| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | blast_seqinfosrc_aux.cpp | 57 list<CRef<CSeq_id> > seqid_list = seqinfo_src->GetId(oid); in BEGIN_SCOPE() local
59 CRef<CSeq_id> id = FindBestChoice(seqid_list, CSeq_id::BestRank); in BEGIN_SCOPE()
65 SerialAssign(*seqid, *(seqid_list.front())); in BEGIN_SCOPE()
79 list<CRef<CSeq_id> > seqid_list = seqinfo_src->GetId(oid); in GetSequenceLengthAndId() local
81 CRef<CSeq_id> id = FindBestChoice(seqid_list, rank_func); in GetSequenceLengthAndId()
101 list< CRef<CSeq_id> > seqid_list = seqinfo_src.GetId(oid); in GetFilteredRedundantGis() local
102 gis.reserve(seqid_list.size()); in GetFilteredRedundantGis()
104 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in GetFilteredRedundantGis()
124 list< CRef<CSeq_id> > seqid_list = seqinfo_src.GetId(oid); in GetFilteredRedundantSeqids() local
126 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in GetFilteredRedundantSeqids()
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| H A D | blast_seqalign.cpp | 1152 if ( !seqid_list.empty() ) { in s_CalculateScoreVectorSize()
1153 retval += seqid_list.size(); in s_CalculateScoreVectorSize()
1211 if ( !seqid_list.empty() ) { in s_BuildScoreList()
1235 const vector<string> & seqid_list) in s_AddUserObjectToSeqAlign() argument
1237 if (seqid_list.empty()) in s_AddUserObjectToSeqAlign()
1242 userObject->AddField("SEQIDS", seqid_list); in s_AddUserObjectToSeqAlign()
1500 s_AddUserObjectToSeqAlign(seqalign, seqid_list); in BLASTHspListToSeqAlign()
1600 vector<string> seqid_list; in BlastHitList2SeqAlign_OMF() local
1612 seqid_list, in BlastHitList2SeqAlign_OMF()
1807 vector<string> seqid_list; in s_BLAST_OneSubjectResults2CSeqAlign() local
[all …]
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| H A D | seqinfosrc_seqvec.cpp | 68 list < CRef<CSeq_id> > seqid_list; in GetId() local
75 seqid_list.push_back(seqid_ref); in GetId()
76 return seqid_list; in GetId()
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| H A D | blast_seqalign.hpp | 81 const vector<string> & seqid_list,
91 const vector<string> & seqid_list,
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | blast_seqinfosrc_aux.cpp | 57 list<CRef<CSeq_id> > seqid_list = seqinfo_src->GetId(oid); in BEGIN_SCOPE() local
59 CRef<CSeq_id> id = FindBestChoice(seqid_list, CSeq_id::BestRank); in BEGIN_SCOPE()
65 SerialAssign(*seqid, *(seqid_list.front())); in BEGIN_SCOPE()
79 list<CRef<CSeq_id> > seqid_list = seqinfo_src->GetId(oid); in GetSequenceLengthAndId() local
81 CRef<CSeq_id> id = FindBestChoice(seqid_list, rank_func); in GetSequenceLengthAndId()
101 list< CRef<CSeq_id> > seqid_list = seqinfo_src.GetId(oid); in GetFilteredRedundantGis() local
102 gis.reserve(seqid_list.size()); in GetFilteredRedundantGis()
104 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in GetFilteredRedundantGis()
124 list< CRef<CSeq_id> > seqid_list = seqinfo_src.GetId(oid); in GetFilteredRedundantSeqids() local
126 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in GetFilteredRedundantSeqids()
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| H A D | blast_seqalign.cpp | 1152 if ( !seqid_list.empty() ) { in s_CalculateScoreVectorSize()
1153 retval += seqid_list.size(); in s_CalculateScoreVectorSize()
1211 if ( !seqid_list.empty() ) { in s_BuildScoreList()
1235 const vector<string> & seqid_list) in s_AddUserObjectToSeqAlign() argument
1237 if (seqid_list.empty()) in s_AddUserObjectToSeqAlign()
1242 userObject->AddField("SEQIDS", seqid_list); in s_AddUserObjectToSeqAlign()
1500 s_AddUserObjectToSeqAlign(seqalign, seqid_list); in BLASTHspListToSeqAlign()
1600 vector<string> seqid_list; in BlastHitList2SeqAlign_OMF() local
1612 seqid_list, in BlastHitList2SeqAlign_OMF()
1807 vector<string> seqid_list; in s_BLAST_OneSubjectResults2CSeqAlign() local
[all …]
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| H A D | seqinfosrc_seqvec.cpp | 68 list < CRef<CSeq_id> > seqid_list; in GetId() local
75 seqid_list.push_back(seqid_ref); in GetId()
76 return seqid_list; in GetId()
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| H A D | blast_seqalign.hpp | 81 const vector<string> & seqid_list,
91 const vector<string> & seqid_list,
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blastdb/ |
