/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/ |
H A D | fix_feature_id.cpp | 44 for (CFeat_CI feat_it(entry); feat_it; ++feat_it) { in s_FindHighestFeatureId() local 45 if (feat_it->IsSetId()) { in s_FindHighestFeatureId() 46 const CFeat_id &id = feat_it->GetId(); in s_FindHighestFeatureId() 70 CFeat_CI feat_it(entry); in s_UpdateFeatureIds() local 71 for ( ; feat_it; ++feat_it ) in s_UpdateFeatureIds() 118 feat_it.Rewind(); in s_UpdateFeatureIds() 119 for ( ; feat_it; ++feat_it ) in s_UpdateFeatureIds() 178 for (CFeat_CI feat_it(entry); feat_it; ++feat_it) { in s_MakeIDPairs() local 179 if (feat_it->IsSetId()) { in s_MakeIDPairs() 180 const CFeat_id &id = feat_it->GetId(); in s_MakeIDPairs() [all …]
|
/dports/misc/openmvg/openMVG-2.0/src/openMVG/features/ |
H A D | svg_features.cpp | 32 for (const features::PointFeature & feat_it : features) { in Features2SVG() local 35 feat_it.x(), feat_it.y(), feature_circle_radius, in Features2SVG() 66 for (const features::SIOPointFeature & feat_it : features) { in Features2SVG() local 69 feat_it.x(), feat_it.y(), feat_it.scale(), in Features2SVG() 125 for (const features::PointFeature & feat_it : left_features) { in Features2SVG() local 127 feat_it.x(), feat_it.y(), feature_circle_radius, in Features2SVG() 130 for (const features::PointFeature & feat_it : right_features) { in Features2SVG() local 132 feat_it.x() + svg_offset_x, feat_it.y() + svg_offset_y, feature_circle_radius, in Features2SVG() 187 for (const features::SIOPointFeature & feat_it : left_features) { in Features2SVG() local 189 feat_it.x(), feat_it.y(), feat_it.scale(), in Features2SVG() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/ |
H A D | fix_feature_id.cpp | 44 for (CFeat_CI feat_it(entry); feat_it; ++feat_it) { in s_FindHighestFeatureId() local 45 if (feat_it->IsSetId()) { in s_FindHighestFeatureId() 145 feat_it; in UpdateFeatureIds() 146 ++feat_it) { in UpdateFeatureIds() 224 CFeat_CI feat_it(entry); in s_UpdateFeatureIds() local 225 for ( ; feat_it; ++feat_it ) in s_UpdateFeatureIds() 262 feat_it.Rewind(); in s_UpdateFeatureIds() 263 for ( ; feat_it; ++feat_it ) in s_UpdateFeatureIds() 341 for (CFeat_CI feat_it(entry); feat_it; ++feat_it) { in s_MakeIDPairs() local 342 if (feat_it->IsSetId()) { in s_MakeIDPairs() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sample/app/objmgr/ |
H A D | objmgr_sample.cpp | 193 for (CFeat_CI feat_it(scope, seq_loc, sel); feat_it; ++feat_it) { in Run() local 196 CSeq_annot_Handle annot = feat_it.GetAnnot(); in Run() 204 for (CFeat_CI feat_it(scope, seq_loc, sel); feat_it; ++feat_it) { in Run() local 217 for (CFeat_CI feat_it(scope, seq_loc, sel); feat_it; ++feat_it) { in Run() local 229 for (CFeat_CI feat_it(scope, in Run() local 230 *bioseq_handle.GetRangeSeq_loc(0, 999), sel); feat_it; ++feat_it) { in Run()
|
H A D | feattree_sample.cpp | 188 CFeat_CI feat_it(CFeat_CI(scope, seq_loc, sel)); in Run() local 189 cout << feat_it.GetSize() << " features found." << endl; in Run() 194 feat_tree.AddFeatures(feat_it); in Run() 205 for (feat_it.Rewind(); feat_it; ++feat_it) { in Run() 208 CConstRef<CSeq_feat> seq_feat_ref(feat_it->GetSeq_feat()); in Run() 222 CMappedFeat parent(feat_tree.GetParent(*feat_it, in Run()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/streamtest/ |
