| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
| H A D | gvf_write_data.cpp | 84 const CMappedFeat& mapped_feat ) in AssignSource() argument
88 if ( mapped_feat.IsSetExt() ) { in AssignSource()
113 const CMappedFeat& mapped_feat, in AssignType() argument
118 if ( mapped_feat.IsSetExt() ) { in AssignType()
179 const CMappedFeat& mapped_feat, in AssignAttributes() argument
183 if ( ! x_AssignAttributeID( mapped_feat ) ) { in AssignAttributes()
186 if ( ! x_AssignAttributeParent( mapped_feat ) ) { in AssignAttributes()
189 if ( ! x_AssignAttributeName( mapped_feat ) ) { in AssignAttributes()
192 if ( ! x_AssignAttributeVarType( mapped_feat ) ) { in AssignAttributes()
198 if ( ! x_AssignAttributeEndRange( mapped_feat ) ) { in AssignAttributes()
[all …]
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| H A D | vcf_writer.cpp | 298 CMappedFeat mapped_feat = *fi; in x_WriteData() local
299 …if (mapped_feat.GetTotalRange().IntersectionWith(range).NotEmpty()) { // This code should be moved… in x_WriteData()
300 CSeq_feat_Handle sfh = mapped_feat.GetSeq_feat_Handle(); in x_WriteData()
302 …CRef<CSeq_feat> trimmed_feat = sequence::CFeatTrim::Apply(*mapped_feat.GetOriginalSeq_feat(), rang… in x_WriteData()
304 if (!x_WriteFeature(mapped_feat)) { in x_WriteData()
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| H A D | bed_writer.cpp | 549 const CMappedFeat& mapped_feat, in xWriteFeature() argument
561 return xWriteFeature(track, mapped_feat); in xWriteFeature()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/hgvs/ |
| H A D | id_resolver.cpp | 127 const auto& mapped_feat = *ci; in x_TryProcessLRG() local
128 if (!mapped_feat.IsSetDbxref()) { in x_TryProcessLRG()
131 ITERATE(CSeq_feat::TDbxref, it, mapped_feat.GetDbxref()) { in x_TryProcessLRG()
136 mapped_feat.IsSetProduct() && in x_TryProcessLRG()
137 mapped_feat.GetProduct().GetId()) in x_TryProcessLRG()
140 idh = sequence::GetId(*mapped_feat.GetProduct().GetId(), in x_TryProcessLRG()
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| H A D | na_irep_to_seqfeat.cpp | 1008 const auto& mapped_feat = *it; in x_GetCDS() local
1009 if (mapped_feat.GetData().IsCdregion()) { in x_GetCDS()
1013 coding_seq = mapped_feat.GetSeq_feat(); in x_GetCDS()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/ |
| H A D | seq_loc_cvt.cpp | 985 mapped_feat.Reset(new CSeq_feat); in ConvertCdregion()
992 mapped_feat->SetData(*new_data); in ConvertCdregion()
1113 mapped_feat->SetData() in ConvertRna()
1117 mapped_feat->SetData() in ConvertRna()
1207 if ( mapped_feat ) { in Convert()
1305 if ( mapped_feat ) { in Convert()
1554 mapped_feat->SetData(*new_data); in ConvertCdregion()
1669 mapped_feat->SetData() in ConvertRna()
1673 mapped_feat->SetData() in ConvertRna()
1727 CRef<CSeq_feat> mapped_feat; in Convert() local
[all …]
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| H A D | annot_collector.cpp | 815 map.SetMappedSeq_feat(*mapped_feat); in GetMappedFeat()
1578 CRef<CSeq_feat> mapped_feat; in GetMappedLocation() local
1580 if ( mapped_feat ) { in GetMappedLocation()
1582 mapped_feat.Reset(); in GetMappedLocation()
1657 CRef<CSeq_feat> mapped_feat; in GetMappedFeature() local
1659 if ( !mapped_feat || !mapped_feat->ReferencedOnlyOnce() ) { in GetMappedFeature()
1680 mapped_feat->SetLocation(*loc); in GetMappedFeature()
1683 mapped_feat->SetProduct(*loc); in GetMappedFeature()
1687 mapped_feat->SetPartial(true); in GetMappedFeature()
1690 mapped_feat->ResetPartial(); in GetMappedFeature()
[all …]
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/ |
| H A D | seq_loc_cvt.cpp | 985 mapped_feat.Reset(new CSeq_feat); in ConvertCdregion()
