Searched refs:orig_cds (Results 1 – 10 of 10) sorted by last modified time
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | feature_propagate.cpp | 1006 …ator::ConstructProteinFeatureForPropagatedCodingRegion(const CSeq_feat& orig_cds, const CSeq_feat&… in ConstructProteinFeatureForPropagatedCodingRegion() argument
1008 if (!orig_cds.IsSetProduct()) { in ConstructProteinFeatureForPropagatedCodingRegion()
1012 CBioseq_Handle prot = m_Scope.GetBioseqHandle(orig_cds.GetProduct()); in ConstructProteinFeatureForPropagatedCodingRegion()
1020 …m_MaxFeatId && *m_MaxFeatId > 0) && (pf->GetOriginalSeq_feat()->IsSetId() || orig_cds.IsSetId())) { in ConstructProteinFeatureForPropagatedCodingRegion()
1029 …if (new_cds.IsSetProduct() && !new_cds.GetProduct().GetId()->Equals(*(orig_cds.GetProduct().GetId(… in ConstructProteinFeatureForPropagatedCodingRegion()
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| H A D | gap_trim.cpp | 333 …justProteinSeq(const CBioseq& seq, const CSeq_feat& feat, const CSeq_feat& orig_cds, CScope& scope) in AdjustProteinSeq() argument
356 if (!feat_prod.Equals(orig_cds.GetProduct().GetWhole())) { in AdjustProteinSeq()
390 new CSeq_loc_Mapper(orig_cds, CSeq_loc_Mapper::eLocationToProduct, &scope)); in AdjustProteinSeq()
404 …SeqLocAdjustForTrim(*new_prot_loc, 0, start - 1, orig_cds.GetProduct().GetId(), complete_cut, remo… in AdjustProteinSeq()
407 …SeqLocAdjustForTrim(*new_prot_loc, stop + 1, orig_len - 1, orig_cds.GetProduct().GetId(), complete… in AdjustProteinSeq()
415 if (!feat_prod.Equals(orig_cds.GetProduct().GetWhole())) { in AdjustProteinSeq()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | feature_propagate.cpp | 1006 …ator::ConstructProteinFeatureForPropagatedCodingRegion(const CSeq_feat& orig_cds, const CSeq_feat&… in ConstructProteinFeatureForPropagatedCodingRegion() argument
1008 if (!orig_cds.IsSetProduct()) { in ConstructProteinFeatureForPropagatedCodingRegion()
1012 CBioseq_Handle prot = m_Scope.GetBioseqHandle(orig_cds.GetProduct()); in ConstructProteinFeatureForPropagatedCodingRegion()
1020 …m_MaxFeatId && *m_MaxFeatId > 0) && (pf->GetOriginalSeq_feat()->IsSetId() || orig_cds.IsSetId())) { in ConstructProteinFeatureForPropagatedCodingRegion()
1029 …if (new_cds.IsSetProduct() && !new_cds.GetProduct().GetId()->Equals(*(orig_cds.GetProduct().GetId(… in ConstructProteinFeatureForPropagatedCodingRegion()
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| H A D | gap_trim.cpp | 333 …justProteinSeq(const CBioseq& seq, const CSeq_feat& feat, const CSeq_feat& orig_cds, CScope& scope) in AdjustProteinSeq() argument
356 if (!feat_prod.Equals(orig_cds.GetProduct().GetWhole())) { in AdjustProteinSeq()
390 new CSeq_loc_Mapper(orig_cds, CSeq_loc_Mapper::eLocationToProduct, &scope)); in AdjustProteinSeq()
404 …SeqLocAdjustForTrim(*new_prot_loc, 0, start - 1, orig_cds.GetProduct().GetId(), complete_cut, remo… in AdjustProteinSeq()
407 …SeqLocAdjustForTrim(*new_prot_loc, stop + 1, orig_len - 1, orig_cds.GetProduct().GetId(), complete… in AdjustProteinSeq()
415 if (!feat_prod.Equals(orig_cds.GetProduct().GetWhole())) { in AdjustProteinSeq()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/edit/ |
| H A D | feature_propagate.hpp | 69 …CRef<CSeq_feat> ConstructProteinFeatureForPropagatedCodingRegion(const CSeq_feat& orig_cds, const …
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| H A D | gap_trim.hpp | 88 …ustProteinSeq(const CBioseq& seq, const CSeq_feat& feat, const CSeq_feat& orig_cds, CScope& scope);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/edit/ |
| H A D | feature_propagate.hpp | 69 …CRef<CSeq_feat> ConstructProteinFeatureForPropagatedCodingRegion(const CSeq_feat& orig_cds, const …
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| H A D | gap_trim.hpp | 88 …ustProteinSeq(const CBioseq& seq, const CSeq_feat& feat, const CSeq_feat& orig_cds, CScope& scope);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/ |
| H A D | suspect_feat.cpp | 136 CRef<CSeq_feat> orig_cds; in FixSuspectProductNames() local
139 orig_cds.Reset(&(CSeq_feat&)*cds.GetOriginalSeq_feat()); in FixSuspectProductNames()
140 return orig_cds; in FixSuspectProductNames()
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| /dports/biology/ncbi-toolkit/ncbi/demo/ |
| H A D | reblobber.c | 1818 SeqFeatPtr orig_cds, new_cds; in CopyProteinId() local
1825 orig_cds = SeqMgrGetCDSgivenProduct (prot_bsp, NULL); in CopyProteinId()
1826 if (orig_cds != NULL) { in CopyProteinId()
1827 orig_nuc = BioseqFindFromSeqLoc (orig_cds->location); in CopyProteinId()
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