| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | feature_match.cpp | 90 for (auto& cds_it : cds_list) in s_SetUpXrefPairs() local
92 CMatchCDS& cds_match = *cds_it; in s_SetUpXrefPairs()
163 vector < CRef<CMatchCDS> >::iterator cds_it = in HasCDSMatch() local
165 for (; cds_it != m_UnderlyingCDSs.end() && !rval; ++cds_it) { in HasCDSMatch()
166 if (!(*cds_it)->HasmRNA()) { in HasCDSMatch()
203 vector < CRef<CMatchCDS> >::iterator cds_it = in MatchesUnderlyingCDS()
205 while (cds_it != m_UnderlyingCDSs.end() && !rval) { in MatchesUnderlyingCDS()
206 if (!(*cds_it)->HasmRNA()) { in MatchesUnderlyingCDS()
224 ++cds_it; in MatchesUnderlyingCDS()
241 while (cds_it != m_UnderlyingCDSs.end() && !rval) { in MatchAnyUnderlyingCDS()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/flatfile/ |
| H A D | fcleanup.cpp | 428 for (CFeat_CI cds_it(entryHandle, sel); cds_it; ++cds_it) { in g_InstantiateMissingProteins() local
429 auto pCds = cds_it->GetSeq_feat(); in g_InstantiateMissingProteins()
438 CSeq_feat_EditHandle pCdsEditHandle(*cds_it); in g_InstantiateMissingProteins()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
| H A D | field_handler.cpp | 254 for (auto& cds_it : cds_feats) { in GetRelatedFeatures() local
255 …vector<CConstRef<CSeq_feat> > this_list = GetRelatedFeatures(cds_it.GetOriginalFeature(), constrai… in GetRelatedFeatures()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
| H A D | field_handler.cpp | 254 for (auto& cds_it : cds_feats) { in GetRelatedFeatures() local
255 …vector<CConstRef<CSeq_feat> > this_list = GetRelatedFeatures(cds_it.GetOriginalFeature(), constrai… in GetRelatedFeatures()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/misc/discrepancy/ |
| H A D | feature_tests.cpp | 2081 auto cds_it = cds.begin(); variable
2082 while (cds_it != cds.end()) {
2083 if (context.IsPseudo(**cds_it)) {
2084 cds_it = cds.erase(cds_it);
2088 if ((*cds_it)->IsSetXref()) {
2094 for (auto xref : (*cds_it)->GetXref()) {
2115 string prod = context.GetProdForFeature(**cds_it);
2117 … m_Objs["[n] coding region[s] [has] mismatching mRNA"].Add(*context.SeqFeatObjRef(**cds_it));
2119 cds_it = cds.erase(cds_it);
2122 ++cds_it;
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/wgs/ |
| H A D | wgsloader_impl.cpp | 793 CWGSFeatureIterator cds_it(file->GetDb(), cds_row_id); in GetRootFileInfo() local
794 if ( !cds_it ) { in GetRootFileInfo()
798 switch ( cds_it.GetLocSeqType() ) { in GetRootFileInfo()
803 root_info.row_id = cds_it.GetLocRowId(); in GetRootFileInfo()
811 root_info.row_id = cds_it.GetLocRowId(); in GetRootFileInfo()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/unit_test/ |
| H A D | unit_test_feature_propagate.cpp | 1691 CFeat_CI cds_it(seh, SAnnotSelector(CSeqFeatData::e_Cdregion)); in BOOST_AUTO_TEST_CASE() local
1695 for (; cds_it; ++cds_it) { in BOOST_AUTO_TEST_CASE()
1696 if (cds_it->IsSetProduct()) { in BOOST_AUTO_TEST_CASE()
1697 cds_withprot = cds_it->GetOriginalSeq_feat(); in BOOST_AUTO_TEST_CASE()
1698 CFeat_CI prot_it(scope.GetBioseqHandle(cds_it->GetProduct())); in BOOST_AUTO_TEST_CASE()
1702 cds_withoutprot = cds_it->GetOriginalSeq_feat(); in BOOST_AUTO_TEST_CASE()