992 mapped_feat->SetData(*new_data); in ConvertCdregion()
1113 mapped_feat->SetData() in ConvertRna()
1117 mapped_feat->SetData() in ConvertRna()
1207 if ( mapped_feat ) { in Convert()
1305 if ( mapped_feat ) { in Convert()
1554 mapped_feat->SetData(*new_data); in ConvertCdregion()
1669 mapped_feat->SetData() in ConvertRna()
1673 mapped_feat->SetData() in ConvertRna()
1727 CRef<CSeq_feat> mapped_feat; in Convert() local
[all …]
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| H A D | annot_collector.cpp | 815 map.SetMappedSeq_feat(*mapped_feat); in GetMappedFeat()
1578 CRef<CSeq_feat> mapped_feat; in GetMappedLocation() local
1580 if ( mapped_feat ) { in GetMappedLocation()
1582 mapped_feat.Reset(); in GetMappedLocation()
1657 CRef<CSeq_feat> mapped_feat; in GetMappedFeature() local
1659 if ( !mapped_feat || !mapped_feat->ReferencedOnlyOnce() ) { in GetMappedFeature()
1680 mapped_feat->SetLocation(*loc); in GetMappedFeature()
1683 mapped_feat->SetProduct(*loc); in GetMappedFeature()
1687 mapped_feat->SetPartial(true); in GetMappedFeature()
1690 mapped_feat->ResetPartial(); in GetMappedFeature()
[all …]
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/snputil/ |
| H A D | snp_utils.cpp | 62 bool NSnp::IsSnp(const CMappedFeat &mapped_feat) in IsSnp() argument
64 return IsSnp(mapped_feat.GetOriginalFeature()); in IsSnp()
109 NSnp::TRsid NSnp::GetRsid(const CMappedFeat &mapped_feat) in GetRsid() argument
111 return GetRsid(mapped_feat.GetOriginalFeature()); in GetRsid()
133 int NSnp::GetLength(const CMappedFeat &mapped_feat) in GetLength() argument
135 return GetLength(mapped_feat.GetOriginalFeature()); in GetLength()
220 CSnpBitfield NSnp::GetBitfield(const CMappedFeat &mapped_feat) in GetBitfield() argument
222 return GetBitfield(mapped_feat.GetOriginalFeature()); in GetBitfield()
237 void NSnp::GetAlleles(const CMappedFeat &mapped_feat, TAlleles& Alleles) in GetAlleles() argument
239 GetAlleles(mapped_feat.GetOriginalFeature(), Alleles); in GetAlleles()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/impl/ |
| H A D | seq_loc_cvt.hpp | 122 CRef<CSeq_feat>& mapped_feat);
125 CRef<CSeq_feat>& mapped_feat);
128 CRef<CSeq_feat>& mapped_feat);
379 CRef<CSeq_feat>& mapped_feat);
382 CRef<CSeq_feat>& mapped_feat);
385 CRef<CSeq_feat>& mapped_feat);
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/impl/ |
| H A D | seq_loc_cvt.hpp | 122 CRef<CSeq_feat>& mapped_feat);
125 CRef<CSeq_feat>& mapped_feat);
128 CRef<CSeq_feat>& mapped_feat);
379 CRef<CSeq_feat>& mapped_feat);
382 CRef<CSeq_feat>& mapped_feat);
385 CRef<CSeq_feat>& mapped_feat);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/snputil/ |
| H A D | snp_utils.hpp | 85 static bool IsSnp(const CMappedFeat &mapped_feat);
103 static CTime GetCreateTime(const CMappedFeat &mapped_feat);
112 static TRsid GetRsid(const CMappedFeat &mapped_feat);
196 static void GetAlleles(const CMappedFeat &mapped_feat, TAlleles& Alleles);
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/writers/ |
| H A D | gff_writer.hpp | 215 const CMappedFeat& mapped_feat);
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| H A D | gff3_writer.hpp | 418 const CMappedFeat& mapped_feat) override;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/format/ |
| H A D | gather_items.cpp | 3756 CMappedFeat mapped_feat = *it; in x_GatherFeaturesOnRange() local
3762 CMappedFeat mapped_feat = s_GetTrimmedMappedFeat(ft, range, scope); in x_GatherFeaturesOnRange() local
3763 feat_loc.Reset( slice_mapper->Map( mapped_feat.GetLocation() ) ); in x_GatherFeaturesOnRange()
3778 item.Reset( x_NewFeatureItem(mapped_feat, ctx, feat_loc, m_Feat_Tree) ); in x_GatherFeaturesOnRange()
