private ConsequenceType findCodingOverlappingConsequenceType(ConsequenceType consequenceType, List<ConsequenceType> consequenceTypeList) { for (ConsequenceType consequenceType1 : consequenceTypeList) { if (isCoding(consequenceType1) && consequenceType.getEnsemblTranscriptId().equals(consequenceType1.getEnsemblTranscriptId()) && consequenceType.getProteinVariantAnnotation().getPosition() .equals(consequenceType1.getProteinVariantAnnotation().getPosition())) { return consequenceType1; } } return null; }
private ConsequenceType findCodingOverlappingConsequenceType(ConsequenceType consequenceType, List<ConsequenceType> consequenceTypeList) { for (ConsequenceType consequenceType1 : consequenceTypeList) { if (isCoding(consequenceType1) && consequenceType.getEnsemblTranscriptId().equals(consequenceType1.getEnsemblTranscriptId()) && consequenceType.getProteinVariantAnnotation().getPosition() .equals(consequenceType1.getProteinVariantAnnotation().getPosition())) { return consequenceType1; } } return null; }
stringBuilder.append(consequenceType.getProteinVariantAnnotation().getPosition()); stringBuilder.append(FIELD_SEPARATOR); stringBuilder.append(consequenceType.getProteinVariantAnnotation().getReference())
case "proteinPosition": if (consequenceType.getProteinVariantAnnotation() != null) { stringBuilder.append(consequenceType.getProteinVariantAnnotation().getPosition());
case "proteinPosition": if (consequenceType.getProteinVariantAnnotation() != null) { stringBuilder.append(consequenceType.getProteinVariantAnnotation().getPosition());
private ProteinVariantAnnotation getProteinAnnotation(ConsequenceType consequenceType) { if (consequenceType.getProteinVariantAnnotation() != null) { QueryResult<ProteinVariantAnnotation> proteinVariantAnnotation = proteinDBAdaptor.getVariantAnnotation( consequenceType.getEnsemblTranscriptId(), consequenceType.getProteinVariantAnnotation().getPosition(), consequenceType.getProteinVariantAnnotation().getReference(), consequenceType.getProteinVariantAnnotation().getAlternate(), new QueryOptions()); if (proteinVariantAnnotation.getNumResults() > 0) { return proteinVariantAnnotation.getResult().get(0); } } return null; }
private ProteinVariantAnnotation getProteinAnnotation(ConsequenceType consequenceType) { if (consequenceType.getProteinVariantAnnotation() != null) { QueryResult<ProteinVariantAnnotation> proteinVariantAnnotation = proteinDBAdaptor.getVariantAnnotation( consequenceType.getEnsemblTranscriptId(), consequenceType.getProteinVariantAnnotation().getPosition(), consequenceType.getProteinVariantAnnotation().getReference(), consequenceType.getProteinVariantAnnotation().getAlternate(), new QueryOptions()); if (proteinVariantAnnotation.getNumResults() > 0) { return proteinVariantAnnotation.getResult().get(0); } } return null; }
.append(protVarAnnotation.getPosition()).append(FIELD_SEP).append(aaChange);
String aaPositionString; if((consequenceType.getProteinVariantAnnotation() == null) || ((aaPosition=consequenceType.getProteinVariantAnnotation().getPosition())==null)) { aaPositionString = "-"; } else {
putNotNull(ct, CT_AA_POSITION_FIELD, proteinVariantAnnotation.getPosition()); putNotNull(ct, CT_AA_REFERENCE_FIELD, proteinVariantAnnotation.getReference()); putNotNull(ct, CT_AA_ALTERNATE_FIELD, proteinVariantAnnotation.getAlternate());
int inPosition = inCT.getProteinVariantAnnotation().getPosition() == null ? 0 : inCT.getProteinVariantAnnotation().getPosition(); int outPosition = outCT.getProteinVariantAnnotation().getPosition() == null ? 0 : outCT.getProteinVariantAnnotation().getPosition(); String inRef = inCT.getProteinVariantAnnotation().getReference() == null ? "" : inCT.getProteinVariantAnnotation().getReference(); String outRef = outCT.getProteinVariantAnnotation().getReference() == null ? "" : outCT.getProteinVariantAnnotation().getReference();
.setUniprotAccession(proteinAnnotation.getUniprotAccession()) .setUniprotName(proteinAnnotation.getUniprotName()) .setPosition(proteinAnnotation.getPosition()) .setReference(proteinAnnotation.getReference()) .setAlternate(proteinAnnotation.getAlternate())