERATE(CSearchResultSet, result, *retval) { m_AncillaryData.push_back((*result)->GetAncillaryData()); } return retval; } void CBl2Seq::RunWithoutSeqalignGeneration() { //m_OptsHandle->GetOptions().DebugDumpText(cerr, "m_OptsHandle", 1); m_OptsHandle->GetOptions().Validate(); // throws an exception on failure SetupSearch(); RunFullSearch(); } void CBl2Seq::SetupSearch() { if ( !mi_bQuerySetUpDone ) { x_ResetQueryDs(); const CBlastOptions& kOptions = m_OptsHandle->GetOptions(); EBlastProgramType prog = kOptions.GetProgramType(); ENa_strand strand_opt = kOptions.GetStrandOption(); if (CBlastNucleotideOptionsHandle *nucl_handle = dynamic_cast(&*m_OptsHandle)) { Blast_FindDustFilterLoc(m_tQueries, nucl_handle); Blast_FindRepeatFilterLoc(m_tQueries, nucl_handle); } SetupQueryInfo(m_tQueries, prog, strand_opt, &mi_clsQueryInfo); m_Messages.resize(mi_clsQueryInfo->num_queries); SetupQueries(m_tQueries, mi_clsQueryInfo, &mi_clsQueries, prog, strand_opt, m_Messages); Blast_Message* blmsg = NULL; double scale_factor = 1.0; short st; st = BLAST_MainSetUp(m_OptsHandle->GetOptions().GetProgramType(), m_OptsHandle->GetOptions().GetQueryOpts(), m_OptsHandle->GetOptions().GetScoringOpts(), mi_clsQueries, mi_clsQueryInfo, scale_factor, &mi_pLookupSegments, &m_ipFilteredRegions, &mi_pScoreBlock, &blmsg, &BlastFindMatrixPath); // TODO: Check that lookup_segments are not filtering the whole // sequence (SSeqRange set to -1 -1) const string error_msg1(blmsg ? blmsg->message : "BLAST_MainSetUp failed"); Blast_Message2TSearchMessages(blmsg, mi_clsQueryInfo, m_Messages); blmsg = Blast_MessageFree(blmsg); if (st != 0) { NCBI_THROW(CBlastException, eCoreBlastError, error_msg1); } st = LookupTableWrapInit(mi_clsQueries, m_OptsHandle->GetOptions().GetLutOpts(), m_OptsHandle->GetOptions().GetQueryOpts(), mi_pLookupSegments, mi_pScoreBlock, &mi_pLookupTable, NULL, &blmsg); const string error_msg2(blmsg ? blmsg->message : "LookupTableWrapInit failed"); Blast_Message2TSearchMessages(blmsg, mi_clsQueryInfo, m_Messages); blmsg = Blast_MessageFree(blmsg); if (st != 0) { NCBI_THROW(CBlastException, eCoreBlastError, error_msg2); } mi_bQuerySetUpDone = true; } x_ResetSubjectDs(); mi_pSeqSrc = MultiSeqBlastSeqSrcInit(m_tSubjects, m_OptsHandle->GetOptions().GetProgramType()); char* error_str = BlastSeqSrcGetInitError(mi_pSeqSrc); if (error_str) { string msg(error_str); sfree(error_str); NCBI_THROW(CBlastException, eSeqSrcInit, msg); } // Set the hitlist size to the total number of subject sequences, to // make sure that no hits are discarded. m_OptsHandle->SetHitlistSize((int) m_tSubjects.size()); } void CBl2Seq::RunFullSearch() { mi_pResults = NULL; mi_pDiagnostics = Blast_DiagnosticsInit(); const CBlastOptions& kOptions = GetOptionsHandle().GetOptions(); auto_ptr opts_mem(kOptions.CreateSnapshot()); BlastHSPStream* hsp_stream = CSetupFactory::CreateHspStream(opts_mem.get(), mi_clsQueryInfo->num_queries, CSetupFactory::CreateHspWriter(opts_mem.get(), mi_clsQueryInfo)); BlastHSPStreamRegisterPipe(hsp_stream, CSetupFactory::CreateHspPipe(opts_mem.get(), mi_clsQueryInfo), eTracebackSearch); TBlastHSPStream thsp_stream(hsp_stream, BlastHSPStreamFree); /* *********** START ************* */ BlastGPUOptions* m_GpuOpts; m_GpuOpts = (BlastGPUOptions*)malloc(sizeof(BlastGPUOptions)); m_GpuOpts->use_gpu = (char)kOptions.GetUseGpu(); m_GpuOpts->num_threadsx = kOptions.GetNumGpuThreads(); m_GpuOpts->num_blocksx = kOptions.GetNumGpuBlocks(); m_GpuOpts->num_sequences_to = kOptions.GetNumGpuSequences(); m_GpuOpts->method = kOptions.GetGpuMethod(); m_GpuOpts->cpu_threads = kOptions.GetNumCpuThreads(); /* ********** FINISH ************* */ SBlastProgressReset(m_ProgressMonitor); Int4 status = Blast_RunFullSearch(kOptions.GetProgramType(), mi_clsQueries, mi_clsQueryInfo, mi_pSeqSrc, mi_pScoreBlock, kOptions.GetScoringOpts(), mi_pLookupTable, kOptions.GetInitWordOpts(), kOptions.GetExtnOpts(), kOptions.GetHitSaveOpts(), kOptions.GetEffLenOpts(), NULL, kOptions.GetDbOpts(), /* *********** START ************* */ m_GpuOpts, /* ********** FINISH ************* */ thsp_stream.GetPointer(), NULL, mi_pDiagnostics, &mi_pResults, m_fnpInterrupt, m_ProgressMonitor); if (status) { NCBI_THROW(CBlastException, eCoreBlastError, BlastErrorCode2String(status)); } } /* Unlike the database search, we want to make sure that a seqalign list is * returned for each query/subject pair, even if it is empty. Also we don't * want subjects to be sorted in seqalign results. */ TSeqAlignVector CBl2Seq::x_Results2SeqAlign() { EBlastProgramType program = m_OptsHandle->GetOptions().GetProgramType(); bool gappedMode = m_OptsHandle->GetGappedMode(); bool outOfFrameMode = m_OptsHandle->GetOptions().GetOutOfFrameMode(); CSeqVecSeqInfoSrc seqinfo_src(m_tSubjects); CObjMgr_QueryFactory qf(m_tQueries); CRef query_data = qf.MakeLocalQueryData(&m_OptsHandle->GetOptions()); return LocalBlastResults2SeqAlign(mi_pResults, *query_data, seqinfo_src, program, gappedMode, outOfFrameMode, m_SubjectMasks, eSequenceComparison); } TSeqLocInfoVector CBl2Seq::GetFilteredQueryRegions() const { CConstRef queries(TSeqLocVector2Packed_seqint(m_tQueries)); EBlastProgramType program(GetOptionsHandle().GetOptions().GetProgramType()); TSeqLocInfoVector retval; Blast_GetSeqLocInfoVector(program, *queries, m_ipFilteredRegions, retval); return retval; } END_SCOPE(blast) END_NCBI_SCOPE /* @} */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/Makefile0000644000175000017500000000200512137167774016760 0ustar ykeyke.SUFFIXES : .cu CC := gcc CXX := g++ NVCC := $(NVCC_PATH) COMMONFLAGS := -c # the "--no-align-double" is necessary. Without it the nvcc compiler aligns structure sizes every 8 bytes which is #incompatible with some NCBI_BLAST data structures, i.e. the "BlastContextInfo" NVCCFLAGS := --compiler-options -fno-strict-aliasing --compiler-options -fno-inline -DUNIX -O3 --no-align-double all: libgpublast.a libgpublast.a : gpu_blastp.o gpu_blastp.cu.o gpu_blastp_kernel.h ar cru libgpublast.a gpu_blastp.o gpu_blastp.cu.o ranlib libgpublast.a cp libgpublast.a $(PROJ_DIR)/lib/ cp $(CUDA_LIB)/libcudart.so $(PROJ_DIR)/lib/ gpu_blastp.o : gpu_blastp.c gpu_blastp.h gpu_blastp_kernel.cu $(CXX) $(COMMONFLAGS) gpu_blastp.c -o gpu_blastp.o -I$(CXX_DIR)/include/ -I$(PROJ_DIR)/inc/ gpu_blastp.cu.o : gpu_blastp.cu gpu_blastp.h gpu_blastp_kernel.cu gpu_blastp_kernel.h $(NVCC) $(COMMONFLAGS) $(NVCCFLAGS) gpu_blastp.cu -o gpu_blastp.cu.o -I$(CXX_DIR)/include/ -I$(PROJ_DIR)/inc/ h-blast-1.0_ncbi-blast-2.2.25/h_blast/gpu_blastp_kernel.cu0000644000175000017500000010445112137171261021343 0ustar ykeyke#include #include "gpu_blastp_kernel.h" #define CHARSIZE 5 //shared and constant memory extern __shared__ int array[]; __constant__ char d_Query_const[40960]; __constant__ int d_x_dropoff_const[500]; __constant__ int d_cutoff_score_const[500]; __constant__ int d_query_offset_const[500]; __constant__ int Group_size_const; /** * Each thread scans on of the subjet sequences and * it returns the score and coordinats of each successful alignment * @param d_Database2Dpadded the formatted sequence database[in] * @param d_RepeatedSubstitutionMatrix multiple copies of the substitution matrix (one for each block for parallel loading from global to shared) [in] * @param SubstitutionMatrix_length the substitution matrix [in] * @param d_RepeatedPV multiple copies of the presence vector (one for each block for parallel loading from global to shared) [in] * @param d_ThickBackbone ThickBackbone as taken from NCBI_BLAST [in] * @param d_overflow overflow array as taken from NCIB_BLAST [in] * @param *d_RepeatedSequenceMaxlength_vector multiple copies of the vector that has the maximum length for each group [in] * @param SequenceMaxlength_vector_stride the stride of the array that holds the maximum lengths of each group [in] * @param NumSequences number of sequences the GPU works on [in] * @param pv_length length of the presence vector [in] * @param Query_length length of the query [in] * @param diag_mask mask for the diagonal array [in] * @param diag_array_length length of the diagonal array used by each thread [in] * @param num_quries number of queries [in] * @param word_length word length [in] * @param charsize char size of the lookup table [in] * @param index_mask mask for the iniatialization of the index [in] * @param window window for the two-hit alignment [in] * @param diag_offset diagonal offset [in] * @param d_diag_array allocated global memory used for storing the diagonal arrays [in] * @param d_Hits returns returns hits found for each sequence [out] * @param d_GPUBlastInitHitList returns the statistics of the successful extensions [out] */ __global__ void GPU_BLASTP_kernelTwoHit( int* d_Database2Dpadded, const int* d_RepeatedSubstitutionMatrix, const int SubstitutionMatrix_length, const PV_ARRAY_TYPE* d_RepeatedPV, const AaLookupSmallboneCell* d_ThickBackbone, const unsigned short* d_overflow, const int* d_RepeatedSequence_length_vector, const int Sequence_length_vector_stride, const int NumSequences, const int pv_length, const int Query_length, const int diag_mask, const int diag_array_length, const int num_queries, const int word_length, const int index_mask, const int window, int diag_offset, short* d_diag_array, int* d_Hits, GPUBlastInitHitList* d_GPUBlastInitHitList, int hit_list_base, unsigned int total_hit_list_length) { int bx = blockIdx.x; int tx = threadIdx.x; int blockDimx = blockDim.x; //total threads in the card int total_threads = blockDim.x*gridDim.x; //total room for results per thread int left_room = total_hit_list_length/total_threads; int current_subject_offset = left_room*( bx*blockDimx + (tx&0xfe0))+ left_room * 2* (tx&0xf); left_room *= 2; int kept_results_count_for_current_subject; if( 0==(tx&0x10) ) { d_GPUBlastInitHitList = &(d_GPUBlastInitHitList[current_subject_offset]); hit_list_base += current_subject_offset; } else { d_GPUBlastInitHitList = &(d_GPUBlastInitHitList[current_subject_offset+left_room-1]); hit_list_base += current_subject_offset+left_room-1; } int* SubstitutionMatrix_shared_int = (int*)array; int* Sequence_length_vector_shared = (int*)&SubstitutionMatrix_shared_int[SubstitutionMatrix_length>>2];//The substitution matrix is 640 bytes or 160 integers long int* result_space_used = (int*) &Sequence_length_vector_shared[Sequence_length_vector_stride]; char* Sequence_AA = (char*) &result_space_used[blockDimx]; PV_ARRAY_TYPE* pv_shared = (PV_ARRAY_TYPE*) &Sequence_AA[3* blockDimx * 4]; //pv array from global to shared memory int pv_Index_global = bx*pv_length + tx; int pv_Index_shared = tx; while( pv_Index_shared < pv_length ) { pv_shared[ pv_Index_shared ] = d_RepeatedPV[ pv_Index_global ]; pv_Index_global += blockDimx; pv_Index_shared += blockDimx; } __syncthreads(); //Substitution Matrix from global to shared memory int SubstitutionMatrix_Index_global = bx*(SubstitutionMatrix_length>>2) + tx; int SubstitutionMatrix_Index_shared = tx; while( SubstitutionMatrix_Index_shared < (SubstitutionMatrix_length>>2) )//SubstitutionMatrix_length is a multiple of 64 which includes some padded zeros so there is some waste of memory space. Can it be recovered? { SubstitutionMatrix_shared_int[ SubstitutionMatrix_Index_shared ] = d_RepeatedSubstitutionMatrix[ SubstitutionMatrix_Index_global ]; SubstitutionMatrix_Index_global += blockDimx; SubstitutionMatrix_Index_shared += blockDimx; } __syncthreads(); //SequenceMaxlength_vector from global to shared memory int Sequence_length_vector_Index_global = bx*Sequence_length_vector_stride + tx; int Sequence_length_vector_Index_shared = tx; while( Sequence_length_vector_Index_shared < Sequence_length_vector_stride ) { Sequence_length_vector_shared[ Sequence_length_vector_Index_shared ] = d_RepeatedSequence_length_vector[ Sequence_length_vector_Index_global ]; Sequence_length_vector_Index_global += blockDimx; Sequence_length_vector_Index_shared += blockDimx; } __syncthreads(); char* SubstitutionMatrix_shared_char = (char*)SubstitutionMatrix_shared_int; int Sequence = (bx * blockDimx + tx); GPUBlastInitHitList data; int Group_size = gridDim.x*blockDimx; int diag_array_base = ((bx*blockDimx+tx)*diag_array_length); Sequence_AA = &Sequence_AA[tx*12]; d_diag_array = &d_diag_array[diag_array_base]; d_Database2Dpadded = &(d_Database2Dpadded[bx*blockDimx + tx+ blockDim.x*gridDim.x ]); int S_AA_buffer; while( Sequence < NumSequences ) { kept_results_count_for_current_subject=0; int Hits = 0; int s_last_off = 0; int hits_extended = 0; int successful_extensions = 0; int Sequence_length = Sequence_length_vector_shared[ Sequence/Group_size ]; ((int*) Sequence_AA)[0] = d_Database2Dpadded[ 0 ]; S_AA_buffer = d_Database2Dpadded[ Group_size ]; int index = (Sequence_AA[ 0 ] << CHARSIZE) | Sequence_AA[ 1 ]; for(int s_off = 0; (s_off <= Sequence_length - word_length); ++s_off) { if ( ((s_off&0x3)==0) && (s_off < Sequence_length-4) ) { ((int*)Sequence_AA)[((s_off>>2)+1)&0x1] = S_AA_buffer; S_AA_buffer = d_Database2Dpadded[ (((s_off>>2) + 2)*Group_size) ]; } index = ((index<= window) { /* We are beyond the window for this diagonal; start a new hit */ /* If the difference is less than the wordsize (i.e. last hit and this hit overlap), give up */ d_diag_array[diag_coord] = (s_off + diag_offset) & 0x7FFF; //set only the 31 LSB's (the flag is zero since we are here) continue; } /* If the difference is less than the wordsize (i.e. last hit and this hit overlap), give up */ if (diff < word_length) continue; /* Extend this pair of hits. The extension to the left must reach the end of the first word in order for extension to the right to proceed. To use the cutoff and X-drop values appropriate for this extension, the query context must first be found */ int k = 0; for(k = num_queries-1; k >= 0; --k) if( query_offset >= d_query_offset_const[k] ) break; int right_extend; s_BlastAaExtendTwoHit(&data, SubstitutionMatrix_shared_char, (d_Database2Dpadded), Sequence_length, d_Query_const, Query_length, last_hit + word_length, s_off, query_offset, d_x_dropoff_const[k], word_length, &s_last_off,&right_extend, Sequence_AA ); ++hits_extended; /* if the hsp meets the score threshold, report it */ if ( data.score >= d_cutoff_score_const[k] ) { data.offset_from_first_position = s_off - data.hsp_s; /// If there is enough space to store this hit if(left_room > 0) { if( 0==(threadIdx.x&0x10) ) d_GPUBlastInitHitList[kept_results_count_for_current_subject] = data; else d_GPUBlastInitHitList[0-kept_results_count_for_current_subject] = data; kept_results_count_for_current_subject++; left_room--; } successful_extensions++; } /* If an extension to the right happened, reset the last hit so that future hits to this diagonal must start over. */ if (right_extend) { d_diag_array[diag_coord] = ( (s_last_off - (word_length - 1) + diag_offset) & 0x7FFF ) | 0x8000;//set the 31 LSB's (the flag is zero size we are here) // and set the MSB which holds the flag (this can be merged in the previous assignment) } else /* Otherwise, make the present hit into the previous hit for this diagonal */ d_diag_array[diag_coord] = (s_off + diag_offset) & 0x7FFF;//set only the 31 LSB's (the flag is zero sinze we are here) }/* if (flag) */ } /* end for - done with this batch of hits*/ diagonal = diagonal_buffer; query_offset = query_offset_buffer1; diag_coord = (query_offset - s_off) & diag_mask; last_hit = diagonal & 0x7FFF; flag = diagonal & 0x8000; /* If the reset bit is set, an extension just happened. */ if (flag) { /* If we've already extended past this hit, skip it. */ if ( (s_off + diag_offset) < last_hit) continue; else /* Otherwise, start a new hit. */ d_diag_array[diag_coord] = (s_off + diag_offset) & 0x7FFF;//set the MSB to zero and the rest to (subject_offset + diag_offset) } else /* If the reset bit is cleared, try to start an extension. */ { /* find the distance to the last hit on this diagonal */ last_hit = last_hit - diag_offset; int diff = s_off - last_hit; if (diff >= window) { /* We are beyond the window for this diagonal; start a new hit */ /* If the difference is less than the wordsize (i.e. last hit and this hit overlap), give up */ d_diag_array[diag_coord] = (s_off + diag_offset) & 0x7FFF; //set only the 31 LSB's (the flag is zero since we are here) continue; } /* If the difference is less than the wordsize (i.e. last hit and this hit overlap), give up */ if (diff < word_length) continue; /* Extend this pair of hits. The extension to the left must reach the end of the first word in order for extension to the right to proceed. To use the cutoff and X-drop values appropriate for this extension, the query context must first be found */ int k = 0; for(k = num_queries-1; k >= 0; --k) if( query_offset >= d_query_offset_const[k] ) break; int right_extend; s_BlastAaExtendTwoHit(&data, SubstitutionMatrix_shared_char, (d_Database2Dpadded), Sequence_length, d_Query_const, Query_length, last_hit + word_length, s_off, query_offset, d_x_dropoff_const[k], word_length, &s_last_off,&right_extend, Sequence_AA ); ++hits_extended; /* if the hsp meets the score threshold, report it */ if ( data.score >= d_cutoff_score_const[k] ) { data.offset_from_first_position = s_off - data.hsp_s; /// If there is enough space to store this hit if(left_room > 0) { if( 0==(threadIdx.x&0x10) ) d_GPUBlastInitHitList[kept_results_count_for_current_subject] = data; else d_GPUBlastInitHitList[0-kept_results_count_for_current_subject] = data; kept_results_count_for_current_subject++; left_room--; } successful_extensions++; } /* If an extension to the right happened, reset the last hit so that future hits to this diagonal must start over. */ if (right_extend) { d_diag_array[diag_coord] = ( (s_last_off - (word_length - 1) + diag_offset) & 0x7FFF ) | 0x8000;//set the 31 LSB's (the flag is zero size we are here) // and set the MSB which holds the flag (this can be merged in the previous assignment) } else /* Otherwise, make the present hit into the previous hit for this diagonal */ d_diag_array[diag_coord] = (s_off + diag_offset) & 0x7FFF;//set only the 31 LSB's (the flag is zero sinze we are here) } /* if (flag) */ } //if (PV_TEST...) }//for Sequence_length loop // end_of_batch: diag_offset += Sequence_length + window; int iTmp = Sequence*4; result_space_used[threadIdx.x] = kept_results_count_for_current_subject; __syncthreads(); int iTmp2; if(threadIdx.x & 0x10) iTmp2 = result_space_used[threadIdx.x - 16]; else iTmp2 = result_space_used[threadIdx.x + 16]; //the subject has to be recalculated if ( (kept_results_count_for_current_subject < successful_extensions) || (left_room < iTmp2) ) { d_Hits[ iTmp+3 ] = -1; left_room += kept_results_count_for_current_subject; } else //the hits of the current subjct have been stored { d_Hits[ iTmp+3 ] = hit_list_base; if(threadIdx.x & 0x10) { d_GPUBlastInitHitList = & (d_GPUBlastInitHitList[0-successful_extensions]); hit_list_base -= successful_extensions; } else { d_GPUBlastInitHitList = & (d_GPUBlastInitHitList[successful_extensions]); hit_list_base += successful_extensions; } left_room -= iTmp2; } d_Hits[ iTmp ] = Hits; d_Hits[ iTmp + 1 ] = successful_extensions; d_Hits[ iTmp + 2 ] = hits_extended; iTmp = Group_size * (Sequence_length>>2); Sequence += Group_size; d_Database2Dpadded = &(d_Database2Dpadded[iTmp]); } //while loop } /** Perform a two-hit extension. Given two hits L and R, begin * at R and extend to the left. If we do not reach L, abort the extension. * Otherwise, begin at R and extend to the right. * * @param matrix substitution matrix [in] * @param subject subject sequence [in] * @param subject_length subject length [in] * @param query query sequence [in] * @param query query length [in] * @param s_left_off left subject offset [in] * @param s_right_off right subject offset [in] * @param q_right_off right query offset [in] * @param dropoff X dropoff parameter [in] * @param word_size number of letters in one word [in] * @return the scores and coordinates of the alignment of the hsp. */ static void __device__ s_BlastAaExtendTwoHit(GPUBlastInitHitList* data, const char* matrix, const int* subject, const int subject_length, const char* query, const int query_length, const int s_left_off, int s_right_off, int q_right_off, const int dropoff, const int word_size, int* s_last_off, int* right_extend, char* AA_shared ) { int left_d = 0, right_d = 0; /* left and right displacements */ int left_score = 0, right_score = 0; /* left and right scores */ int i, score = 0; /* find one beyond the position (up to word_size-1 letters to the right) that gives the largest starting score */ /* Use "one beyond" to make the numbering consistent with how it's done for BlastAaExtendOneHit and the "Extend" functions called here. */ for (i = 0; i < word_size; ++i) { score += matrix[ query[q_right_off + i] + (AA_shared[(s_right_off+i) &0x7]<<5) ]; if (score > left_score) { left_score = score; right_d = i + 1; /* Position is one beyond the end of the word. */ } } q_right_off += right_d; s_right_off += right_d; right_d = 0; (*right_extend) = FALSE; (*s_last_off) = s_right_off; /* first, try to extend left, from the second hit to the first hit. */ ExtendLeftReturn ReturnLeftValue = s_BlastAaExtendLeft(matrix, subject, query, s_right_off-1, q_right_off-1, dropoff, 0); left_score = ReturnLeftValue.maxscore; left_d = ReturnLeftValue.length; /* Extend to the right only if left extension reached the first hit. */ ExtendRightReturn ReturnRightValue; if (left_d >= (s_right_off - s_left_off)) { (*right_extend) = TRUE; ReturnRightValue = s_BlastAaExtendRight(matrix, subject, query, s_right_off, q_right_off, dropoff, left_score, subject_length, query_length); right_score = ReturnRightValue.maxscore; right_d = ReturnRightValue.length; } (*s_last_off) = ReturnRightValue.s_last_off; (*data).hsp_q = q_right_off - left_d; (*data).hsp_s = s_right_off - left_d;; (*data).hsp_len = left_d + right_d; (*data).score = MAX(left_score, right_score); } /* * Beginning at s_off and q_off in the subject and query, respectively, * extend to the left until the cumulative score drops by at least * 'dropoff', or the end of at least one sequence is reached. * * @param matrix the substitution matrix [in] * @param subject subject sequence [in] * @param query query sequence [in] * @param s_off subject offset [in] * @param q_off query offset [in] * @param dropoff the X dropoff parameter [in] * @param length the length of the computed extension [out] * @param maxscore the best running score from a previous extension; * the running score of the current extension must exceed * this value if the extension is to be of nonzero size [in] * @return The score and the length of the extension */ __device__ ExtendLeftReturn s_BlastAaExtendLeft(const char* matrix, const int* subject, const char* query, const int s_off, const int q_off, const int dropoff, int maxscore) { int n, best_i; int score = maxscore; int subject_buffer1, subject_buffer2; int temp = gridDim.x*blockDim.x; int index = ((s_off)>>2)*temp; subject_buffer1 = subject[index]; index -= temp; subject_buffer2 = subject[index ]; char* subject_buffer1_ptr = (char*) &subject_buffer1; n = MIN(s_off, q_off); best_i = n + 1; int temp2 = ((s_off)&0x3); int n1=n-temp2; int n2 = n1>>2; int k = n; if(n>0) { char query_temp = 0, sequence_temp = 0, flag = 0; for(int i=temp2; i>=0; i--) { score += matrix[ (query[q_off - n+k]<<5) + subject_buffer1_ptr[i] ]; if (score > maxscore) { maxscore = score; best_i = k; } if ((maxscore - score) >= dropoff) { flag = 1; break; } k--; } if ( (flag == 0) && (n1>0) ) { for (int i = 0; i < n2; i++) { subject_buffer1=subject_buffer2; index=index- temp; subject_buffer2 = subject[index]; //0 sequence_temp = subject_buffer1_ptr[3]; query_temp = query[q_off - n+k]; score += matrix[ (query_temp<<5) + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if ((maxscore - score) >= dropoff) { flag = 1; break; } //1 k--; sequence_temp = subject_buffer1_ptr[2]; query_temp = query[q_off - n+k]; score += matrix[ (query_temp<<5) + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if ((maxscore - score) >= dropoff) { flag = 1; break; } //2 k--; sequence_temp = subject_buffer1_ptr[1]; query_temp = query[q_off - n+k]; score += matrix[ (query_temp<<5) + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if ((maxscore - score) >= dropoff) { flag = 1; break; } //3 k--; sequence_temp = subject_buffer1_ptr[0]; query_temp = query[q_off - n+k]; score += matrix[ (query_temp<<5) + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if ((maxscore - score) >= dropoff) { flag = 1; break; } k--; } if(0==flag) { subject_buffer1 = subject_buffer2; for(int j=0; j<(n1 &0x3); j++) { sequence_temp = subject_buffer1_ptr[3-j]; query_temp = query[q_off - n+k]; score += matrix[ (query_temp<<5) + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if ((maxscore - score) >= dropoff) break; k--; } } } } ExtendLeftReturn ReturnValues; ReturnValues.maxscore = maxscore; ReturnValues.length = n - best_i + 1; return ReturnValues; } /* * Beginning at s_off and q_off in the subject and query, respectively, * extend to the right until the cumulative score drops by at least * 'dropoff', or the end of at least one sequence is reached. * * @param matrix the substitution matrix [in] * @param subject subject sequence [in] * @param query query sequence [in] * @param s_off subject offset [in] * @param q_off query offset [in] * @param dropoff the X dropoff parameter [in] * @param maxscore the best running score from a previous extension; * the running score of the current extension must exceed * this value if the extension is to be of nonzero size [in] * @param Sequence_length the length of the subject sequence [in] * @param Query_length the length of the query sequence [in] * @return The score, lenght, and coordinates of the extension */ __device__ ExtendRightReturn s_BlastAaExtendRight(const char* matrix, const int* subject, const char* query, const int s_off, const int q_off, const int dropoff, int maxscore, const int Sequence_length, const int Query_length) { int n, best_i = -1; int score = maxscore; int subject_buffer1, subject_buffer2; int temp = gridDim.x*blockDim.x; int index = ((s_off)>>2)*temp; subject_buffer1 = subject[index]; index += temp; subject_buffer2 = subject[index ]; char* subject_buffer1_ptr = (char*) &subject_buffer1; n = MIN(Sequence_length - s_off, Query_length - q_off); char query_temp = 0, sequence_temp = 0, flag = 0; int temp2 = 4-(s_off&0x3); int n1=n-temp2; int n2 = n1>>2; int k=0; if(n>0) { for(k=0; k maxscore) { maxscore = score; best_i = k; } if (score <= 0 || (maxscore - score) >= dropoff) { flag = 1; break; } } if ( (0==flag) && (n>temp2) ) { for (int i = 0; i < n2; i++) { subject_buffer1=subject_buffer2; index=index + temp; subject_buffer2 = subject[index]; //0 sequence_temp = subject_buffer1_ptr[0]; query_temp = query[q_off+k]; score += matrix[ query_temp*32 + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if (score <= 0 || (maxscore - score) >= dropoff) { flag = 1; break; } //1 k++; sequence_temp = subject_buffer1_ptr[1]; query_temp = query[q_off+k]; score += matrix[ query_temp*32 + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if (score <= 0 || (maxscore - score) >= dropoff) { flag = 1; break; } //2 k++; sequence_temp = subject_buffer1_ptr[2]; query_temp = query[q_off+k]; score += matrix[ query_temp*32 + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if (score <= 0 || (maxscore - score) >= dropoff) { flag = 1; break; } //3 k++; sequence_temp = subject_buffer1_ptr[3]; query_temp = query[q_off+k]; score += matrix[ query_temp*32 + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if (score <= 0 || (maxscore - score) >= dropoff) { flag = 1; break; } k++; } if(0==flag) { subject_buffer1=subject_buffer2; for(int j=0; j<(n1 &0x3); j++,k++) { sequence_temp = subject_buffer1_ptr[j]; query_temp = query[q_off+k]; score += matrix[ query_temp*32 + sequence_temp ]; if (score > maxscore) { maxscore = score; best_i = k; } if (score <= 0 || (maxscore - score) >= dropoff) break; } } } } ExtendRightReturn ReturnValues; ReturnValues.length = best_i + 1; ReturnValues.s_last_off = s_off + k; ReturnValues.maxscore = maxscore; return ReturnValues; } h-blast-1.0_ncbi-blast-2.2.25/h_blast/gpu_blastp_kernel.h0000644000175000017500000000737612137171332021172 0ustar ykeyke#ifndef GPU_BLASTP_KERNEL_H #define GPU_BLASTP_KERNEL_H typedef struct ExtendLeftReturn { int maxscore; int length; } ExtendLeftReturn; typedef struct ExtendRightReturn { int s_last_off; int maxscore; int length; } ExtendRightReturn; typedef struct ExtendTwoHitReturn { int s_last_off; int hsp_q; int hsp_s; int hsp_len; int MAX_score; int right_extend; int left_score; int left_disp; int right_disp; } ExtendTwoHitReturn; texture texRef; #define AA_HITS_PER_CELL 3 /**< maximum number of hits in one lookup table cell */ __global__ void GPU_BLASTP_kernel_TwoHit( int* d_Database2Dpadded, const int *d_RepeatedSubstitutionMatrix, const int SubstitutionMatrix_length, const PV_ARRAY_TYPE* d_RepeatedPV, const AaLookupSmallboneCell* d_ThickBackbone, const unsigned short* d_overflow, const int* d_RepeatedSequenceMaxlength_vector, const int SequenceMaxlength_vector_stride, const int NumSequences, const int pv_length, const int Query_length, const int diag_mask, const int diag_array_length, const int num_queries, const int word_length, const int index_mask, const int window, int diag_offset, short* d_diag_array, int* d_Hits, GPUBlastInitHitList* d_GPUBlastInitHitList, int hit_list_base, unsigned int total_hit_list_length); static void __device__ s_BlastAaExtendTwoHit(GPUBlastInitHitList* data, const char* matrix, const int* subject, const int subject_length, const char* query, const int query_length, const int s_left_off, int s_right_off, int q_right_off, const int dropoff, const int word_size, int* s_last_off, int* right_extend, char* AA_shared ); __device__ ExtendLeftReturn s_BlastAaExtendLeft(const char* matrix, const int* subject, const char * query, const int s_off, const int q_off, const int dropoff, int maxscore); __device__ ExtendRightReturn s_BlastAaExtendRight(const char* matrix, const int* subject, const char* query, const int s_off, const int q_off, const int dropoff, int maxscore, const int Sequence_actual_length, const int Query_length); #endif /* GPU_BLASTP_KERNEL_H */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/modify0000644000175000017500000003307212001215332016510 0ustar ykeyke#blast!/bin/bash ############# New modify script support blastx ############### ############# May 16, 2012 Weicai Ye ###################### cxx_dir=$1 #Files related to GPU BLAST cp ./ncbi_blast_files/functions.cpp $cxx_dir/src/algo/blast/core/functions.cpp if [ -f $cxx_dir/src/algo/blast/core/blast_engine.c ]; then cp $cxx_dir/src/algo/blast/core/blast_engine.c $cxx_dir/src/algo/blast/core/blast_engine.c.backup cp ./ncbi_blast_files/blast_engine.c $cxx_dir/src/algo/blast/core/ else echo "\"$cxx_dir/src/algo/blast/core/blast_engine.c\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/core/blast_seqsrc.c ]; then cp $cxx_dir/src/algo/blast/core/blast_seqsrc.c $cxx_dir/src/algo/blast/core/blast_seqsrc.c.backup cp ./ncbi_blast_files/blast_seqsrc.c $cxx_dir/src/algo/blast/core/ else echo "\"$cxx_dir/src/algo/blast/core/blast_seqsrc.c\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/api/seqsrc_seqdb.cpp ]; then cp $cxx_dir/src/algo/blast/api/seqsrc_seqdb.cpp $cxx_dir/src/algo/blast/api/seqsrc_seqdb.cpp.backup cp ./ncbi_blast_files/seqsrc_seqdb.cpp $cxx_dir/src/algo/blast/api/ else echo "\"$cxx_dir/src/algo/blast/api/seqsrc_seqdb.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_reader/seqdb.cpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_reader/seqdb.cpp $cxx_dir/src/objtools/blast/seqdb_reader/seqdb.cpp.backup cp ./ncbi_blast_files/seqdb.cpp $cxx_dir/src/objtools/blast/seqdb_reader/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_reader/seqdb.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.cpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.cpp $cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.cpp.backup cp ./ncbi_blast_files/seqdbimpl.cpp $cxx_dir/src/objtools/blast/seqdb_reader/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.hpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.hpp $cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.hpp.backup cp ./ncbi_blast_files/seqdbimpl.hpp $cxx_dir/src/objtools/blast/seqdb_reader/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_reader/seqdbimpl.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/blastinput/cmdline_flags.cpp ]; then cp $cxx_dir/src/algo/blast/blastinput/cmdline_flags.cpp $cxx_dir/src/algo/blast/blastinput/cmdline_flags.cpp.backup cp ./ncbi_blast_files/cmdline_flags.cpp $cxx_dir/src/algo/blast/blastinput/ else echo "\"$cxx_dir/src/algo/blast/blastinput/cmdline_flags.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/blastinput/blast_args.cpp ]; then cp $cxx_dir/src/algo/blast/blastinput/blast_args.cpp $cxx_dir/src/algo/blast/blastinput/blast_args.cpp.backup cp ./ncbi_blast_files/blast_args.cpp $cxx_dir/src/algo/blast/blastinput/ else echo "\"$cxx_dir/src/algo/blast/blastinput/blast_args.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/blastinput/blastp_args.cpp ]; then cp $cxx_dir/src/algo/blast/blastinput/blastp_args.cpp $cxx_dir/src/algo/blast/blastinput/blastp_args.cpp.backup cp ./ncbi_blast_files/blastp_args.cpp $cxx_dir/src/algo/blast/blastinput/ else echo "\"$cxx_dir/src/algo/blast/blastinput/blastp_args.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/blastinput/blastx_args.cpp ]; then cp $cxx_dir/src/algo/blast/blastinput/blastx_args.cpp $cxx_dir/src/algo/blast/blastinput/blastx_args.cpp.backup cp ./ncbi_blast_files/blastx_args.cpp $cxx_dir/src/algo/blast/blastinput/ else echo "\"$cxx_dir/src/algo/blast/blastinput/blastx_args.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/api/blast_options_cxx.cpp ]; then cp $cxx_dir/src/algo/blast/api/blast_options_cxx.cpp $cxx_dir/src/algo/blast/api/blast_options_cxx.cpp.backup cp ./ncbi_blast_files/blast_options_cxx.cpp $cxx_dir/src/algo/blast/api/ else echo "\"$cxx_dir/src/algo/blast/api/blast_options_cxx.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/api/blast_options_local_priv.hpp ]; then cp $cxx_dir/src/algo/blast/api/blast_options_local_priv.hpp $cxx_dir/src/algo/blast/api/blast_options_local_priv.hpp.backup cp ./ncbi_blast_files/blast_options_local_priv.hpp $cxx_dir/src/algo/blast/api/ else echo "\"$cxx_dir/src/algo/blast/api/blast_options_local_priv.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/api/bl2seq.cpp ]; then cp $cxx_dir/src/algo/blast/api/bl2seq.cpp $cxx_dir/src/algo/blast/api/bl2seq.cpp.backup cp ./ncbi_blast_files/bl2seq.cpp $cxx_dir/src/algo/blast/api/ else echo "\"$cxx_dir/src/algo/blast/api/bl2seq.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/api/blast_memento_priv.hpp ]; then cp $cxx_dir/src/algo/blast/api/blast_memento_priv.hpp $cxx_dir/src/algo/blast/api/blast_memento_priv.hpp.backup cp ./ncbi_blast_files/blast_memento_priv.hpp $cxx_dir/src/algo/blast/api/ else echo "\"$cxx_dir/src/algo/blast/api/blast_memento_priv.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/algo/blast/api/prelim_search_runner.hpp ]; then cp $cxx_dir/src/algo/blast/api/prelim_search_runner.hpp $cxx_dir/src/algo/blast/api/prelim_search_runner.hpp.backup cp ./ncbi_blast_files/prelim_search_runner.hpp $cxx_dir/src/algo/blast/api/ else echo "\"$cxx_dir/src/algo/blast/api/prelim_search_runner.hpp\" could not be found. Exiting..." exit 1 fi cp ./ncbi_blast_files//gpu_cpu_common.h $cxx_dir/include/algo/blast/core/gpu_cpu_common.h if [ -f $cxx_dir/include/algo/blast/core/blast_engine.h ]; then cp $cxx_dir/include/algo/blast/core/blast_engine.h $cxx_dir/include/algo/blast/core/blast_engine.h.backup cp ./ncbi_blast_files/blast_engine.h $cxx_dir/include/algo/blast/core/ else echo "\"$cxx_dir/include/algo/blast/core/blast_engine.h\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/algo/blast/core/blast_options.h ]; then cp $cxx_dir/include/algo/blast/core/blast_options.h $cxx_dir/include/algo/blast/core/blast_options.h.backup cp ./ncbi_blast_files/blast_options.h $cxx_dir/include/algo/blast/core else echo "\"$cxx_dir/include/algo/blast/core/blast_options.h\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/algo/blast/core/blast_seqsrc_impl.h ]; then cp $cxx_dir/include/algo/blast/core/blast_seqsrc_impl.h $cxx_dir/include/algo/blast/core/blast_seqsrc_impl.h.backup cp ./ncbi_blast_files/blast_seqsrc_impl.h $cxx_dir/include/algo/blast/core/ else echo "\"$cxx_dir/include/algo/blast/core/blast_seqsrc_impl.h\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/objtools/blast/seqdb_reader/seqdb.hpp ]; then cp $cxx_dir/include/objtools/blast/seqdb_reader/seqdb.hpp $cxx_dir/include/objtools/blast/seqdb_reader/seqdb.hpp.backup cp ./ncbi_blast_files/seqdb.hpp $cxx_dir/include/objtools/blast/seqdb_reader/ else echo "\"$cxx_dir/include/objtools/blast/seqdb_reader/seqdb.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/algo/blast/blastinput/blast_args.hpp ]; then cp $cxx_dir/include/algo/blast/blastinput/blast_args.hpp $cxx_dir/include/algo/blast/blastinput/blast_args.hpp.backup cp ./ncbi_blast_files/blast_args.hpp $cxx_dir/include/algo/blast/blastinput/ else echo "\"$cxx_dir/include/algo/blast/blastinput/blast_args.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/algo/blast/blastinput/cmdline_flags.hpp ]; then cp $cxx_dir/include/algo/blast/blastinput/cmdline_flags.hpp $cxx_dir/include/algo/blast/blastinput/cmdline_flags.hpp.backup cp ./ncbi_blast_files/cmdline_flags.hpp $cxx_dir/include/algo/blast/blastinput/ else echo "\"$cxx_dir/include/algo/blast/blastinput/cmdline_flags.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/algo/blast/api/blast_options.hpp ]; then cp $cxx_dir/include/algo/blast/api/blast_options.hpp $cxx_dir/include/algo/blast/api/blast_options.hpp.backup cp ./ncbi_blast_files/blast_options.hpp $cxx_dir/include/algo/blast/api/ else echo "\"$cxx_dir/include/algo/blast/api/blast_options.hpp\" could not be found. Exiting..." exit 1 fi #Files related to makeblastdb if [ -f $cxx_dir/src/app/blastdb/makeblastdb.cpp ]; then cp $cxx_dir/src/app/blastdb/makeblastdb.cpp $cxx_dir/src/app/blastdb/makeblastdb.cpp.backup cp ./ncbi_blast_files/makeblastdb.cpp $cxx_dir/src/app/blastdb/ else echo "\"$cxx_dir/src/app/blastdb/makeblastdb.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_writer/writedb.cpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_writer/writedb.cpp $cxx_dir/src/objtools/blast/seqdb_writer/writedb.cpp.backup cp ./ncbi_blast_files/writedb.cpp $cxx_dir/src/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/writedb.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/objtools/blast/seqdb_writer/writedb.hpp ]; then cp $cxx_dir/include/objtools/blast/seqdb_writer/writedb.hpp $cxx_dir/include/objtools/blast/seqdb_writer/writedb.hpp.backup cp ./ncbi_blast_files/writedb.hpp $cxx_dir/include/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/include/objtools/blast/seqdb_writer/writedb.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_writer/build_db.cpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_writer/build_db.cpp $cxx_dir/src/objtools/blast/seqdb_writer/build_db.cpp.backup cp ./ncbi_blast_files/build_db.cpp $cxx_dir/src/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/build_db.