stringBuilder.append(consequenceType.getCdnaPosition()); break; case "cdsPosition":
stringBuilder.append(consequenceType.getCdnaPosition()); break; case "cdsPosition":
|| (conseqType.getCdnaPosition() != null && conseqType.getCdnaPosition() > 0) || (conseqType.getCdsPosition() != null && conseqType.getCdsPosition() > 0)) { } else { trans.append(FIELD_SEP) .append(conseqType.getCdnaPosition() == null ? 0 : conseqType.getCdnaPosition()) .append(FIELD_SEP) .append(conseqType.getCdsPosition() == null ? 0 : conseqType.getCdsPosition());
int cdnaPosition = consequenceType1.getCdnaPosition(); int cdsPosition = consequenceType1.getCdsPosition(); String codon = null;
if((cdnaPosition=consequenceType.getCdnaPosition())==null) { cdnaPositionString = "-"; } else {
int cdnaPosition = consequenceType1.getCdnaPosition(); int cdsPosition = consequenceType1.getCdsPosition(); String codon = null;
putNotNull(ct, CT_C_DNA_POSITION_FIELD, consequenceType.getCdnaPosition()); putNotNull(ct, CT_CDS_POSITION_FIELD, consequenceType.getCdsPosition());
int inCdnaPosition = inCT.getCdnaPosition() == null ? 0 : inCT.getCdnaPosition(); int inCdsPosition = inCT.getCdsPosition() == null ? 0 : inCT.getCdsPosition(); int outCdnaPosition = outCT.getCdnaPosition() == null ? 0 : outCT.getCdnaPosition(); int outCdsPosition = outCT.getCdsPosition() == null ? 0 : outCT.getCdsPosition(); String inCodon = inCT.getCodon() == null ? "" : inCT.getCodon().trim();
public static VariantAnnotationProto.ConsequenceType createConsequenceType(ConsequenceType type) { VariantAnnotationProto.ConsequenceType.Builder builder= VariantAnnotationProto.ConsequenceType.newBuilder() .setGeneName(type.getGeneName()) .setEnsemblGeneId(type.getEnsemblGeneId()) .setEnsemblTranscriptId(type.getEnsemblTranscriptId()) .setStrand(type.getStrand()) .setBiotype(type.getBiotype()) .setCDnaPosition(type.getCdnaPosition()) .setCdsPosition(type.getCdsPosition()) .setCodon(type.getCodon()) .setProteinVariantAnnotation(createProteinVariantAnnotation(type.getProteinVariantAnnotation())); List<SequenceOntologyTerm> sequenceOntologyTerms = type.getSequenceOntologyTerms(); if (sequenceOntologyTerms != null) { for (SequenceOntologyTerm so : sequenceOntologyTerms) { VariantAnnotationProto.SequenceOntologyTerm.Builder soBuilder = VariantAnnotationProto.SequenceOntologyTerm.newBuilder() .setAccession(so.getAccession()) .setName(so.getName()); builder.addSequenceOntologyTerms(soBuilder.build()); } } return builder.build(); }