H A D | process_gene_overlap.hpp | 101 for (CFeat_CI feat_it(bsh, sel); feat_it; ++feat_it) { in SeqEntryProcess() local 102 const CMappedFeat mf = *feat_it; in SeqEntryProcess() 240 for (CFeat_CI feat_it(bsh, sel); feat_it; ++feat_it) { in SeqEntryProcess() local 241 const CMappedFeat mf = *feat_it; in SeqEntryProcess() 245 for (CFeat_CI feat_it(bsh, sel); feat_it; ++feat_it) { in SeqEntryProcess() local 246 const CMappedFeat mf = *feat_it; in SeqEntryProcess()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/wgs/test/ |
H A D | test_wgs_loader.cpp | 414 CFeat_CI feat_it(bh); in sx_ExtractAnnot() local 415 if ( feat_it ) { in sx_ExtractAnnot() 417 for ( ; feat_it; ++feat_it ) { in sx_ExtractAnnot() 1609 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local 1641 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local 1674 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local 1706 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local 1740 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local 1773 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local 1807 CFeat_CI feat_it(bsh); in BOOST_AUTO_TEST_CASE() local [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | validerror_annot.cpp | 172 FOR_EACH_SEQFEAT_ON_SEQANNOT(feat_it, annot) { in ValidateSeqAnnotContext() 174 ReportLocationGI0(**feat_it, label); in ValidateSeqAnnotContext() 175 if (!(*feat_it)->IsSetLocation() || IsLocationUnindexed((*feat_it)->GetLocation())) { in ValidateSeqAnnotContext() 177 "Feature is not indexed on Bioseq " + label, **feat_it); in ValidateSeqAnnotContext() 182 for (CSeq_loc_CI loc_it((*feat_it)->GetLocation()); loc_it; ++loc_it) { in ValidateSeqAnnotContext() 307 FOR_EACH_SEQFEAT_ON_SEQANNOT (feat_it, annot) { in ValidateSeqAnnotContext() 308 ReportLocationGI0(**feat_it, "?"); in ValidateSeqAnnotContext() 309 if (!(*feat_it)->IsSetLocation() || IsLocationUnindexed((*feat_it)->GetLocation())) { in ValidateSeqAnnotContext() 311 "Feature is not indexed on Bioseq ?", **feat_it); in ValidateSeqAnnotContext() 317 } else if ((*feat_it)->IsSetLocation() && in ValidateSeqAnnotContext() [all …]
|
H A D | tax_validation_and_cleanup.cpp | 690 if ((*feat_it)->IsSetData() && (*feat_it)->GetData().IsBiosrc() in x_GatherSources() 693 feat.Reset(*feat_it); in x_GatherSources() 735 ++feat_it; in GetTaxonomyLookupRequest() 853 && feat_it != m_SrcFeats.end()) { in ReportTaxLookupErrors() 863 ++feat_it; in ReportTaxLookupErrors() 914 ++feat_it; in ReportIncrementalTaxLookupErrors() 918 feat_it != m_SrcFeats.end()) { in ReportIncrementalTaxLookupErrors() 928 ++feat_it; in ReportIncrementalTaxLookupErrors() 1019 while (feat_it != m_SrcFeats.end()) { in x_CreateQualifierMap() 1020 lookup.AddFeat(*feat_it); in x_CreateQualifierMap() [all …]
|
H A D | dup_feats.cpp | 55 … for (CFeat_CI feat_it(tse, SAnnotSelector(CSeqFeatData::eSubtype_cdregion)); feat_it; ++feat_it) in BEGIN_SCOPE() local 57 if (feat_it->IsSetProduct()) in BEGIN_SCOPE() 59 CSeq_feat_Handle fh = feat_it->GetSeq_feat_Handle(); in BEGIN_SCOPE()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/test/ |
H A D | test_helper.cpp | 1155 feat_it; ++feat_it) { in ProcessBioseq() 1166 feat_it; ++feat_it) { in ProcessBioseq() 1178 feat_it; ++feat_it) { in ProcessBioseq() 1201 for ( CFeat_CI feat_it(scope, loc); feat_it; ++feat_it) { in ProcessBioseq() local 1217 feat_it; ++feat_it) { in ProcessBioseq() 1236 feat_it; ++feat_it) { in ProcessBioseq() 1255 feat_it; ++feat_it) { in ProcessBioseq() 1277 for ( CSeq_annot_ftable_CI feat_it(*annot_it); feat_it; ++feat_it ) { in ProcessBioseq() local 1295 feat_it; ++feat_it) { in ProcessBioseq() 1306 feat_it; ++feat_it) { in ProcessBioseq() [all …]
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/ |
H A D | unit_test_polya.cpp | 97 for(CFeat_CI feat_it(handle, SAnnotSelector(CSeqFeatData::e_Region)); in BOOST_AUTO_TEST_CASE() local 98 feat_it; ++feat_it) in BOOST_AUTO_TEST_CASE() 99 if(feat_it->GetData().GetRegion() == "polya") in BOOST_AUTO_TEST_CASE() 100 expected_polya = feat_it->GetRange(); in BOOST_AUTO_TEST_CASE()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/data_loaders/snp/test/ |
H A D | test_snp_loader.cpp | 119 CFeat_CI feat_it) in s_CheckSource() argument 122 for ( ; feat_it; ++feat_it ) { in s_CheckSource() 218 if ( feat_it ) { in s_TestNoNA() 219 s_CheckSource(descr, eFromGB, feat_it); in s_TestNoNA() 246 BOOST_CHECK(feat_it); in s_TestNA() 247 BOOST_CHECK_EQUAL(feat_it.GetSize(), snp_count); in s_TestNA() 248 s_CheckSource(descr, source, feat_it); in s_TestNA() 282 BOOST_CHECK(feat_it); in s_TestPTIS() 283 BOOST_CHECK_GE(feat_it.GetSize(), snp_count); in s_TestPTIS() 284 BOOST_CHECK_LT(feat_it.GetSize(), snp_count*2); in s_TestPTIS() [all …]
|
/dports/textproc/apertium/apertium-3.6.1/apertium/ |
H A D | feature_vec.cc | 64 FeatureVec::Map::const_iterator feat_it = fv.data.begin(); in operator <<() local 65 for (; feat_it != fv.data.end(); feat_it++) in operator <<() 67 FeatureKey::const_iterator bc_it = feat_it->first.begin(); in operator <<() 69 for (;bc_it != feat_it->first.end(); bc_it++) in operator <<() 72 if (bc_it + 1 != feat_it->first.end()) in operator <<() 77 out << ": " << feat_it->second << "\n"; in operator <<()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/edit/ |
H A D | external_annots.cpp | 123 CFeat_CI feat_it(annot_handle); in x_GetCompleteSeqAnnot() local 124 for (; feat_it; ++feat_it) { in x_GetCompleteSeqAnnot() 126 feat->Assign(feat_it->GetMappedFeature()); in x_GetCompleteSeqAnnot()
|
H A D | link_cds_mrna.cpp | 116 for (CSeq_annot::TData::TFtable::iterator feat_it = ftable.begin(); in xLinkCDSmRNAbyLabelAndLocation() local 117 ftable.end() != feat_it; ++feat_it) in xLinkCDSmRNAbyLabelAndLocation() 119 CRef<CSeq_feat> feature = (*feat_it); in xLinkCDSmRNAbyLabelAndLocation() 131 CSeq_annot::TData::TFtable::iterator opp_it = feat_it; in xLinkCDSmRNAbyLabelAndLocation()
|
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/edit/ |
H A D | external_annots.cpp | 123 CFeat_CI feat_it(annot_handle); in x_GetCompleteSeqAnnot() local 124 for (; feat_it; ++feat_it) { in x_GetCompleteSeqAnnot() 126 feat->Assign(feat_it->GetMappedFeature()); in x_GetCompleteSeqAnnot()
|