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/objtools/blast/seqdb_writer/build_db.hpp ]; then cp $cxx_dir/include/objtools/blast/seqdb_writer/build_db.hpp $cxx_dir/include/objtools/blast/seqdb_writer/build_db.hpp.backup cp ./ncbi_blast_files/build_db.hpp $cxx_dir/include/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/include/objtools/blast/seqdb_writer/build_db.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.cpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.cpp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.cpp.backup cp ./ncbi_blast_files/writedb_impl.cpp $cxx_dir/src/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.hpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.hpp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.hpp.backup cp ./ncbi_blast_files/writedb_impl.hpp $cxx_dir/src/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/writedb_impl.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.cpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.cpp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.cpp.backup cp ./ncbi_blast_files/writedb_volume.cpp $cxx_dir/src/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.cpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.hpp ]; then cp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.hpp $cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.hpp.backup cp ./ncbi_blast_files/writedb_volume.hpp $cxx_dir/src/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/writedb_volume.hpp\" could not be found. Exiting..." exit 1 fi if [ -f $cxx_dir/include/objtools/blast/seqdb_writer/writedb_files.hpp ]; then cp $cxx_dir/include/objtools/blast/seqdb_writer/writedb_files.hpp $cxx_dir/include/objtools/blast/seqdb_writer/writedb_files.hpp.backup cp ./ncbi_blast_files/writedb_files.hpp $cxx_dir/include/objtools/blast/seqdb_writer/ else echo "\"$cxx_dir/src/objtools/blast/seqdb_writer/writedb_files.hpp\" could not be found. Exiting..." exit 1 fi exit 0 h-blast-1.0_ncbi-blast-2.2.25/h_blast/gpu_blastp.h0000644000175000017500000000113012001215332017575 0ustar ykeyke#ifndef GPU_BLASTP_H #define GPU_BLASTP_H #define WIDTH_MULTIPLE 64 /* --------------- protein blast defines -----------------------------*/ typedef uint PV_ARRAY_TYPE; void ReadSubstitutionMatrix(char *SubstitutionMatrix, char *h_RepeatedSubstitutionMatrix, int SubstitutionMatrix_length, int num_blocksx); void MultipleCopyPV(PV_ARRAY_TYPE* h_RepeatedPV, PV_ARRAY_TYPE* h_pv, int pv_length, int num_blocksx); void MultipleCopyMaxlength(int* h_Repeated_SequenceMaxlength_vector, const int* Sequence_Maxlength_vector, int Group_number, int stride, int NumSequences); #endif /*GPU_BLASTP_H */ h-blast-1.0_ncbi-blast-2.2.25/h_blast/gpu_blastp.c0000644000175000017500000001645712001215333017613 0ustar ykeyke#include #include #include #include #include #include "gpu_blastp.h" #include void Round2Multiple(int* const MaxLength) { int remainder = *MaxLength % WIDTH_MULTIPLE; if( 0 != remainder) *MaxLength += (WIDTH_MULTIPLE - remainder); } void MultipleCopyPV(PV_ARRAY_TYPE* h_RepeatedPV, PV_ARRAY_TYPE* h_pv, int pv_length, int num_blocksx) { int offset = 0; for(int block = 0; block < num_blocksx; ++block) { memcpy(&h_RepeatedPV[offset], h_pv, pv_length*sizeof(PV_ARRAY_TYPE)); offset += pv_length; } } void MultipleCopyMaxlength(int* h_Repeated_SequenceMaxlength_vector, const int* Sequence_Maxlength_vector, const int Group_number, const int stride, const int NumSequences) { int offset = 0; for(int i = 0; i < NumSequences; ++i) { memcpy(&h_Repeated_SequenceMaxlength_vector[offset], Sequence_Maxlength_vector, Group_number*sizeof(int)); offset += stride; } } void ReadSubstitutionMatrix(char *h_SubstitutionMatrix, char *h_RepeatedSubstitutionMatrix, int SubstitutionMatrix_length, int num_blocksx) { char Blosum62[28][32] = { {-128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128, -128}, // (00) {-128, 4, -2, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -1, -2, -1, -1, -4, -1, -1, -128, -128, -128, -128}, //A (01) {-128, -2, 4, -3, 4, 1, -3, -1, 0, -3, 0, -4, -3, 4, -2, 0, -1, 0, -1, -3, -4, -1, -3, 0, -1, -4, -1, -3, -128, -128, -128, -128}, //B (02) {-128, 0, -3, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -1, -2, -3, -1, -4, -1, -1, -128, -128, -128, -128}, //C (03) {-128, -2, 4, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -1, -3, 1, -1, -4, -1, -3, -128, -128, -128, -128}, //D (04) {-128, -1, 1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -1, -2, 4, -1, -4, -1, -3, -128, -128, -128, -128}, //E (05) {-128, -2, -3, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, -1, 3, -3, -1, -4, -1, 0, -128, -128, -128, -128}, //F (06) {-128, 0, -1, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -1, -3, -2, -1, -4, -1, -4, -128, -128, -128, -128}, //G (07) {-128, -2, 0, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, -1, 2, 0, -1, -4, -1, -3, -128, -128, -128, -128}, //H (08) {-128, -1, -3, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1, -1, -3, -1, -4, -1, 3, -128, -128, -128, -128}, //I (09) {-128, -1, 0, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -1, -2, 1, -1, -4, -1, -3, -128, -128, -128, -128}, //K (10) {-128, -1, -4, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1, -1, -3, -1, -4, -1, 3, -128, -128, -128, -128}, //L (11) {-128, -1, -3, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1, -1, -1, -1, -4, -1, 2, -128, -128, -128, -128}, //M (12) {-128, -2, 4, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -1, -2, 0, -1, -4, -1, -3, -128, -128, -128, -128}, //N (13) {-128, -1, -2, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -1, -3, -1, -1, -4, -1, -3, -128, -128, -128, -128}, //P (14) {-128, -1, 0, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1, -1, 4, -1, -4, -1, -2, -128, -128, -128, -128}, //Q (15) {-128, -1, -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -1, -2, 0, -1, -4, -1, -2, -128, -128, -128, -128}, //R (16) {-128, 1, 0, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -1, -2, 0, -1, -4, -1, -2, -128, -128, -128, -128}, //S (17) {-128, 0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -1, -2, -1, -1, -4, -1, -1, -128, -128, -128, -128}, //T (18) {-128, 0, -3, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1, -1, -2, -1, -4, -1, 2, -128, -128, -128, -128}, //V (19) {-128, -3, -4, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, -1, 2, -2, -1, -4, -1, -2, -128, -128, -128, -128}, //W (20) {-128, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -4, -1, -1, -128, -128, -128, -128}, //X (21) {-128, -2, -3, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, -1, 7, -2, -1, -4, -1, -1, -128, -128, -128, -128}, //Y (22) {-128, -1, 0, -3, 1, 4, -3, -2, 0, -3, 1, -3, -1, 0, -1, 4, 0, 0, -1, -2, -2, -1, -2, 4, -1, -4, -1, -3, -128, -128, -128, -128}, //Z (23) {-128, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -4, -1, -1, -128, -128, -128, -128}, // (24) {-128, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1, -4, -4, -128, -128, -128, -128}, // (25) {-128, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -4, -1, -1, -128, -128, -128, -128}, // (26) {-128, -1, -3, -1, -3, -3, 0, -4, -3, 3, -3, 3, 2, -3, -3, -2, -2, -2, -1, 2, -2, -1, -1, -3, -1, -4, -1, 3, -128, -128, -128, -128} // (27) }; memcpy(h_SubstitutionMatrix, Blosum62,SubstitutionMatrix_length*sizeof(char) ); int offset = 0; for(int block = 0; block < num_blocksx; ++block) { memcpy(&h_RepeatedSubstitutionMatrix[offset], h_SubstitutionMatrix, SubstitutionMatrix_length*sizeof(char)); offset += SubstitutionMatrix_length*sizeof(char); } } h-blast-1.0_ncbi-blast-2.2.25/h_blast/gpu_blastp.cu0000644000175000017500000014252412137173253020011 0ustar ykeyke#include #include #include #include // includes, kernels #include "gpu_blastp.h" #include "gpu_blastp_kernel.cu" #include #include "gpu_blastp_kernel.h" #include #include #include using namespace std; #define CUDA_DEVICE_MAXNUMBER 100 /// The macro "NO_CELL_LEVELS" shows the statistic /// function will report at most 2^(NO_CELL_LEVELS-1) /// results can be stored within a subject. #define NO_CELL_LEVELS 7 typedef struct { int GPU_device_id; char* h_db_access_entry; //database first ptr int* h_db_Sequence_Maxlength_vector; //the vector addressed max length of each group of subjects Int4 number_of_Groups; // the size of vector @h_db_Sequence_Maxlength_vector Int4 num_seq_to; // the no. of sequence in a part of one file volumne unsigned long h_GPU_BLASTP_database_bytes; // the total bytes of the related database section Int4 h_Hits_offset; // The first address of the location in the space @h_Hits Int4 h_GPUBlastInitHitList_offset; //The first address of the location in the space @h_GPUBlastInitHitList Int4 h_Hits_bytes; Int4 h_GPUBlastInitHitList_bytes; Int4* h_Hits; GPUBlastInitHitList* h_GPUBlastInitHitList; Int4* d_Hits; GPUBlastInitHitList* d_GPUBlastInitHitList; Int4* d_Database2Dpadded; Int4* d_RepeatedSubstitutionMatrix; Int4* d_RepeatedSequence_length_vector; PV_ARRAY_TYPE* d_RepeatedPV; AaLookupSmallboneCell* d_ThickBackbone; Uint2* d_overflow; short* d_RepeatedDiag_array; cudaStream_t stream_id; cudaEvent_t event_id, start; } GPU_Stream_Block; static unsigned int MAX_SUCCESSFUL_HITS_PER_SEQUENCE=19; /// For query adjustment void static small_bobbo_sorting(unsigned short* short_array, int array_count ) { int i,j; Uint2 tmp=0; for(i=0; ithick_backbone; unsigned short* h_overflow = (unsigned short*)lookup->overflow; unsigned long int h_overflow_count = lookup->overflow_size; vector overflow_vector (h_overflow, h_overflow+h_overflow_count); int i; for(i=0; ibackbone_size; i++) { if(h_ThickBackbone[i].num_used > AA_HITS_PER_CELL) sort(overflow_vector.begin()+ h_ThickBackbone[i].payload.overflow_cursor, overflow_vector.begin() + h_ThickBackbone[i].payload.overflow_cursor + h_ThickBackbone[i].num_used ); else if(h_ThickBackbone[i].num_used > 0 ) small_bobbo_sorting( h_ThickBackbone[i].payload.entries, h_ThickBackbone[i].num_used); } for(i=0; iCUDA_DEVICE_MAXNUMBER) { printf("Warning: The no. of avalible gpu cards are more then %d.\nNow, uses %d cards only!\nTo use all cards, please modify the constant CUDA_DEVICE_MAXNUMBER\n", CUDA_DEVICE_MAXNUMBER, num_of_gpu_cards_used); num_of_gpu_cards_used = CUDA_DEVICE_MAXNUMBER; } if( (num_of_gpu_cards_used>=expected_num_of_cards) && (0!=expected_num_of_cards)) num_of_gpu_cards_used = expected_num_of_cards; else if(num_of_gpu_cards_used < expected_num_of_cards) { printf("Warning: There is not enough gpu cards avalible, uses %d cards only!\n", num_of_gpu_cards_used); } } void gpu_quit() { /// !!!!!!!!!!!!!!!!!!!! /// Note that this function will reset the device immediately. /// It is the caller's responsibility to ensure that the device /// is not being accessed by any other host threads from the /// process when this function is called. /// !!!!!!!!!!!!!!!!!!!! cudaDeviceReset(); } void gpu_abnormally_exit(int exit_code) { /// !!!!!!!!!!!!!!!!!!!! /// Note that this function will reset the device immediately. /// It is the caller's responsibility to ensure that the device /// is not being accessed by any other host threads from the /// process when this function is called. /// !!!!!!!!!!!!!!!!!!!! gpu_quit(); exit(exit_code); } void all_gpu_quit() { /// !!!!!!!!!!!!!!!!!!!! /// Note that this function will reset the device immediately. /// It is the caller's responsibility to ensure that the device /// is not being accessed by any other host threads from the /// process when this function is called. /// !!!!!!!!!!!!!!!!!!!! int gpu_device_count=num_of_gpu_cards_used, i; for(i=0; iaverage_sequence_bytes) { stream_blocks[i].h_db_Sequence_Maxlength_vector=&(Sequence_length_vector[last_group_ptr+1]); stream_blocks[i].number_of_Groups=group_ptr-last_group_ptr; stream_blocks[i].num_seq_to = stream_blocks[i].number_of_Groups*Group_size; if(group_ptr==last_group_ptr) { printf("Error: The size of a group of subject sequences is greater than the amount of average sequence bytes of a part! \ Please decrease the gpu thread size or the gpu block size!\n"); exit(-1); } else { stream_blocks[i].h_GPU_BLASTP_database_bytes = sequence_bytes_of_a_part - Sequence_length_vector[group_ptr+1]*Group_size; } stream_blocks[i].h_Hits_offset = (last_group_ptr+1)*Group_size*H_HITS_SIZE_BYTE; stream_blocks[i].h_GPUBlastInitHitList_offset = i*total_init_hsp_list_length/cuda_device_count; last_total_database_bytes += stream_blocks[i].h_GPU_BLASTP_database_bytes; sequence_bytes_of_a_part = 0; last_group_ptr=group_ptr; break; } group_ptr ++; } if(group_ptr+1 == Group_number-1) { if(0==flag) { stream_blocks[i].h_GPU_BLASTP_database_bytes = total_sequence_bytes - last_total_database_bytes; if((group_ptr==last_group_ptr) && (stream_blocks[i].h_GPU_BLASTP_database_bytes > average_sequence_bytes)) { printf("Error: The size of the last group of subject sequences is greater than the amount of average sequence bytes of a part! \ Please decrease the gpu thread size or the gpu block size!\n"); exit(-1); } else if(stream_blocks[i].h_GPU_BLASTP_database_bytes > average_sequence_bytes) { flag = 1; stream_blocks[i].h_GPU_BLASTP_database_bytes = sequence_bytes_of_a_part; stream_blocks[i].h_db_Sequence_Maxlength_vector=&(Sequence_length_vector[last_group_ptr+1]); stream_blocks[i].number_of_Groups=group_ptr-last_group_ptr; stream_blocks[i].h_Hits_offset = (last_group_ptr+1)*Group_size*H_HITS_SIZE_BYTE; stream_blocks[i].h_GPUBlastInitHitList_offset = i*total_init_hsp_list_length/cuda_device_count; stream_blocks[i].num_seq_to = stream_blocks[i].number_of_Groups*Group_size; last_group_ptr=group_ptr; last_total_database_bytes += stream_blocks[i].h_GPU_BLASTP_database_bytes; sequence_bytes_of_a_part=0; } else { stream_blocks[i].h_db_Sequence_Maxlength_vector=&(Sequence_length_vector[Group_number-1]); stream_blocks[i].number_of_Groups=1; stream_blocks[i].h_Hits_offset = (last_group_ptr+1)*Group_size*H_HITS_SIZE_BYTE; stream_blocks[i].h_GPUBlastInitHitList_offset = i*total_init_hsp_list_length/cuda_device_count; stream_blocks[i].num_seq_to = num_seq_to - (last_group_ptr+1)*Group_size; flag = 2; group_ptr++; last_total_database_bytes = total_sequence_bytes; last_group_ptr = Group_number-1; } } else if(1==flag) { stream_blocks[i].h_db_Sequence_Maxlength_vector=&(Sequence_length_vector[last_group_ptr+1]); stream_blocks[i].number_of_Groups=1; stream_blocks[i].h_GPU_BLASTP_database_bytes = total_sequence_bytes - last_total_database_bytes; if(stream_blocks[i].h_GPU_BLASTP_database_bytes > average_sequence_bytes) { printf("Error: The size of the last group of subject sequences is greater than the \n amount of average sequence bytes of a part! \n \ Please decrease the gpu thread size or the gpu block size!\n"); exit(-1); } stream_blocks[i].h_Hits_offset = (Group_number-1)*Group_size*H_HITS_SIZE_BYTE; stream_blocks[i].h_GPUBlastInitHitList_offset = i*total_init_hsp_list_length/cuda_device_count; stream_blocks[i].num_seq_to = num_seq_to - (Group_number-1)*Group_size; flag=2; group_ptr++; last_total_database_bytes = total_sequence_bytes; last_group_ptr = Group_number-1; } } if(group_ptr+1 == Group_number) { stream_blocks[i].h_db_Sequence_Maxlength_vector=Sequence_length_vector; stream_blocks[i].number_of_Groups=0; stream_blocks[i].h_GPU_BLASTP_database_bytes = 0; stream_blocks[i].h_Hits_offset = 0; stream_blocks[i].h_GPUBlastInitHitList_offset = 0; stream_blocks[i].num_seq_to = 0; } } if(group_ptr+1 == Group_number) { stream_blocks[cuda_device_count-1].h_db_access_entry= h_GPU_BLASTP_database; stream_blocks[cuda_device_count-1].h_db_Sequence_Maxlength_vector=Sequence_length_vector; stream_blocks[cuda_device_count-1].number_of_Groups=0; stream_blocks[cuda_device_count-1].h_GPU_BLASTP_database_bytes = 0; stream_blocks[cuda_device_count-1].h_Hits_offset = 0; stream_blocks[cuda_device_count-1].h_GPUBlastInitHitList_offset = 0; stream_blocks[cuda_device_count-1].num_seq_to = 0; } else { stream_blocks[cuda_device_count-1].h_db_access_entry= &(h_GPU_BLASTP_database[last_total_database_bytes]); stream_blocks[cuda_device_count-1].h_db_Sequence_Maxlength_vector=&(Sequence_length_vector[last_group_ptr+1]); stream_blocks[cuda_device_count-1].number_of_Groups=Group_number-last_group_ptr-1; stream_blocks[cuda_device_count-1].h_GPU_BLASTP_database_bytes = total_sequence_bytes - last_total_database_bytes; if((group_ptr==last_group_ptr) && (stream_blocks[cuda_device_count-1].h_GPU_BLASTP_database_bytes > average_sequence_bytes)) { printf("Warning: The size of the last group of subject sequences is greater than the amount of average sequence bytes of a part! \ Please decrease the gpu thread size or the gpu block size!\n"); } stream_blocks[cuda_device_count-1].h_Hits_offset = (last_group_ptr+1)*Group_size*H_HITS_SIZE_BYTE; stream_blocks[cuda_device_count-1].h_GPUBlastInitHitList_offset = (cuda_device_count-1)*total_init_hsp_list_length/cuda_device_count; stream_blocks[cuda_device_count-1].num_seq_to = num_seq_to - (last_group_ptr+1)*Group_size; } } for(i=0; inum_blocksx * gpu_options->num_threadsx, gpu_options->num_sequences_to, h_Database2Dpadded_bytes, h_GPUBlastInitHitList_bytes/sizeof(GPUBlastInitHitList)); for(int cuda_device_id=0; cuda_device_idnum_blocksx, num_threadsx = gpu_options->num_threadsx, num_sequences = stream_blocks[cuda_device_id].num_seq_to;//gpu_options->num_sequences_to; if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Number of processed sequences by the GPU = %5d\n", num_sequences); int Group_number = (num_sequences / (num_threadsx*num_blocksx) ) + (( (num_sequences % (num_threadsx*num_blocksx) ) == 0)?0:1); int Sequence_length_vector_stride = ( Group_number / PITCH + ((Group_number % PITCH)?1:0) ) * PITCH; int h_RepeatedSequence_length_vector_integers = Sequence_length_vector_stride * num_blocksx; unsigned long int h_RepeatedSequence_length_vector_bytes = Sequence_length_vector_stride * num_blocksx * sizeof(int); int* h_RepeatedSequence_length_vector=(int*) calloc( h_RepeatedSequence_length_vector_integers, sizeof(int) ); MultipleCopyMaxlength(h_RepeatedSequence_length_vector, Sequence_length_vector, Group_number, Sequence_length_vector_stride, num_blocksx); BlastAaLookupTable *lookup = (BlastAaLookupTable*) lookup_wrap->lut; PV_ARRAY_TYPE *h_pv = lookup->pv; int pv_length = (lookup->backbone_size >> PV_ARRAY_BTS) + 1; Round2Multiple(&pv_length); unsigned long int h_RepeatedPV_bytes = num_blocksx * pv_length * sizeof(PV_ARRAY_TYPE); PV_ARRAY_TYPE* h_RepeatedPV = (PV_ARRAY_TYPE*) calloc( h_RepeatedPV_bytes, sizeof(char)); MultipleCopyPV(h_RepeatedPV, h_pv, pv_length, num_blocksx); AaLookupSmallboneCell* h_ThickBackbone = (AaLookupSmallboneCell*) lookup->thick_backbone; Uint2* h_overflow = (Uint2*)lookup->overflow; unsigned long int h_ThickBackbone_bytes = (lookup->backbone_size+1) * sizeof(AaLookupSmallboneCell); unsigned long int h_overflow_bytes = (lookup->overflow_size+1) * sizeof(Uint2); unsigned int diag_array_length = ewp->diag_table->diag_array_length; unsigned long long int h_RepeatedDiag_array_bytes = (unsigned long long int)diag_array_length * num_blocksx*num_threadsx*sizeof(short); int diag_mask = ewp->diag_table->diag_mask; int window = ewp->diag_table->window; int Query_length = query->length; unsigned char* h_Query = query->sequence; int num_contexts_invoked = query_info->last_context - query_info->first_context +1; int* h_x_dropoff = (int*)malloc(num_contexts_invoked * sizeof(int) ); int* h_cutoff_score = (int*)malloc(num_contexts_invoked * sizeof(int) ); int* h_query_offset = (int*)malloc((num_contexts_invoked+1) * sizeof(int) ); for(int i = 0; i < num_contexts_invoked; ++i) { h_x_dropoff[i] = word_params->cutoffs[i].x_dropoff; h_cutoff_score[i] = word_params->cutoffs[i].cutoff_score; h_query_offset[i] = query_info->contexts[i].query_offset; } h_query_offset[num_contexts_invoked] = query->length; //Read Substitution Matrix char* h_SubstitutionMatrix = (char*) calloc( SUBSTITUTION_MATRIX_LENGTH * sizeof(char), sizeof(char) ); unsigned int h_RepeatedSubstitutionMatrix_bytes = SUBSTITUTION_MATRIX_LENGTH * num_blocksx * sizeof(char); char* h_RepeatedSubstitutionMatrix = (char*) calloc ( h_RepeatedSubstitutionMatrix_bytes, sizeof(char) ); ReadSubstitutionMatrix( h_SubstitutionMatrix, h_RepeatedSubstitutionMatrix, SUBSTITUTION_MATRIX_LENGTH, num_blocksx ); if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Global memory allocated memory size = %lf Mb\n", (double)(stream_blocks[cuda_device_id].h_GPU_BLASTP_database_bytes + num_blocksx * num_threadsx * sizeof(int) + h_RepeatedSubstitutionMatrix_bytes + h_RepeatedSequence_length_vector_bytes + stream_blocks[cuda_device_id].h_Hits_bytes + h_RepeatedPV_bytes+ h_ThickBackbone_bytes+ h_overflow_bytes+ h_RepeatedDiag_array_bytes + stream_blocks[cuda_device_id].h_GPUBlastInitHitList_bytes)/1e6); unsigned long long int BytesTransferredToGlobalMemory = stream_blocks[cuda_device_id].h_GPU_BLASTP_database_bytes + 2* num_blocksx * num_threadsx * sizeof(int) + h_RepeatedSubstitutionMatrix_bytes + h_RepeatedSequence_length_vector_bytes + h_RepeatedPV_bytes+ h_ThickBackbone_bytes+ h_overflow_bytes; if( GPU_VERBOSE ) { fprintf(stderr,"\nthreadId = 0: Bytes transferred to global memory\n"); fprintf(stderr,"\n\nthreadId = 0: Bytes allocated on host\n"); fprintf(stderr,"threadId = 0: Database = %d bytes\n",stream_blocks[cuda_device_id].h_GPU_BLASTP_database_bytes ); fprintf(stderr,"threadId = 0: SubstitutionMatrix = %d bytes\n",h_RepeatedSubstitutionMatrix_bytes ); fprintf(stderr,"threadId = 0: SequenceMaxlength = %d bytes\n",h_RepeatedSequence_length_vector_bytes ); fprintf(stderr,"threadId = 0: Hits = %d bytes\n",stream_blocks[cuda_device_id].h_Hits_bytes ); fprintf(stderr,"threadId = 0: PV = %d bytes\n",h_RepeatedPV_bytes ); fprintf(stderr,"threadId = 0: ThickBackbone = %d bytes\n",h_ThickBackbone_bytes ); fprintf(stderr,"threadId = 0: Overflow = %d bytes\n",h_overflow_bytes ); fprintf(stderr,"threadId = 0: RepeatedDiagArray = %d bytes\n",h_RepeatedDiag_array_bytes) ; fprintf(stderr,"threadId = 0: InitHitList = %d bytes\n",stream_blocks[cuda_device_id].h_GPUBlastInitHitList_bytes ) ; fprintf(stderr,"\nthreadId = 0: Bytes transferred to global memory\n"); fprintf(stderr,"threadId = 0: Database = %10.1f Mb\n",(float)stream_blocks[cuda_device_id].h_GPU_BLASTP_database_bytes / 1e6); fprintf(stderr,"threadId = 0: SubstitutionMatrix = %10.1f Mb\n",(float)h_RepeatedSubstitutionMatrix_bytes / 1e6); fprintf(stderr,"threadId = 0: SequenceMaxlength = %10.1f Mb\n",(float)h_RepeatedSequence_length_vector_bytes / 1e6); fprintf(stderr,"threadId = 0: PV = %10.1f Mb\n",(float)h_RepeatedPV_bytes / 1e6); fprintf(stderr,"threadId = 0: ThickBackbone = %10.1f Mb\n",(float)h_ThickBackbone_bytes / 1e6); fprintf(stderr,"threadId = 0: Overflow = %10.1f Mb\n",(float)h_overflow_bytes / 1e6); fprintf(stderr,"threadId = 0: Total = %10.1f Mb\n",(double)BytesTransferredToGlobalMemory/1e6); } if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Allocating GPU memory...\n"); gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_Database2Dpadded), stream_blocks[cuda_device_id].h_GPU_BLASTP_database_bytes + 2*num_blocksx * num_threadsx * sizeof(int) ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_RepeatedSubstitutionMatrix), h_RepeatedSubstitutionMatrix_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_RepeatedSequence_length_vector), h_RepeatedSequence_length_vector_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_Hits), stream_blocks[cuda_device_id].h_Hits_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_RepeatedPV), h_RepeatedPV_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_ThickBackbone), h_ThickBackbone_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_overflow), h_overflow_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_RepeatedDiag_array), h_RepeatedDiag_array_bytes ) ; gpu_device_calloc( (void**) &(stream_blocks[cuda_device_id].d_GPUBlastInitHitList), stream_blocks[cuda_device_id].h_GPUBlastInitHitList_bytes ) ; if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Done with allocating GPU memory\n"); // copy host memory to device if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Copying to GPU memory...\n"); gpu_memcpy( stream_blocks[cuda_device_id].d_RepeatedSubstitutionMatrix, h_RepeatedSubstitutionMatrix, h_RepeatedSubstitutionMatrix_bytes, cudaMemcpyHostToDevice) ; gpu_memcpy( stream_blocks[cuda_device_id].d_RepeatedSequence_length_vector, h_RepeatedSequence_length_vector, h_RepeatedSequence_length_vector_bytes, cudaMemcpyHostToDevice) ; gpu_memcpy( stream_blocks[cuda_device_id].d_RepeatedPV, h_RepeatedPV, h_RepeatedPV_bytes, cudaMemcpyHostToDevice) ; gpu_memcpy( stream_blocks[cuda_device_id].d_ThickBackbone, h_ThickBackbone, h_ThickBackbone_bytes, cudaMemcpyHostToDevice) ; gpu_memcpy( stream_blocks[cuda_device_id].d_overflow, h_overflow, h_overflow_bytes, cudaMemcpyHostToDevice) ; if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Done with copying GPU memory\n"); // setup execution parameters dim3 grid( num_blocksx, num_blocksy, 1); dim3 threads( num_threadsx, num_threadsy, 1); int total_shared_mem_size_requested = 0, total_const_mem_size_requested=0; total_shared_mem_size_requested = pv_length*sizeof(PV_ARRAY_TYPE) + SUBSTITUTION_MATRIX_LENGTH*sizeof(char) + Sequence_length_vector_stride*sizeof(int) + 3 * num_threadsx * 4 * sizeof(char) + num_threadsx*sizeof(int); total_const_mem_size_requested = Query_length + (num_contexts_invoked+1)*sizeof(int)*3; cudaDeviceProp deviceProp; cudaGetDeviceProperties(&deviceProp, cuda_device_id); if(total_shared_mem_size_requested > deviceProp.sharedMemPerBlock) { fprintf(stderr,"ERROR: Shared memory requirements (%d bytes per block) bigger than available memory (%d bytes)!!\n", total_shared_mem_size_requested, deviceProp.sharedMemPerBlock); all_gpu_abnormally_exit(-1); } if(total_const_mem_size_requested > deviceProp.totalConstMem) { fprintf(stderr,"ERROR: Constant memory requirements (%d bytes per block) bigger than available memory (%d bytes)!!\n", total_const_mem_size_requested, deviceProp.totalConstMem); all_gpu_abnormally_exit(-1); } if((num_threadsx/32)*32 != num_threadsx) { fprintf(stderr,"ERROR: The no. of threads must be a multipy of 32!\n"); all_gpu_abnormally_exit(-1); } int total_subject_length_offset_per_gpu_thread = 0; for(int i=0; i (1<<15) )// greater than { fprintf(stderr, "ERROR: the diag. array can not handle this query group!\n"); all_gpu_abnormally_exit(-1); } int hash_subject_length = 0; for(int i=0; idiag_table->window; } if(hash_subject_length>(1<<15)) { fprintf(stderr,"ERROR: the diag. array is not big enough, please make the size of each DB volumn smaller!\n") ; all_gpu_abnormally_exit(-1); } gpu_memcpy_to_symbol( d_Query_const, h_Query, Query_length) ; gpu_memcpy_to_symbol( (char*)d_x_dropoff_const, h_x_dropoff, num_contexts_invoked*sizeof(int)); gpu_memcpy_to_symbol( (char*)d_cutoff_score_const, h_cutoff_score, num_contexts_invoked*sizeof(int)); gpu_memcpy_to_symbol( (char*)d_query_offset_const, h_query_offset, (num_contexts_invoked+1)*sizeof(int)); /// For record time elaspsed gpu_memcpy( & (stream_blocks[cuda_device_id].d_Database2Dpadded[num_blocksx * num_threadsx]), stream_blocks[cuda_device_id].h_db_access_entry, stream_blocks[cuda_device_id].h_GPU_BLASTP_database_bytes, cudaMemcpyHostToDevice) ; cudaEventRecord(stream_blocks[cuda_device_id].start,stream_blocks[cuda_device_id].stream_id); if(NULL == stream_blocks[cuda_device_id].h_db_access_entry) { printf("Error, the h_db entry is NULL, and the card id is %d\n", cuda_device_id); gpu_abnormally_exit(-1); } // execute the kernel if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Kernel execution...\n"); GPU_BLASTP_kernelTwoHit<<< grid, threads, total_shared_mem_size_requested, stream_blocks[cuda_device_id].stream_id >>>( stream_blocks[cuda_device_id].d_Database2Dpadded, stream_blocks[cuda_device_id].d_RepeatedSubstitutionMatrix, SUBSTITUTION_MATRIX_LENGTH, stream_blocks[cuda_device_id].d_RepeatedPV, stream_blocks[cuda_device_id].d_ThickBackbone, stream_blocks[cuda_device_id].d_overflow, stream_blocks[cuda_device_id].d_RepeatedSequence_length_vector, Sequence_length_vector_stride, num_sequences, pv_length, Query_length, diag_mask, diag_array_length, num_contexts_invoked, lookup->word_length, lookup->mask, window, window, stream_blocks[cuda_device_id].d_RepeatedDiag_array, stream_blocks[cuda_device_id].d_Hits, stream_blocks[cuda_device_id].d_GPUBlastInitHitList, stream_blocks[cuda_device_id].h_GPUBlastInitHitList_offset, stream_blocks[cuda_device_id].h_GPUBlastInitHitList_bytes/sizeof(GPUBlastInitHitList) ); if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Done with kernel execution\n"); cudaEventRecord(stream_blocks[cuda_device_id].event_id, stream_blocks[cuda_device_id].stream_id); printf("Finished submitted, and the card id is %d\n", cuda_device_id); free(h_x_dropoff); free(h_cutoff_score); free(h_query_offset); free(h_SubstitutionMatrix); free(h_RepeatedSequence_length_vector); free(h_RepeatedPV); free(h_RepeatedSubstitutionMatrix); } void memory_defrag( const Int4 h_Hits_bytes, const Int4 h_GPUBlastInitHitList_bytes, const Int4 num_sequences) { int i=0, current_hit_id=0, total_sucessful_extention_for_subject=0; GPUBlastInitHitList* GPUBlastInitHitList_tmp= (GPUBlastInitHitList*)malloc(h_GPUBlastInitHitList_bytes*sizeof(char)); GPUBlastInitHitList* current_hit_list_in_this_subject=NULL; if((NULL==local_h_Hits) || (NULL==local_h_GPUBlastInitHitList)) { printf("Error: the memory address of local_h_Hits or local_h_GPUBlastInitHitList is unaccessable!\n"); gpu_abnormally_exit(-1); } if(NULL==GPUBlastInitHitList_tmp) { printf("Error: there is no enough memory space to varialbe GPUBlastInitHitList_tmp!\n"); gpu_abnormally_exit(-1); } for(i=0; i0) ) { total_sucessful_extention_for_subject = local_h_Hits[i*4+1]; current_hit_list_in_this_subject = & (local_h_GPUBlastInitHitList[local_h_Hits[i*4+3]]); local_h_Hits[i*4+3] = current_hit_id; if( 0==(i&0x10) ) { memcpy( GPUBlastInitHitList_tmp+current_hit_id,current_hit_list_in_this_subject,total_sucessful_extention_for_subject*sizeof(GPUBlastInitHitList)); } else { memcpy( GPUBlastInitHitList_tmp+current_hit_id, current_hit_list_in_this_subject-total_sucessful_extention_for_subject+1, total_sucessful_extention_for_subject*sizeof(GPUBlastInitHitList)); } current_hit_id += total_sucessful_extention_for_subject; } } gpu_host_mem_free((void**)&local_h_GPUBlastInitHitList); local_h_GPUBlastInitHitList = GPUBlastInitHitList_tmp; GPUBlastInitHitList_tmp = NULL; } void GPU_BLASTP_get_data( Int4* h_Hits, const Int4 h_Hits_bytes, GPUBlastInitHitList* h_GPUBlastInitHitList, const Int4 h_GPUBlastInitHitList_bytes, const Int4 num_sequences) { // copy result from device to host if( GPU_VERBOSE ) fprintf(stderr,"threadId = 0: Transferring data from GPU...\n"); int gpu_device_count=num_of_gpu_cards_used; for(int i=0; i NUM_QUERIES_MAX ) return FALSE; if( query_length > QUERY_LENGTH_MAX ) return FALSE; int h_RepeatedSubstitutionMatrix_bytes = SUBSTITUTION_MATRIX_LENGTH * (gpu_options->num_blocksx) * sizeof(char); int Sequence_length_vector_stride = ( Group_number / PITCH + ((Group_number % PITCH)?1:0) ) * PITCH; long int h_RepeatedSequence_length_vector_bytes = Sequence_length_vector_stride * (gpu_options->num_blocksx) * sizeof(int); BlastAaLookupTable *lookup = (BlastAaLookupTable*) lookup_wrap->lut; int pv_length = (lookup->backbone_size >> PV_ARRAY_BTS) + 1; Round2Multiple(&pv_length); int h_RepeatedPV_bytes = (gpu_options->num_blocksx) * pv_length * sizeof(PV_ARRAY_TYPE); int h_ThickBackbone_bytes = (lookup->backbone_size +1) * sizeof(AaLookupSmallboneCell); int h_overflow_bytes = (lookup->overflow_size+1) * sizeof(Uint2); int diag_array_length = ewp->diag_table->diag_array_length; unsigned long long int h_RepeatedDiag_array_bytes = (unsigned long long int)diag_array_length * (gpu_options->num_blocksx)*(gpu_options->num_threadsx)*sizeof(short); if(0==num_of_gpu_cards_used) { printf("Error: num_of_gpu_cards_used is zero!\n"); exit(-1); } int acutal_h_Database2Dpadded_bytes = h_Database2Dpadded_bytes / num_of_gpu_cards_used; if(num_of_gpu_cards_used>0) acutal_h_Database2Dpadded_bytes *=IMB_factor_of_gpudb_group; unsigned long long int Total_global_memory_bytes = acutal_h_Database2Dpadded_bytes + gpu_options->num_blocksx * gpu_options->num_threadsx * sizeof(int) + h_RepeatedSubstitutionMatrix_bytes + h_RepeatedSequence_length_vector_bytes + h_Hits_bytes + h_RepeatedPV_bytes + h_ThickBackbone_bytes + h_overflow_bytes + h_RepeatedDiag_array_bytes + h_GPUBlastInitHitList_bytes; cudaDeviceProp deviceProp; cudaGetDeviceProperties(&deviceProp, 0); unsigned long long int GPU_global_memory = (unsigned long long int) (deviceProp.totalGlobalMem*0.93); if( Total_global_memory_bytes > GPU_global_memory) { printf("Not enough mem: %d bytes ,just has %d \n", Total_global_memory_bytes, GPU_global_memory); return FALSE; } return TRUE; } Boolean GPU_BLAST_check_availability() { int deviceCount = 0; if (cudaGetDeviceCount(&deviceCount) != 0) return FALSE; if ( 0 == deviceCount ) return FALSE; return TRUE; } void GPU_BLASTP_check_rehit_ratio(const Int4* _h_Hits, const Int4 _num_sequences) { long rehit_count[NO_CELL_LEVELS], re_extension_count[NO_CELL_LEVELS], re_succ_extension_count[NO_CELL_LEVELS], total_successful_extension=0, total_hits=0, total_hits_extended=0; int icounter, i; for(i=0; i (1< %3d | %13ld | %13ld | %13ld \n", (1<0) && (total_hits_extended>0) && (total_successful_extension>0) ) { printf("\n=========== re-comp. ratio ( '%' ) statistic =========\n"); printf("cell no. | re-hit | re-extened | re-succ-extended\n"); printf("--------------------------------------------------------\n"); printf("autual | %7lg | %7lg | %7lg\n", 100.0*rehit_count[0]/total_hits, 100.0*re_extension_count[0]/total_hits_extended, 100.0*re_succ_extension_count[0]/total_successful_extension ); printf("--------------------------------------------------------\n"); for(i=1; i %3d | %7lg | %7lg | %7lg\n", (1<sp|Q8CG65|SSPO_MOUSE SCO-spondin OS=Mus musculus GN=Sspo PE=2 SV=1 MLPLALLFGMLWTQANGHWCEQIETVHVEEEVTPRQEDLVPCTSLYHYSRLGWQLDLSWS GRVGLTRPPALGLCAIYKPPETRPATWNRTVRACCPGWGGAHCTDALAETSPKGHCFVTW HCQPLAGSANSSAGSLEDPADELGVWPLTLNDPILFPGMSLQWQGDWLVLSGGLGVVVRL DRSSSISISVDQEFWGRTQGLCGLYNGRPEDDFVEPGGGLATLAATFGNSWKLPGSEPGC LDAVEVAWGCESLLGGTLTDLEAVKLQAQAQDMCHQLLEGPFWQCHGQVQPDEYHETCLF AYCVGATAGNGPEGQLEAVCATFANYAQACARQHIYVHWRKPGFCERVCPGGQLYSDCVS SCPPSCSAVAQGEEGSCGKECVSGCECPTGLFWDGALCVPAAHCPCYHRRQRYAPGDTVK QQCNPCVCQDGRWHCAQALCPAECAVGGDGHYFTFDGRSFFFRGTPGCHYSLVQDSVKGQ LLVVLEHGACDTGSCLHALSVFLGNTHIQLRYSGAVLVDGEDVDLPWIGVEGFNISWASS TFLLLHWPGAWVLWGVAEPAAYITLDPRHAYQVQGLCGTFTWKQQDDFLTPAGDIETSVT AFASKFQVSGDGRCPLVDKSPLFCSSYSQHLTFTEAACAILHGHAFQECHGLVDREPFRL RCLEAVCGCAPGRDCLCPVLSAYTRHCAQEGVLLQWRNETLCPVSCPGGQVYQECAPVCG HHCGEPEDCKELGICVAGCNCPPGLLWDLEGQCVPPSMCHCQFGGHRYTINTTTVRDCSH CICQERGLWNCTAHHCPRQWALCPRELIYVPGACLLTCDSPRANHSCWAGSTDGCVCPPG TVLLDKHCVSPDLCPCRHNGQWYPPNATIQEDCNICVCQGQRWHCTGQRCSGWCQASGAP HYVTFDGLVFTFPGACEYLLVREAGGRFSVSVQNLPCGASGLTCTKALVVRLDSTVVHML RGQAVTVNGVSIRLPKVYTGPGLSLHHAGLFLLLTTRLGLTLLWDGGTRVLVQLSPHFHG RVAGLCGNFDSDASNDLRSRQGLLEPTAYLTAHSWRLNPLCPEPGDLPHPWNAHRANWAP ARCEVILQPIFAPCHTEVPPQQYYEWCVYDACGCDTGGDCECLCSAIATYADECARHRHH VRWRSQELCPLQCEGGQVYEPCGSTCPPTCHDHHSELRWHCQVITCVEGCFCPEGTLLHG GACMKLAACPCEWQGSFFPPGTVLQKDCGNCTCQGSQWHCDRGGAPCEDMEPGCAEGETL CRENGHCVPLEWLCDNQDDCGDGSDEEGCATSVCGEGQMSCQSGHCLPLSLICDGQDDCG DGTDEQGCLCPHGSLACADGRCLPPALLCNGHPDCLDAADEESCLGPVSCISGEVSCVDG TCVRTIQLCDGVWDCPDGADEGPSHCSLPSLPTPPGGIGQNPSTSSLDTAPSPVGSTSPA SPCSLLEFQCNSGECTPRGWRCDQEEDCTDGSDELDCGGPCMLYQVPCAHSPHCVSPGQL CDGVTQCPDGSDEDPDVCEEQSASGGANRTGAPCPEFSCPDGTCIDFLLVCDGNPDCELA DETEPSLDEQGCGAWGSWGPWAPCSQTCGSGTRSRNRNCSTSSLQVLQNCPGLQHQSQAC FTEACPVDGEWSSWSPWSPCSEPCGGTTTRHRQCRPPQNGGQDCALLPGSTHSTRQTSPC PQEGCLNATCFGELVFRTCAPCPLTCDDISGQAACPPDRPCSSPGCWCPDGKVLNTEGQC VRPRQCPCLVDGAHYWPGQRIKMDCQLCGLDCGWSSWSPWAECLGPCSSQSLQWSFRSPN NPRLSGHGRQCRGIHRKARRCQTEACEGCEQWGLMYNVGERWRGGPCMVCECLHSSITHC SPYCPIGSCPQGWVLVEGMGESCCHCALPEKNQTVIHMTTPAPAPASAPSPQIGAHLVTY VLPPTADACYSPLGLAGLPMWAPSQHWEHITRADPVEAPMAGPGPREGASAEWHTQPLYL QLDLRRPRNLTGIIVQRAGSSAAYVSTLSLQFSSDNLQWHNYVNSLSSTLSPPKPSPESS NHMAPEVWTFDQMVQARYIRVWPHSGHLRDNNQHDIFLWVELLGLSPLAPLCPGSRHRCA SGECAPKGGPCDGAVDCDDGSDEEGCGSLHASTTSRTPALSPTQPGKFPREVSEDLRQGA EAMTSHSPPSSGETAGLIPASEGTLPVSGQPMQTLSATSTFPPGAKSLHPGMAAVTVHPP HSVTPGAPVGQTVSPRPFPPMPCGPGQVPCDVLGCVEQEQLCDGREDCLDGSDEQHCASA EPFTVPTTALPGLPASKALCSPSQLRCGSGECLPFEHRCDLQVNCQDGSDEDNCVDCVLA PWSGWSDCSRSCGLGLIFQHRELLRLPLPGGSCLLDQFRSQSCFVQACPVAGAWAEWGPW TACSVSCGGGHQSRQRSCVDPPPKNGGAPCPGPSHEKAPCNLQLCPGDTDCEPGLVHVNA ELCQKGLVPPCPPSCLDPEANRSCSGHCMEGCRCPPGLLLQDSHCLPLSECPCLVGQKLI QPRLAFLLDNCSQCICEKGTLLCKPGACSQSCGWSAWSPWTACDRSCGSGVRARFRSPTN PPVAFGGSPCEGDRQELQACYTDCGTEIPGWTPWTSWSSCSQSCLVPGGDPGWRQRSRLC PSSRDTFCPGEATQEEPCSPPVCPVPSAWGLWASWSTCSASCNGGIQTRGRSCSGSAPGN PVCLGPHTQTRDCNMHPCTAQCPGNMVFRSAEQCLEEGGPCPQLCLAQDPGVECTGSCAP SCNCPPGLFLHNASCLPRSQCPCQLHGQLYAPGAVAHLDCNNCTCISGEMVCTSKRCPVA CGWSPWTPWSPCSQSCNVGIRRRFRAGTEPPAAFGGAECQGPNLDAEFCSLRPCRGPGAA WSSWTPCSVPCGGGYRNRTQGSGPHSPIEFSTCSLQPCAGPVPGVCPEDQQWLDCAQGPA SCAHLSIPGEANQTCHPGCYCLSGMLLLNNVCVPVQDCPCAHRGRLYSPGSAVHLPCENC SCISGLITNCSSWPCEEGQPAWSSWTPWSVCSASCNPARRHRHRFCARPPHRAPFSLVLL TTVAAPTTLCPGPEAEEEPCLLPGCNQAGGWSPWSPWSGCSRSCGGGLRSRTRACDQPSP QGLGDFCEGPQAQGEACQAQPCPVTNCSAMEGAEYSPCGPPCPRSCDDLVHCVWRCQPGC YCPLGKVLSADGAICVKPSYCSCLDLLTGKRHHAGTQLMRPDGCNHCTCMEGRLNCTDLP CQVSGDWCPWSKWTACSQPCRGQTRTRSRACVCPAPQHGGSPCPEESGGTGVQHQMEACP NATACPVDGAWSPWGPWSSCDACLGQSYRSRVCSHPPISDGGKPCLGGYQQSRPCRNSST LCTDCGGGQDLLPCGQPCRHSCQDLSLGSTCQPGSAGCQSGCGCPPGQLSQHGLCVFPVD CHCHFQPRAMGIPENRSRSVGSTLSSWESLEPGEVVTGPCDNCTCVAGILQCHEVPSCPG PGIWSSWGPWEKCSVSCGGGEQLRSRQCARPPCPGLAQQSRICHIHVCRETGCPAGRLYR ECQPSDGCPFSCAHVTGQVACFSERCKEGCHCPEGTFQHHVACVQECPCVLTVLLLQELG LASAALGSYPTLLGDEGKPLGPGVELLPGQMLQTDCGNCSCVHGKLSCSMVECSRVHGSF GPWGMWSLCSRSCGGLGTRTRTRQCVLPTLAPGGLSCRGPLQDLEYCFSPECPGTAGSTV EPVTGLAGGWGPWSPWSPCSHSCTDPAHPAWRSRTRLCLANCTVGDSSQERPCNLPSCAA LLPCPGPGCGSGNCFWTSWAPWEPCSRSCGVGQQRRLRAYHPPGPGGHWCPDILTAYQER RFCNLRACPVPGGWSHWSPWSWCDRSCGGGRSLRSRSCSSPPPKNGGTSCVGERHHVRPC NPMPCEEGCPAGMEMVSCANHCPYSCSDLQEGGMCQEDQACQLGCRCSEGFLEQDGGCVP VGHCECTDAQGRSWAPGSQHQDACNNCSCQAGQLSCTAQLCSPPAHCAWSHWSAWSSCSH SCGPQGQQSRFRSSTSGSWALECQKEQSQSQPCPEVPCPPLCLHEAHLHELGDNWLHGEC QQCSCTPEGAICKDTDCAVPRGWTLWSSWSYCSVSCGGGSQVRTRSCTVSAPPHGSLSCE GPDTQTRHCGQQLCLQKLERCSWGPWGPCSRSCGTGLASRSGSCPCLLTKEDSKCNDTFL GLDTQACYSGPCQDDCTWGDWSSWTRCSCKVLVQQRYRHQVPAPGQAGEGTPCTRLDGHF RPCTIGNCSEDSCPPPFEFQSCGSPCAGLCATHLNHRLCQDLPPCQPGCYCPKGLLEQAG SCILPEQCNCWHISGEGARVTLAPGDRLQLGCKECVCRRGELQCSSQGCEGLLPLTGWSE WSPCGPCLPQSALAPASRTALEGHWPLNTSDLPPPSVTLLASEQYRHRLCLDPETRRPWA GDPALCTVPLSQQRLCPDPGACNDTCQWGPWGPWSPCQMPCSGGFKLRWRVARDTSAGEC PGPWAQTESCNMGSCPGESCETRDTVFTLDCANQCPRSCADLWDGVQCLQGPCSPGCRCP PGQLVQDGHCVPISSCRCGLPSANASWELAPTQVVQLDCHNCTCINGTLMCPHLECPVLG PWSAWSECSAVCGKGTMVRHRSCEEHPDREPCQALDLQQWQECNLQACPECPPGQVLSTC ATMCPSLCSHLWPGTICVREPCQLGCGCPGGQLLYNGTCIPPEACPCTQFSLPWGLTLPL EEQARELPSGTVLTRNCTHCTCQGGAFICSLTDCQECAPGEIWQHGKLGPCEKTCPEMNM TQAWSNCTEAQAPGCVCQLGYFRSQTGLCVPEDHCECWHHGSPHLPGSEWQEACESCRCL HGKSVCIRHCPELSCAQGEVIMQEPGSCCPICQQDTLKEEPVSCRYLTELRNLTKGPCHL DQIEVSYCSGHCRSSTNVMTEEPYLQSQCDCCSYRLDPDSPVRILNLLCPDGHTEPVVLP VIHSCQCSACQGGDFSKH >sp|Q8BRH4|MLL3_MOUSE Histone-lysine N-methyltransferase MLL3 OS=Mus musculus GN=Mll3 PE=2 SV=2 MSSEEDRSAEQQQPPPAPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGK STVEDEDSMDGLETTETENIVETEIKEQSVEEDAETEVDSSKQPVSALQRSVSEESANSL VSVGVEAKISEQLCAFCYCGEKSSLGQGDLKQFRVTPGLTLPWKDQPSNKDIDDNSSGTC EKIQNYAPRKQRGQRKERPPQQSAVSCVSVSTQTACEDQAGKLWDELSLVGLPDAIDVQA LFDSTGTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEK CTQMYHYPCAAGAGTFQDFSHFFLLCPEHIDQAPERSKEDANCAVCDSPGDLLDQFFCTT CGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV MKSVPTNGWKCKNCRICIECGTRSSTQWHHNCLICDTCYQQQDNLCPFCGKCYHPELQKD MLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYCKHLGAEIDPLHPGNEVEMPELPTD YASGMEIEGTEDEVVFLEQTVNKDVSDHQCRPGIVPDVQVYTEEPQKSNPLESPDTVGLI TSESSDNKMNPDLANEIAHEVDTEKTEMLSKGRHVCEEDQNEDRMEVTENIEVLPHQTIV PQEDLLLSEDSEVASKELSPPKSAPETAAPEALLSPHSERSLSCKEPLLTERVQEEMEQK ENSEFSTGCVDFEMTLAVDSCDKDSSCQGDKYVELPAEEESTFSSATDLNKADVSSSSTL CSDLPSCDMLHGYPPAFNSAAGSIMPTTYISVTPKIGMGKPAITKRKFSPGRPRSKQGAW SNHNTVSPPSWAPDTSEGREIFKPRQLSGSAIWSIKVGRGSGFPGKRRPRGAGLSGRGGR GRSKLKSGIGAVVLPGVSAADISSNKDEEENSMHNTVVLFSSSDKFTLQQDMCVVCGSFG QGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECTVCEACGKATDPGRLLLCDD CDISYHTYCLDPPLQTVPKGGWKCKWCVWCRHCGATSAGLRCEWQNNYTQCAPCASLSSC PVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMCRPYMPVSNVPS SDCCDSSLVAQIVTKVKELDPPKTYTQDGVCLTESGMSQLQSLTVTAPRRKRTKPKLKLK IINQNSVAVLQTPPDIQSEHSRDGEMDDSREGELMDCDGKSESSPEREAGDDETKGIEGT DAIKKRKRKPYRPGIGGFMVRQRSRTGQGKAKRSVVRKDSSGSISEQLPSRDDGWREQLP DTLVDEPVSVAENTDKIKKRYRKRKNKLEETFPAYLQEAFFGKDLLDTSRQNKLSVDNLS EDAAQLSFKTGFLDPSSDPLLSSSSTSAKPGTQGTADDPLADISEVLNTDDDILGIISDD LAKSVDHSDIGPTTADASSLPQPGVSQSSRPLTEEQLDGILSPELDKMVTDGAILGKLYK IPELGGKDVEDLFTAVLSPATTQPAPLPQPPPPPQLLPMHNQDVFSRMPLMNGLIGPSPH LPHNSLPPGSGLGTFPAIAQSPYTDVRDKSPAFNAIASDPNSSWAPTTPSMEGENDTLSN AQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERA PYVQKARDNRAALRINKVQMSNDSMKRQQQQDSIDPSSRIDSDLFKDPLKQRESEHEQEW KFRQQMRQKSKQQAKIEATQKLEQVKNEQQQQQQQQQQQQQQQLASQHLLVAPGSDTPSS GAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPPPPSTPSRIPV QESLSQSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVE NCVPLSSVPRPIHMNETSATRPSPARDLCASSMTNSDPYAKPPDTPRPMMTDQFSKPFSL PRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTP LHPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTE SFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR PNTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRP RTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGPGRIDTF THASSSAVRDPYDQPPVTPRPHSESFGTSQVVHDLVDRPVPGSEGNFSTSSNLPVSSQGQ QFSSVSQLPGPVPTSGGTDTQNTVNMSQADTEKLRQRQKLREIILQQQQQKKIASRQEKG PQDTAVVPHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAVFPKDQRGPYP PEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPHIRRPMSMEMPRPSNN PPLNNPVGLPQHFPPQGLPVQQHNILGQAFIELRHRAPDGRSRLPFAASPSSVIESPSHP RHGNFLPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP LNHPLSGEFSEAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKELDVKDLEGVE VKDLDDEDLENLNLDTEDGKGDDLDTLDNLETNDPNLDDLLRSGEFDIIAYTDPELDLGD KKSMFNEELDLNVPIDDKLDNQCASVEPKTRDQGDKTMVLEDKDLPQRKSSVSSEIKTEA LSPYSKEEIQSEIKNHDDSRGDADTACSQAASAQTNHSDRGKTALLTTDQDMLEKRCNQE NAGPVVSAIQGSTPLPARDVMNSCDITGSTPVLSSLLSNEKCDDSDIRPSGSSPPSLPIS PSTHGSSLPPTLIVPPSPLLDNTVNSNVTVVPRINHAFSQGVPVNPGFIQGQSSVNHNLG TGKPTNQTVPLTNQSSTMSGPQQLMIPQTLAQQNRERPLLLEEQPLLLQDLLDQERQEQQ QQRQMQAMIRQRSEPFFPNIDFDAITDPIMKAKMVALKGINKVMAQNSLGMPPMVMSRFP FMGPSVAGTQNNDGQTLVPQAVAQDGSITHQISRPNPPNFGPGFVNDSQRKQYEEWLQET QQLLQMQQKYLEEQIGAHRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQ LEQIRKQQKEHAELIEDYRIKQQQQQQQCALAPPILMPGVQPQPPLVPGATSLTMSQPNF PMVPQQLQHQQHTAVISGHTSPARMPSLPGWQSNSASAHLPLNPPRIQPPIAQLSLKTCT PAPGTVSSANPQNGPPPRVEFDDNNPFSESFQERERKERLREQQERQRVQLMQEVDRQRA LQQRMEMEQHCLMGAELANRTPVSQMPFYGSDRPCDFLQPPRPLQQSPQHQQQIGPVLQQ QNVQQGSVNSPPNQTFMQTNEQRQVGPPSFVPDSPSASGGSPNFHSVKPGHGNLPGSSFQ QSPLRPPFTPILPGTSPVANSNVPCGQDPAVTQGQNYSGSSQSLIQLYSDIIPEEKGKKK RTRKKKKDDDAESGKAPSTPHSDCAAPLTPGLSETTSTPAVSSPSELPQQRQQEPVEPVP VPTPNVSAGQPCIESENKLPNSEFIKETSNQQTHVNAEADKPSVETPNKTEEIKLEKAET QPSQEDTKVEEKTGNKIKDIVAGPVSSIQCPSHPVGTPTTKGDTGNELLKHLLKNKKASS LLTQKPEGTLSSDESSTKDGKLIEKQSPAEGLQTLGAQMQGGFGGGNSQLPKTDGASENK KQRSKRTQRTGEKAAPRSKKRKKDEEEKQAMYSSSDSFTHLKQQNNLSNPPTPPASLPPT PPPMACQKMANGFATTEELAGKAGVLVSHEVARALGPKPFQLPFRPQDDLLARAIAQGPK TVDVPASLPTPPHNNHEELRIQDHYGDRDTPDSFVPSSSPESVVGVEVNKYPDLSLVKEE PPEPVPSPIIPILPSISGKNSESRRNDIKTEPGTLFFTSPFGSSPNGPRSGLISVAITLH PTAAENISSVVAAFSDLLHVRIPNSYEVSNAPDVPPMGLVSSHRVNPSLEYRQHLLLRGP PPGSANPPRLATSYRLKQPNVPFPPTSNGLSGYKDSSHGPAEGASLRPQWCCHCKVVILG SGVRKSCKDLTFVNKGSRENTKRMEKDIVFCSNNCFILYSSAAQAKNSDNKESLPSLPQS PMKEPSKAFHQYSNNISTLDVHCLPQFQEKVSPPASPPISFPPAFEAAKVESKPDELKVT VKLKPRLRTVPVGLEDCRPLNKKWRGMKWKKWSIHIVIPKGTFKPPCEDEIDEFLKKLGT CLKPDPVPKDCRKCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALI NVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMFFKDKTMLCPMHKP KGIHEQQLSYFAVFRRVYVQRDEVRQIASIVQRGERDHTFRVGSLIFHTIGQLLPQQMQA FHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEEKDGRPVFVIRIVEQGHEDLVLSDS SPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYT FRYGRNPLMELPLAVNPTGCARSEPKMSAHVKRFVLRPHTLNSTSTSKSFQSTVTGELNA PYSKQFVHSKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNE VANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVVTFERGHKI IISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN h-blast-1.0_ncbi-blast-2.2.25/queries/3SequenceLength_00014606.txt0000600000175000017500000003544611746751572022106 0ustar ykeyke>sp|Q8CG65|SSPO_MOUSE SCO-spondin OS=Mus musculus GN=Sspo PE=2 SV=1 MLPLALLFGMLWTQANGHWCEQIETVHVEEEVTPRQEDLVPCTSLYHYSRLGWQLDLSWS GRVGLTRPPALGLCAIYKPPETRPATWNRTVRACCPGWGGAHCTDALAETSPKGHCFVTW HCQPLAGSANSSAGSLEDPADELGVWPLTLNDPILFPGMSLQWQGDWLVLSGGLGVVVRL DRSSSISISVDQEFWGRTQGLCGLYNGRPEDDFVEPGGGLATLAATFGNSWKLPGSEPGC LDAVEVAWGCESLLGGTLTDLEAVKLQAQAQDMCHQLLEGPFWQCHGQVQPDEYHETCLF AYCVGATAGNGPEGQLEAVCATFANYAQACARQHIYVHWRKPGFCERVCPGGQLYSDCVS SCPPSCSAVAQGEEGSCGKECVSGCECPTGLFWDGALCVPAAHCPCYHRRQRYAPGDTVK QQCNPCVCQDGRWHCAQALCPAECAVGGDGHYFTFDGRSFFFRGTPGCHYSLVQDSVKGQ LLVVLEHGACDTGSCLHALSVFLGNTHIQLRYSGAVLVDGEDVDLPWIGVEGFNISWASS TFLLLHWPGAWVLWGVAEPAAYITLDPRHAYQVQGLCGTFTWKQQDDFLTPAGDIETSVT AFASKFQVSGDGRCPLVDKSPLFCSSYSQHLTFTEAACAILHGHAFQECHGLVDREPFRL RCLEAVCGCAPGRDCLCPVLSAYTRHCAQEGVLLQWRNETLCPVSCPGGQVYQECAPVCG HHCGEPEDCKELGICVAGCNCPPGLLWDLEGQCVPPSMCHCQFGGHRYTINTTTVRDCSH CICQERGLWNCTAHHCPRQWALCPRELIYVPGACLLTCDSPRANHSCWAGSTDGCVCPPG TVLLDKHCVSPDLCPCRHNGQWYPPNATIQEDCNICVCQGQRWHCTGQRCSGWCQASGAP HYVTFDGLVFTFPGACEYLLVREAGGRFSVSVQNLPCGASGLTCTKALVVRLDSTVVHML RGQAVTVNGVSIRLPKVYTGPGLSLHHAGLFLLLTTRLGLTLLWDGGTRVLVQLSPHFHG RVAGLCGNFDSDASNDLRSRQGLLEPTAYLTAHSWRLNPLCPEPGDLPHPWNAHRANWAP ARCEVILQPIFAPCHTEVPPQQYYEWCVYDACGCDTGGDCECLCSAIATYADECARHRHH VRWRSQELCPLQCEGGQVYEPCGSTCPPTCHDHHSELRWHCQVITCVEGCFCPEGTLLHG GACMKLAACPCEWQGSFFPPGTVLQKDCGNCTCQGSQWHCDRGGAPCEDMEPGCAEGETL CRENGHCVPLEWLCDNQDDCGDGSDEEGCATSVCGEGQMSCQSGHCLPLSLICDGQDDCG DGTDEQGCLCPHGSLACADGRCLPPALLCNGHPDCLDAADEESCLGPVSCISGEVSCVDG TCVRTIQLCDGVWDCPDGADEGPSHCSLPSLPTPPGGIGQNPSTSSLDTAPSPVGSTSPA SPCSLLEFQCNSGECTPRGWRCDQEEDCTDGSDELDCGGPCMLYQVPCAHSPHCVSPGQL CDGVTQCPDGSDEDPDVCEEQSASGGANRTGAPCPEFSCPDGTCIDFLLVCDGNPDCELA DETEPSLDEQGCGAWGSWGPWAPCSQTCGSGTRSRNRNCSTSSLQVLQNCPGLQHQSQAC FTEACPVDGEWSSWSPWSPCSEPCGGTTTRHRQCRPPQNGGQDCALLPGSTHSTRQTSPC PQEGCLNATCFGELVFRTCAPCPLTCDDISGQAACPPDRPCSSPGCWCPDGKVLNTEGQC VRPRQCPCLVDGAHYWPGQRIKMDCQLCGLDCGWSSWSPWAECLGPCSSQSLQWSFRSPN NPRLSGHGRQCRGIHRKARRCQTEACEGCEQWGLMYNVGERWRGGPCMVCECLHSSITHC SPYCPIGSCPQGWVLVEGMGESCCHCALPEKNQTVIHMTTPAPAPASAPSPQIGAHLVTY VLPPTADACYSPLGLAGLPMWAPSQHWEHITRADPVEAPMAGPGPREGASAEWHTQPLYL QLDLRRPRNLTGIIVQRAGSSAAYVSTLSLQFSSDNLQWHNYVNSLSSTLSPPKPSPESS NHMAPEVWTFDQMVQARYIRVWPHSGHLRDNNQHDIFLWVELLGLSPLAPLCPGSRHRCA SGECAPKGGPCDGAVDCDDGSDEEGCGSLHASTTSRTPALSPTQPGKFPREVSEDLRQGA EAMTSHSPPSSGETAGLIPASEGTLPVSGQPMQTLSATSTFPPGAKSLHPGMAAVTVHPP HSVTPGAPVGQTVSPRPFPPMPCGPGQVPCDVLGCVEQEQLCDGREDCLDGSDEQHCASA EPFTVPTTALPGLPASKALCSPSQLRCGSGECLPFEHRCDLQVNCQDGSDEDNCVDCVLA PWSGWSDCSRSCGLGLIFQHRELLRLPLPGGSCLLDQFRSQSCFVQACPVAGAWAEWGPW TACSVSCGGGHQSRQRSCVDPPPKNGGAPCPGPSHEKAPCNLQLCPGDTDCEPGLVHVNA ELCQKGLVPPCPPSCLDPEANRSCSGHCMEGCRCPPGLLLQDSHCLPLSECPCLVGQKLI QPRLAFLLDNCSQCICEKGTLLCKPGACSQSCGWSAWSPWTACDRSCGSGVRARFRSPTN PPVAFGGSPCEGDRQELQACYTDCGTEIPGWTPWTSWSSCSQSCLVPGGDPGWRQRSRLC PSSRDTFCPGEATQEEPCSPPVCPVPSAWGLWASWSTCSASCNGGIQTRGRSCSGSAPGN PVCLGPHTQTRDCNMHPCTAQCPGNMVFRSAEQCLEEGGPCPQLCLAQDPGVECTGSCAP SCNCPPGLFLHNASCLPRSQCPCQLHGQLYAPGAVAHLDCNNCTCISGEMVCTSKRCPVA CGWSPWTPWSPCSQSCNVGIRRRFRAGTEPPAAFGGAECQGPNLDAEFCSLRPCRGPGAA WSSWTPCSVPCGGGYRNRTQGSGPHSPIEFSTCSLQPCAGPVPGVCPEDQQWLDCAQGPA SCAHLSIPGEANQTCHPGCYCLSGMLLLNNVCVPVQDCPCAHRGRLYSPGSAVHLPCENC SCISGLITNCSSWPCEEGQPAWSSWTPWSVCSASCNPARRHRHRFCARPPHRAPFSLVLL TTVAAPTTLCPGPEAEEEPCLLPGCNQAGGWSPWSPWSGCSRSCGGGLRSRTRACDQPSP QGLGDFCEGPQAQGEACQAQPCPVTNCSAMEGAEYSPCGPPCPRSCDDLVHCVWRCQPGC YCPLGKVLSADGAICVKPSYCSCLDLLTGKRHHAGTQLMRPDGCNHCTCMEGRLNCTDLP CQVSGDWCPWSKWTACSQPCRGQTRTRSRACVCPAPQHGGSPCPEESGGTGVQHQMEACP NATACPVDGAWSPWGPWSSCDACLGQSYRSRVCSHPPISDGGKPCLGGYQQSRPCRNSST LCTDCGGGQDLLPCGQPCRHSCQDLSLGSTCQPGSAGCQSGCGCPPGQLSQHGLCVFPVD CHCHFQPRAMGIPENRSRSVGSTLSSWESLEPGEVVTGPCDNCTCVAGILQCHEVPSCPG PGIWSSWGPWEKCSVSCGGGEQLRSRQCARPPCPGLAQQSRICHIHVCRETGCPAGRLYR ECQPSDGCPFSCAHVTGQVACFSERCKEGCHCPEGTFQHHVACVQECPCVLTVLLLQELG LASAALGSYPTLLGDEGKPLGPGVELLPGQMLQTDCGNCSCVHGKLSCSMVECSRVHGSF GPWGMWSLCSRSCGGLGTRTRTRQCVLPTLAPGGLSCRGPLQDLEYCFSPECPGTAGSTV EPVTGLAGGWGPWSPWSPCSHSCTDPAHPAWRSRTRLCLANCTVGDSSQERPCNLPSCAA LLPCPGPGCGSGNCFWTSWAPWEPCSRSCGVGQQRRLRAYHPPGPGGHWCPDILTAYQER RFCNLRACPVPGGWSHWSPWSWCDRSCGGGRSLRSRSCSSPPPKNGGTSCVGERHHVRPC NPMPCEEGCPAGMEMVSCANHCPYSCSDLQEGGMCQEDQACQLGCRCSEGFLEQDGGCVP VGHCECTDAQGRSWAPGSQHQDACNNCSCQAGQLSCTAQLCSPPAHCAWSHWSAWSSCSH SCGPQGQQSRFRSSTSGSWALECQKEQSQSQPCPEVPCPPLCLHEAHLHELGDNWLHGEC QQCSCTPEGAICKDTDCAVPRGWTLWSSWSYCSVSCGGGSQVRTRSCTVSAPPHGSLSCE GPDTQTRHCGQQLCLQKLERCSWGPWGPCSRSCGTGLASRSGSCPCLLTKEDSKCNDTFL GLDTQACYSGPCQDDCTWGDWSSWTRCSCKVLVQQRYRHQVPAPGQAGEGTPCTRLDGHF RPCTIGNCSEDSCPPPFEFQSCGSPCAGLCATHLNHRLCQDLPPCQPGCYCPKGLLEQAG SCILPEQCNCWHISGEGARVTLAPGDRLQLGCKECVCRRGELQCSSQGCEGLLPLTGWSE WSPCGPCLPQSALAPASRTALEGHWPLNTSDLPPPSVTLLASEQYRHRLCLDPETRRPWA GDPALCTVPLSQQRLCPDPGACNDTCQWGPWGPWSPCQMPCSGGFKLRWRVARDTSAGEC PGPWAQTESCNMGSCPGESCETRDTVFTLDCANQCPRSCADLWDGVQCLQGPCSPGCRCP PGQLVQDGHCVPISSCRCGLPSANASWELAPTQVVQLDCHNCTCINGTLMCPHLECPVLG PWSAWSECSAVCGKGTMVRHRSCEEHPDREPCQALDLQQWQECNLQACPECPPGQVLSTC ATMCPSLCSHLWPGTICVREPCQLGCGCPGGQLLYNGTCIPPEACPCTQFSLPWGLTLPL EEQARELPSGTVLTRNCTHCTCQGGAFICSLTDCQECAPGEIWQHGKLGPCEKTCPEMNM TQAWSNCTEAQAPGCVCQLGYFRSQTGLCVPEDHCECWHHGSPHLPGSEWQEACESCRCL HGKSVCIRHCPELSCAQGEVIMQEPGSCCPICQQDTLKEEPVSCRYLTELRNLTKGPCHL DQIEVSYCSGHCRSSTNVMTEEPYLQSQCDCCSYRLDPDSPVRILNLLCPDGHTEPVVLP VIHSCQCSACQGGDFSKH >sp|Q8BRH4|MLL3_MOUSE Histone-lysine N-methyltransferase MLL3 OS=Mus musculus GN=Mll3 PE=2 SV=2 MSSEEDRSAEQQQPPPAPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGK STVEDEDSMDGLETTETENIVETEIKEQSVEEDAETEVDSSKQPVSALQRSVSEESANSL VSVGVEAKISEQLCAFCYCGEKSSLGQGDLKQFRVTPGLTLPWKDQPSNKDIDDNSSGTC EKIQNYAPRKQRGQRKERPPQQSAVSCVSVSTQTACEDQAGKLWDELSLVGLPDAIDVQA LFDSTGTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEK CTQMYHYPCAAGAGTFQDFSHFFLLCPEHIDQAPERSKEDANCAVCDSPGDLLDQFFCTT CGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV MKSVPTNGWKCKNCRICIECGTRSSTQWHHNCLICDTCYQQQDNLCPFCGKCYHPELQKD MLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYCKHLGAEIDPLHPGNEVEMPELPTD YASGMEIEGTEDEVVFLEQTVNKDVSDHQCRPGIVPDVQVYTEEPQKSNPLESPDTVGLI TSESSDNKMNPDLANEIAHEVDTEKTEMLSKGRHVCEEDQNEDRMEVTENIEVLPHQTIV PQEDLLLSEDSEVASKELSPPKSAPETAAPEALLSPHSERSLSCKEPLLTERVQEEMEQK ENSEFSTGCVDFEMTLAVDSCDKDSSCQGDKYVELPAEEESTFSSATDLNKADVSSSSTL CSDLPSCDMLHGYPPAFNSAAGSIMPTTYISVTPKIGMGKPAITKRKFSPGRPRSKQGAW SNHNTVSPPSWAPDTSEGREIFKPRQLSGSAIWSIKVGRGSGFPGKRRPRGAGLSGRGGR GRSKLKSGIGAVVLPGVSAADISSNKDEEENSMHNTVVLFSSSDKFTLQQDMCVVCGSFG QGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECTVCEACGKATDPGRLLLCDD CDISYHTYCLDPPLQTVPKGGWKCKWCVWCRHCGATSAGLRCEWQNNYTQCAPCASLSSC PVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMCRPYMPVSNVPS SDCCDSSLVAQIVTKVKELDPPKTYTQDGVCLTESGMSQLQSLTVTAPRRKRTKPKLKLK IINQNSVAVLQTPPDIQSEHSRDGEMDDSREGELMDCDGKSESSPEREAGDDETKGIEGT DAIKKRKRKPYRPGIGGFMVRQRSRTGQGKAKRSVVRKDSSGSISEQLPSRDDGWREQLP DTLVDEPVSVAENTDKIKKRYRKRKNKLEETFPAYLQEAFFGKDLLDTSRQNKLSVDNLS EDAAQLSFKTGFLDPSSDPLLSSSSTSAKPGTQGTADDPLADISEVLNTDDDILGIISDD LAKSVDHSDIGPTTADASSLPQPGVSQSSRPLTEEQLDGILSPELDKMVTDGAILGKLYK IPELGGKDVEDLFTAVLSPATTQPAPLPQPPPPPQLLPMHNQDVFSRMPLMNGLIGPSPH LPHNSLPPGSGLGTFPAIAQSPYTDVRDKSPAFNAIASDPNSSWAPTTPSMEGENDTLSN AQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERA PYVQKARDNRAALRINKVQMSNDSMKRQQQQDSIDPSSRIDSDLFKDPLKQRESEHEQEW KFRQQMRQKSKQQAKIEATQKLEQVKNEQQQQQQQQQQQQQQQLASQHLLVAPGSDTPSS GAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPPPPSTPSRIPV QESLSQSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVE NCVPLSSVPRPIHMNETSATRPSPARDLCASSMTNSDPYAKPPDTPRPMMTDQFSKPFSL PRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTP LHPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTE SFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR PNTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRP RTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGPGRIDTF THASSSAVRDPYDQPPVTPRPHSESFGTSQVVHDLVDRPVPGSEGNFSTSSNLPVSSQGQ QFSSVSQLPGPVPTSGGTDTQNTVNMSQADTEKLRQRQKLREIILQQQQQKKIASRQEKG PQDTAVVPHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAVFPKDQRGPYP PEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPHIRRPMSMEMPRPSNN PPLNNPVGLPQHFPPQGLPVQQHNILGQAFIELRHRAPDGRSRLPFAASPSSVIESPSHP RHGNFLPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP LNHPLSGEFSEAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKELDVKDLEGVE VKDLDDEDLENLNLDTEDGKGDDLDTLDNLETNDPNLDDLLRSGEFDIIAYTDPELDLGD KKSMFNEELDLNVPIDDKLDNQCASVEPKTRDQGDKTMVLEDKDLPQRKSSVSSEIKTEA LSPYSKEEIQSEIKNHDDSRGDADTACSQAASAQTNHSDRGKTALLTTDQDMLEKRCNQE NAGPVVSAIQGSTPLPARDVMNSCDITGSTPVLSSLLSNEKCDDSDIRPSGSSPPSLPIS PSTHGSSLPPTLIVPPSPLLDNTVNSNVTVVPRINHAFSQGVPVNPGFIQGQSSVNHNLG TGKPTNQTVPLTNQSSTMSGPQQLMIPQTLAQQNRERPLLLEEQPLLLQDLLDQERQEQQ QQRQMQAMIRQRSEPFFPNIDFDAITDPIMKAKMVALKGINKVMAQNSLGMPPMVMSRFP FMGPSVAGTQNNDGQTLVPQAVAQDGSITHQISRPNPPNFGPGFVNDSQRKQYEEWLQET QQLLQMQQKYLEEQIGAHRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQ LEQIRKQQKEHAELIEDYRIKQQQQQQQCALAPPILMPGVQPQPPLVPGATSLTMSQPNF PMVPQQLQHQQHTAVISGHTSPARMPSLPGWQSNSASAHLPLNPPRIQPPIAQLSLKTCT PAPGTVSSANPQNGPPPRVEFDDNNPFSESFQERERKERLREQQERQRVQLMQEVDRQRA LQQRMEMEQHCLMGAELANRTPVSQMPFYGSDRPCDFLQPPRPLQQSPQHQQQIGPVLQQ QNVQQGSVNSPPNQTFMQTNEQRQVGPPSFVPDSPSASGGSPNFHSVKPGHGNLPGSSFQ QSPLRPPFTPILPGTSPVANSNVPCGQDPAVTQGQNYSGSSQSLIQLYSDIIPEEKGKKK RTRKKKKDDDAESGKAPSTPHSDCAAPLTPGLSETTSTPAVSSPSELPQQRQQEPVEPVP VPTPNVSAGQPCIESENKLPNSEFIKETSNQQTHVNAEADKPSVETPNKTEEIKLEKAET QPSQEDTKVEEKTGNKIKDIVAGPVSSIQCPSHPVGTPTTKGDTGNELLKHLLKNKKASS LLTQKPEGTLSSDESSTKDGKLIEKQSPAEGLQTLGAQMQGGFGGGNSQLPKTDGASENK KQRSKRTQRTGEKAAPRSKKRKKDEEEKQAMYSSSDSFTHLKQQNNLSNPPTPPASLPPT PPPMACQKMANGFATTEELAGKAGVLVSHEVARALGPKPFQLPFRPQDDLLARAIAQGPK TVDVPASLPTPPHNNHEELRIQDHYGDRDTPDSFVPSSSPESVVGVEVNKYPDLSLVKEE PPEPVPSPIIPILPSISGKNSESRRNDIKTEPGTLFFTSPFGSSPNGPRSGLISVAITLH PTAAENISSVVAAFSDLLHVRIPNSYEVSNAPDVPPMGLVSSHRVNPSLEYRQHLLLRGP PPGSANPPRLATSYRLKQPNVPFPPTSNGLSGYKDSSHGPAEGASLRPQWCCHCKVVILG SGVRKSCKDLTFVNKGSRENTKRMEKDIVFCSNNCFILYSSAAQAKNSDNKESLPSLPQS PMKEPSKAFHQYSNNISTLDVHCLPQFQEKVSPPASPPISFPPAFEAAKVESKPDELKVT VKLKPRLRTVPVGLEDCRPLNKKWRGMKWKKWSIHIVIPKGTFKPPCEDEIDEFLKKLGT CLKPDPVPKDCRKCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALI NVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMFFKDKTMLCPMHKP KGIHEQQLSYFAVFRRVYVQRDEVRQIASIVQRGERDHTFRVGSLIFHTIGQLLPQQMQA FHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEEKDGRPVFVIRIVEQGHEDLVLSDS SPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYT FRYGRNPLMELPLAVNPTGCARSEPKMSAHVKRFVLRPHTLNSTSTSKSFQSTVTGELNA PYSKQFVHSKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNE VANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVVTFERGHKI IISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN >sp|Q9VW71|FAT2_DROME Putative fat-like cadherin-related tumor suppressor homolog OS=Drosophila melanogaster GN=fat2 PE=1 SV=2 MKIKKYVTPVKRKAFTILQWISLLCSLWLIPTVQSKADEKHTATLEYRLENQLQDLYRFS HSVYNVTIPENSLGKTYAKGVLHERLAGLRVGLNAEVKYRIISGDKEKLFKAEEKLVGDF AFLAIRTRTNNVVLNREKTEEYVIRVKAHVHLHDRNVSSYETEANIHIKVLDRNDLSPLF YPTQYTVVIPEDTPKYQSILKVTADDADLGINGEIYYSLLMDSEYFAIHPTTGEITLLQQ LQYAENSHFELTVVAYDRGSWVNHQNHQASKTKVSISVKQVNFYAPEIFTKTFSSVTPTS NPLIYGIVRVNDKDTGINGNIGRLEIVDGNPDGTFLLKAAETKDEYYIELNQFAHLNQQH FIYNLTLLAEDLGTPRRFAYKSVPIQIKPESKNIPIFTQEIYEVSIPETAPINMPVIRLK VSDPDLGKNALVYLEIVGGNEGDEFRINPDSGMLYTAKQLDAEKKSSYTLTVSAIDQANV GSRKQSSAKVKISVQDMNDNDPIFENVNKVISINENNLAGSFVVKLTAKDRDSGENSYIS YSIANLNAVPFEIDHFSGIVKTTSLLDFETMKRNYELIIRASDWGLPYRRQTEIKLSIVV KDINDNRPQFERVNCYGKVTKSAPMGTEVFVTSAIDFDAGDIISYRLSDGNEDGCFNLDP TSGSLSISCDLKKTTLTNRILKVSATDGTHFSDDLIINVHLMPEDLGGDSSILHGFGSFE CRETGVARRLAETLSLAEKNNVKSASPSVFSDLSLTPSRYGQNVHRPEFVNFPQELSINE SVQLGETVAWIEAKDRDLGYNGKLVFAISDGDYDSVFRIDPDRGELQIIGYLDRERQNEY VLNITVYDLGNPTKSTSKMLPITILDVNDNRPVIQKTLATFRLTESARIGTVVHCLHATD ADSGINAQVTYALSVECSDFTVNATTGCLRLNKPLDREKQDNYALHITAKDGGSPVLSSE ALVYVLVDDVNDNAPVFGVQEYIFKVREDLPRGTVLAVIEAVDEDIGPNAEIQFSLKEET QDEELFRIDKHTGAIRTQGYLDYENKQVHNLIVSAIDGGDPSLTSDMSIVIMIIDVNENR FAPEFDDFVYEGKVKENKPKGTFVMNVTARDMDTVDLNSKITYSITGGDGLGIFAVNDQG SITSLSQLDAETKNFYWLTLCAQDCAIVPLSNCVEVYIQVENENDNIPLTDKPVYYVNVT EASVENVEIITLKAFDPDIDPTQTITYNIVSGNLVGYFEIDSKTGVIKTTERKLDRENQA EHILEVAISDNGSPVLSSTSRIVVSVLDINDNSPEFDQRVYKVQVPSSATVNQSIFQVHA IDSDSGENGRITYSIKSGKGKNKFRIDSQRGHIHIAKPLDSDNEFEIHIKAEDNGIPKKS QTARVNIVVVPVNPNSQNAPLIVRKTSENVVDLTENDKPGFLVTQILAVDDDNDQLWYNI SNGNDDNTFYIGQDNGNILLSKYLDYETQQSYNLTISVTDGTFTAFTNLLVQVIDINDNP PQFAKDVYHVNISENIEEESVIMQLHATDRDEDKKLFYHLHATQDPSSLALFRIDSISGN VIVTQRLDFEKTAQHILIVFVKDQGAPGKRNYAKIIVNVHDHNDHHPEFTAKIIQSKVPE SAAIGSKLAEVRAIDRDSGHNAEIQYSIITGNVGSVFEIDPTFGIITLAGNLNINKIQEY MLQVKAVDLGNPPLSSQIPVHIIVTMSENDPPKFPTNNIAIEIFENLPIGTFVTQVTARS SSSIFFNIISGNINESFRINPSTGVIVINGNIDYESIKVFNLTVKGTNMAAESSCQNIII HILDANDNIPYFVQNEYVGALPESAAIGSYVLKVHDSSKDHLTLQVKDADVGVNGMVEYH IVDDLAKNFFKIDSTTGAIELLRQLDYETNAGYTFDVTVSDMGKPKLHSTTTAHVTIRVI NVNDCPPVFNERELNVTLFLPTFENVFVRQVSAKDADNDTLRFDIVDGNTNECFQIEKYT GIITTRNFEILNNENDRDYALHVRASDGIFSAILIVKIKVLSAIDSNFAFQRESYRFSAF ENNTKVATIGLVNVIGNTLDENVEYRILNPTQLFDIGISSGALKTTGVIFDREVKDLYRL FVEAKSMLYDGMNSNVRRAVTSIDISVLDVNDNCPLFVNMPYYATVSIDDPKGTIIMQVK AIDLDSAENGEVRYELKKGNGELFKLDRKSGELSIKQHVEGHNRNYELTVAAYDGAITPC SSEAPLQVKVIDRSMPVFEKQFYTVSVKEDVEMYSALSVSIEAESPLGRSLIYTISSESQ SFEIDYNTGSIFVVNELDYEKISSHDVSIRATDSLSGVYAEVVLSVSIMDVNDCYPEIES DIYNLTIPENASFGTQILKINATDNDSGANAKLSYYIESINGQNNSELFYIDVTDGNLYL KTPLDYEQIKYHHIVVNVKDHGSPSLSSRSNVFITGRILCRFISYKLIYDSIIPVKDLND NAPCFVEPSYFTKVSVAAVRGQFVALPKAYDKDISDTDSLEYKIVYGNELQTYSIDKLTG VISLQNMLNFTDKSSTVLNISVSDGVHTAYARLKISLLPENVYSPLFDQSTYEAQVPENL LHGHNIITVKASDGDFGTYANLYYEIVSEEMKKIFLIDQTTGVITSKVTFDREKKDEYVV LLKVSDGGGKFGFASLKVIVVDVNDNVPYFLLKEYKMVVSTTVEANQTILTVKAKDDDIV DNGSVHFQIVQKSNDKAVKDVIEINEKTGDIVFKSKAESYGVNSYQFFVRASDRGEPQFH SEVPVSIEIIETDANIPTFEKSSVLLKIIESTPPGTVLTKLHMIGNYTFKFSIAADQDHF MISDSGELILQQTLDREQQESHNLIVVAETSTVPVFFAYADVLIDVRDENDNYPKFDNTF YSASVAENSEKVISLVKVSATDADTGPNGDIRYYLESDTENIQNIFDIDIYSGWITLLTS LDREVQSEYNFKVIAADNGHPKHDAKVPVTIKIVDYNDNAPVFKLPIEGLSVFENALPGT VLINLLLIDPDIEKQEMDFFIVSGDKQAQFQIGKSGELFIAKPLDREQLMFYNLSIIATD GKFTAKANVEIDVKDINDNTPYCLKPRYHISTNESISIGTTLVEVKAIDFDFQSKLRFYL SGKGADDFSIGKESGILKVASALDRETTPKYKLVAHVQDGKDFTQECFSEIIITVNDIND NMPIFSMAQYRVSVPEDAQLNTLITKVHAMDKDFGVNRQIKYSLMGENHDYFKISKSTGI IRLHKSLDRETISLFNLTVKAEDCGVPKLHSIATVAVNILDINDNPPEFSMRQYSCKILE NATHGTEVCKVYATSIDIGVNADIHYFIMSGNEQGKFKMDSTTGDLVLNATLDYEMSKFY FLTIQAIDGGTPPLSNNAYVNISILDINDNSPTFLQNLYRINVNEDIFVGSKILDVKATD EDSDVNGLVTYNIERGDNIGQFSIDPKNGTISVSRPLDRETISHYTLEIQACDQGDPQRC NSVPININILDTNDNAPIFSSSNYSVVLQENRLLGYVFLTFKISDADETPNTTPYTFDIR SGNEGGLFRLEQDGSLRTASRFNHNLQDEFVIQVRVFDNGTPPLYSDAWVVVKIIEESQY PPIVTPLEVTINSFEDDFSGAFIGKVHASDQDKYDELNFSLVSGPDDMYQSSKLFNISNN TGKIYAISNLDIGLYKLNVSVSDGKFHVFSIVKINVELVTNDMLKESVVIRFRRISASEF LLSHRKTFMRSIRNIMRCRQKDVILITLQSDYQKASQHAVGNRRARSIDSDLNVVFAVRK QQIIPDSDEFFTSDEIRQTLIDKKNEIENETNLVVEDVLPSTCQSNKNDCVHGECKQILQ ILKNNVTTTFTDVISFAAPSYIPVNTCVCRPGFDGKHCKETVNACSTDPCSPQRICMPSG SALGYQCVCPKGFSGTYCERKSSKCSNESCDMGLFTAVSFGGKSYAHYKINKVKAKFTLE NGFSYSLQIRTVQQTGTLLYASGKVDYNILEIINGAVQYRFDLGSGEGVISVSSINISDG EWHQISLERSLNSAKVMVDNKHVSHGSAPGVNGILNIQSNDIFVGAEVRPHPSIIGYEDI QRGFIGCMANIKIAKESLPLYISGGSTIAALKRFTNVEFKCDPSNVLVRLGICGSQPCAN SGICKELDTDVFECACQPRYSGKHCEIDLDPCSSGPCLFGGRCDYHGPNNYSCTCPIHLS GKRCEYGKFCTPNPCKNGGICEEGDGISHCMCRGYTGPTCEIDVDECENQPCGNGATCIN EPGSFRCICPSYLTGASCGDPLYSNSISTKLKNFSIEHISGIISGVAVVLVIISCVLCCV VLKRSSSSKRRNRLEKDKNKSSYKEANLNSLVDKDNYCKPNVKLSNLEVNQRPISYTAVP NDNLVLSNRNFVNNLDILRSYGSAGDELENVPFEYQKVNRNKQHVNINSCHSTDADNAYK QEWCEQMHLRTFSENKLNNELKRDFGPSVSRFSTGKLIQVEMPNVCHSSSANFVDYSALA NGQYHWDCSDWVRKSHNPLPDITEVPGAEIADSSSLHSNDSNESKSKKAFFVHREDGDVD PTRDIAALNEDIGSEYLDSEAESCLEPFMLPRSSNQPLSRLSSFNNIENEDYKSNTGKVY LRHPDSYLPTMHFPSETDGESSMTEGPISRMEIKTRRTISENSEEAYLFPCTVGEIGSNS NISVRLCEIEDSELEEFLPQQQTNN h-blast-1.0_ncbi-blast-2.2.25/queries/4SequenceLength_00015806.txt0000600000175000017500000004012611746752055022076 0ustar ykeyke>sp|Q8CG65|SSPO_MOUSE SCO-spondin OS=Mus musculus GN=Sspo PE=2 SV=1 MLPLALLFGMLWTQANGHWCEQIETVHVEEEVTPRQEDLVPCTSLYHYSRLGWQLDLSWS GRVGLTRPPALGLCAIYKPPETRPATWNRTVRACCPGWGGAHCTDALAETSPKGHCFVTW HCQPLAGSANSSAGSLEDPADELGVWPLTLNDPILFPGMSLQWQGDWLVLSGGLGVVVRL DRSSSISISVDQEFWGRTQGLCGLYNGRPEDDFVEPGGGLATLAATFGNSWKLPGSEPGC LDAVEVAWGCESLLGGTLTDLEAVKLQAQAQDMCHQLLEGPFWQCHGQVQPDEYHETCLF AYCVGATAGNGPEGQLEAVCATFANYAQACARQHIYVHWRKPGFCERVCPGGQLYSDCVS SCPPSCSAVAQGEEGSCGKECVSGCECPTGLFWDGALCVPAAHCPCYHRRQRYAPGDTVK QQCNPCVCQDGRWHCAQALCPAECAVGGDGHYFTFDGRSFFFRGTPGCHYSLVQDSVKGQ LLVVLEHGACDTGSCLHALSVFLGNTHIQLRYSGAVLVDGEDVDLPWIGVEGFNISWASS TFLLLHWPGAWVLWGVAEPAAYITLDPRHAYQVQGLCGTFTWKQQDDFLTPAGDIETSVT AFASKFQVSGDGRCPLVDKSPLFCSSYSQHLTFTEAACAILHGHAFQECHGLVDREPFRL RCLEAVCGCAPGRDCLCPVLSAYTRHCAQEGVLLQWRNETLCPVSCPGGQVYQECAPVCG HHCGEPEDCKELGICVAGCNCPPGLLWDLEGQCVPPSMCHCQFGGHRYTINTTTVRDCSH CICQERGLWNCTAHHCPRQWALCPRELIYVPGACLLTCDSPRANHSCWAGSTDGCVCPPG TVLLDKHCVSPDLCPCRHNGQWYPPNATIQEDCNICVCQGQRWHCTGQRCSGWCQASGAP HYVTFDGLVFTFPGACEYLLVREAGGRFSVSVQNLPCGASGLTCTKALVVRLDSTVVHML RGQAVTVNGVSIRLPKVYTGPGLSLHHAGLFLLLTTRLGLTLLWDGGTRVLVQLSPHFHG RVAGLCGNFDSDASNDLRSRQGLLEPTAYLTAHSWRLNPLCPEPGDLPHPWNAHRANWAP ARCEVILQPIFAPCHTEVPPQQYYEWCVYDACGCDTGGDCECLCSAIATYADECARHRHH VRWRSQELCPLQCEGGQVYEPCGSTCPPTCHDHHSELRWHCQVITCVEGCFCPEGTLLHG GACMKLAACPCEWQGSFFPPGTVLQKDCGNCTCQGSQWHCDRGGAPCEDMEPGCAEGETL CRENGHCVPLEWLCDNQDDCGDGSDEEGCATSVCGEGQMSCQSGHCLPLSLICDGQDDCG DGTDEQGCLCPHGSLACADGRCLPPALLCNGHPDCLDAADEESCLGPVSCISGEVSCVDG TCVRTIQLCDGVWDCPDGADEGPSHCSLPSLPTPPGGIGQNPSTSSLDTAPSPVGSTSPA SPCSLLEFQCNSGECTPRGWRCDQEEDCTDGSDELDCGGPCMLYQVPCAHSPHCVSPGQL CDGVTQCPDGSDEDPDVCEEQSASGGANRTGAPCPEFSCPDGTCIDFLLVCDGNPDCELA DETEPSLDEQGCGAWGSWGPWAPCSQTCGSGTRSRNRNCSTSSLQVLQNCPGLQHQSQAC FTEACPVDGEWSSWSPWSPCSEPCGGTTTRHRQCRPPQNGGQDCALLPGSTHSTRQTSPC PQEGCLNATCFGELVFRTCAPCPLTCDDISGQAACPPDRPCSSPGCWCPDGKVLNTEGQC VRPRQCPCLVDGAHYWPGQRIKMDCQLCGLDCGWSSWSPWAECLGPCSSQSLQWSFRSPN NPRLSGHGRQCRGIHRKARRCQTEACEGCEQWGLMYNVGERWRGGPCMVCECLHSSITHC SPYCPIGSCPQGWVLVEGMGESCCHCALPEKNQTVIHMTTPAPAPASAPSPQIGAHLVTY VLPPTADACYSPLGLAGLPMWAPSQHWEHITRADPVEAPMAGPGPREGASAEWHTQPLYL QLDLRRPRNLTGIIVQRAGSSAAYVSTLSLQFSSDNLQWHNYVNSLSSTLSPPKPSPESS NHMAPEVWTFDQMVQARYIRVWPHSGHLRDNNQHDIFLWVELLGLSPLAPLCPGSRHRCA SGECAPKGGPCDGAVDCDDGSDEEGCGSLHASTTSRTPALSPTQPGKFPREVSEDLRQGA EAMTSHSPPSSGETAGLIPASEGTLPVSGQPMQTLSATSTFPPGAKSLHPGMAAVTVHPP HSVTPGAPVGQTVSPRPFPPMPCGPGQVPCDVLGCVEQEQLCDGREDCLDGSDEQHCASA EPFTVPTTALPGLPASKALCSPSQLRCGSGECLPFEHRCDLQVNCQDGSDEDNCVDCVLA PWSGWSDCSRSCGLGLIFQHRELLRLPLPGGSCLLDQFRSQSCFVQACPVAGAWAEWGPW TACSVSCGGGHQSRQRSCVDPPPKNGGAPCPGPSHEKAPCNLQLCPGDTDCEPGLVHVNA ELCQKGLVPPCPPSCLDPEANRSCSGHCMEGCRCPPGLLLQDSHCLPLSECPCLVGQKLI QPRLAFLLDNCSQCICEKGTLLCKPGACSQSCGWSAWSPWTACDRSCGSGVRARFRSPTN PPVAFGGSPCEGDRQELQACYTDCGTEIPGWTPWTSWSSCSQSCLVPGGDPGWRQRSRLC PSSRDTFCPGEATQEEPCSPPVCPVPSAWGLWASWSTCSASCNGGIQTRGRSCSGSAPGN PVCLGPHTQTRDCNMHPCTAQCPGNMVFRSAEQCLEEGGPCPQLCLAQDPGVECTGSCAP SCNCPPGLFLHNASCLPRSQCPCQLHGQLYAPGAVAHLDCNNCTCISGEMVCTSKRCPVA CGWSPWTPWSPCSQSCNVGIRRRFRAGTEPPAAFGGAECQGPNLDAEFCSLRPCRGPGAA WSSWTPCSVPCGGGYRNRTQGSGPHSPIEFSTCSLQPCAGPVPGVCPEDQQWLDCAQGPA SCAHLSIPGEANQTCHPGCYCLSGMLLLNNVCVPVQDCPCAHRGRLYSPGSAVHLPCENC SCISGLITNCSSWPCEEGQPAWSSWTPWSVCSASCNPARRHRHRFCARPPHRAPFSLVLL TTVAAPTTLCPGPEAEEEPCLLPGCNQAGGWSPWSPWSGCSRSCGGGLRSRTRACDQPSP QGLGDFCEGPQAQGEACQAQPCPVTNCSAMEGAEYSPCGPPCPRSCDDLVHCVWRCQPGC YCPLGKVLSADGAICVKPSYCSCLDLLTGKRHHAGTQLMRPDGCNHCTCMEGRLNCTDLP CQVSGDWCPWSKWTACSQPCRGQTRTRSRACVCPAPQHGGSPCPEESGGTGVQHQMEACP NATACPVDGAWSPWGPWSSCDACLGQSYRSRVCSHPPISDGGKPCLGGYQQSRPCRNSST LCTDCGGGQDLLPCGQPCRHSCQDLSLGSTCQPGSAGCQSGCGCPPGQLSQHGLCVFPVD CHCHFQPRAMGIPENRSRSVGSTLSSWESLEPGEVVTGPCDNCTCVAGILQCHEVPSCPG PGIWSSWGPWEKCSVSCGGGEQLRSRQCARPPCPGLAQQSRICHIHVCRETGCPAGRLYR ECQPSDGCPFSCAHVTGQVACFSERCKEGCHCPEGTFQHHVACVQECPCVLTVLLLQELG LASAALGSYPTLLGDEGKPLGPGVELLPGQMLQTDCGNCSCVHGKLSCSMVECSRVHGSF GPWGMWSLCSRSCGGLGTRTRTRQCVLPTLAPGGLSCRGPLQDLEYCFSPECPGTAGSTV EPVTGLAGGWGPWSPWSPCSHSCTDPAHPAWRSRTRLCLANCTVGDSSQERPCNLPSCAA LLPCPGPGCGSGNCFWTSWAPWEPCSRSCGVGQQRRLRAYHPPGPGGHWCPDILTAYQER RFCNLRACPVPGGWSHWSPWSWCDRSCGGGRSLRSRSCSSPPPKNGGTSCVGERHHVRPC NPMPCEEGCPAGMEMVSCANHCPYSCSDLQEGGMCQEDQACQLGCRCSEGFLEQDGGCVP VGHCECTDAQGRSWAPGSQHQDACNNCSCQAGQLSCTAQLCSPPAHCAWSHWSAWSSCSH SCGPQGQQSRFRSSTSGSWALECQKEQSQSQPCPEVPCPPLCLHEAHLHELGDNWLHGEC QQCSCTPEGAICKDTDCAVPRGWTLWSSWSYCSVSCGGGSQVRTRSCTVSAPPHGSLSCE GPDTQTRHCGQQLCLQKLERCSWGPWGPCSRSCGTGLASRSGSCPCLLTKEDSKCNDTFL GLDTQACYSGPCQDDCTWGDWSSWTRCSCKVLVQQRYRHQVPAPGQAGEGTPCTRLDGHF RPCTIGNCSEDSCPPPFEFQSCGSPCAGLCATHLNHRLCQDLPPCQPGCYCPKGLLEQAG SCILPEQCNCWHISGEGARVTLAPGDRLQLGCKECVCRRGELQCSSQGCEGLLPLTGWSE WSPCGPCLPQSALAPASRTALEGHWPLNTSDLPPPSVTLLASEQYRHRLCLDPETRRPWA GDPALCTVPLSQQRLCPDPGACNDTCQWGPWGPWSPCQMPCSGGFKLRWRVARDTSAGEC PGPWAQTESCNMGSCPGESCETRDTVFTLDCANQCPRSCADLWDGVQCLQGPCSPGCRCP PGQLVQDGHCVPISSCRCGLPSANASWELAPTQVVQLDCHNCTCINGTLMCPHLECPVLG PWSAWSECSAVCGKGTMVRHRSCEEHPDREPCQALDLQQWQECNLQACPECPPGQVLSTC ATMCPSLCSHLWPGTICVREPCQLGCGCPGGQLLYNGTCIPPEACPCTQFSLPWGLTLPL EEQARELPSGTVLTRNCTHCTCQGGAFICSLTDCQECAPGEIWQHGKLGPCEKTCPEMNM TQAWSNCTEAQAPGCVCQLGYFRSQTGLCVPEDHCECWHHGSPHLPGSEWQEACESCRCL HGKSVCIRHCPELSCAQGEVIMQEPGSCCPICQQDTLKEEPVSCRYLTELRNLTKGPCHL DQIEVSYCSGHCRSSTNVMTEEPYLQSQCDCCSYRLDPDSPVRILNLLCPDGHTEPVVLP VIHSCQCSACQGGDFSKH >sp|Q8BRH4|MLL3_MOUSE Histone-lysine N-methyltransferase MLL3 OS=Mus musculus GN=Mll3 PE=2 SV=2 MSSEEDRSAEQQQPPPAPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGK STVEDEDSMDGLETTETENIVETEIKEQSVEEDAETEVDSSKQPVSALQRSVSEESANSL VSVGVEAKISEQLCAFCYCGEKSSLGQGDLKQFRVTPGLTLPWKDQPSNKDIDDNSSGTC EKIQNYAPRKQRGQRKERPPQQSAVSCVSVSTQTACEDQAGKLWDELSLVGLPDAIDVQA LFDSTGTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEK CTQMYHYPCAAGAGTFQDFSHFFLLCPEHIDQAPERSKEDANCAVCDSPGDLLDQFFCTT CGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV MKSVPTNGWKCKNCRICIECGTRSSTQWHHNCLICDTCYQQQDNLCPFCGKCYHPELQKD MLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYCKHLGAEIDPLHPGNEVEMPELPTD YASGMEIEGTEDEVVFLEQTVNKDVSDHQCRPGIVPDVQVYTEEPQKSNPLESPDTVGLI TSESSDNKMNPDLANEIAHEVDTEKTEMLSKGRHVCEEDQNEDRMEVTENIEVLPHQTIV PQEDLLLSEDSEVASKELSPPKSAPETAAPEALLSPHSERSLSCKEPLLTERVQEEMEQK ENSEFSTGCVDFEMTLAVDSCDKDSSCQGDKYVELPAEEESTFSSATDLNKADVSSSSTL CSDLPSCDMLHGYPPAFNSAAGSIMPTTYISVTPKIGMGKPAITKRKFSPGRPRSKQGAW SNHNTVSPPSWAPDTSEGREIFKPRQLSGSAIWSIKVGRGSGFPGKRRPRGAGLSGRGGR GRSKLKSGIGAVVLPGVSAADISSNKDEEENSMHNTVVLFSSSDKFTLQQDMCVVCGSFG QGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECTVCEACGKATDPGRLLLCDD CDISYHTYCLDPPLQTVPKGGWKCKWCVWCRHCGATSAGLRCEWQNNYTQCAPCASLSSC PVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMCRPYMPVSNVPS SDCCDSSLVAQIVTKVKELDPPKTYTQDGVCLTESGMSQLQSLTVTAPRRKRTKPKLKLK IINQNSVAVLQTPPDIQSEHSRDGEMDDSREGELMDCDGKSESSPEREAGDDETKGIEGT DAIKKRKRKPYRPGIGGFMVRQRSRTGQGKAKRSVVRKDSSGSISEQLPSRDDGWREQLP DTLVDEPVSVAENTDKIKKRYRKRKNKLEETFPAYLQEAFFGKDLLDTSRQNKLSVDNLS EDAAQLSFKTGFLDPSSDPLLSSSSTSAKPGTQGTADDPLADISEVLNTDDDILGIISDD LAKSVDHSDIGPTTADASSLPQPGVSQSSRPLTEEQLDGILSPELDKMVTDGAILGKLYK IPELGGKDVEDLFTAVLSPATTQPAPLPQPPPPPQLLPMHNQDVFSRMPLMNGLIGPSPH LPHNSLPPGSGLGTFPAIAQSPYTDVRDKSPAFNAIASDPNSSWAPTTPSMEGENDTLSN AQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERA PYVQKARDNRAALRINKVQMSNDSMKRQQQQDSIDPSSRIDSDLFKDPLKQRESEHEQEW KFRQQMRQKSKQQAKIEATQKLEQVKNEQQQQQQQQQQQQQQQLASQHLLVAPGSDTPSS GAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPPPPSTPSRIPV QESLSQSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVE NCVPLSSVPRPIHMNETSATRPSPARDLCASSMTNSDPYAKPPDTPRPMMTDQFSKPFSL PRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTP LHPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTE SFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR PNTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRP RTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGPGRIDTF THASSSAVRDPYDQPPVTPRPHSESFGTSQVVHDLVDRPVPGSEGNFSTSSNLPVSSQGQ QFSSVSQLPGPVPTSGGTDTQNTVNMSQADTEKLRQRQKLREIILQQQQQKKIASRQEKG PQDTAVVPHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAVFPKDQRGPYP PEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPHIRRPMSMEMPRPSNN PPLNNPVGLPQHFPPQGLPVQQHNILGQAFIELRHRAPDGRSRLPFAASPSSVIESPSHP RHGNFLPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP LNHPLSGEFSEAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKELDVKDLEGVE VKDLDDEDLENLNLDTEDGKGDDLDTLDNLETNDPNLDDLLRSGEFDIIAYTDPELDLGD KKSMFNEELDLNVPIDDKLDNQCASVEPKTRDQGDKTMVLEDKDLPQRKSSVSSEIKTEA LSPYSKEEIQSEIKNHDDSRGDADTACSQAASAQTNHSDRGKTALLTTDQDMLEKRCNQE NAGPVVSAIQGSTPLPARDVMNSCDITGSTPVLSSLLSNEKCDDSDIRPSGSSPPSLPIS PSTHGSSLPPTLIVPPSPLLDNTVNSNVTVVPRINHAFSQGVPVNPGFIQGQSSVNHNLG TGKPTNQTVPLTNQSSTMSGPQQLMIPQTLAQQNRERPLLLEEQPLLLQDLLDQERQEQQ QQRQMQAMIRQRSEPFFPNIDFDAITDPIMKAKMVALKGINKVMAQNSLGMPPMVMSRFP FMGPSVAGTQNNDGQTLVPQAVAQDGSITHQISRPNPPNFGPGFVNDSQRKQYEEWLQET QQLLQMQQKYLEEQIGAHRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQ LEQIRKQQKEHAELIEDYRIKQQQQQQQCALAPPILMPGVQPQPPLVPGATSLTMSQPNF PMVPQQLQHQQHTAVISGHTSPARMPSLPGWQSNSASAHLPLNPPRIQPPIAQLSLKTCT PAPGTVSSANPQNGPPPRVEFDDNNPFSESFQERERKERLREQQERQRVQLMQEVDRQRA LQQRMEMEQHCLMGAELANRTPVSQMPFYGSDRPCDFLQPPRPLQQSPQHQQQIGPVLQQ QNVQQGSVNSPPNQTFMQTNEQRQVGPPSFVPDSPSASGGSPNFHSVKPGHGNLPGSSFQ QSPLRPPFTPILPGTSPVANSNVPCGQDPAVTQGQNYSGSSQSLIQLYSDIIPEEKGKKK RTRKKKKDDDAESGKAPSTPHSDCAAPLTPGLSETTSTPAVSSPSELPQQRQQEPVEPVP VPTPNVSAGQPCIESENKLPNSEFIKETSNQQTHVNAEADKPSVETPNKTEEIKLEKAET QPSQEDTKVEEKTGNKIKDIVAGPVSSIQCPSHPVGTPTTKGDTGNELLKHLLKNKKASS LLTQKPEGTLSSDESSTKDGKLIEKQSPAEGLQTLGAQMQGGFGGGNSQLPKTDGASENK KQRSKRTQRTGEKAAPRSKKRKKDEEEKQAMYSSSDSFTHLKQQNNLSNPPTPPASLPPT PPPMACQKMANGFATTEELAGKAGVLVSHEVARALGPKPFQLPFRPQDDLLARAIAQGPK TVDVPASLPTPPHNNHEELRIQDHYGDRDTPDSFVPSSSPESVVGVEVNKYPDLSLVKEE PPEPVPSPIIPILPSISGKNSESRRNDIKTEPGTLFFTSPFGSSPNGPRSGLISVAITLH PTAAENISSVVAAFSDLLHVRIPNSYEVSNAPDVPPMGLVSSHRVNPSLEYRQHLLLRGP PPGSANPPRLATSYRLKQPNVPFPPTSNGLSGYKDSSHGPAEGASLRPQWCCHCKVVILG SGVRKSCKDLTFVNKGSRENTKRMEKDIVFCSNNCFILYSSAAQAKNSDNKESLPSLPQS PMKEPSKAFHQYSNNISTLDVHCLPQFQEKVSPPASPPISFPPAFEAAKVESKPDELKVT VKLKPRLRTVPVGLEDCRPLNKKWRGMKWKKWSIHIVIPKGTFKPPCEDEIDEFLKKLGT CLKPDPVPKDCRKCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALI NVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMFFKDKTMLCPMHKP KGIHEQQLSYFAVFRRVYVQRDEVRQIASIVQRGERDHTFRVGSLIFHTIGQLLPQQMQA FHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEEKDGRPVFVIRIVEQGHEDLVLSDS SPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYT FRYGRNPLMELPLAVNPTGCARSEPKMSAHVKRFVLRPHTLNSTSTSKSFQSTVTGELNA PYSKQFVHSKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNE VANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVVTFERGHKI IISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN >sp|Q9VW71|FAT2_DROME Putative fat-like cadherin-related tumor suppressor homolog OS=Drosophila melanogaster GN=fat2 PE=1 SV=2 MKIKKYVTPVKRKAFTILQWISLLCSLWLIPTVQSKADEKHTATLEYRLENQLQDLYRFS HSVYNVTIPENSLGKTYAKGVLHERLAGLRVGLNAEVKYRIISGDKEKLFKAEEKLVGDF AFLAIRTRTNNVVLNREKTEEYVIRVKAHVHLHDRNVSSYETEANIHIKVLDRNDLSPLF YPTQYTVVIPEDTPKYQSILKVTADDADLGINGEIYYSLLMDSEYFAIHPTTGEITLLQQ LQYAENSHFELTVVAYDRGSWVNHQNHQASKTKVSISVKQVNFYAPEIFTKTFSSVTPTS NPLIYGIVRVNDKDTGINGNIGRLEIVDGNPDGTFLLKAAETKDEYYIELNQFAHLNQQH FIYNLTLLAEDLGTPRRFAYKSVPIQIKPESKNIPIFTQEIYEVSIPETAPINMPVIRLK VSDPDLGKNALVYLEIVGGNEGDEFRINPDSGMLYTAKQLDAEKKSSYTLTVSAIDQANV GSRKQSSAKVKISVQDMNDNDPIFENVNKVISINENNLAGSFVVKLTAKDRDSGENSYIS YSIANLNAVPFEIDHFSGIVKTTSLLDFETMKRNYELIIRASDWGLPYRRQTEIKLSIVV KDINDNRPQFERVNCYGKVTKSAPMGTEVFVTSAIDFDAGDIISYRLSDGNEDGCFNLDP TSGSLSISCDLKKTTLTNRILKVSATDGTHFSDDLIINVHLMPEDLGGDSSILHGFGSFE CRETGVARRLAETLSLAEKNNVKSASPSVFSDLSLTPSRYGQNVHRPEFVNFPQELSINE SVQLGETVAWIEAKDRDLGYNGKLVFAISDGDYDSVFRIDPDRGELQIIGYLDRERQNEY VLNITVYDLGNPTKSTSKMLPITILDVNDNRPVIQKTLATFRLTESARIGTVVHCLHATD ADSGINAQVTYALSVECSDFTVNATTGCLRLNKPLDREKQDNYALHITAKDGGSPVLSSE ALVYVLVDDVNDNAPVFGVQEYIFKVREDLPRGTVLAVIEAVDEDIGPNAEIQFSLKEET QDEELFRIDKHTGAIRTQGYLDYENKQVHNLIVSAIDGGDPSLTSDMSIVIMIIDVNENR FAPEFDDFVYEGKVKENKPKGTFVMNVTARDMDTVDLNSKITYSITGGDGLGIFAVNDQG SITSLSQLDAETKNFYWLTLCAQDCAIVPLSNCVEVYIQVENENDNIPLTDKPVYYVNVT EASVENVEIITLKAFDPDIDPTQTITYNIVSGNLVGYFEIDSKTGVIKTTERKLDRENQA EHILEVAISDNGSPVLSSTSRIVVSVLDINDNSPEFDQRVYKVQVPSSATVNQSIFQVHA IDSDSGENGRITYSIKSGKGKNKFRIDSQRGHIHIAKPLDSDNEFEIHIKAEDNGIPKKS QTARVNIVVVPVNPNSQNAPLIVRKTSENVVDLTENDKPGFLVTQILAVDDDNDQLWYNI SNGNDDNTFYIGQDNGNILLSKYLDYETQQSYNLTISVTDGTFTAFTNLLVQVIDINDNP PQFAKDVYHVNISENIEEESVIMQLHATDRDEDKKLFYHLHATQDPSSLALFRIDSISGN VIVTQRLDFEKTAQHILIVFVKDQGAPGKRNYAKIIVNVHDHNDHHPEFTAKIIQSKVPE SAAIGSKLAEVRAIDRDSGHNAEIQYSIITGNVGSVFEIDPTFGIITLAGNLNINKIQEY MLQVKAVDLGNPPLSSQIPVHIIVTMSENDPPKFPTNNIAIEIFENLPIGTFVTQVTARS SSSIFFNIISGNINESFRINPSTGVIVINGNIDYESIKVFNLTVKGTNMAAESSCQNIII HILDANDNIPYFVQNEYVGALPESAAIGSYVLKVHDSSKDHLTLQVKDADVGVNGMVEYH IVDDLAKNFFKIDSTTGAIELLRQLDYETNAGYTFDVTVSDMGKPKLHSTTTAHVTIRVI NVNDCPPVFNERELNVTLFLPTFENVFVRQVSAKDADNDTLRFDIVDGNTNECFQIEKYT GIITTRNFEILNNENDRDYALHVRASDGIFSAILIVKIKVLSAIDSNFAFQRESYRFSAF ENNTKVATIGLVNVIGNTLDENVEYRILNPTQLFDIGISSGALKTTGVIFDREVKDLYRL FVEAKSMLYDGMNSNVRRAVTSIDISVLDVNDNCPLFVNMPYYATVSIDDPKGTIIMQVK AIDLDSAENGEVRYELKKGNGELFKLDRKSGELSIKQHVEGHNRNYELTVAAYDGAITPC SSEAPLQVKVIDRSMPVFEKQFYTVSVKEDVEMYSALSVSIEAESPLGRSLIYTISSESQ SFEIDYNTGSIFVVNELDYEKISSHDVSIRATDSLSGVYAEVVLSVSIMDVNDCYPEIES DIYNLTIPENASFGTQILKINATDNDSGANAKLSYYIESINGQNNSELFYIDVTDGNLYL KTPLDYEQIKYHHIVVNVKDHGSPSLSSRSNVFITGRILCRFISYKLIYDSIIPVKDLND NAPCFVEPSYFTKVSVAAVRGQFVALPKAYDKDISDTDSLEYKIVYGNELQTYSIDKLTG VISLQNMLNFTDKSSTVLNISVSDGVHTAYARLKISLLPENVYSPLFDQSTYEAQVPENL LHGHNIITVKASDGDFGTYANLYYEIVSEEMKKIFLIDQTTGVITSKVTFDREKKDEYVV LLKVSDGGGKFGFASLKVIVVDVNDNVPYFLLKEYKMVVSTTVEANQTILTVKAKDDDIV DNGSVHFQIVQKSNDKAVKDVIEINEKTGDIVFKSKAESYGVNSYQFFVRASDRGEPQFH SEVPVSIEIIETDANIPTFEKSSVLLKIIESTPPGTVLTKLHMIGNYTFKFSIAADQDHF MISDSGELILQQTLDREQQESHNLIVVAETSTVPVFFAYADVLIDVRDENDNYPKFDNTF YSASVAENSEKVISLVKVSATDADTGPNGDIRYYLESDTENIQNIFDIDIYSGWITLLTS LDREVQSEYNFKVIAADNGHPKHDAKVPVTIKIVDYNDNAPVFKLPIEGLSVFENALPGT VLINLLLIDPDIEKQEMDFFIVSGDKQAQFQIGKSGELFIAKPLDREQLMFYNLSIIATD GKFTAKANVEIDVKDINDNTPYCLKPRYHISTNESISIGTTLVEVKAIDFDFQSKLRFYL SGKGADDFSIGKESGILKVASALDRETTPKYKLVAHVQDGKDFTQECFSEIIITVNDIND NMPIFSMAQYRVSVPEDAQLNTLITKVHAMDKDFGVNRQIKYSLMGENHDYFKISKSTGI IRLHKSLDRETISLFNLTVKAEDCGVPKLHSIATVAVNILDINDNPPEFSMRQYSCKILE NATHGTEVCKVYATSIDIGVNADIHYFIMSGNEQGKFKMDSTTGDLVLNATLDYEMSKFY FLTIQAIDGGTPPLSNNAYVNISILDINDNSPTFLQNLYRINVNEDIFVGSKILDVKATD EDSDVNGLVTYNIERGDNIGQFSIDPKNGTISVSRPLDRETISHYTLEIQACDQGDPQRC NSVPININILDTNDNAPIFSSSNYSVVLQENRLLGYVFLTFKISDADETPNTTPYTFDIR SGNEGGLFRLEQDGSLRTASRFNHNLQDEFVIQVRVFDNGTPPLYSDAWVVVKIIEESQY PPIVTPLEVTINSFEDDFSGAFIGKVHASDQDKYDELNFSLVSGPDDMYQSSKLFNISNN TGKIYAISNLDIGLYKLNVSVSDGKFHVFSIVKINVELVTNDMLKESVVIRFRRISASEF LLSHRKTFMRSIRNIMRCRQKDVILITLQSDYQKASQHAVGNRRARSIDSDLNVVFAVRK QQIIPDSDEFFTSDEIRQTLIDKKNEIENETNLVVEDVLPSTCQSNKNDCVHGECKQILQ ILKNNVTTTFTDVISFAAPSYIPVNTCVCRPGFDGKHCKETVNACSTDPCSPQRICMPSG SALGYQCVCPKGFSGTYCERKSSKCSNESCDMGLFTAVSFGGKSYAHYKINKVKAKFTLE NGFSYSLQIRTVQQTGTLLYASGKVDYNILEIINGAVQYRFDLGSGEGVISVSSINISDG EWHQISLERSLNSAKVMVDNKHVSHGSAPGVNGILNIQSNDIFVGAEVRPHPSIIGYEDI QRGFIGCMANIKIAKESLPLYISGGSTIAALKRFTNVEFKCDPSNVLVRLGICGSQPCAN SGICKELDTDVFECACQPRYSGKHCEIDLDPCSSGPCLFGGRCDYHGPNNYSCTCPIHLS GKRCEYGKFCTPNPCKNGGICEEGDGISHCMCRGYTGPTCEIDVDECENQPCGNGATCIN EPGSFRCICPSYLTGASCGDPLYSNSISTKLKNFSIEHISGIISGVAVVLVIISCVLCCV VLKRSSSSKRRNRLEKDKNKSSYKEANLNSLVDKDNYCKPNVKLSNLEVNQRPISYTAVP NDNLVLSNRNFVNNLDILRSYGSAGDELENVPFEYQKVNRNKQHVNINSCHSTDADNAYK QEWCEQMHLRTFSENKLNNELKRDFGPSVSRFSTGKLIQVEMPNVCHSSSANFVDYSALA NGQYHWDCSDWVRKSHNPLPDITEVPGAEIADSSSLHSNDSNESKSKKAFFVHREDGDVD PTRDIAALNEDIGSEYLDSEAESCLEPFMLPRSSNQPLSRLSSFNNIENEDYKSNTGKVY LRHPDSYLPTMHFPSETDGESSMTEGPISRMEIKTRRTISENSEEAYLFPCTVGEIGSNS NISVRLCEIEDSELEEFLPQQQTNN >sp|Q9SX33|ALA9_ARATH Putative phospholipid-transporting ATPase 9 OS=Arabidopsis thaliana GN=ALA9 PE=2 SV=1 MVGGGTKRRRRRLQLSKLYTLTCAQACFKQDHSQIGGPGFSRVVYCNEPDSPEADSRNYS DNYVRTTKYTLATFLPKSLFEQFRRVANFYFLVTGVLAFTPLAPYTASSAIVPLLFVIGA TMVKEGVEDWRRQKQDNEVNNRKVKVHRGDGSFDAKEWKTLSIGDIVKVEKNEFFPADLV LLSSSYEDAICYVETMNLDGETNLKVKQGLEVTSSLRDEFNFKGFEAFVKCEDPNANLYS FVGTMELKGAKYPLSPQQLLLRDSKLRNTDFIFGAVIFTGHDTKVIQNSTDPPSKRSMIE KKMDKIIYLMFFMVITMAFIGSVIFGVTTRDDLKDGVMKRWYLRPDSSSIFFDPKRAPVA AIYHFLTAVMLYSYFIPISLYVSIEIVKVLQSIFINQDIHMYYEEADKPARARTSNLNEE LGQVDTILSDKTGTLTCNSMEFIKCSVAGTAYGRGVTEVEMAMGRRKGGPLVFQSDENDI DMEYSKEAITEESTVKGFNFRDERIMNGNWVTETHADVIQKFFRLLAVCHTVIPEVDEDT EKISYEAESPDEAAFVIAARELGFEFFNRTQTTISVRELDLVSGKRVERLYKVLNVLEFN STRKRMSVIVQEEDGKLLLLCKGADNVMFERLSKNGREFEEETRDHVNEYADAGLRTLIL AYRELDEKEYKVFNERISEAKSSVSADRESLIEEVTEKIEKDLILLGATAVEDKLQNGVP DCIDKLAQAGIKIWVLTGDKMETAINIGFACSLLRQDMKQIIINLETPEIQSLEKTGEKD VIAKASKENVLSQIINGKTQLKYSGGNAFALIIDGKSLAYALDDDIKHIFLELAVSCASV ICCRSSPKQKALVTRLVKSGNGKTTLAIGDGANDVGMLQEADIGVGISGVEGMQAVMSSD IAIAQFRYLERLLLVHGHWCYRRISTMICYFFYKNITFGFTLFLYETYTTFSSTPAYNDW FLSLYNVFFSSLPVIALGVFDQDVSARYCLKFPLLYQEGVQNVLFSWRRILGWMFNGFYS AVIIFFLCKSSLQSQAFNHDGKTPGREILGGTMYTCIVWVVNLQMALAISYFTLIQHIVI WSSIVVWYFFITVYGELPSRISTGAYKVFVEALAPSLSYWLITLFVVVATLMPYFIYSAL QMSFFPMYHGMIQWLRYEGQCNDPEYCDIVRQRSIRPTTVGFTARLEAKKRSVRISEPAS h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002404.txt0000600000175000017500000000471711455416572022004 0ustar ykeyke>sp|Q9QX47|SON_MOUSE SON protein OS=Mus musculus GN=Son PE=1 SV=1 MAADIEQVFRSFVVSKFREIQQELSSGRSEGQLNGETNPPIEGNQAGDTAASARSLPNEE IVQKIEEVLSGVLDTELRYKPDLKEASRKSRCVSVQTDPTDEVPTKKSKKHKKHKNKKKK KKKEKEKKYKRQPEESESKLKSHHDGNLESDSFLKFDSEPSAAALEHPVRAFGLSEASET ALVLEPPVVSMEVQESHVLETLKPATKAAELSVVSTSVISEQSEQPMPGMLEPSMTKILD SFTAAPVPMSTAALKSPEPVVTMSVEYQKSVLKSLETMPPETSKTTLVELPIAKVVEPSE TLTIVSETPTEVHPEPSPSTMDFPESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELP KTTAVELQESTVASALELPGPPATSILELQGPPVTPVPELPGPSATPVPELSGPLSTPVP ELPGPPATVVPELPGPSVTPVPQLSQELPGPPAPSMGLEPPQEVPEPPVMAQELSGVPAV SAAIELTGQPAVTVAMELTEQPVTTTEFEQPVAMTTVEHPGHPEVTTATGLLGQPEAAMV LELPGQPVATTALELSGQPSVTGVPELSGLPSATRALELSGQSVATGALELPGQLMATGA LEFSGQSGAAGALELLGQPLATGVLELPGQPGAPELPGQPVATVALEISVQSVVTTSELS TMTVSQSLEVPSTTALESYNTVAQELPTTLVGETSVTVGVDPLMAQESHMLASNTMETHM LASNTMDSQMLASNTMDSQMLASNTMDSQMLASSTMDSQMLASSTMDSQMLATSTMDSQM LATSSMDSQMLATSSMDSQMLATSSMDSQMLATSSMESQMLASGAMDSQMLASGTMDAQM LASGTMDAQMLASSTQDSAMMGSKSPDPYRLAQDPYRLAQDPYRLGHDPYRLGHDAYRLG QDPYRLGHDPYRLTPDPYRVSPRPYRIAPRSYRIAPRPYRLAPRPLMLASRRSMMMSYAA ERSMMSSYERSMMSYERSMMSPMAERSMMSAYERSMMSAYERSMMSPMAERSMMSAYERS MMSAYERSMMSPMADRSMMSMGADRSMMSSYSAADRSMMSSYSAADRSMMSSYTDRSMMS MAADSYTDSYTDSYTEAYMVPPLPPEEPPTMPPLPPEEPPMTPPLPPEEPPEGPALSTEQ SALTADNTWSTEVTLSTGESLSQPEPPVSQSEISEPMAVPANYSMSESETSMLASEAVMT VPEPAREPESSVTSAPVESAVVAEHEMVPERPMTYMVSETTMSVEPAVLTSEASVISETS ETYDSMRPSGHAISEVTMSLLEPAVTISQPAEDSLELPSMTVPAPSTMTTTESPVVAVTE IPPVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEPPTMATPELCSLSVSEPPVAV SELPALADPEHAITAVSGVSSLEPSVPILEPAVSVLQPVMIVSEPSVPVQEPTVAVSEPA VIVSEHTQITSPEMAVESSPVIVDSSVMSSQIMKGMNLLGGDENLGPEVGMQETLLHPGE EPRDGGHLKSDLYENEYDRNADLTVNSHLIVKDAEHNTVCATTVGPVGEASEEKILPISE TKEITELATCAAVSEADIGRSLSSQLALELDTVGTSKGFEFVTASALISESKYDVEVSVT TQDTEHDMVISTSPSGGSEADIEGPLPAKDIHLDLPSTNFVCKDVEDSLPIKESAQAVAV ALSPKESSEDTEVLLPNKEIVPESGYSASIDEINEADLVRPLLPKDMERLTSLRAGIEGP LLASEVERDKSAASPVVISIPERASESSSEEKDDYEIFVKVKDTHEKSKKNKNRDKGEKE KKRDSSLRSRSKRSKSSEHKSRKRTSESRSRARKRSSKSKSHRSQTRSRSRSRRRRRSSR SRSKSRGRRSVSKEKRKRSPKHRSKSRERKRKRSSSRDNRKAARARSRTPSRRSRSHTPS RRRRSISVGRRRSFSISPSRRSRTPSRRSRTPSRRSRTPSRRSRTPSRRSRTPSRRRRSR SAVRRRSFSISPVRLRRSRTPLRRRFSRSPIRRKRSRSSERGRSPKRLTDLDKAQLLEIA KANAAAMCAKAGVPLPPNLKPAPPPTIEEKVAKKSGGATIEELTEKCKQIAQSKEDDDVI VNKPHVSDEEEEEPPFYHHPFKLSEPKPIFFNLNIAAAKPTPPKSQVTLTKEFPVSSGSQ HRKKEADSVYGEWVPVEKNGEESKDDDNVFSSSLPSEPVDISTAMSERALAQKRLSENAF DLEAMSMLNRAQERIDAWAQLNSIPGQFTGSTGVQVLTQEQLANTGAQAWIKKDQFLRAA PVTGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAVGERAQKRSGNFSA AMKDLSGKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPNCMFF LNRY h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000100.txt0000600000175000017500000000032211455416572021757 0ustar ykeyke>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 MGVYKFCYNKKKEVGQVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKC CKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002701.txt0000600000175000017500000000542511455416572022001 0ustar ykeyke>sp|Q02224|CENPE_HUMAN Centromere-associated protein E OS=Homo sapiens GN=CENPE PE=1 SV=2 MAEEGAVAVCVRVRPLNSREESLGETAQVYWKTDNNVIYQVDGSKSFNFDRVFHGNETTK NVYEEIAAPIIDSAIQGYNGTIFAYGQTASGKTYTMMGSEDHLGVIPRAIHDIFQKIKKF PDREFLLRVSYMEIYNETITDLLCGTQKMKPLIIREDVNRNVYVADLTEEVVYTSEMALK WITKGEKSRHYGETKMNQRSSRSHTIFRMILESREKGEPSNCEGSVKVSHLNLVDLAGSE RAAQTGAAGVRLKEGCNINRSLFILGQVIKKLSDGQVGGFINYRDSKLTRILQNSLGGNA KTRIICTITPVSFDETLTALQFASTAKYMKNTPYVNEVSTDEALLKRYRKEIMDLKKQLE EVSLETRAQAMEKDQLAQLLEEKDLLQKVQNEKIENLTRMLVTSSSLTLQQELKAKRKRR VTWCLGKINKMKNSNYADQFNIPTNITTKTHKLSINLLREIDESVCSESDVFSNTLDTLS EIEWNPATKLLNQENIESELNSLRADYDNLVLDYEQLRTEKEEMELKLKEKNDLDEFEAL ERKTKKDQEMQLIHEISNLKNLVKHAEVYNQDLENELSSKVELLREKEDQIKKLQEYIDS QKLENIKMDLSYSLESIEDPKQMKQTLFDAETVALDAKRESAFLRSENLELKEKMKELAT TYKQMENDIQLYQSQLEAKKKMQVDLEKELQSAFNEITKLTSLIDGKVPKDLLCNLELEG KITDLQKELNKEVEENEALREEVILLSELKSLPSEVERLRKEIQDKSEELHIITSEKDKL FSEVVHKESRVQGLLEEIGKTKDDLATTQSNYKSTDQEFQNFKTLHMDFEQKYKMVLEEN ERMNQEIVNLSKEAQKFDSSLGALKTELSYKTQELQEKTREVQERLNEMEQLKEQLENRD STLQTVEREKTLITEKLQQTLEEVKTLTQEKDDLKQLQESLQIERDQLKSDIHDTVNMNI DTQEQLRNALESLKQHQETINTLKSKISEEVSRNLHMEENTGETKDEFQQKMVGIDKKQD LEAKNTQTLTADVKDNEIIEQQRKIFSLIQEKNELQQMLESVIAEKEQLKTDLKENIEMT IENQEELRLLGDELKKQQEIVAQEKNHAIKKEGELSRTCDRLAEVEEKLKEKSQQLQEKQ QQLLNVQEEMSEMQKKINEIENLKNELKNKELTLEHMETERLELAQKLNENYEEVKSITK ERKVLKELQKSFETERDHLRGYIREIEATGLQTKEELKIAHIHLKEHQETIDELRRSVSE KTAQIINTQDLEKSHTKLQEEIPVLHEEQELLPNVKEVSETQETMNELELLTEQSTTKDS TTLARIEMERLRLNEKFQESQEEIKSLTKERDNLKTIKEALEVKHDQLKEHIRETLAKIQ ESQSKQEQSLNMKEKDNETTKIVSEMEQFKPKDSALLRIEIEMLGLSKRLQESHDEMKSV AKEKDDLQRLQEVLQSESDQLKENIKEIVAKHLETEEELKVAHCCLKEQEETINELRVNL SEKETEISTIQKQLEAINDKLQNKIQEIYEKEEQFNIKQISEVQEKVNELKQFKEHRKAK DSALQSIESKMLELTNRLQESQEEIQIMIKEKEEMKRVQEALQIERDQLKENTKEIVAKM KESQEKEYQFLKMTAVNETQEKMCEIEHLKEQFETQKLNLENIETENIRLTQILHENLEE MRSVTKERDDLRSVEETLKVERDQLKENLRETITRDLEKQEELKIVHMHLKEHQETIDKL RGIVSEKTNEISNMQKDLEHSNDALKAQDLKIQEELRIAHMHLKEQQETIDKLRGIVSEK TDKLSNMQKDLENSNAKLQEKIQELKANEHQLITLKKDVNETQKKVSEMEQLKKQIKDQS LTLSKLEIENLNLAQKLHENLEEMKSVMKERDNLRRVEETLKLERDQLKESLQETKARDL EIQQELKTARMLSKEHKETVDKLREKISEKTIQISDIQKDLDKSKDELQKKIQELQKKEL QLLRVKEDVNMSHKKINEMEQLKKQFEAQNLSMQSVRMDNFQLTKKLHESLEEIRIVAKE RDELRRIKESLKMERDQFIATLREMIARDRQNHQVKPEKRLLSDGQQHLTESLREKCSRI KELLKRYSEMDDHYECLNRLSLDLEKEIEFQKELSMRVKANLSLPYLQTKHIEKLFTANQ RCSMEFHRIMKKLKYVLSYVTKIKEEQHESINKFEMDFIDEVEKQKELLIKIQHLQQDCD VPSRELRDLKLNQNMDLHIEEILKDFSESEFPSIKTEFQQVLSNRKEMTQFLEEWLNTRF DIEKLKNGIQKENDRICQVNNFFNNRIIAIMNESTEFEERSATISKEWEQDLKSLKEKNE KLFKNYQTLKTSLASGAQVNPTTQDNKNPHVTSRATQLTTEKIRELENSLHEAKESAMHK ESKIIKMQKELEVTNDIIAKLQAKVHESNKCLEKTKETIQVLQDKVALGAKPYKEEIEDL KMKLVKIDLEKMKNAKEFEKEISATKATVEYQKEVIRLLRENLRRSQQAQDTSVISEHTD PQPSNKPLTCGGGSGIVQNTKALILKSEHIRLEKEISKLKQQNEQLIKQKNELLSNNQHL SNEVKTWKERTLKREAHKQVTCENSPKSPKVTGTASKKKQITPSQCKERNLQDPVPKESP KSCFFDSRSKSLPSPHPVRYFDNSSLGLCPEVQNAGAESVDSQPGPWHASSGKDVPECKT Q h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004705.txt0000600000175000017500000001145711455416572022011 0ustar ykeyke>sp|Q9VW71|FAT2_DROME Putative fat-like cadherin-related tumor suppressor homolog OS=Drosophila melanogaster GN=fat2 PE=1 SV=2 MKIKKYVTPVKRKAFTILQWISLLCSLWLIPTVQSKADEKHTATLEYRLENQLQDLYRFS HSVYNVTIPENSLGKTYAKGVLHERLAGLRVGLNAEVKYRIISGDKEKLFKAEEKLVGDF AFLAIRTRTNNVVLNREKTEEYVIRVKAHVHLHDRNVSSYETEANIHIKVLDRNDLSPLF YPTQYTVVIPEDTPKYQSILKVTADDADLGINGEIYYSLLMDSEYFAIHPTTGEITLLQQ LQYAENSHFELTVVAYDRGSWVNHQNHQASKTKVSISVKQVNFYAPEIFTKTFSSVTPTS NPLIYGIVRVNDKDTGINGNIGRLEIVDGNPDGTFLLKAAETKDEYYIELNQFAHLNQQH FIYNLTLLAEDLGTPRRFAYKSVPIQIKPESKNIPIFTQEIYEVSIPETAPINMPVIRLK VSDPDLGKNALVYLEIVGGNEGDEFRINPDSGMLYTAKQLDAEKKSSYTLTVSAIDQANV GSRKQSSAKVKISVQDMNDNDPIFENVNKVISINENNLAGSFVVKLTAKDRDSGENSYIS YSIANLNAVPFEIDHFSGIVKTTSLLDFETMKRNYELIIRASDWGLPYRRQTEIKLSIVV KDINDNRPQFERVNCYGKVTKSAPMGTEVFVTSAIDFDAGDIISYRLSDGNEDGCFNLDP TSGSLSISCDLKKTTLTNRILKVSATDGTHFSDDLIINVHLMPEDLGGDSSILHGFGSFE CRETGVARRLAETLSLAEKNNVKSASPSVFSDLSLTPSRYGQNVHRPEFVNFPQELSINE SVQLGETVAWIEAKDRDLGYNGKLVFAISDGDYDSVFRIDPDRGELQIIGYLDRERQNEY VLNITVYDLGNPTKSTSKMLPITILDVNDNRPVIQKTLATFRLTESARIGTVVHCLHATD ADSGINAQVTYALSVECSDFTVNATTGCLRLNKPLDREKQDNYALHITAKDGGSPVLSSE ALVYVLVDDVNDNAPVFGVQEYIFKVREDLPRGTVLAVIEAVDEDIGPNAEIQFSLKEET QDEELFRIDKHTGAIRTQGYLDYENKQVHNLIVSAIDGGDPSLTSDMSIVIMIIDVNENR FAPEFDDFVYEGKVKENKPKGTFVMNVTARDMDTVDLNSKITYSITGGDGLGIFAVNDQG SITSLSQLDAETKNFYWLTLCAQDCAIVPLSNCVEVYIQVENENDNIPLTDKPVYYVNVT EASVENVEIITLKAFDPDIDPTQTITYNIVSGNLVGYFEIDSKTGVIKTTERKLDRENQA EHILEVAISDNGSPVLSSTSRIVVSVLDINDNSPEFDQRVYKVQVPSSATVNQSIFQVHA IDSDSGENGRITYSIKSGKGKNKFRIDSQRGHIHIAKPLDSDNEFEIHIKAEDNGIPKKS QTARVNIVVVPVNPNSQNAPLIVRKTSENVVDLTENDKPGFLVTQILAVDDDNDQLWYNI SNGNDDNTFYIGQDNGNILLSKYLDYETQQSYNLTISVTDGTFTAFTNLLVQVIDINDNP PQFAKDVYHVNISENIEEESVIMQLHATDRDEDKKLFYHLHATQDPSSLALFRIDSISGN VIVTQRLDFEKTAQHILIVFVKDQGAPGKRNYAKIIVNVHDHNDHHPEFTAKIIQSKVPE SAAIGSKLAEVRAIDRDSGHNAEIQYSIITGNVGSVFEIDPTFGIITLAGNLNINKIQEY MLQVKAVDLGNPPLSSQIPVHIIVTMSENDPPKFPTNNIAIEIFENLPIGTFVTQVTARS SSSIFFNIISGNINESFRINPSTGVIVINGNIDYESIKVFNLTVKGTNMAAESSCQNIII HILDANDNIPYFVQNEYVGALPESAAIGSYVLKVHDSSKDHLTLQVKDADVGVNGMVEYH IVDDLAKNFFKIDSTTGAIELLRQLDYETNAGYTFDVTVSDMGKPKLHSTTTAHVTIRVI NVNDCPPVFNERELNVTLFLPTFENVFVRQVSAKDADNDTLRFDIVDGNTNECFQIEKYT GIITTRNFEILNNENDRDYALHVRASDGIFSAILIVKIKVLSAIDSNFAFQRESYRFSAF ENNTKVATIGLVNVIGNTLDENVEYRILNPTQLFDIGISSGALKTTGVIFDREVKDLYRL FVEAKSMLYDGMNSNVRRAVTSIDISVLDVNDNCPLFVNMPYYATVSIDDPKGTIIMQVK AIDLDSAENGEVRYELKKGNGELFKLDRKSGELSIKQHVEGHNRNYELTVAAYDGAITPC SSEAPLQVKVIDRSMPVFEKQFYTVSVKEDVEMYSALSVSIEAESPLGRSLIYTISSESQ SFEIDYNTGSIFVVNELDYEKISSHDVSIRATDSLSGVYAEVVLSVSIMDVNDCYPEIES DIYNLTIPENASFGTQILKINATDNDSGANAKLSYYIESINGQNNSELFYIDVTDGNLYL KTPLDYEQIKYHHIVVNVKDHGSPSLSSRSNVFITGRILCRFISYKLIYDSIIPVKDLND NAPCFVEPSYFTKVSVAAVRGQFVALPKAYDKDISDTDSLEYKIVYGNELQTYSIDKLTG VISLQNMLNFTDKSSTVLNISVSDGVHTAYARLKISLLPENVYSPLFDQSTYEAQVPENL LHGHNIITVKASDGDFGTYANLYYEIVSEEMKKIFLIDQTTGVITSKVTFDREKKDEYVV LLKVSDGGGKFGFASLKVIVVDVNDNVPYFLLKEYKMVVSTTVEANQTILTVKAKDDDIV DNGSVHFQIVQKSNDKAVKDVIEINEKTGDIVFKSKAESYGVNSYQFFVRASDRGEPQFH SEVPVSIEIIETDANIPTFEKSSVLLKIIESTPPGTVLTKLHMIGNYTFKFSIAADQDHF MISDSGELILQQTLDREQQESHNLIVVAETSTVPVFFAYADVLIDVRDENDNYPKFDNTF YSASVAENSEKVISLVKVSATDADTGPNGDIRYYLESDTENIQNIFDIDIYSGWITLLTS LDREVQSEYNFKVIAADNGHPKHDAKVPVTIKIVDYNDNAPVFKLPIEGLSVFENALPGT VLINLLLIDPDIEKQEMDFFIVSGDKQAQFQIGKSGELFIAKPLDREQLMFYNLSIIATD GKFTAKANVEIDVKDINDNTPYCLKPRYHISTNESISIGTTLVEVKAIDFDFQSKLRFYL SGKGADDFSIGKESGILKVASALDRETTPKYKLVAHVQDGKDFTQECFSEIIITVNDIND NMPIFSMAQYRVSVPEDAQLNTLITKVHAMDKDFGVNRQIKYSLMGENHDYFKISKSTGI IRLHKSLDRETISLFNLTVKAEDCGVPKLHSIATVAVNILDINDNPPEFSMRQYSCKILE NATHGTEVCKVYATSIDIGVNADIHYFIMSGNEQGKFKMDSTTGDLVLNATLDYEMSKFY FLTIQAIDGGTPPLSNNAYVNISILDINDNSPTFLQNLYRINVNEDIFVGSKILDVKATD EDSDVNGLVTYNIERGDNIGQFSIDPKNGTISVSRPLDRETISHYTLEIQACDQGDPQRC NSVPININILDTNDNAPIFSSSNYSVVLQENRLLGYVFLTFKISDADETPNTTPYTFDIR SGNEGGLFRLEQDGSLRTASRFNHNLQDEFVIQVRVFDNGTPPLYSDAWVVVKIIEESQY PPIVTPLEVTINSFEDDFSGAFIGKVHASDQDKYDELNFSLVSGPDDMYQSSKLFNISNN TGKIYAISNLDIGLYKLNVSVSDGKFHVFSIVKINVELVTNDMLKESVVIRFRRISASEF LLSHRKTFMRSIRNIMRCRQKDVILITLQSDYQKASQHAVGNRRARSIDSDLNVVFAVRK QQIIPDSDEFFTSDEIRQTLIDKKNEIENETNLVVEDVLPSTCQSNKNDCVHGECKQILQ ILKNNVTTTFTDVISFAAPSYIPVNTCVCRPGFDGKHCKETVNACSTDPCSPQRICMPSG SALGYQCVCPKGFSGTYCERKSSKCSNESCDMGLFTAVSFGGKSYAHYKINKVKAKFTLE NGFSYSLQIRTVQQTGTLLYASGKVDYNILEIINGAVQYRFDLGSGEGVISVSSINISDG EWHQISLERSLNSAKVMVDNKHVSHGSAPGVNGILNIQSNDIFVGAEVRPHPSIIGYEDI QRGFIGCMANIKIAKESLPLYISGGSTIAALKRFTNVEFKCDPSNVLVRLGICGSQPCAN SGICKELDTDVFECACQPRYSGKHCEIDLDPCSSGPCLFGGRCDYHGPNNYSCTCPIHLS GKRCEYGKFCTPNPCKNGGICEEGDGISHCMCRGYTGPTCEIDVDECENQPCGNGATCIN EPGSFRCICPSYLTGASCGDPLYSNSISTKLKNFSIEHISGIISGVAVVLVIISCVLCCV VLKRSSSSKRRNRLEKDKNKSSYKEANLNSLVDKDNYCKPNVKLSNLEVNQRPISYTAVP NDNLVLSNRNFVNNLDILRSYGSAGDELENVPFEYQKVNRNKQHVNINSCHSTDADNAYK QEWCEQMHLRTFSENKLNNELKRDFGPSVSRFSTGKLIQVEMPNVCHSSSANFVDYSALA NGQYHWDCSDWVRKSHNPLPDITEVPGAEIADSSSLHSNDSNESKSKKAFFVHREDGDVD PTRDIAALNEDIGSEYLDSEAESCLEPFMLPRSSNQPLSRLSSFNNIENEDYKSNTGKVY LRHPDSYLPTMHFPSETDGESSMTEGPISRMEIKTRRTISENSEEAYLFPCTVGEIGSNS NISVRLCEIEDSELEEFLPQQQTNN h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001800.txt0000600000175000017500000000366311455416572022002 0ustar ykeyke>sp|A5AB61|UTP10_ASPNC U3 small nucleolar RNA-associated protein 10 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=utp10 PE=3 SV=1 MASSLAAQLSQIAAKSTNQLNLKAQRIAHSQSLIFDWKTATTQDFDTVYQICFEGFQELC QLDPRFAPFERTIFSEQSKAEDRTEMNAAQNKELDTVVEAFLALVGGHLLLSPAVKAVDW LIRRFRVHEYNTEFTILTFLPYYTTPLFLNLLSILPEDLTPTFKILNPYKKSQINPPRHP LVHSATTNKHFLAAVNRYTLQVSKQRAHHHALLSFWAGTLTEAVAGMLDSSRSGRREVEK EKHEDVVMKVLPVLNDGLALKDVSELVIGCYMVCVVLAQKSSLQDKLLDGLMEAVAGSWT DETKESGLICLSVLAQKKSDARIPKRAFKAVLRLEDPVQQLSAISAQYPTSHLLLGLVAG CVDDLSKQKDLSRLDLLSLLFETNLLGEQEAGKAMAVILQAVSHAHTEGVLSLDAQTHLA ELVQHFTQSESLQPIFQKTIEDSSIDVAALEHNLQTVIESVPTTTPAIGDVEMEDVQQEA VEDNFASVLESVAGKNLESSALSAQSMPAYESLVQTFALAVGSQEKLQAFVDLPALKKAD ASTSPQYLSFFIRTFSGSYPIGTRITALNQISSLLNSATPDVDLQALLPFLLVALADSSE RVRREAAGVLAAIGSLYKKSKKGDANVWARDTIYGKQSKNVQWIAGRDVQKIVERAFLPG LEEYVLDQAHIGRVLEATLRGSSTSDSGATELKKPLRLSLFTFLCSHAVQMPLYAPKLSL LKLLNRVDKAGGTTRTKELGPFLKTWRDMKEHTAKDVCERERVSVADVDREAVMTVTPKD KDAISLLLSNVSPYSDSLRPSFVTAIFNRMKAVWGTVAEELQVDAAEKLFEISLEDVQTP LVHGCRDVLRSVQLTGSVLLQFLRKIPVSITDMESLGPAPKRRRTSQNNMVAMTIKDEAK LSQLMEKMTFILELVDSSTPEAHPELADGLFQTLAALHHFKSQIQSGLSYLLSLTLGSLL AIVNRSKGTAKAQFDTSVIRADLVVDCVRTTDSPQVQNAALLLVAGLSVIAPELVLHSVM PIFTFMGSSVLRKDDEYSVSVIDQTIDQVVPALIQSLRNQKRDVVSGTSELLLSFTAAFE HIPSHRRLRLFHALVTKLGTQDFLFAVLAMLANRYALDKDVLILMTGLVSDASAPVELNT YSKFLDLVKDSLSSKPGISQVLLGIGSDDGRDPQKVAVDLLRALAYLFKHSSLKVKMAKD FATEGDKVVGQIRTLFSRILEQVLAIGESMQNVKPVSQASGDVLSALFGTLSLVDFLDTI EVLLQRRNDELRRKVLRLLEGRLRQNPERDGASQHRMLDFLPTLVNIIQSSPDILLKHAA VACIDRIAEKYGRKEPTKVIHAAQVVASEACIGQDDERIRIMGVLCLASMAEVLGEAMIP ALPDALSRSLALLEQSLEDGKENARLHDAVYSFFSALFIHIPFMVSGSHLDKILVLSYKS AVSEGVEDESREEALQLMARKVDVAATYAAIDRNWQHAVKAGPDATRETLGVVSLAIEKH PKSATVKNIAVLTSILFKAFDLRREQVSLDTQATFELSDVDEIEDIINEVTIKMIYKLND TTFRPIFTKLLEWATTGVPKKDARGSLARLTTFYRFLQVFFGTLQSIVTGYSSYIIENVV SVLGKANPSNQDTKSLWLATMRMLKNSFEHDQDEFWQSPSHLTVIAQPLISQLAHAKNSS TASIVIAEAVPALTELAVAADSTDNHKELNTVLMRLLRPSAGPSGKTAGGENPHTRLAAL KAQQSLTEQLGEEWLALLPEMLPYISELMEDEDENVEREVRKWVKQIEDVLGERLDDMLT h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000900.txt0000600000175000017500000000173511455416572022000 0ustar ykeyke>sp|O88990|ACTN3_MOUSE Alpha-actinin-3 OS=Mus musculus GN=Actn3 PE=2 SV=1 MMMVMQPEGLGAGEGPFSGGGGGEYMEQEEDWDRDLLLDPAWEKQQRKTFTAWCNSHLRK AGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKL VSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQ NFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDI VNTPKPDEKAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENEKLMEEYEKLASELL EWIRRTVPWLENRVGEPSMSAMQRKLEDFRDYRRLHKPPRVQEKCQLEINFNTLQTKLRL SHRPAFMPSEGKLVSDIANAWRGLEQVEKGYEDWLLSEIRRLQRLQHLAEKFQQKASLHE AWTRGKEEMLNQHDYESASLQEVRALLRRHEAFESDLAAHQDRVEHIAALAQELNELDYH EAASVNSRCQAICDQWDNLGTLTQKRRDALERMEKLLETIDQLQLEFARRAAPFNNWLDG AIEDLQDVWLVHSVEETQSLLTAHEQFKATLPEADRERGAILGIQGEIQKICQTYGLRPK SGNPYITLSSQDINNKWDTVRKLVPSRDQTLQEELARQQVNERLRRQFAAQANAIGPWIQ GKVEEVGRLAAGLAGSLEEQMAGLRQQEQNIINYKSNIDRLEGDHQLLQESLVFDNKHTV YSMEHIRVGWEQLLTSIARTINEVENQVLTRDAKGLSQEQLNEFRASFNHFDRKRNGMME PDDFRACLISMGYDLGEVEFARIMTMVDPNAAGVVTFQAFIDFMTRETAETDTAEQVVAS FKILAGDKNYITPEELRRELPAEQAEYCIRRMAPYKGSGAPSGALDYVAFSSALYGESDL h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003503.txt0000600000175000017500000000707211455416572022002 0ustar ykeyke>sp|Q24292|DS_DROME Protein dachsous OS=Drosophila melanogaster GN=ds PE=1 SV=3 MLRSSLLILLAIVLLGSSQAASHDQERERKLEVFEGVAVDYQIGYIGDFGGIDSGPPYII VAEAGVETDLAIDRATGEIRTKVKLDRETRASYSLVAIPLSGRNIRVLVTVKDENDNAPT FPQTSMHIEFPENTPREVKRTLLPARDLDLEPYNTQRYNIVSGNVNDAFRLSSHRERDGV LYLDLQISGFLDRETTPGYSLLIEALDGGTPPLRGFMTVNITIQDVNDNQPIFNQSRYFA TVPENATVGTSVLQVYASDTDADENGLVEYAINRRQSDKEQMFRIDPRTGAIYINKALDF ETKELHELVVVAKDHGEQPLETTAFVSIRVTDVNDNQPTINVIFLSDDASPKISESAQPG EFVARISVHDPDSKTEYANVNVTLNGGDGHFALTTRDNSIYLVIVHLPLDREIVSNYTLS VVATDKGTPPLHASKSIFLRITDVNDNPPEFEQDLYHANVMEVADPGTSVLQVLAHDRDE GLNSALTYSLAETPETHAQWFQIDPQTGLITTRSHIDCETEPVPQLTVVARDGGVPPLSS TATVLVTIHDVNDNEPIFDQSFYNVSVAENEPVGRCILKVSASDPDCGVNAMVNYTIGEG FKHLTEFEVRSASGEICIAGELDFERRSSYEFPVLATDRGGLSTTAMIKMQLTDVNDNRP VFYPREYKVSLRESPKASSQASSTPIVAVVATDPDYGNFGQVSYRIVAGNEAGIFRIDRS TGEIFVVRPDMLSVRTQPMHMLNISATDGGNLRSNADAVVFLSIIDAMQRPPIFEKARYN YYVKEDIPRGTVVGSVIAASGDVAHRSPVRYSIYSGDPDGYFSIETNSGNIRIAKPLDHE AKSQVLLNIQATLGEPPVYGHTQVNIEVEDVNDNAPEFEASMVRISVPESAELGAPLYAA HAHDKDSGSSGQVTYSLVKESGKGLFAIDARSGHLILSQHLDYESSQRHTLIVTATDGGV PSLSTNLTILVDVQDVNDNPPVFEKDEYSVNVSESRSINAQIIQVNASDLDTGNNARITY RIVDAGVDNVTNSISSSDVSQHFGIFPNSGWIYLRAPLDRETRDRYQLTVLATDNGTPAA HAKTRVIVRVLDANDNDPKFQKSKYEFRIEENLRRGSVVGVVTASDLDLGENAAIRYSLL PINSSFQVHPVTGEISTREPLDRELRELYDLVVEARDQGTPVRSARVPVRIHVSDVNDNA PEIADPQEDVVSVREEQPPGTEVVRVRAVDRDHGQNASITYSIVKGRDSDGHGLFSIDPT SGVIRTRVVLDHEERSIYRLGVAASDGGNPPRETVRMLRVEVLDLNDNRPTFTSSSLVFR VREDAALGHVVGSISPIERPADVVRNSVEESFEDLRVTYTLNPLTKDLIEAAFDIDRHSG NLVVARLLDREVQSEFRLEIRALDTTASNNPQSSAITVKIEVADVNDNAPEWPQDPIDLQ VSEATPVGTIIHNFTATDADTGTNGDLQYRLIRYFPQLNESQEQAMSLFRMDSLTGALSL QAPLDFEAVQEYLLIVQALDQSSNVTERLQTSVTVRLRILDANDHAPHFVSPNSSGGKTA SLFISDATRIGEVVAHIVAVDEDSGDNGQLTYEITGGNGEGRFRINSQTGIIELVKSLPP ATEDVEKGGRFNLIIGAKDHGQPEPKKSSLNLHLIVQGSHNNPPRFLQAVYRATILENVP SGSFVLQVTAKSLHGAENANLSYEIPAGVANDLFHVDWQRGIITTRGQFDRESQASYVLP VYVRDANRQSTLSSSAVRKQRSSDSIGDTSNGQHFDVATIYITVGDVNDNSPEFRPGSCY GLSVPENSEPGVIHTVVASDLDEGPNADLIYSITGGNLGNKFSIDSSSGELSARPLDREQ HSRYTLQIQASDRGQPKSRQGHCNITIFVEDQNDNAPRFKLSKYTGSVQEDAPLGTSVVQ ISAVDADLGVNARLVYSLANETQWQFAIDGQSGLITTVGKLDRELQASYNFMVLATDGGR YEVRSATVPVQINVLDINDNRPIFERYPYIGQVPALIQPGQTLLKVQALDADLGANAEIV YSLNAENSAVSAKFRINPSTGALSASQSLASESGKLLHLEVVARDKGNPPQSSLGLIELL IGEAPQGTPVLRFQNETYRVMLKENSPSGTRLLQVVALRSDGRRQKVQFSFGAGNEDGIL SLDSLSGEIRVNKPHLLDYDRFSTPSMSALSRGRALHYEEEIDESSEEDPNNSTRSQRAL TSSSFALTNSQPNEIRVVLVARTADAPFLASYAELVIELEDENDNSPKFSQKQFVATVSE GNNKGTFVAQVHAFDSDAGSNARLRYHIVDGNHDNAFVIEPAFSGIVRTNIVLDREIRDI YKLKIIATDEGVPQMTGTATIRVQIVDVNDNQPTFPPNNLVTVSEATELGAVITSISAND VDTYPALTYRLGAESTVDIENMSIFALDRYSGKLVLKRRLDYELQQEYELDVIASDAAHE ARTVLTVRVNDENDNAPVFLAQQPPAYFAILPAISEISESLSVDFDLLTVNATDADSEGN NSKVIYIIEPAQEGFSVHPSNGVVSVNMSRLQPAVSSSGDYFVRIIAKDAGKPALKSSTL LRVQANDNGSGRSQFLQNQYRAQISEAAPLGSVVLQLGQDALDQSLAIIAGNEESAFELL QSKAIVLVKPLDRERNDLYKLRLVLSHPHGPPLISSLNSSSGISVIITILDANDNFPIFD RSAKYEAEISELAPLRYSIAQLQAIDADQENTPNSEVVYDITSGNDEHMFTIDLVTGVLF VNNRLDYDSGAKSYELIIRACDSHHQRPLCSLQPFRLELHDENDNEPKFPLTEYVHFLAE NEPVGSSVFRAHASDLDKGPFGQLNYSIGPAPSDESSWKMFRVDSESGLVTSAFVFDYEQ RQRYDMELLASDMGGKKASVAVRVEIESRDEFTPQFTERTYRFVLPAAVALPQGYVVGQV TATDSDSGPDGRVVYQLSAPHSHFKVNRSSGAVLIKRKLKLDGDGDGNLYMDGRDISLVI SASSGRHNSLSSMAVVEIALDPLAHPGTNLASAGGSSSGSIGDWAIGLLVAFLLVLCAAA GIFLFIHMRSRKPRNAVKPHLATDNAGVGNTNSYVDPSAFDTIPIRGSISGGAAGAASGQ FAPPKYDEIPPFGAHAGSSGAATTSELSGSEQSGSSGRGSAEDDGEDEEIRMINEGPLHH RNGGAGAGSDDGRISDISVQNTQEYLARLGIVDHDPSGAGGGASSMAGSSHPMHLYHDDD ATARSDITNLIYAKLNDVTGAGSEIGSSADDAGTTAGSIGTIGTAITHGHGVMSSYGEVP VPVPVVVGGSNVGGSLSSIVHSEEELTGSYNWDYLLDWGPQYQPLAHVFSEIARLKDDTL SEHSGSGASSSAKSKHSSSHSSAGAGSVVLKPPPSAPPTHIPPPLLTNVAPRAINLPMRL PPHLSLAPAHLPRSPIGHEASGSFSTSSAMSPSFSPSLSPLATRSPSISPLGAGPPTHLP HVSLPRHGHAPQPSQRGNVGTRM h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003000.txt0000600000175000017500000000612511455416572021770 0ustar ykeyke>sp|Q9Y4D8|K0614_HUMAN Probable E3 ubiquitin-protein ligase KIAA0614 OS=Homo sapiens GN=KIAA0614 PE=2 SV=4 MKELELLCSMKEVSFDGNDLENMVLSLREKFLQEVNSLIQKPSHPLAKTKTLVKSLMNRA ELLLHVTIAAQSGLTRSISGTPAETPACKSASETKVISHAVRQPVFLRSMSAPSDLEMIG NEDLEFTRANQRRRHVTSHRSSSFTLLQSLAIEDSRDKPTYSVLLGQLFAFIGTNPDQAV SSSSFLLAAQTRWRRGNTRKQALVHMRELLTAAVRVGGVTHLVGPVTMVLQGGPRIEELT CGGMVEQVQEAFGETMTSVVSLCARYPIACANSIGLLCTIPYTRSEEKCLVRSGLVQLMD RLCSLSNQTESSSSEKQTKKQKVATMAWAAFQVLANRCVEWEKEEGGSTEAVHSGLARQV SSLLTNHLARATECCGNQAAGNDALQDVLSLLNDLSRSHIGKAILSQPACVSKLLSLLLD QRPSPKLVLIILQLCRAALPLMSVEDCGNVELPPWSYSVPSLNSEQEDPSDPASKIASLL LAKLADYVVPGCQTVLSPTASEPDTTLTKTSPKNSLKGDKDPGEESEAVDGKLSIFIHKR EDQSSHEVLQPLLSSSEGRPFRLGTGANMEKVVKMDRDMTKGGCCEVITEEAAAALRKAT KWAQSGLIVSIGPPVESINPETVSGLSTGDKKKTAQTSICRERNSELARTDPVRPFISGH VANSMAAEVIALLHSLLMAPESNAAQIWTTTAEKVLSRALMYIPQLGKYAESILENGSSS GRKLAKLQRIARQAVAALCALGGFKETIKIGSEVQVLGRGISGSIGVVASINEQEGIATV RFPPIDCRKTSQASDTLTIPLSRLCVPRSEALPLHKLSITEKVVQAVQSMLLPQEGSLSI HTSLPATGDGSAPVMAVVRLLAEIRTRACLVMAQLLEDSLFCEEFIQQCPAAVEVLNLVA QECSAGERLAVVEVQCERLRMLYRDCARPPPPPLQADRRQPKEITWSPSRVFPPVRACMF SSHLTSVTFLADPSAGGGLPRGTFIYATSPLPVQAPSFYWEIEIVSYGDTDDDTGPIVSF GFTTEAEKRDGAWTNPVGTCLFHNNGRAVHYNGSSLLQWKSVRLDVTLSPGDVAGIGWER TEGTPPPPGQPAKGRVYFTYCGQRLSPYLEDVSGGMWPVVHIQKKNTKTRANFGSRPFAY AEGQAHRNAADLCTDLAEEISANFEALPFAMASDSDNDAGTSIASDPGTHGPPCRIAAVA TAQQQYDSDTSCHYKVELSYENFITSGPDPHPPPIADDESDDDDDDDIPQEDHYALLVKA WETKVFPTIRRRFRNEAERKSGLDQIKGALQLGMVDIARQTVEFLYEENGGIPRDLYLPT IEDIKDEANKFTIDKVRKGLTVVTRSPDSNNVASSAVGTALPKFAIRGMLKTFGLHGVVL DVDSVNELVQVETYLRSEGVLVRYWYPIDMLERPPAGYRRTATNGLVTLDNTNLQIHREL LRCEAALARLYCRMALLNIFAPKLPHLFTRLFHIPAIRDITLEHLQLLSNQLLAPPLPDG TISSSSILLAQSLQHCIHSQNCSATDLFYQGNSQTVREWLNVAITRTLHQGEESLLELTK QICSFLQTAPEQFPSEEFPISESKVNMDVNFPGAAFVVVSCKESQSGFRKDSSLYKAPWA RVLVYGLGHKVKRNGQLNLIEAACYPRDASPANTGLAPPPTADQYPSVVLSTDRVHIKLG VSPPPGAVLVLHSLPLEFPLAMAFAEQLLSWKSEDSEGKSEDEPDTIPTSVLLQVVELLG NFLWTTDMAACVKELVFHLLAELLRTVHTLEQRRHPAGLSSSIALQLNPCLAMLMALQSE LHKLYDEETQNWVSGGACGGSGGAAAGDQGRFSTYFHALMEGCLAVAEVTLPTNMSVTAS GVTSATAPNLSDSSSSSSSSPGQTPQSPSLLSKRKKVKMKREKASSSGKRQSSRTVDSDP TVLSIGGSKPEDMLWFHRALTLLIILRHLTRKDPQGLGVTSDAIADACQALVGPTAHSRL LVISGIPTHLDEGVVRGAIRKACNAHGGVFKDEIYIPLQEEDTKKPKDKAEGGDGKVEPE KTLAFPGTDSMEVSTSSSLTPAMSISASASTSQASICSSQGISQTVSDLSVDPLPAGLEL PIPPGLLEPHAVSSQESLDISLCSTGSLGSLGSLGEPLDNAETASVSDMGSMYTVTSLDN QPLAARPIKGFAVVEIRSRAKIEKIRASLFNNNDLIGLSSLDGEDELMEMSTEEILTVSV VNQSLFDTQGSPGLEDYFNDKSIKGEKLVPGAREVLTEIFKSCAHSEQTLSLTPAKPIRV SDIYLSKEQINSQTPGNLLHLFFTNVRPPKKVLEDQLTQILRKYGVPKPKFDKSKYSKAG KEQHPVKVVSTKRPITKPPAKDKAVLNSVSRTALSEKKPTVKPKSPEKSKPDEKDPEKSP TKKQEVPEEKYLTLEGFHKFVIDRARQDIRSVWRAILSCGYDLHFERCACIDVRHAQKAS RKWTLEMDVALVQYINQLCRHLAITPARLHPHEVYLDPADAADPRVACLLNVPIESLRLR FALLQSLNTTLETFFLPLVELRQTPMYTHSIAALLKEAKGLIFYDTKVTVMNRVLNATVQ RTADHAAPEITLDPLEIVGGEIRASENSYFCQAARQLASVPSSQLCVKLASGGDPTYAFN IRFTGEEVHGTSGSFRHFLWQVCKELQSSSLSLLLLCPSSAVNKNKGKYILTPSPITYGE EQLLHFLGQLLGIAIRADVPLPLDLLPSFWKTLVGEPLDPEQDLQEADILTYNYVKKFES INDETELEALCAEIASQHLATESPDSPNKPCCRFTYLTMTGEEVELCSRGRHILVAWENK DIYAAAIRSLRLRELQNVECVTAVRAGLGSIIPLQLLTMLSPLEMELRTCGLPYINLEFL KAHTMYQVGLMETDQHIEFFWGALEMFTQEELCKFIKFACNQERIPFTCPCKDGGPDTAH VPPYPMKIAPPDGTAGSPDSRYIRVETCMFMIKLPQYSSLEIMLEKLRCAIHYREDPLSG h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003206.txt0000600000175000017500000000643411455416572022003 0ustar ykeyke>sp|P29152|POLG_PSBMV Genome polyprotein OS=Pea seed-borne mosaic virus (strain DPD1) PE=2 SV=1 MSTLVCQAVAAPVWSNGARTRRIRDADGEYRCTQCDMGFDSMTMARPVNHCCDGIMIDEY NLYDDDPIMHLVDSKTPIKRGSQETEGDGMAAEAIKVTGAEPVNCFMVGTIKCKINENSI VAKGVMAAIPRQLTQDEVFMRKARLQAAVAKSTIEREEKERQFAFSKLEEKLRARREKLK DGIVIKTRKGLEWREATPNQQRGKLQSTSFDASGGKTLTPHTIYCKTKSSKFSNGGVKCA TSKKMRTVRKPQSLKMKTESIDVLIEQVMTIAGKHAKQVTLIDKQKTNRVWIRRVNGVRL LQVETKHHKGIISQKDASLNNLTKRVARHFARKTAYIHPSDSITHGHSGVVFLRANISGS KSYSIDDLFVVRGKRNGKLMESRNKVAWRKMFQIDHFSIVGIKIWNAFDAEYVKLRDESV SDHDCVGGITPEECGILAAQILRVFYPCWRITCTKCISNWLSKPTSEQIEHIYERGNLAI QDLNKRIPSAHHVTQMVELLRQRIKNTTFDMGNNTKVHELIGHRQDGVFRHLNRLNNSIL AANGSSTIEWESMNESLLELARWHNKRTESIASGGISSFRNKISAKAQINFALMCDNQLD TNGNFVWGERGYHAKRFFSEFFTKIDPKDGYSHHTVRATPTGVRHLAIGNLIIPGDLQKL REKLEGVSITAVGISEKCVSRRNGDFVYPCSCVTSENGKPVLSDVILPTRNHLVIGNTGD PKLVDLPKTETGRMWIAKEGYCYINIFFAMLVNVSEKDAKDFTKFVRDEIMPQLGKWPTM MDVATACYKLAIIYPDVRDAQLPRILVDHSEQIFHVIDSYGSMTTGYHILKAGTVSQLIS FAHGALLGEMKMYRVGGTQKMEINMCCCQRKNLLIKQLIRAIYRPKLLTEIIETEPFVLM LAIVSPSILKAMFRSGTFNQAIKFYMHRSKPTAQTLAFLEALSERVSRSRVLSEQFNIID GALKELKSLANMSMRTQHTYPIVQNQLDIMIERVSADAELLRDGFVVSKGRVQALIEKNY QDDLRNSFTDLPYVQQLQQTMSFSRVKHGFGELCESKDLSFSKEAWMGHLSSFSAGGKQI IRLARTKSQQMLASGGRRVTLAARNITMRMVTATFSEIMKFVNMLLVLSMIFKLWKQANT LLEEREKDKWEKFDRSQNELRRQLRYTLWRFEAQEGRQVTREEFFDYLKYNEGIENRHEL INELIANQPLFSIQAKKHGEIRFEQTVALMALLAMMFGSDRSDAVFSTLSKVRTIFTTMA QEVRCQSIDDIHDVFDEKKATIDFELATDQPAQVQMDKTFCEWWQNQMEQNRTVPHYRTG GKFIEFTRSNAASVANEIAHTPDFSEYLIRGAVGSGKSTGLPCYLSAKGRVLLLEPTRPL TENVCAQLRGSPFHKSPSMSMRNGHTFGSTPIHVMTTGYALHFFCNNVERIREYDFVIFD ECHVIDSSAMSFYCALKEYSYQGKILKVSATPPGREVEFKTQFPVTIATEDSLSFDQFVQ AQGSGANCDILKKGHNILVYVSSYNEVDRLSKLLVDRGFKVTKVDGRTMKLGGVEINTSG TAEKPHFIVATNIIENGVTLDIDVVVDFGVKVVAELDADARTMRYNKQAISYGERIQRLG RVGRLKDGHALRIGHTEKGITEIPVAIAVESAFQCFAYGLPVMTSNVSTSIIGNCTVKQA RTMMNFELSPFFTVELVKYNGTMHPEIHKILVPYKLRDSSMQLCKEAIPNSGVSRWHTAH EYISHGIVLETLKSDVRIPFYLKGVPEKVYEKIWNAVCVFKSDSGFGRMSTASACNVAYT LKTDPLSITRTIAHIDALLIEEQEKKSQFDLMSSHVTNSSSISLAGLVNRLRSKWMVDHS GENIVKLQNARSQLLEFRGMDINLDDVESFRKFGCAETVRCQSKSEVSKTLQLKGKWNKP LITSDFFVVCMVSIGCVVLMYQIFMAKWNEPVKLEGKSKAKTLRFRQARDNNAKYEVFAD EDTKRHYFGEAYTKKGKKSGKARGMGVKTKKFVNVYGFDPCEYSLVRFVDPLTGLTYDRH PMEHMMDVQETIGDDRREAMWNDELDKQLFVTRPTIEAYYIKDKTTPALKIDLNPHNPMR VCDKAETIAGFPEREFELRQSGSATLVPYSEVPVQNEKQEFDEEHVRTEAASLHFGLRDY NPIAQAVCRITNTGVDYDRSIFGIGFGQFLITNAHCFKLNEGETRIVSRHGQFTIEKTHS LPIHQVKDKDMVIVRLPKDFPPFPQRLQFRAPQEREKICLVGSNFQEKSIQSVITESCMT FKHNGGKYWKHWITTKEGHCGLPAVALKDGHIVGIHNLGGENTNINYFTPFDADILDKYL LNAEALQWTKGWKYNKNKVCWGGLELLDDNEPEESGLFRMVKLLKSLEEDGVRTQSRDDA WLEKEIKGSLKVVARCPGQLVTKHVVKGPCAMFQLYLELHEDAKSFFTPRMGSYGKSRLS KGAFIKDIMKYSSNTVVGNVDCDVFENAIDNVEKILWKAGMMQCEYVTDAEAIFQSLNMN AAVGAMYQGKKKDYFEDFTAADRELIVKQSCERLFLGKKGVWNGSLKAELRPIEKVHENK TRTFTAAPLDTLLGGKVCVDDFNNFFYSCHLRGPWTVGITKFYAGWNEFLSKLPDGWLYC DADGSRFDSSLTPYLINAVLELRLRFMEEWDAGEQMLKNLYTEIIYTPIATPDGSVIKKT KGNNSGQPSTVVDNTLMVILAMQYSLQLLGVDFETQDEVVRYFANGDDLLIAVRPDCEFV LKGLEIHFSNLGLNYNFSARHHDKKDVWFMSTRGILRDGILIPKLEEERIVAILEWDRSR EFSHRLDAICAAMIEAWGYDELLQHIRKFYYWLLEQEPYRSIAQEGKAPYIAETALRHLY TNAMATQSELEKYTEAINQHYNDEGGDGSIKVRLQAGDETKDDERRRKEEEDRKKREESI DASQFGSNRDNKKNKNKESDTPNKLIVKSDRDVDAGSSGTITVPRLEKISAKIRMPKHKG GVAISLQHLVDYNPAQVDISNTRATQSQFDNWWRAVSQEYGVGDNEMQVLASGLMVWCIE NGTSPNINGMWTMMDGEEQVEYPLKPVMDNARPTFRQIMAHFSDVAEAYIEKRNSTEVYI PRYALQRNLRDPSLARYGFDFYEITAKTPVRAREAHFQMKAAAIRGKSNSLFGLDGNVGT QEENTERHTAEDVNQNMHNLLGMRAM h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002900.txt0000600000175000017500000000600211455416572021772 0ustar ykeyke>sp|P0C657|MED13_CAEBR Mediator of RNA polymerase II transcription subunit 13 OS=Caenorhabditis briggsae GN=let-19 PE=3 SV=1 MASSKEGEKDASRKVKVPKRPEVNNGGSLEDCISNVFSLLELPGIKWKCFRPKLNAPRGV PLTSDLVLKAYSRCLTDGILCTWRRKPSPPTGNNELLPPTHFFSNDSPKELWVFWYDAEP TALGKYCEGLDSDEELSSANQMNIVSYEVRTILFKALHVVLERDLTKDGFVRFGRWFTMP LVARDHYLHFMYPSHSPAIRFNFFVHGTSTICASIQAQRQPTLIKLARRHFECKTPKRFP VVIGPWSMRGYLIADQMTLLADQKIQEAAEKEWNQWKEYLQLEEKEPENVTEERQKTPEA EPPAPPQTTRVLLASSSDEDQEKNGGELKSEEVSQKIRWMFEPDLRQDKPKEETAAEKEK RMAAREVRRLRRQRREERRREMEKQRRADDNLEDYDSDVVTDQDEDEAGKEEIVNNDVPK MILIEIDNVRLLYPSKFVCITVEEDRQMLESMGFKCHPMPQELQVPGRRPRNKNVVNMSN PLLSTMAVYQYVQNEKRAEREHFYPRNKPVEIETDTNFEILSNPKARRVAPPKSPTFLSW ESQRANHFDTTDIFVNRLFEKYQPYHRKRPAKSVKEKKKKAKRKVKKFVRYNSPEQFLAS MSRTRKKFNAWKQKKKGPPPKKDLAKKEAAADKDKDKDKEKDKEKDKDNDDDPFVMDKVS QLDWANFSEDETNGNSFADIEEIFFRKIIFLNKKYVSKKCILKFRNRALVSEEHIKFSSL YNPAGGDIEEGDETSNESPDEKTPEGSPNGSPRPKEEIEPFFPITYLAAKPSNIESDLGP DVDDMTEEQFNTEYVPKEYDITQDPKKVKNGQIPISEFSKDNQFYHGEICRLGLRGYKKI CAERDREEAARRTKWLQLYRLKVEKRSIKTARQCHRDYLRQIAKRCLRKALRRLRITAKK DALAPPPPKPKPVDPVLKKKEDAKKFEMSLKIMERDLGNLDMSAFCQVREKAGPHGVSFP EIILLTNPKWLKVRSTAGYMKPNYFNSPHGSFDHDSEPEFDEQRTGLGEGTSDQYQDGES VDMIDIERELANDPSSYLSNAEHIRTLGEHIGPDGMLSPPASNEMPKGGPLSVGPASIES QGLNQIYPTPPSVQMLQADASQAHSPSIGGKFRSTANDDIDRAAASGKTIVDIEIEDIET GNMQRWNKIANQSKLSKFLVASRDNPILKGRKTKYDTPATDKFEIRCQVERVTVPMAYES MVTRNFECAPPHTFAELIRQSRTGIKKYTRPLQIQSTLARPPPGATSPLPPPTPMFNPHT LPLHHTSPFSAGPMSHHSMGPPAYPPTPGPYPPTTPTYPGMTPRPGSSYGPGYPNHHQMM PPGYPNQMGMGPIGMQRQFSNPQMYQHHQMMRMQQMRMQGGLPGYGAPGVPQYPQQSPVS GGPGGFGVPSGPSSVQRLNNFVNQSQFGPSSGPQNPYGTQMPPMIPQSPSFNQPYPGMGN QMMSPMQQHQFQQQQMMQQQQQQQLQLQRSQAHQIQHQPNQQTMQSLQLTPEQLQIQQSQ QVQAVFQQLPDREKRKYQRRQIQLMNGLMPTSLQPASIKALKNPPDANIPYKRQDIIYNP PNPAHPRGDSLTIAIVLSDTLLDLHFDSVFDACPICSCSVSIRSRDLGMYIIPHAVLSSR EIGETNKREYTTGTWSGFHVNSATSCTCGFSAIRHRYLSCCAGLFDEDADEATASEHANA PVIPPLFARNTTKTRDMMWFDPQSVHDLALTDQIRQMAFSNSLGKAVSQMATEKEHRRNI TNAVDIGTDITVPTEYVLSHVDTLELMMLGMSALGPMQTPETTGNQFTPQSKYLSYFHPW GFQTANEIAELESSEWVDLLDIITPTLESSMKQARRPSVETPFVIEGPMTWKQVVTKAIR GKPPTDEDEDFSLAEPVPAVMRALEQEAVRAAPNIEQYYDQAELGPVDQPKDVMYITIIP DNDDIYERTVKFMHTMTETYERMRLGRHIPFPVSTGTASRFREVLKTYQHQFPYQEQNQQ LVEFTNNRLEAVPQELSNNPDPLNTDPEKWSKRLKRKLELSEELKKADEHPAPPSTQSEN SEGNAATPAAETLSSIFSDEVHDTLPEGFYEREGILRVGKPLEPLRISHTVVSTREFDNM TQHLSDAQGFVSKLRIFLQQMEDLVFHTLSGSSEAFERRGYRYQMAVEGRLKRQKHKRDI EEERLRYEAAKVQDEADKREKMDEADLFPGAEVGEETPSPWVDDELEEKKRNKQKENEQY PAEESQAPSPVPAGMIHIPETLSEQERKVQPTLADMFADPSTVAPINAQNIPWKQRDTRV QNPFPYSNQPPVAFEAVGSNDTDAYSTLPHVIVLYVVNPFSYGAEGQSALHMRIALLSFI RAYNSIVGRLPFTKRTQLQLEIIGMESLDDMVKGIPDYLNDSQVPFDILHDYPVRNERPS ESGQEAAARSLSVAVYTHPRVFTPEVYKAVSARCMTAFGPGSQLINTVNNIEKINQEAFY QMSKRSKTALNNMDGYMGMMGSHQVETKAHISYRVPSNIVCLAPPPAIYQMDEEGKPILN QLDEQTLFISYCLVGTEYLVATATDSQGKLIDNCIANMKPRRLHNQVYRYKNKTQILDGM GKLWSFILGVMSSDIKNWRLVVGRLGRIGHGEFRAWTHLLNKTSLLRYSSSLKDICGACR SMPSAIGTPAILSACLITLEPEPSIRIMPKFHDIDESIKKNLIFQTPGDLSCTHILTFPV GTEINLEVQDQTADTKGDENWEFGDLDIMEGLDDGDTEIMKDLGLETPSSAAIRQTGGVS MFFSEDSSSIEIQNQPLASGYYISTAPAPELPSWFWATCPSAKRHSPVHLKSSLHINISE VKNDDIAMESAKDKEKEKEEKDIHPLESRQTEEVLRHVLESYNALSWLNLNRQTGDRYSC LPIHVQHLLRLYHSVARLLV h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001200.txt0000600000175000017500000000246011455416572021766 0ustar ykeyke>sp|Q9SX33|ALA9_ARATH Putative phospholipid-transporting ATPase 9 OS=Arabidopsis thaliana GN=ALA9 PE=2 SV=1 MVGGGTKRRRRRLQLSKLYTLTCAQACFKQDHSQIGGPGFSRVVYCNEPDSPEADSRNYS DNYVRTTKYTLATFLPKSLFEQFRRVANFYFLVTGVLAFTPLAPYTASSAIVPLLFVIGA TMVKEGVEDWRRQKQDNEVNNRKVKVHRGDGSFDAKEWKTLSIGDIVKVEKNEFFPADLV LLSSSYEDAICYVETMNLDGETNLKVKQGLEVTSSLRDEFNFKGFEAFVKCEDPNANLYS FVGTMELKGAKYPLSPQQLLLRDSKLRNTDFIFGAVIFTGHDTKVIQNSTDPPSKRSMIE KKMDKIIYLMFFMVITMAFIGSVIFGVTTRDDLKDGVMKRWYLRPDSSSIFFDPKRAPVA AIYHFLTAVMLYSYFIPISLYVSIEIVKVLQSIFINQDIHMYYEEADKPARARTSNLNEE LGQVDTILSDKTGTLTCNSMEFIKCSVAGTAYGRGVTEVEMAMGRRKGGPLVFQSDENDI DMEYSKEAITEESTVKGFNFRDERIMNGNWVTETHADVIQKFFRLLAVCHTVIPEVDEDT EKISYEAESPDEAAFVIAARELGFEFFNRTQTTISVRELDLVSGKRVERLYKVLNVLEFN STRKRMSVIVQEEDGKLLLLCKGADNVMFERLSKNGREFEEETRDHVNEYADAGLRTLIL AYRELDEKEYKVFNERISEAKSSVSADRESLIEEVTEKIEKDLILLGATAVEDKLQNGVP DCIDKLAQAGIKIWVLTGDKMETAINIGFACSLLRQDMKQIIINLETPEIQSLEKTGEKD VIAKASKENVLSQIINGKTQLKYSGGNAFALIIDGKSLAYALDDDIKHIFLELAVSCASV ICCRSSPKQKALVTRLVKSGNGKTTLAIGDGANDVGMLQEADIGVGISGVEGMQAVMSSD IAIAQFRYLERLLLVHGHWCYRRISTMICYFFYKNITFGFTLFLYETYTTFSSTPAYNDW FLSLYNVFFSSLPVIALGVFDQDVSARYCLKFPLLYQEGVQNVLFSWRRILGWMFNGFYS AVIIFFLCKSSLQSQAFNHDGKTPGREILGGTMYTCIVWVVNLQMALAISYFTLIQHIVI WSSIVVWYFFITVYGELPSRISTGAYKVFVEALAPSLSYWLITLFVVVATLMPYFIYSAL QMSFFPMYHGMIQWLRYEGQCNDPEYCDIVRQRSIRPTTVGFTARLEAKKRSVRISEPAS h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003907.txt0000600000175000017500000000774411455416572022020 0ustar ykeyke>sp|Q96662|POLG_BVDVC Genome polyprotein OS=Bovine viral diarrhea virus (strain CP7) PE=1 SV=1 MELITNELLYKTYKQKPAGVEEPVYDQAGNPLFGERGVIHPQSTLKLPHKRGEREVPTNL ASLPKRGDCRSGNSKGPVSGIYLKPGPLFYQDYKGPVYHRAPLEFFEEASMCETTKRIGR VTGSDSRLYHIYVCIDGCIIVKSATKDRQKVLKWVHNKLNCPLWVSSCSDTKDEGVVRKK QQKPDRLEKGRMKITPKESEKDSKTKPPDATIVVDGVKYQVKKKGKVKSKNTQDGLYHNK NKPQESRKKLEKALLAWAIIALVFFQVTMGENITQWNLQDNGTEGIQRAMFQRGVNRSLH GIWPEKICTGVPSHLATDTELKAIHGMMDASEKTNYTCCRLQRHEWNKHGWCNWYNIEPW ILLMNKTQANLTEGQPLRECAVTCRYDRDSDLNVVTQARDSPTPLTGCKKGKNFSFAGIL VQGPCNFEIAVSDVLFKEHDCTSVIQDTAHYLVDGMTNSLESARQGTAKLTTWLGRQLGI LGKKLENKSKTWFGAYAASPYCEVERKLGYIWYTKNCTPACLPRNTKIIGPGRFDTNAED GKILHEMGGHLSEVLLLSVVVLSDFAPETASVIYLILHFSIPQGHTDIQDCDKNQLNLTV ELTTAEVIPGSVWNLGKYVCVRPDWWPYETATVLVIEEVGQVIKVVLRALKDLTRIWTAA TTTAFLVCLVKVVRGQVLQGILWLMLITGAQGYPDCKPGFSYAIAKNDEIGPLGATGLTT QWYEYSDGMRLQDSVVEVWCKNGEIKYLIRCGREARYLAVLHTRALPTSVVFEKIFDGKE QEDIVEMDDNFEFGLCPCDARPLIRGKFNTTLLNGPAFQMVCPIGWTGTVSCTLANKDTL ATIVVRTYKRVRPFPYRQDCVTQKTIGEDLYDCALGGNWTCVPGDALRYVAGPVESCEWC GYKFLKSEGLPHFPIGKCRLKNESGYRQVDETSCNRNGVAIVPSGTVKCKIGDTVVQVIA MDDKLGPMPCKPHEIISSEGPVEKTACTFNYTRTLKNKYFEPRDNYFQQYMLKGEYQYWF DLEITDHHRDYFAESLLVIVVALLGGRYVLWLLVTYMILSEQMASGVQYGAGEIVMMGNL LTHDSVEVVTYFLLLYLLLREENTKKWVILIYHIIVMHPLKSVTVILLMVGGMAKAEPGA QGYLEQVDLSFTMITIIVIGLVIARRDPTVVPLVTIVAALKITGLGFGPGVDAAMAVLTL TLLMTSYVTDYFRYKRWIQCILSLVAGVFLIRTLKHLGELKTPELTIPNWRPLTFILLYL TSATVVTRWKIDIAGIFLQGAPILLMIATLWADFLTLVLILPTYELAKLYYLKNVKTDVE KSWGVPYPDPQTLGGLDYRTIDSVYDVDESGEGVYLFPSRQKKNKNISILLPLIRATLIS CISSKWQMVYMAYLTLDFMYYMHRKVIEEISGSTNVMSRVIAALIELNWSMEEEESKGLK KFFILSGRLRNLIIKHKVRNQTVASWYGEEEVYGMPKVVTIIRACTLNKNKHCIICTVCE ARKWKGGNCPKCGRHGKPIICGMTLADFEERHYKRIFIREGNFEGPFRQEYNGFVQYTAR GQLFLRNLPILATKVKMIMVGNLGEEIGDLEHLGWILRGPAVCKKITEHEKCHVNILDKL TAFFGVMPRGTTPRAPVRFPTALLKVRRGLETGWAYTHQGGISSVDHVTAGKDLLVCDSM GRTRVVCQSNNKLTDETEYGVKTDSGCPDGARCYVLNPEAVNISGSKGAVVHLQKTGGEF TCVTASGTPAFFDLKNLKGWSGLPIFEASSGRVVGRVKVGKNEESKPTKLMSGIQTVSKN TADLTEMVKKITSMNRGDFRQITLATGAGKTTELPKAVIEEIGRHKRVLVLIPLRAAAES VYQYMRLKHPSISFNLRIGDMKEGDMATGITYASYGYFCQMPQPKLRAAMIEYSYIFLDE YHCATPEQLAVIGKIHRFSESIRVVAMTATPAGSVTTTGQKHPIEEFIAPEVMKGEDLGS QFLDIAGLKIPVEEMKGNMLVFVPTRNMAVEVAKKLKAKGYNSGYYYSGEDPANLRVVTS QSPYVVVATNAIESGVTLPDLDTVVDTGLKCEKRVRVSSKIPFIVTGLKRMAVTVGEQAQ RRGRVGRVKPGRYYRSQETATGSKDYHYDLLQAQRYGIEDGINVTKSFREMNYDWSLYEE DSLLITQLEILNNLLISEDLPAAVKNIMARTDHPEPIQLAYNSYEVQVPVLFPKIRNGEV TDTYENYSFLNARKLGEDVPVYVYATEDEDLAVDLLGLDWPDPGNQQVVETGKALKQVVG LSSAENALLIALFGYVGYQALSKRHVPMITDIYTIEDQRLEDTTHLQYAPNAIRTEGKET ELKELAVGDLDKIMGSISDYASEGLNFVRSQAEKMRSAPAFKENVEAAKGYVQKFIDSLI ENKETIIRYGLWGTHTALYKSIAARLGHETAFATLVIKWLAFGGESVSDHMRQAAVDLVV YYVINKPSFPGDSETQQEGRRFVASLFISALATYTYKTWNYNNLSKVVEPALAYLPYATN ALKMFTPTRLESVVILSTTIYKTYLSIRKGKSDGLLGTGISAAMEILSQNPVSVGISVML GVGAIAAHNAIESSEQKRTLLMKVFVKNFLDQAATDELVKENPEKIIMALFEAVQTIGNP LRLIYHLYGVYYKGWEAKELSERTAGRNLFTLIMFEAFELLGMDSEGKIRNLSGNYVLDL IYSLHKQINRGLKKIVLGWAPAPFSCDWTPSDERIRLPTNNYLRVETKCPCGYEMKALRN VGGSLTKVEEKGPFLCRNRLGRGPVNYRVTKYYDDNLKEIKPVAKLEGFVDHYYKGVTAR IDYGRGKMLLATDKWEVEHGVVTRLAKRYTGVGFKGAYLGDEPNHRDLVERDCATITKNT VQFLKMKKGCAFTYDLTLSNLTRLIELVHKNNLEEKDIPAATVTTWLAYTFVNEDIGTIK PVLGERVVTDPVVDVNLQPEVQVDTSEVGITLVGRAALMTTGTTPVVEKTEPNADGGPSS IKIGLDEGRYPGPGLQDRTLTDEIHSRDERPFVLVLGSKNSMSNRAKTARNINLYKGNNP REIRDLMAQGRMLVVALKDFNPELSELVDFKGTFLDREALEALSLGRPKSKQVTTATVRE LLEQEVQVEIPSWFGAGDPVFLEVTLKGDRYHLVGDVDRVKDQAKELGATDQTRIVKEVG ARTYTMKLSSWFLQATNKQMSLTPLFEELLLRCPPKIKSNKGHMASAYQLAQGNWEPLDC GVHLGTIPARRVKIHPYEAYLKLKDLLEEEEKKPKCRDTVIREHNKWILKKVRHQGNLNT KKILNPGKLSEQLDREGHKRNIYNNQIGTIMTEAGSRLEKLPVVRAQTDTKSFHEAIRDK IDKNENQQSPGLHDKLLEIFHTIAQPSLRHTYSDVTWEQLEAGVNRKGAAGFLEKKNVGE VLDSEKHLVEQLIRDLKTGRKIRYYETAIPKNEKRDVSDDWQSGDLVDEKKPRVIQYPEA KTRLAITKVMYNWVKQQPVVIPGYEGKTPLFNIFNKVRKEWDLFNEPVAVSFDTKAWDTQ VTSRDLRLIGEIQKYYYRKEWHKFIDTITDHMVEVPVITADGEVYIRNGQRGSGQPDTSA GNSMLNVLTMMYAFCESTGVPYKSFNRVARIHVCGDDGFLITEKGLGLKFANNGMQILHE AGKPQKITEGERMKVAYRFEDIEFCSHTPVPVRWSDNTSSYMAGRDTAVILSKMATRLDS SGERGTIAYEKAVAFSFLLMYSWNPLVRRICLLVLSQQPETTPSTQTTYYYKGDPIGAYK DVIGKNLCELKRTGFEKLANLNLSLSTLGIWSKHTSKRIIQDCVTIGKEEGNWLVNADRL ISSKTGHLYIPDKGYTLQGKHYEQLQLQARTSPVTGVGTERYKLGPIVNLLLRRLRVLLM AAVGASS h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002504.txt0000600000175000017500000000507511455416572022003 0ustar ykeyke>sp|P19096|FAS_MOUSE Fatty acid synthase OS=Mus musculus GN=Fasn PE=1 SV=2 MEEVVIAGMSGKLPESENLQEFWANLIGGVDMVTDDDRRWKAGLYGLPKRSGKLKDLSKF DASFFGVHPKQAHTMDPQLRLLLEVSYEAIVDGGINPASLRGTNTGVWVGVSGSEASEAL SRDPETLLGYSMVGCQRAMMANRLSFFFDFKGPSIALDTACSSSLLALQNAYQAIRSGEC PAALVGGINLLLKPNTSVQFMKLGMLSPDGTCRSFDDSGSGYCRSEAVVAVLLTKKSLAR RVYATILNAGTNTDGSKEQGVTFPSGEVQEQLICSLYQPAGLAPESLEYIEAHGTGTKVG DPQELNGITRSLCAFRQAPLLIGSTKSNMGHPEPASGLAALTKVLLSLEHGVWAPNLHFH NPNPEIPALLDGRLQVVDRPLPVRGGNVGINSFGFGGSNVHVILQPNTRQAPAPTAHAAL PHLLHASGRTLEAVQDLLEQGRQHSQDLAFVSMLNDIAATPTAAMPFRGYTVLGVEGRVQ EVQQVSTNKRPLWFICSGMGTQWRGMGLSLMRLDSFRESILRSDEAVKPLGVKVSDLLLS TDERTFDDIVHAFVSLTAIQIALIDLLTSVGLKPDGIIGHSLGEVACGYADGCLSQREAV LAAYWRGQCIKDAHLPPGSMAAVGLSWEECKQRCPAGVVPACHNSEDTVTISGPQAAVNE FVEQLKQEGVFAKEVRTGGLAFHSYFMEGIAPTLLQALKKVIREPRPRSARWLSTSIPEA QWQSSLARTSSAEYNVNNLVSPVLFQEALWHIPEHAVVLEIAPHALLQAVLKRGVKSSCT IIPLMKRDHKDNLEFFLTNLGKVHLTGINVNPNALFPPVEFPAPRGTPLISPHIKWDHSQ TWDVPVAEDFPNGSSSSSATVYSIDASPESPDHYLVDHCIDGRVIFPGTGYLCLVWKTLA RSLGLSLEETPVVFENVSFHQATILPKTGTVALEVRLLEASHAFEVSDTGNLIVSGKVYL WEDPNSKLFDHPEVPTPPESASVSRLTQGEVYKELRLRGYDYGPQFQGICEATLEGEQGK LLWKDNWVTFMDTMLQVSILGSSQQSLQLPTRVTAIYIDPATHRQKVYRLKEDTQVADVT TSRCLGITVSGGIHISRLQTTATSRRQQEQLVPTLEKFVFTPHMEAECLSESTALQKELQ LCKGLARALQTKATQQGLKAAMLGQEDPPQHGLPRLLAAACQLQLNGNLQLELGEALAQE RLLLPEDPLISGLLNSQALKACVDTALENLSTLKMKVAEVLAGEGHLYSRIPALLNTQPM LQLEYTATDRHPQALKDVQTKLQQHDVAQGQWNPSDPAPSSLGALDLLVCNCALATLGDP ALALDNMVAALKEGGFLLVHTVLKGHALGETLACLPSEVQPAPSLLSQEEWESLFSRKAL HLVGLKRSFYGTALFLCRRAIPQEKPIFLSVEDTSFQWVDSLKSTLATSSSQPVWLTAMD CPTSGVVGLVNCLRKEPGGHRIRCILLSNLSNTSHAPKLDPGSPELQQVLKHDLVMNVYR DGAWGAFRHFQLEQDKPKEQTAHAFVNVLTRGDLASIRWVSSPLKHTQPSSSGAQLCTVY YASLNFRDIMLATGKLSPDAIPGKWASRDCMLGMEFSGRDRCGRRVMGLVPAEGLATSVL LSSDFLWDVPSSWTLEEAASVPVVYTTAYYSLVVRGRIQRGETVLIHSGSGGVGQAAISI ALSLGCRVFTTVGSAEKRAYLQARFPQLDDTSFANSRDTSFEQHVLLHTGGKGVDLVLNS LAEEKLQASVRCLAQHGRFLEIGKFDLSNNHPLGMAIFLKNVTFHGILLDALFEEANDSW REVAALLKAGIRDGVVKPLKCTVFPKAQVEDAFRYMAQGKHIGKVLVQVREEEPEAVLPG AQPTLISAISKTFCPAHKSYIITGGLGGFGLELARWLVLRGAQRLVLTSRSGIRTGYQAK HIREWRRQGIQVLVSTSNVSSLEGARALIAEATKLGPVGGVFNLAMVLRDAMLENQTPEL FQDVNKPKYNGTLNLDRATREACPELDYFVAFSSVSCGRGNAGQTNYGFANSTMERICEQ RRHDGLPGLAVQWGAIGDVGIVLEAMGTNDTVIGGTLPQRISSCMEVLDLFLNQPHAVLS SFVLAEKKAVAHGDGDTQRDLVKAVAHILGIRDLAGINLDSTLADLGLDSLMGVEVRQIL EREHDLVLPMREVRQLTLRKLQEMSSKTDSATDTTAPKSRSDTSLKQNQLNLSTLLVNPE GPTLTQLNSVQSSERPLFLVHPIEGSTTVFHSLAAKLSVPTYGLQCTQAAPLDSIPNLAA YYIDCIKQVQPEGPYRIAGYSFGACVAFEMCSQLQAQQGPAPTHNNLFLFDGSHTYVLAY TQSYRAKMTPGCEAEAEAEALCFFIKQFLDVEHSKVLEALLPLKSLEDRVAASVDLITKS HHSLDRRELSFAAVSFYHKLRAADQYKPKAKYHGNVTLLRAKTGGTYGEDLGADYNLSQV CDGKVSVHIIEGDHRTLLEGSGLESIINIIHSSLAEPRVSVREG h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003101.txt0000600000175000017500000000626711455416572022001 0ustar ykeyke>sp|Q54FP8|PKS32_DICDI Probable polyketide synthase 32 OS=Dictyostelium discoideum GN=pks32 PE=3 SV=1 MVQNTDNNTYDQLIRERNDYDDDAGSSGDVAVIGIGLRFPSGSLKESISKPYQLFNELLN GLDGIVSTFERWFDNYYLNGEIVSKFAGLLPLDEWKQFDPIFFAINPSNDNVSSIDPQQR LLLKCVWEALEDSGIDPISLRGTNTSTFIGSSTIDYCNLQKSPSETQNNIFGSSTHSIAN RIGFCFDFRGESLTIDTACSSSSNAINCGYNSIKSNKSNVSIVGGVNFILDPHISKSFTQ LGLLSPTGRCHTFSSDADGYVRSEGVGIVVLKKLKDAIKDSNNIYCVIKGSNSNIDGNFD KLNFYSPSKSSQCENIKLAIKSTNGQINESDIDYCETHGTGTPTGDPIELEGISRVFNTT KISSATTITTNNNNKQVLVGSIKSNIGHTEACSGVASLIKCCLMFKNKLFLQNINFKEPN PLINFKEWGLKVVTEPIKFNENKQTVMLINNFGVTGSNVCLILSEFKNNHYGNDYHKMKI DNKFNEKKRYLIPFSSNSSTSLNNYKSSIIKHSNSSSTTTSFKEFVHNQIKFKSTSLIQK SVIIASDWNEFQDESNQIKLNSSDNLISNITVEKKKSPLTVMVLCGQGSQYNKMALSLYD NEPIFRESVNRFDKELFKYYGYSVLDKLRSIDDKDLISIHQPILAQPANIMIQVSLYELY KHWGVSADIIIGHSLGEVSSAYCSGMIDFETLCYLTYHRSVAQNRTTGTGRMLSVNISSD EFINNYQSTTKYESLEIACYNSPTSIVIAGKEDLLNEITNEFKSNDIFCSMLGSLSSFHT SSQQMIKDEVCSLNISSKQPSIAVFSTVTTNLFNHQTSPFNANYVFDNIIQPVYFTQTIT NLYKHIESNDMGNEITFIEVSPHPTLQYYLNQMKSTQSSYFNNGKNITIYSPLNKKKNDY NEFLKTISLLYVNNNFDINFKSQLINNNNSNNNYENQLNNLPLYQWDDKEYFKLNSSLEK IKSEGPSINNLGNNTDSPYPSYQTFIDIKKSPFQWLKGHQVSDKFYYPGMGYVHNLLSIY PNQDITISSLEFKSPLVLTEGNNQCLQTIITPLSKNEFNIKSHYKDQKTNQWILSSLGNF SLTKHNSIISNKLINIQSLKDKCNFTSISKQDLYETIRIKTNLTYKGLFQGVKQCHIGNN CSLAIVSLNEIYNQKEYNHLINNTNMNSFFNAAILDTCLHGSLVAVTQPVVLDRIEGFKY YSSNIPSFKNGNNNDDDEESNNNNNNNNNNNNNNNNNIKELYVFSDIKSRTNSQTYSISV KIILPNGTLLVDISNVVCTLVSLPNPESAIICKPPSNDIYTPYLQSKDSVINKPEQFKHL YRVDEFSVNEEDNQFISNELLLSLFYKHINNRCPSINLESLTTLEYNQFKQLYYNSSVNE NLFKFIFENLKRYSNILNHDNNHSNIKSENEELYIRTTKIMAKQLFPLKDDDSITDTPQS LFESGFLDDFYKNSRVVQPLNNLLSEIIVETLKPILNEPIVFRILEAGGGTGSLSLLILE KICKLLNDNSTTSIINIEFTWSDISASFFAEIKEKFSSFTNHNNLNIIYRVLDLEKPLLD QDLKASYYDFVVMSNVMHVVKKLKPTLNEIHNILTPNGQLMFIEPPYKSFYYDSIFGCFS QWWPSYDSDIELRPDRCCMKQEKWINLLNQCNYRDTIMSGNDNLVFLIQTRKPTINEIIS EQSISLDQLNSFNNIILFSNNNNSNDKNRNSCSSSILDLIRLNQELKHKIININNYNEFQ SWITNNQNKDGCNKTLIIFLKSIESKMNTFNFKEITFEYIQINQLILKLELSNNFKHLLL SLNSTTDNYLSSSIVGAARYFVEFPQLDLYILNYDNVSIENNQQLSLINYLINPNNNIQK EFTINNNKVYYERYCRRSNNIKSIFQSESFETNKDNLYIQLNSNLEYQLYSKKDELNSNE VEIEIKANGINYKDYLMYIGMIGSDLDIKYGKEYEIENGIGIDNPNIGNDFSGIITRLGS NVKKFKVGDQVCGVGSKTNSSHVIVDYNYIYYKPLNYNHSVSASIPSIYITSLHSIYSIG NLKSNESILIHSAAGGIGISSLDLLKSKQHQGYIFLTVGSKDKEEYLTKKYGSLITAIYS SRNKDYVYEIKNKLIELSVVEQHQQGVDLILNTLSSEYMDSNFQCLNLSGRIVDLSITHL TPNDYMINNHYKFNMGYNNVEVVDFPSKLFKGYLKKIIKMANSNKLELSVPIIEYSNNQF KDAIEYINQRKHIGKIIVNHNQDEFNRVYNNYQNNNNHIIMKHSYDISKLNIGKNILLTG QTGIVLEILKYLIKYSNHSIENIIILSKSKLKWELELLINQSKFKKDNNIKFHFNQIDIE DSNKVNQVLNQLELNENITNIDSIIHFAFMNDIGDVQQVDMNRLNNTHGAKTIGAINLHN QSINRSWNIKQFIMASSVVSIFGSDQQCCYVSACSVIDSLSKYRHSIGLPSLAINLGAIS STGFVSRNNAIETMLKSSILNLFSPQLVISSLDLFIQNQHQYPNYCLSDFNFEILPSTLT NHFLKKFDYQINIVKKSNQIKSSSGGNGGDNNEIIRSTILNKISELLSIDESKINEDLQL TQYGMDSLVIVQLKNFIDNQLGHNIITIQQLQNNKINQSIEIIKSANNKNNKNNNNNNNN KTNKNNNNLVKKEQQSLDEFIKHETKLNESIISRPYSIKNILNNNNNKSIFLTGSTGFLG AYLLTELIKMKNVSKIYCLIRNNSKLTNPIDAIINNLKKHQLINMNKESPNQRSSKILNH TGNISNDKLSIIENSENNNKQIREDQLIKIIPMIGDISKDKFGLTEQDYLKLSNECDIII NSAADLNLKSNYEESKTVNVDSINQVIKLSVSNNSSQKLIVHFSSIAVFINHQLKDGETF EETNILPNFDTTPVGYIQSKVISEKLLTNAAESRGIPSIIIRPPDIFSNPITGIGHSNDF ISLFLKVSKEIGYYPNIHKPIFTTPVTTIAKTTIDLIFNENSWNQNKSKPISIYSLNGNS IEMKSIYEFLENKFNCKEIDYQEWIKLVSKSNGKSSKRYSAFHIHDNQNLLISNFKINSL FKMSNSTKELLISIGSYNHQDWEINESIILNNINNNNKEIK h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001500.txt0000600000175000017500000000310411455416572021765 0ustar ykeyke>sp|Q63041|A1M_RAT Alpha-1-macroglobulin OS=Rattus norvegicus GN=A1m PE=1 SV=1 MRRNQLPIPVFLLLLLLLPRDATAATGKPRYVVLVPSELYAGVPEKVCVHLNHLNETVTL NVTLEYGVQYSNLLIDQAVDKDSSYCSSFTISRPLSPSALIAVEIKGPTHHFIKKKSMWI TKAESPVFVQTDKPIYKPGQTVKFRVVSVDISFRPVNETFPVVYIENPKRNRIFQWQNVD LPGGLHQLSFPLSVEPALGIYKVVVQKDSGKKIEHSFEVKEYVLPKFEVQVKMPKTMAFL EEELVVTACGLYTYGKPVPGLVTMKVCRKYTQSYSNCHGQHSKSICEEFSKQADEKGCFR QVVKTKVFQPRQKGYDMKIEVEAKIKEDGTGIELTGTGSCEIANTLSKLKFTKANTFYRP GLPFFGQVLLVDEKGQPIPNKNLTVQVNSVRSQFTFTTDEHGLANILIDTTNFTFSFMGI RVIYKQNNICFDNWWVDEYHTQADHSAARIFSPSRSYIQLELVLGTLACGQTQEIRIHFL LNEDALKDAKDLTFYYLIKARGSIFNSGSHVLPLEQGKVKGVVSFPIRVEPGMAPVAKLI VYTILPNEELIADVQKFDIEKCFANTVNLSFPSAQSLPASDTHLTVKATPLSLCALTAVD QSVLLLKPEAKLSPQSIYNLLPQKAEQGAYLGPLPYKGGENCIKAEDITHNGIVYTPKQD LNDNDAYSVFQSIGLKIFTNTRVHKPRYCPMYQAYPPLPYVGEPQALAMSAIPGAGYRSS NIRTSSMMMMGASEVAQEVEVRETVRKYFPETWIWDMVPLDLSGDGELPVKVPDTITEWK ASAFCLSGTTGLGLSSTISHKVFQPFFLELTLPYSVVRGEAFILKATVLNYMPHCIRIHV SLEMSPDFLAVPVGSHEDSHCICGNERKTVSWAVTPKSLGEVNFTATAEALQSPELCGNK VAEVPALVQKDTVVKPVIVEPEGIEKEQTYNTLLCPQDAELQENWTLDLPANVVEGSARA TQSVLGDILGSAMQNLQNLLQMPYGCGEQNMVLFVPNIYVLEYLNETQQLTEAIKSKAIS YLISGYQRQLNYQHSDGSYSTFGDRGMRHSQGNTWLTAFVLKAFAQAQSYIYIEKTHITN AFNWLSMKQRENGCFQQSGSLLNNAMKGGVDDEVTLSAYITIALLEMPLPVTHSVVRNAL FCLETAWASISNSQESHVYTKALLAYAFALAGNRAKRSEVLESLNKDAVNEEESVHWQRP KNVEENVREMRSFSYKPRAPSAEVEMTAYVLLAYLTSASSRPTRDLSSSDLTTASKIVKW ISKQQNSHGGFSSTQDTVVALQALSKYGAATFTKSNKEVSVTIESSGTVSGTLHVNNGNR LLLQEVRLADLPGNYITKVSGSGCVYLQTSLKYNILPEAEGEAPFTLKVNTLPLNFDKAE HHRKFQIHINVSYIGERPNSNMVIVDVKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVL IYIEKLTNQTMGFSFAVEQDIPVKNLKPAPVKVYDYYETDEFAIEEYSAPFSSDSEQGNA h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000800.txt0000600000175000017500000000162411455416572021774 0ustar ykeyke>sp|A6QR56|A16A1_BOVIN Aldehyde dehydrogenase family 16 member A1 OS=Bos taurus GN=ALDH16A1 PE=2 SV=1 MAATRTASRACEIFTTLEYGPAPESHACALAWLDTQDRHLGHYVNGQWLKPEHRSSVPCQ DPITGENLASCLQAQSEDVAAAVEAARASLENWSTQPGAIRAQHLTRLAKVIQKHQRLLW TLESLVTGRAVREVRDRDVPLAQQLLQYHAVQAHTQEEALAGWEPMGVIGLILSPTFPFL DMMWRICPALAVGCTVVVLVPPASPTPLLLAQLAGELGPFPGILNVISGPASLGPVLAAQ PGVQKVAFCGAIEEGRALRRTLAGWVPELGLALGAESLLLLTEVADVDSAVEGIVDAAWS DRSPGGLRLLIQEAVWDETMRRLQERMGRLRCGHGLDGAVDMGARGAAARDLAQRYVSEA QSQGAQVFQAGSEPSDSPFFPPTLVSDLPPASPCTQAEVPWPLVVASPFRTAKEALAVAN GTPRGGSASVWSERLGQALELAYGLQVGTVWINAHGLRDPAVPTGGCKESGSSWHGGQDG LYEYLRPSGTPAWIPYLSKTLNYDAFGLALPSTLPAGPETGPAPPYGLFVGGRFQAPGAR SSRPIQDSQGSLQGYVAEGGAKDIRGAVEAAHQAAPGWMSQSPAARAALLWALAAALQRR EPNLVSRLERHGVELKVAKAEVELSVKRLRAWGARVQAQGCALQVAELRGPVLRLREPLG VLAIVCPDEWPLLAFVSLLAPALAHGNTVVLVPSGACPIPALEVCQEMATLLPAGLVNVV TGDRDHLTRCLALHQDIQALWYFGSAQGSQFVEWASAGNLKPVWVNRGCPRAWDQEAEGA GPELGRRAARTKALWLPMGD h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001000.txt0000600000175000017500000000213611455416572021764 0ustar ykeyke>sp|Q6XPR4|BRO1_EMENI Vacuolar protein-sorting protein bro1 OS=Emericella nidulans GN=broA PE=3 SV=2 MVQSPMISCPLKQTNEIDWIQPLKDYIRQSYGEDPERYSQECATLNRLRQDMRGAGKDSA TGRDLLYRYYGQLELLDLRFPVDENHIKISFTWYDAFTHKPTSQYSLAFEKASIIFNISA VLSCHAANQNRADDIGLKTAYHNFQASAGMFTYINENFLHAPSTDLNRETVKTLINITLA QGQEVFLEKQIMDHKKAGFLAKLASQASYLYAQAIEGTQEHAKGIFDKSWVTLLQVKSAH MGSVASYYQALADGESGSHGVAVARLQLAEKHSTSALSWAKSLPSSISPNTNLTSEAGPS LVDIVKFHLANVQSQLATFVKDNDFIYHQPVPSEAGLSAVSKLPAAKAIPVSELYQGQDI QRIIGPDIFQKLVPMSVTETASLYDEEKAKLIRAETEKVETADGEMAASLDYFKLPGSLN ILKGGMDQEVMVDEEFQRWCQELAGHDSFAKAFDTLQDRKSEVLATLDQCAKQLDLEESV CEKMRSKYGADWSQQPSSRLNMTLRNDIRTYRDTVHEASASDAQLSATLRQYESDFDEMR SAGETDEADVLFQRAMIKAGSKQGKTKNGVTSPYSATEGSLLDDVYDDGVPSVAEQIARV ESILKKLNLVKRERTQVLKDLKEKVRNDDISNVLILNKKSITGQESQLFEAELEKFHPHQ MRIVQANHKQTALMKELTKTYGDLLQDKRVRAEQSKYESITRQRNSVMARYKKIYDSFNN LGSGIKQAQTFYAEMTETVDSLKKNVDTFINNRRSEGAQLLGQIEREKAAGTSDHEERER EKLRQLMERLSTEPKPPSVPPGSSTAGPAKAKSPPPPVKAPAYPTNIAPPKASPHFAPTV PQQHGTPVSHSPAPYSQYVPPGAGVSYLPSQSFQQGAAAPLSEGYNPMAYPIPASSMSPP PSQPFYSPTPTPFYTSPTPPVPSGQYMPQGYVPPPPPPRPQQPTYPPSTGPFPSGPGGYA QSRPYGSSQHHKAHSQSSPQTGPSVSANSSDPWAGLNAWK h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004614.txt0000600000175000017500000001126411455416572022004 0ustar ykeyke>sp|Q9P2P6|STAR9_HUMAN StAR-related lipid transfer protein 9 OS=Homo sapiens GN=STARD9 PE=2 SV=2 MANVQVAVRVRPLSKRETKEGGRIIVEVDGKVAKIRNLKVDNRPDGFGDSREKVMAFGFD YCYWSVNPEDPQYASQDVVFQDLGMEVLSGVAKGYNICLFAYGQTGSGKTYTMLGTPVSV GLTPRICEGLFVREKDCASLPSSCRIKVSFLEIYNERVRDLLKQSGQKKSYTLRVREHPE MGPYVQGLSQHVVTNYKQVIQLLEEGIANRITAATHVHEASSRSHAIFTIHYTQAILENN LPSEMASKINLVDLAGSERADPSYCKDRIAEGANINKSLVTLGIVISTLAQNSQVFSSCQ SLNSSVSNGGDSGILSSPSGTSSGGAPSRRQSYIPYRDSVLTWLLKDSLGGNSKTIMVAI TRQTMSTLRYASSAKNIINKPRVNEVRPFQKNFSSLSDENLKELVLQNELKVDQLTKDWT QKWNDWQALMEHYSVDINRRRAGVVIDSSLPHLMALEDDVLSTGVVLYHLKGQWIERDHC TITSACGVVVLRPARGARCTVNGREVTASCRLTQGAVITLGKAQKFRFNHPAEAAVLRQR RQVGEAAAGRGSLEWLDLDGDLAASRLGLSPLLWKERRALEEQCDEDHQTPRDGETSHRA QIQQQQSYVEDLRHQILAEEIRAAKELEFDQAWISQQIKENQQCLLREETWLASLQQQQQ EDQVAEKELEASVALDAWLQTDPEIQPSPFVQSQKRVVHLQLLRRHTLRAAERNVRRKKV SFQLERIIKKQRLLEAQKRLEKLTTLCWLQDDSTQEPPYQVLSPDATVPRPPCRSKLTSC SSLSPQRLCSKHMPQLHSIFLSWDPSTTLPPRPDPTHQTSEKTSSEEHLPQAASYPARTG CLRKNGLHSSGHGQPCTARAALARKGASAPDACLTMSPNSVGIQEMEMGVKQPHQMVSQG LASLRKSANKLKPRHEPKIFTSTTQTRGAKGLADPSHTQAGWRKEGNLGTHKAAKGASCN SLYPHGPRQTAGHGKAVKTFWTEYKPPSPSRASKRHQRVLATRVRNITKKSSHLPLGSPL KRQQNTRDPDTMVPLTDFSPVMDHSREKDNDLSDTDSNYSLDSLSCVYAKALIEPLKPEE RKWDFPEPENSESDDSQLSEDSLAEKRYQSPKNRLGGNRPTNNRGQPRTRTRASVRGFTA ASDSDLLAQTHRSFSLDSLIDAEEELGEDQQEEPFPGSADEIPTETFWHLEDSSLPVMDQ EAICRLGPINYRTAARLDAVLPMSSSFYLDPQFQPHCMQLSRESPLMSMDSWFSCDSKIN PSSPPGIVGSLCPSPDMQEFHSCKGERPGYWPNTEELKPSDAETVLPYSSKLHQGSTELL CSARDEHTASAADTSRLSLWGIQRLIQPGADGTFQGRCIPDMTQQGSSEASHNSSVSNVL AASATTLTHVGSTHERDWSALQQKYLLELSCPVLEAIGAPKPAYPYLEEDSGSLAQASSK GGDTLLPVGPRVSSNLNLNNFPVHLSRIRRLRAEKEQDSLNAKLEGVSDFFSTSEKEASY DETYSADLESLSASRSTNAQVFATENAIPDSMTEACEVKQNNLEECLQSCRKPGLMTSSD EDFFQKNACHSNVTTATKADHWSQGWAPLRKNSAVQPGQLSPDSHYPLEEEKTDCQESSK EAVRRHINVSFALPSGPELYLHSAPWNPLSSSLQPPLLETFYVTKSRDALTETALEIPAC REVRVPSPPPREAWGFGHNHQALQGAYLKNNLPVLLQNQNSKIASSQQVTAEIPVDLNTR EVIRESGKCPGNITEESHDSVYSSVTQNRHFLPSTSTKVCEFENQVVILNKKHSFPALEG GEVTAQSCCGASSDSTESGKSLLFRESEAREEEELDQNTVLRQTINVSLEKDMPGESAVS LKSRSVDRRVSSPVMVAQGGGPTPKWEGKNETGLLEKGLRPKDSSEEFKLPGTKPAYERF QLVACPQERNPSECKSQEMLNPNREPSGKKQNKRVNNTDEMARLIRSVMQLENGILEIES KQNKQVHASHTPGTDKELVFQDQKEQEKTDHAFRPDSSGNPLPSKDQPSSPRQTDDTVFR DSEAGAMEVNSIGNHPQVQKITPNPFRSREGVRESEPVREHTHPAGSDRPARDICDSLGK HTTCREFTNTSLHPQRMKALARALPLQPRLERSSKNNGQFVKASASLKGQPWGLGSLEEL ETVKGFQESQVAEHVSSSNQEEPKAQGKVEEMPMQRGGSLQEENKVTQKFPSLSQLCRDT FFRQETVSPLLSRTEFCTAPLHQDLSNTLPLNSPRWPRRCLHVPVALGISSLDCVLDLTM LKIHNSPLVTGVEHQDQSTETRSHSPEGNVRGRSSEAHTAWCGSVRSMAMGSHSQSGVPE SIPLGTEDRISASTSPQDHGKDLRITLLGFSTSEDFASEAEVAVQKEIRVSSLNKVSSQP EKRVSFSLEEDSDQASKPRQKAEKETEDVGLTSGVSLAPVSLPRVPSPEPRLLEPSDHAS MCLAILEEIRQAKAQRKQLHDFVARGTVLSYCETLLEPECSSRVAGRPQCKQIDQSSSDQ TRNEGEAPGFHVASLSAEAGQIDLLPDERKVQATSLSADSFESLPNTETDREPWDPVQAF SHAAPAQDRKRRTGELRQFAGASEPFICHSSSSEIIEKKKDATRTPSSADPLAPDSPRSS APVEEVRRVVSKKVVAALPSQAPYDDPRVTLHELSQSVPQETAEGIPPGSQDSSPEHQEP RTLDTTYGEVSDNLLVTAQGEKTAHFESQSVTCDVQNSTSASGPKQDHVQCPEASTGFEE GRASPKQDTILPGALTRVALEAPTQQCVQCKESVGSGLTEVCRAGSKHSRPIPLPDQRPS ANPGGIGEEAPCRHPREALDGPVFSRNPEGSRTLSPSRGKESRTLPCRQPCSSQPVATHA YSSHSSTLLCFRDGDLGKEPFKAAPHTIHPPCVVPSRAYEMDETGEISRGPDVHLTHGLE PKDVNREFRLTESSTCEPSTVAAVLSRAQGCRSPSAPDVRTGSFSHSATDGSVGLIGVPE KKVAEKQASTELEAASFPAGMYSEPLRQFRDSSVGDQNAQVCQTNPEPPATTQGPHTLDL SEGSAESKLVVEPQHECLENTTRCFLEKPQFSTELRDHNRLDSQAKFVARLKHTCSPQED SPWQEEEQHRDQASGGGEGFAQGVNPLPDEDGLDGCQILDAGREEVAVAKPPVSKILSQG FKDPATVSLRQNETPQPAAQRSGHLYTGREQPAPNHRGSLPVTTIFSGPKHSRSSPTPQF SVVGSSRSLQELNLSVEPPSPTDEDTQGPNRLWNPHLRGYSSGKSVARTSLQAEDSNQKA SSRLDDGTTDHRHLKPATPPYPMPSTLSHMPTPDFTTSWMSGTLEQAQQGKREKLGVQVR PENWCSQMDKGMLHFGSSDISPYALPWRPEEPARISWKQYMSGSAVDVSCSQKPQGLTLS NVARCSSMDNGLEDQNSPFHSHLSTYANICDLSTTHSSTENAQGSNEAWEVFRGSSSIAL GDPHIPTSPEGVAPTSGHDRRPQFRGPSGEADCLRSKPPLAKGSAAGPVDEIMLLYPSEA GCPVGQTRTNTFEQGTQTLGSRRHWSSTDISFAQPEASAVSAFDLASWTSMHNLSLHLSQ LLHSTSELLGSLSQPDVARREQNTKRDIPDKAPQALMMDGSTQTTVDEGSQTDLTLPTLC LQTSEAEPQGANVILEGLGSDTSTVSQEEGDVPGVPQKREAEETAQKMAQLLYLQEESTP YKPQSPSIPSSHLRFQKAPVGQHLPSVSPSVSDAFLPPSSQPEESYCLVVSSPSPSSPHS PGLFPSTSEYPGDSRVQKKLGPTSALFVDRASSPILTLSASTQEPGLSPGSLTLSAPSTH PVEGHQKLDSSPDPVDAPRTPMDNYSQTTDELGGSQRGRSSLQRSNGRSFLELHSPHSPQ QSPKLQFSFLGQHPQQLQPRTTIGVQSRLLPPPLRHRSQRLGNSFVPEKVASPEHCPLSG REPSQWQSRTENGGESSASPGEPQRTLDRPSSWGGLQHLSPCPVSELTDTAGLRGSALGL PQACQPEELLCFSCQMCMAPEHQHHSLRDLPVHNKFSNWCGVQKGSPGGLDMTEEELGAS GDLSSEKQEQSPPQPPNDHSQDSEWSKREQIPLQVGAQNLSLSVELTEAKLHHGFGEADA LLQVLQSGTGEALAADEPVTSTWKELYARQKKAIETLRRERAERLGNFCRTRSLSPQKQL SLLPNKDLFIWDLDLPSRRREYLQQLRKDVVETTRYPESVSRSAHTPSDIELMLQDYQQA HEEAKVEIARARDQLRERTEQEKLRIHQKIISQLLKEEDKLHTLANSSSLCTSSNGSLSS GMTSGYNSSPALSGQLQFPENMGHTNLPDSRDVWIGDERGGHSAVRKNSAYSHRASLGSC CCSPSSLSSLGTCFSSSYQDLAKHVVDTSMADVMAACSDNLHNLFSCQATAGWNYQGEEQ AVQLYYKVFSPTRHGFLGAGVVSQPLSRVWAAVSDPTVWPLYYKPIQTARLHQRVTNSIS LVYLVCNTTLCALKQPRDFCCVCVEAKEGHLSVMAAQSVYDTSMPRPSRKMVRGEILPSA WILQPITVEGKEVTRVIYLAQVELGAPGFPPQLLSSFIKRQPLVIARLASFLGR h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004903.txt0000600000175000017500000001173111455416572022004 0ustar ykeyke>sp|Q8BRH4|MLL3_MOUSE Histone-lysine N-methyltransferase MLL3 OS=Mus musculus GN=Mll3 PE=2 SV=2 MSSEEDRSAEQQQPPPAPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGK STVEDEDSMDGLETTETENIVETEIKEQSVEEDAETEVDSSKQPVSALQRSVSEESANSL VSVGVEAKISEQLCAFCYCGEKSSLGQGDLKQFRVTPGLTLPWKDQPSNKDIDDNSSGTC EKIQNYAPRKQRGQRKERPPQQSAVSCVSVSTQTACEDQAGKLWDELSLVGLPDAIDVQA LFDSTGTCWAHHRCVEWSLGICQMEEPLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEK CTQMYHYPCAAGAGTFQDFSHFFLLCPEHIDQAPERSKEDANCAVCDSPGDLLDQFFCTT CGQHYHGMCLDIAVTPLKRAGWQCPECKVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQPV MKSVPTNGWKCKNCRICIECGTRSSTQWHHNCLICDTCYQQQDNLCPFCGKCYHPELQKD MLHCNMCKRWVHLECDKPTDQELDSQLKEDYICMYCKHLGAEIDPLHPGNEVEMPELPTD YASGMEIEGTEDEVVFLEQTVNKDVSDHQCRPGIVPDVQVYTEEPQKSNPLESPDTVGLI TSESSDNKMNPDLANEIAHEVDTEKTEMLSKGRHVCEEDQNEDRMEVTENIEVLPHQTIV PQEDLLLSEDSEVASKELSPPKSAPETAAPEALLSPHSERSLSCKEPLLTERVQEEMEQK ENSEFSTGCVDFEMTLAVDSCDKDSSCQGDKYVELPAEEESTFSSATDLNKADVSSSSTL CSDLPSCDMLHGYPPAFNSAAGSIMPTTYISVTPKIGMGKPAITKRKFSPGRPRSKQGAW SNHNTVSPPSWAPDTSEGREIFKPRQLSGSAIWSIKVGRGSGFPGKRRPRGAGLSGRGGR GRSKLKSGIGAVVLPGVSAADISSNKDEEENSMHNTVVLFSSSDKFTLQQDMCVVCGSFG QGAEGRLLACSQCGQCYHPYCVSIKITKVVLSKGWRCLECTVCEACGKATDPGRLLLCDD CDISYHTYCLDPPLQTVPKGGWKCKWCVWCRHCGATSAGLRCEWQNNYTQCAPCASLSSC PVCCRNYREEDLILQCRQCDRWMHAVCQNLNTEEEVENVADIGFDCSMCRPYMPVSNVPS SDCCDSSLVAQIVTKVKELDPPKTYTQDGVCLTESGMSQLQSLTVTAPRRKRTKPKLKLK IINQNSVAVLQTPPDIQSEHSRDGEMDDSREGELMDCDGKSESSPEREAGDDETKGIEGT DAIKKRKRKPYRPGIGGFMVRQRSRTGQGKAKRSVVRKDSSGSISEQLPSRDDGWREQLP DTLVDEPVSVAENTDKIKKRYRKRKNKLEETFPAYLQEAFFGKDLLDTSRQNKLSVDNLS EDAAQLSFKTGFLDPSSDPLLSSSSTSAKPGTQGTADDPLADISEVLNTDDDILGIISDD LAKSVDHSDIGPTTADASSLPQPGVSQSSRPLTEEQLDGILSPELDKMVTDGAILGKLYK IPELGGKDVEDLFTAVLSPATTQPAPLPQPPPPPQLLPMHNQDVFSRMPLMNGLIGPSPH LPHNSLPPGSGLGTFPAIAQSPYTDVRDKSPAFNAIASDPNSSWAPTTPSMEGENDTLSN AQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERA PYVQKARDNRAALRINKVQMSNDSMKRQQQQDSIDPSSRIDSDLFKDPLKQRESEHEQEW KFRQQMRQKSKQQAKIEATQKLEQVKNEQQQQQQQQQQQQQQQLASQHLLVAPGSDTPSS GAQSPLTPQAGNGNVSPAQTFHKDLFSKHLPGTPASTPSDGVFVKPQPPPPPSTPSRIPV QESLSQSQNSQPPSPQMFSPGSSHSRPPSPVDPYAKMVGTPRPPPGGHSFPRRNSVTPVE NCVPLSSVPRPIHMNETSATRPSPARDLCASSMTNSDPYAKPPDTPRPMMTDQFSKPFSL PRSPVISEQSTKGPLTTGTSDHFTKPSPRTDAFQRQRLPDPYAGPSLTPAPLGNGPFKTP LHPPPSQDPYGSVSQTSRRLSVDPYERPALTPRPVDNFSHSQSNDPYSHPPLTPHPAMTE SFTHASRAFPQPGTISRSASQDPYSQPPGTPRPLIDSYSQTSGTARSNPDPYSQPPGTPR PNTIDPYSQQPPTPRPSPQTDMFVSSVANQRHTDPYTHHLGPPRPGISVPYSQPPAVPRP RTSEGFTRPSSARPALMPNQDPFLQAAQNRVPGLPGPLIRPPDTCSQTPRPPGPGRIDTF THASSSAVRDPYDQPPVTPRPHSESFGTSQVVHDLVDRPVPGSEGNFSTSSNLPVSSQGQ QFSSVSQLPGPVPTSGGTDTQNTVNMSQADTEKLRQRQKLREIILQQQQQKKIASRQEKG PQDTAVVPHPVPLPHWQPESINQAFTRPPPPYPGSTRSPVIPPLGPRYAVFPKDQRGPYP PEVAGMGMRPHGFRFGFPGAGHGPMPSQDRFHVPQQIQGSGIPPHIRRPMSMEMPRPSNN PPLNNPVGLPQHFPPQGLPVQQHNILGQAFIELRHRAPDGRSRLPFAASPSSVIESPSHP RHGNFLPRPDFPGPRHTDPIRQPSQCLSNQLPVHPNLEQVPPSQQEQGHPAHQSSIVMRP LNHPLSGEFSEAPLSTSTPAETSPDNLEIAGQSSAGLEEKLDSDDPSVKELDVKDLEGVE VKDLDDEDLENLNLDTEDGKGDDLDTLDNLETNDPNLDDLLRSGEFDIIAYTDPELDLGD KKSMFNEELDLNVPIDDKLDNQCASVEPKTRDQGDKTMVLEDKDLPQRKSSVSSEIKTEA LSPYSKEEIQSEIKNHDDSRGDADTACSQAASAQTNHSDRGKTALLTTDQDMLEKRCNQE NAGPVVSAIQGSTPLPARDVMNSCDITGSTPVLSSLLSNEKCDDSDIRPSGSSPPSLPIS PSTHGSSLPPTLIVPPSPLLDNTVNSNVTVVPRINHAFSQGVPVNPGFIQGQSSVNHNLG TGKPTNQTVPLTNQSSTMSGPQQLMIPQTLAQQNRERPLLLEEQPLLLQDLLDQERQEQQ QQRQMQAMIRQRSEPFFPNIDFDAITDPIMKAKMVALKGINKVMAQNSLGMPPMVMSRFP FMGPSVAGTQNNDGQTLVPQAVAQDGSITHQISRPNPPNFGPGFVNDSQRKQYEEWLQET QQLLQMQQKYLEEQIGAHRKSKKALSAKQRTAKKAGREFPEEDAEQLKHVTEQQSMVQKQ LEQIRKQQKEHAELIEDYRIKQQQQQQQCALAPPILMPGVQPQPPLVPGATSLTMSQPNF PMVPQQLQHQQHTAVISGHTSPARMPSLPGWQSNSASAHLPLNPPRIQPPIAQLSLKTCT PAPGTVSSANPQNGPPPRVEFDDNNPFSESFQERERKERLREQQERQRVQLMQEVDRQRA LQQRMEMEQHCLMGAELANRTPVSQMPFYGSDRPCDFLQPPRPLQQSPQHQQQIGPVLQQ QNVQQGSVNSPPNQTFMQTNEQRQVGPPSFVPDSPSASGGSPNFHSVKPGHGNLPGSSFQ QSPLRPPFTPILPGTSPVANSNVPCGQDPAVTQGQNYSGSSQSLIQLYSDIIPEEKGKKK RTRKKKKDDDAESGKAPSTPHSDCAAPLTPGLSETTSTPAVSSPSELPQQRQQEPVEPVP VPTPNVSAGQPCIESENKLPNSEFIKETSNQQTHVNAEADKPSVETPNKTEEIKLEKAET QPSQEDTKVEEKTGNKIKDIVAGPVSSIQCPSHPVGTPTTKGDTGNELLKHLLKNKKASS LLTQKPEGTLSSDESSTKDGKLIEKQSPAEGLQTLGAQMQGGFGGGNSQLPKTDGASENK KQRSKRTQRTGEKAAPRSKKRKKDEEEKQAMYSSSDSFTHLKQQNNLSNPPTPPASLPPT PPPMACQKMANGFATTEELAGKAGVLVSHEVARALGPKPFQLPFRPQDDLLARAIAQGPK TVDVPASLPTPPHNNHEELRIQDHYGDRDTPDSFVPSSSPESVVGVEVNKYPDLSLVKEE PPEPVPSPIIPILPSISGKNSESRRNDIKTEPGTLFFTSPFGSSPNGPRSGLISVAITLH PTAAENISSVVAAFSDLLHVRIPNSYEVSNAPDVPPMGLVSSHRVNPSLEYRQHLLLRGP PPGSANPPRLATSYRLKQPNVPFPPTSNGLSGYKDSSHGPAEGASLRPQWCCHCKVVILG SGVRKSCKDLTFVNKGSRENTKRMEKDIVFCSNNCFILYSSAAQAKNSDNKESLPSLPQS PMKEPSKAFHQYSNNISTLDVHCLPQFQEKVSPPASPPISFPPAFEAAKVESKPDELKVT VKLKPRLRTVPVGLEDCRPLNKKWRGMKWKKWSIHIVIPKGTFKPPCEDEIDEFLKKLGT CLKPDPVPKDCRKCCFCHEEGDGLTDGPARLLNLDLDLWVHLNCALWSTEVYETQAGALI NVELALRRGLQMKCVFCHKTGATSGCHRFRCTNIYHFTCATKAQCMFFKDKTMLCPMHKP KGIHEQQLSYFAVFRRVYVQRDEVRQIASIVQRGERDHTFRVGSLIFHTIGQLLPQQMQA FHSPKALFPVGYEASRLYWSTRYANRRCRYLCSIEEKDGRPVFVIRIVEQGHEDLVLSDS SPKDVWDKILEPVACVRKKSEMLQLFPAYLKGEDLFGLTVSAVARIAESLPGVEACENYT FRYGRNPLMELPLAVNPTGCARSEPKMSAHVKRFVLRPHTLNSTSTSKSFQSTVTGELNA PYSKQFVHSKSSQYRRMKTEWKSNVYLARSRIQGLGLYAARDIEKHTMVIEYIGTIIRNE VANRKEKLYESQNRGVYMFRMDNDHVIDATLTGGPARYINHSCAPNCVAEVVTFERGHKI IISSNRRIQKGEELCYDYKFDFEDDQHKIPCHCGAVNCRKWMN h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003801.txt0000600000175000017500000000756111455416572022006 0ustar ykeyke>sp|Q99698|LYST_HUMAN Lysosomal-trafficking regulator OS=Homo sapiens GN=LYST PE=1 SV=3 MSTDSNSLAREFLTDVNRLCNAVVQRVEAREEEEEETHMATLGQYLVHGRGFLLLTKLNS IIDQALTCREELLTLLLSLLPLVWKIPVQEEKATDFNLPLSADIILTKEKNSSSQRSTQE KLHLEGSALSSQVSAKVNVFRKSRRQRKITHRYSVRDARKTQLSTSDSEANSDEKGIAMN KHRRPHLLHHFLTSFPKQDHPKAKLDRLATKEQTPPDAMALENSREIIPRQGSNTDILSE PAALSVISNMNNSPFDLCHVLLSLLEKVCKFDVTLNHNSPLAASVVPTLTEFLAGFGDCC SLSDNLESRVVSAGWTEEPVALIQRMLFRTVLHLLSVDVSTAEMMPENLRKNLTELLRAA LKIRICLEKQPDPFAPRQKKTLQEVQEDFVFSKYRHRALLLPELLEGVLQILICCLQSAA SNPFYFSQAMDLVQEFIQHHGFNLFETAVLQMEWLVLRDGVPPEASEHLKALINSVMKIM STVKKVKSEQLHHSMCTRKRHRRCEYSHFMHHHRDLSGLLVSAFKNQVSKNPFEETADGD VYYPERCCCIAVCAHQCLRLLQQASLSSTCVQILSGVHNIGICCCMDPKSVIIPLLHAFK LPALKNFQQHILNILNKLILDQLGGAEISPKIKKAACNICTVDSDQLAQLEETLQGNLCD AELSSSLSSPSYRFQGILPSSGSEDLLWKWDALKAYQNFVFEEDRLHSIQIANHICNLIQ KGNIVVQWKLYNYIFNPVLQRGVELAHHCQHLSVTSAQSHVCSHHNQCLPQDVLQIYVKT LPILLKSRVIRDLFLSCNGVSQIIELNCLNGIRSHSLKAFETLIISLGEQQKDASVPDID GIDIEQKELSSVHVGTSFHHQQAYSDSPQSLSKFYAGLKEAYPKRRKTVNQDVHINTINL FLCVAFLCVSKEAESDRESANDSEDTSGYDSTASEPLSHMLPCISLESLVLPSPEHMHQA ADIWSMCRWIYMLSSVFQKQFYRLGGFRVCHKLIFMIIQKLFRSHKEEQGKKEGDTSVNE NQDLNRISQPKRTMKEDLLSLAIKSDPIPSELGSLKKSADSLGKLELQHISSINVEEVSA TEAAPEEAKLFTSQESETSLQSIRLLEALLAICLHGARTSQQKMELELPNQNLSVESILF EMRDHLSQSKVIETQLAKPLFDALLRVALGNYSADFEHNDAMTEKSHQSAEELSSQPGDF SEEAEDSQCCSFKLLVEEEGYEADSESNPEDGETQDDGVDLKSETEGFSASSSPNDLLEN LTQGEIIYPEICMLELNLLSASKAKLDVLAHVFESFLKIIRQKEKNVFLLMQQGTVKNLL GGFLSILTQDDSDFQACQRVLVDLLVSLMSSRTCSEELTLLLRIFLEKSPCTKILLLGIL KIIESDTTMSPSQYLTFPLLHAPNLSNGVSSQKYPGILNSKAMGLLRRARVSRSKKEADR ESFPHRLLSSWHIAPVHLPLLGQNCWPHLSEGFSVSLWFNVECIHEAESTTEKGKKIKKR NKSLILPDSSFDGTESDRPEGAEYINPGERLIEEGCIHIISLGSKALMIQVWADPHNATL IFRVCMDSNDDMKAVLLAQVESQENIFLPSKWQHLVLTYLQQPQGKRRIHGKISIWVSGQ RKPDVTLDFMLPRKTSLSSDSNKTFCMIGHCLSSQEEFLQLAGKWDLGNLLLFNGAKVGS QEAFYLYACGPNHTSVMPCKYGKPVNDYSKYINKEILRCEQIRELFMTKKDVDIGLLIES LSVVYTTYCPAQYTIYEPVIRLKGQMKTQLSQRPFSSKEVQSILLEPHHLKNLQPTEYKT IQGILHEIGGTGIFVFLFARVVELSSCEETQALALRVILSLIKYNQQRVHELENCNGLSM IHQVLIKQKCIVGFYILKTLLEGCCGEDIIYMNENGEFKLDVDSNAIIQDVKLLEELLLD WKIWSKAEQGVWETLLAALEVLIRADHHQQMFNIKQLLKAQVVHHFLLTCQVLQEYKEGQ LTPMPREVCRSFVKIIAEVLGSPPDLELLTIIFNFLLAVHPPTNTYVCHNPTNFYFSLHI DGKIFQEKVRSIMYLRHSSSGGRSLMSPGFMVISPSGFTASPYEGENSSNIIPQQMAAHM LRSRSLPAFPTSSLLTQSQKLTGSLGCSIDRLQNIADTYVATQSKKQNSLGSSDTLKKGK EDAFISSCESAKTVCEMEAVLSAQVSVSDVPKGVLGFPVVKADHKQLGAEPRSEDDSPGD ESCPRRPDYLKGLASFQRSHSTIASLGLAFPSQNGSAAVGRWPSLVDRNTDDWENFAYSL GYEPNYNRTASAHSVTEDCLVPICCGLYELLSGVLLILPDVLLEDVMDKLIQADTLLVLV NHPSPAIQQGVIKLLDAYFARASKEQKDKFLKNRGFSLLANQLYLHRGTQELLECFIEMF FGRHIGLDEEFDLEDVRNMGLFQKWSVIPILGLIETSLYDNILLHNALLLLLQILNSCSK VADMLLDNGLLYVLCNTVAALNGLEKNIPMSEYKLLACDIQQLFIAVTIHACSSSGSQYF RVIEDLIVMLGYLQNSKNKRTQNMAVALQLRVLQAAMEFIRTTANHDSENLTDSLQSPSA PHHAVVQKRKSIAGPRKFPLAQTESLLMKMRSVANDELHVMMQRRMSQENPSQATETELA QRLQRLTVLAVNRIIYQEFNSDIIDILRTPENVTQSKTSVFQTEISEENIHHEQSSVFNP FQKEIFTYLVEGFKVSIGSSKASGSKQQWTKILWSCKETFRMQLGRLLVHILSPAHAAQE RKQIFEIVHEPNHQEILRDCLSPSLQHGAKLVLYLSELIHNHQGELTEEELGTAELLMNA LKLCGHKCIPPSASTKADLIKMIKEEQKKYETEEGVNKAAWQKTVNNNQQSLFQRLDSKS KDISKIAADITQAVSLSQGNERKKVIQHIRGMYKVDLSASRHWQELIQQLTHDRAVWYDP IYYPTSWQLDPTEGPNRERRRLQRCYLTIPNKYLLRDRQKSEDVVKPPLSYLFEDKTHSS FSSTVKDKAASESIRVNRRCISVAPSRETAGELLLGKCGMYFVEDNASDTVESSSLQGEL EPASFSWTYEEIKEVHKRWWQLRDNAVEIFLTNGRTLLLAFDNTKVRDDVYHNILTNNLP NLLEYGNITALTNLWYTGQITNFEYLTHLNKHAGRSFNDLMQYPVFPFILADYVSETLDL NDLLIYRNLSKPIAVQYKEKEDRYVDTYKYLEEEYRKGAREDDPMPPVQPYHYGSHYSNS GTVLHFLVRMPPFTKMFLAYQDQSFDIPDRTFHSTNTTWRLSSFESMTDVKELIPEFFYL PEFLVNREGFDFGVRQNGERVNHVNLPPWARNDPRLFILIHRQALESDYVSQNICQWIDL VFGYKQKGKASVQAINVFHPATYFGMDVSAVEDPVQRRALETMIKTYGQTPRQLFHMAHV SRPGAKLNIEGELPAAVGLLVQFAFRETREQVKEITYPSPLSWIKGLKWGEYVGSPSAPV PVVCFSQPHGERFGSLQALPTRAICGLSRNFCLLMTYSKEQGVRSMNSTDIQWSAILSWG YADNILRLKSKQSEPPVNFIQSSQQYQVTSCAWVPDSCQLFTGSKCGVITAYTNRFTSST PSEIEMETQIHLYGHTEEITSLFVCKPYSILISVSRDGTCIIWDLNRLCYVQSLAGHKSP VTAVSASETSGDIATVCDSAGGGSDLRLWTVNGDLVGHVHCREIICSVAFSNQPEGVSIN VIAGGLENGIVRLWSTWDLKPVREITFPKSNKPIISLTFSCDGHHLYTANSDGTVIAWCR KDQQRLKQPMFYSFLSSYAAG h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002800.txt0000600000175000017500000000562411455416572022002 0ustar ykeyke>sp|Q1ZXD6|ROCO5_DICDI Probable serine/threonine-protein kinase roco5 OS=Dictyostelium discoideum GN=roco5 PE=3 SV=1 MEVIKKEKKDKEKKDKEEKKDKEKKDKSEKKEKKDKEKKEKEKKEKKEKEKEKEKDKEKD GGLFSIVGGWVGNLTEPTPPPPPPPSSVSAQSTAEANAILLNPTTQENHKKAMDFWVTNT STTTTTTTTTSSNNIPSLVSVQNNNTSNNNINNNNKTSNTTGSNVSSSNNKETVKINVTS LDSGGNNNASGKDISNEHSPKNRKEKEKEKDKDNKEDSINESPVDENRRKLVEGFMKSLQ GCSDAIKVILDVFYQPLKKADLLSQEELKAIFSLIESISSFQQTILIDFKKYISNWNSTT QAQLHSTFLQFVGYLKLYKVYGLQYNYSLSSLCLLMFDNQRFESFINNAESKLVNEHKYS LAPLVPTSSSSSCVKPVSLSEILGSQYDQTTSQSTNNSSGSSFPAVTLRRTGHTFTGINS ANSNNNNNNSGGGSSGINNSNSVTGKFTQEYTYSNLASLLILPIHFLARFHQFFKSLIDS IAVLNPDYKPYNNLYKQIVQVVKDIVNESVNINKVISISKSIKSPTIGLFNSSDIVQNRK FLKEGILIEQFNNQRISYYTFLFSDIILFTEKIEDTSTINNNTMMAYDGSFYLLKKLERI VNIQVDDPELGFEYRKGFQIKTKESSIFYMTSSEKEKSTWFQVLSQASLKSNQNQNQNQN NLTNSYSSTVAGGRNSTIGLGGIDDFNNNNNGNNNGSNNDDGPDEFEDAKDIALFCKMII SGQRPKVELTSQMLKISDPKPLFAALASTHFVNQLIFIPLTMNDKYMQMTLGMMSLNKSI THLTLSQNSINDPCAVALGDMLRYNHSLIQMDLSENTIADKGLISLIDGILSHPSITVVI LTQNQITDTGAKHISKLLKFNQTLNALFLEDNNITQSMGAEIIDQWVSCHSTVLSRITLP SIPPEYSDRIKLKAISVTNRLDKKKKQLQVNQKSTTPSTSTSTTSSTIINNNKGLLDLGS CDYSEISLQLLNKLNMLSLDSRRISDLKELYLDHNCISSIPVSILKELKNLQILDLSNNQ LSSLPSEISEMKELKLLNVSHNNLSSLPIELGTLCKLNHLDISFNFIETINVNSLSQLVN LKVLMMQRNYFNRLPIEIFTRLKSLESFSIAGSPCFHPIKQRIYEAIAIKATKLDLSDCG LSALPIEIGSISSLIELDLTNNRIKDLPPQIGKLSSLQTLNLSNNAIESLPWQLSQLTTL KVLNITGNPISFDGASNAKISIPDVLSGDDLIGILKYLKLASTKEKPCMRMKLMLVGQEN VGKTSIAKCLKKEIIPVGKKLRQTIGLGTKKSKTPTLTEANGSIDFNAPQSINPLNTSLN ISTDGINMDDWRPPSEDQSPPVTFSIWDFAGQEVYYSTHQFFISSRSVFIVVFDMSVYNP DETSRVPYWLQCIEAFGGNSPVILVGTHLDDLPNGVDVNQITQDIHSKYFTKFPNVKFFL PVSCKSGKNINKLQNHIVKLGKAEKKLGDLFSRSYFQLENLILSEREMNTPPIITLSEFT EMAISCGIPQTSITAAADFLKELGVIVYFDDPKSGLDQFIFIDPPWLTRLMATIITSKPN FVQSGVLDQSNLHQIWKPPDFPQHLHHVLLAILQKFEIVHPLPDPKATISSSSSSPSTTQ KSLNNSGSNLKSSGSAISTSSSSTTNGNKTLHRTNSTTNTTSLLNVSRFGNGSISKGSSL SIIKKINDQSTSPSNSTTPSPNTSSNNFSDSITLVPKSSTKHLVPILLSEERPNSIEKLY DQILLKSQQQQPFLERIYQFEFLPIGFFSKLMIRTMHFTTVKEFWKNGLLVEKDDSQCLI ESIQQFNQINFKAWGKNPASLLRFIIETAEVLISGWYKLHFHFLVPCNCINCNSILISNI GSINIINSTINLSSNNNNNVNIVNMSQQQHHQQQQSPSTSTSSSSSLTSSQPSLSTPLTS SQPSLSTSQPQLSTTTTTTATTTTSSSSQSLASQQSSSQIQLTHSSSLSSMSGSISTNSL NSNVSSSSSTPSLLSPPLLNPDSTSSSNETSGDILDLDFADYYDGESVSPGGTLKGKRKK NPSKFLTLYRNTNKPKINGTTGSGSSSSIVTTAVSSSSSSSSSTSLSNTSSRQLDLSKIS HLINQQLSFGPSKTQDLRTMFLYEEIERIFLSKKFEVVCRSSITGEETIVRLDSLVPELM MSDIGPNFTLEYKDLEIIEKVGEGGFGIVYKGKLRGQLVAIKQITIDSGQAEAASEIYRE FRREVWLSNTLTHPSIVSLKGYCLDPCCIVMEYIPNGTLYSHLRKSFSSITWQLKLKIAI NIADAIKHMHGFTPKICHRDLKSPNILMLSDMNAAVVCKVSDFGETRAVVTSALGRDKLS NPIWLSPEIMRGDEYTEKADVYSFGIVLWEILTGLLPFDEYPVAHSSFMYQLEDEITNGL RPTIPQNSVCGHPDFITLITDCWQNDPLKRPTFIDIHSRLLIMSGLNPATATTTNSAKST ISTGFNSNSGATTTTKPKSSTISSGSGTTSPPQPHPQLVRKLTQNFTPIATSPTPSVIVS SVPTTTTTTTTSVATTPTVQTILAGGNITPKPSVPTAMKPNITPKPTLISSQKPPAPNPV PILKTPTPTNLSPTSISTPTTPTTPTTPTTPTTPTNSTSSNLKPTPTSKSNPSSPPQIAT TATATQTPTPSPISVLKPPRSLPQKPVGTTQTTSTPPTNQTPNPTIVTRPPLPSSLSSNS INKPPSKPLPTPGGVTSPPPPPTTSSTTPIKFNSISAGNKTIGQSSTLPSSTLKQFTANN NTSPSGSSSLPNSTVSSPSSSFLLRPTGGTISKKLPAIPK h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004513.txt0000600000175000017500000001115611455416572022002 0ustar ykeyke>sp|Q9MBF8|DYH1B_CHLRE Dynein-1-beta heavy chain, flagellar inner arm I1 complex OS=Chlamydomonas reinhardtii GN=DHC10 PE=1 SV=1 MEPGDEGKGHQLTADATCIAWVRSKLQLLKPESLGDSDGAEWLSSVWHNDVHTPVVSTFL MSVKATRMFAALDGGHEGGSSPKLVLALEVPKQFEQMVYFVRDPSKFVTRENVGSVIFFG VMRGGDPLHSLLNIMHGLYVPVVVANTTWPETVKSDFTAQMHKFMANLTETVYEVKGKTI LYIPQEDLRDPKAAAKQKDLVQRLESTIIHWTRQVKELLNQQDSVDASEQAGPLAEIEFW RERSVDLSGIRAQLDDGAVSSIVSVLEYAKSSYLAPFLSLRNLIHREAVAAEDNLKFLLC LEEPCQQLASAHPQTIPSLLPPILNCIRMVWNLSRFYNTPERLSVLLRKLSNEIINRCCS VISLPDVWSGDVDNVMVALRQSMEAGERWKELYKRTAAAVAVRSPKPWDFDISSIFAHID AFLQRCNDLLEVCEAQLQFAPRTPLPVFGGTYGPEVKKSILDIQESFQGLVQGLQALKYD ILDVKATRWHDDFNGFKGGVKDLEVMMANVIQRAFDTQPCLAARGELLEGFQTMAKRDYI RRFVEKKTVEFFALFNAEINTVKKLFDAVKRSQPKSPILPRYAGLAKYAMNLMRRLEQSH KVVDSVRYTLPQVSEAADVMQQYELAHQAIEQYISNTHNDWFSTIESSIAKELQACLLTQ DKASGGLLSMNFHKDLLSMGQEVHFWERMRLAVPLVAMEINAQREKYRVLRDNILMVVRD YNKILTALDKEERKLFHDRIRYLDRRIMPGVTKLQWTADKHALEFYYREARKFCRDADMA VGDYKTANSRLDAICRSISELVLVDVEKKKIYQHAEFANLQESHHAKIKDRLVSAVDEIR DIMASIHRVFEQDSEEVQREWVRFTQKVDRKLEDALRHVIKKSLQELSRLLNGDNKTEVM PIFHVTMVLERTNRVELRPTIQALFDTINSVARNLILVLQSVPRVALQLTDKQRRDMEDA GLPLPKPLPTLYETISADEDAVLRTIMQITSGITSIIDKVQAFLTYWEKKYRQVWEADRD AYIRRYEKAQKPLSSFEADISRYLQCIDEIRGEDGATNMRFLRIDCGPLKLTLVGHCEAW VSKFTGLLGQLAATELRTLHTYFRENKDSLMLAPSTLEQLAELVGLHRRLADERRRTEAR FEPLRDKYKLLERYEVGAKEEEAALLEGLEPAWTQFQALLDETAGKLERYKDNFREKVKS LLDTFLKDVAQLCEDFSRDAPYSSEVPTPDALDFIQASKQADEDTRKRAAEIKNGMDIFN IPQPQYKDLAAMEKDLDFLDRIWGLKDEWEQLYYGWKDGSFTDIKVEEMEEAAVRIGKNV AKLGRDIRQWTVWSSLKDTLDAFKRTMPLITDLRNPAMRPRHWQNLQDHIGVRFDPHSRD FTLDSLVALRLDQHVEFVAELSVNATKELAIENNIKAIAATWSALGLDMAEYKSTFKLRS TEEIFTSLEENIVTLSTMKASKYFIVFEKDIAYWEKTLSHISETIEIILQVQRNWMYLEN IFIGSEDIRKQLPQESQMFDAVHNNFMRLMKQLYSTANCLKACTAQGLLESFQDMNNKLE RIQKSLDNYLENKRQQFPRFYFLSSDDLLEILGQAKDPLNVQPHLKKCFEGIKKLDMHLP GEDRKQTISVGITSPDGEYLPFANPVITEGRPEEWLNRVEDAMFLTTKKHLYKVLEESKA QKKEKWVKENQGQMIITAGQIVWTHECEKALADADSARKNLKLLKKKWISYLNKLTAVTR SKLNKIERNKVVALITIEVHARDVIEKLGKSNCSSTNDFEWVSQLRFYWDREKNDCIVKQ VLSVFYYGYEYQGNNGRLVITPLTDRCYMTLGAAMFTRRGGNPLGPAGTGKTETVKDFGK ALARYVIVFNCSDGVDYKMTGKMFSGLAQTGAWACLDEFNRIEVEVLSVVATQIAAVMQA IKESKKRFLFLGQEIRLNPSCGIFVTMNPGYAGRSELPDNLKAMLRPVSMMVPDFTLIAE IMMFSEGFSSAKVLAKKMIAIMELSQQQLSKQDHYDYGLRSFVIPIARAAGSLKRLDPEG SEEVILYRTMLDLIKPKLVYLDLPLFMALLSDLFPGVELPPADGGSLRRAIEAELRESNL QIVPEFVTKIIQVFDCKVARHGNMIVGRTGSGKSEAWKCLQRALGRLRKEEPDDDRFQKV HVHTINPLALSNDELYGCFEAATHEWQDGVLARIMRTVCKDETHEQKWILFDGPVDTLWI ESMNTTLDDNKLLTLLSGERIAMTPAVSLLFEVEDLSQASPATVSRAGMIYLNVEDLGWR PFITSWLAAKQAAPGADAAIIDQVSKLVDKYMEAALEHKRLHCRELVPTDRLSCVRAFTR LWDALAVPENGVGTMPVDESAGPPGSKAAAAAAAAAAAAAPPEETSGGTGGNLVEMWFLF CLIWGIGGPLDEEGRKKFDAFMREMDTRYPSSDTVFEYFVEPKAKSWLAWETKLTGAFKP AMDQPFFKILVPTVDTVRNRFVGSALVRVSQHTLIVGNVGVGKTMIVGSLLEGLPGDRMS SMTINFSAQTSSNSLQDTIEGKLEKRTKGVFAPAGGKRLVCFIDDLNMPQKSKFGFIPPL ELLKLWVDNGFWYDRAKCEVKHIKDMQLLAAMAPPGGGRNAFSQRVQACFATLNVTAPND NQLKRIFGTILNAKLADFDDEVKPLSEPITMATIGIYRAVSKELLPTPSKSHYLFNTRDL AKIIQGMMQATKAFYNSKEEVLQLWCHECMRIIADRMWDHADKEWLVRQLDEKLGTTFST SFGTLFEAYNETVPPFVTFMRQNVDVPVYEAVRDMVALKDLLTERLEDYALEPGHSAMDL VLFRDALSHVCRIHRILGQPRGNALLVGVGGSGRKSLARLAAFVAELKCFTIEITKNYRQ TEFREDLKGLYRQAGVANKPTVFLFDETQIVYETFLEDVNNILTSGEVPNLFPKDELGSV LDELRPAAKAAGAGETADALYGFLLERVRTNLHVVLCLSPVGEAFRERCRMFPGLVNCTT IDWFTEWPADALFEVAQKQLMDVDLGSTEVKTAVCKVFVTAHQSVENTSAKMFAALKRRN YVTPTNYLETVRGYKGLLAEKRTELGEKAAKLQGGLHKLDETSVQVAAMKKVAEEKKVVV AQAKADCEELLVEIVQDKRVADEQEKQVNAEAQKIGKEAEEANIIAAQVQQELDKALPAL REAEAALDVLTKKDMSELKAYAKPPEKVEMTLNAVLTVLRRPPNWDEAKKRLSDANFMQS LKEFDKDKLDDSLLKKIGKFTANPDFTYEKINTVSAAASGMCKWVHAMETYGYVAKDVAP KRAKLKSAQDTLARKQAALALAQEQLAVVLAKVQALKDKYDTSIARKQALEEELADLEGK LERAEKLVTGLAGERVRWEASISEYNIALGCLPGDVVVAAAFMSYAGPFPSEYRDELVKH TWLPQVKALNIPASEHFDFALFLANPAMVRDWNIQGLPSDSFSTENGVMVTRGRRWPLMI DPQGQANKWIKNMEGRGGRLKVLNLQMSDMARQIENAIQFGQPVLMQDILQEIDPILEPV LAKSFIKRGNQTLIKLGDKEVDYNFDFRLYLTTKLANPLYTPEISTKVMIVNFAVKEQGL EAQLLATVVKNERPDLDKQKNDLVVKVAAGKRTQAELEDTILHLLSTATGSLLDNVTLIN TLDQSKTTWEEVNASLAVAEETQKKIEAASQLYRPCSVRASVLYFVLNDLSTIDPMYQFS LDAYNDLFLLSIKNSPKNDNLAERIKSLNDFHTYAVYKYTSRGLFERHKLLLSLQMCVRI LQTANQVNTEEWQFFLRGGTVLDRSSQPNNPSQEWISEEAWDNITELDALPNFKGVVSSF ESNLGEWEAWYRKGDPEASELPAEWESKCNELQRLILVRCLRPDRVIFAATTYVSNALGR KYVEPPVLDLAETLKDSTALSPLIFVLSAGVDPTDNLRKLATEKGMTSRFFTVALGQGQA PTATRLIEDGLREGNWVFLANCHLMTSWLPTLDKIIEGFETKQPHENFRLWLSSNPSPSF PIAILQRGIKMTTEPPKGLRANLLRLYNSVSDASYAQCKTQIKYQKLLFALTYFHSVLLE RRKFRTLGFNIPYDFNDTDFSVSDDLLKSYLDSYEQTPWDALKYLIAEANYGGRVTDELD RRVLASYLNKFYCEDALAVPGYLLSPLSTYYVPENGPLQSFKDYILTLPAGDRPEAFGQH PNAEISYLIEDSKVLLDSLLSLQPRTEGAAGGAGTRREDVVMAIATDLLDQVPQPFNLEE VMKAKADDPSALHVVLFQEVERYNALLVAVRRSCVELQRGIKGLVVMSADLDLIFESLYA AKVPAAWLKTYPSLKPLGPWTRDLLQRIEQLATWVEETYPRVYWLSGFTYPTGFLTAVLQ TTARKASVPIDTLSFEFSIINLDEREINAPPKEGVYIKGLFLEGAGWDFENGCLCEPNPM ELIVPMPILLFRPVENKKRTAKGIYTCPLYLYPLRTGTRERPSFMINVDLRSGSADPDHW IMRGTALLLSLAT h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000300.txt0000600000175000017500000000062711455416572021771 0ustar ykeyke>sp|Q4V8X4|ACBD6_DANRE Acyl-CoA-binding domain-containing protein 6 OS=Danio rerio GN=acbd6 PE=2 SV=1 MASRSPSSSPDSATGSGTDPARPDTGEPLGGGSDSDSDFGLGKFDCSAGDASARLEGADL ENEFESAADRVRDLVQTASREQLLYLYARFKQVKVGKCNTSKPGFFDFEGQRKWSAWKQL GDMSAEQAMQEYVTCVHALDPEGSQKSSERRGGEKRTGFGGPAVSSLYQEEKIREEDKNI FDYCRENNIEHVSKAISSKTVDVNTRDEEGRALLHWACDRGHKDLVSLLLQNNADINSQD DEGQTALHYASACEFAEIVELLLKAGADPSIKDQEGSLPEEVTESSAISSLLRQYTAPKG h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004829.txt0000600000175000017500000001162411455416572022014 0ustar ykeyke>sp|Q9NR09|BIRC6_HUMAN Baculoviral IAP repeat-containing protein 6 OS=Homo sapiens GN=BIRC6 PE=1 SV=1 MAAAAAAASGPGCSSAAGAGAAGVSEWLVLRDGCMHCDADGLHSLSYHPALNAILAVTSR GTIKVIDGTSGATLQASALSAKPGGQVKCQYISAVDKVIFVDDYAVGCRKDLNGILLLDT ALQTPVSKQDDVVQLELPVTEAQQLLSACLEKVDISSTEGYDLFITQLKDGLKNTSHETA ANHKVAKWATVTFHLPHHVLKSIASAIVNELKKINQNVAALPVASSVMDRLSYLLPSARP ELGVGPGRSVDRSLMYSEANRRETFTSWPHVGYRWAQPDPMAQAGFYHQPASSGDDRAMC FTCSVCLVCWEPTDEPWSEHERHSPNCPFVKGEHTQNVPLSVTLATSPAQFPCTDGTDRI SCFGSGSCPHFLAAATKRGKICIWDVSKLMKVHLKFEINAYDPAIVQQLILSGDPSSGVD SRRPTLAWLEDSSSCSDIPKLEGDSDDLLEDSDSEEHSRSDSVTGHTSQKEAMEVSLDIT ALSILQQPEKLQWEIVANVLEDTVKDLEELGANPCLTNSKSEKTKEKHQEQHNIPFPCLL AGGLLTYKSPATSPISSNSHRSLDGLSRTQGESISEQGSTDNESCTNSELNSPLVRRTLP VLLLYSIKESDEKAGKIFSQMNNIMSKSLHDDGFTVPQIIEMELDSQEQLLLQDPPVTYI QQFADAAANLTSPDSEKWNSVFPKPGTLVQCLRLPKFAEEENLCIDSITPCADGIHLLVG LRTCPVESLSAINQVEALNNLNKLNSALCNRRKGELESNLAVVNGANISVIQHESPADVQ TPLIIQPEQRNVSGGYLVLYKMNYATRIVTLEEEPIKIQHIKDPQDTITSLILLPPDILD NREDDCEEPIEDMQLTSKNGFEREKTSDISTLGHLVITTQGGYVKILDLSNFEILAKVEP PKKEGTEEQDTFVSVIYCSGTDRLCACTKGGELHFLQIGGTCDDIDEADILVDGSLSKGI EPSSEGSKPLSNPSSPGISGVDLLVDQPFTLEILTSLVELTRFETLTPRFSATVPPCWVE VQQEQQQRRHPQHLHQQHHGDAAQHTRTWKLQTDSNSWDEHVFELVLPKACMVGHVDFKF VLNSNITNIPQIQVTLLKNKAPGLGKVNALNIEVEQNGKPSLVDLNEEMQHMDVEESQCL RLCPFLEDHKEDILCGPVWLASGLDLSGHAGMLTLTSPKLVKGMAGGKYRSFLIHVKAVN ERGTEEICNGGMRPVVRLPSLKHQSNKGYSLASLLAKVAAGKEKSSNVKNENTSGTRKSE NLRGCDLLQEVSVTIRRFKKTSISKERVQRCAMLQFSEFHEKLLNTLCRKTDDGQITEHA QSLVLDTLCWLAGVHSNGPGSSKEGNENLLSKTRKFLSDIVRVCFFEAGRSIAHKCARFL ALCISNGKCDPCQPAFGPVLLKALLDNMSFLPAATTGGSVYWYFVLLNYVKDEDLAGCST ACASLLTAVSRQLQDRLTPMEALLQTRYGLYSSPFDPVLFDLEMSGSSCKNVYNSSIGVQ SDEIDLSDVLSGNGKVSSCTAAEGSFTSLTGLLEVEPLHFTCVSTSDGTRIERDDAMSSF GVTPAVGGLSSGTVGEASTALSSAAQVALQSLSHAMASAEQQLQVLQEKQQQLLKLQQQK AKLEAKLHQTTAAAAAAASAVGPVHNSVPSNPVAAPGFFIHPSDVIPPTPKTTPLFMTPP LTPPNEAVSVVINAELAQLFPGSVIDPPAVNLAAHNKNSNKSRMNPLGSGLALAISHASH FLQPPPHQSIIIERMHSGARRFVTLDFGRPILLTDVLIPTCGDLASLSIDIWTLGEEVDG RRLVVATDISTHSLILHDLIPPPVCRFMKITVIGRYGSTNARAKIPLGFYYGHTYILPWE SELKLMHDPLKGEGESANQPEIDQHLAMMVALQEDIQCRYNLACHRLETLLQSIDLPPLN SANNAQYFLRKPDKAVEEDSRVFSAYQDCIQLQLQLNLAHNAVQRLKVALGASRKMLSET SNPEDLIQTSSTEQLRTIIRYLLDTLLSLLHASNGHSVPAVLQSTFHAQACEELFKHLCI SGTPKIRLHTGLLLVQLCGGERWWGQFLSNVLQELYNSEQLLIFPQDRVFMLLSCIGQRS LSNSGVLESLLNLLDNLLSPLQPQLPMHRRTEGVLDIPMISWVVMLVSRLLDYVATVEDE AAAAKKPLNGNQWSFINNNLHTQSLNRSSKGSSSLDRLYSRKIRKQLVHHKQQLNLLKAK QKALVEQMEKEKIQSNKGSSYKLLVEQAKLKQATSKHFKDLIRLRRTAEWSRSNLDTEVT TAKESPEIEPLPFTLAHERCISVVQKLVLFLLSMDFTCHADLLLFVCKVLARIANATRPT IHLCEIVNEPQLERLLLLLVGTDFNRGDISWGGAWAQYSLTCMLQDILAGELLAPVAAEA MEEGTVGDDVGATAGDSDDSLQQSSVQLLETIDEPLTHDITGAPPLSSLEKDKEIDLELL QDLMEVDIDPLDIDLEKDPLAAKVFKPISSTWYDYWGADYGTYNYNPYIGGLGIPVAKPP ANTEKNGSQTVSVSVSQALDARLEVGLEQQAELMLKMMSTLEADSILQALTNTSPTLSQS PTGTDDSLLGGLQAANQTSQLIIQLSSVPMLNVCFNKLFSMLQVHHVQLESLLQLWLTLS LNSSSSGNKENGADIFLYNANRIPVISLNQASITSFLTVLAWYPNTLLRTWCLVLHSLTL MTNMQLNSGSSSAIGTQESTAHLLVSDPNLIHVLVKFLSGTSPHGTNQHSPQVGPTATQA MQEFLTRLQVHLSSTCPQIFSEFLLKLIHILSTERGAFQTGQGPLDAQVKLLEFTLEQNF EVVSVSTISAVIESVTFLVHHYITCSDKVMSRSGSDSSVGARACFGGLFANLIRPGDAKA VCGEMTRDQLMFDLLKLVNILVQLPLSGNREYSARVSVTTNTTDSVSDEEKVSGGKDGNG SSTSVQGSPAYVADLVLANQQIMSQILSALGLCNSSAMAMIIGASGLHLTKHENFHGGLD AISVGDGLFTILTTLSKKASTVHMMLQPILTYMACGYMGRQGSLATCQLSEPLLWFILRV LDTSDALKAFHDMGGVQLICNNMVTSTRAIVNTARSMVSTIMKFLDSGPNKAVDSTLKTR ILASEPDNAEGIHNFAPLGTITSSSPTAQPAEVLLQATPPHRRARSAAWSYIFLPEEAWC DLTIHLPAAVLLKEIHIQPHLASLATCPSSVSVEVSADGVNMLPLSTPVVTSGLTYIKIQ LVKAEVASAVCLRLHRPRDASTLGLSQIKLLGLTAFGTTSSATVNNPFLPSEDQVSKTSI GWLRLLHHCLTHISDLEGMMASAAAPTANLLQTCAALLMSPYCGMHSPNIEVVLVKIGLQ STRIGLKLIDILLRNCAASGSDPTDLNSPLLFGRLNGLSSDSTIDILYQLGTTQDPGTKD RIQALLKWVSDSARVAAMKRSGRMNYMCPNSSTVEYGLLMPSPSHLHCVAAILWHSYELL VEYDLPALLDQELFELLFNWSMSLPCNMVLKKAVDSLLCSMCHVHPNYFSLLMGWMGITP PPVQCHHRLSMTDDSKKQDLSSSLTDDSKNAQAPLALTESHLATLASSSQSPEAIKQLLD SGLPSLLVRSLASFCFSHISSSESIAQSIDISQDKLRRHHVPQQCNKMPITADLVAPILR FLTEVGNSHIMKDWLGGSEVNPLWTALLFLLCHSGSTSGSHNLGAQQTSARSASLSSAAT TGLTTQQRTAIENATVAFFLQCISCHPNNQKLMAQVLCELFQTSPQRGNLPTSGNISGFI RRLFLQLMLEDEKVTMFLQSPCPLYKGRINATSHVIQHPMYGAGHKFRTLHLPVSTTLSD VLDRVSDTPSITAKLISEQKDDKEKKNHEEKEKVKAENGFQDNYSVVVASGLKSQSKRAV SATPPRPPSRRGRTIPDKIGSTSGAEAANKIITVPVFHLFHKLLAGQPLPAEMTLAQLLT LLYDRKLPQGYRSIDLTVKLGSRVITDPSLSKTDSYKRLHPEKDHGDLLASCPEDEALTP GDECMDGILDESLLETCPIQSPLQVFAGMGGLALIAERLPMLYPEVIQQVSAPVVTSTTQ EKPKDSDQFEWVTIEQSGELVYEAPETVAAEPPPIKSAVQTMSPIPAHSLAAFGLFLRLP GYAEVLLKERKHAQCLLRLVLGVTDDGEGSHILQSPSANVLPTLPFHVLRSLFSTTPLTT DDGVLLRRMALEIGALHLILVCLSALSHHSPRVPNSSVNQTEPQVSSSHNPTSTEEQQLY WAKGTGFGTGSTASGWDVEQALTKQRLEEEHVTCLLQVLASYINPVSSAVNGEAQSSHET RGQNSNALPSVLLELLSQSCLIPAMSSYLRNDSVLDMARHVPLYRALLELLRAIASCAAM VPLLLPLSTENGEEEEEQSECQTSVGTLLAKMKTCVDTYTNRLRSKRENVKTGVKPDASD QEPEGLTLLVPDIQKTAEIVYAATTSLRQANQEKKLGEYSKKAAMKPKPLSVLKSLEEKY VAVMKKLQFDTFEMVSEDEDGKLGFKVNYHYMSQVKNANDANSAARARRLAQEAVTLSTS LPLSSSSSVFVRCDEERLDIMKVLITGPADTPYANGCFEFDVYFPQDYPSSPPLVNLETT GGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWNPQTSSFLQVLVSVQSLILVAEPYFNE PGYERSRGTPSGTQSSREYDGNIRQATVKWAMLEQIRNPSPCFKEVIHKHFYLKRVEIMA QCEEWIADIQQYSSDKRVGRTMSHHAAALKRHTAQLREELLKLPCPEGLDPDTDDAPEVC RATTGAEETLMHDQVKPSSSKELPSDFQL h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002601.txt0000600000175000017500000000530211455416572021772 0ustar ykeyke>sp|Q9C0D2|K1731_HUMAN Leucine-rich repeat-containing protein KIAA1731 OS=Homo sapiens GN=KIAA1731 PE=2 SV=3 MKRKVVNTHKLRLSPNEEAFILKEDYERRRKLRLLQVREQERDIALQIREDIKQRRNQQF TRLAEELRAEWEESQTQKIQNLEKLYLASLRSMGEGHRQAKENEPDLDALAQRAAERKRK ADLRHKEALKVQKNQKEILLKQKTWHIKARKEALLVEKERSAKITSLPPPPPTLFENIEV KRISAVKTNSSTYHHLHTFVNRETDTKRPDARLAAEEEAKRLEELQKQAAQERMERFEKA HVRGFQAMKKIHLAQNQEKLMKELKQLQQEDLARRRQTVAQMPPQLVELPYKRSEMKEDW QRELEFAFEDMYNADRKVKGNLILHLEPEPLPTVTNQIQDEELDLSMEQENLGAAEDLPV TEAEICSSETDVPLVMKTQQIPSKVLFKKLLNKIRSQKSLWTIKSMSEDESEMITTVSEI ESKAPTVESGTIASKERTLSSGQEQVVESDTLTIESGPLASEDKPLSCGTNSGKEQEINE TLPITTVAQSSVLLHPQEAAARIRMSARQKQIMEIEEQKQKQLELLEQIEQQKLRLETDC FRAQLEEEKRKKTQPTGVGIAPASCPVISDEDSHRQMIRNYQHQLLQQNRLHRQSVETAR KQLLEYQTMLKGRCPSVSAPSLITDSVISVPSWKSERPTAISEHWDQGQRLKLSPNKYQP IQPIQTSKLEQDHFQVARQNHFPQRQVETTETLRASDILTNQALESQEHLRQFSQTETQQ RDYKLVPKDSETLSRALSHDRQLISQDARKISETFGATTFQSLESQQLFSENSENISYHL TEPSSFVPLVPQHSFSSLPVKVESGKIQEPFSAMSKSTVSTSHSIISQMHDRPLLPSENI TAQQGNMKALQEQLDLQKKVLQATQEAQEQLLLCKQKEVEQQTGLSVFLPLVTPDSSALL PSAKADLGRIQESSPTKNNIAVSSDHHVISQLQDKRLSLSQPILSQQNNFKFLQEQLNIQ KDSLQARREAQEVLYVHKQSELDRRVCSEQAEPSFPFQVAQHTFTSLPSADTKSGKIQEQ HSSKSEKGLVSCQSDIPISQDGSLSFLQQFLPLHDSLKLLQEQLTKQRDTLQARHEAQVE LLLHRQRDLGDSKSGLVSSSSSPVVVQHSVASQASAKAEPRRIQELYLSEKENVGPSCHL IIPTFQDKSLSFPQHSLAQQENLTILQEQSQIQRVILGAKEGTQEFVHTESELEKRISSE QTGTSSSLSQVDESERFQECISIKSDSTIPLSHPKIPRCQERLLRVSQHMLPLQDNLEEH QAWLDTEKEAFHFSQKTQENTSSEQTGSSSFIPQLVQLSFTSLASAESGTILEPLFTESE SKIFSSHLQIPQLQDRLLRISQLIQPQQDNLKALQEQLATQREAIILARQEAREELLLHQ SEWEGRISPEQVDTSSLPLVPQHSFASLPLNESERNQEPCSINSDNIVSSGHSEIPTLPD GLLGLSHLVLPQQDNLIALEEHLHAQTDFLPSIEKTQKELVLSKPCKFEEKVSSEHFIQS HHGDLQALQQQLDTQKKAIRSIQEVQEELLLQRLSELEKRVSSEQVCSSSFVSQVPVADS ERTQKSFPTKSNDTLPSSHREIPRLQDRLLSLSKPILPQQDNMTAQLDAQREVMYSYEKP QEELSLNKQRKLNKSESAEHTIPSLFLPKETEHSFIPLPFAEAKPKSTCELYSSQNEHAA PPSNPVIPGFQDRLLSFSQSVLTQQDNLGLQKQLDLQREVLHYSQKAQEKLLVQRQTALQ QQIQKHEETLKDFFKDSQISKPTVENDLKTQKMGQLRDWFPNTQDLAGNDQENIRHADRN NSDDNHLASEDTSAKQSGEHLEKDLGRRSSKPPVAKVKCGLDLNQHELSAIQEVESPAIG RTSILGKPGIYEDRDPLRVSISREQSFFGSPLAHDPFSCLQLVGQENVCGDDYDEAVKLK ESVVENHAVLSYAVEEEHAYLGPTVKPDDKAKTLSYEPLSSATVSTGSLLSYENTDLSLT DPESFSEHMDDSKQESTTSKEEETNIISSIVPSTQDIYQRQNSSDVHKSLLPAVDETTCG HTHFQQMIDKYINEANLIPEKTDLQELEHIFPNLHHQLFKPLEPHPDFDLSSSSSGISPD NRDFYQRSDSSSESHCATGLSKSTVYFTALRRTSMHSSLNTSPNQQPDTNLAHVGAHSFA TENIIGGSEQCFEQLQPEYSSQEESQHADLPSIFSIEARDSSQGMKNQNYPSEEHTEILQ NKKKIVHFQLSIGNLSSVYSSSDEANVFDQLNVQHSTPCGSNSSECSTKHQLESRKESMG FEELSKRGVVTMLQSQGLIEDNKNETCRVLDINPQVEETDSRLCVRTVEMGTSIQAPYSL TTQNEKYFENSAETDIPKITKKLSQLGESELFASSGSFSLQSSIPVWETETGHGIMEEPE LTLISTTDTSIAEMDFANLTLEEKSENEAKCFFQVSVFLPLVSATEASDYPAVSELSIEK PRTASTETPRRLTPVPGSLQEAFIKRKKSFMERSHQRQKEIRNKIHVSENSQIKTVKEKP SISSSVSRLKGVNKVRASFPEDRKTTQALRHQRGLRLYNQLAEVKQQKEEKTKQEAYAQN RARAKEFHKKTLEKLRAKNTC h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002100.txt0000600000175000017500000000426311455416572021771 0ustar ykeyke>sp|Q1E702|ATG2_COCIM Autophagy-related protein 2 OS=Coccidioides immitis GN=ATG2 PE=3 SV=1 MPFSLPSFAQKLVLRYALSRLGLVDTDTLDLATLGITWGQRSTFELRNVGLKLEKLSAHL PPYCTLTKGSVSLLRVTVPANLHNSSIIVEVDGVDARVRLLPDKPEQNAPPTRSKGTAED EGQDGHSVLPSTADLAQSFLESEPKEETEELQAAILSQSQYPEHLDAQSDDGEEDLGLYD GLSLPAFIAGFLKGVIDRLQLNIANVSLRVDTEVQRDGVLKDETQDPISGLFTIQEIAID STATSASEDSRLKIGKRMVSLSGIHAMIMSDAEVFSNYSRFNAPDIPSTVHSKSTHTPLR PRSPQPSSSGSDSCGDMSRSTILDPSSMYGSRLTVDSHGDESRHLESSVYSTTGRFSDAD SDDENDLEFYSQATTGMLDSHYDERLLDNPAYLDEALKSQFDDHLEDSTIFPKDCPSTPV RDQTPRPHVSKSPSSSPEHYMYHSVHESNFPVGGGIRDNEPDSATSARGKTPDCQTEQES PSTSKICPAVSQPEDLSASRIFTHEEAQSMYMSAMSQSSTTSFDPDMPGAWGSSKRIDTS DPDQKEQPLSGDTDTEAKGASHDFDTSQNSPEAQTGEDDERESVHNSPQYISGVVKEILA IDRIIIWLPSVDSQDSEEIPKTDIDSKPVDPMVESTITLADSVTPDLLANTRSRLAQSAF RRGSVSSIVSSRHLPISRTKPTTQKHEDFDGLNDPQTTRAVEIDITSLTAKLDIASGWLL VKIGQRITDVSTSTSKQTKISEAASEESSPSFFRLNLTSCSLKFLERVPAQPYPLSSAPS LSQLQSGIPIEETILHLTLSGTSIDFAAIGNTTKLRLDVMKFVLGHMSYDIISFDESLRM RESTRDVTSPGQKDISLRVIKSSESTTVNLTTLPICLSLDLQELDETLGWFGGLSTVLEL GSSIASASTVKGEQPCSPPRPRRGVHFADPVPPSSPSTTNHAALKANCRIGGIVLRVIGE HCTVQLGTTAAKLVSRFEGIALQIDKASVGGPHLRKEPSPSPPSLDFENIRFEYLYGPKE VDLDRLLGLLTPSKDKFDEDDDIMLDTLFRQRRQGAVLRLTVGHADFAVPNPTALQPLSH LGEELAKLATVAKYLPQDDRPGILILALVREFEGRVHVNNEAGDITIISHNLEAGYVTFP SLLATRISTVTVVRNGSEELVAEVIPEDTEEARTHDPLPMIMARFIADEMEPTVKIKLYN VRVEYTVPSITAFLGLNNQMAAEDVAANMAQSVLNLADLKAHHEPGSDLSERDSIGSGDD RSAMLPRLSVGMKDCGIGLNPRKSPAKALVIFTRASFSGALHETKPSEALLDIRKASVMI IDNVENLGSAENYRHRMSSGARSGQIQHLQSIGFVPVCDISSASVALKVMQLDVEGEKSL DIEVRDDLLVLETCADSTQTLISILSGLAPLSPPITERKYRTEVIRIEDMLNSLSGDAFA TDIVPDSDYEVEGENDGQDGDGAEEIEYVSVFYPSHGDSGPQGRGATTPRFGNEGSASAG TSRILGSFHSEAQMSSSIPELEFQEDHFAKQSAVGDTAHRWDSSRNTYTLATEVKLRDSP LRIRVRDVHVIWNLYDGYDWQRTRDTISKAVRDVQAKAAEKFARRPGNRLSADFEEDEES VIGDFLFNSVYIGIPANRDPRELSHDINRNIDDLASETMSFATSTTVTGLQNQVPGTKRE KLRLARSKHHKMTFELKGISADLIVFPPHSGETQSSLDIRVEDLEIFDHIPTSTWKKFAT YMRDVGEREIGTSMVHLEILNVKPVPDLAASEVVLKATVLPLRLHVDQDALDFLSRFFEF KDDSAPSEPSPEDVPFLQRAEVNAIRVRLDFKPKRVDYAGLRSGRTTEFMNFFVLDEADM VLQHVIIYGVSGFDRLGRTLNDIWMPDIKANQLPTVLAGIAPVRSLVNIGGGVKDLVLVP MREYKKDGRIVRSIQKGAVQFAKTTTNELLRFGAKLAIGTQTALQSAEDFLNSPRGSPSR PSTSDGRWDDNGVDEGERPRISLYADQPLGVAQGLRGAYSSLERDILMTRDAIVAMPSEV LESGSATEAARRLLGRTPTVVLRPAIGASKAVSQTLLGVSNALDPKNRRKIDDKYKKHKV h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001600.txt0000600000175000017500000000333211455416572021771 0ustar ykeyke>sp|Q811B3|ATS12_MOUSE A disintegrin and metalloproteinase with thrombospondin motifs 12 OS=Mus musculus GN=Adamts12 PE=1 SV=1 MPCARGSWLAKLSIVAQLINFGAFCHGRQTQPWPVRFPDPRQEHFIKSLPEYHIVSPVQV DAGGHVLSYGLHHPVTSSRKKRAAGGSGDQLYYRISHEEKDLFFNLTVNWEFLSNGYVVE KRYGNLSHVKMVASSGQPCHLRGTVLQQGTTVGIGTAALSACQGLTGFFHLPHGDFFIEP VKKHPLTEEGSYPHVVYRRQSIRAPETKEPICGLKDSLDNSVKQELQREKWERKTLRSRS LSRRSISKERWVETLVVADTKTVEYHGSENVESYILTIMNMVTGLFHSPSIGNLVHIVVV RLILLEEEEQGLKIVHHAEKTLSSFCKWQKSINPKSDLNPVHHDVAVLITRKDICAGVNR PCETLGLSQLSGMCQPHRSCNINEDSGLPLAFTIAHELGHSFGIQHDGKENDCEPVGRHP YIMSQQIQYDPTPLTWSKCSKEYITRFLDRGRGFCLDDIPSKKGLKSNVIAPGVIYDVHH QCQLQYGPNATFCQEVENVCQTLWCSVKGFCRSKLDAAADGTRCGEKKWCMAGKCITVGK KPESIPGGWGRWSPWSHCSRTCGAGAQSAERLCNNPEPKFGGKYCTGERKRYRLCNVHPC RSDTPTFRQMQCSEFDTVPYKNQFYRWFPVFNAAHPCELYCRPIDEQFSERMLEAVIDGT PCFEGGNSRNVCINGICKRVGCDYEIDSNATEDRCGVCLGDGSACQTVKKLFRQKEGSGY VDIGLIPKGARDIRVMEIKAAGNFLAIRSEDPEKYYLNGGFIIQWNGNYKLAGTVFQYDR KGDLEKLIAPGPTNESVWLQLLFQVTNPGIKYEYTVRKDGLDNDVEKLLYFWQFGRWTEC SVTCGTGIRRQAAHCVKKGHGIVKTTFCNPETQPSVRQKKCHEKDCPPRWWAGEWEACST TCGPYGEKKRTVLCIQTMGSDEQALPATDCQHLLKPKALVSCNRDILCPSDWTVGNWSEC SVSCGGGVRIRSVTCAKNLNEPCDKTRKPNSRALCGLQQCPFSRRVLKPHKDIAPSGKNQ STAEHDPFKPIPAPTSRPTPLSTPTVPESMSTSTPTINSLGSTIASQEDANGMGWQNNST QAEEGSHFPTSSGSTSQVPVTSWSLSIQPDDENVSSSAIGPTSEGDFWATTTSDSGLSSS DAMTWQVTPFYSTMTTDPEVEIHSGSGEDSDQPLNKDKSNSVIWNKIGVPEHDAPMETDA ELPLGPPPTSYMGEEPSWPPFSTKMEGSLPAWSFKNETPRDDGMIAEKSRKIPLPLAGDH HPATSEKLENHDKLALPNTTNPTQGFGPVLTEEDASNLIAEGFLLNASDYKHLMKDHSPA YWIVGNWSKCSTTCGLGAYWRSVECSSGVDADCTTIQRPDPAKKCHLRPCAGWRVGNWSK CSRNCSGGFKIREVQCMDSLDHHRSLRPFHCQFLAGAPPPLSMSCNLEPCGEWQVEPWSQ CSRSCGGGVQERGVSCPGGLCDWTKRPATTVPCNRHLCCHWATGNWELCNTSCGGGSQKR TIHCIPSENSTTEDQDQCLCDHQVKPPEFQTCNQQACRKSADLTCLKDRLSISFCQTLKS MRKCSVPSVRAQCCLSCPQAPSIHTQRQRKQQLLQNHDML h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000400.txt0000600000175000017500000000105711455416572021770 0ustar ykeyke>sp|Q52813|AAPQ_RHIL3 General L-amino acid transport system permease protein aapQ OS=Rhizobium leguminosarum bv. viciae (strain 3841) GN=aapQ PE=3 SV=1 MTHEAVDTTPLHGTGWSFRSAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNT ASGFGFLRGRAGFEIGQSLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIG RLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLA FPKPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVF VVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQS EAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTIL NQSGQAIEIVCIWGIVYLSLSILTSLFMNWFNAKMALVER h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001700.txt0000600000175000017500000000342611455416572021776 0ustar ykeyke>sp|Q03376|BAR3_CHITE Balbiani ring protein 3 OS=Chironomus tentans GN=BR3 PE=2 SV=1 MKTLSSLLLVLAVNVLLIQASPDPDNRCPARKYWNERKQACVCKRENRCYPIGAIFDPES CTFSMCQSKGCSAKQIFNKDKCACECRNDQPKDGCGAGRYWCNQDCSCKCSTPMSAGGCS GSQIWCEKSCACVCPNADKCTAPQVWNKDTCCCGCPVNMQEPADGCTKPLIWDKVDCRCE CPLKKDCGKNRDWSDSSCSCECKGDGKCQGSKIWCKNNCRCICPTAEPAGGCSAPLKWDD DKCSCACPAKMEEKKEKCVESGKIWNPNTCECGCAQLNCPDNKKANKETCQCECKEVKKC NGGQVFCKDSCSCVCPGGDKDKTCTAPQVYDGVACSCSCPVNMQKPADGCPRPQKWDKEE CRCECPVKHDCKNGKVWDETICQCICPRDAPVCTAGKERCGESCECKCINREPKEGCAKP LVWNENTCKCVCPADKQMSPGGCGSGKSFNKLTCQCECDQSASKCGLKRWNADTCKCECQ PGMPPEGCGKQTWISDKCKCECSPTITCQAPQILDLNTCECKCPVNMLAQKEKCKSPRQW TDSKCLCECSTTPATCEGKQTWCGEACQCICPGGDKNCGNKKFFDKPSCECKCKNNPTCT SPQVWDADDCECKCPKDKQKPQGGCDGGQKWNDRVCSCGCPVPRPDCTNGQIYNINTCAC GCGIDKPSCPKQQIYNWKTCDCECPNGMKEPVGGCGAKTWLDDECQCDCVPGKPKGGCTG AQKWCDKTCKCKCEKEMPTGGCENNKKWCDETCDCVCPQKNTCIAPKVWDAKTCSCICVN PPKCNSPQVLKDTCCCGCQNVKSCKAPQKFIENICDCACPNKKQCKAPLVWSDEFCDCVC PNSASMKTCLSPKEWNKVTCTCDCNPPKPDCCPGTQKWMDDKCKCGCPNAQTDCAGGKKF NDFTCSCGCPSGKLDCTGNTKWSAETCTCGCGDVNRNCGNLKNFNDNLCQCECKNKQEMA NCKSPRTWNYDTCKCVCKNADDSDDCVKPQIWLDDQCKCGCPASAQMTCPANKRFIEKSC SCECKSPMPSPIPQGKKWNEDKCVVECANVKTCEGPQRWCDNQCKCICPQVNTKCSDKQK FIESKCECGCETQTQCKDGFRWSNLECGCLCDDKKCPGKQVFDKNTCQCKCPNQKPGDTC GNGKDFCPLDCSCKCKNPKPANGCTGVQEWNEEKCQCECPKDKPKKQCPGGQDWNNHQCQ CGCPTPAPTCSNNQKYSNVSCSCGCNPGKPKNGCPGNQIWCDNTCRCVCPKNMEKPADNC KTKWWNDEMCQCVCKPGCPEGGCKGVMKWNANTCSCECPADKAKPASCGDKKSWNDDSCS CQCKSKMPCGGCPPNQQWNEKDCECKCSATGNCPAGQTWNSQTCQCSCPATGKCTGAQVW CSKACKCVCPAQKKCDSPKTWDENSCSCQCPKNMRPPTGGCNAGRTWDDATCSEKCAATP KCDSPKVFDPTTCGCKCGNKPNKLDAGRTWDEQKCKMTCDLPAIPCCHYEGQVYDSNTCK CGCPKEETCKQGFSFSPKSGCKCILECNKKDPGCGAKKIWCQETCKCECASEPPRMGCGP NRYWDKEDCACQCLKTKVCTDSDFSFFSHDTCDCECSNAKDFILNCNQKLNKVSCQPQCI QRPPPEGCAEKFGEFFSWDPKACECKCIEQKTTVKGRVFDKATCNFKCTNEPKTNPKCAN