1800 CFeat_CI cds_it(seh, SAnnotSelector(CSeqFeatData::e_Cdregion)); in BOOST_AUTO_TEST_CASE() local
1804 for (; cds_it; ++cds_it) { in BOOST_AUTO_TEST_CASE()
1805 if (cds_it->IsSetProduct()) { in BOOST_AUTO_TEST_CASE()
1806 cds_withprot = cds_it->GetOriginalSeq_feat(); in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/ |
| H A D | cleanup.cpp | 2674 for (CFeat_CI cds_it(entry, sel); cds_it; ++cds_it) { in WGSCleanup() local
2677 new_cds->Assign(*(cds_it->GetSeq_feat())); in WGSCleanup()
2678 if (sequence::IsPseudo(*(cds_it->GetSeq_feat()), entry.GetScope())) { in WGSCleanup()
2737 … CConstRef<CSeq_feat> mrna = sequence::GetmRNAforCDS(*(cds_it->GetSeq_feat()), entry.GetScope()); in WGSCleanup()
2771 CSeq_feat_EditHandle cds_h(*cds_it); in WGSCleanup()
2925 for (CFeat_CI cds_it(entry, sel); cds_it; ++cds_it) { in x_AddLowQualityException() local
2928 new_cds->Assign(*(cds_it->GetSeq_feat())); in x_AddLowQualityException()
2929 if (!sequence::IsPseudo(*(cds_it->GetSeq_feat()), entry.GetScope()) && in x_AddLowQualityException()
2930 x_HasShortIntron(cds_it->GetLocation())) { in x_AddLowQualityException()
2935 CSeq_feat_EditHandle cds_h(*cds_it); in x_AddLowQualityException()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/ |
| H A D | cleanup.cpp | 2674 for (CFeat_CI cds_it(entry, sel); cds_it; ++cds_it) { in WGSCleanup() local
2677 new_cds->Assign(*(cds_it->GetSeq_feat())); in WGSCleanup()
2678 if (sequence::IsPseudo(*(cds_it->GetSeq_feat()), entry.GetScope())) { in WGSCleanup()
2737 … CConstRef<CSeq_feat> mrna = sequence::GetmRNAforCDS(*(cds_it->GetSeq_feat()), entry.GetScope()); in WGSCleanup()
2771 CSeq_feat_EditHandle cds_h(*cds_it); in WGSCleanup()
2925 for (CFeat_CI cds_it(entry, sel); cds_it; ++cds_it) { in x_AddLowQualityException() local
2928 new_cds->Assign(*(cds_it->GetSeq_feat())); in x_AddLowQualityException()
2929 if (!sequence::IsPseudo(*(cds_it->GetSeq_feat()), entry.GetScope()) && in x_AddLowQualityException()
2930 x_HasShortIntron(cds_it->GetLocation())) { in x_AddLowQualityException()
2935 CSeq_feat_EditHandle cds_h(*cds_it); in x_AddLowQualityException()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/test/ |
| H A D | unit_test_extended_cleanup.cpp | 713 CFeat_CI cds_it(bsh, CSeqFeatData::e_Cdregion); in BOOST_AUTO_TEST_CASE() local
714 while (cds_it) { in BOOST_AUTO_TEST_CASE()
716 replace->Assign(*(cds_it->GetSeq_feat())); in BOOST_AUTO_TEST_CASE()
718 ++cds_it; in BOOST_AUTO_TEST_CASE()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/unit_test/ |
| H A D | unit_test_validator.cpp | 16406 …CSeq_annot::TData::TFtable::iterator cds_it = entry->SetSet().SetAnnot().front()->SetData().SetFta… in BOOST_AUTO_TEST_CASE() local
16408 CRef<CSeq_feat> mrna = unit_test_util::MakemRNAForCDS (*cds_it); in BOOST_AUTO_TEST_CASE()
16411 CRef<CSeq_feat> gene = unit_test_util::MakeGeneForFeature (*cds_it); in BOOST_AUTO_TEST_CASE()
16425 ++cds_it; in BOOST_AUTO_TEST_CASE()
16426 CRef<CSeq_feat> new_mrna = unit_test_util::MakemRNAForCDS (*cds_it); in BOOST_AUTO_TEST_CASE()
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