| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
| H A D | cuSequence.cpp | 112 int GetMMDBId(const CBioseq& bioseq) { in GetMMDBId()
139 TTaxId GetTaxIdInBioseq(const CBioseq& bioseq) { in GetTaxIdInBioseq()
184 bool IsEnvironmentalSeq(const CBioseq& bioseq) { in IsEnvironmentalSeq()
190 string GetSpeciesFromBioseq(const CBioseq& bioseq) { in GetSpeciesFromBioseq()
216 int GetSeqLength(const CBioseq& bioseq) in GetSeqLength()
292 const CBioseq& bioseq = Seq->GetSeq(); in GetNcbieaaString() local
298 bool GetNcbieaaString(const CBioseq& bioseq, string & Str) in GetNcbieaaString()
315 bool GetNcbistdSeq(const CBioseq& bioseq, vector<char>& seqData) in GetNcbistdSeq()
349 string GetRawSequenceString(const CBioseq& bioseq) in GetRawSequenceString()
486 bool checkAndFixPdbBioseq(CRef< CBioseq > bioseq) in checkAndFixPdbBioseq()
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| H A D | cuSequenceTable.cpp | 69 void SequenceTable::addSequence(CRef< CBioseq > bioseq) in addSequence()
89 CRef< CBioseq > bioseq(&(seqEntry.SetSeq())); in addSequences() local
131 CRef< CBioseq > bioseq; in findSequence() local
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| H A D | cuPssmScorer.cpp | 76 int PssmScorer::score(const CRef<CSeq_align> align, const CRef<CBioseq> bioseq) in score()
81 int PssmScorer::score(BlockModelPair& bmp, const CRef<CBioseq> bioseq) in score()
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| /dports/biology/ncbi-toolkit/ncbi/object/ |
| H A D | objseq.h | 423 typedef struct bioseq { struct
440 SeqEntryPtr seqentry; /* internal seqentry that points to this bioseq */ argument
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
| H A D | seq_table_ci.cpp | 57 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq) in CSeq_table_CI()
66 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
77 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
88 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
100 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
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| H A D | feat_ci.cpp | 84 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq) in CFeat_CI()
94 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
106 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
118 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
131 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
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| H A D | align_ci.cpp | 56 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
67 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
78 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
90 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
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| H A D | graph_ci.cpp | 235 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq) in CGraph_CI()
245 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
257 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
269 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
282 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
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| H A D | annot_ci.cpp | 81 CAnnot_CI::CAnnot_CI(const CBioseq_Handle& bioseq) in CAnnot_CI()
95 CAnnot_CI::CAnnot_CI(const CBioseq_Handle& bioseq, in CAnnot_CI()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
| H A D | seq_table_ci.cpp | 57 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq) in CSeq_table_CI()
66 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
77 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
88 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
100 CSeq_table_CI::CSeq_table_CI(const CBioseq_Handle& bioseq, in CSeq_table_CI()
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| H A D | feat_ci.cpp | 84 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq) in CFeat_CI()
94 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
106 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
118 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
131 CFeat_CI::CFeat_CI(const CBioseq_Handle& bioseq, in CFeat_CI()
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| H A D | align_ci.cpp | 56 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
67 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
78 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
90 CAlign_CI::CAlign_CI(const CBioseq_Handle& bioseq, in CAlign_CI()
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| H A D | graph_ci.cpp | 235 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq) in CGraph_CI()
245 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
257 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
269 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
282 CGraph_CI::CGraph_CI(const CBioseq_Handle& bioseq, in CGraph_CI()
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| H A D | annot_ci.cpp | 81 CAnnot_CI::CAnnot_CI(const CBioseq_Handle& bioseq) in CAnnot_CI()
95 CAnnot_CI::CAnnot_CI(const CBioseq_Handle& bioseq, in CAnnot_CI()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
| H A D | citation.cpp | 88 void CPubInfo::SetBioseq(const objects::CBioseq* bioseq) in SetBioseq()