TAESWDSQICACKVCSTCKH h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000500.txt0000600000175000017500000000122011455416572021761 0ustar ykeyke>sp|Q28647|2A5B_RABIT Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform OS=Oryctolagus cuniculus GN=PPP2R5B PE=2 SV=1 METKLPPASTPTSPSSPGLSPVPPADKVDGFSRRSLRRARPRRSHSSSQFRYQSNQQELT PLPLLKDVPASELHDLLSRKLAQCGVMFDFLDCVADLKGKEVKRAALNELVECVGSTRGV LIEPVYPDIIRMISVNIFRTLPPSENPEFDPEEDEPNLEPSWPHLQLVYEFFLRFLESPD FQPSVAKRYVDQKFVLMLLELFDSEDPREREYLKTILHRVYGKFLGLRAYIRKQCNHIFL RFIYEFEHFNGVAELLEILGSIINGFALPLKTEHKQFLVRVLIPLHSVKSLSVFHAQLAY CVVQFLEKDATLTEHVIRGLLKYWPKTCTQKEVMFLGEVEEILDVIEPSQFVKIQEPLFK QVARCVSSPHFQVAERALYFWNNEYILSLIEDNCHTVLPAVFGTLYQVSKEHWNQTIVSL IYNVLKTFMEMNGKLFDELTASYKLEKQQEQQKARERQELWQGLEELRLRRLQGTQGTQG AREAPLQRFVPQVAATGGQS h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000200.txt0000600000175000017500000000050511455416572021763 0ustar ykeyke>sp|Q5WGN4|3MGH_BACSK Putative 3-methyladenine DNA glycosylase OS=Bacillus clausii (strain KSM-K16) GN=ABC1936 PE=3 SV=1 MEQQKALDLSFFEQSTIEVAKGLIGMHLVHELDGVTLIGRITETEAYLGVLDRACHSYGR RRTKRTAILYEEAGRCYTYTMHTHCLLNVVCEQKGQPEAVLIRAIEPISGVKEMERLRGK PHTSREFANGPGKLTKAMGITMADYGRLLTEPPLYFAKGDHTNASIVATKRIGIKGAGPC SHHPWRFIDGNSRAVSAYRP h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000600.txt0000600000175000017500000000133711455416572021773 0ustar ykeyke>sp|P23745|ABRA_PLAFG 101 kDa malaria antigen (Fragment) OS=Plasmodium falciparum (isolate FCR-3 / Gambia) GN=ABRA PE=2 SV=1 QYTDSVTYLMDGFKSANNSANNGKKNNAEEMKNLVNFLQSHKKLIKALKKNIESIQNKKH LIYKNKSYNPLLLSCVKKMNMLKENVDYIQKNQNLFKELMNQKATYSFVNTKKKIISLKS QGHKKETSQNQNENNDNQKYQEVNDEDDVNDEEDTNDDEDTNDEEDTNDDEDTNDDEDTN DEEDTNDEEDHENNNATAYELGIVPVNDVLNVNMKNMITGNNFMDVVKSTLAQSGGLGSN DLINFLNQGKEIGENLLNITKMNLGDKNNLESFPLDQLNMLKDNLINYEFILNNLKTSVL NKLKDLLLRLLYKAYVSYKKRKAQEKGLPEPTVTNEEYVEELKKGILDMGIKLLFSKVKS LLKKLKNKIFPKKKEDNQAVDTKSMEEPKVKAQPALRGVEPTEDSNIMNSINNVMDEIDF FEKELIENNNTPNVVPPTQSKKKNKNETVSGMDENFDNHPENYFKEEYYYDENDDMEVKV KKIGVTLKKFEPLKNGNVSETIKLIHLGNKDKKHIEAINNDIQIIKQELQAIYNELMNYT NGNKNIQQIFQQNILENDVLNQETEEEMEKQVEAITKQIEAEVDALAPKNKEEEEKEKEK h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004303.txt0000600000175000017500000001053411455416572021776 0ustar ykeyke>sp|P98161|PKD1_HUMAN Polycystin-1 OS=Homo sapiens GN=PKD1 PE=1 SV=2 MPPAAPARLALALGLGLWLGALAGGPGRGCGPCEPPCLCGPAPGAACRVNCSGRGLRTLG PALRIPADATALDVSHNLLRALDVGLLANLSALAELDISNNKISTLEEGIFANLFNLSEI NLSGNPFECDCGLAWLPRWAEEQQVRVVQPEAATCAGPGSLAGQPLLGIPLLDSGCGEEY VACLPDNSSGTVAAVSFSAAHEGLLQPEACSAFCFSTGQGLAALSEQGWCLCGAAQPSSA SFACLSLCSGPPPPPAPTCRGPTLLQHVFPASPGATLVGPHGPLASGQLAAFHIAAPLPV TATRWDFGDGSAEVDAAGPAASHRYVLPGRYHVTAVLALGAGSALLGTDVQVEAAPAALE LVCPSSVQSDESLDLSIQNRGGSGLEAAYSIVALGEEPARAVHPLCPSDTEIFPGNGHCY RLVVEKAAWLQAQEQCQAWAGAALAMVDSPAVQRFLVSRVTRSLDVWIGFSTVQGVEVGP APQGEAFSLESCQNWLPGEPHPATAEHCVRLGPTGWCNTDLCSAPHSYVCELQPGGPVQD AENLLVGAPSGDLQGPLTPLAQQDGLSAPHEPVEVMVFPGLRLSREAFLTTAEFGTQELR RPAQLRLQVYRLLSTAGTPENGSEPESRSPDNRTQLAPACMPGGRWCPGANICLPLDASC HPQACANGCTSGPGLPGAPYALWREFLFSVAAGPPAQYSVTLHGQDVLMLPGDLVGLQHD AGPGALLHCSPAPGHPGPQAPYLSANASSWLPHLPAQLEGTWACPACALRLLAATEQLTV LLGLRPNPGLRMPGRYEVRAEVGNGVSRHNLSCSFDVVSPVAGLRVIYPAPRDGRLYVPT NGSALVLQVDSGANATATARWPGGSVSARFENVCPALVATFVPGCPWETNDTLFSVVALP WLSEGEHVVDVVVENSASRANLSLRVTAEEPICGLRATPSPEARVLQGVLVRYSPVVEAG SDMVFRWTINDKQSLTFQNVVFNVIYQSAAVFKLSLTASNHVSNVTVNYNVTVERMNRMQ GLQVSTVPAVLSPNATLALTAGVLVDSAVEVAFLWNFGDGEQALHQFQPPYNESFPVPDP SVAQVLVEHNVMHTYAAPGEYLLTVLASNAFENLTQQVPVSVRASLPSVAVGVSDGVLVA GRPVTFYPHPLPSPGGVLYTWDFGDGSPVLTQSQPAANHTYASRGTYHVRLEVNNTVSGA AAQADVRVFEELRGLSVDMSLAVEQGAPVVVSAAVQTGDNITWTFDMGDGTVLSGPEATV EHVYLRAQNCTVTVGAASPAGHLARSLHVLVFVLEVLRVEPAACIPTQPDARLTAYVTGN PAHYLFDWTFGDGSSNTTVRGCPTVTHNFTRSGTFPLALVLSSRVNRAHYFTSICVEPEV GNVTLQPERQFVQLGDEAWLVACAWPPFPYRYTWDFGTEEAAPTRARGPEVTFIYRDPGS YLVTVTASNNISAANDSALVEVQEPVLVTSIKVNGSLGLELQQPYLFSAVGRGRPASYLW DLGDGGWLEGPEVTHAYNSTGDFTVRVAGWNEVSRSEAWLNVTVKRRVRGLVVNASRTVV PLNGSVSFSTSLEAGSDVRYSWVLCDRCTPIPGGPTISYTFRSVGTFNIIVTAENEVGSA QDSIFVYVLQLIEGLQVVGGGRYFPTNHTVQLQAVVRDGTNVSYSWTAWRDRGPALAGSG KGFSLTVLEAGTYHVQLRATNMLGSAWADCTMDFVEPVGWLMVTASPNPAAVNTSVTLSA ELAGGSGVVYTWSLEEGLSWETSEPFTTHSFPTPGLHLVTMTAGNPLGSANATVEVDVQV PVSGLSIRASEPGGSFVAAGSSVPFWGQLATGTNVSWCWAVPGGSSKRGPHVTMVFPDAG TFSIRLNASNAVSWVSATYNLTAEEPIVGLVLWASSKVVAPGQLVHFQILLAAGSAVTFR LQVGGANPEVLPGPRFSHSFPRVGDHVVSVRGKNHVSWAQAQVRIVVLEAVSGLQMPNCC EPGIATGTERNFTARVQRGSRVAYAWYFSLQKVQGDSLVILSGRDVTYTPVAAGLLEIQV RAFNALGSENRTLVLEVQDAVQYVALQSGPCFTNRSAQFEAATSPSPRRVAYHWDFGDGS PGQDTDEPRAEHSYLRPGDYRVQVNASNLVSFFVAQATVTVQVLACREPEVDVVLPLQVL MRRSQRNYLEAHVDLRDCVTYQTEYRWEVYRTASCQRPGRPARVALPGVDVSRPRLVLPR LALPVGHYCFVFVVSFGDTPLTQSIQANVTVAPERLVPIIEGGSYRVWSDTRDLVLDGSE SYDPNLEDGDQTPLSFHWACVASTQREAGGCALNFGPRGSSTVTIPRERLAAGVEYTFSL TVWKAGRKEEATNQTVLIRSGRVPIVSLECVSCKAQAVYEVSRSSYVYLEGRCLNCSSGS KRGRWAARTFSNKTLVLDETTTSTGSAGMRLVLRRGVLRDGEGYTFTLTVLGRSGEEEGC ASIRLSPNRPPLGGSCRLFPLGAVHALTTKVHFECTGWHDAEDAGAPLVYALLLRRCRQG HCEEFCVYKGSLSSYGAVLPPGFRPHFEVGLAVVVQDQLGAAVVALNRSLAITLPEPNGS ATGLTVWLHGLTASVLPGLLRQADPQHVIEYSLALVTVLNEYERALDVAAEPKHERQHRA QIRKNITETLVSLRVHTVDDIQQIAAALAQCMGPSRELVCRSCLKQTLHKLEAMMLILQA ETTAGTVTPTAIGDSILNITGDLIHLASSDVRAPQPSELGAESPSRMVASQAYNLTSALM RILMRSRVLNEEPLTLAGEEIVAQGKRSDPRSLLCYGGAPGPGCHFSIPEAFSGALANLS DVVQLIFLVDSNPFPFGYISNYTVSTKVASMAFQTQAGAQIPIERLASERAITVKVPNNS DWAARGHRSSANSANSVVVQPQASVGAVVTLDSSNPAAGLHLQLNYTLLDGHYLSEEPEP YLAVYLHSEPRPNEHNCSASRRIRPESLQGADHRPYTFFISPGSRDPAGSYHLNLSSHFR WSALQVSVGLYTSLCQYFSEEDMVWRTEGLLPLEETSPRQAVCLTRHLTAFGASLFVPPS HVRFVFPEPTADVNYIVMLTCAVCLVTYMVMAAILHKLDQLDASRGRAIPFCGQRGRFKY EILVKTGWGRGSGTTAHVGIMLYGVDSRSGHRHLDGDRAFHRNSLDIFRIATPHSLGSVW KIRVWHDNKGLSPAWFLQHVIVRDLQTARSAFFLVNDWLSVETEANGGLVEKEVLAASDA ALLRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYG AVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPA GQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSW PDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEG VSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTG LVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASF LGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEE ARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRS EELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSD YDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLH NWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLP LLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAAD RQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLC RALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESW HLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLW MGLSKVKEFRHKVRFEGMEPLPSRSSRGSKVSPDVPPPSAGSDASHPSTSSSQLDGLSVS LGRLGTRCEPEPSRLQAVFEALLTQFDRLNQATEDVYQLEQQLHSLQGRRSSRAPAGSSR GPSPGLRPALPSRLARASRGVDLATGPSRTPLRAKNKVHPSST h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003411.txt0000600000175000017500000000675211455416572022004 0ustar ykeyke>sp|P03314|POLG_YEFV1 Genome polyprotein OS=Yellow fever virus (strain 17D vaccine) PE=1 SV=1 MSGRKAQGKTLGVNMVRRGVRSLSNKIKQKTKQIGNRPGPSRGVQGFIFFFLFNILTGKK ITAHLKRLWKMLDPRQGLAVLRKVKRVVASLMRGLSSRKRRSHDVLTVQFLILGMLLMTG GVTLVRKNRWLLLNVTSEDLGKTFSVGTGNCTTNILEAKYWCPDSMEYNCPNLSPREEPD DIDCWCYGVENVRVAYGKCDSAGRSRRSRRAIDLPTHENHGLKTRQEKWMTGRMGERQLQ KIERWFVRNPFFAVTALTIAYLVGSNMTQRVVIALLVLAVGPAYSAHCIGITDRDFIEGV HGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCP STGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKI QYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYI AEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLK TALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGH GTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSY IIVGRGDSRLTYQWHKEGSSIGKLFTQTMKGVERLAVMGDTAWDFSSAGGFFTSVGKGIH TVFGSAFQGLFGGLNWITKVIMGAVLIWVGINTRNMTMSMSMILVGVIMMFLSLGVGADQ GCAINFGKRELKCGDGIFIFRDSDDWLNKYSYYPEDPVKLASIVKASFEEGKCGLNSVDS LEHEMWRSRADEINAIFEENEVDISVVVQDPKNVYQRGTHPFSRIRDGLQYGWKTWGKNL VFSPGRKNGSFIIDGKSRKECPFSNRVWNSFQIEEFGTGVFTTRVYMDAVFEYTIDCDGS ILGAAVNGKKSAHGSPTFWMGSHEVNGTWMIHTLEALDYKECEWPLTHTIGTSVEESEMF MPRSIGGPVSSHNHIPGYKVQTNGPWMQVPLEVKREACPGTSVIIDGNCDGRGKSTRSTT DSGKVIPEWCCRSCTMPPVSFHGSDGCWYPMEIRPRKTHESHLVRSWVTAGEIHAVPFGL VSMMIAMEVVLRKRQGPKQMLVGGVVLLGAMLVGQVTLLDLLKLTVAVGLHFHEMNNGGD AMYMALIAAFSIRPGLLIGFGLRTLWSPRERLVLTLGAAMVEIALGGVMGGLWKYLNAVS LCILTINAVASRKASNTILPLMALLTPVTMAEVRLAAMFFCAVVIIGVLHQNFKDTSMQK TIPLVALTLTSYLGLTQPFLGLCAFLATRIFGRRSIPVNEALAAAGLVGVLAGLAFQEME NFLGPIAVGGLLMMLVSVAGRVDGLELKKLGEVSWEEEAEISGSSARYDVALSEQGEFKL LSEEKVPWDQVVMTSLALVGAALHPFALLLVLAGWLFHVRGARRSGDVLWDIPTPKIIEE CEHLEDGIYGIFQSTFLGASQRGVGVAQGGVFHTMWHVTRGAFLVRNGKKLIPSWASVKE DLVAYGGSWKLEGRWDGEEEVQLIAAVPGKNVVNVQTKPSLFKVRNGGEIGAVALDYPSG TSGSPIVNRNGEVIGLYGNGILVGDNSFVSAISQTEVKEEGKEELQEIPTMLKKGMTTVL DFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGLDVKFHTQAFSAHG SGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARGWAAHRARANESAT ILMTATPPGTSDEFPHSNGEIEDVQTDIPSEPWNTGHDWILADKRPTAWFLPSIRAANVM AASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANLCVERVLDCRTAFKP VLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEAS MLLDNMEVRGGMVAPLYGVEGTKTPVSPGEMRLRDDQRKVFRELVRNCDLPVWLSWQVAK AGLKTNDRKWCFEGPEEHEILNDSGETVKCRAPGGAKKPLRPRWCDERVSSDQSALSEFI KFAEGRRGAAEVLVVLSELPDFLAKKGGEAMDTISVFLHSEEGSRAYRNALSMMPEAMTI VMLFILAGLLTSGMVIFFMSPKGISRMSMAMGTMAGCGYLMFLGGVKPTHISYVMLIFFV LMVVVIPEPGQQRSIQDNQVAYLIIGILTLVSAVAANELGMLEKTKEDLFGKKNLIPSSA SPWSWPDLDLKPGAAWTVYVGIVTMLSPMLHHWIKVEYGNLSLSGIAQSASVLSFMDKGI PFMKMNISVIMLLVSGWNSITVMPLLCGIGCAMLHWSLILPGIKAQQSKLAQRRVFHGVA ENPVVDGNPTVDIEEAPEMPALYEKKLALYLLLALSLASVAMCRTPFSLAEGIVLASAAL GPLIEGNTSLLWNGPMAVSMTGVMRGNHYAFVGVMYNLWKMKTGRRGSANGKTLGEVWKR ELNLLDKRQFELYKRTDIVEVDRDTARRHLAEGKVDTGVAVSRGTAKLRWFHERGYVKLE GRVIDLGCGRGGWCYYAAAQKEVSGVKGFTLGRDGHEKPMNVQSLGWNIITFKDKTDIHR LEPVKCDTLLCDIGESSSSSVTEGERTVRVLDTVEKWLACGVDNFCVKVLAPYMPDVLEK LELLQRRFGGTVIRNPLSRNSTHEMYYVSGARSNVTFTVNQTSRLLMRRMRRPTGKVTLE ADVILPIGTRSVETDKGPLDKEAIEERVERIKSEYMTSWFYDNDNPYRTWHYCGSYVTKT SGSAASMVNGVIKILTYPWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKI MKVVNRWLFRHLAREKNPRLCTKEEFIAKVRSHAAIGAYLEEQEQWKTANEAVQDPKFWE LVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWLGARYLEFEALGFLN EDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWDTRITEADLDDEQEI LNYMSPHHKKLAQAVMEMTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALNTI TNLKVQLIRMAEAEMVIHHQHVQDCDESVLTRLEAWLTEHGCDRLKRMAVSGDDCVVRPI DDRFGLALSHLNAMSKVRKDISEWQPSKGWNDWENVPFCSHHFHELQLKDGRRIVVPCRE QDELIGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLSLAVSSAVPTSWVPQ GRTTWSIHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTMVKKWRDVPYLTKRQDKLCGSL IGMTNRATWASHIHLVIHRIRTLIGQEKYTDYLTVMDRYSVDADLQLGELI h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000700.txt0000600000175000017500000000146411455416572021775 0ustar ykeyke>sp|Q54GQ6|ACOX1_DICDI Peroxisomal acyl-coenzyme A oxidase 1 OS=Dictyostelium discoideum GN=acox1 PE=3 SV=1 MYCPKAYENEKKNEDLEFERSQSTFSVSELNFILNNNDHNIINIKNEIKKFIDNDEIISK PQEIHFLSREEQYKRALYVSSKLIEIKKRFGEIGRDQYYQSLFEEIPFVINDIVFACAFK SLASDEQMNRLYSKFENYQYFGSYSQTEIGHGSNVQGIETTCTFIKETGEFELNSPNLTS TKFWIGGLGKLATHTIVFAQLLIPSSIDGKLKNYGPHPFILQVRSLDDHSPLPGVTVGDI GPKLGFNSIDNGFLRLDHVRIPRENMLSRFFRVNEQGEYEKPKHPKLIYAGMVGVRSSMI ENSFVSLSRAVTIAIRYSTIRKQFKSNRLDKQEKKIIEYSNQMNRIIPYLAQTFAYFFTG KRFSIEFDQMMKAVKHNQDTTLLSELHANSSGLKSLMTQSTSDGIESCRLSCGGHGYSQF SGLPYLWSNYVHMSSAEGESNLLPQQTTKYLLTILRKVLSGGGGSSDTTTADDDNKPIGK SVKYINDEFQSSFENINQFIQEKGLNSIIHPDSLLQLFKHRSFILIKSIAESIQEQMSNG NKDIPQIWSDLNVEINHCSKAHCQLYVIQSFYDQILLLSSNSSSCSSSITTVLIQLLQTY SIWIINSNLVDFLQDQYVELSQIDFLKKSLINFYKLLRPNLVPLVDSFDLCNTTLGSALG SYNGDVYSTLYKWASTQPFNKNSLPLGFNETIKPLINSKL h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002300.txt0000600000175000017500000000456211455416572021775 0ustar ykeyke>sp|Q01631|CYAA_NEUCR Adenylate cyclase OS=Neurospora crassa GN=cr-1 PE=3 SV=2 MTRNDGGSRYSSIDSAQSSITAKPFPLTPTSSLGSSMTRPLSPSLQAGSSSSNGGHNVSR SASQGARRPAPTRLKTDDGTQFASRSSRDFESSQSQSQPSHTQTRSHSLSQATLQSCSQP QLSLNSQQSQSPSQYHSQQTPTQQQPQQQVSPTGGSRLTQSPTTPSNASIREHRMSELGG YRREMAAMLDTTGGALSRTSSHSQQQPQQPQQQQQQQQQQQGHAAGSVSGTFSNLSQYAP YLGGNNGGGMSMGSFLNDSTDNLSVISQLSPGIRPMTARPSQASAGSMEFPDSAYYDDER RPSIASITTTASSQGSRTSKTRGGLQKLQQFFGDRDDWPGRDSSEISLPQPSHSGPMSTG KEHRSHSYSLPGSGRSHRDRNYSNATDHHPSTFGSVSTVGGRDRDASPVPSRPRTPVPAP EVVPFLYQEADDIARYGEAPVRTSLTGPDRDRYIDSSQNPPKTSSSARSGHSIVHLPGHH KHNKSNEDPRALKPSLSREDSAASFARDFRNGSSSMMGTRSRAQSPAPSWTGTSRGLKAN SISDGTSSPAPSHKKGILGRFRRHNKDKEDGSSLRSGSNHTLVHRPSRQDLTRAAESTYP ASVYVSDPSEQREVPVRPGYVRQTTAPGFTTKLFTSKKSSSAKQPQDDMDEDIGPTDMHM GGGTVYHLDTNLNDMEGILTKPQPMTPLDNSISMRRESEKMIVPITTDPEGAWAAPDSWA VRDNKKSLAPQVNEDLCSRQPSEEKEKKSNYYIRVFRSDSTWTTLTLPLTATAEDVIMGV AKKTYLPPGAQDSYSLLIKKHDLFRVLNSAEQPLRIQKRLFQQIGYQEKDGIDEIGREDN SYICRWVFLKEKEADMHLLSPDINFRNQKLNHVDLSGRNLITIPVPLYRKAAEIVSLNLS RNLSLDVPRDFIQACTALRDIKYNNNEAQALPKSFATASKLTYLDVSNNRLQDLDHSELS KLTGLLKLNLANNCLRSLPPTLGAYKSLRTLNISSNFLDVFPSFICELETIVDLDLSFNS INNLPDNLMKLRNLEKFVITNNRLSGPISESVRDLVSLRELDIRYNQISTIDVLSDLPRL EILSADHNQISKFSGSFERLRSLKLNSNPIVKFEVKAPVPTLKILNLSNAQLASIDESID NLMNLERLILDSNYFVSLPNQIGNLKKLDHLSMANNHLGELPPEIGCLTELRTLDVHGNN MRKLPNEIWWANKLEHLNASSNILTEFPKPASRAPQAPGEASPSPGAYPFPNANKNGLLS RTPSMDDLNGDASRRPSQASSTLLGVAVSPVPSGPDNRKSSMVSLYGKGGRKTSVVSRST TQSSTGVITPSNGPRKDSSLSYRFTHTFSGSLKNLYLADNQLDDDVFEELKHLPELRVLN LSCNDLSDMPQGTIRSWPQLVELYLSGNELTSLPAEDFLEEHCLLQTLHINGNKFINLPA EISRAKKLQVLDCSSNNLKYNVTNVPYDWNWNFNRDLRYLNLSGNKRLEIKNNYRQPQSY RDDDFADTDFSKLTNLRVLGLMEVTHTLPNIPDQTEDRRVRTSEMKAGAYLPYGMADTLG KNEHLSLFDLVVPRLGSVETDTLVALFDGKELSTGGSKIAKFLYEEFSRLFILELEKVKG KPNENPADALRRTFLSVNKLLMSLSNSADERGLDSHPSRNYAHTVLTKEDLNSGCVATVA YLSELKLYVANVGDVQGMLIQANGSFKMLTKKHDPADPVERSRIRNAGGWVSRNGRLNDV LNVSRAFGYTELLPAVQAAPDITEHTIDDKDETVLIASKELWEHLRPELIVDVARECRSD LMKASQKLRDLAIAYGSTNKLLIMMIGVANLKQRQAQQFKGQLNATFSMPQDDPSHVPPS GNKRRKVRAEGPLDSNLMRLNAEVPPPTGQLSIVFTDIKNSTQLWENYPEAMRLAIKLHN EVMRRQLRMIGGFEVKTEGDAFMVSFPTATSALLWCFAVQMKLLTVDWPPEVLSNSSCQP IYDRNNNLITRGLSVRMGAHWGEPLAERDPVTRRMDYYGPMVNKASRISAVADGGQITAS SDFITEIHRCLETYKESVDVDEDSLEDDATAKAIRAELRALSSQGFEVKDMGEKKLKGLE NPELVYSVYPHALVGRTEQHHAHTESTQNQAALQPYGALATPKPATMDPDSEIQFEPETI WALWRVALRLEMLCSTLEEPNARGLQAPETELLERMKQRAGEVTDHFLLNFMEHQISRIE TCITSLAVRHIAIGSGPITKLNDLRAPMNDVLSTLKEQMDELARYKAKYGSLDQAETDDA TDNNSSGDVDTLDGSDTEQE h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003603.txt0000600000175000017500000000725611455416572022007 0ustar ykeyke>sp|P94459|PPSD_BACSU Plipastatin synthetase subunit D OS=Bacillus subtilis GN=ppsD PE=1 SV=2 MTKANSIQDIYPLSYMQEGMLFHSLLQKDSQAYVEQASFTIEGKVNPQFFQNSINALVER HDIFRTIFISQNVSSPQQVVLRERNVIVLEEDITHLNEAEQSQFIEQWKEKDRDRGFHLQ KDVLMRIALIQTGESQYSCIWTFHHIMMDGWCLSIVLKEFLHIYASYVNASPITLEPVQP YGKYIKWLMEQDKEQAVSYWDHYLSGHEQQTVLPKQKKTKGKSRQEHVTFSFSKEESSRL SELAAREEVTLSTIFHTIWGILLQKYNNNDDAVFGSVISGRPAEIEGIEHMVGLFINTMP VRVQGAKTPFLQLIKDMQKDRLAAEAYSYHPLYEIQSRSAVKQGLIDHILVFENYPVQQE IQMLNKQEHASDLFQIHNFTVADETNYSFYLMVAPGEEIHIKMNYDAEQHDRSFVLSVKE HLLNAVSQILNNPNLPPEEIDITTDTEKRQLIGEITDQTPVYETIHAMFEKQAEKTPDAH AVIDQACSLTYRELNKAANRLARHLRMKGVVRQEPVAIMMERSAAFITGVLGILKAGGAI VPVDPHYPADRIRYILHDCGCSHVVSQAHLPSSLEDNYIITHPEDIESKVDGSNIKSVNN ADDLLYMIYTSGTTGKPKGVQFEHRNMANLLKFEYTHSGIDFEADVLQFATPSFDVCYQE IFSALLKGGTLHIVPEAIKRDVPQLFAFINKHQTNIVFLPTAFIKMIFSERELANSFPDG VKHLIAAGEQLMISDLFQDVLRKRGIHLHNHYGPSETHVVSTYTIHPGDPIPELPPIGKP IGCTDLYILNHQKQLQPCGVPGELYISGASVARGYVNHDKLTSDKFSSDPFKPDVIMYRT GDLARRLEDGNIEYIGRADNQVKIRGYRIEPQEIEVTLMNHPDISEAAILIWQDQNGEHE LCAYYCSVQKLNTIDLRSYMASELPEYMIPAKWIWVDSIPLTPNGKVDRAALPEPDASIS GNPYTAPRNLLEAKLSQLFEDVLKNGHIGIQDNFFDNGGHSLKATVLMSRIAKEFHVQVS LKDIFAHPTVEGLALIIREAEQNLYAAIEPAEKRDTYPVSSAQKRIYVLQQLDEGVAYNM PAVLELEGALDVAKLSAVCKELISRHEPLRTSFVSGADDEPVQRIHTEVPFTLSKETTIE GFVRPFDLSQAPLFRAGLIEVSNEKHVLLVDMHHIISDGVSVQLLIREFTDLYANRQLKP LRIQYKDYAVWQQKFKKGDSYQKQETYWQQQFSGDLPILELPTDKRRPAERQFIGGKVTF QLDKEITARIKRLAHKNRSTLYMTLLALYSAFLSRLSGQDDIVIGSPIAGRPHADLEAVL GMFVNTLALRTRPAGNKTFEEFLKEVRQTALEAYEHQDYPFEELVDKLGVQREMSRNPLF DTTLVLQNMEQQKLKMNDVQLQWNDLEHPISKFDISLYVTEHDSELFCQFEYSTALFEKE TIQRWASLFTTLVEHTAASPETELDNIPILTKEEERDFIESCHLFEETGYSMNQTLHYAL EQQAEKTPDQAAVIFEDGVMTYKELNEQANRIAWELIGRGVKPETTVAIIGKRSPEMLLG IYGILKAGGAYLPIDPDYPEERISFLLEDSGTNILLLQSAGLHVPEFTGEIVYLNQTNSG LAHRLSNPNVDVLPQSLAYVIYTSGSTGMPKGVEIEHRSAVNFLNSLQSRYQLKHSDMIM HKTSYSFDASIWELFWWPYAGASVYLLPQGGEKEPEVIAKAIEEQKITAMHFVPSMLHAF LEHIKYRSVPIKTNRLKRVFSGGEQLGTHLVSRFYELLPNVSITNSYGPTEATVEAAFFD CPPHEKLERIPIGKPVHHVRLYLLNQNQRMLPVGCIGELYIAGAGVARGYLNRPALTEER FLEDPFYPGERMYKTGDVARWLPDGNVEFLGRTDDQVKIRGYRIEPGEIEAALRSIEGVR EAAVTVRTDSGEPELCAYVEGLQRNEVRAQLERLLPGYMVPAYMIEMEQWPVTPSGKLDR NALPAPGGAADAETYTAPRNVTEMKLSQLWEDVLKNGPVGIHDNFFDRGGHSLKATALVS RITKEFDVQVPLKDVFAHPTVEGLATVIREGTDSPYEAIKPAEKQETYPVSSAQKRIYVL QQLEDGGTGYNMPAVLELEGKLNPERMDRAFQELIKRHESLRTSFEQDEGGDPVQRIHDE VPFTLQTTVLGARTEQEAAAAFIKPFDLSQAPLFRAQIVKVSDERHLLLVDMHHIISDGV SVNILIQEFGELYNNRKLPALRIQYKDYAVWQEGFKTGDAYKMQEAYWLKQLEGELPVLD LPADHARPPVRSFAGDKVSFTLEPEVASGLHKLARENGSTLYMVLLAAYTAFLSRLSGQE DIIVGSPIAGRPHKDLEPILGMFVNTLALRTRPEGGKPFVQYLQEVRETALEAFEHQNYP FEELVDKLELTRDMSRNPVFDAMLVVQNNDYEPLHLHDLQMKPAQVSHLVSKFDLTLQAS EGDGNIHFLFEYSTALFEKTTIERWASHLTNVLSIIGKNPKVTLNHIDILTQEERHQLLN EFNTGQANQYGVQTISQLFEQQAARTPKASALVSGDKTLTYQELDEWSNGIARALRSRGV KPDTPVGIMMHRSFSMIASILGVWKAGGCYVPIDPEYPKERKRYILSDSGTKLLMTINEA DLGVLADFEGEILTIESVEEDDKSPLPQMSSAHHLAYIIYTSGTTGRPKGVMVEHKGIAN TLQWRRNAYAFNETDTILQLFSFSFDGFITSMFTPLLSGAKAVLLHEEEAKDILAIKHQL SRQRITHMIIVPVLYRALLDVVQPEDVKTLRVVTLAGEAADRELIARSLAICPHTELANE YGPTENSVATTVMRHMEKQAYVSIGQPIDGTQVLILNSNHQLQPIGVAGELCIAGTGLAR GYVNLPELTERAFTQNPFKPEARMYRTGDAARWMADGTLEYLGRIDDQVKIRGYRVETKE IESVIRCIKGVKDAAVVAHVTASGQTELSAYVVTKPGLSTNAVRSELQNKLPVFMHPAFI EKLDSLPLSPNGKLDRGALPKPVYNHEGERPFLPPSSKMEQILADIWKEVLGAEKIGTAD SFFELGGDSIKALQVSARLHRIGKQMAVKDLFSHPTIQELAAYIRDSDTSSSQAAVEGDV QWSPVQKWFLSQDIKEKHHFNQSVMLHRSTSVQEDALRKTLKAITCHHDALRMVFTQNEQ GKWDQYNRPLSHSDDALYGLQMIDLSAPDGTDGNRPYEPLIKRHVLDIQQKMDLKNGPLL QAGLFHTIDGDFLFLSAHHLVVDGISWRVLLEDLALGYRQAAGGEDIKLPPKTSSFKAYA KKLSDYAESQQLMKQLKYWREAEEYQTEALPFDQIDGTRAHEGQRSTISFTLNDKETAAL LKDANSAYNTDTQDMLLASVILALRHWTNQSAFKLSLEGHGREDVLKGIDVSRTIGWFTA IYPLLIKLNADLPDSEESMVHVLKTTKDTLRRVPDKGFGYGVIKYLTPPGKKDINFTGAP EISFNYLGQFESGRTAEVPEEDAFSFSPLGAGGDISTTWNREQSLDISAIAAEGKLTVNM TYDNARFQRKTIEQLSETCRQFLLQLIEHCQNKSETEKTISDFDDQELTEDALQEIADML SFH h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001100.txt0000600000175000017500000000225711455416572021771 0ustar ykeyke>sp|P16638|ACLY_RAT ATP-citrate synthase OS=Rattus norvegicus GN=Acly PE=1 SV=1 MSAKAISEQTGKELLYKYICTTSAIQNRFKYARVTPDTDWAHLLQDHPWLLSQSLVVKPD QLIKRRGKLGLVGVNLSLDGVKSWLKPRLGHEATVGKAKGFLKNFLIEPFVPHSQAEEFY VCIYATREGDYVLFHHEGGVDVGDVDTKAQKLLVGVDEKLNAEDIKRHLLVHAPEDKKEI LASFISGLFNFYEDLYFTYLEINPLVVTKDGVYILDLAAKVDATADYICKVKWGDIEFPP PFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNE LANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRA IRDYQGSLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMAWA PAIPNQPPTAAHTANFLLNASGSTSTPAPSRTASFSESRADEVAPAKKAKPAMPQDSVPS PRSLQGKSATLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKF YWGHKEILIPVFKNMADAMKKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGI PEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVS RSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGG TEEYKICRGIKEGRLTKPVVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKE AGVFVPRSFDELGEIIQSVYEDLVAKGAIVPAQEVPPPTVPMDYSWARELGLIRKPASFM TSICDERGQELIYAGMPITEVFKEEMGIGGVLGLLWFQRRLPKYSCQFIEMCLMVTADHG PAVSGAHNTIICARAGKDLVSSLTSGLLTIGDRFGGALDAAAKMFSKAFDSGIIPMEFVN KMKKEGKLIMGIGHRVKSINNPDMRVQILKDFVKQHFPATPLLDYALEVEKITTSKKPNL ILNVDGFIGVAFVDMLRNCGSFTREEADEYVDIGALNGVFVLGRSMGFIGHYLDQKRLKQ GLYRHPWDDISYVLPEHMSM h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000002.txt0000600000175000017500000000011011455416572021753 0ustar ykeyke>sp|P83570|GWA_SEPOF Neuropeptide GWa OS=Sepia officinalis PE=1 SV=1 GW h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002200.txt0000600000175000017500000000444511455416572021774 0ustar ykeyke>sp|Q9BMN8|LAR_CAEEL Tyrosine-protein phosphatase Lar-like OS=Caenorhabditis elegans GN=ptp-3 PE=1 SV=1 MIQFRNKNNSMNRIARHLRNVARRKGSSLLLFLMLSTVLVAAKEDDPARLVVRPDSSTVV DESKISFFCRADGNPLPSVIWRVNGKSITDHNRISIKSLATGLSTLRFERVSLDDNATVV SCSADNGVANPVVAEASLTVVPRDKVPIGFPQIELHPSLKSVEQGKTAYVSCRVRGDPRA KVLWLRDLIPLDIRADGRYSVSTIGNPGALMIQHAREEDQGKYECIARNTLGVAHSKAAN LYVKVRRVPPYFSYKLERQYVVGVGGNINLTCVAVGYPMPRVFWKKTDLMVLDDPSTAPI GKNVLTLTHVESTENFTCVAVSALGNIEATTTVIAKELPPPPVNIVVSSVTSESVVITWK PPKYNEAINKYVVNYRLKYSEGRSSRGKTMETLENSLVIDGLVAFQTYEFTVRSAGPVGV GLESLPVEAQTKPSKPATAPVSPQARSLNRDSILVKWGPCEQPNGLITGYKVYYTNDLVT TPIREWKQHDAKSDEFMTTINGLEPDSRYFVRVIAQNSEGDSPLSTLVTVATRQGIPGQP PMLTVKALDSRRMQLTWDKPLYSSPVVGYTVRYNTSDGEKELTLTSPHEKHVVTGLHPDK YYYFRVAAYSDRGQGEFTEPMISKTIASIPLSSPTIVSAAATSSKSVEIRWKGPEQKKLN GVLTAYRINYFRLEDSKTANLESVEYDEDMDDSSSFLDRMSVVVPSDATSYVLSDLLPYS SYEITVAASTMDGYGPESSIRVVKTLEDVPSAPRNFNAELTSATSVKLTWDAPAAANGAL LGYYVYLDRMVNGEPVVEKGSKKRIVMIRDSSKRYFELDSLDPNTEYSFRLNAFNRNGDG EFSERKSIITQGIPPEAPEIVSVSLDRDEPPVVARIEWKMPKMKPNETPIEKYNLWLRAQ GYPDSYVKAKTVDGTDLSTTISGLWMGVVYDVLLAAENREGRSQNATETIATPVGSPDGE PIDVQYEVMKGKIVVSWRPPSEEKRNGNITSYKAILSAMDATADRYEQPVPAPSTSSTFE VNVRRAYLFKVAAATMKGIGPYSPVLTINPDPAALVGPPTNVRVEATSNSTAVVQWDFES QKADSFVVKYMHEPGNRMDTEKWKQLPVVSIDKENPKRFAVVSDLNAHKPYAFCVLAVKN NLTLNEQFNKVRVTNYMTNFQRQGPCSDPPTVLESVTPTYMVQNLRVLWKTSNSVQLTWE YNGPRNVGFYVNHTGRKDYVNHELQEKTMSTPGFGQDVDEKHREYLWTNLRPHMMYTIHV GVRTLPPGARKYWPQEVVTITDPTGPPFVDVPKLVDSSGTQPGQQMIRLTPATEEYGPIS HYWIILVPANYSTEDVVNLDPIELEKATAEKRAQLARSLSVSPSKKLKRKASEVGDDSQS ASYHPKEKRARRATVPGAYVTARLSADRVKQQYRNNQPFIVGDSQLYDGFTNYPLEHNLH YRLMMRAFAKNDVRTKDSFEQRAPMSEKLSRMYSDSVLTEPFTIKSALRGASQKSSPWVG ACIAFLVLFSIVGMLICWWLRCNKKSAGRHPRHGSITKVALTGNIMNGGGGIPGETSKLL STSNEYGRQIMNPYEQMNGNHHMESSMDLYPLPTSHSRSNGYAPVPVAIPSLPNNGNNMT TVSHPAVPIAELANHIERLRMNNNAGFQSEFESIETGQHFTWEHSSADMNKHKNRYANVA AYDHSRVVLSNVEGYPGMDYINANYVDGYDKPRSYIATQGPLPETFSDFWRMVWEEQSVT IVMLTNLEERSRVKCDQYWPSRGTATYGDIEVTLLESVHLAHYTMRTMRLKMVGEPEVRE IKHLQYTAWPDHGVPDHPTPFLIFLKRVKTLNPNDAGPIISHCSAGIGRTGAFIVIDCML ERLRYDNTVDIYGCVTALRAQRSYMVQTEEQYIFIHDAVLDAVNSGSTEVPASRLHQHLH ILSQPSADQLSGIDMEFRHLTTLKWTSNRCTVANLPVNRPKNRMLSAVPYDSNRVIMRLL PGADGSDYINASWIDGYKERGAYIATQAPTNETAADFWRAIWEHNSPIIAMLVRTNERGQ EQCSDYWPLETGVQVGMLVVEPMAEYDMKHYHLREFRISDINTREVRTVRQFHFMEWPDV GKPHTADHFLDFVTQVHNTYAQFGCTGPITVHCCSGAGRTAVFIALSIILDRMRAEHVVD VFTTVKLLRTERQNMIQEPEQYHFLYLAAYEYLAAYDNFS h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004241.txt0000600000175000017500000001053011455416572021773 0ustar ykeyke>sp|Q55EI3|VP13E_DICDI Putative vacuolar protein sorting-associated protein 13E OS=Dictyostelium discoideum GN=vps13E PE=3 SV=1 MVSKILPGLLKKILGNYIEGLDTLSIPWWKGQIVLENLKFKKELFSSNELPFDLLSGVVK RVVITIPILHFLKDPIVVNIDGVFLLFGPKDIINTFSNYGNDKSNKKDIVIDDNDGGISI DSNSNNNNKKNAPSSSSSNDDFFKKPNLTKEELKKIQIQIDKEQSKESNDGYSADSESFK FRMIKKLLKCIRIQLNNLHICYQDDSTSPGEIFSVGITMESFTFQTTDSQWVPLSKNTST HQQQQPTFNPYVGSQQQQQQQPQQNTEINYENDSEHNPFMNNKNSDEGISSSSSSSSFNN NNLNIPTLNLNDNYMDSEAYTTNTQPTPKSEQYQQQQQQQQPLGQIVDQIITYKLASIFN FSIYWDSQFGKTRMVTPEDMDVLLMHSIPRQKAKINHKYILQPISGFLKICLTEDSIESV NKEGVFNSIANNFNVSIGLKQIDLQLMDIQYRDMLNLLSFYQDWRRVLRYHKFRPHCRVK GNARIWWHFAFRSIISDFRSKKTEMTWKEIEDSKRVRECYIKLYTEKFIKGKLGRLDQNL IDEIEKKVTYEDIVLFRTIAEKDLKVTKRKDLDQFTESSGWWLGGWLGFQHHHQNNNQDK ITLTNEQLTFLERYLKVNLKVLAGKPHSSVSLIFFLNVKRLSISILDWQENHTVVPLANI DITEVNLQMEQSHNTKLKFSAESLDIFDRCSPNTKFENIILEKSRFNSSNINPDNSANSI GSFILDRQISNSEFLNGVYTGVNGTNNNNNKKFIDISIVLNPPEDTTDYFIYFKLEPFYF INSKPFVDTMIPFFTHANQEALDRLKYSFIKKIKILQEYLINELKHLVRNQKVADIKLDI AIPGLVFPESYDREDTMVLVCNMGNLILKTQPHNSEWDSMDFSEINEQDETDEIFVRYCN LLKDRVKWWSDNCPIKKINEPIEKQSYIINYVQQHRQTIENLGTGNGINNNNSGGGGNGG NASNSSEDDGKYPEQDDLDDSKVEKEGFDSCDTDWNKVSVNINNAQFYDGIVLTISDIYV KVCDCTQINNFNYLISPFSLDIFLELCSRPYDLKLPQIKCKAELSELNLQVSDKELYEIA KIVGKNGILEYFMDMDRKSSKELADMYEIVQVKKPKKKSFEVQFSLFSDTKSILNSRKRT KERLVKTTLLRFFFTSNAINMKLNYLDSCTLSLTMDQIRCRSLVKFMQMNIQFDISSIEI KDSNSITPVLSIFPYNLNNNNNNNNNNNNNNNNNNNNNNNRNLNNNNNNNNNNQKPECLN EFPISITAKSISKNSLDYDYIDFVLTLTTQYIRINFPKECVMALIAIIGTVVTNTTNFYE TKKSILTVEGSFYQGRVGQFTQSNTTTTTSPRYHHQNHHNHQHKKQNRHRLSTRLETNEF DPNDLKSKITINIPSFGLTLSTIENDLVAFQFEDISIDGIFQLPLIDCELKVRDMKFIDY TGSDGPYPYMLITQKSQSPMVPVVRMHLVCHSNSKTQEWGFSRLINIAVGKIQITFLLQT INLIRLFIHDITSSLKEYCPFLFKVMAIVDDNNKPSSKDNNNNNNNNNNSDSDSDSDTDS SSSSENNYNNNIDLNSPVVEIVKKKKNLTNLEIEIDNNVVIVPKNSRSRSAIRFSVGRIL LGLDQMDPTVDAVFVKIYGINMASKYEDSIDPIISDPIKMDIRFIHMFETSLKDKSIEVI IKIDKIHLKLSQYQYNLLYNTYQQNINQSIVPAPPSNSYSTVERQDILLDIRLEFKDFVE LNLENEKTNDSRFFSMLIQRPIICCSVWNNGDSDFLIKTTGISVRDKNKLVVVPNGFQEM INITPYDLDVPIKNVINQSINEVFFDIVKMNIDDNGIDINITIEYLSIFFDLPWVSKLIT FLSPIIDADYIGNSCSNSTNKSSTTINTQLLPPPPPPPPISLNKSGVNLTNQQQNEEFNS KFNKDWKIFLKVEVSAKNANIMVGDLNSKNELVLLMNSSLLINSQFGTEGLMKIILEYQC IKGLIGNKTKDPIYSTKNPSATTMSFISASSRDLGAQKNTTHYLWKELKKSSKLFLETFK TNIQVCLVPEGNQFYFCELNDLSLVFSGKAYKYLLDIYECVSDIIYGVSKSKDITNNNLV QKHSRSSSISTDLPIPINLRRSSIISTNLMQQQQQQQQQQQQQQQQQQQQQQQQQQNNNN NQNNQASSNNNNNNNNNVSGNTINNKSVPNVHDKTKNQFYQIKTRSVEMLRAHQTRVTEK YQASLPSNGKIAETEENENGDHTFTSDDDDDEGEDEDIGEGFSLDHSTSSAPTSRSNYNN INEPMIDLKSSKKQDDSNMVTKIQFSQISISIKNLNIIIMDDLSKHKMNTPIFNMKLNYG FMKAVLKTTRIEVEFDSVFQMNYFNNRIAYWEPFIEPWLFKSMMTLGKELSIDIYSTDLL NINFTIPLMDNISLFLRTYSKEFGYPFNLICAPSDSNNTDNSSNNGKKSHSNRHSLIGQI KKIKEKKTKTSYSPFFIRNRTGSRLRYRLETQDGKPVAGVNHKMEGSTVRVVNIENYGLF FELDSGDCSPIKFLPDVQINLETFSQLVLAVELLGVEKSISIPLDKIKIYDYQVYLDSST STKLYANIGIKNGTKLITIQFPIVLKNLTSFPIDIATVTSGFGDTQMPNYSTTIRVGQAR APLPINRMRNVQIKFKPSGDQYKWSTEALDVNNVIEGEDKFSCILKNGEKIYYIKGYIFK KNQCFIIKLCHMLKVKNLLPYPIQFKLKSPIENIPLLKRETQATVQDQEKTEVYEIPLLD KFKIQVRIADKDGTFEKSEWSEIRSIVEREDNNEIGVITISDSNNLIVDYLHLNVEFESY KGEKKIVFYNQYWIFNKSGLNLYCKKSYHSKDYSESQTHFNHPLQQLDSSNTNTTIKPSD AIIVTPDQWYSHQLIKESPLLFSFKKLKDMENSIRIRVGDSKWSHKISIAAIGDRGTIVI DSSEKRHSRSYHLGLSVDLAPNLKTKIVVFTPRFVFHNLFPYTILVQQCGANTDSTTIRI PPSCSVPFYYFINNTGESSKPTLKFKIDYQEFDWSPPFSIQTFSDFTFNVFNNNNNDNVE NYKQPDIHCNPYIRIKTCLEVATILVIISELKEPPYRILNNTKYQLSIQQKKVGKVLTVE PSSSIPYVWDLPLEDHILEVLVHISTNQSEKASYKMDKIKTFRPMEFNDDHNPVVIKAIV EADESTRVLTLSDKTSFQISKYEEENLRQSFRIHFTGIGISVINANPTELLYVSIHDILC EYFISSFLQKLEMKITNIQVDNQLSKVTPYSHPVLLFADNLLPNTPFLQVRIVRSMKMKN IDYYHHVSLKMQELNIKVEEKFLYVLLDFFNSLDFSFWTGNKKTNTLHNMDMLTPMYNED IGEGFIDEMVARALPSIYGKKMYFESLDIEPISMFLTFDLSNKSGSIASLEQAPMVKAFR RIGFVIVSFQHAHIFLHGFSLSHAFGSNEELLAPIFNHYFSEGLSEVYKILGAFNLFGNP VGLVTNFGIGFKEFFVSMGKGLVGNSFTDSFGQGSKSLAKHSVYGIFDSGAKLTGSAGKV LSTLSMDQRYILERQYIIGESPNTFMQGLILGGRAAKTAVYRGFSGFVKLPYEGGKEAGP KGVVKGIGKGTAGLVLKPIAAGFDFASKVSEGIKNSTQLSIERKRIRFPRPLFSDSPLET YDSAESYGHFLFLTYIITAGKLRRISADQINLPLMEVVSKDEKYVSHLIYKNRKTLLFTN KRIIYLYDTDGFRTKFDIKYTRIHGVSEKSDHIDIKIDKKHKLSFLYNEKNKKIDYRIKC VGEEKSYIFYRIIEMIKTYKPFADEELTVNGLKADPTTMIPIPPPPPPPLQQQLLYGSNI IQQQPPIQYFNDGSSSSSNLTGGRTIQPIIFTNDAGPMRNDLNPILENLLAQQPNKNMEI PIWISQGFNPPKPPDTLIPQRFRDPNLINNNNNYYYPNGSGYVYSQPPLYDQYGNQIPPP PPLPSHPLAIDRPTTTTTTNTTTTPYQSSQNIHSTPYPTETPQSVVLKEDISKAIHTPSA SSLKKLKTPHHYNVRFEPSSSLGPQDFDIHTIRLQNQQYQHSGSGAPPPPPIITTTTNST IPPPSSNINQRQLQHQFSSNSIIETPRYKSMARQQQFQQPPPPPPLPSNNRLSLTPSGSG NINYSDKFEVALNTIIQIQKIQSQQMSSLQKNQRDLQKLLFQQQSTEFDTLRNQQEQIQN IISQYHPLSPSKASLVSKLSNELESTNSNVVISPPTGGASN h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004998.txt0000600000175000017500000001203611741454135022014 0ustar ykeyke>sp|Q8CG65|SSPO_MOUSE SCO-spondin OS=Mus musculus GN=Sspo PE=2 SV=1 MLPLALLFGMLWTQANGHWCEQIETVHVEEEVTPRQEDLVPCTSLYHYSRLGWQLDLSWS GRVGLTRPPALGLCAIYKPPETRPATWNRTVRACCPGWGGAHCTDALAETSPKGHCFVTW HCQPLAGSANSSAGSLEDPADELGVWPLTLNDPILFPGMSLQWQGDWLVLSGGLGVVVRL DRSSSISISVDQEFWGRTQGLCGLYNGRPEDDFVEPGGGLATLAATFGNSWKLPGSEPGC LDAVEVAWGCESLLGGTLTDLEAVKLQAQAQDMCHQLLEGPFWQCHGQVQPDEYHETCLF AYCVGATAGNGPEGQLEAVCATFANYAQACARQHIYVHWRKPGFCERVCPGGQLYSDCVS SCPPSCSAVAQGEEGSCGKECVSGCECPTGLFWDGALCVPAAHCPCYHRRQRYAPGDTVK QQCNPCVCQDGRWHCAQALCPAECAVGGDGHYFTFDGRSFFFRGTPGCHYSLVQDSVKGQ LLVVLEHGACDTGSCLHALSVFLGNTHIQLRYSGAVLVDGEDVDLPWIGVEGFNISWASS TFLLLHWPGAWVLWGVAEPAAYITLDPRHAYQVQGLCGTFTWKQQDDFLTPAGDIETSVT AFASKFQVSGDGRCPLVDKSPLFCSSYSQHLTFTEAACAILHGHAFQECHGLVDREPFRL RCLEAVCGCAPGRDCLCPVLSAYTRHCAQEGVLLQWRNETLCPVSCPGGQVYQECAPVCG HHCGEPEDCKELGICVAGCNCPPGLLWDLEGQCVPPSMCHCQFGGHRYTINTTTVRDCSH CICQERGLWNCTAHHCPRQWALCPRELIYVPGACLLTCDSPRANHSCWAGSTDGCVCPPG TVLLDKHCVSPDLCPCRHNGQWYPPNATIQEDCNICVCQGQRWHCTGQRCSGWCQASGAP HYVTFDGLVFTFPGACEYLLVREAGGRFSVSVQNLPCGASGLTCTKALVVRLDSTVVHML RGQAVTVNGVSIRLPKVYTGPGLSLHHAGLFLLLTTRLGLTLLWDGGTRVLVQLSPHFHG RVAGLCGNFDSDASNDLRSRQGLLEPTAYLTAHSWRLNPLCPEPGDLPHPWNAHRANWAP ARCEVILQPIFAPCHTEVPPQQYYEWCVYDACGCDTGGDCECLCSAIATYADECARHRHH VRWRSQELCPLQCEGGQVYEPCGSTCPPTCHDHHSELRWHCQVITCVEGCFCPEGTLLHG GACMKLAACPCEWQGSFFPPGTVLQKDCGNCTCQGSQWHCDRGGAPCEDMEPGCAEGETL CRENGHCVPLEWLCDNQDDCGDGSDEEGCATSVCGEGQMSCQSGHCLPLSLICDGQDDCG DGTDEQGCLCPHGSLACADGRCLPPALLCNGHPDCLDAADEESCLGPVSCISGEVSCVDG TCVRTIQLCDGVWDCPDGADEGPSHCSLPSLPTPPGGIGQNPSTSSLDTAPSPVGSTSPA SPCSLLEFQCNSGECTPRGWRCDQEEDCTDGSDELDCGGPCMLYQVPCAHSPHCVSPGQL CDGVTQCPDGSDEDPDVCEEQSASGGANRTGAPCPEFSCPDGTCIDFLLVCDGNPDCELA DETEPSLDEQGCGAWGSWGPWAPCSQTCGSGTRSRNRNCSTSSLQVLQNCPGLQHQSQAC FTEACPVDGEWSSWSPWSPCSEPCGGTTTRHRQCRPPQNGGQDCALLPGSTHSTRQTSPC PQEGCLNATCFGELVFRTCAPCPLTCDDISGQAACPPDRPCSSPGCWCPDGKVLNTEGQC VRPRQCPCLVDGAHYWPGQRIKMDCQLCGLDCGWSSWSPWAECLGPCSSQSLQWSFRSPN NPRLSGHGRQCRGIHRKARRCQTEACEGCEQWGLMYNVGERWRGGPCMVCECLHSSITHC SPYCPIGSCPQGWVLVEGMGESCCHCALPEKNQTVIHMTTPAPAPASAPSPQIGAHLVTY VLPPTADACYSPLGLAGLPMWAPSQHWEHITRADPVEAPMAGPGPREGASAEWHTQPLYL QLDLRRPRNLTGIIVQRAGSSAAYVSTLSLQFSSDNLQWHNYVNSLSSTLSPPKPSPESS NHMAPEVWTFDQMVQARYIRVWPHSGHLRDNNQHDIFLWVELLGLSPLAPLCPGSRHRCA SGECAPKGGPCDGAVDCDDGSDEEGCGSLHASTTSRTPALSPTQPGKFPREVSEDLRQGA EAMTSHSPPSSGETAGLIPASEGTLPVSGQPMQTLSATSTFPPGAKSLHPGMAAVTVHPP HSVTPGAPVGQTVSPRPFPPMPCGPGQVPCDVLGCVEQEQLCDGREDCLDGSDEQHCASA EPFTVPTTALPGLPASKALCSPSQLRCGSGECLPFEHRCDLQVNCQDGSDEDNCVDCVLA PWSGWSDCSRSCGLGLIFQHRELLRLPLPGGSCLLDQFRSQSCFVQACPVAGAWAEWGPW TACSVSCGGGHQSRQRSCVDPPPKNGGAPCPGPSHEKAPCNLQLCPGDTDCEPGLVHVNA ELCQKGLVPPCPPSCLDPEANRSCSGHCMEGCRCPPGLLLQDSHCLPLSECPCLVGQKLI QPRLAFLLDNCSQCICEKGTLLCKPGACSQSCGWSAWSPWTACDRSCGSGVRARFRSPTN PPVAFGGSPCEGDRQELQACYTDCGTEIPGWTPWTSWSSCSQSCLVPGGDPGWRQRSRLC PSSRDTFCPGEATQEEPCSPPVCPVPSAWGLWASWSTCSASCNGGIQTRGRSCSGSAPGN PVCLGPHTQTRDCNMHPCTAQCPGNMVFRSAEQCLEEGGPCPQLCLAQDPGVECTGSCAP SCNCPPGLFLHNASCLPRSQCPCQLHGQLYAPGAVAHLDCNNCTCISGEMVCTSKRCPVA CGWSPWTPWSPCSQSCNVGIRRRFRAGTEPPAAFGGAECQGPNLDAEFCSLRPCRGPGAA WSSWTPCSVPCGGGYRNRTQGSGPHSPIEFSTCSLQPCAGPVPGVCPEDQQWLDCAQGPA SCAHLSIPGEANQTCHPGCYCLSGMLLLNNVCVPVQDCPCAHRGRLYSPGSAVHLPCENC SCISGLITNCSSWPCEEGQPAWSSWTPWSVCSASCNPARRHRHRFCARPPHRAPFSLVLL TTVAAPTTLCPGPEAEEEPCLLPGCNQAGGWSPWSPWSGCSRSCGGGLRSRTRACDQPSP QGLGDFCEGPQAQGEACQAQPCPVTNCSAMEGAEYSPCGPPCPRSCDDLVHCVWRCQPGC YCPLGKVLSADGAICVKPSYCSCLDLLTGKRHHAGTQLMRPDGCNHCTCMEGRLNCTDLP CQVSGDWCPWSKWTACSQPCRGQTRTRSRACVCPAPQHGGSPCPEESGGTGVQHQMEACP NATACPVDGAWSPWGPWSSCDACLGQSYRSRVCSHPPISDGGKPCLGGYQQSRPCRNSST LCTDCGGGQDLLPCGQPCRHSCQDLSLGSTCQPGSAGCQSGCGCPPGQLSQHGLCVFPVD CHCHFQPRAMGIPENRSRSVGSTLSSWESLEPGEVVTGPCDNCTCVAGILQCHEVPSCPG PGIWSSWGPWEKCSVSCGGGEQLRSRQCARPPCPGLAQQSRICHIHVCRETGCPAGRLYR ECQPSDGCPFSCAHVTGQVACFSERCKEGCHCPEGTFQHHVACVQECPCVLTVLLLQELG LASAALGSYPTLLGDEGKPLGPGVELLPGQMLQTDCGNCSCVHGKLSCSMVECSRVHGSF GPWGMWSLCSRSCGGLGTRTRTRQCVLPTLAPGGLSCRGPLQDLEYCFSPECPGTAGSTV EPVTGLAGGWGPWSPWSPCSHSCTDPAHPAWRSRTRLCLANCTVGDSSQERPCNLPSCAA LLPCPGPGCGSGNCFWTSWAPWEPCSRSCGVGQQRRLRAYHPPGPGGHWCPDILTAYQER RFCNLRACPVPGGWSHWSPWSWCDRSCGGGRSLRSRSCSSPPPKNGGTSCVGERHHVRPC NPMPCEEGCPAGMEMVSCANHCPYSCSDLQEGGMCQEDQACQLGCRCSEGFLEQDGGCVP VGHCECTDAQGRSWAPGSQHQDACNNCSCQAGQLSCTAQLCSPPAHCAWSHWSAWSSCSH SCGPQGQQSRFRSSTSGSWALECQKEQSQSQPCPEVPCPPLCLHEAHLHELGDNWLHGEC QQCSCTPEGAICKDTDCAVPRGWTLWSSWSYCSVSCGGGSQVRTRSCTVSAPPHGSLSCE GPDTQTRHCGQQLCLQKLERCSWGPWGPCSRSCGTGLASRSGSCPCLLTKEDSKCNDTFL GLDTQACYSGPCQDDCTWGDWSSWTRCSCKVLVQQRYRHQVPAPGQAGEGTPCTRLDGHF RPCTIGNCSEDSCPPPFEFQSCGSPCAGLCATHLNHRLCQDLPPCQPGCYCPKGLLEQAG SCILPEQCNCWHISGEGARVTLAPGDRLQLGCKECVCRRGELQCSSQGCEGLLPLTGWSE WSPCGPCLPQSALAPASRTALEGHWPLNTSDLPPPSVTLLASEQYRHRLCLDPETRRPWA GDPALCTVPLSQQRLCPDPGACNDTCQWGPWGPWSPCQMPCSGGFKLRWRVARDTSAGEC PGPWAQTESCNMGSCPGESCETRDTVFTLDCANQCPRSCADLWDGVQCLQGPCSPGCRCP PGQLVQDGHCVPISSCRCGLPSANASWELAPTQVVQLDCHNCTCINGTLMCPHLECPVLG PWSAWSECSAVCGKGTMVRHRSCEEHPDREPCQALDLQQWQECNLQACPECPPGQVLSTC ATMCPSLCSHLWPGTICVREPCQLGCGCPGGQLLYNGTCIPPEACPCTQFSLPWGLTLPL EEQARELPSGTVLTRNCTHCTCQGGAFICSLTDCQECAPGEIWQHGKLGPCEKTCPEMNM TQAWSNCTEAQAPGCVCQLGYFRSQTGLCVPEDHCECWHHGSPHLPGSEWQEACESCRCL HGKSVCIRHCPELSCAQGEVIMQEPGSCCPICQQDTLKEEPVSCRYLTELRNLTKGPCHL DQIEVSYCSGHCRSSTNVMTEEPYLQSQCDCCSYRLDPDSPVRILNLLCPDGHTEPVVLP VIHSCQCSACQGGDFSKH h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001400.txt0000600000175000017500000000275111455416572021773 0ustar ykeyke>sp|Q9ESU6|BRD4_MOUSE Bromodomain-containing protein 4 OS=Mus musculus GN=Brd4 PE=1 SV=1 MSTESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAASTNPPPPETSNPNKPKRQT NQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYW NAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRG RGRKETGAAKPGVSTVPNTTQASTSPQTQTPQQNPPPPVQATTHPFPAVTPDLIAQPPVM TMVPPQPLQTPSPVPPQPPPPPAPVPQPVQSHPPIIATTPQPVKTKKGVKRKADTTTPTT IDPIHEPPSLAPEPKTAKLGPRRESSRPVKPPKKDVPDSQQHPGPEKSSKISEQLKCCSG ILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFG ADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVTVSSPAVPPPTKV VAPPSSSDSSSDSSSDSDSSTDDSEEERAQRLAELQEQLKAVHEQLAALSQPQQNKPKKK EKDKKEKKKEKHKKKEEVEENKKSKTKELPPKKTKKNNSSNSNVSKKEPVPTKTKPPPTY ESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETL KPSTLRELERYVTSCLRKKRKPQAEKVDVIAGSSKMKGFSSSESESTSESSSSDSEDSET EMAPKSKKKGHTGRDQKKHHHHHHPQMQPAPAPVPQQPPPPPQQPPPPPPPQQQQQQPPP PPPPPSMPQQTAPAMKSSPPPFITAQVPVLEPQLPGSVFDPIGHFTQPILHLPQPELPPH LPQPPEHSTPPHLNQHAVVSPPALHNALPQQPSRPSNRAAALPPKPTRPPAVSPALAQPP LLPQPPMVQPPQVLLEDEEPPAPPLTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPL PPPPHPSVQQQQLQPQPPPPPPPQPQPPPQQQHQPPPRPVHLPSMPFSAHIQQPPPPPGQ QPTHPPPGQQPPPPQPAKPQQVIQHHPSPRHHKSDPYSAGHLREAPSPLMIHSPQMPQFQ SLTHQSPPQQNVQPKKQVKGRAEPQPPGPVMGQGQGCPPASPAAVPMLSQELRPPSVVQP QPLVVVKEEKIHSPIIRSEPFSTSLRPEPPKHPENIKAPVHLPQRPEMKPVDIGRPVIRP PEQSAPPPGAPDKDKQKQEPKTPVAPKKDLKIKNMGSWASLVQKHPTTPSSTAKSSSDSF EHFRRAAREKEEREKALKAQAEHAEKEKERLRQERMRSREDEDALEQARRAHEEARRRQE QQQQQQQQRQEQQQQQQQAAAVAAASAPQAQSSQPQSMLDQQRELARKREQERRRREAMA ATIDMNFQSDLLSIFEENLF h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001900.txt0000600000175000017500000000376311455416572022004 0ustar ykeyke>sp|P37297|STT4_YEAST Phosphatidylinositol 4-kinase STT4 OS=Saccharomyces cerevisiae GN=STT4 PE=1 SV=1 MRFTRGLKASSSLRAKAIGRLTKLSTGAPNDQNSNGTTLDLITHTLPIFYSTNTSKIYTI PLTLSEWEVLTSLCVAIPTTLDLVETMLKEIIAPYFLETPRQRISDVLSSKFKLEQMRNP IELLTFQLTKFMIQACEQYPVLYENIGGIISTYFERVLKIFTIKQSGLLSLVGFINAFIQ FPNSTELTKFTWKKLAKLVLRGSFLNEVDKILNSSATFTNDSIVQYYDAGNELSSAYLLE LISRLQVSLISHLLNTSHVGANLSEFLLNQQYQFYKFDQEVADENDDTKCIDDFFFNVRS NKQFFTDMCKISLQFCSESHILDLSTDNRARFSFDTRAHYLQTLCLIPFIEDTESELFES FTNVVSESIDKFFLSDVVTPSLIKAIVASASLLNFFTEKLSLTLIRMFPLLVASPHITTE TVNDVAKIFTTGLYPLNEDAIVSTIYSMNNLLAVSEDGSPVPVLRERQLTITSGKNIEKD YFPLRNSSASLDGTGALLGNTTVGQLSSHDVNSGATMTYHASLISNCVAATTTIASYYNT QSITALTISILTQKVNSMSKELDGVILNSLARLAPNTSLTEFSLLLKFFKSRTVIATKID DSALLKNIIKAKCVISKELLARHFSSDLYFMYLHDLLDSIIASGEVERLEHHRPQTEISR VADQIATYLEPLAALLPVPGDTPLDINKDEVTTNKFRNAWFNFVIHGYHLGGPIVKRNFS FLLTIAYNSPPLASEFPANNKELSLEMNTILRRGSSNENIKQQKQQITEYFNTNIVQYRT TSSSKIMFLAAAVLLETIRCEAGDCSKTLLYFSDPSILSGSIEKCIAVLSVSMIRKYARL IQKGNDAIFNSKMIAQQLNNLLLCLSHREPTLQDAAFHACEIFIRSIPSSLCHHLSLYTL LDMLTALFDSILDSEAHKFEPRYEFKLKHSKTTILVPSSSSWRATTLSRLHKSAKEWVRI LLNRSNQDTKILLQSYISDLGEYSRLNSVEFGVSFAMDMAGLILPADKELSRLTYYGPEK PNTISGFISLHSWRSKYLFDTAITSSPEDIKRQIGISTQNIRKNLTLGNKIITKDVTDFL DMATALLILGNGAPASLIYDIVHIPFEVFTSASLKIATNVWLTIITEKPEVAHLLLVEVC YCWMRSIDDNIGLYSRDHDLKGEEYQKMEYSPYDKAGINRDAKNASQAMQPHLHVIKFFA SHFEGTLFQSDFLLKIFTKCALYGIKNLYKASLHPFARMIRHELLLFATLVLNASYKQGS KYMGRLSQEITNGALSWFKRPVAWPFGSNELKIKADLSVTRDLFLQLNKLSSLMSRHCGK DYKILNYFLASEIQQIQTWLTPTEKIEGADSNELTSDIVEATFAKDPTLAINLLQRCYSK KAEDVLVGLVAKHALMCVGSPSALDLFIKGSHLSSKKDLHATLYWAPVSPLKSINLFLPE WQGNSFILQFSIYSLESQDVNLAFFYVPQIVQCLRYDKTGYVERLILDTAKISVLFSHQI IWNMLANCYKDDEGIQEDEIKPTLDRIRERMVSSFSQSHRDFYEREFEFFDEVTGISGKL KPYIKKSKAEKKHKIDEEMSKIEVKPDVYLPSNPDGVVIDIDRKSGKPLQSHAKAPFMAT FKIKKDVKDPLTGKNKEVEKWQAAIFKVGDDCRQDVLALQLISLFRTIWSSIGLDVYVFP YRVTATAPGCGVIDVLPNSVSRDMLGREAVNGLYEYFTSKFGNESTIEFQNARNNFVKSL AGYSVISYLLQFKDRHNGNIMYDDQGHCLHIDFGFIFDIVPGGIKFEAVPFKLTKEMVKV MGGSPQTPAYLDFEELCIKAYLAARPHVEAIIECVNPMLGSGLPCFKGHKTIRNLRARFQ PQKTDHEAALYMKALIRKSYESIFTKGYDEFQRLTNGIPY h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003301.txt0000600000175000017500000000660611455416572022000 0ustar ykeyke>sp|Q91ZI0|CELR3_MOUSE Cadherin EGF LAG seven-pass G-type receptor 3 OS=Mus musculus GN=Celsr3 PE=2 SV=1 MARRPLWWGLPGPSTPVLLLLLLSLFPFSREELGGGGDQDWDPGVATTTGPRAQIGSGAV ALCPESPGVWEDGDPGLGVREPVFMRLRVGRQNARNGRGAPEQPNAEVVVQALGSREQEA GQGPGYLLCWHPEISSCGRTGPLRRGSLPLDALSPGDSDLRNSSPHPSELLAQPDGSRPV AFQRNARRSIRKRVETSRCCGKLWEPGHKGQGERSATSTVERGPFRRDCLPGSLGSGLGE DSAPRAVRTAPTPGSAPRESRTAPGRMRSRGLFRRRFLFERPGPRPPGFPTGPEAKQILS TNQARPRRAANRHPQFPQYNYQTLVPENEAAGTSVLRVVAQDPDPGEAGRLIYSLAALMN SRSLELFSIDPQSGLIRTAAALDRESMERHYLRVTAQDHGSPRLSATTMVAVTVADRNDH APVFEQAQYRETLRENVEEGYPILQLRATDGDAPPNANLRYRFVGSPAVRTAAAAAFEID PRSGLISTSGRVDREHMESYELVVEASDQGQEPGPRSATVRVHITVLDENDNAPQFGEKR YVAQVREDVRPHTVVLRVTATDKDKDANGLVHYNIISGNSRGHFAIDSLTGEIQVMAPLD FEAEREYALRIRAQDAGRPPLSNNTGLASIQVVDINDHAPIFVSTPFQVSVLENAPLGHS VIHIQAVDADHGENSRLEYSLTGVASDTPFVINSATGWVSVSGPLDRESVEHYFFGVEAR DHGSPPLSASASVTVTVLDVNDNRPEFTMKEYHLRLNEDAAVGTSVVSVTAVDRDANSAI SYQITGGNTRNRFAISTQGGVGLVTLALPLDYKQERYFKLVLTASDRALHDHCYVHINIT DANTHRPVFQSAHYSVSMNEDRPVGSTVVVISASDDDVGENARITYLLEDNLPQFRIDAD SGAITLQAPLDYEDQVTYTLAITARDNGIPQKADTTYVEVMVNDVNDNAPQFVASHYTGL VSEDAPPFTSVLQISATDRDAHANGRVQYTFQNGEDGDGDFTIEPTSGIVRTVRRLDREA VPVYELTAYAVDRGVPPLRTPVSIQVTVQDVNDNAPVFPAEEFEVRVKENSIVGSVVAQI TAVDPDDGPNAHIMYQIVEGNIPELFQMDIFSGELTALIDLDYEARQEYVIVVQATSAPL VSRATVHVRLVDQNDNSPVLNNFQILFNNYVSNRSDTFPSGIIGRIPAYDPDVSDHLFYS FERGNELQLLVVNRTSGELRLSRKLDNNRPLVASMLVTVTDGLHSVTAQCVLRVVIITEE LLANSLTVRLENMWQERFLSPLLGHFLEGVAAVLATPTEDVFIFNIQNDTDVGGTVLNVS FSALAPRGAGAGAAGPWFSSEELQEQLYVRRAALAARSLLDVLPFDDNVCLREPCENYMK CVSVLRFDSSAPFLASTSTLFRPIQPIAGLRCRCPPGFTGDFCETELDLCYSNPCRNGGA CARREGGYTCVCRPRFTDCELDTEAGRCVPGVCRNGGTCTNAPNGGFRCQCPAGGAFEGP RCEVAARSFPPSSFVMFRGLRQRFHLTLSLSFATVQPSGLLFYNGRLNEKHDFLALELVA GQVRLTYSTGESNTVVSPTVPGGLSDGQWHTVHLRYYNKPRTDALGGAQGPSKDKVAVLS VDDCNVAVALQFGAEIGNYSCAAAGVQTSSKKSLDLTGPLLLGGVPNLPENFPVSHKDFI GCMRDLHIDGRRMDMAAFVANNGTMAGCQAKSHFCASGPCKNNGFCSERWGGFSCDCPVG FGGKDCRLTMAHPYHFQGNGTLSWDFGNDMAVSVPWYLGLSFRTRATKGILMQVQLGPHS VLLCKLDRGLLSVTLNRASGHTVHLLLDQMTVSDGRWHDLRLELQEEPGGRRGHHIFMVS LDFTLFQDTMAMGGELQGLKVKQLHVGGLPPSSKEEGHQGLVGCIQGVWIGFTPFGSSAL LPPSHRVNVEPGCTVTNPCASGPCPPHADCKDLWQTFSCTCRPGYYGPGCVDACLLNPCQ NQGSCRHLQGAPHGYTCDCVSGYFGQHCEHRVDQQCPRGWWGSPTCGPCNCDVHKGFDPN CNKTNGQCHCKEFHYRPRGSDSCLPCDCYPVGSTSRSCAPHSGQCPCRPGALGRQCNSCD SPFAEVTASGCRVLYDACPKSLRSGVWWPQTKFGVLATVPCPRGALGAAVRLCDEDQGWL EPDLFNCTSPAFRELSLLLDGLELNKTALDTVEAKKLAQRLREVTGQTDHYFSQDVRVTA RLLAYLLAFESHQQGFGLTATQDAHFNENLLWAGSALLAPETGHLWAALGQRAPGGSPGS AGLVQHLEEYAATLARNMELTYLNPVGLVTPNIMLSIDRMEHPSSTQGARRYPRYHSNLF RGQDAWDPHTHVLLPSQASQPSPSEVLPTSSNAENATASSVVSPPAPLEPESEPGISIVI LLVYRALGGLLPAQFQAERRGARLPQNPVMNSPVVSVAVFHGRNFLRGVLVSPINLEFRL LQTANRSKAICVQWDPPGPTDQHGMWTARDCELVHRNGSHARCRCSRTGTFGVLMDASPR ERLEGDLELLAVFTHVVVAVSVTALVLTAAVLLSLRSLKSNVRGIHANVAAALGVAELLF LLGIHRTHNQLLCTAVAILLHYFFLSTFAWLLVQGLHLYRMQVEPRNVDRGAMRFYHALG WGVPAVLLGLAVGLDPEGYGNPDFCWISIHEPLIWSFAGPIVLVIVMNGTMFLLAARTSC STGQREAKKTSVLTLRSSFLLLLLVSASWLFGLLAVNHSILAFHYLHAGLCGLQGLAVLL LFCVLNADARAAWTPACLGKKAAPEETRPAPGPGSGAYNNTALFEESGLIRITLGASTVS SVSSARSGRAQDQDSQRGRSYLRDNVLVRHGSTAEHTERSLQAHAGPTDLDVAMFHRDAG ADSDSDSDLSLEEERSLSIPSSESEDNGRTRGRFQRPLRRAAQSERLLAHPKDVDGNDLL SYWPALGECEAAPCALQAWGSERRLGLDSNKDAANNNQPELALTSGDETSLGRAQRQRKG ILKNRLQYPLVPQSRGTPELSWCRAATLGHRAVPAASYGRIYAGGGTGSLSQPASRYSSR EQLDLLLRRQLSKERLEEVPVPAPVLHPLSRPGSQERLDTAPARLEARDRGSTLPRRQPP RDYPGTMAGRFGSRDALDLGAPREWLSTLPPPRRNRDLDPQHPPLPLSPQRQLSRDPLLP SRPLDSLSRISNSREGLDQVPSRHPSREALGPAPQLLRAREDPASGPSHGPSTEQLDILS SILASFNSSALSSVQSSSTPSGPHTTATASALGPSTPRSATSHSISELSPDSEVPRSEGH S h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00001300.txt0000600000175000017500000000264011455416572021767 0ustar ykeyke>sp|A2AH22|AMRA1_MOUSE Activating molecule in BECN1-regulated autophagy protein 1 OS=Mus musculus GN=Ambra1 PE=1 SV=1 MKVVPEKNAVRILWGRERGTRAMGAQRLLQELVEDKTRWMKWEGKRVELPDSPRSTFLLA FSPDRTLLASTHVNHNIYITEVKTGKCVHSLIGHRRTPWCVTFHPTISGLIASGCLDGEV