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Searched refs:annot_handle (Results 1 – 20 of 20) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/
H A Dexternal_annots.cpp100 CRef<CSeq_annot> CAnnotGetter::x_GetCompleteSeqAnnot(const CSeq_annot_Handle& annot_handle) in x_GetCompleteSeqAnnot() argument
102 CConstRef<CSeq_annot> annot = annot_handle.GetCompleteSeq_annot(); in x_GetCompleteSeqAnnot()
123 CFeat_CI feat_it(annot_handle); in x_GetCompleteSeqAnnot()
H A Dapply_object.cpp161 const CSeq_annot_Handle& annot_handle = oh.GetAnnot(); in ApplyChange() local
162 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in ApplyChange()
H A Dcds_fix.cpp441 const CSeq_annot_Handle& annot_handle = f->GetAnnot(); in AdjustForCDSPartials() local
442 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in AdjustForCDSPartials()
996 const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot(); in DemoteCDSToNucSeq() local
997 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in DemoteCDSToNucSeq()
1016 CSeq_annot_EditHandle old_annot = annot_handle.GetEditHandle(); in DemoteCDSToNucSeq()
H A Dloc_edit.cpp845 const CSeq_annot_Handle& annot_handle = fh.GetAnnot(); in ApplyPolicyToFeature() local
846 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in ApplyPolicyToFeature()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/
H A Dexternal_annots.cpp100 CRef<CSeq_annot> CAnnotGetter::x_GetCompleteSeqAnnot(const CSeq_annot_Handle& annot_handle) in x_GetCompleteSeqAnnot() argument
102 CConstRef<CSeq_annot> annot = annot_handle.GetCompleteSeq_annot(); in x_GetCompleteSeqAnnot()
123 CFeat_CI feat_it(annot_handle); in x_GetCompleteSeqAnnot()
H A Dapply_object.cpp161 const CSeq_annot_Handle& annot_handle = oh.GetAnnot(); in ApplyChange() local
162 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in ApplyChange()
H A Dcds_fix.cpp441 const CSeq_annot_Handle& annot_handle = f->GetAnnot(); in AdjustForCDSPartials() local
442 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in AdjustForCDSPartials()
996 const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot(); in DemoteCDSToNucSeq() local
997 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in DemoteCDSToNucSeq()
1016 CSeq_annot_EditHandle old_annot = annot_handle.GetEditHandle(); in DemoteCDSToNucSeq()
H A Dloc_edit.cpp845 const CSeq_annot_Handle& annot_handle = fh.GetAnnot(); in ApplyPolicyToFeature() local
846 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in ApplyPolicyToFeature()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/
H A Dbed_writer.cpp550 CSeq_annot_Handle annot_handle, in xWriteFeature() argument
557 if ( ! track.Assign(*(annot_handle.GetCompleteSeq_annot())) ) { in xWriteFeature()
574 const auto& annot_handle = feat_it.GetAnnot(); in xWriteFeature() local
580 if ( ! track.Assign(*(annot_handle.GetCompleteSeq_annot())) ) { in xWriteFeature()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/edit/
H A Dexternal_annots.hpp62 static CRef<CSeq_annot> x_GetCompleteSeqAnnot(const CSeq_annot_Handle& annot_handle);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/edit/
H A Dexternal_annots.hpp62 static CRef<CSeq_annot> x_GetCompleteSeqAnnot(const CSeq_annot_Handle& annot_handle);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/writers/
H A Dbed_writer.hpp127 CSeq_annot_Handle annot_handle,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/
H A Dannot_collector.hpp201 const CSeq_annot_Handle& annot_handle);
203 const CSeq_annot_Handle& annot_handle,
206 CAnnotObject_Ref(const CSeq_annot_Handle& annot_handle,
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/