4389 CMappedFeat mapped_feat = *it; in x_GetFeatsOnCdsProductIdx() local
4397 feat->Assign(mapped_feat.GetMappedFeature()); in x_GetFeatsOnCdsProductIdx()
4400 mapped_feat = s_GetTrimmedMappedFeat(*feat, range, scope); in x_GetFeatsOnCdsProductIdx()
4502 CMappedFeat mapped_feat = *it; in x_GetFeatsOnCdsProduct() local
4510 feat->Assign(mapped_feat.GetMappedFeature()); in x_GetFeatsOnCdsProduct()
4513 mapped_feat = s_GetTrimmedMappedFeat(*feat, range, scope); in x_GetFeatsOnCdsProduct()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/format/ |
| H A D | gather_items.cpp | 3756 CMappedFeat mapped_feat = *it; in x_GatherFeaturesOnRange() local
3762 CMappedFeat mapped_feat = s_GetTrimmedMappedFeat(ft, range, scope); in x_GatherFeaturesOnRange() local
3763 feat_loc.Reset( slice_mapper->Map( mapped_feat.GetLocation() ) ); in x_GatherFeaturesOnRange()
3778 item.Reset( x_NewFeatureItem(mapped_feat, ctx, feat_loc, m_Feat_Tree) ); in x_GatherFeaturesOnRange()
4387 CMappedFeat mapped_feat = *it; in x_GetFeatsOnCdsProductIdx() local
4395 feat->Assign(mapped_feat.GetMappedFeature()); in x_GetFeatsOnCdsProductIdx()
4398 mapped_feat = s_GetTrimmedMappedFeat(*feat, range, scope); in x_GetFeatsOnCdsProductIdx()
4500 CMappedFeat mapped_feat = *it; in x_GetFeatsOnCdsProduct() local
4508 feat->Assign(mapped_feat.GetMappedFeature()); in x_GetFeatsOnCdsProduct()
4511 mapped_feat = s_GetTrimmedMappedFeat(*feat, range, scope); in x_GetFeatsOnCdsProduct()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | seq_entry_edit.cpp | 3141 CMappedFeat mapped_feat(feat_h); in DeleteProteinAndRenormalizeNucProtSet() local
3142 if ( mapped_feat.IsSetData() && in DeleteProteinAndRenormalizeNucProtSet()
3143 mapped_feat.GetData().Which() == CSeqFeatData::e_Cdregion && in DeleteProteinAndRenormalizeNucProtSet()
3144 mapped_feat.IsSetProduct() ) in DeleteProteinAndRenormalizeNucProtSet()
3148 mapped_feat.GetScope().GetBioseqHandle(mapped_feat.GetProduct()); in DeleteProteinAndRenormalizeNucProtSet()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | seq_entry_edit.cpp | 3141 CMappedFeat mapped_feat(feat_h); in DeleteProteinAndRenormalizeNucProtSet() local
3142 if ( mapped_feat.IsSetData() && in DeleteProteinAndRenormalizeNucProtSet()
3143 mapped_feat.GetData().Which() == CSeqFeatData::e_Cdregion && in DeleteProteinAndRenormalizeNucProtSet()
3144 mapped_feat.IsSetProduct() ) in DeleteProteinAndRenormalizeNucProtSet()
3148 mapped_feat.GetScope().GetBioseqHandle(mapped_feat.GetProduct()); in DeleteProteinAndRenormalizeNucProtSet()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
| H A D | gene_model.cpp | 2449 CRef<CSeq_feat> mapped_feat; in x_MapFeature() local
2451 mapped_feat.Reset(new CSeq_feat()); in x_MapFeature()
2452 mapped_feat->Assign(*feature_on_mrna); in x_MapFeature()
2453 mapped_feat->ResetId(); in x_MapFeature()
2455 mapped_feat->SetLocation(*mapped_loc); in x_MapFeature()
2457 return mapped_feat; in x_MapFeature()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | validerror_bioseq.cpp | 7270 for (const auto& mapped_feat : *m_AllFeatIt) { in x_ValidateCDSmRNAmatch()
7271 if (!mapped_feat.IsSetData()) { in x_ValidateCDSmRNAmatch()
7275 if (mapped_feat.GetData().IsCdregion()) { in x_ValidateCDSmRNAmatch()
7276 const auto& cds_feat = *mapped_feat.GetSeq_feat(); in x_ValidateCDSmRNAmatch()
7291 } else if (mapped_feat.GetData().GetSubtype() == CSeqFeatData::eSubtype_mRNA) { in x_ValidateCDSmRNAmatch()
7292 const auto& feat = *mapped_feat.GetSeq_feat(); in x_ValidateCDSmRNAmatch()
7293 mrna_map[mapped_feat.GetSeq_feat()] = Ref(new CMrnaMatchInfo(feat, m_Scope)); in x_ValidateCDSmRNAmatch()
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