H A D | link_cds_mrna.cpp | 116 for (CSeq_annot::TData::TFtable::iterator feat_it = ftable.begin(); in xLinkCDSmRNAbyLabelAndLocation() local 117 ftable.end() != feat_it; ++feat_it) in xLinkCDSmRNAbyLabelAndLocation() 119 CRef<CSeq_feat> feature = (*feat_it); in xLinkCDSmRNAbyLabelAndLocation() 131 CSeq_annot::TData::TFtable::iterator opp_it = feat_it; in xLinkCDSmRNAbyLabelAndLocation()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | micro_introns.cpp | 155 CFeat_CI feat_it(range ? CFeat_CI(bsh, *range, sel) : CFeat_CI(bsh, sel)); in CreateMicroIntrons() local 156 feat_tree.AddFeatures(feat_it); in CreateMicroIntrons() 166 …for(CFeat_CI feat_it(range ? CFeat_CI(bsh, *range, orig_sel) : CFeat_CI(bsh, orig_sel)); feat_it; … in CreateMicroIntrons() local 167 CSeq_feat_Handle cur_feat = feat_it->GetSeq_feat_Handle(); in CreateMicroIntrons()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
H A D | gvf_writer.cpp | 145 CFeat_CI feat_it) in xWriteFeature() argument 148 if (!feat_it) { in xWriteFeature() 151 CGffFeatureContext fc(feat_it, CBioseq_Handle(), feat_it.GetAnnot()); in xWriteFeature() 152 return xWriteFeature(fc, *feat_it); in xWriteFeature()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/ |
H A D | feature_table_reader.cpp | 574 if ((**feat_it).IsSetId() && (**feat_it).GetId().Equals(id)) in _FindFeature() 575 return *feat_it; in _FindFeature() 1017 auto feat_it = seq_ftable.begin(); in _MoveCdRegions() local 1023 ++feat_it; in _MoveCdRegions() 1053 ++feat_it; in _MoveCdRegions() 1065 feat_it = seq_ftable.erase(feat_it); in _MoveCdRegions() 1070 ++feat_it; in _MoveCdRegions() 1377 …if ((*feat_it)->IsSetData() && (*feat_it)->GetData().IsProt() && !(*feat_it)->GetData().GetProt().… in AddEmptyProteinFeatureToProtein() 1378 prot_feat = *feat_it; in AddEmptyProteinFeatureToProtein() 1943 for (auto feat_it = ftable.begin(); feat_it != ftable.end(); ++feat_it) { in s_GatherRegionIterators() local [all …]
|
H A D | visitors.hpp | 122 for (objects::CFeat_CI feat_it(entry_h); feat_it; ++feat_it) in VisitAllFeatures() local 124 m(*(CSeq_feat*)feat_it->GetOriginalSeq_feat().GetPointer()); in VisitAllFeatures()
|
H A D | table2asn_context.cpp | 509 for (CFeat_CI feat_it(*bioseq_it, SAnnotSelector(CSeqFeatData::e_Rna) ); feat_it; ++feat_it) in CopyFeatureIdsToComments() local 519 CSeq_feat& feature = (CSeq_feat&) feat_it->GetOriginalFeature(); in CopyFeatureIdsToComments() 544 for (CFeat_CI feat_it(h_entry); feat_it; ++feat_it) in SmartFeatureAnnotation() local 546 if (!feat_it->IsSetData()) in SmartFeatureAnnotation() 549 switch (feat_it->GetData().Which()) in SmartFeatureAnnotation() 555 cds.push_back((CSeq_feat*) &feat_it->GetOriginalFeature()); in SmartFeatureAnnotation() 558 rnas.push_back((CSeq_feat*) &feat_it->GetOriginalFeature()); in SmartFeatureAnnotation()
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objmgr/util/ |
H A D | weight.cpp | 159 CFeat_CI feat_it(bsh, CSeqFeatData::e_Prot); in GetProteinWeight() local 160 for ( ; feat_it; ++feat_it) { in GetProteinWeight() 161 switch (feat_it->GetData().GetProt().GetProcessed()) { in GetProteinWeight()
|
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objmgr/util/ |
H A D | weight.cpp | 159 CFeat_CI feat_it(bsh, CSeqFeatData::e_Prot); in GetProteinWeight() local 160 for ( ; feat_it; ++feat_it) { in GetProteinWeight() 161 switch (feat_it->GetData().GetProt().GetProcessed()) { in GetProteinWeight()
|