| /dports/biology/jalview/jalview/src/jalview/ws/dbsources/ |
| H A D | Uniprot.java | 229 String cdsId = getProperty(dbref.getProperty(), in uniprotEntryToSequence() local
231 if (cdsId != null && cdsId.trim().length() > 0) in uniprotEntryToSequence()
234 String[] vrs = cdsId.split("\\."); in uniprotEntryToSequence()
251 String cdsId = getProperty(dbref.getProperty(), in uniprotEntryToSequence() local
253 if (cdsId != null && cdsId.trim().length() > 0) in uniprotEntryToSequence()
256 DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim()); in uniprotEntryToSequence()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/ |
| H A D | store_io_ucsc.h | 60 TId cdsId = length(fragStore.annotationStore); in _storeAnnotationRecord() local
63 resize(fragStore.annotationStore, cdsId + 1 + length(record.exonBegin), Generous()); in _storeAnnotationRecord()
64 resize(fragStore.annotationNameStore, cdsId + 1 + length(record.exonBegin), Generous()); in _storeAnnotationRecord()
80 TAnnotation & cds = fragStore.annotationStore[cdsId]; in _storeAnnotationRecord()
91 TAnnotation & exon = fragStore.annotationStore[cdsId + 1 + i]; in _storeAnnotationRecord()
|
| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/ |
| H A D | store_io_ucsc.h | 60 TId cdsId = length(fragStore.annotationStore); in _storeAnnotationRecord() local
63 resize(fragStore.annotationStore, cdsId + 1 + length(record.exonBegin), Generous()); in _storeAnnotationRecord()
64 resize(fragStore.annotationNameStore, cdsId + 1 + length(record.exonBegin), Generous()); in _storeAnnotationRecord()
80 TAnnotation & cds = fragStore.annotationStore[cdsId]; in _storeAnnotationRecord()
91 TAnnotation & exon = fragStore.annotationStore[cdsId + 1 + i]; in _storeAnnotationRecord()
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/ |
| H A D | store_io_ucsc.h | 60 TId cdsId = length(fragStore.annotationStore); in _storeAnnotationRecord() local
63 resize(fragStore.annotationStore, cdsId + 1 + length(record.exonBegin), Generous()); in _storeAnnotationRecord()
64 resize(fragStore.annotationNameStore, cdsId + 1 + length(record.exonBegin), Generous()); in _storeAnnotationRecord()
80 TAnnotation & cds = fragStore.annotationStore[cdsId]; in _storeAnnotationRecord()
91 TAnnotation & exon = fragStore.annotationStore[cdsId + 1 + i]; in _storeAnnotationRecord()
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
| H A D | gff3_reader.cpp | 82 string cdsId = parentId; in xMakeRecordId() local
83 if (cdsId.empty()) { in xMakeRecordId()
84 cdsId = (id.empty() ? xNextGenericId() : id); in xMakeRecordId()
87 cdsId += ":cds"; in xMakeRecordId()
89 return cdsId; in xMakeRecordId()
542 string cdsId = xMakeRecordId(record); in xUpdateAnnotCds() local
543 mpLocations->AddRecordForId(cdsId, record); in xUpdateAnnotCds()
545 auto pExistingFeature = m_MapIdToFeature.find(cdsId); in xUpdateAnnotCds()
550 m_MapIdToFeature[cdsId] = pFeature; in xUpdateAnnotCds()
|
| H A D | gff2_data.cpp | 536 string cdsId; in UpdateFeature() local
537 GetAttribute("ID", cdsId); in UpdateFeature()
538 if (!cdsId.empty()) { in UpdateFeature()
539 pFeature->AddOrReplaceQualifier("ID", cdsId); in UpdateFeature()
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
| H A D | gff3_reader.cpp | 82 string cdsId = parentId; in xMakeRecordId() local
83 if (cdsId.empty()) { in xMakeRecordId()
84 cdsId = (id.empty() ? xNextGenericId() : id); in xMakeRecordId()
87 cdsId += ":cds"; in xMakeRecordId()
89 return cdsId; in xMakeRecordId()
542 string cdsId = xMakeRecordId(record); in xUpdateAnnotCds() local
543 mpLocations->AddRecordForId(cdsId, record); in xUpdateAnnotCds()
545 auto pExistingFeature = m_MapIdToFeature.find(cdsId); in xUpdateAnnotCds()
550 m_MapIdToFeature[cdsId] = pFeature; in xUpdateAnnotCds()
|
| H A D | gff2_data.cpp | 536 string cdsId; in UpdateFeature() local
537 GetAttribute("ID", cdsId); in UpdateFeature()
538 if (!cdsId.empty()) { in UpdateFeature()
539 pFeature->AddOrReplaceQualifier("ID", cdsId); in UpdateFeature()
|
| /dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
| H A D | store_io_ucsc.h | 284 TId cdsId = TAnnotation::INVALID_ID; in _storeOneAnnotationKnownGene() local
288 cdsId = length(fragStore.annotationNameStore); in _storeOneAnnotationKnownGene()
294 if (annoStoreLen <= cdsId) in _storeOneAnnotationKnownGene()
295 annoStoreLen = cdsId + 1; in _storeOneAnnotationKnownGene()
310 TAnnotation &cds = fragStore.annotationStore[cdsId]; in _storeOneAnnotationKnownGene()
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/writers/ |
| H A D | gff3_writer.cpp | 2601 string cdsId = pCds->Id(); in xWriteFeatureCds() local
2611 pExon->SetRecordId(cdsId); in xWriteFeatureCds()
|