Home
last modified time | relevance | path

Searched refs:annot_name (Results 1 – 25 of 42) sorted by relevance

12

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/sra/
H A Dcsraread.hpp745 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 …]
H A Dgraphread.hpp268 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,
H A Dsnpread.hpp555 const string& annot_name,
563 const string& annot_name,
575 const string& annot_name,
584 const string& annot_name,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dmicro_introns.cpp115 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/pubseq_gateway/server/
H A Dosg_annot.cpp245 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/bam/test/
H A Dtest_bam_loader.cpp388 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/csra/test/
H A Dtest_csra_loader.cpp857 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/sra/
H A Dgraphread.cpp369 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 …]
H A Dcsraread.cpp744 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 …]
H A Dsnpread.cpp1120 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/patcher/
H A Dloaderpatcher.cpp722 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/sra/readers/bam/
H A Dbamread.hpp777 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()
H A Dbamindex.hpp303 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,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/pubseq_gateway/impl/cassandra/changelog/
H A Dna_record.hpp58 string annot_name, in CNAnnotChangelogRecord() argument
65 , m_AnnotName(annot_name) in CNAnnotChangelogRecord()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/
H A Dtse_chunk_info.hpp157 void x_AddAnnotType(const CAnnotName& annot_name,
160 void x_AddAnnotType(const CAnnotName& annot_name,
164 void x_AddAnnotType(const CAnnotName& annot_name,
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/
H A Dtse_chunk_info.hpp157 void x_AddAnnotType(const CAnnotName& annot_name,
160 void x_AddAnnotType(const CAnnotName& annot_name,
164 void x_AddAnnotType(const CAnnotName& annot_name,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dtse_chunk_info.cpp377 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dtse_chunk_info.cpp377 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()
/dports/biology/py-biopython/biopython-1.79/Bio/SearchIO/HmmerIO/
H A Dhmmer3_text.py392 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)
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dgene_model.hpp219 const string& annot_name = "",
228 static void x_SetAnnotName(objects::SAnnotSelector& sel, const string& annot_name);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/
H A Dbamindex.cpp1045 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/data_loaders/lds2/
H A Dlds2_dataloader.cpp373 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()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/pubseq_gateway/cassandra/nannot_task/
H A Dfetch.cpp271 string annot_name = record.GetAnnotName(); in Wait1() local
273 m_LastConsumedAnnot = move(annot_name); in Wait1()
/dports/textproc/p5-UML-Sequence/UML-Sequence-0.08/lib/UML/Sequence/
H A DSvg.pm588 $annot_name, $annot_span) = @_;
621 <AREA SHAPE=RECT COORDS='$x2,$y4,$x3,$y3' HREF='#$annot_name'>
627 <a name='$annot_name'></a>
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/lds2/
H A Dlds2.cpp86 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()

12