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Searched refs:feat_it (Results 1 – 25 of 86) sorted by relevance

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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/cleanup/
H A Dfix_feature_id.cpp44 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()
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/dports/misc/openmvg/openMVG-2.0/src/openMVG/features/
H A Dsvg_features.cpp32 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/cleanup/
H A Dfix_feature_id.cpp44 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sample/app/objmgr/
H A Dobjmgr_sample.cpp193 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 Dfeattree_sample.cpp188 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 Dprocess_gene_overlap.hpp101 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 Dtest_wgs_loader.cpp414 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
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/
H A Dvaliderror_annot.cpp172 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()
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H A Dtax_validation_and_cleanup.cpp690 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()
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H A Ddup_feats.cpp55 … 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 Dtest_helper.cpp1155 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/unit_test/
H A Dunit_test_polya.cpp97 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 Dtest_snp_loader.cpp119 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()
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/dports/textproc/apertium/apertium-3.6.1/apertium/
H A Dfeature_vec.cc64 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 Dexternal_annots.cpp123 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 Dlink_cds_mrna.cpp116 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 Dexternal_annots.cpp123 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 Dlink_cds_mrna.cpp116 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 Dmicro_introns.cpp155 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 Dgvf_writer.cpp145 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 Dfeature_table_reader.cpp574 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
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H A Dvisitors.hpp122 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 Dtable2asn_context.cpp509 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 Dweight.cpp159 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 Dweight.cpp159 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()

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