private SequenceOntologyTerm newSequenceOntologyTerm(String name) { return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name); }
private SequenceOntologyTerm newSequenceOntologyTerm(String name) { return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name); }
private SequenceOntologyTerm newSequenceOntologyTerm(String name) { return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name); }
public static SequenceOntologyTerm newSequenceOntologyTerm(String name) throws SOTermNotAvailableException { return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name); }
public static SequenceOntologyTerm newSequenceOntologyTerm(String name) throws SOTermNotAvailableException { return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name); }
private ConsequenceType buildConsequenceType(String geneName, String ensemblGeneId, String ensemblTranscriptId, String strand, String biotype, List<Document> exonOverlap, List<String> transcriptAnnotationFlags, Integer cDnaPosition, Integer cdsPosition, String codon, List<String> soNameList, ProteinVariantAnnotation proteinVariantAnnotation) { List<SequenceOntologyTerm> soTerms = new ArrayList<>(soNameList.size()); for (String soName : soNameList) { soTerms.add(new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(soName), soName)); } List<ExonOverlap> exonOverlapList = new ArrayList<>(exonOverlap.size()); for (Document document : exonOverlap) { ExonOverlap e = new ExonOverlap( document.getString(CT_EXON_OVERLAP_NUMBER_FIELD), getDefault(document, CT_EXON_OVERLAP_PERCENTAGE_FIELD, 0F)); exonOverlapList.add(e); } return new ConsequenceType(geneName, ensemblGeneId, ensemblTranscriptId, strand, biotype, exonOverlapList, transcriptAnnotationFlags, cDnaPosition, cdsPosition, codon, proteinVariantAnnotation, soTerms); }
.add(new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(newSoName), newSoName));
@Override public SequenceOntologyTerm build() { try { SequenceOntologyTerm record = new SequenceOntologyTerm(); record.accession = fieldSetFlags()[0] ? this.accession : (java.lang.String) defaultValue(fields()[0]); record.name = fieldSetFlags()[1] ? this.name : (java.lang.String) defaultValue(fields()[1]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
.add(new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(newSoName), newSoName));
SequenceOntologyTerm sequenceOntologyTerm = new SequenceOntologyTerm(); sequenceOntologyTerm.setAccession("SO:" + String.format("%07d", soAcc)); sequenceOntologyTerm.setName(ConsequenceTypeMappings.accessionToTerm.get(soAcc)); SequenceOntologyTerm sequenceOntologyTerm = new SequenceOntologyTerm(); sequenceOntologyTerm.setAccession("SO:" + String.format("%07d", soAcc)); sequenceOntologyTerm.setName(ConsequenceTypeMappings.accessionToTerm.get(soAcc));