| H A D | blastdb_aliastool.cpp | 458 string seqid_list = args[kArgSeqIdList].AsString(); in CreateAliasFile() local
459 if ( !seqid_list.empty() ) { in CreateAliasFile()
460 if ( !CFile(seqid_list).Exists() ) { in CreateAliasFile()
461 NCBI_THROW(CSeqDBException, eFileErr, seqid_list + " not found"); in CreateAliasFile()
466 seq_type, seqid_list, in CreateAliasFile()
574 vector<string> seqid_list; in x_ConvertSeqIDFile() local
581 seqid_list.push_back(line); in x_ConvertSeqIDFile()
591 return WriteBlastSeqidlistFile(seqid_list, output, title, &seqdb); in x_ConvertSeqIDFile()
594 return WriteBlastSeqidlistFile(seqid_list, output, title); in x_ConvertSeqIDFile()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blastdb/ |
| H A D | blastdb_aliastool.cpp | 458 string seqid_list = args[kArgSeqIdList].AsString(); in CreateAliasFile() local
459 if ( !seqid_list.empty() ) { in CreateAliasFile()
460 if ( !CFile(seqid_list).Exists() ) { in CreateAliasFile()
461 NCBI_THROW(CSeqDBException, eFileErr, seqid_list + " not found"); in CreateAliasFile()
466 seq_type, seqid_list, in CreateAliasFile()
574 vector<string> seqid_list; in x_ConvertSeqIDFile() local
581 seqid_list.push_back(line); in x_ConvertSeqIDFile()
591 return WriteBlastSeqidlistFile(seqid_list, output, title, &seqdb); in x_ConvertSeqIDFile()
594 return WriteBlastSeqidlistFile(seqid_list, output, title); in x_ConvertSeqIDFile()
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| /dports/biology/ncbi-toolkit/ncbi/tools/ |
| H A D | blast.h | 514 …BCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
518 …BCALLBACK *index_callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
645 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
649 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
651 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
653 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
674 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
676 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
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| H A D | mblast.h | 229 SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list,
237 SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list,
251 SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, Int4 gi_list_total,
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| H A D | blastpri.h | 758 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
760 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4…
770 SeqIdPtr seqid_list, BlastDoubleInt4Ptr
896 …eadDBFILEPtr rdfp_list, Int8Ptr db_length, Int4Ptr db_number, SeqIdPtr seqid_list, BlastDoubleInt4…
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| H A D | blastutl.c | 4936 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BioseqBlastEngineEx() argument
4944 …, progname, database, options, other_returns, error_returns, callback, seqid_list, gi_list, gi_lis… in BioseqBlastEngineEx()
4989 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BioseqBlastEngineByLocEx() argument
4992 …, progname, database, options, other_returns, error_returns, callback, seqid_list, gi_list, gi_lis… in BioseqBlastEngineByLocEx()
4996 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BioseqBlastEngineByLocWithCallback() argument
4998 …, progname, database, options, other_returns, error_returns, callback, seqid_list, gi_list, gi_lis… in BioseqBlastEngineByLocWithCallback()
5096 …ocWithReadDbEx(slp, progname, SeqLocLen(slp), database, options, NULL, seqid_list, gi_list, gi_lis… in BioseqBlastEngineByLocWithCallbackMult()
5233 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BioseqHitRangeEngine() argument
5240 …, progname, database, options, other_returns, error_returns, callback, seqid_list, gi_list, gi_lis… in BioseqHitRangeEngine()
5315 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BioseqHitRangeEngineByLoc() argument
[all …]
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| H A D | mblast.c | 770 SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, in BioseqMegaBlastEngine() argument
802 seqid_list, gi_list, gi_list_total, in BioseqMegaBlastEngine()
826 SeqIdPtr seqid_list, BlastDoubleInt4Ptr gi_list, in BioseqMegaBlastEngineByLoc() argument
