/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/sra/ |
H A D | csraread.hpp | 745 return x_GetSeq_annot(&annot_name); in GetSeq_annot() 764 return x_GetMatchEntry(&annot_name); in GetMatchEntry() 780 return x_GetEmptyMatchAnnot(&annot_name); in GetEmptyMatchAnnot() 796 return x_GetMatchAnnot(&annot_name); in GetMatchAnnot() 812 return x_GetQualityGraphAnnot(&annot_name); in GetQualityGraphAnnot() 828 return m_RefIter.x_GetSeq_annot(annot_name); in x_GetSeq_annot() 834 CCSraAlignIterator::GetSeq_annot(const string& annot_name) const in GetSeq_annot() 836 return x_GetSeq_annot(&annot_name); in GetSeq_annot() 850 CCSraAlignIterator::MakeSeq_annot(const string& annot_name) in MakeSeq_annot() argument 852 return CCSraRefSeqIterator::MakeSeq_annot(annot_name); in MakeSeq_annot() [all …]
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H A D | graphread.hpp | 268 const string& annot_name = kEmptyStr, 278 CRef<CSeq_graph> x_MakeGraph(const string& annot_name, 286 CRef<CSeq_table> x_MakeTable(const string& annot_name,
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H A D | snpread.hpp | 555 const string& annot_name, 563 const string& annot_name, 575 const string& annot_name, 584 const string& annot_name,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | micro_introns.cpp | 115 const string& annot_name) in x_SetAnnotName() argument 118 if(!annot_name.empty()) { in x_SetAnnotName() 120 if(annot_name =="Unnamed") { in x_SetAnnotName() 123 sel.AddNamedAnnots(annot_name); in x_SetAnnotName() 125 if (NStr::StartsWith(annot_name, "NA0")) { in x_SetAnnotName() 126 sel.IncludeNamedAnnotAccession(annot_name.find(".") == string::npos ? in x_SetAnnotName() 127 annot_name + ".1" in x_SetAnnotName() 129 annot_name); in x_SetAnnotName() 140 const string& annot_name, in CreateMicroIntrons() argument 151 x_SetAnnotName(sel, annot_name); in CreateMicroIntrons() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/pubseq_gateway/server/ |
H A D | osg_annot.cpp | 245 string annot_name; member 354 if ( annot_name.empty() ) { in SetAnnotName() 355 annot_name = name; in SetAnnotName() 357 else if ( annot_name != name ) { in SetAnnotName() 358 ERR_POST("OSG-annot: multiple annot accessions: "<<annot_name<<" <> "<<name); in SetAnnotName() 459 string annot_name; in SendReplies() local 462 annot_name = info.annot_name; in SendReplies() 483 annot_name = ai->GetName(); in SendReplies() 496 if ( m_NamesToProcess.count(annot_name) ) { in SendReplies() 497 GetReply()->PrepareNamedAnnotationData(annot_name, GetName(), in SendReplies() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/bam/test/ |
H A D | test_bam_loader.cpp | 388 string bam_name, id, annot_name; in BOOST_AUTO_TEST_CASE() local 420 if ( annot_name.empty() ) { in BOOST_AUTO_TEST_CASE() 455 string bam_name, id, annot_name; in BOOST_AUTO_TEST_CASE() local 481 if ( annot_name.empty() ) { in BOOST_AUTO_TEST_CASE() 541 if ( annot_name.empty() ) { in BOOST_AUTO_TEST_CASE() 629 if ( annot_name.empty() ) { in BOOST_AUTO_TEST_CASE() 720 if ( annot_name.empty() ) { in BOOST_AUTO_TEST_CASE() 1233 annot_name = base_name; in BOOST_AUTO_TEST_CASE() 1264 if ( annot_name.empty() ) { in BOOST_AUTO_TEST_CASE() 1339 annot_name = base_name; in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/ |
H A D | test_csra_loader.cpp | 857 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 934 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 1013 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 1183 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 1347 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 1554 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 1739 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local 1931 string annot_name = csra_name; 1957 sel.AddNamedAnnots(annot_name); 2647 string annot_name = csra_name; in BOOST_AUTO_TEST_CASE() local [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/ |