136 …CitInDescr(std::vector<CPubInfo>& pubs, const TSeqdescList& descrs, const objects::CBioseq* bioseq) in FindCitInDescr()
292 …onst std::vector<CPubInfo>& pubs, objects::CBioseq::TAnnot& annots, const objects::CBioseq* bioseq) in ProcessCit()
359 for (CTypeConstIterator<objects::CBioseq> bioseq(Begin(*(*entry))); bioseq; ++bioseq) in ProcessCitations() local
377 for (CTypeIterator<objects::CBioseq> bioseq(Begin(*(*entry))); bioseq; ++bioseq) in ProcessCitations() local
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| H A D | fcleanup.cpp | 136 for (CTypeIterator<objects::CBioseq> bioseq(Begin(entry)); bioseq; ++bioseq) in MoveSourceDescrToTop() local
224 const objects::CBioseq& bioseq = (*entry)->GetSeq(); in MoveBiomolToTop() local
245 objects::CBioseq& bioseq = (*entry)->SetSeq(); in MoveBiomolToTop() local
502 for (CTypeIterator<objects::CBioseq> bioseq(Begin(**entry)); bioseq; ++bioseq) { in FinalCleanup() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
| H A D | sequence_tests.cpp | 78 const CBioseq& bioseq = context.CurrentBioseq(); variable
118 const CBioseq& bioseq = context.CurrentBioseq(); variable
138 const CBioseq& bioseq = context.CurrentBioseq(); variable
185 const CBioseq& bioseq = context.CurrentBioseq(); variable
218 const CBioseq& bioseq = context.CurrentBioseq(); variable
256 const CBioseq& bioseq = context.CurrentBioseq(); variable
288 const CBioseq& bioseq = context.CurrentBioseq(); variable
305 const CBioseq& bioseq = context.CurrentBioseq(); variable
325 const CBioseq& bioseq = context.CurrentBioseq(); variable
347 const CBioseq& bioseq = context.CurrentBioseq(); variable
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| H A D | discrepancy_case.cpp | 63 const CBioseq& bioseq = context.CurrentBioseq(); variable
84 const CBioseq& bioseq = context.CurrentBioseq(); variable
115 const CBioseq& bioseq = context.CurrentBioseq(); variable
131 const CBioseq& bioseq = context.CurrentBioseq(); variable
183 const CBioseq& bioseq = context.CurrentBioseq(); variable
207 const CBioseq& bioseq = context.CurrentBioseq(); variable
345 const CBioseq& bioseq = context.CurrentBioseq(); variable
521 const CBioseq& bioseq = context.CurrentBioseq(); variable
579 const CBioseq& bioseq = context.CurrentBioseq(); variable
664 const CBioseq& bioseq = context.CurrentBioseq(); variable
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| H A D | seqdesc_per_bioseq.cpp | 54 const CBioseq& bioseq = context.CurrentBioseq(); variable
87 const CBioseq& bioseq = context.CurrentBioseq(); variable
133 const CBioseq& bioseq = context.CurrentBioseq(); variable
286 const CBioseq& bioseq = context.CurrentBioseq(); variable
359 const CBioseq& bioseq = context.CurrentBioseq(); variable
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/streamtest/ |
| H A D | process_prosplign.hpp | 87 const CBioseq& bioseq = *bit; in SeqEntryProcess() local
95 const CBioseq& bioseq = *bit; in SeqEntryProcess() local
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| H A D | process_title.hpp | 92 void x_TitleSeqIdWrite(const CBioseq& bioseq) in x_TitleSeqIdWrite()
147 const CBioseq& bioseq = *bit; in SeqEntryProcess() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | gaps_edit.cpp | 242 CGapsEditor::CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos gap_length) in CreateGap()
249 CGapsEditor::CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos nominal_length, bool length_unkn… in CreateGap()
315 void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq) in ConvertNs2Gaps()
426 void CGapsEditor::ConvertBioseqToDelta(CBioseq& bioseq) in ConvertBioseqToDelta()
438 void CGapsEditor::AppendGap(CBioseq& bioseq) in AppendGap()
450 void CGapsEditor::AddBioseqAsLiteral(CBioseq& parent, CBioseq& bioseq) in AddBioseqAsLiteral()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | gaps_edit.cpp | 242 CGapsEditor::CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos gap_length) in CreateGap()
249 CGapsEditor::CreateGap(CBioseq& bioseq, TSeqPos gap_start, TSeqPos nominal_length, bool length_unkn… in CreateGap()
315 void CGapsEditor::ConvertNs2Gaps(CBioseq& bioseq) in ConvertNs2Gaps()
426 void CGapsEditor::ConvertBioseqToDelta(CBioseq& bioseq) in ConvertBioseqToDelta()
438 void CGapsEditor::AppendGap(CBioseq& bioseq) in AppendGap()
450 void CGapsEditor::AddBioseqAsLiteral(CBioseq& parent, CBioseq& bioseq) in AddBioseqAsLiteral()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/macro/ |
| H A D | Location_constraint.cpp | 97 …_DoesBioseqMatchSequenceType(CConstRef <CBioseq> bioseq, const ESeqtype_constraint& seq_type) const in x_DoesBioseqMatchSequenceType()
157 …int :: x_DoesLocationMatchDistanceConstraint(CConstRef <CBioseq> bioseq, const CSeq_loc& loc) const in x_DoesLocationMatchDistanceConstraint()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/macro/ |
| H A D | Location_constraint.cpp | 97 …_DoesBioseqMatchSequenceType(CConstRef <CBioseq> bioseq, const ESeqtype_constraint& seq_type) const in x_DoesBioseqMatchSequenceType()
157 …int :: x_DoesLocationMatchDistanceConstraint(CConstRef <CBioseq> bioseq, const CSeq_loc& loc) const in x_DoesLocationMatchDistanceConstraint()
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