RIWDLHGGSESWFTDSNNAIASLAFHPTAQLLLIATANEIHFWDWSRREPFAVVKTASEM ERVRLVRFDPLGHYLLTAIVNPSNQQGDDEPEIPIDGTELSHYRQRALLQSQPVRRTPLL HNFLHMLSSRSSGIQVGEQSTVQDSATPSPPPPPPQPSTERPRTSAYIRLRQRVSYPTTV ECCQHPGILCLCSRCAGTRVPSLLPHQDSVPPASARATTPSFSFVQTEPFHPPEQASSTQ QDQGLLNRPSAFSTVQSSTAGNTLRNLSLGPTRRSLGGPLSSHPSRYHRELAPGLTGSEW TRTVLTLNSRSEVESMPPPRTSASSVSLLSVLRQQEGGSQASVYTSATEGRGFPSSGLAT ESDGGNGSSQNNSGSIRHELQCDLRRFFLEYDRLQELDQSLSGETPQTQQAQEMLNNNIE SERPGPSHLPTPHSSENNSNLSRGHLNRCRACHNLLTFNNDTLRWERTTPNYSSGEASSS WHVSTTFEGMPPSGNQLPPLERTEGQMPSSSRLELSSSASSQEERTVGVAFNQETGHWER IYTQSSRSGTVSQEALHQDMPEESSEEDSLRRRLLESSLISLSRYDGAGSREHPIYPDPA RLSPAAYYAQRMIQYLSRRDSIRQRSMRYQQNRLRSSTSSSSSDNQGPSVEGTDLEFEDF EDNGDRSRHRAPRNARMSAPSLGRFVPRRFLLPEYLPYAGIFHERGQPGLATHSSVNRVL AGAVIGDGQSAVASNIANTTYRLQWWDFTKFDLPEISNASVNVLVQNCKIYNDASCDISA DGQLLAAFIPSSQRGFPDEGILAVYSLAPHNLGEMLYTKRFGPNAISVSLSPMGRYVMVG LASRRILLHPSTEHMVAQVFRLQQAHGGETSMRRVFNVLYPMPADQRRHVSINSARWLPE PGLGLAYGTNKGDLVICRPEALNSGIEYYWDQLSETVFTVHSSSRSSERPGTSRATWRTD RDMGLMNAIGLQPRNPTTSVTSQGTQTLALQLQNAETQTEREEEEPGAASSGPGEGEGSE YGGSGEDALSRIQRLMAEGGMTAVVQREQSTTMASMGGFGNNIIVSHRIHRSSQTGTESG AARTSSPQPSTSRGLPSEPGQLAERALSPRTASWDQPSTSGRELPQPALSSSSPVPIPVP LASNEGPTMHCNVTNNSHLPEGDGSNRGEAAGPSGEPQNR h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00002000.txt0000600000175000017500000000412611455416572021766 0ustar ykeyke>sp|Q12873|CHD3_HUMAN Chromodomain-helicase-DNA-binding protein 3 OS=Homo sapiens GN=CHD3 PE=1 SV=3 MKAADTVILWARSKNDQLRISFPPGLCWGDRMPDKDDIRLLPSALGVKKRKRGPKKQKEN KPGKPRKRKKRDSEEEFGSERDEYREKSESGGSEYGTGPGRKRRRKHREKKEKKTKRRKK GEGDGGQKQVEQKSSATLLLTWGLEDVEHVFSEEDYHTLTNYKAFSQFMRPLIAKKNPKI PMSKMMTILGAKWREFSANNPFKGSAAAVAAAAAAAAAAVAEQVSAAVSSATPIAPSGPP ALPPPPAADIQPPPIRRAKTKEGKGPGHKRRSKSPRVPDGRKKLRGKKMAPLKIKLGLLG GKRKKGGSYVFQSDEGPEPEAEESDLDSGSVHSASGRPDGPVRTKKLKRGRPGRKKKKVL GCPAVAGEEEVDGYETDHQDYCEVCQQGGEIILCDTCPRAYHLVCLDPELDRAPEGKWSC PHCEKEGVQWEAKEEEEEYEEEGEEEGEKEEEDDHMEYCRVCKDGGELLCCDACISSYHI HCLNPPLPDIPNGEWLCPRCTCPVLKGRVQKILHWRWGEPPVAVPAPQQADGNPDVPPPR PLQGRSEREFFVKWVGLSYWHCSWAKELQLEIFHLVMYRNYQRKNDMDEPPPLDYGSGED DGKSDKRKVKDPHYAEMEEKYYRFGIKPEWMTVHRIINHSVDKKGNYHYLVKWRDLPYDQ STWEEDEMNIPEYEEHKQSYWRHRELIMGEDPAQPRKYKKKKKELQGDGPPSSPTNDPTV KYETQPRFITATGGTLHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYK EGHTKGPFLVSAPLSTIINWEREFQMWAPKFYVVTYTGDKDSRAIIRENEFSFEDNAIKG GKKAFKMKREAQVKFHVLLTSYELITIDQAALGSIRWACLVVDEAHRLKNNQSKFFRVLN GYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLL GPHMLRRLKADVFKNMPAKTELIVRVELSPMQKKYYKYILTRNFEALNSRGGGNQVSLLN IMMDLKKCCNHPYLFPVAAMESPKLPSGAYEGGALIKSSGKLMLLQKMLRKLKEQGHRVL IFSQMTKMLDLLEDFLDYEGYKYERIDGGITGALRQEAIDRFNAPGAQQFCFLLSTRAGG LGINLATADTVIIFDSDWNPHNDIQAFSRAHRIGQANKVMIYRFVTRASVEERITQVAKR KMMLTHLVVRPGLGSKAGSMSKQELDDILKFGTEELFKDENEGENKEEDSSVIHYDNEAI ARLLDRNQDATEDTDVQNMNEYLSSFKVAQYVVREEDKIEEIEREIIKQEENVDPDYWEK LLRHHYEQQQEDLARNLGKGKRVRKQVNYNDAAQEDQDNQSEYSVGSEEEDEDFDERPEG RRQSKRQLRNEKDKPLPPLLARVGGNIEVLGFNTRQRKAFLNAVMRWGMPPQDAFTTQWL VRDLRGKTEKEFKAYVSLFMRHLCEPGADGSETFADGVPREGLSRQQVLTRIGVMSLVKK KVQEFEHINGRWSMPELMPDPSADSKRSSRASSPTKTSPTTPEASATNSPCTSKPATPAP SEKGEGIRTPLEKEEAENQEEKPEKNSRIGEKMETEADAPSPAPSLGERLEPRKIPLEDE VPGVPGEMEPEPGYRGDREKSATESTPGERGEEKPLDGQEHRERPEGETGDLGKREDVKG DRELRPGPRDEPRSNGRREEKTEKPRFMFNIADGGFTELHTLWQNEERAAISSGKLNEIW HRRHDYWLLAGIVLHGYARWQDIQNDAQFAIINEPFKTEANKGNFLEMKNKFLARRFKLL EQALVIEEQLRRAAYLNLSQEPAHPAMALHARFAEAECLAESHQHLSKESLAGNKPANAV LHKVLNQLEELLSDMKADVTRLPATLSRIPPIAARLQMSERSILSRLASKGTEPHPTPAY PPGPYATPPGYGAAFSAAPVGALAAAGANYSQMPAGSFITAATNGPPVLVKKEKEMVGAL VSDGLDRKEPRAGEVICIDD h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004114.txt0000600000175000017500000001027511455416572022000 0ustar ykeyke>sp|O43103|SID2_USTMA Ferrichrome siderophore peptide synthetase OS=Ustilago maydis GN=SID2 PE=3 SV=2 MSVSKNAHAPFPDVTGLRTSGPDFSRVGPQCKLLRVQQSLHLDARAASSFSGQDLHLALL SAWCVILFHYGSHEATNIEVLHTSQHGHETLVELDFAEQRELVPFTPSQLAAFVHQARQQ QLPAKDLDHGYAAFYQPSHTNEPSPHFQQLQLSSRPDISLALSYHLQGSAQLVLEMKAAP SVHSHQSAQLQLRQVAALLESYHSDTQQHALSVERFDWKLRASDNPNYQHLPDPNHIQDR HADRLETEFEYFAATTPDALALDFRFDLQDLKSTKWSYAEMNQRAEKVKHLLWSHGVGSA SSDPQADHIVALYLEKSPETYLSFIGVLKAGAAWCPIDTDWPASRRQALLAKSNAKIVLT HDDKISEQLRHDLESQLVKDKGEITAIRLDQLDAELSQVQVVPPANANRSIQQLAYMIWT SGTTGLPKGVGIQHLAIIQAMRALRIYIPYGKDKIGTDQIRYLQYSAYNFDLSIMDCFYT WGLGGTICSCPRGVLLQDLVEVGNSLQPTHTLLTPAVMAMTERHRVPSLKVVISGGEKLS QVVADEWSKDCCLLNLYGPAEATLIAMNRRVPFGDRVKAPNIGVALPTVSCHALDKYDQI VIKGAVGELVLGGPQLARGYVGDPVKTADKFFPHPQLGRVYRTGDLVRQLDNQEFEYLGR IDDQVKINGIRIELLEINAAIKNSHDKIKDSETMAFSKKDNESEQQIINFSALPGGEPGQ LLRTDQDAIAVARELQANAKDSLPSYMVPNLFVILSHFPRTSSAKIDRVALKNVLASFDQ LDWENKLANEGDDDQVDPATAQAEACLRKWLAKLCNVDASKIGRKTPFTSVGLDSIRAMM FSKRVSEEGFAVSVLDVARFPTLKSLGEHLQSSGASSEERAKRAASFLADFDAAFRPVVS SWVKQRKADASAIQSILPCTPLQEGMLAESQRDSSSYRIQRQYRLASDCDQARLSKALIE TVAHFDSLRTSFADVGSLDVGLHQREWPFQPHFLQIVWKSFTPLIEQLDVDDGSDAEQAI LSAAKTKLDLDPFGTSPPVAFLFVKQALSRSLVVVAHHSTYDARSLGIFEDHVEAVYNRQ KPPTSLQFSTALAQILPIDQTEAQRHADVWQKALSNYPRGEYASFPTLSLTRPSEADADQ ASLHQSRYLEANINWAKIESACRELGVSARPLVQTAWALVLSAFTESQHLILGDSVSGRT LSAELDLAYGPVLSTVPVPFMLRPEQKLGNLIKQMDDFQTSIMEAQHTDLGAIRRMLQVP PRESLFHSVFVLEPAPEQPEDIDSSQFRLSKMADLGVATEHVLGVEVLPASDGSVKLGLS WQKNIISEGFGGLILEQFDRSLTALCSSLDADVGSLLYCHPRSDQQASSFYSVTKPVSKQ KCSSATFTGVASSLNKQAISDNSNAVEIYQDMADSPSSRKPAATMSYPELEQASNGVANL FRHLPRNSVVGVCLERGLESYIVPLAILKAGHAYLPLDATLPLDRKKELVKDSGAALIVA SSKFTDFDSLTGVEMLGTDSRQFKDAVKDGKATVSVESRSDDVAFIIYTSGSTGKPKGCL LTQANLAAAVEGFYYNYEKEAPGSFESRARFLARSAEAFDVHLLEIFLSLRVGATIVTGP RALIHDDIAKTMSTLEVTHACVVPSLFFSKGKRIEPSVVPSLRVLIIGGEALTQDLCQIW GSEGSERPVVLNAYGPSEATIGNSVARVSKKSRPSNIGAPFPGTQYLVLKDVNGQLVPTL RGEPGELYIGGEQVAKGYLNRPDSSSFITYQGQQIYRTGDMVRLHPSDEAEYLGRIDGSQ VKVRGARLELAEVDAALSASLNENLGTVGTAVTIHADHPKIEGAARLVSFFAQDCVRTKA QDSVDPGALLVQAPEAVKQSAELRRSVRARLPQYMVPSLVLALTYLPISPLSGKADRRLL KELYHSIDPSKLSTLSDKNESRQRELTDSEQTVAELVRSSVRLSSDVHLMHDLDLIMAGL DSLTVVTLANKLRKHGYDATVSSIMNEPTIEAIAGRRIDKLSSNETSDVEWKQTVSQLTD KVRSLPQYRGTQIETALPCVPIQVALVSQAVSDDRSTPRYITTISIDLSSNEFSADRIRN AWMTALSRHEIYRTVFAEVDRTLVQVVLSAESLTSNWSATSEPIPSPDSLADYHASTAKD IVANISSVPALRLKLWQGENGAPTLTLTCSHAIYDGDSIRMLLKEASDCLVTKSKVVPAL PFQEAARCIVGDAEDEEAKQFWTTTLADFLPTTVPNLTGVRPEHNVSRGEELTIASHLSF TQLEKAARAAKVTIQSILVAAFAHLLGLYAGESDVTLGLVLSGRSIPVDGVESIHGPCVT TVPLRLTDARSNASSDLCKRAHQAVNAILPHQHVSLPQLMRWLDLSKAPFEALFSYLGQS ERSSEKPYFSERASQMERDYSLALEVSAVGDAVNLHLAFDTRSMPAEQAKRMLCQYDGFL TVFTGTKRVDDDGKHLSILNKSCYVPTSANETIVARFTEHVKANPDAPAIVFASSMQEPP KVTSYAELDSLSTKIAFHLVHAAGPFVGVHLNKEGPELYATILAIWKAGKAYLPLDPSLP VERLSYMIESVGDCPVVASHSTKENLASFRCKVLDLKELVKPRSGAHELPSQNLDALCYL LFTSGSTGKPKAVQINQRALAGALYSWERILPFTRTSRFLQLASIGFDVCLIEMCMPLSL GFSIGTAPKQELLEDLTHSIKHLGITIADLPAALAGAVHPEDVRLEWLMSGGDVIDSRVV DEWNHAKRLLINAWGPTEATIGNTLGQVKRGATRNLIGGVYPSSSMFVLDENSTRILPSG AIGELAVGGPQLADCYYGREELTAEKFILLEDGTRVYRTGDLGRFLVDDTVECLGRIGSD RQVKVNGQRMELDEVCSVISAQAGVYDADVQYLKHPSMGSKQLVAFVAAAETQAKQGDMD VRDDDKAIDLCIRLEQEAAKRLATYMVPTHWIVMKHGLPLTHNNKTDHKALAAFYGRMDA TLLRSLGAKREGAISSHAWTQSELKLRALVSDFCNVPQDQLARNTSFHRLGIDSISAIRL VKQLRTSGFTFSVADVLSTPNIAALADKQMQSSACSSDHAQPNEGLNEWIGQISSVAENE AWKWSSKDSLVSVLPCTPLQSGMIAQSLASAGGLYFHHHAFELQSTEKQHVVAAWRKLVE RLDILRTTFHPVDGLHPWTQAVHSEVQPRIVQHSGSFQSCGLDAIDGQPSFQDEQAFRTP PFALHLWSQEGKLVVLISIHHALYDGSSLPQLLEDFEALITGNQAKLTSRLPFYKLVPSL LSQDEDVQHWVNALHAFQPTLLCKRSNKPSGAAVLLEKRLALTSQELESRCRAIGVSPQV LCNLTFGKLLAIESQTRDVCFGQLFGLLDLMPEADTCVGPAFNTTATRIRFQELDAPVSK LATTLQQANDAGRPHRRAALRDVQAKLGRGQLFDALFDYQRSYDQEDSKLRQIELQSDGT ERAQYTLNVAFVQGPSQMSIVAKADGNRYDQKALEGVVYRLEHLLEHLSIRVEEPISVLP DVFGETAFPLHLAQVSVANGTSTSKASAQNSANQALSQDGSKLASIISQIAGIDEMELHG ETRLSQLGLDSISAIRIASQARKAGLNLRMGEIVAGETINAILSARSQTNATKSSDHVNR NGRGNGHARVSLETAKRVAARLAIDFEQVERVLPVLPGQKLWLATWAQSQGGGGFSFAYR LAGAEADKVKETWQKLRQLQPILRTAFLVHHDGGASQVVLKADSVSAGSGFAEVQVERDA ELTAKDVVGRRAAQGWPDLTSPPVELTLVGEIVVFSLHHVLYDAFSIEFLARDFGSLYNA GELVSSNQWPEVVEHIVEEQQRTRGDAQEYWCRALAPGSSGLLADRPGSTGEAWHVQHNA ISLSSAVDVRIRKAGLTLAGVLLAAWSTLLSERMHDASPVFGLYQLGRSSSFESIDKVHG PLLNCLPIQLRGGSLLDKARAAVSELRLRAKFEQTDLQDAHRWAGLSQHQACYNTFVNIL FGDQLDQHLEMHQLDLGHPLDYSHHSQHSTHDRTPPSTPHVALPWQPDVNLDVVLKNHAV DIAIKANTSVVAQADLHTLVNRLVQLVHATLELL h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004416.txt0000600000175000017500000001075011455416572022003 0ustar ykeyke>sp|P0C6U9|R1A_CVM2 Replicase polyprotein 1a OS=Murine coronavirus (strain 2) GN=1a PE=3 SV=1 MAKMGKYGLGFKWAPEFPWMLPNASEKLGSPERSEEDGFCPSAAQEPKTKGKTLINHVRV DCSRLPALECCVQSAIIRDIFVDEDPLNVEASTMMALQFGSAVLVKPSKRLSIQAWAKLG VLPKTPAMGLFKRFCLCNTRECVCDAHVAFQLFTVQPDGVCLGNGRFIGWFVPVTAIPAY AKQWLQPWSILLRKGGNKGSVTSGHFRRAVTMPVYDFNVEDACEEVHLNPKGKYSRKAYA LLKGYRGVKSILFLDQYGCDYTGRLAKGLEDYGDCTLEEMKELFPVWCDSLDNEVVVAWH VDRDPRAVMRLQTLATIRSIGYVGQPTEDLVDGDVVVREPAHLLAANAIVKRLPRLVETM LYTDSSVTEFCYKTKLCDCGFITQFGYVDCCGDACDFRGWVPGNMMDGFLCPGCSKSYMP WELEAQSSGVIPKGGVLFTQSTDTVNRESFKLYGHAVVPFGSAVYWSPYPGMWLPVIWSS VKSYADLTYTGVVGCKAIVQETDAICRSLYMDYVQHKCGNLEQRAILGLDDVYHRQLLVN RGDYSLLLENVDLFVKRRAEFACKFATCGDGLVPLLLDGLVPRSYYLIKSGQAFTSMMVN FSHEVTDMCMDMALLFMHDVKVATKYVKKVTGKLAVRFKALGVAVVRKITEWFDLAVDTA ASAAGWLCYQLVNGLFAVANGGITFLSDVPELVKNFVDKFKVFFKVLIDSMSVSVLSGLT VVKTASNRVCLAGCKVYEVVQKRLSAYVMPVGCNEATCLVGEIEPAVVEDDVVDVVKAPL TYQGCCKPPTSFEKICVVDKLYMAKCGDQFYPVVVDNDTIGVLDQCWRFPCAGKKVEFND KPKVKEIPSTRKIKINFALDATFDSVLSKACSEFEVDKDVTLDELLDVVLDAVESTLSPC KEHDVIGTKVCALLNRLAEDYVYLFDEGGEEVIAPKMYCSFSAPDDEDCVAADVVDADEN QGDDADDSAALVTDTQEEDGVAKGQVGVAESDARLDQVEAFDIEKVEDPILNELSAELNA PADKTYEDVLAFDAIYSEALSAFYAVPGDETHFKVCGFYSPAIERTNCWLRSTLIVMQSL PLEFKDLEMQKLWLSYKSSYNKEFVDKLVKSVPKSIILPQGGYVADFAYFFLSQCSFKAY ANWRCLKCDMDLKLQGLDAMFFYGDVVSHVCKCGTGMTLLSADIPYTLHFGLRDDKFCAF YTPRKVFRAACVVDVNDCHSMAVVDGKQIDGKVVTKFNGDKYDFMVGHGMAFSMSAFEIA QLYGSCITPNVCFVKGDVIKVLRRVGAEVIVNPANGRMAHGAGVAGAIAKAAGKSFIKET ADMVKNQGVCQVGECYESTGGNLCKTVLNIVGPDARGHGKQCYSFLERAYQHINKCDDVV TTLISAGIFSVPTDVSLTYLIGVVTKNVILVSNNKDDFDVIEKCQVTSIAGTKALSLQLA KNLCRDVKFETNACDSLFSDSCFVSSYDVLQEVELLRHDIQLDDDARVFVQAHMDNLPAD WRLVNKFDSVDGVRTVKYFECPGEIFVSSQGKKFGYVQNGSFKVASVSQIRALLANKVDV LCTVDGVNFRSCCVAEGEVFGKTLGSVFCDGINVTKVRCSAIHKGKVFFQYSGLSAADLV AVTDAFGFDEPQLLKYYNMLGMCKWPVVVCGNYFAFKQSNNNCYINVACLMLQHLSLKFH KWQWQEAWNEFRSGKPLRFVSLVLAKGSFKFNEPSDSTDFMRVVLREADLSGATCDFEFV CKCGVKQEQRKGVDAVMHFGTLDKGDLAKGYTIACTCGNKLVHCTQLNVPFLICSNKPEG KKLPDDVVAANIFTGGSLGHYTHVKCKPKYQLYDACNVSKVSEAKGNFTDCLYLKNLKQT FSSKLTTFYLDDVKCVEYNPDLSQYYCESGKYYTKPIIKAQFRTFEKVEGVYTNFKLVGH SIAEKFNAKLGFDCNSPFTEYKITEWPTATGDVVLASDDLYVSRYSGGCVTFGKPVIWLG HEEASLKSLTYFNRPSVVCENKFNVLPVDVSEPTDKGPVPAAVLVTGALSGAATAPGTAK EQKVCASDSVVDQVVSGFLSDLSGATVDVKEVKLNGVKKPIKVEDSVVVNDPTSETKVVK SLSIVDVYDMFLTGCRYVVWMANELSRLVNSPTVREYVKWGMTKIVIPAKLVLLRDEKQE FVAPKVVKAKVIACYSAVKWFFLYCFSWIKFNTDNKVIYTTEVASKLTFNLCCLAFKNAL QTFNWNVVSRGFFLVATVFLLWFNFLYANVILSDFYLPNIGFFPTFVGQIVAWVKTTFGI FTLCDLYQVSDVGYRSSFCNGSMVCELCFSGFDMLDNYDAINVVQHVVDRRVSFDYISLF KLVVELVIGYSLYTVCFYPLFGLIGMQLLTTWLPEFFMLETMHWSARFFVFVANMLPAFT LLRFYIVVTAMYKIFCLCRHVMYGCSRPGCLFCYKRNRSVRVKCSTVVGGTLRYYDVMAN GGTGFCAKHQWNCLNCSAFGPGNTFITHEAAADLSKELKRPVNPTDSAYYLVTEVKQVGC SMRLFYERDGQRVYDDVSASLFVDMNGLLHSKVKGVPETHVVVVENEADKAGFLNAAVFY AQSLYRPMLLVEKKLITTANTGLSVSQTMFDLYVDSLLGVLDVDRKSLTSFVNAAHNSLK EGVQLEQVMDTFIGCARRKCAIDSDVETKSITKSIMSAVNAGVDFTDESCNNLVPTYVKS DTIVAADLGVLIQNNAKHVQANVAKAANVACIWSVDAFNQLSADLQHRLRKACSKTGLKI KLTYNKQEANVPILTTPFSLKGGAVFSKVLQWLFVVNLICFIVLWALMPTYAVHKSDMQL PLYASFKVIDNGVLRDVTVTDACFANKFIQFDQWYESTFGLVYYRNSRACPVVVAVIDQD IGYTLFNVPTKVLRYGFHVLHFITHAFATDSVQCYTPHMQIPYDNFYASGCVLSSLCTML AHADGTPHPYCYTEGIMHNASLYDSLAPHVRYNLANSNGYIRFPEVVSEGIVRIVRTRSM TYCRVGLCEDAEEGVCFNFNSSWVLNNPYYRAMPGTFCGRNAFDLIHQVLGGLVRPIDFF ALTASSVAGAILAIIVVLAFYYLIKLKRAFGDYTSVVVINVIVWCINFLMLFVFQVYPTL SCLYACFYFYTTLYFPSEISVVMHLQWLVMYGAIMPLWFCIIYVAVVVSNHALWLFSYCR KLGTEVRSDGTFEEMSLTTFMITKESYCKLKNSVSDVAFNRYLSLYNKYRYFSGKMDTAA YREAACSQLAKAMETFNHNNGNDVLYQPPTASVTTSFLQSGIVKMVFPTSKVEPCVVSVT YGNMTLNGLWLDDKVYCPRHVICSSADMTDPDYSNLLCRVISSDFCVMSGRMSLTVMSYQ MQGSLLVLTVTLQNPNTPKYSFGVVKPGETFTVLAAYNGKSQGAFHVTMRSSYTIKGSFL CGSCGSVGYVLTGDSVRFVYMHQLELSTGCHTGTDFSGNFYGPYRDAQVVQLPVQDYTQT VNVVAWLYAAILNRCNWFVQSDSCSLEEFNVWAMTNGFSSIKADLVLDALASMTGVTVEQ ILAAIKRLYSGFQGKQILGSCVLEDELTPSDVYQQLAGVKLQSKRTRVVKGTCCWILAST LLFCSIISAFVKWTMFMYVTTHMLGVTLCALCFVSFAMLLVKHKHLYLTMFIMPVLCTLF YTNYLVVYKQSFRGLAYAWLSHFVPAVDYTYMDEVLYGVVLLVAMVFVTMRSINHDVFSV MFLVGRLVSLVSMWYFGANLEEEVLLFLTSLFGTYTWTTMLSLATAKVIAKWLAVNVLYF TDVPQVKLVLLSYLCIGYVCCCYWGVLSLLNSIFRMPLGVYNYKISVQELRYMNANGLRP PRNSFEALVLNFKLLGIGGVPVIEVSQIQSRLTDVKCVNVVLLNCLQHLHIASSSKLWQY CSTLHNEILATSDLSVAFDKLAQLLVVLFANPAAVDSKCLASIEEVSDDYVRDSTVLQAL QSEFVNMASFVEYELAKKNLDEAKASGSANQQQIKQLEKACNIAKSAYERDRAVARKLER MADLALTNMYKEARINDKKSKVVSALQTMLFSMIRKLDNQALNSILDNAVKGCVPLNAIP SLTSNTLTIIVPDKQVFDQVVDNVYVTYAGNVWHIQSIQDADGAVKQLNEIDVNITWPLV IAANRHNEVSSVVLQNNELMPQKLRTQVVNSGSDMNCNTPTQCYYNTTGMGKIVYAILSD CDGLKYTKIVKEDGNCVVLELDPPCKFSVQDVKGLKIKYLYFVKGCNTLARGWVVGTLSS TVRLQAGTATEYASNSAIRSLCAFSVDPKKTYLDYIQQGGAPVTNCVKMLCDHAGTGMAI TIKPEATTNQDSYGGASVCIYCRSRVEHPDVDGLCKLRGKFVQVPLGIKDPVSYVLTHDV CQVCGFWRDGSCSCVGTGSQFQSKDTNFLNGFGVQV h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00003703.txt0000600000175000017500000000741611455416572022006 0ustar ykeyke>sp|Q15911|ZFHX3_HUMAN Zinc finger homeobox protein 3 OS=Homo sapiens GN=ZFHX3 PE=1 SV=2 MEGCDSPVVSGKDNGCGIPQHQQWTELNSTHLPDKPSSMEQSTGESHGPLDSLRAPFNER LAESTASAGPPSEPASKEVTCNECSASFASLQTYMEHHCPSARPPPPLREESASDTGEEG DEESDVENLAGEIVYQPDGSAYIVESLSQLTQGGGACGSGSGSGPLPSLFLNSLPGAGGK QGDPSCAAPVYPQIINTFHIASSFGKWFEGPDQAFPNTSALAGLSPVLHSFRVFDVRHKS NKDYLNSDGSAKSSCVSKDVPNNVDLSKFDGFVLYGKRKPILMCFLCKLSFGYVRSFVTH AVHDHRMTLSEDERKILSNKNISAIIQGIGKDKEPLVSFLEPKNKNFQHPLVSTANLIGP GHSFYGKFSGIRMEGEEALPAGSAAGPEQPQAGLLTPSTLLNLGGLTSSVLKTPITSVPL GPLASSPTKSSEGKDSGAAEGEKQEVGDGDCFSEKVEPAEEEAEEEEEEEEAEEEEEEEE EEEEEEEDEGCKGLFPSELDEELEDRPHEEPGAAAGSSSKKDLALSNQSISNSPLMPNVL QTLSRGTASTSSNSASSFVVFDGANRRNRLSFNSEGVRANVAEGGRRLDFADESANKDNA TAPEPNESTEGDDGGFVPHHQHAGSLCELGVGECPSGSGVECPKCDTVLGSSRSLGGHMT MMHSRNSCKTLKCPKCNWHYKYQQTLEAHMKEKHPEPGGSCVYCKSGQPHPRLARGESYT CGYKPFRCEVCNYSTTTKGNLSIHMQSDKHLNNMQNLQNGGGEQVFSHTAGAAAAAVAAA AAAANISSSCGAPSPTKPKTKPTWRCEVCDYETNVARNLRIHMTSEKHMHNMMLLQQNMT QIQHNRHLGLGSLPSPAEAELYQYYLAQNMNLPNLKMDSAASDAQFMMSGFQLDPAGPMA AMTPALVGGEIPLDMRLGGGQLVSEELMNLGESFIQTNDPSLKLFQCAVCNKFTTDNLDM LGLHMNVERSLSEDEWKAVMGDSYQCKLCRYNTQLKANFQLHCKTDKHVQKYQLVAHIKE GGKANEWRLKCVAIGNPVHLKCNACDYYTNSLEKLRLHTVNSRHEASLKLYKHLQQHESG VEGESCYYHCVLCNYSTKAKLNLIQHVRSMKHQRSESLRKLQRLQKGLPEEDEDLGQIFT IRRCPSTDPEEAIEDVEGPSETAADPEELAKDQEGGASSSQAEKELTDSPATSKRISFPG SSESPLSSKRPKTAEEIKPEQMYQCPYCKYSNADVNRLRVHAMTQHSVQPMLRCPLCQDM LNNKIHLQLHLTHLHSVAPDCVEKLIMTVTTPEMVMPSSMFLPAAVPDRDGNSNLEEAGK QPETSEDLGKNILPSASTEQSGDLKPSPADPGSVREDSGFICWKKGCNQVFKTSAALQTH FNEVHAKRPQLPVSDRHVYKYRCNQCSLAFKTIEKLQLHSQYHVIRAATMCCLCQRSFRT FQALKKHLETSHLELSEADIQQLYGGLLANGDLLAMGDPTLAEDHTIIVEEDKEEESDLE DKQSPTGSDSGSVQEDSGSEPKRALPFRKGPNFTMEKFLDPSRPYKCTVCKESFTQKNIL LVHYNSVSHLHKLKRALQESATGQPEPTSSPDNKPFKCNTCNVAYSQSSTLEIHMRSVLH QTKARAAKLEAASGSSNGTGNSSSISLSSSTPSPVSTSGSNTFTTSNPSSAGIAPSSNLL SQVPTESVGMPPLGNPIGANIASPSEPKEANRKKLADMIASRQQQQQQQQQQQQQQQQQQ QAQTLAQAQAQVQAHLQQELQQQAALIQSQLFNPTLLPHFPMTTETLLQLQQQQHLLFPF YIPSAEFQLNPEVSLPVTSGALTLTGTGPGLLEDLKAQVQVPQQSHQQILPQQQQNQLSI AQSHSALLQPSQHPEKKNKLVIKEKEKESQRERDSAEGGEGNTGPKETLPDALKAKEKKE LAPGGGSEPSMLPPRIASDARGNATKALLENFGFELVIQYNENKQKVQKKNGKTDQGENL EKLECDSCGKLFSNILILKSHQEHVHQNYFPFKQLERFAKQYRDHYDKLYPLRPQTPEPP PPPPPPPPPPLPAAPPQPASTPAIPASAPPITSPTIAPAQPSVPLTQLSMPMELPIFSPL MMQTMPLQTLPAQLPPQLGPVEPLPADLAQLYQHQLNPTLLQQQNKRPRTRITDDQLRVL RQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQRNKDSPYNFSNPPITSLE ELKIDSRPPSPEPPKQEYWGSKRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLN LPTRVIVVWFQNARQKARKNYENQGEGKDGERRELTNDRYIRTSNLNYQCKKCSLVFQRI FDLIKHQKKLCYKDEDEEGQDDSQNEDSMDAMEILTPTSSSCSTPMPSQAYSAPAPSANN TASSAFLQLTAEAEELATFNSKTEAGDEKPKLAEAPSAQPNQTQEKQGQPKPELQQQEQP EQKTNTPQQKLPQLVSLPSLPQPPPQAPPPQCPLPQSSPSPSQLSHLPLKPLHTSTPQQL ANLPPQLIPYQCDQCKLAFPSFEHWQEHQQLHFLSAQNQFIHPQFLDRSLDMPFMLFDPS NPLLASQLLSGAIPQIPASSATSPSTPTSTMNTLKRKLEEKASASPGENDSGTGGEEPQR DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKGQ FRAVGPAQAHRRCPFCRALFKAKTALEAHIRSRHWHEAKRAGYNLTLSAMLLDCDGGLQM KGDIFDGTSFSHLPPSSSDGQGVPLSPVSKTMELSPRTLLSPSSIKVEGIEDFESPSMSS VNLNFDQTKLDNDDCSSVNTAITDTTTGDEGNADNDSATGIATETKSSSAPNEGLTKAAM MAMSEYEDRLSSGLVSPAPSFYSKEYDNEGTVDYSETSSLADPCSPSPGASGSAGKSGDS GDRPGQKRFRTQMTNLQLKVLKSCFNDYRTPTMLECEVLGNDIGLPKRVVQVWFQNARAK EKKSKLSMAKHFGINQTSYEGPKTECTLCGIKYSARLSVRDHIFSQQHISKVKDTIGSQL DKEKEYFDPATVRQLMAQQELDRIKKANEVLGLAAQQQGMFDNTPLQALNLPTAYPALQG IPPVLLPGLNSPSLPGFTPSNTALTSPKPNLMGLPSTTVPSPGLPTSGLPNKPSSASLSS PTPAQATMAMGPQQPPQQQQQQQQPQVQQPPPPPAAQPPPTPQLPLQQQQQRKDKDSEKV KEKEKAHKGKGEPLPVPKKEKGEAPTATAATISAPLPTMEYAVDPAQLQALQAALTSDPT ALLTSQFLPYFVPGFSPYYAPQIPGALQSGYLQPMYGMEGLFPYSPALSQALMGLSPGSL LQQYQQYQQSLQEAIQQQQQRQLQQQQQQKVQQQQPKASQTPVPPGAPSPDKDPAKESPK PEEQKNTPREVSPLLPKLPEEPEAESKSADSLYDPFIVPKVQYKLVCRKCQAGFSDEEAA RSHLKSLCFFGQSVVNLQEMVLHVPTGGGGGGSGGGGGGGGGGGGGGSYHCLACESALCG EEALSQHLESALHKHRTITRAARNAKEHPSLLPHSACFPDPSTASTSQSAAHSNDSPPPP SAAAPSSASPHASRKSWPQVVSRASAAKPPSFPPLSSSSTVTSSSCSTSGVQPSMPTDDY SEESDTDLSQKSDGPASPVEGPKDPSCPKDSGLTSVGTDTFRL h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00004001.txt0000600000175000017500000001013511455416572021766 0ustar ykeyke>sp|Q9VCA8|ANKHM_DROME Ankyrin repeat and KH domain-containing protein mask OS=Drosophila melanogaster GN=mask PE=1 SV=2 MNNDAKNHESDDLNVRSTAYFNQQTTTNQPKAPATSKNNTGSGSGSNNNNNNTNQNPNRQ LNHNLPRIAAARQSIAAALLKNSGRKILTAKNEPLTTTESSGVLTNTPLPSNSRLKVNNN NNTNNTAKMSGTSSSQSSATPTPPTASSSTTTTTTTNISTGGGGSGSSGGGGGSTTVIAN PASVTNTGAGSAAKFRAAVASAPSPALPATNAPANATAAAAIAAIATAPAPSSSSSSSSS SKKTRAAVAALKRQVALQQQQPVTGNAPNMTSKDSAHLKFATTTLLMGAAAAAADSNAGA ALGGSGAGGSGSSSSVGAVGGARMALNPAVDMANAAVLLKQKLKDAAAAASASASNRSAT SSMSSTASSLSSSAGIVNAISSALQNIITPDTDTDTEFYPQPVTTDLSESEEESVSEDDI PESDPDSCPHEGEVREDEDETEEESEDSDESEGEEEEEDEEEIDVLQDNDADDEEIDDED EEEDAPEVSSFLLDANNKRSSNISALLEAAANEKAPVLRHATHAIDETKQALTKMRCASS PRDKNSGFSRSLVAACTDNDVNTVKRLLCKGNVNLNDAAASTDDGESLLSMACSAGYYEL AQVLLAMSAAQVEDKGQKDSTPLMEAASAGHLDIVKLLLNHNADVNAHCATGNTPLMFAC AGGQVDVVKVLLKHGANVEEQNENGHTPLMEAASAGHVEVAKVLLEHGAGINTHSNEFKE SALTLACYKGHLDMVRFLLQAGADQEHKTDEMHTALMEASMDGHVEVARLLLDSGAQVNM PTDSFESPLTLAACGGHVELATLLIERGANIEEVNDEGYTPLMEAAREGHEEMVALLLSK GANINATTEETQETALTLACCGGFMEVAAFLIKEGANLELGASTPLMEASQEGHTDLVSF LLKKKANVHAETQTGDTALTHACENGHTDAAGVLLSYGAELEHESEGGRTPLMKACRAGH LCTVKFLIQKGANVNKQTTSNDHTALSLACAGGHQSVVELLLKNNADPFHKLKDNSTMLI EASKGGHTRVVELLFRYPNISPTENAASANVTQAAPTSNQPGPNQMRQKIMKQQLQHQLQ QLNAPPGLHELSEAARASNQQHFHQQQFSSAGNGSSNIVAMGTGDFLDAGELQLTATAGM SAGAGTSTTGSETGMEEYGEVGGIDLTTLGAQQQEGLIAKSRLFHLQQQQQQQQQQQQQQ QQQQQQQQQQQQQQQQPPAAGQHQLVPCKHFDLDMEHINSLQPPQKAPPAPPVLFHTVCQ QPVMQQQQQQLQPGQLKLKAMLPNRNRALKTAEVVEFIDCPVDQQQPGEQVRTQPLGEDG KTPQFACAGEDPRLQRRRGFMPELKKGELPPESSSSDPNELALKGADNNQPVPTALDNSA CAQIPARNSGGAITHSSEVLQSTAISDRPKVKATNKNNRKQAAAAAAAAAAAAAAAAAAA QHAQQVLPNPMVSIYNNLHLQHLQHPHLQFQQQLQLHHQRVAGLDNAAAAAAAAASSANM AYSISPASPLPSPTGSGNYVDQQLQQQSMDVALQRKTAMDDFRGMLETAVNGPRGRKDLA LNTPQLNFFKDGWHMVGVHNFFGDQPKSPTETPPEMEETTMSSPTEADRLGSEPRAEMKN LATLCSAAAAAAAVAAVNKDQVEISSDLESECEDDAEGGAGADCEENTLPPEPIELAAAL REDGIIVEEEEDDEEEDDDDEEQDTNSGEVDKLNYDDEDAEVDNDGEVDYIDEDEGGGEG EEEEDDADDDEFFLDEPDSDQGTGNNNNNSKSGASSLPLKQRKMATRLENLILNSQTVCD FPPELSNSELVHVLPQISNLKAAANSNAALNSVLQQQLAAASAAAAHAKASVVHQKQQHG EGDQQCEDDGSASASELYSGLEHFANDGEMEDIFQELASSLNYPELAEFSLNQMCKGRFA GNWAQSSGKWTGQEQLVGVVRSPGLINPGDVPQDAQRQANLVLLDYPMQQNIQLEQRLLD AEEMHLQQHQQTPLSLLPFTDEQQQQLHHQALSNASDFQQHQQLALENDPELKQQLQQNS NARIIKAVAAQHQQQPPTNFVYNVESGDKNAPPVQLLFQLPPHMAQHQAQQQQGVGEPLT EQQQQQLHAEQAHLFQHRTGGQRPPTQSELEQVAQELLLQRSGQVPAGAPVVGVQAIPLK QKHFNLHPPPCPPTCVQHQVATQTHPASVVVPQPAVGYTQFALQASQQQQMQQNELSIWP MATPTPAPSSGVSSTKSMPGGIAKKAIDKQSRKERRCVVRQTPAGIQENTKLHLQPQVAT AQQQFLVQNQLAVATTVSLDKTIEIDSETESNHDTALTLACAGGHEELVELLINRGANIE HRDKKGFTPLILAATAGHDKVVDILLKHSAELEAQSERTKDTPLSLACSGGRYEVVELLL SVGANKEHRNVSDYTPLSLAASGGYVNIIKLLLSHGAEINSRTGSKLGISPLMLAAMNGH TPAVKLLLDQGSDINAQIETNRNTALTLACFQGRHEVVSLLLDRRANVEHRAKTGLTPLM EAASGGYIEVGRVLLDKGADVNAAPVPTSRDTALTIAADKGHQKFVELLLSRNASVEVKN KKGNSPLWLAAHGGHLSVVELLYDHNADIDSQDNRRVSCLMAAFRKGHTKIVKWMVQYVS QFPSDQEMIRFIGTISDKELIDKCFDCMKILRSAKEAQAVKANKNASILLEELDLERTRE ESRKAAAARRRERKKKKKMEKKEEKRRQQQGNGPGGDDMQGDDDDASDKDDDSDKDDEDE EAAPAAAREEGDSGIDQGSCSSGDTKGARFGGSQSAQAAEAAANSVSTNSQGKKNKKQAK NKVLISVEPTQPVITSNSVLKGVCAKKHPAVEVVKQPPATQQAAPLKRQLDVKKEEPALK KKEEKNSSSSSSSKREKENLAPKEVALPAKQQPSSSSKLQSSESASNINSSTATNTSSAN TTRKEVAKPASQTASATTLNPAKRTEVDGWKEVVRKSSAQQTTAVGASGAPLPVTATSSA TSVQHHPHHHLANSSSNSSSSLTTSTTTAASSVPEMTCKKVQVPVNAISRVIGRGGSNIN AIRATTGAHIEVEKQGKNQSERCITIKGLTDATKQAHMLILALIKDPDVDILQMLPRINS SIKQASSGGASTPMSVGTWDNRTAAGVNAYTFSSAASTTSTSSSSSASSTTPAGASYSNA HKQHQQQPQSVKGPSGRSSTSVKSNGSSTKVSASSGSGSRSGRAGSSYLAQQQPGRSSGG GSSNGVIKSKSESSSKSLPAAQKSSTTLGKSSTVSPGAQNFAKAAAIGQSSPKKAEGGAT SAVVTSAGGRSSGVVAPFGRGKPVAGQGGPAATAASNVAQLGSVSGNSNILAGPIGTFNV ADVAAVNAAAAAGAAAATNSNVKPIAPIAPPSKRVGSPTQVQQQHQTQQQQQQQLPQPAP VPGPQPQQQPLQQQQQQQAPQQQPQQPNQQQQPQTSQQNLVINTNLLNDLMAASAANTTS DSFSAQLAAKLSSAYSLFSDYQQSQWGKLGDPGIGGGAGAVGDGLPQADASKAPGYNRNI LSSPVGSSKASSNHSTSPPVGNVIQQQQQQQPQSSQQALNIITSGPGGPATAPARSPMVS ANEGNPAVGQPSMNGTQGLGETAPAHSPGVIKPPTATVPIQRHVPMPISAPEAGAPPTFG AIGSNPASGNNSAAAQAAAAAAASAMIDRQQQNLQNLQTLQNLQRMVGASQQQQPQQQLN YPMDPTSSFIVDANNVLRLNPRVIFPQGNTKPPQPPPQGGTQSNVFGGNPGRQPPGTGAR QPGGAAAQRWYGGTLEYPSYTGRDMLHLENGAGGMAGMGSPSAMSPNHDDIRKMPRPIGT ERAASWKYNNFNVGGPSLNMEDALASVLPPWAHELKAQPPGLQQPPPPPQSQQQQQQPLN WLKQQPQQQQYRAYNNGPYPQQQQQHEPMNMPMDYHNMQAPPNMSQQQQQHVNLMPSYGY QHFVGAPGAVDISAHMPDKMEVWDHHDKHMPWTNYTTNWSN h-blast-1.0_ncbi-blast-2.2.25/queries/24Sequence_length_30k.txt0000644000175000017500000010040012012642730022032 0ustar ykeyke>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 MGVYKFCYNKKKEVGQVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKC CKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI >sp|Q5WGN4|3MGH_BACSK Putative 3-methyladenine DNA glycosylase OS=Bacillus clausii (strain KSM-K16) GN=ABC1936 PE=3 SV=1 MEQQKALDLSFFEQSTIEVAKGLIGMHLVHELDGVTLIGRITETEAYLGVLDRACHSYGR RRTKRTAILYEEAGRCYTYTMHTHCLLNVVCEQKGQPEAVLIRAIEPISGVKEMERLRGK PHTSREFANGPGKLTKAMGITMADYGRLLTEPPLYFAKGDHTNASIVATKRIGIKGAGPC SHHPWRFIDGNSRAVSAYRP >sp|Q4V8X4|ACBD6_DANRE Acyl-CoA-binding domain-containing protein 6 OS=Danio rerio GN=acbd6 PE=2 SV=1 MASRSPSSSPDSATGSGTDPARPDTGEPLGGGSDSDSDFGLGKFDCSAGDASARLEGADL ENEFESAADRVRDLVQTASREQLLYLYARFKQVKVGKCNTSKPGFFDFEGQRKWSAWKQL GDMSAEQAMQEYVTCVHALDPEGSQKSSERRGGEKRTGFGGPAVSSLYQEEKIREEDKNI FDYCRENNIEHVSKAISSKTVDVNTRDEEGRALLHWACDRGHKDLVSLLLQNNADINSQD DEGQTALHYASACEFAEIVELLLKAGADPSIKDQEGSLPEEVTESSAISSLLRQYTAPKG >sp|Q52813|AAPQ_RHIL3 General L-amino acid transport system permease protein aapQ OS=Rhizobium leguminosarum bv. viciae (strain 3841) GN=aapQ PE=3 SV=1 MTHEAVDTTPLHGTGWSFRSAMYDPKYRSIFYQILTIVILVGFVWWVAHNTAVNLARSNT ASGFGFLRGRAGFEIGQSLITFSSDSTYARALLVGILNTLLVAVTGIFTATIIGFLIGIG RLSRNWLIAKLCTVYVEVFRNIPPLLVIFFWYLGVLSVLPQPRESVGLPFSMYLNNRGLA FPKPIFDTGMIAVGIALVIAIVASIIIARWAHKRQAATGQPFHTVWTAIALIVGLPLLVF VVSGFPLTFDVPVAGKFNLTGGSVVGPEFMSLFLALSFYTASFIAEIVRGGIRGVPKGQS EAAGALGLHPSSVTRLVVVPQALRIIIPPLTSQYLNLTKNSSLAIAIGFSDLVAVGGTIL NQSGQAIEIVCIWGIVYLSLSILTSLFMNWFNAKMALVER >sp|Q28647|2A5B_RABIT Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform OS=Oryctolagus cuniculus GN=PPP2R5B PE=2 SV=1 METKLPPASTPTSPSSPGLSPVPPADKVDGFSRRSLRRARPRRSHSSSQFRYQSNQQELT PLPLLKDVPASELHDLLSRKLAQCGVMFDFLDCVADLKGKEVKRAALNELVECVGSTRGV LIEPVYPDIIRMISVNIFRTLPPSENPEFDPEEDEPNLEPSWPHLQLVYEFFLRFLESPD FQPSVAKRYVDQKFVLMLLELFDSEDPREREYLKTILHRVYGKFLGLRAYIRKQCNHIFL RFIYEFEHFNGVAELLEILGSIINGFALPLKTEHKQFLVRVLIPLHSVKSLSVFHAQLAY CVVQFLEKDATLTEHVIRGLLKYWPKTCTQKEVMFLGEVEEILDVIEPSQFVKIQEPLFK QVARCVSSPHFQVAERALYFWNNEYILSLIEDNCHTVLPAVFGTLYQVSKEHWNQTIVSL IYNVLKTFMEMNGKLFDELTASYKLEKQQEQQKARERQELWQGLEELRLRRLQGTQGTQG AREAPLQRFVPQVAATGGQS >sp|P23745|ABRA_PLAFG 101 kDa malaria antigen (Fragment) OS=Plasmodium falciparum (isolate FCR-3 / Gambia) GN=ABRA PE=2 SV=1 QYTDSVTYLMDGFKSANNSANNGKKNNAEEMKNLVNFLQSHKKLIKALKKNIESIQNKKH LIYKNKSYNPLLLSCVKKMNMLKENVDYIQKNQNLFKELMNQKATYSFVNTKKKIISLKS QGHKKETSQNQNENNDNQKYQEVNDEDDVNDEEDTNDDEDTNDEEDTNDDEDTNDDEDTN DEEDTNDEEDHENNNATAYELGIVPVNDVLNVNMKNMITGNNFMDVVKSTLAQSGGLGSN DLINFLNQGKEIGENLLNITKMNLGDKNNLESFPLDQLNMLKDNLINYEFILNNLKTSVL NKLKDLLLRLLYKAYVSYKKRKAQEKGLPEPTVTNEEYVEELKKGILDMGIKLLFSKVKS LLKKLKNKIFPKKKEDNQAVDTKSMEEPKVKAQPALRGVEPTEDSNIMNSINNVMDEIDF FEKELIENNNTPNVVPPTQSKKKNKNETVSGMDENFDNHPENYFKEEYYYDENDDMEVKV KKIGVTLKKFEPLKNGNVSETIKLIHLGNKDKKHIEAINNDIQIIKQELQAIYNELMNYT NGNKNIQQIFQQNILENDVLNQETEEEMEKQVEAITKQIEAEVDALAPKNKEEEEKEKEK >sp|Q54GQ6|ACOX1_DICDI Peroxisomal acyl-coenzyme A oxidase 1 OS=Dictyostelium discoideum GN=acox1 PE=3 SV=1 MYCPKAYENEKKNEDLEFERSQSTFSVSELNFILNNNDHNIINIKNEIKKFIDNDEIISK PQEIHFLSREEQYKRALYVSSKLIEIKKRFGEIGRDQYYQSLFEEIPFVINDIVFACAFK SLASDEQMNRLYSKFENYQYFGSYSQTEIGHGSNVQGIETTCTFIKETGEFELNSPNLTS TKFWIGGLGKLATHTIVFAQLLIPSSIDGKLKNYGPHPFILQVRSLDDHSPLPGVTVGDI GPKLGFNSIDNGFLRLDHVRIPRENMLSRFFRVNEQGEYEKPKHPKLIYAGMVGVRSSMI ENSFVSLSRAVTIAIRYSTIRKQFKSNRLDKQEKKIIEYSNQMNRIIPYLAQTFAYFFTG KRFSIEFDQMMKAVKHNQDTTLLSELHANSSGLKSLMTQSTSDGIESCRLSCGGHGYSQF SGLPYLWSNYVHMSSAEGESNLLPQQTTKYLLTILRKVLSGGGGSSDTTTADDDNKPIGK SVKYINDEFQSSFENINQFIQEKGLNSIIHPDSLLQLFKHRSFILIKSIAESIQEQMSNG NKDIPQIWSDLNVEINHCSKAHCQLYVIQSFYDQILLLSSNSSSCSSSITTVLIQLLQTY SIWIINSNLVDFLQDQYVELSQIDFLKKSLINFYKLLRPNLVPLVDSFDLCNTTLGSALG SYNGDVYSTLYKWASTQPFNKNSLPLGFNETIKPLINSKL >sp|A6QR56|A16A1_BOVIN Aldehyde dehydrogenase family 16 member A1 OS=Bos taurus GN=ALDH16A1 PE=2 SV=1 MAATRTASRACEIFTTLEYGPAPESHACALAWLDTQDRHLGHYVNGQWLKPEHRSSVPCQ DPITGENLASCLQAQSEDVAAAVEAARASLENWSTQPGAIRAQHLTRLAKVIQKHQRLLW TLESLVTGRAVREVRDRDVPLAQQLLQYHAVQAHTQEEALAGWEPMGVIGLILSPTFPFL DMMWRICPALAVGCTVVVLVPPASPTPLLLAQLAGELGPFPGILNVISGPASLGPVLAAQ PGVQKVAFCGAIEEGRALRRTLAGWVPELGLALGAESLLLLTEVADVDSAVEGIVDAAWS DRSPGGLRLLIQEAVWDETMRRLQERMGRLRCGHGLDGAVDMGARGAAARDLAQRYVSEA QSQGAQVFQAGSEPSDSPFFPPTLVSDLPPASPCTQAEVPWPLVVASPFRTAKEALAVAN GTPRGGSASVWSERLGQALELAYGLQVGTVWINAHGLRDPAVPTGGCKESGSSWHGGQDG LYEYLRPSGTPAWIPYLSKTLNYDAFGLALPSTLPAGPETGPAPPYGLFVGGRFQAPGAR SSRPIQDSQGSLQGYVAEGGAKDIRGAVEAAHQAAPGWMSQSPAARAALLWALAAALQRR EPNLVSRLERHGVELKVAKAEVELSVKRLRAWGARVQAQGCALQVAELRGPVLRLREPLG VLAIVCPDEWPLLAFVSLLAPALAHGNTVVLVPSGACPIPALEVCQEMATLLPAGLVNVV TGDRDHLTRCLALHQDIQALWYFGSAQGSQFVEWASAGNLKPVWVNRGCPRAWDQEAEGA GPELGRRAARTKALWLPMGD >sp|O88990|ACTN3_MOUSE Alpha-actinin-3 OS=Mus musculus GN=Actn3 PE=2 SV=1 MMMVMQPEGLGAGEGPFSGGGGGEYMEQEEDWDRDLLLDPAWEKQQRKTFTAWCNSHLRK AGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKL VSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQ NFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDI VNTPKPDEKAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENEKLMEEYEKLASELL EWIRRTVPWLENRVGEPSMSAMQRKLEDFRDYRRLHKPPRVQEKCQLEINFNTLQTKLRL SHRPAFMPSEGKLVSDIANAWRGLEQVEKGYEDWLLSEIRRLQRLQHLAEKFQQKASLHE AWTRGKEEMLNQHDYESASLQEVRALLRRHEAFESDLAAHQDRVEHIAALAQELNELDYH EAASVNSRCQAICDQWDNLGTLTQKRRDALERMEKLLETIDQLQLEFARRAAPFNNWLDG AIEDLQDVWLVHSVEETQSLLTAHEQFKATLPEADRERGAILGIQGEIQKICQTYGLRPK SGNPYITLSSQDINNKWDTVRKLVPSRDQTLQEELARQQVNERLRRQFAAQANAIGPWIQ GKVEEVGRLAAGLAGSLEEQMAGLRQQEQNIINYKSNIDRLEGDHQLLQESLVFDNKHTV YSMEHIRVGWEQLLTSIARTINEVENQVLTRDAKGLSQEQLNEFRASFNHFDRKRNGMME PDDFRACLISMGYDLGEVEFARIMTMVDPNAAGVVTFQAFIDFMTRETAETDTAEQVVAS FKILAGDKNYITPEELRRELPAEQAEYCIRRMAPYKGSGAPSGALDYVAFSSALYGESDL >sp|Q6XPR4|BRO1_EMENI Vacuolar protein-sorting protein bro1 OS=Emericella nidulans GN=broA PE=3 SV=2 MVQSPMISCPLKQTNEIDWIQPLKDYIRQSYGEDPERYSQECATLNRLRQDMRGAGKDSA TGRDLLYRYYGQLELLDLRFPVDENHIKISFTWYDAFTHKPTSQYSLAFEKASIIFNISA VLSCHAANQNRADDIGLKTAYHNFQASAGMFTYINENFLHAPSTDLNRETVKTLINITLA QGQEVFLEKQIMDHKKAGFLAKLASQASYLYAQAIEGTQEHAKGIFDKSWVTLLQVKSAH MGSVASYYQALADGESGSHGVAVARLQLAEKHSTSALSWAKSLPSSISPNTNLTSEAGPS LVDIVKFHLANVQSQLATFVKDNDFIYHQPVPSEAGLSAVSKLPAAKAIPVSELYQGQDI QRIIGPDIFQKLVPMSVTETASLYDEEKAKLIRAETEKVETADGEMAASLDYFKLPGSLN ILKGGMDQEVMVDEEFQRWCQELAGHDSFAKAFDTLQDRKSEVLATLDQCAKQLDLEESV CEKMRSKYGADWSQQPSSRLNMTLRNDIRTYRDTVHEASASDAQLSATLRQYESDFDEMR SAGETDEADVLFQRAMIKAGSKQGKTKNGVTSPYSATEGSLLDDVYDDGVPSVAEQIARV ESILKKLNLVKRERTQVLKDLKEKVRNDDISNVLILNKKSITGQESQLFEAELEKFHPHQ MRIVQANHKQTALMKELTKTYGDLLQDKRVRAEQSKYESITRQRNSVMARYKKIYDSFNN LGSGIKQAQTFYAEMTETVDSLKKNVDTFINNRRSEGAQLLGQIEREKAAGTSDHEERER EKLRQLMERLSTEPKPPSVPPGSSTAGPAKAKSPPPPVKAPAYPTNIAPPKASPHFAPTV PQQHGTPVSHSPAPYSQYVPPGAGVSYLPSQSFQQGAAAPLSEGYNPMAYPIPASSMSPP PSQPFYSPTPTPFYTSPTPPVPSGQYMPQGYVPPPPPPRPQQPTYPPSTGPFPSGPGGYA QSRPYGSSQHHKAHSQSSPQTGPSVSANSSDPWAGLNAWK >sp|P16638|ACLY_RAT ATP-citrate synthase OS=Rattus norvegicus GN=Acly PE=1 SV=1 MSAKAISEQTGKELLYKYICTTSAIQNRFKYARVTPDTDWAHLLQDHPWLLSQSLVVKPD QLIKRRGKLGLVGVNLSLDGVKSWLKPRLGHEATVGKAKGFLKNFLIEPFVPHSQAEEFY VCIYATREGDYVLFHHEGGVDVGDVDTKAQKLLVGVDEKLNAEDIKRHLLVHAPEDKKEI LASFISGLFNFYEDLYFTYLEINPLVVTKDGVYILDLAAKVDATADYICKVKWGDIEFPP PFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNE LANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRA IRDYQGSLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMAWA PAIPNQPPTAAHTANFLLNASGSTSTPAPSRTASFSESRADEVAPAKKAKPAMPQDSVPS PRSLQGKSATLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKF YWGHKEILIPVFKNMADAMKKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGI PEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVS RSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGG TEEYKICRGIKEGRLTKPVVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKE AGVFVPRSFDELGEIIQSVYEDLVAKGAIVPAQEVPPPTVPMDYSWARELGLIRKPASFM TSICDERGQELIYAGMPITEVFKEEMGIGGVLGLLWFQRRLPKYSCQFIEMCLMVTADHG PAVSGAHNTIICARAGKDLVSSLTSGLLTIGDRFGGALDAAAKMFSKAFDSGIIPMEFVN KMKKEGKLIMGIGHRVKSINNPDMRVQILKDFVKQHFPATPLLDYALEVEKITTSKKPNL ILNVDGFIGVAFVDMLRNCGSFTREEADEYVDIGALNGVFVLGRSMGFIGHYLDQKRLKQ GLYRHPWDDISYVLPEHMSM >sp|Q9SX33|ALA9_ARATH Putative phospholipid-transporting ATPase 9 OS=Arabidopsis thaliana GN=ALA9 PE=2 SV=1 MVGGGTKRRRRRLQLSKLYTLTCAQACFKQDHSQIGGPGFSRVVYCNEPDSPEADSRNYS DNYVRTTKYTLATFLPKSLFEQFRRVANFYFLVTGVLAFTPLAPYTASSAIVPLLFVIGA TMVKEGVEDWRRQKQDNEVNNRKVKVHRGDGSFDAKEWKTLSIGDIVKVEKNEFFPADLV LLSSSYEDAICYVETMNLDGETNLKVKQGLEVTSSLRDEFNFKGFEAFVKCEDPNANLYS FVGTMELKGAKYPLSPQQLLLRDSKLRNTDFIFGAVIFTGHDTKVIQNSTDPPSKRSMIE KKMDKIIYLMFFMVITMAFIGSVIFGVTTRDDLKDGVMKRWYLRPDSSSIFFDPKRAPVA AIYHFLTAVMLYSYFIPISLYVSIEIVKVLQSIFINQDIHMYYEEADKPARARTSNLNEE LGQVDTILSDKTGTLTCNSMEFIKCSVAGTAYGRGVTEVEMAMGRRKGGPLVFQSDENDI DMEYSKEAITEESTVKGFNFRDERIMNGNWVTETHADVIQKFFRLLAVCHTVIPEVDEDT EKISYEAESPDEAAFVIAARELGFEFFNRTQTTISVRELDLVSGKRVERLYKVLNVLEFN STRKRMSVIVQEEDGKLLLLCKGADNVMFERLSKNGREFEEETRDHVNEYADAGLRTLIL AYRELDEKEYKVFNERISEAKSSVSADRESLIEEVTEKIEKDLILLGATAVEDKLQNGVP DCIDKLAQAGIKIWVLTGDKMETAINIGFACSLLRQDMKQIIINLETPEIQSLEKTGEKD VIAKASKENVLSQIINGKTQLKYSGGNAFALIIDGKSLAYALDDDIKHIFLELAVSCASV ICCRSSPKQKALVTRLVKSGNGKTTLAIGDGANDVGMLQEADIGVGISGVEGMQAVMSSD IAIAQFRYLERLLLVHGHWCYRRISTMICYFFYKNITFGFTLFLYETYTTFSSTPAYNDW FLSLYNVFFSSLPVIALGVFDQDVSARYCLKFPLLYQEGVQNVLFSWRRILGWMFNGFYS AVIIFFLCKSSLQSQAFNHDGKTPGREILGGTMYTCIVWVVNLQMALAISYFTLIQHIVI WSSIVVWYFFITVYGELPSRISTGAYKVFVEALAPSLSYWLITLFVVVATLMPYFIYSAL QMSFFPMYHGMIQWLRYEGQCNDPEYCDIVRQRSIRPTTVGFTARLEAKKRSVRISEPAS >sp|A2AH22|AMRA1_MOUSE Activating molecule in BECN1-regulated autophagy protein 1 OS=Mus musculus GN=Ambra1 PE=1 SV=1 MKVVPEKNAVRILWGRERGTRAMGAQRLLQELVEDKTRWMKWEGKRVELPDSPRSTFLLA FSPDRTLLASTHVNHNIYITEVKTGKCVHSLIGHRRTPWCVTFHPTISGLIASGCLDGEV RIWDLHGGSESWFTDSNNAIASLAFHPTAQLLLIATANEIHFWDWSRREPFAVVKTASEM ERVRLVRFDPLGHYLLTAIVNPSNQQGDDEPEIPIDGTELSHYRQRALLQSQPVRRTPLL HNFLHMLSSRSSGIQVGEQSTVQDSATPSPPPPPPQPSTERPRTSAYIRLRQRVSYPTTV ECCQHPGILCLCSRCAGTRVPSLLPHQDSVPPASARATTPSFSFVQTEPFHPPEQASSTQ QDQGLLNRPSAFSTVQSSTAGNTLRNLSLGPTRRSLGGPLSSHPSRYHRELAPGLTGSEW TRTVLTLNSRSEVESMPPPRTSASSVSLLSVLRQQEGGSQASVYTSATEGRGFPSSGLAT ESDGGNGSSQNNSGSIRHELQCDLRRFFLEYDRLQELDQSLSGETPQTQQAQEMLNNNIE SERPGPSHLPTPHSSENNSNLSRGHLNRCRACHNLLTFNNDTLRWERTTPNYSSGEASSS WHVSTTFEGMPPSGNQLPPLERTEGQMPSSSRLELSSSASSQEERTVGVAFNQETGHWER IYTQSSRSGTVSQEALHQDMPEESSEEDSLRRRLLESSLISLSRYDGAGSREHPIYPDPA RLSPAAYYAQRMIQYLSRRDSIRQRSMRYQQNRLRSSTSSSSSDNQGPSVEGTDLEFEDF EDNGDRSRHRAPRNARMSAPSLGRFVPRRFLLPEYLPYAGIFHERGQPGLATHSSVNRVL AGAVIGDGQSAVASNIANTTYRLQWWDFTKFDLPEISNASVNVLVQNCKIYNDASCDISA DGQLLAAFIPSSQRGFPDEGILAVYSLAPHNLGEMLYTKRFGPNAISVSLSPMGRYVMVG LASRRILLHPSTEHMVAQVFRLQQAHGGETSMRRVFNVLYPMPADQRRHVSINSARWLPE PGLGLAYGTNKGDLVICRPEALNSGIEYYWDQLSETVFTVHSSSRSSERPGTSRATWRTD RDMGLMNAIGLQPRNPTTSVTSQGTQTLALQLQNAETQTEREEEEPGAASSGPGEGEGSE YGGSGEDALSRIQRLMAEGGMTAVVQREQSTTMASMGGFGNNIIVSHRIHRSSQTGTESG AARTSSPQPSTSRGLPSEPGQLAERALSPRTASWDQPSTSGRELPQPALSSSSPVPIPVP LASNEGPTMHCNVTNNSHLPEGDGSNRGEAAGPSGEPQNR >sp|Q9ESU6|BRD4_MOUSE Bromodomain-containing protein 4 OS=Mus musculus GN=Brd4 PE=1 SV=1 MSTESGPGTRLRNLPVMGDGLETSQMSTTQAQAQPQPANAASTNPPPPETSNPNKPKRQT NQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYW NAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRG RGRKETGAAKPGVSTVPNTTQASTSPQTQTPQQNPPPPVQATTHPFPAVTPDLIAQPPVM TMVPPQPLQTPSPVPPQPPPPPAPVPQPVQSHPPIIATTPQPVKTKKGVKRKADTTTPTT IDPIHEPPSLAPEPKTAKLGPRRESSRPVKPPKKDVPDSQQHPGPEKSSKISEQLKCCSG ILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFG ADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVTVSSPAVPPPTKV VAPPSSSDSSSDSSSDSDSSTDDSEEERAQRLAELQEQLKAVHEQLAALSQPQQNKPKKK EKDKKEKKKEKHKKKEEVEENKKSKTKELPPKKTKKNNSSNSNVSKKEPVPTKTKPPPTY ESEEEDKCKPMSYEEKRQLSLDINKLPGEKLGRVVHIIQSREPSLKNSNPDEIEIDFETL KPSTLRELERYVTSCLRKKRKPQAEKVDVIAGSSKMKGFSSSESESTSESSSSDSEDSET EMAPKSKKKGHTGRDQKKHHHHHHPQMQPAPAPVPQQPPPPPQQPPPPPPPQQQQQQPPP PPPPPSMPQQTAPAMKSSPPPFITAQVPVLEPQLPGSVFDPIGHFTQPILHLPQPELPPH LPQPPEHSTPPHLNQHAVVSPPALHNALPQQPSRPSNRAAALPPKPTRPPAVSPALAQPP LLPQPPMVQPPQVLLEDEEPPAPPLTSMQMQLYLQQLQKVQPPTPLLPSVKVQSQPPPPL PPPPHPSVQQQQLQPQPPPPPPPQPQPPPQQQHQPPPRPVHLPSMPFSAHIQQPPPPPGQ QPTHPPPGQQPPPPQPAKPQQVIQHHPSPRHHKSDPYSAGHLREAPSPLMIHSPQMPQFQ SLTHQSPPQQNVQPKKQVKGRAEPQPPGPVMGQGQGCPPASPAAVPMLSQELRPPSVVQP QPLVVVKEEKIHSPIIRSEPFSTSLRPEPPKHPENIKAPVHLPQRPEMKPVDIGRPVIRP PEQSAPPPGAPDKDKQKQEPKTPVAPKKDLKIKNMGSWASLVQKHPTTPSSTAKSSSDSF EHFRRAAREKEEREKALKAQAEHAEKEKERLRQERMRSREDEDALEQARRAHEEARRRQE QQQQQQQQRQEQQQQQQQAAAVAAASAPQAQSSQPQSMLDQQRELARKREQERRRREAMA ATIDMNFQSDLLSIFEENLF >sp|Q63041|A1M_RAT Alpha-1-macroglobulin OS=Rattus norvegicus GN=A1m PE=1 SV=1 MRRNQLPIPVFLLLLLLLPRDATAATGKPRYVVLVPSELYAGVPEKVCVHLNHLNETVTL NVTLEYGVQYSNLLIDQAVDKDSSYCSSFTISRPLSPSALIAVEIKGPTHHFIKKKSMWI TKAESPVFVQTDKPIYKPGQTVKFRVVSVDISFRPVNETFPVVYIENPKRNRIFQWQNVD LPGGLHQLSFPLSVEPALGIYKVVVQKDSGKKIEHSFEVKEYVLPKFEVQVKMPKTMAFL EEELVVTACGLYTYGKPVPGLVTMKVCRKYTQSYSNCHGQHSKSICEEFSKQADEKGCFR QVVKTKVFQPRQKGYDMKIEVEAKIKEDGTGIELTGTGSCEIANTLSKLKFTKANTFYRP GLPFFGQVLLVDEKGQPIPNKNLTVQVNSVRSQFTFTTDEHGLANILIDTTNFTFSFMGI RVIYKQNNICFDNWWVDEYHTQADHSAARIFSPSRSYIQLELVLGTLACGQTQEIRIHFL LNEDALKDAKDLTFYYLIKARGSIFNSGSHVLPLEQGKVKGVVSFPIRVEPGMAPVAKLI VYTILPNEELIADVQKFDIEKCFANTVNLSFPSAQSLPASDTHLTVKATPLSLCALTAVD QSVLLLKPEAKLSPQSIYNLLPQKAEQGAYLGPLPYKGGENCIKAEDITHNGIVYTPKQD LNDNDAYSVFQSIGLKIFTNTRVHKPRYCPMYQAYPPLPYVGEPQALAMSAIPGAGYRSS NIRTSSMMMMGASEVAQEVEVRETVRKYFPETWIWDMVPLDLSGDGELPVKVPDTITEWK ASAFCLSGTTGLGLSSTISHKVFQPFFLELTLPYSVVRGEAFILKATVLNYMPHCIRIHV SLEMSPDFLAVPVGSHEDSHCICGNERKTVSWAVTPKSLGEVNFTATAEALQSPELCGNK VAEVPALVQKDTVVKPVIVEPEGIEKEQTYNTLLCPQDAELQENWTLDLPANVVEGSARA TQSVLGDILGSAMQNLQNLLQMPYGCGEQNMVLFVPNIYVLEYLNETQQLTEAIKSKAIS YLISGYQRQLNYQHSDGSYSTFGDRGMRHSQGNTWLTAFVLKAFAQAQSYIYIEKTHITN AFNWLSMKQRENGCFQQSGSLLNNAMKGGVDDEVTLSAYITIALLEMPLPVTHSVVRNAL FCLETAWASISNSQESHVYTKALLAYAFALAGNRAKRSEVLESLNKDAVNEEESVHWQRP KNVEENVREMRSFSYKPRAPSAEVEMTAYVLLAYLTSASSRPTRDLSSSDLTTASKIVKW ISKQQNSHGGFSSTQDTVVALQALSKYGAATFTKSNKEVSVTIESSGTVSGTLHVNNGNR LLLQEVRLADLPGNYITKVSGSGCVYLQTSLKYNILPEAEGEAPFTLKVNTLPLNFDKAE HHRKFQIHINVSYIGERPNSNMVIVDVKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVL IYIEKLTNQTMGFSFAVEQDIPVKNLKPAPVKVYDYYETDEFAIEEYSAPFSSDSEQGNA >sp|Q811B3|ATS12_MOUSE A disintegrin and metalloproteinase with thrombospondin motifs 12 OS=Mus musculus GN=Adamts12 PE=1 SV=1 MPCARGSWLAKLSIVAQLINFGAFCHGRQTQPWPVRFPDPRQEHFIKSLPEYHIVSPVQV DAGGHVLSYGLHHPVTSSRKKRAAGGSGDQLYYRISHEEKDLFFNLTVNWEFLSNGYVVE KRYGNLSHVKMVASSGQPCHLRGTVLQQGTTVGIGTAALSACQGLTGFFHLPHGDFFIEP VKKHPLTEEGSYPHVVYRRQSIRAPETKEPICGLKDSLDNSVKQELQREKWERKTLRSRS LSRRSISKERWVETLVVADTKTVEYHGSENVESYILTIMNMVTGLFHSPSIGNLVHIVVV RLILLEEEEQGLKIVHHAEKTLSSFCKWQKSINPKSDLNPVHHDVAVLITRKDICAGVNR PCETLGLSQLSGMCQPHRSCNINEDSGLPLAFTIAHELGHSFGIQHDGKENDCEPVGRHP YIMSQQIQYDPTPLTWSKCSKEYITRFLDRGRGFCLDDIPSKKGLKSNVIAPGVIYDVHH QCQLQYGPNATFCQEVENVCQTLWCSVKGFCRSKLDAAADGTRCGEKKWCMAGKCITVGK KPESIPGGWGRWSPWSHCSRTCGAGAQSAERLCNNPEPKFGGKYCTGERKRYRLCNVHPC RSDTPTFRQMQCSEFDTVPYKNQFYRWFPVFNAAHPCELYCRPIDEQFSERMLEAVIDGT PCFEGGNSRNVCINGICKRVGCDYEIDSNATEDRCGVCLGDGSACQTVKKLFRQKEGSGY VDIGLIPKGARDIRVMEIKAAGNFLAIRSEDPEKYYLNGGFIIQWNGNYKLAGTVFQYDR KGDLEKLIAPGPTNESVWLQLLFQVTNPGIKYEYTVRKDGLDNDVEKLLYFWQFGRWTEC SVTCGTGIRRQAAHCVKKGHGIVKTTFCNPETQPSVRQKKCHEKDCPPRWWAGEWEACST TCGPYGEKKRTVLCIQTMGSDEQALPATDCQHLLKPKALVSCNRDILCPSDWTVGNWSEC SVSCGGGVRIRSVTCAKNLNEPCDKTRKPNSRALCGLQQCPFSRRVLKPHKDIAPSGKNQ STAEHDPFKPIPAPTSRPTPLSTPTVPESMSTSTPTINSLGSTIASQEDANGMGWQNNST QAEEGSHFPTSSGSTSQVPVTSWSLSIQPDDENVSSSAIGPTSEGDFWATTTSDSGLSSS DAMTWQVTPFYSTMTTDPEVEIHSGSGEDSDQPLNKDKSNSVIWNKIGVPEHDAPMETDA ELPLGPPPTSYMGEEPSWPPFSTKMEGSLPAWSFKNETPRDDGMIAEKSRKIPLPLAGDH HPATSEKLENHDKLALPNTTNPTQGFGPVLTEEDASNLIAEGFLLNASDYKHLMKDHSPA YWIVGNWSKCSTTCGLGAYWRSVECSSGVDADCTTIQRPDPAKKCHLRPCAGWRVGNWSK CSRNCSGGFKIREVQCMDSLDHHRSLRPFHCQFLAGAPPPLSMSCNLEPCGEWQVEPWSQ CSRSCGGGVQERGVSCPGGLCDWTKRPATTVPCNRHLCCHWATGNWELCNTSCGGGSQKR TIHCIPSENSTTEDQDQCLCDHQVKPPEFQTCNQQACRKSADLTCLKDRLSISFCQTLKS MRKCSVPSVRAQCCLSCPQAPSIHTQRQRKQQLLQNHDML >sp|Q03376|BAR3_CHITE Balbiani ring protein 3 OS=Chironomus tentans GN=BR3 PE=2 SV=1 MKTLSSLLLVLAVNVLLIQASPDPDNRCPARKYWNERKQACVCKRENRCYPIGAIFDPES CTFSMCQSKGCSAKQIFNKDKCACECRNDQPKDGCGAGRYWCNQDCSCKCSTPMSAGGCS GSQIWCEKSCACVCPNADKCTAPQVWNKDTCCCGCPVNMQEPADGCTKPLIWDKVDCRCE CPLKKDCGKNRDWSDSSCSCECKGDGKCQGSKIWCKNNCRCICPTAEPAGGCSAPLKWDD DKCSCACPAKMEEKKEKCVESGKIWNPNTCECGCAQLNCPDNKKANKETCQCECKEVKKC NGGQVFCKDSCSCVCPGGDKDKTCTAPQVYDGVACSCSCPVNMQKPADGCPRPQKWDKEE CRCECPVKHDCKNGKVWDETICQCICPRDAPVCTAGKERCGESCECKCINREPKEGCAKP LVWNENTCKCVCPADKQMSPGGCGSGKSFNKLTCQCECDQSASKCGLKRWNADTCKCECQ PGMPPEGCGKQTWISDKCKCECSPTITCQAPQILDLNTCECKCPVNMLAQKEKCKSPRQW TDSKCLCECSTTPATCEGKQTWCGEACQCICPGGDKNCGNKKFFDKPSCECKCKNNPTCT SPQVWDADDCECKCPKDKQKPQGGCDGGQKWNDRVCSCGCPVPRPDCTNGQIYNINTCAC GCGIDKPSCPKQQIYNWKTCDCECPNGMKEPVGGCGAKTWLDDECQCDCVPGKPKGGCTG AQKWCDKTCKCKCEKEMPTGGCENNKKWCDETCDCVCPQKNTCIAPKVWDAKTCSCICVN PPKCNSPQVLKDTCCCGCQNVKSCKAPQKFIENICDCACPNKKQCKAPLVWSDEFCDCVC PNSASMKTCLSPKEWNKVTCTCDCNPPKPDCCPGTQKWMDDKCKCGCPNAQTDCAGGKKF NDFTCSCGCPSGKLDCTGNTKWSAETCTCGCGDVNRNCGNLKNFNDNLCQCECKNKQEMA NCKSPRTWNYDTCKCVCKNADDSDDCVKPQIWLDDQCKCGCPASAQMTCPANKRFIEKSC SCECKSPMPSPIPQGKKWNEDKCVVECANVKTCEGPQRWCDNQCKCICPQVNTKCSDKQK FIESKCECGCETQTQCKDGFRWSNLECGCLCDDKKCPGKQVFDKNTCQCKCPNQKPGDTC GNGKDFCPLDCSCKCKNPKPANGCTGVQEWNEEKCQCECPKDKPKKQCPGGQDWNNHQCQ CGCPTPAPTCSNNQKYSNVSCSCGCNPGKPKNGCPGNQIWCDNTCRCVCPKNMEKPADNC KTKWWNDEMCQCVCKPGCPEGGCKGVMKWNANTCSCECPADKAKPASCGDKKSWNDDSCS CQCKSKMPCGGCPPNQQWNEKDCECKCSATGNCPAGQTWNSQTCQCSCPATGKCTGAQVW CSKACKCVCPAQKKCDSPKTWDENSCSCQCPKNMRPPTGGCNAGRTWDDATCSEKCAATP KCDSPKVFDPTTCGCKCGNKPNKLDAGRTWDEQKCKMTCDLPAIPCCHYEGQVYDSNTCK CGCPKEETCKQGFSFSPKSGCKCILECNKKDPGCGAKKIWCQETCKCECASEPPRMGCGP NRYWDKEDCACQCLKTKVCTDSDFSFFSHDTCDCECSNAKDFILNCNQKLNKVSCQPQCI QRPPPEGCAEKFGEFFSWDPKACECKCIEQKTTVKGRVFDKATCNFKCTNEPKTNPKCAN TAESWDSQICACKVCSTCKH >sp|A5AB61|UTP10_ASPNC U3 small nucleolar RNA-associated protein 10 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=utp10 PE=3 SV=1 MASSLAAQLSQIAAKSTNQLNLKAQRIAHSQSLIFDWKTATTQDFDTVYQICFEGFQELC QLDPRFAPFERTIFSEQSKAEDRTEMNAAQNKELDTVVEAFLALVGGHLLLSPAVKAVDW LIRRFRVHEYNTEFTILTFLPYYTTPLFLNLLSILPEDLTPTFKILNPYKKSQINPPRHP LVHSATTNKHFLAAVNRYTLQVSKQRAHHHALLSFWAGTLTEAVAGMLDSSRSGRREVEK EKHEDVVMKVLPVLNDGLALKDVSELVIGCYMVCVVLAQKSSLQDKLLDGLMEAVAGSWT DETKESGLICLSVLAQKKSDARIPKRAFKAVLRLEDPVQQLSAISAQYPTSHLLLGLVAG CVDDLSKQKDLSRLDLLSLLFETNLLGEQEAGKAMAVILQAVSHAHTEGVLSLDAQTHLA ELVQHFTQSESLQPIFQKTIEDSSIDVAALEHNLQTVIESVPTTTPAIGDVEMEDVQQEA VEDNFASVLESVAGKNLESSALSAQSMPAYESLVQTFALAVGSQEKLQAFVDLPALKKAD ASTSPQYLSFFIRTFSGSYPIGTRITALNQISSLLNSATPDVDLQALLPFLLVALADSSE RVRREAAGVLAAIGSLYKKSKKGDANVWARDTIYGKQSKNVQWIAGRDVQKIVERAFLPG LEEYVLDQAHIGRVLEATLRGSSTSDSGATELKKPLRLSLFTFLCSHAVQMPLYAPKLSL LKLLNRVDKAGGTTRTKELGPFLKTWRDMKEHTAKDVCERERVSVADVDREAVMTVTPKD KDAISLLLSNVSPYSDSLRPSFVTAIFNRMKAVWGTVAEELQVDAAEKLFEISLEDVQTP LVHGCRDVLRSVQLTGSVLLQFLRKIPVSITDMESLGPAPKRRRTSQNNMVAMTIKDEAK