872 seqid_list, gi_list, in BioseqMegaBlastEngineByLoc()
998 SeqIdPtr seqid_list, in MegaBlastSetUpSearchWithReadDbInternal() argument
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| H A D | blast.c | 5657 SeqIdPtr seqid_list, BlastDoubleInt4Ptr in BLASTSetUpSearchWithReadDbInternalEx() argument
5665 seqid_list, gi_list, in BLASTSetUpSearchWithReadDbInternalEx()
5671 seqid_list, gi_list, in BLASTSetUpSearchWithReadDbInternalEx()
5677 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BLASTSetUpSearchWithReadDbInternal() argument
5679 …Mult(query_slp, query_bsp, prog_name, qlen, dbname, options, callback, seqid_list, gi_list, gi_lis… in BLASTSetUpSearchWithReadDbInternal()
5714 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BLASTSetUpSearchWithReadDbInternalMult() argument
5847 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BLASTSetUpSearchWithReadDbEx() argument
5850 …Internal (NULL, query_bsp, prog_name, qlen, dbname, options, callback, seqid_list, gi_list, gi_lis… in BLASTSetUpSearchWithReadDbEx()
5868 …nt (LIBCALLBACK *callback)PROTO((Int4 done, Int4 positives)), SeqIdPtr seqid_list, BlastDoubleInt4… in BLASTSetUpSearchByLocWithReadDbEx() argument
5872 …rnalMult (query_slp, NULL, prog_name, qlen, dbname, options, callback, seqid_list, gi_list, gi_lis… in BLASTSetUpSearchByLocWithReadDbEx()
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| H A D | readdb.h | 1893 CharPtr FDFGetAccessionFromSeqIdChain(SeqIdPtr seqid_list);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastdb/unit_test/ |
| H A D | defline_unit_test.cpp | 88 list<CRef<CSeq_id> >& seqid_list = defline->SetSeqid(); in s_MakeDefline() local
89 CSeq_id::ParseFastaIds(seqid_list, id); in s_MakeDefline()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/align_format/ |
| H A D | seqalignfilter.cpp | 177 list< CRef<CSeq_id> > seqid_list = db->GetSeqIDs(oid); in s_GetFilteredRedundantGis() local
178 gis.reserve(seqid_list.size()); in s_GetFilteredRedundantGis()
180 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in s_GetFilteredRedundantGis()
585 list< CRef<CSeq_id> > seqid_list = filteredDB->GetSeqIDs(oid); in s_UpdateSeqAlnWithFilteredSeqIDs() local
586 seqids.reserve(seqid_list.size()); in s_UpdateSeqAlnWithFilteredSeqIDs()
588 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in s_UpdateSeqAlnWithFilteredSeqIDs()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/align_format/ |
| H A D | seqalignfilter.cpp | 177 list< CRef<CSeq_id> > seqid_list = db->GetSeqIDs(oid); in s_GetFilteredRedundantGis() local
178 gis.reserve(seqid_list.size()); in s_GetFilteredRedundantGis()
180 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in s_GetFilteredRedundantGis()
584 list< CRef<CSeq_id> > seqid_list = filteredDB->GetSeqIDs(oid); in s_UpdateSeqAlnWithFilteredSeqIDs() local
585 seqids.reserve(seqid_list.size()); in s_UpdateSeqAlnWithFilteredSeqIDs()
587 ITERATE(list< CRef<CSeq_id> >, id, seqid_list) { in s_UpdateSeqAlnWithFilteredSeqIDs()
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| /dports/biology/ncbi-toolkit/ncbi/biostruc/cdd/ |
| H A D | cddposutil.h | 103 SeqIdPtr seqid_list,
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| H A D | cddposutil.c | 1989 SeqIdPtr seqid_list, in CddSetUpSearchWithReadDb() argument
2033 …if (seqid_list) BlastAdjustDbNumbers(search->rdfp, &(dblen), &(search->dbseq_num), seqid_list, NUL… in CddSetUpSearchWithReadDb()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/services/ |
| H A D | blast_services.cpp | 223 list< CRef< CSeq_id > > & seqid_list = in s_BuildGetSeqRequest() local
227 seqid_list.push_back(*iter); in s_BuildGetSeqRequest()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/services/ |
| H A D | blast_services.cpp | 223 list< CRef< CSeq_id > > & seqid_list = in s_BuildGetSeqRequest() local
227 seqid_list.push_back(*iter); in s_BuildGetSeqRequest()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/seqdb_reader/ |
| H A D | seqdb_unit_test.cpp | 843 const char * seqid_list[] = { in BOOST_AUTO_TEST_CASE() local
861 size_t L_seqid = ArraySize(seqid_list); in BOOST_AUTO_TEST_CASE()
869 string arr_seqid(seqid_list[i]); in BOOST_AUTO_TEST_CASE()
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