H A D | graphread.cpp | 369 CVDBGraphSeqIterator::x_MakeGraph(const string& annot_name, in x_MakeGraph() argument 383 if ( !annot_name.empty() ) { in x_MakeGraph() 384 graph->SetTitle(annot_name); in x_MakeGraph() 488 CVDBGraphSeqIterator::x_MakeTable(const string& annot_name, in x_MakeTable() argument 664 const string& annot_name, in GetAnnot() argument 677 if ( !annot_name.empty() ) { in GetAnnot() 679 desc->SetName(annot_name); in GetAnnot() 724 graph = x_MakeGraph(annot_name, *loc, info, range, in GetAnnot() 728 graph = x_MakeGraph(annot_name, *loc, info, range, in GetAnnot() 732 graph = x_MakeGraph(annot_name, *loc, info, range, in GetAnnot() [all …]
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H A D | csraread.cpp | 744 CRef<CSeq_annot> annot = GetSeq_annot(annot_name); in GetCoverageAnnot() 751 CCSraRefSeqIterator::MakeSeq_annot(const string& annot_name) in MakeSeq_annot() argument 756 desc->SetName(annot_name); in MakeSeq_annot() 767 if ( annot_name ) { in x_GetSeq_annot() 769 desc->SetName(*annot_name); in x_GetSeq_annot() 1744 CRef<CSeq_annot> annot = x_GetSeq_annot(annot_name); in x_GetEmptyMatchAnnot() 1759 CRef<CSeq_annot> annot = MakeSeq_annot(annot_name); in MakeEmptyMatchAnnot() 1777 CRef<CSeq_annot> annot = x_GetSeq_annot(annot_name); in x_GetQualityGraphAnnot() 2280 if ( annot_name ) { in x_GetSeq_annot() 2282 desc->SetName(*annot_name); in x_GetSeq_annot() [all …]
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H A D | snpread.cpp | 1120 annot->SetNameDesc(annot_name); in x_NewAnnot() 1184 const string& annot_name, in GetOverviewAnnot() argument 1191 CRef<CSeq_annot> annot = x_NewAnnot(annot_name); in GetOverviewAnnot() 1216 const string& annot_name, in GetCoverageAnnot() argument 1221 CRef<CSeq_annot> annot = x_NewAnnot(annot_name); in GetCoverageAnnot() 1567 CRef<CSeq_annot> GetAnnot(const string& annot_name, 1672 CRef<CSeq_annot> table_annot = x_NewAnnot(annot_name); in GetAnnot() 1758 SSeqTableConverter::GetAnnots(const string& annot_name) in GetAnnots() argument 1764 m_Tables[k][i].GetAnnot(annot_name, *m_Seq_id); in GetAnnots() 1771 m_RegularAnnot->SetNameDesc(annot_name); in GetAnnots() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/patcher/ |
H A D | loaderpatcher.cpp | 722 CAnnotName annot_name; in x_ApplyCmd() local 724 annot_name.SetNamed(cmd.GetName()); in x_ApplyCmd() 747 CAnnotName annot_name; in x_ApplyCmd() local 749 annot_name.SetNamed(cmd.GetName()); in x_ApplyCmd() 760 annot_obj = finder.Find(info, annot_name, in x_ApplyCmd() 764 annot_obj = finder.Find(info, annot_name, in x_ApplyCmd() 826 CAnnotName annot_name; in x_ApplyCmd() local 828 annot_name.SetNamed(cmd.GetName()); in x_ApplyCmd() 833 x_MakeReplace(tse,info, annot_name, in x_ApplyCmd() 838 x_MakeReplace(tse, info, annot_name, in x_ApplyCmd() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/bam/ |
H A D | bamread.hpp | 777 CRef<CSeq_entry> GetMatchEntry(const string& annot_name) const; 779 CRef<CSeq_annot> GetSeq_annot(const string& annot_name) const; 819 CRef<CSeq_entry> x_GetMatchEntry(const string* annot_name) const; 820 CRef<CSeq_annot> x_GetSeq_annot(const string* annot_name) const; 894 CBamAlignIterator::GetMatchEntry(const string& annot_name) const in GetMatchEntry() 896 return x_GetMatchEntry(&annot_name); in GetMatchEntry() 909 CBamAlignIterator::GetSeq_annot(const string& annot_name) const in GetSeq_annot() 911 return x_GetSeq_annot(&annot_name); in GetSeq_annot()
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H A D | bamindex.hpp | 303 const string& annot_name, 310 const string& annot_name, 318 const string& annot_name, 324 const string& annot_name, 331 const string& annot_name, 338 const string& annot_name,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/pubseq_gateway/impl/cassandra/changelog/ |
H A D | na_record.hpp | 58 string annot_name, in CNAnnotChangelogRecord() argument 65 , m_AnnotName(annot_name) in CNAnnotChangelogRecord()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/ |
H A D | tse_chunk_info.hpp | 157 void x_AddAnnotType(const CAnnotName& annot_name, 160 void x_AddAnnotType(const CAnnotName& annot_name, 164 void x_AddAnnotType(const CAnnotName& annot_name,
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/ |