H A Dannot_collector.hpp201 const CSeq_annot_Handle& annot_handle);
203 const CSeq_annot_Handle& annot_handle,
206 CAnnotObject_Ref(const CSeq_annot_Handle& annot_handle,
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/unit_test/
H A Dunit_test_loc_edit.cpp379 CSeq_annot_Handle annot_handle = scope.AddSeq_annot(*(entry->GetAnnot().front())); in BOOST_AUTO_TEST_CASE() local
388 cds = annot_handle.GetCompleteSeq_annot()->GetData().GetFtable().front(); in BOOST_AUTO_TEST_CASE()
396 cds = annot_handle.GetCompleteSeq_annot()->GetData().GetFtable().front(); in BOOST_AUTO_TEST_CASE()
404 cds = annot_handle.GetCompleteSeq_annot()->GetData().GetFtable().front(); in BOOST_AUTO_TEST_CASE()
410 cds = annot_handle.GetCompleteSeq_annot()->GetData().GetFtable().front(); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/
H A Dannot_collector.cpp488 const CSeq_annot_Handle& annot_handle) in CAnnotObject_Ref() argument
489 : m_Seq_annot(annot_handle), in CAnnotObject_Ref()
521 const CSeq_annot_Handle& annot_handle, in CAnnotObject_Ref() argument
524 : m_Seq_annot(annot_handle), in CAnnotObject_Ref()
559 CAnnotObject_Ref::CAnnotObject_Ref(const CSeq_annot_Handle& annot_handle, in CAnnotObject_Ref() argument
562 : m_Seq_annot(annot_handle), in CAnnotObject_Ref()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/
H A Dannot_collector.cpp488 const CSeq_annot_Handle& annot_handle) in CAnnotObject_Ref() argument
489 : m_Seq_annot(annot_handle), in CAnnotObject_Ref()
521 const CSeq_annot_Handle& annot_handle, in CAnnotObject_Ref() argument
524 : m_Seq_annot(annot_handle), in CAnnotObject_Ref()
559 CAnnotObject_Ref::CAnnotObject_Ref(const CSeq_annot_Handle& annot_handle, in CAnnotObject_Ref() argument
562 : m_Seq_annot(annot_handle), in CAnnotObject_Ref()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/
H A Dfeature.cpp3935 const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot(); in PromoteCDSToNucProtSet() local
3936 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in PromoteCDSToNucProtSet()
3967 CSeq_annot_EditHandle old_annot = annot_handle.GetEditHandle(); in PromoteCDSToNucProtSet()
4080 const CSeq_annot_Handle& annot_handle = f->GetAnnot(); in AdjustForCDSPartials() local
4081 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in AdjustForCDSPartials()
4148 const CSeq_annot_Handle& annot_handle = f->GetAnnot(); in RetranslateCDS() local
4149 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in RetranslateCDS()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/
H A Dfeature.cpp3935 const CSeq_annot_Handle& annot_handle = orig_feat.GetAnnot(); in PromoteCDSToNucProtSet() local
3936 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in PromoteCDSToNucProtSet()
3967 CSeq_annot_EditHandle old_annot = annot_handle.GetEditHandle(); in PromoteCDSToNucProtSet()
4080 const CSeq_annot_Handle& annot_handle = f->GetAnnot(); in AdjustForCDSPartials() local
4081 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in AdjustForCDSPartials()
4148 const CSeq_annot_Handle& annot_handle = f->GetAnnot(); in RetranslateCDS() local
4149 CSeq_entry_EditHandle eh = annot_handle.GetParentEntry().GetEditHandle(); in RetranslateCDS()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/
H A Dfeature_tests.cpp2162 CSeq_annot_EditHandle annot_handle = cds_edit_handle.GetAnnot(); in AddmRNAForCDS() local
2163 annot_handle.AddFeat(*new_mRNA); in AddmRNAForCDS()
2201 CSeq_annot_EditHandle annot_handle = GetAnnotHandle(scope, bh); in DISCREPANCY_AUTOFIX() local
2202 annot_handle.AddFeat(*new_mRNA); in DISCREPANCY_AUTOFIX()