LSQLMEKMTFILELVDSSTPEAHPELADGLFQTLAALHHFKSQIQSGLSYLLSLTLGSLL AIVNRSKGTAKAQFDTSVIRADLVVDCVRTTDSPQVQNAALLLVAGLSVIAPELVLHSVM PIFTFMGSSVLRKDDEYSVSVIDQTIDQVVPALIQSLRNQKRDVVSGTSELLLSFTAAFE HIPSHRRLRLFHALVTKLGTQDFLFAVLAMLANRYALDKDVLILMTGLVSDASAPVELNT YSKFLDLVKDSLSSKPGISQVLLGIGSDDGRDPQKVAVDLLRALAYLFKHSSLKVKMAKD FATEGDKVVGQIRTLFSRILEQVLAIGESMQNVKPVSQASGDVLSALFGTLSLVDFLDTI EVLLQRRNDELRRKVLRLLEGRLRQNPERDGASQHRMLDFLPTLVNIIQSSPDILLKHAA VACIDRIAEKYGRKEPTKVIHAAQVVASEACIGQDDERIRIMGVLCLASMAEVLGEAMIP ALPDALSRSLALLEQSLEDGKENARLHDAVYSFFSALFIHIPFMVSGSHLDKILVLSYKS AVSEGVEDESREEALQLMARKVDVAATYAAIDRNWQHAVKAGPDATRETLGVVSLAIEKH PKSATVKNIAVLTSILFKAFDLRREQVSLDTQATFELSDVDEIEDIINEVTIKMIYKLND TTFRPIFTKLLEWATTGVPKKDARGSLARLTTFYRFLQVFFGTLQSIVTGYSSYIIENVV SVLGKANPSNQDTKSLWLATMRMLKNSFEHDQDEFWQSPSHLTVIAQPLISQLAHAKNSS TASIVIAEAVPALTELAVAADSTDNHKELNTVLMRLLRPSAGPSGKTAGGENPHTRLAAL KAQQSLTEQLGEEWLALLPEMLPYISELMEDEDENVEREVRKWVKQIEDVLGERLDDMLT >sp|P37297|STT4_YEAST Phosphatidylinositol 4-kinase STT4 OS=Saccharomyces cerevisiae GN=STT4 PE=1 SV=1 MRFTRGLKASSSLRAKAIGRLTKLSTGAPNDQNSNGTTLDLITHTLPIFYSTNTSKIYTI PLTLSEWEVLTSLCVAIPTTLDLVETMLKEIIAPYFLETPRQRISDVLSSKFKLEQMRNP IELLTFQLTKFMIQACEQYPVLYENIGGIISTYFERVLKIFTIKQSGLLSLVGFINAFIQ FPNSTELTKFTWKKLAKLVLRGSFLNEVDKILNSSATFTNDSIVQYYDAGNELSSAYLLE LISRLQVSLISHLLNTSHVGANLSEFLLNQQYQFYKFDQEVADENDDTKCIDDFFFNVRS NKQFFTDMCKISLQFCSESHILDLSTDNRARFSFDTRAHYLQTLCLIPFIEDTESELFES FTNVVSESIDKFFLSDVVTPSLIKAIVASASLLNFFTEKLSLTLIRMFPLLVASPHITTE TVNDVAKIFTTGLYPLNEDAIVSTIYSMNNLLAVSEDGSPVPVLRERQLTITSGKNIEKD YFPLRNSSASLDGTGALLGNTTVGQLSSHDVNSGATMTYHASLISNCVAATTTIASYYNT QSITALTISILTQKVNSMSKELDGVILNSLARLAPNTSLTEFSLLLKFFKSRTVIATKID DSALLKNIIKAKCVISKELLARHFSSDLYFMYLHDLLDSIIASGEVERLEHHRPQTEISR VADQIATYLEPLAALLPVPGDTPLDINKDEVTTNKFRNAWFNFVIHGYHLGGPIVKRNFS FLLTIAYNSPPLASEFPANNKELSLEMNTILRRGSSNENIKQQKQQITEYFNTNIVQYRT TSSSKIMFLAAAVLLETIRCEAGDCSKTLLYFSDPSILSGSIEKCIAVLSVSMIRKYARL IQKGNDAIFNSKMIAQQLNNLLLCLSHREPTLQDAAFHACEIFIRSIPSSLCHHLSLYTL LDMLTALFDSILDSEAHKFEPRYEFKLKHSKTTILVPSSSSWRATTLSRLHKSAKEWVRI LLNRSNQDTKILLQSYISDLGEYSRLNSVEFGVSFAMDMAGLILPADKELSRLTYYGPEK PNTISGFISLHSWRSKYLFDTAITSSPEDIKRQIGISTQNIRKNLTLGNKIITKDVTDFL DMATALLILGNGAPASLIYDIVHIPFEVFTSASLKIATNVWLTIITEKPEVAHLLLVEVC YCWMRSIDDNIGLYSRDHDLKGEEYQKMEYSPYDKAGINRDAKNASQAMQPHLHVIKFFA SHFEGTLFQSDFLLKIFTKCALYGIKNLYKASLHPFARMIRHELLLFATLVLNASYKQGS KYMGRLSQEITNGALSWFKRPVAWPFGSNELKIKADLSVTRDLFLQLNKLSSLMSRHCGK DYKILNYFLASEIQQIQTWLTPTEKIEGADSNELTSDIVEATFAKDPTLAINLLQRCYSK KAEDVLVGLVAKHALMCVGSPSALDLFIKGSHLSSKKDLHATLYWAPVSPLKSINLFLPE WQGNSFILQFSIYSLESQDVNLAFFYVPQIVQCLRYDKTGYVERLILDTAKISVLFSHQI IWNMLANCYKDDEGIQEDEIKPTLDRIRERMVSSFSQSHRDFYEREFEFFDEVTGISGKL KPYIKKSKAEKKHKIDEEMSKIEVKPDVYLPSNPDGVVIDIDRKSGKPLQSHAKAPFMAT FKIKKDVKDPLTGKNKEVEKWQAAIFKVGDDCRQDVLALQLISLFRTIWSSIGLDVYVFP YRVTATAPGCGVIDVLPNSVSRDMLGREAVNGLYEYFTSKFGNESTIEFQNARNNFVKSL AGYSVISYLLQFKDRHNGNIMYDDQGHCLHIDFGFIFDIVPGGIKFEAVPFKLTKEMVKV MGGSPQTPAYLDFEELCIKAYLAARPHVEAIIECVNPMLGSGLPCFKGHKTIRNLRARFQ PQKTDHEAALYMKALIRKSYESIFTKGYDEFQRLTNGIPY >sp|Q12873|CHD3_HUMAN Chromodomain-helicase-DNA-binding protein 3 OS=Homo sapiens GN=CHD3 PE=1 SV=3 MKAADTVILWARSKNDQLRISFPPGLCWGDRMPDKDDIRLLPSALGVKKRKRGPKKQKEN KPGKPRKRKKRDSEEEFGSERDEYREKSESGGSEYGTGPGRKRRRKHREKKEKKTKRRKK GEGDGGQKQVEQKSSATLLLTWGLEDVEHVFSEEDYHTLTNYKAFSQFMRPLIAKKNPKI PMSKMMTILGAKWREFSANNPFKGSAAAVAAAAAAAAAAVAEQVSAAVSSATPIAPSGPP ALPPPPAADIQPPPIRRAKTKEGKGPGHKRRSKSPRVPDGRKKLRGKKMAPLKIKLGLLG GKRKKGGSYVFQSDEGPEPEAEESDLDSGSVHSASGRPDGPVRTKKLKRGRPGRKKKKVL GCPAVAGEEEVDGYETDHQDYCEVCQQGGEIILCDTCPRAYHLVCLDPELDRAPEGKWSC PHCEKEGVQWEAKEEEEEYEEEGEEEGEKEEEDDHMEYCRVCKDGGELLCCDACISSYHI HCLNPPLPDIPNGEWLCPRCTCPVLKGRVQKILHWRWGEPPVAVPAPQQADGNPDVPPPR PLQGRSEREFFVKWVGLSYWHCSWAKELQLEIFHLVMYRNYQRKNDMDEPPPLDYGSGED DGKSDKRKVKDPHYAEMEEKYYRFGIKPEWMTVHRIINHSVDKKGNYHYLVKWRDLPYDQ STWEEDEMNIPEYEEHKQSYWRHRELIMGEDPAQPRKYKKKKKELQGDGPPSSPTNDPTV KYETQPRFITATGGTLHMYQLEGLNWLRFSWAQGTDTILADEMGLGKTIQTIVFLYSLYK EGHTKGPFLVSAPLSTIINWEREFQMWAPKFYVVTYTGDKDSRAIIRENEFSFEDNAIKG GKKAFKMKREAQVKFHVLLTSYELITIDQAALGSIRWACLVVDEAHRLKNNQSKFFRVLN GYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKEDQIKKLHDLL GPHMLRRLKADVFKNMPAKTELIVRVELSPMQKKYYKYILTRNFEALNSRGGGNQVSLLN IMMDLKKCCNHPYLFPVAAMESPKLPSGAYEGGALIKSSGKLMLLQKMLRKLKEQGHRVL IFSQMTKMLDLLEDFLDYEGYKYERIDGGITGALRQEAIDRFNAPGAQQFCFLLSTRAGG LGINLATADTVIIFDSDWNPHNDIQAFSRAHRIGQANKVMIYRFVTRASVEERITQVAKR KMMLTHLVVRPGLGSKAGSMSKQELDDILKFGTEELFKDENEGENKEEDSSVIHYDNEAI ARLLDRNQDATEDTDVQNMNEYLSSFKVAQYVVREEDKIEEIEREIIKQEENVDPDYWEK LLRHHYEQQQEDLARNLGKGKRVRKQVNYNDAAQEDQDNQSEYSVGSEEEDEDFDERPEG RRQSKRQLRNEKDKPLPPLLARVGGNIEVLGFNTRQRKAFLNAVMRWGMPPQDAFTTQWL VRDLRGKTEKEFKAYVSLFMRHLCEPGADGSETFADGVPREGLSRQQVLTRIGVMSLVKK KVQEFEHINGRWSMPELMPDPSADSKRSSRASSPTKTSPTTPEASATNSPCTSKPATPAP SEKGEGIRTPLEKEEAENQEEKPEKNSRIGEKMETEADAPSPAPSLGERLEPRKIPLEDE VPGVPGEMEPEPGYRGDREKSATESTPGERGEEKPLDGQEHRERPEGETGDLGKREDVKG DRELRPGPRDEPRSNGRREEKTEKPRFMFNIADGGFTELHTLWQNEERAAISSGKLNEIW HRRHDYWLLAGIVLHGYARWQDIQNDAQFAIINEPFKTEANKGNFLEMKNKFLARRFKLL EQALVIEEQLRRAAYLNLSQEPAHPAMALHARFAEAECLAESHQHLSKESLAGNKPANAV LHKVLNQLEELLSDMKADVTRLPATLSRIPPIAARLQMSERSILSRLASKGTEPHPTPAY PPGPYATPPGYGAAFSAAPVGALAAAGANYSQMPAGSFITAATNGPPVLVKKEKEMVGAL VSDGLDRKEPRAGEVICIDD >sp|Q1E702|ATG2_COCIM Autophagy-related protein 2 OS=Coccidioides immitis GN=ATG2 PE=3 SV=1 MPFSLPSFAQKLVLRYALSRLGLVDTDTLDLATLGITWGQRSTFELRNVGLKLEKLSAHL PPYCTLTKGSVSLLRVTVPANLHNSSIIVEVDGVDARVRLLPDKPEQNAPPTRSKGTAED EGQDGHSVLPSTADLAQSFLESEPKEETEELQAAILSQSQYPEHLDAQSDDGEEDLGLYD GLSLPAFIAGFLKGVIDRLQLNIANVSLRVDTEVQRDGVLKDETQDPISGLFTIQEIAID STATSASEDSRLKIGKRMVSLSGIHAMIMSDAEVFSNYSRFNAPDIPSTVHSKSTHTPLR PRSPQPSSSGSDSCGDMSRSTILDPSSMYGSRLTVDSHGDESRHLESSVYSTTGRFSDAD SDDENDLEFYSQATTGMLDSHYDERLLDNPAYLDEALKSQFDDHLEDSTIFPKDCPSTPV RDQTPRPHVSKSPSSSPEHYMYHSVHESNFPVGGGIRDNEPDSATSARGKTPDCQTEQES PSTSKICPAVSQPEDLSASRIFTHEEAQSMYMSAMSQSSTTSFDPDMPGAWGSSKRIDTS DPDQKEQPLSGDTDTEAKGASHDFDTSQNSPEAQTGEDDERESVHNSPQYISGVVKEILA IDRIIIWLPSVDSQDSEEIPKTDIDSKPVDPMVESTITLADSVTPDLLANTRSRLAQSAF RRGSVSSIVSSRHLPISRTKPTTQKHEDFDGLNDPQTTRAVEIDITSLTAKLDIASGWLL VKIGQRITDVSTSTSKQTKISEAASEESSPSFFRLNLTSCSLKFLERVPAQPYPLSSAPS LSQLQSGIPIEETILHLTLSGTSIDFAAIGNTTKLRLDVMKFVLGHMSYDIISFDESLRM RESTRDVTSPGQKDISLRVIKSSESTTVNLTTLPICLSLDLQELDETLGWFGGLSTVLEL GSSIASASTVKGEQPCSPPRPRRGVHFADPVPPSSPSTTNHAALKANCRIGGIVLRVIGE HCTVQLGTTAAKLVSRFEGIALQIDKASVGGPHLRKEPSPSPPSLDFENIRFEYLYGPKE VDLDRLLGLLTPSKDKFDEDDDIMLDTLFRQRRQGAVLRLTVGHADFAVPNPTALQPLSH LGEELAKLATVAKYLPQDDRPGILILALVREFEGRVHVNNEAGDITIISHNLEAGYVTFP SLLATRISTVTVVRNGSEELVAEVIPEDTEEARTHDPLPMIMARFIADEMEPTVKIKLYN VRVEYTVPSITAFLGLNNQMAAEDVAANMAQSVLNLADLKAHHEPGSDLSERDSIGSGDD RSAMLPRLSVGMKDCGIGLNPRKSPAKALVIFTRASFSGALHETKPSEALLDIRKASVMI IDNVENLGSAENYRHRMSSGARSGQIQHLQSIGFVPVCDISSASVALKVMQLDVEGEKSL DIEVRDDLLVLETCADSTQTLISILSGLAPLSPPITERKYRTEVIRIEDMLNSLSGDAFA TDIVPDSDYEVEGENDGQDGDGAEEIEYVSVFYPSHGDSGPQGRGATTPRFGNEGSASAG TSRILGSFHSEAQMSSSIPELEFQEDHFAKQSAVGDTAHRWDSSRNTYTLATEVKLRDSP LRIRVRDVHVIWNLYDGYDWQRTRDTISKAVRDVQAKAAEKFARRPGNRLSADFEEDEES VIGDFLFNSVYIGIPANRDPRELSHDINRNIDDLASETMSFATSTTVTGLQNQVPGTKRE KLRLARSKHHKMTFELKGISADLIVFPPHSGETQSSLDIRVEDLEIFDHIPTSTWKKFAT YMRDVGEREIGTSMVHLEILNVKPVPDLAASEVVLKATVLPLRLHVDQDALDFLSRFFEF KDDSAPSEPSPEDVPFLQRAEVNAIRVRLDFKPKRVDYAGLRSGRTTEFMNFFVLDEADM VLQHVIIYGVSGFDRLGRTLNDIWMPDIKANQLPTVLAGIAPVRSLVNIGGGVKDLVLVP MREYKKDGRIVRSIQKGAVQFAKTTTNELLRFGAKLAIGTQTALQSAEDFLNSPRGSPSR PSTSDGRWDDNGVDEGERPRISLYADQPLGVAQGLRGAYSSLERDILMTRDAIVAMPSEV LESGSATEAARRLLGRTPTVVLRPAIGASKAVSQTLLGVSNALDPKNRRKIDDKYKKHKV >sp|Q9BMN8|LAR_CAEEL Tyrosine-protein phosphatase Lar-like OS=Caenorhabditis elegans GN=ptp-3 PE=1 SV=1 MIQFRNKNNSMNRIARHLRNVARRKGSSLLLFLMLSTVLVAAKEDDPARLVVRPDSSTVV DESKISFFCRADGNPLPSVIWRVNGKSITDHNRISIKSLATGLSTLRFERVSLDDNATVV SCSADNGVANPVVAEASLTVVPRDKVPIGFPQIELHPSLKSVEQGKTAYVSCRVRGDPRA KVLWLRDLIPLDIRADGRYSVSTIGNPGALMIQHAREEDQGKYECIARNTLGVAHSKAAN LYVKVRRVPPYFSYKLERQYVVGVGGNINLTCVAVGYPMPRVFWKKTDLMVLDDPSTAPI GKNVLTLTHVESTENFTCVAVSALGNIEATTTVIAKELPPPPVNIVVSSVTSESVVITWK PPKYNEAINKYVVNYRLKYSEGRSSRGKTMETLENSLVIDGLVAFQTYEFTVRSAGPVGV GLESLPVEAQTKPSKPATAPVSPQARSLNRDSILVKWGPCEQPNGLITGYKVYYTNDLVT TPIREWKQHDAKSDEFMTTINGLEPDSRYFVRVIAQNSEGDSPLSTLVTVATRQGIPGQP PMLTVKALDSRRMQLTWDKPLYSSPVVGYTVRYNTSDGEKELTLTSPHEKHVVTGLHPDK YYYFRVAAYSDRGQGEFTEPMISKTIASIPLSSPTIVSAAATSSKSVEIRWKGPEQKKLN GVLTAYRINYFRLEDSKTANLESVEYDEDMDDSSSFLDRMSVVVPSDATSYVLSDLLPYS SYEITVAASTMDGYGPESSIRVVKTLEDVPSAPRNFNAELTSATSVKLTWDAPAAANGAL LGYYVYLDRMVNGEPVVEKGSKKRIVMIRDSSKRYFELDSLDPNTEYSFRLNAFNRNGDG EFSERKSIITQGIPPEAPEIVSVSLDRDEPPVVARIEWKMPKMKPNETPIEKYNLWLRAQ GYPDSYVKAKTVDGTDLSTTISGLWMGVVYDVLLAAENREGRSQNATETIATPVGSPDGE PIDVQYEVMKGKIVVSWRPPSEEKRNGNITSYKAILSAMDATADRYEQPVPAPSTSSTFE VNVRRAYLFKVAAATMKGIGPYSPVLTINPDPAALVGPPTNVRVEATSNSTAVVQWDFES QKADSFVVKYMHEPGNRMDTEKWKQLPVVSIDKENPKRFAVVSDLNAHKPYAFCVLAVKN NLTLNEQFNKVRVTNYMTNFQRQGPCSDPPTVLESVTPTYMVQNLRVLWKTSNSVQLTWE YNGPRNVGFYVNHTGRKDYVNHELQEKTMSTPGFGQDVDEKHREYLWTNLRPHMMYTIHV GVRTLPPGARKYWPQEVVTITDPTGPPFVDVPKLVDSSGTQPGQQMIRLTPATEEYGPIS HYWIILVPANYSTEDVVNLDPIELEKATAEKRAQLARSLSVSPSKKLKRKASEVGDDSQS ASYHPKEKRARRATVPGAYVTARLSADRVKQQYRNNQPFIVGDSQLYDGFTNYPLEHNLH YRLMMRAFAKNDVRTKDSFEQRAPMSEKLSRMYSDSVLTEPFTIKSALRGASQKSSPWVG ACIAFLVLFSIVGMLICWWLRCNKKSAGRHPRHGSITKVALTGNIMNGGGGIPGETSKLL STSNEYGRQIMNPYEQMNGNHHMESSMDLYPLPTSHSRSNGYAPVPVAIPSLPNNGNNMT TVSHPAVPIAELANHIERLRMNNNAGFQSEFESIETGQHFTWEHSSADMNKHKNRYANVA AYDHSRVVLSNVEGYPGMDYINANYVDGYDKPRSYIATQGPLPETFSDFWRMVWEEQSVT IVMLTNLEERSRVKCDQYWPSRGTATYGDIEVTLLESVHLAHYTMRTMRLKMVGEPEVRE IKHLQYTAWPDHGVPDHPTPFLIFLKRVKTLNPNDAGPIISHCSAGIGRTGAFIVIDCML ERLRYDNTVDIYGCVTALRAQRSYMVQTEEQYIFIHDAVLDAVNSGSTEVPASRLHQHLH ILSQPSADQLSGIDMEFRHLTTLKWTSNRCTVANLPVNRPKNRMLSAVPYDSNRVIMRLL PGADGSDYINASWIDGYKERGAYIATQAPTNETAADFWRAIWEHNSPIIAMLVRTNERGQ EQCSDYWPLETGVQVGMLVVEPMAEYDMKHYHLREFRISDINTREVRTVRQFHFMEWPDV GKPHTADHFLDFVTQVHNTYAQFGCTGPITVHCCSGAGRTAVFIALSIILDRMRAEHVVD VFTTVKLLRTERQNMIQEPEQYHFLYLAAYEYLAAYDNFS >sp|Q01631|CYAA_NEUCR Adenylate cyclase OS=Neurospora crassa GN=cr-1 PE=3 SV=2 MTRNDGGSRYSSIDSAQSSITAKPFPLTPTSSLGSSMTRPLSPSLQAGSSSSNGGHNVSR SASQGARRPAPTRLKTDDGTQFASRSSRDFESSQSQSQPSHTQTRSHSLSQATLQSCSQP QLSLNSQQSQSPSQYHSQQTPTQQQPQQQVSPTGGSRLTQSPTTPSNASIREHRMSELGG YRREMAAMLDTTGGALSRTSSHSQQQPQQPQQQQQQQQQQQGHAAGSVSGTFSNLSQYAP YLGGNNGGGMSMGSFLNDSTDNLSVISQLSPGIRPMTARPSQASAGSMEFPDSAYYDDER RPSIASITTTASSQGSRTSKTRGGLQKLQQFFGDRDDWPGRDSSEISLPQPSHSGPMSTG KEHRSHSYSLPGSGRSHRDRNYSNATDHHPSTFGSVSTVGGRDRDASPVPSRPRTPVPAP EVVPFLYQEADDIARYGEAPVRTSLTGPDRDRYIDSSQNPPKTSSSARSGHSIVHLPGHH KHNKSNEDPRALKPSLSREDSAASFARDFRNGSSSMMGTRSRAQSPAPSWTGTSRGLKAN SISDGTSSPAPSHKKGILGRFRRHNKDKEDGSSLRSGSNHTLVHRPSRQDLTRAAESTYP ASVYVSDPSEQREVPVRPGYVRQTTAPGFTTKLFTSKKSSSAKQPQDDMDEDIGPTDMHM GGGTVYHLDTNLNDMEGILTKPQPMTPLDNSISMRRESEKMIVPITTDPEGAWAAPDSWA VRDNKKSLAPQVNEDLCSRQPSEEKEKKSNYYIRVFRSDSTWTTLTLPLTATAEDVIMGV AKKTYLPPGAQDSYSLLIKKHDLFRVLNSAEQPLRIQKRLFQQIGYQEKDGIDEIGREDN SYICRWVFLKEKEADMHLLSPDINFRNQKLNHVDLSGRNLITIPVPLYRKAAEIVSLNLS RNLSLDVPRDFIQACTALRDIKYNNNEAQALPKSFATASKLTYLDVSNNRLQDLDHSELS KLTGLLKLNLANNCLRSLPPTLGAYKSLRTLNISSNFLDVFPSFICELETIVDLDLSFNS INNLPDNLMKLRNLEKFVITNNRLSGPISESVRDLVSLRELDIRYNQISTIDVLSDLPRL EILSADHNQISKFSGSFERLRSLKLNSNPIVKFEVKAPVPTLKILNLSNAQLASIDESID NLMNLERLILDSNYFVSLPNQIGNLKKLDHLSMANNHLGELPPEIGCLTELRTLDVHGNN MRKLPNEIWWANKLEHLNASSNILTEFPKPASRAPQAPGEASPSPGAYPFPNANKNGLLS RTPSMDDLNGDASRRPSQASSTLLGVAVSPVPSGPDNRKSSMVSLYGKGGRKTSVVSRST TQSSTGVITPSNGPRKDSSLSYRFTHTFSGSLKNLYLADNQLDDDVFEELKHLPELRVLN LSCNDLSDMPQGTIRSWPQLVELYLSGNELTSLPAEDFLEEHCLLQTLHINGNKFINLPA EISRAKKLQVLDCSSNNLKYNVTNVPYDWNWNFNRDLRYLNLSGNKRLEIKNNYRQPQSY RDDDFADTDFSKLTNLRVLGLMEVTHTLPNIPDQTEDRRVRTSEMKAGAYLPYGMADTLG KNEHLSLFDLVVPRLGSVETDTLVALFDGKELSTGGSKIAKFLYEEFSRLFILELEKVKG KPNENPADALRRTFLSVNKLLMSLSNSADERGLDSHPSRNYAHTVLTKEDLNSGCVATVA YLSELKLYVANVGDVQGMLIQANGSFKMLTKKHDPADPVERSRIRNAGGWVSRNGRLNDV LNVSRAFGYTELLPAVQAAPDITEHTIDDKDETVLIASKELWEHLRPELIVDVARECRSD LMKASQKLRDLAIAYGSTNKLLIMMIGVANLKQRQAQQFKGQLNATFSMPQDDPSHVPPS GNKRRKVRAEGPLDSNLMRLNAEVPPPTGQLSIVFTDIKNSTQLWENYPEAMRLAIKLHN EVMRRQLRMIGGFEVKTEGDAFMVSFPTATSALLWCFAVQMKLLTVDWPPEVLSNSSCQP IYDRNNNLITRGLSVRMGAHWGEPLAERDPVTRRMDYYGPMVNKASRISAVADGGQITAS SDFITEIHRCLETYKESVDVDEDSLEDDATAKAIRAELRALSSQGFEVKDMGEKKLKGLE NPELVYSVYPHALVGRTEQHHAHTESTQNQAALQPYGALATPKPATMDPDSEIQFEPETI WALWRVALRLEMLCSTLEEPNARGLQAPETELLERMKQRAGEVTDHFLLNFMEHQISRIE TCITSLAVRHIAIGSGPITKLNDLRAPMNDVLSTLKEQMDELARYKAKYGSLDQAETDDA TDNNSSGDVDTLDGSDTEQE >sp|Q9QX47|SON_MOUSE SON protein OS=Mus musculus GN=Son PE=1 SV=1 MAADIEQVFRSFVVSKFREIQQELSSGRSEGQLNGETNPPIEGNQAGDTAASARSLPNEE IVQKIEEVLSGVLDTELRYKPDLKEASRKSRCVSVQTDPTDEVPTKKSKKHKKHKNKKKK KKKEKEKKYKRQPEESESKLKSHHDGNLESDSFLKFDSEPSAAALEHPVRAFGLSEASET ALVLEPPVVSMEVQESHVLETLKPATKAAELSVVSTSVISEQSEQPMPGMLEPSMTKILD SFTAAPVPMSTAALKSPEPVVTMSVEYQKSVLKSLETMPPETSKTTLVELPIAKVVEPSE TLTIVSETPTEVHPEPSPSTMDFPESSTTDVQRLPEQPVEAPSEIADSSMTRPQESLELP KTTAVELQESTVASALELPGPPATSILELQGPPVTPVPELPGPSATPVPELSGPLSTPVP ELPGPPATVVPELPGPSVTPVPQLSQELPGPPAPSMGLEPPQEVPEPPVMAQELSGVPAV SAAIELTGQPAVTVAMELTEQPVTTTEFEQPVAMTTVEHPGHPEVTTATGLLGQPEAAMV LELPGQPVATTALELSGQPSVTGVPELSGLPSATRALELSGQSVATGALELPGQLMATGA LEFSGQSGAAGALELLGQPLATGVLELPGQPGAPELPGQPVATVALEISVQSVVTTSELS TMTVSQSLEVPSTTALESYNTVAQELPTTLVGETSVTVGVDPLMAQESHMLASNTMETHM LASNTMDSQMLASNTMDSQMLASNTMDSQMLASSTMDSQMLASSTMDSQMLATSTMDSQM LATSSMDSQMLATSSMDSQMLATSSMDSQMLATSSMESQMLASGAMDSQMLASGTMDAQM LASGTMDAQMLASSTQDSAMMGSKSPDPYRLAQDPYRLAQDPYRLGHDPYRLGHDAYRLG QDPYRLGHDPYRLTPDPYRVSPRPYRIAPRSYRIAPRPYRLAPRPLMLASRRSMMMSYAA ERSMMSSYERSMMSYERSMMSPMAERSMMSAYERSMMSAYERSMMSPMAERSMMSAYERS MMSAYERSMMSPMADRSMMSMGADRSMMSSYSAADRSMMSSYSAADRSMMSSYTDRSMMS MAADSYTDSYTDSYTEAYMVPPLPPEEPPTMPPLPPEEPPMTPPLPPEEPPEGPALSTEQ SALTADNTWSTEVTLSTGESLSQPEPPVSQSEISEPMAVPANYSMSESETSMLASEAVMT VPEPAREPESSVTSAPVESAVVAEHEMVPERPMTYMVSETTMSVEPAVLTSEASVISETS ETYDSMRPSGHAISEVTMSLLEPAVTISQPAEDSLELPSMTVPAPSTMTTTESPVVAVTE IPPVAVPEPPIMAVPELPTMAVVKTPAVAVPEPLVAAPEPPTMATPELCSLSVSEPPVAV SELPALADPEHAITAVSGVSSLEPSVPILEPAVSVLQPVMIVSEPSVPVQEPTVAVSEPA VIVSEHTQITSPEMAVESSPVIVDSSVMSSQIMKGMNLLGGDENLGPEVGMQETLLHPGE EPRDGGHLKSDLYENEYDRNADLTVNSHLIVKDAEHNTVCATTVGPVGEASEEKILPISE TKEITELATCAAVSEADIGRSLSSQLALELDTVGTSKGFEFVTASALISESKYDVEVSVT TQDTEHDMVISTSPSGGSEADIEGPLPAKDIHLDLPSTNFVCKDVEDSLPIKESAQAVAV ALSPKESSEDTEVLLPNKEIVPESGYSASIDEINEADLVRPLLPKDMERLTSLRAGIEGP LLASEVERDKSAASPVVISIPERASESSSEEKDDYEIFVKVKDTHEKSKKNKNRDKGEKE KKRDSSLRSRSKRSKSSEHKSRKRTSESRSRARKRSSKSKSHRSQTRSRSRSRRRRRSSR SRSKSRGRRSVSKEKRKRSPKHRSKSRERKRKRSSSRDNRKAARARSRTPSRRSRSHTPS RRRRSISVGRRRSFSISPSRRSRTPSRRSRTPSRRSRTPSRRSRTPSRRSRTPSRRRRSR SAVRRRSFSISPVRLRRSRTPLRRRFSRSPIRRKRSRSSERGRSPKRLTDLDKAQLLEIA KANAAAMCAKAGVPLPPNLKPAPPPTIEEKVAKKSGGATIEELTEKCKQIAQSKEDDDVI VNKPHVSDEEEEEPPFYHHPFKLSEPKPIFFNLNIAAAKPTPPKSQVTLTKEFPVSSGSQ HRKKEADSVYGEWVPVEKNGEESKDDDNVFSSSLPSEPVDISTAMSERALAQKRLSENAF DLEAMSMLNRAQERIDAWAQLNSIPGQFTGSTGVQVLTQEQLANTGAQAWIKKDQFLRAA PVTGGMGAVLMRKMGWREGEGLGKNKEGNKEPILVDFKTDRKGLVAVGERAQKRSGNFSA AMKDLSGKHPVSALMEICNKRRWQPPEFLLVHDSGPDHRKHFLFRVLRNGSPYQPNCMFF LNRY h-blast-1.0_ncbi-blast-2.2.25/queries/2SequenceLength_00000400.txt0000600000175000017500000000102711741230651022035 0ustar ykeyke>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 MGVYKFCYNKKKEVGQVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKC CKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI >sp|Q5WGN4|3MGH_BACSK Putative 3-methyladenine DNA glycosylase OS=Bacillus clausii (strain KSM-K16) GN=ABC1936 PE=3 SV=1 MEQQKALDLSFFEQSTIEVAKGLIGMHLVHELDGVTLIGRITETEAYLGVLDRACHSYGR RRTKRTAILYEEAGRCYTYTMHTHCLLNVVCEQKGQPEAVLIRAIEPISGVKEMERLRGK PHTSREFANGPGKLTKAMGITMADYGRLLTEPPLYFAKGDHTNASIVATKRIGIKGAGPC SHHPWRFIDGNSRAVSAYRP h-blast-1.0_ncbi-blast-2.2.25/queries/2SequenceLength_00005898.txt0000600000175000017500000001377311741454234022107 0ustar ykeyke>sp|Q8CG65|SSPO_MOUSE SCO-spondin OS=Mus musculus GN=Sspo PE=2 SV=1 MLPLALLFGMLWTQANGHWCEQIETVHVEEEVTPRQEDLVPCTSLYHYSRLGWQLDLSWS GRVGLTRPPALGLCAIYKPPETRPATWNRTVRACCPGWGGAHCTDALAETSPKGHCFVTW HCQPLAGSANSSAGSLEDPADELGVWPLTLNDPILFPGMSLQWQGDWLVLSGGLGVVVRL DRSSSISISVDQEFWGRTQGLCGLYNGRPEDDFVEPGGGLATLAATFGNSWKLPGSEPGC LDAVEVAWGCESLLGGTLTDLEAVKLQAQAQDMCHQLLEGPFWQCHGQVQPDEYHETCLF AYCVGATAGNGPEGQLEAVCATFANYAQACARQHIYVHWRKPGFCERVCPGGQLYSDCVS SCPPSCSAVAQGEEGSCGKECVSGCECPTGLFWDGALCVPAAHCPCYHRRQRYAPGDTVK QQCNPCVCQDGRWHCAQALCPAECAVGGDGHYFTFDGRSFFFRGTPGCHYSLVQDSVKGQ LLVVLEHGACDTGSCLHALSVFLGNTHIQLRYSGAVLVDGEDVDLPWIGVEGFNISWASS TFLLLHWPGAWVLWGVAEPAAYITLDPRHAYQVQGLCGTFTWKQQDDFLTPAGDIETSVT AFASKFQVSGDGRCPLVDKSPLFCSSYSQHLTFTEAACAILHGHAFQECHGLVDREPFRL RCLEAVCGCAPGRDCLCPVLSAYTRHCAQEGVLLQWRNETLCPVSCPGGQVYQECAPVCG HHCGEPEDCKELGICVAGCNCPPGLLWDLEGQCVPPSMCHCQFGGHRYTINTTTVRDCSH CICQERGLWNCTAHHCPRQWALCPRELIYVPGACLLTCDSPRANHSCWAGSTDGCVCPPG TVLLDKHCVSPDLCPCRHNGQWYPPNATIQEDCNICVCQGQRWHCTGQRCSGWCQASGAP HYVTFDGLVFTFPGACEYLLVREAGGRFSVSVQNLPCGASGLTCTKALVVRLDSTVVHML RGQAVTVNGVSIRLPKVYTGPGLSLHHAGLFLLLTTRLGLTLLWDGGTRVLVQLSPHFHG RVAGLCGNFDSDASNDLRSRQGLLEPTAYLTAHSWRLNPLCPEPGDLPHPWNAHRANWAP ARCEVILQPIFAPCHTEVPPQQYYEWCVYDACGCDTGGDCECLCSAIATYADECARHRHH VRWRSQELCPLQCEGGQVYEPCGSTCPPTCHDHHSELRWHCQVITCVEGCFCPEGTLLHG GACMKLAACPCEWQGSFFPPGTVLQKDCGNCTCQGSQWHCDRGGAPCEDMEPGCAEGETL CRENGHCVPLEWLCDNQDDCGDGSDEEGCATSVCGEGQMSCQSGHCLPLSLICDGQDDCG DGTDEQGCLCPHGSLACADGRCLPPALLCNGHPDCLDAADEESCLGPVSCISGEVSCVDG TCVRTIQLCDGVWDCPDGADEGPSHCSLPSLPTPPGGIGQNPSTSSLDTAPSPVGSTSPA SPCSLLEFQCNSGECTPRGWRCDQEEDCTDGSDELDCGGPCMLYQVPCAHSPHCVSPGQL CDGVTQCPDGSDEDPDVCEEQSASGGANRTGAPCPEFSCPDGTCIDFLLVCDGNPDCELA DETEPSLDEQGCGAWGSWGPWAPCSQTCGSGTRSRNRNCSTSSLQVLQNCPGLQHQSQAC FTEACPVDGEWSSWSPWSPCSEPCGGTTTRHRQCRPPQNGGQDCALLPGSTHSTRQTSPC PQEGCLNATCFGELVFRTCAPCPLTCDDISGQAACPPDRPCSSPGCWCPDGKVLNTEGQC VRPRQCPCLVDGAHYWPGQRIKMDCQLCGLDCGWSSWSPWAECLGPCSSQSLQWSFRSPN NPRLSGHGRQCRGIHRKARRCQTEACEGCEQWGLMYNVGERWRGGPCMVCECLHSSITHC SPYCPIGSCPQGWVLVEGMGESCCHCALPEKNQTVIHMTTPAPAPASAPSPQIGAHLVTY VLPPTADACYSPLGLAGLPMWAPSQHWEHITRADPVEAPMAGPGPREGASAEWHTQPLYL QLDLRRPRNLTGIIVQRAGSSAAYVSTLSLQFSSDNLQWHNYVNSLSSTLSPPKPSPESS NHMAPEVWTFDQMVQARYIRVWPHSGHLRDNNQHDIFLWVELLGLSPLAPLCPGSRHRCA SGECAPKGGPCDGAVDCDDGSDEEGCGSLHASTTSRTPALSPTQPGKFPREVSEDLRQGA EAMTSHSPPSSGETAGLIPASEGTLPVSGQPMQTLSATSTFPPGAKSLHPGMAAVTVHPP HSVTPGAPVGQTVSPRPFPPMPCGPGQVPCDVLGCVEQEQLCDGREDCLDGSDEQHCASA EPFTVPTTALPGLPASKALCSPSQLRCGSGECLPFEHRCDLQVNCQDGSDEDNCVDCVLA PWSGWSDCSRSCGLGLIFQHRELLRLPLPGGSCLLDQFRSQSCFVQACPVAGAWAEWGPW TACSVSCGGGHQSRQRSCVDPPPKNGGAPCPGPSHEKAPCNLQLCPGDTDCEPGLVHVNA ELCQKGLVPPCPPSCLDPEANRSCSGHCMEGCRCPPGLLLQDSHCLPLSECPCLVGQKLI QPRLAFLLDNCSQCICEKGTLLCKPGACSQSCGWSAWSPWTACDRSCGSGVRARFRSPTN PPVAFGGSPCEGDRQELQACYTDCGTEIPGWTPWTSWSSCSQSCLVPGGDPGWRQRSRLC PSSRDTFCPGEATQEEPCSPPVCPVPSAWGLWASWSTCSASCNGGIQTRGRSCSGSAPGN PVCLGPHTQTRDCNMHPCTAQCPGNMVFRSAEQCLEEGGPCPQLCLAQDPGVECTGSCAP SCNCPPGLFLHNASCLPRSQCPCQLHGQLYAPGAVAHLDCNNCTCISGEMVCTSKRCPVA CGWSPWTPWSPCSQSCNVGIRRRFRAGTEPPAAFGGAECQGPNLDAEFCSLRPCRGPGAA WSSWTPCSVPCGGGYRNRTQGSGPHSPIEFSTCSLQPCAGPVPGVCPEDQQWLDCAQGPA SCAHLSIPGEANQTCHPGCYCLSGMLLLNNVCVPVQDCPCAHRGRLYSPGSAVHLPCENC SCISGLITNCSSWPCEEGQPAWSSWTPWSVCSASCNPARRHRHRFCARPPHRAPFSLVLL TTVAAPTTLCPGPEAEEEPCLLPGCNQAGGWSPWSPWSGCSRSCGGGLRSRTRACDQPSP QGLGDFCEGPQAQGEACQAQPCPVTNCSAMEGAEYSPCGPPCPRSCDDLVHCVWRCQPGC YCPLGKVLSADGAICVKPSYCSCLDLLTGKRHHAGTQLMRPDGCNHCTCMEGRLNCTDLP CQVSGDWCPWSKWTACSQPCRGQTRTRSRACVCPAPQHGGSPCPEESGGTGVQHQMEACP NATACPVDGAWSPWGPWSSCDACLGQSYRSRVCSHPPISDGGKPCLGGYQQSRPCRNSST LCTDCGGGQDLLPCGQPCRHSCQDLSLGSTCQPGSAGCQSGCGCPPGQLSQHGLCVFPVD CHCHFQPRAMGIPENRSRSVGSTLSSWESLEPGEVVTGPCDNCTCVAGILQCHEVPSCPG PGIWSSWGPWEKCSVSCGGGEQLRSRQCARPPCPGLAQQSRICHIHVCRETGCPAGRLYR ECQPSDGCPFSCAHVTGQVACFSERCKEGCHCPEGTFQHHVACVQECPCVLTVLLLQELG LASAALGSYPTLLGDEGKPLGPGVELLPGQMLQTDCGNCSCVHGKLSCSMVECSRVHGSF GPWGMWSLCSRSCGGLGTRTRTRQCVLPTLAPGGLSCRGPLQDLEYCFSPECPGTAGSTV EPVTGLAGGWGPWSPWSPCSHSCTDPAHPAWRSRTRLCLANCTVGDSSQERPCNLPSCAA LLPCPGPGCGSGNCFWTSWAPWEPCSRSCGVGQQRRLRAYHPPGPGGHWCPDILTAYQER RFCNLRACPVPGGWSHWSPWSWCDRSCGGGRSLRSRSCSSPPPKNGGTSCVGERHHVRPC NPMPCEEGCPAGMEMVSCANHCPYSCSDLQEGGMCQEDQACQLGCRCSEGFLEQDGGCVP VGHCECTDAQGRSWAPGSQHQDACNNCSCQAGQLSCTAQLCSPPAHCAWSHWSAWSSCSH SCGPQGQQSRFRSSTSGSWALECQKEQSQSQPCPEVPCPPLCLHEAHLHELGDNWLHGEC QQCSCTPEGAICKDTDCAVPRGWTLWSSWSYCSVSCGGGSQVRTRSCTVSAPPHGSLSCE GPDTQTRHCGQQLCLQKLERCSWGPWGPCSRSCGTGLASRSGSCPCLLTKEDSKCNDTFL GLDTQACYSGPCQDDCTWGDWSSWTRCSCKVLVQQRYRHQVPAPGQAGEGTPCTRLDGHF RPCTIGNCSEDSCPPPFEFQSCGSPCAGLCATHLNHRLCQDLPPCQPGCYCPKGLLEQAG SCILPEQCNCWHISGEGARVTLAPGDRLQLGCKECVCRRGELQCSSQGCEGLLPLTGWSE WSPCGPCLPQSALAPASRTALEGHWPLNTSDLPPPSVTLLASEQYRHRLCLDPETRRPWA GDPALCTVPLSQQRLCPDPGACNDTCQWGPWGPWSPCQMPCSGGFKLRWRVARDTSAGEC PGPWAQTESCNMGSCPGESCETRDTVFTLDCANQCPRSCADLWDGVQCLQGPCSPGCRCP PGQLVQDGHCVPISSCRCGLPSANASWELAPTQVVQLDCHNCTCINGTLMCPHLECPVLG PWSAWSECSAVCGKGTMVRHRSCEEHPDREPCQALDLQQWQECNLQACPECPPGQVLSTC ATMCPSLCSHLWPGTICVREPCQLGCGCPGGQLLYNGTCIPPEACPCTQFSLPWGLTLPL EEQARELPSGTVLTRNCTHCTCQGGAFICSLTDCQECAPGEIWQHGKLGPCEKTCPEMNM TQAWSNCTEAQAPGCVCQLGYFRSQTGLCVPEDHCECWHHGSPHLPGSEWQEACESCRCL HGKSVCIRHCPELSCAQGEVIMQEPGSCCPICQQDTLKEEPVSCRYLTELRNLTKGPCHL DQIEVSYCSGHCRSSTNVMTEEPYLQSQCDCCSYRLDPDSPVRILNLLCPDGHTEPVVLP VIHSCQCSACQGGDFSKH >sp|O88990|ACTN3_MOUSE Alpha-actinin-3 OS=Mus musculus GN=Actn3 PE=2 SV=1 MMMVMQPEGLGAGEGPFSGGGGGEYMEQEEDWDRDLLLDPAWEKQQRKTFTAWCNSHLRK AGTQIENIEEDFRNGLKLMLLLEVISGERLPRPDKGKMRFHKIANVNKALDFIASKGVKL VSIGAEEIVDGNLKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNVQ NFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLDAEDI VNTPKPDEKAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENEKLMEEYEKLASELL EWIRRTVPWLENRVGEPSMSAMQRKLEDFRDYRRLHKPPRVQEKCQLEINFNTLQTKLRL SHRPAFMPSEGKLVSDIANAWRGLEQVEKGYEDWLLSEIRRLQRLQHLAEKFQQKASLHE AWTRGKEEMLNQHDYESASLQEVRALLRRHEAFESDLAAHQDRVEHIAALAQELNELDYH EAASVNSRCQAICDQWDNLGTLTQKRRDALERMEKLLETIDQLQLEFARRAAPFNNWLDG AIEDLQDVWLVHSVEETQSLLTAHEQFKATLPEADRERGAILGIQGEIQKICQTYGLRPK SGNPYITLSSQDINNKWDTVRKLVPSRDQTLQEELARQQVNERLRRQFAAQANAIGPWIQ GKVEEVGRLAAGLAGSLEEQMAGLRQQEQNIINYKSNIDRLEGDHQLLQESLVFDNKHTV YSMEHIRVGWEQLLTSIARTINEVENQVLTRDAKGLSQEQLNEFRASFNHFDRKRNGMME PDDFRACLISMGYDLGEVEFARIMTMVDPNAAGVVTFQAFIDFMTRETAETDTAEQVVAS FKILAGDKNYITPEELRRELPAEQAEYCIRRMAPYKGSGAPSGALDYVAFSSALYGESDL h-blast-1.0_ncbi-blast-2.2.25/queries/SequenceLength_00000100x.txt0000600000175000017500000000032211455416572022147 0ustar ykeyke>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1 MGVYKFCYNKKKEVGQVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKC CKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI h-blast-1.0_ncbi-blast-2.2.25/README0000644000175000017500000003062112152342732014553 0ustar ykeyke************************ H-BLAST v1.0 release [Dec. 30, 2012] ****************** H-BLAST is developed to accelerate the protein sequence alignment algorithms of the NCBI-BLAST implementation based on a GPU+CPU heterogeneous computer, with preserving the same output results as those obtained by NCBI-BLAST. It can take advantage of multiply CPU cores and GPUs. It has been tested on CentOS 5.4 and Ubuntu 11.04 with three NVIDIA Tesla Fermi C2050 GPUs and two NVIDIA Geforce GTX 560 GPUs, respectively. H-BLAST is free for academic and non-commercial use. The current implementation is an enhancing variation of GPU-BLAST. Further imformation about GPU-BLAST, please refer to the paper Panagiotis D. Vouzis and Nikolaos V. Sahinidis, "GPU-BLAST: Using graphics processors to accelerate protein sequence alignment," Vol. 27, no. 2, pages 182-188, Bioinformatics, 2011 (Open Access). And imformation about H-BLAST, please refer to the paper Weicai Ye, Yongdong Zhang, Ying Chen and Yuesheng Xu, "H-BLASTP: A Fast Scalable Protein Sequence Alignment Toolkit on Heterogeneous Computers". Please cite the authors in any work or product based on this material: Weicai Ye, Yongdong Zhang, Ying Chen and Yuesheng Xu, "H-BLASTP: A Fast Scalable Protein Sequence Alignment Toolkit on Heterogeneous Computers". For any questions and feedback about H-BLAST, contact cai_rcy@mail.tom.com or lnszyd@mail.sysu.edu.cn. I. Supported features ===================== H-BLAST v1.0 supports protein alignment algorithms "blastp" and “blastx” (for test only). It can handle input files with multiple protein queries and take advantage of multiply CPU cores and GPUs. H-BLAST v1.0 does not support PSI BLAST. The substitution matrix is fixed with the Blosum62 matrix. II. Files in this folder. ===================== ./queries The folder contains all queries for benchmark test. For example, the file with the name "24Sequence_length_30k.txt" contains 24 sequences with total length 30kbp. ./h_blast The folder contains all source code of h-blast. ./install The script for installation the h-blast into NCBI-BLAST. ./README The current file for your eyes. ./gpu_db_used_ratioq The file address additional parameters for H-BLAST. III. Quick start ===================== The following scenario shows a procedure to build and use the H-BLAST software with “blastp” algorithm (H-BLASTP). There are three steps, installation of H-BLAST, making databases and sequence alignment with H-BLAST. All commands are on a CentOS 5.4 with CUDA 4.0, and the login shell is bash. We assume that there are 12 CPU cores and 2 GPU cards on the given computer, and the database in fasta format and the query sequence are located at “/home/Blast/db” folder. The pre-built NCBI-BLAST-2.25+ software with source code is located at “/home/Blast/ncbi_blast/blast/ncbi-blast-2.2.25+-src/c++/GCC412-ReleaseMT64/bin” folder. The procedure to use the H-BLAST software with “blastx” algorithm (H-BLASTX) is the same except using the blastx interface. Step one: Installation of H-BLAST $tar -xzf h-blast-1.0_ncbi-blast-2.2.25.tar.gz $cd h-blast-1.0_ncbi-blast-2.2.25 $./install ncbi-blast-2.2.25 Do you want to install H-BLAST on an existing installation of "blastp" [yes/no] yes: you will be asked for the installation directory of the "blastp" executable no: will download and install "ncbi-blast-2.2.25+-src" yes Please input the installation directory of "blastp" of "ncbi-blast-2.2.25+-src" /home/Blast/ncbi_blast/blast/ncbi-blast-2.2.25+-src/c++/GCC412-ReleaseMT64/bin "blastp" version 2.2.25+ is compatible Continuing with the installation of H-BLAST... Modifying NCBI BLAST files Compiling CUDA code .gpu_blastp.cu(484): warning: variable "result" was set but never used gpu_blastp.cu(484): warning: variable "result" was set but never used .gpu_blastp.cu: In function ‘void GPU_BLASTP(int, const BLAST_SequenceBlk*, const BlastQueryInfo*, const LookupTableWrap*, const Blast_ExtendWord*, const BlastInitialWordParameters*, const BlastGPUOptions*, const Int4*)’: gpu_blastp.cu:858: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’ gpu_blastp.cu:860: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’ gpu_blastp.cu:862: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’ gpu_blastp.cu:863: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’ gpu_blastp.cu:864: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long unsigned int’ gpu_blastp.cu:865: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ gpu_blastp.cu:924: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘size_t’ gpu_blastp.cu:932: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘size_t’ gpu_blastp.cu: In function ‘Boolean GPU_BLASTP_check_memory(const LookupTableWrap*, const Blast_ExtendWord*, const BlastGPUOptions*, int, Int4, Int4, Int4, Int4, Int4)’: gpu_blastp.cu:1230: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘long long unsigned int’ gpu_blastp.cu:1230: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ gpu_blastp.cu: In function ‘void GPU_BLASTP_check_rehit_ratio(const Int4*, Int4)’: gpu_blastp.cu:1312: warning: unknown conversion type character ‘)’ in format Compiling CUDA code Building NCBI-BLAST with H-BLAST ......................................................................................... ......................................................................................... ...................................................................................... $cp /home/Blast/ncbi_blast/blast/ncbi-blast-2.2.25+-src/c++/GCC412-ReleaseMT64/bin/makeblastdb /home/Blast/db $cp /home/Blast/ncbi_blast/blast/ncbi-blast-2.2.25+-src/c++/GCC412-ReleaseMT64/bin/blastp /home/Blast/db $cp gpu_db_used_ratioq /home/Blast/db Step two: Make a BLAST Database and a GPU database $cd /home/Blast/db $./makeblastdb -in nr.fasta -out sorted_nr -sort_volumes -max_file_sz 250MB $./blastp -query SequenceLength_00001000.txt -db sorted_nr -gpu t -method -1 -gpu_blocks 256 -gpu_threads 64 > create_db_out.txt Step three: Sequence alignment with H-BLAST $./blastp -db sorted_nr -query 24Sequence_length_30k.txt -out result_30k -num_threads 12 -gpu t –method 2 &> output.txt IV. FAQ ===================== Q1. How to use H-BLAST? Since the H-BLAST modifies NCBI-BLAST with GPU functionality, the interface of “blastp” and “blastx” in H-BLAST is identical to those from NCBI-BLAST except additional options. Q2. What are the additional options of using H-BLAST? The additional options are shown as follows: -gpu Use GPU for “blastp” or “blastx” Default = `F' -gpu_threads Number of GPU threads per block Default = `64' -gpu_blocks Number of GPU block per grid Default = `512' -method Method to be used x >= 1 = for GPU-based sequence alignment with x GPU cards (default x = 1), 0 = for GPU-based sequence alignment with all GPU cards in the computer -1 = for GPU database creation Default = `1' * “-method -1” is incompatible with: num_threads Typing "./blastp -help" will print the above options towards the end of the output. Q3. Are there any relationships among the options “-max_file_sz”, “-gpu_threads” and “-gpu_blocks” in H-BLAST? Yes, they are very close. The max. size of a GPU database volume and the number of gpu threads are limited by the memory size on a GPU card. H-BLAST will reject any unacceptable option combos. Furthermore, different option combos affect performance. In our tests, two option combos are good for different GPU cards, listed as follows: a. -max_file_sz 250MB -gpu_threads 64 -gpu_blocks 256 b. -max_file_sz 500MB -gpu_threads 64 -gpu_blocks 512 Option a fits for any GPU cards with at least 1GB memory, such as NVIDIA Geforce GTX 560. And Option b fits for any GPU cards with at least 2GB memory, such as NVIDA Tesla C2050. And the option a is our first choice, even using NVIDA Tesla C2050 GPU cards. Q4. Is the option “-sort_volumes” necessary? Yes, if you want to use GPU cards. And the sorted database produces identical alignments with the unsorted one. Q5. What is the file “gpu_db_used_ratioq” used for? The file “gpu_db_used_ratioq” list some parameters using in H-BLAST, including the initial load assignment ratio for GPU cards, using self-adaptive load balancer or not, the computational capacity ratio between a GPU card and a CPU core and the number of max. successful hits per subject sequence to be saved. Since some parameters depend on empirical experience, we show the parameters with two different computers. The initial load assignment ratios are listed in tables. a. A cluster node has 2 six-core Intel Xeon E5650 2.6GHz CPUs, 6 NVIDIA Tesla C2050 GPUs, and 72GB memory with GCC 4.1.2 compiler and CUDA 4.0 on CentOS 5.4. ///=================== file content in gpu_db_used_ratioq =========== # The gpu_db_used_ratio is 1 # the gpu_db_used_ratio is fixed or not, '1' for fixed, others for changed by program itself 0 # gpu_cpu_capacity_rate is 4 # MAX_SUCCESSFUL_HITS_PER_SEQUENCE is 19 ///============= table of initial load assignment ratios =========== CPU threads\ GPU cards | 1 | 2 | 3 ------------------------------------------------------------------------------ 1 | 1 | 1 | 1 ------------------------------------------------------------------------------ 2 | 1 | 1 | 1 ------------------------------------------------------------------------------ 4 | 1 | 1 | 1 ------------------------------------------------------------------------------ 6 | 0.8 | 1 | 1 ------------------------------------------------------------------------------ 8 | 0.7 | 1 | 1 ------------------------------------------------------------------------------ 12 | 0.5 | 0.8 | 1 ------------------------------------------------------------------------------ b. A desktop PC has an i5-2300 2.8GHz quad-core CPU, 2 NVIDIA GTX560 GPUs, and 8G memory with GCC 4.4.6 compiler and CUDA 4.0 on Ubuntu 11.04. ///=================== file content in gpu_db_used_ratioq =========== # The gpu_db_used_ratio is 1 # the gpu_db_used_ratio is fixed or not, '1' for fixed, others for changed by program itself 0 # gpu_cpu_capacity_rate is 2 # MAX_SUCCESSFUL_HITS_PER_SEQUENCE is 19 ///============= table of initial load assignment ratios =========== CPU threads\ GPU cards | 1 | 2 | ------------------------------------------------------------------------------ 1 | 1 | 1 | ------------------------------------------------------------------------------ 2 | 1 | 1 | ------------------------------------------------------------------------------ 4 | 0.8 | 1 | ------------------------------------------------------------------------------ Q6. What is the screen output used for? The screen output shows the details of the H-BLAST execution, including the execution time for each database volume with CPU cores and GPU cards, the realignment ratio and any error messages. Q7 What are the options of H-BLAST used for installation configures with NCBI-BLAST? The installation configures H-BLAST with the following options: ./configure --without-debug --with-mt --without-sybase --without-ftds --without-fastcgi --without-fltk --without-wxwin --without-ncbi-c --without-sssdb --without-sss --without-geo --without-sp --without-orbacus --without-boost h-blast-1.0_ncbi-blast-2.2.25/gpu_db_used_ratioq0000644000175000017500000000030212137167274017457 0ustar ykeyke# The gpu_db_used_ratio is 1 # the gpu_db_used_ratio is fixed or not, '1' for fixed, others for changed by program itself 0 # gpu_cpu_capacity_rate is 2 # MAX_SUCCESSFUL_HITS_PER_SEQUENCE is 19 h-blast-1.0_ncbi-blast-2.2.25/install0000755000175000017500000001345712152342007015272 0ustar ykeyke#!/bin/bash # # Progress Indicator # function progress_ind { # Sleep at least 1 second otherwise this algoritm will consume # a lot system resources. interval=1 while true do echo -ne "." sleep $interval done } # # Stop distraction # function stop_progress_ind { exec 2>/dev/null kill $1 echo -en "\n" } ncbi_blast_version=$1 working_dir=`pwd` nvcc=`which nvcc` if [ $? -ne 0 ]; then echo -e "\nError: nvcc cannot be found. Exiting..." exit 1 fi if [ -z $ncbi_blast_version ]; then echo -e "Error: NCBI BLAST version not provided.\nE.g.: install ncbi-blast-2.2.25+-src. Exiting..." exit 1 fi echo "Do you want to install H-BLAST on an existing installation of \"blastp\" [yes/no]" echo "yes: you will be asked for the installation directory of the \"blastp\" executable" echo "no: will download and install \"${ncbi_blast_version}\"" read user_input if [ $user_input == "yes" ]; then echo "Please input the installation directory of \"blastp\" of \"${ncbi_blast_version}\"" read installed_dir #check if the executable "blastp" exists in the given directory if [ ! -x $installed_dir/blastp ]; then echo "Executable \"blastp\" cannot be found" echo "Exiting..." exit 0 else blastp_version=`$installed_dir/blastp -version | grep blastp | awk '{print $NF}'` if [ $blastp_version == "2.2.25+" ]; then echo "\"blastp\" version $blastp_version is compatible" else echo "\"blastp\" version $blastp_version is not supported" echo "Exiting..." exit 0 fi fi #check if the source file "blast_engine.c" as a first check that the source code exists if [ ! -f "$installed_dir/../../src/algo/blast/core/blast_engine.c" ]; then echo "Source code not detected." echo "You must have the source code of \"$ncbi_blast_version\" to add H-BLAST" echo "Exiting..." exit 0 else echo "Continuing with the installation of H-BLAST..." download=0 fi elif [ $user_input == "no" ]; then echo "Continuing with the downloading of $ncbi_blast_version..." download=1 else echo "Please enter \"yes\" or \"no\"" echo "Exiting.." exit 0 fi if [ $download == 1 ]; then #Download the version 2.2.25 of NCBI BLAST echo "Downloading NBCI BLAST" wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.25/${ncbi_blast_version}.tar.gz if [ $? -ne 0 ]; then echo -e "\nError downloading ${ncbi_blast_version}. Verify that the file exists in the server. Exiting..." exit 1 fi echo -e "\nExtracting NCBI BLAST" progress_ind & pid=$! trap "stop_progress_ind $pid; exit" INT TERM EXIT tar -xzf ${ncbi_blast_version}.tar.gz stop_progress_ind $pid #Move to the c++ directory which contains the configuration script cd ${working_dir}/${ncbi_blast_version}/c++/ #Configure NCBI BLAST progress_ind & pid=$! trap "stop_progress_ind $pid; exit" INT TERM EXIT configuration_options="./configure --without-debug --with-mt --without-sybase --without-ftds --without-fastcgi --without-fltk --without-wxwin --without-ncbi-c --without-sssdb --without-sss --without-geo --without-sp --without-orbacus --without-boost" echo -e "\nConfiguring ${ncbi_blast_version} with options:" echo -e "\n${configuration_options}" echo -e "\nIf you want to change these options edit the file \"install\", delete the directory ${ncbi_blast_version}, and rerun install" $configuration_options > ${working_dir}/configure.output if [ $? -ne 0 ]; then echo -e "\nError in configuring NCBI BLAST installation. Look at \"configure.output\" for more information" exit 1 fi stop_progress_ind $pid #extract the installation directory makefile_line=`cat ../../configure.output | grep Tools` makefile=`echo $makefile_line | awk -F" " '{print $NF}'` build_dir=`dirname $makefile` proj_dir=`dirname $build_dir` cxx_dir=`dirname $proj_dir` else build_dir="$installed_dir/../build/" proj_dir="$installed_dir/../" cxx_dir="$installed_dir/../../" fi #Modify NCBI BLAST files echo -e "\nModifying NCBI BLAST files" cd ${working_dir}/h_blast/ sh ./modify ${cxx_dir} > ${working_dir}/modify.output if [ $? -ne 0 ]; then echo -e "\nError: while modirying the source code files. See \"modify.output\" for more details. Exiting..." exit 1 fi #Compile GPU code progress_ind & pid=$! trap "stop_progress_ind $pid; exit" INT TERM EXIT echo -e "\nCompiling CUDA code" bin_dir=`dirname ${nvcc}` cuda_dir=`dirname ${bin_dir}` os_version=`uname -m` if [[ "$os_version" = "i686" ]]; then cudart_lib=${cuda_dir}/lib fi if [[ "$os_version" = "x86_64" ]]; then cudart_lib=${cuda_dir}/lib64 fi if [[ ! -d ${cudart_lib} ]]; then echo "CUDA library directory cannot be found. Exiting installation..." exit 1 fi #make -f makefile.shared -B NVCC_PATH=${nvcc} PROJ_DIR=${proj_dir} CXX_DIR=${cxx_dir} CUDA_LIB=${cudart_lib} #> ${working_dir}/gpu_blast.output make -f Makefile -B NVCC_PATH=${nvcc} PROJ_DIR=${proj_dir} CXX_DIR=${cxx_dir} CUDA_LIB=${cudart_lib} > ${working_dir}/gpu_blast.output #Modify CONF_LIB of Makefile.mk to inlcude the libraries -lgpublast and -lcudart cp ${build_dir}/Makefile.mk ${build_dir}/Makefile.mk.backup conf_libs_line=`cat ${build_dir}/Makefile.mk | grep ^CONF_LIB` conf_libs_line=${conf_libs_line}" -lgpublast -lcudart" sed "/^CONF_LIBS/ c\ ${conf_libs_line}" ${build_dir}/Makefile.mk > ${build_dir}/Makefile.mk.temp mv ${build_dir}/Makefile.mk.temp ${build_dir}/Makefile.mk stop_progress_ind $pid #Compile NCBI BLAST echo "Building NCBI BLAST with H-BLAST" cd $build_dir progress_ind & pid=$! trap "stop_progress_ind $pid; exit" INT TERM EXIT make all_r -j4 &> ${working_dir}/ncbi_blast.output if [ $? -ne 0 ]; then echo -e "\nError in NCBI BLAST installation. Look at \"ncbi_blast.output\" for more information" exit 1 fi stop_progress_ind $pid exit 0; h-blast-1.0_ncbi-blast-2.2.25/h_blast/ncbi_blast_files/0000755000175000017500000000000012137172302020564 5ustar ykeykeh-blast-1.0_ncbi-blast-2.2.25/h_blast/0000755000175000017500000000000012152342063015302 5ustar ykeykeh-blast-1.0_ncbi-blast-2.2.25/queries/0000755000175000017500000000000012137177242015353 5ustar ykeykeh-blast-1.0_ncbi-blast-2.2.25/0000755000175000017500000000000012152342733013672 5ustar ykeyke