H A D | tse_chunk_info.hpp | 157 void x_AddAnnotType(const CAnnotName& annot_name, 160 void x_AddAnnotType(const CAnnotName& annot_name, 164 void x_AddAnnotType(const CAnnotName& annot_name,
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
H A D | tse_chunk_info.cpp | 377 void CTSE_Chunk_Info::x_AddAnnotType(const CAnnotName& annot_name, in x_AddAnnotType() argument 383 TLocationSet& dst = m_AnnotContents[annot_name][annot_type]; in x_AddAnnotType() 388 void CTSE_Chunk_Info::x_AddAnnotType(const CAnnotName& annot_name, in x_AddAnnotType() argument 393 TLocationSet& dst = m_AnnotContents[annot_name][annot_type]; in x_AddAnnotType() 399 void CTSE_Chunk_Info::x_AddAnnotType(const CAnnotName& annot_name, in x_AddAnnotType() argument 404 TLocationSet& dst = m_AnnotContents[annot_name][annot_type]; in x_AddAnnotType()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
H A D | tse_chunk_info.cpp | 377 void CTSE_Chunk_Info::x_AddAnnotType(const CAnnotName& annot_name, in x_AddAnnotType() argument 383 TLocationSet& dst = m_AnnotContents[annot_name][annot_type]; in x_AddAnnotType() 388 void CTSE_Chunk_Info::x_AddAnnotType(const CAnnotName& annot_name, in x_AddAnnotType() argument 393 TLocationSet& dst = m_AnnotContents[annot_name][annot_type]; in x_AddAnnotType() 399 void CTSE_Chunk_Info::x_AddAnnotType(const CAnnotName& annot_name, in x_AddAnnotType() argument 404 TLocationSet& dst = m_AnnotContents[annot_name][annot_type]; in x_AddAnnotType()
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/dports/biology/py-biopython/biopython-1.79/Bio/SearchIO/HmmerIO/ |
H A D | hmmer3_text.py | 392 annot_name = regx.group(3) 393 if annot_name in annot: 394 annot[annot_name] += regx.group(2) 396 annot[annot_name] = regx.group(2)
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/ |
H A D | gene_model.hpp | 219 const string& annot_name = "", 228 static void x_SetAnnotName(objects::SAnnotSelector& sel, const string& annot_name);
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/ |
H A D | bamindex.cpp | 1045 const string& annot_name, in MakeEstimatedCoverageAnnot() argument 1050 …return MakeEstimatedCoverageAnnot(header, ref_name, id, annot_name, min_index_level, max_index_lev… in MakeEstimatedCoverageAnnot() 1058 const string& annot_name, in MakeEstimatedCoverageAnnot() argument 1067 return MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, in MakeEstimatedCoverageAnnot() 1075 const string& annot_name, in MakeEstimatedCoverageAnnot() argument 1081 …return MakeEstimatedCoverageAnnot(ref_index, id, annot_name, length, min_index_level, max_index_le… in MakeEstimatedCoverageAnnot() 1088 const string& annot_name, in MakeEstimatedCoverageAnnot() argument 1092 …return MakeEstimatedCoverageAnnot(ref_index, seq_id, annot_name, kInvalidSeqPos, min_index_level, … in MakeEstimatedCoverageAnnot() 1099 const string& annot_name, in MakeEstimatedCoverageAnnot() argument 1119 const string& annot_name, in MakeEstimatedCoverageAnnot() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/lds2/ |
H A D | lds2_dataloader.cpp | 373 CAnnotName annot_name; in x_LoadTSE() local 375 annot_name.SetNamed(annot.name); in x_LoadTSE() 378 annot_name.SetUnnamed(); in x_LoadTSE() 397 annot_name, in x_LoadTSE()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/pubseq_gateway/cassandra/nannot_task/ |
H A D | fetch.cpp | 271 string annot_name = record.GetAnnotName(); in Wait1() local 273 m_LastConsumedAnnot = move(annot_name); in Wait1()
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/dports/textproc/p5-UML-Sequence/UML-Sequence-0.08/lib/UML/Sequence/ |
H A D | Svg.pm | 588 $annot_name, $annot_span) = @_; 621 <AREA SHAPE=RECT COORDS='$x2,$y4,$x3,$y3' HREF='#$annot_name'> 627 <a name='$annot_name'></a>
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/lds2/ |
H A D | lds2.cpp | 86 const string* annot_name, 852 const string* annot_name, in AddAnnot() argument 857 annot->is_named = (annot_name != NULL); in AddAnnot() 858 if ( annot_name ) { in AddAnnot() 859 annot->name = *annot_name; in AddAnnot()
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