stringBuilder.append(consequenceType.getProteinVariantAnnotation().getReference()) .append("/") .append(consequenceType.getProteinVariantAnnotation().getAlternate()); stringBuilder.append(FIELD_SEPARATOR); if (consequenceType.getProteinVariantAnnotation().getSubstitutionScores() != 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; }
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; }
&& StringUtils.isNotEmpty(protVarAnnotation.getAlternate())) { aaChange = protVarAnnotation.getReference() + "/" + protVarAnnotation.getAlternate();
|| consequenceType.getProteinVariantAnnotation().getAlternate()==null) { aaChange = "-"; } else { aaChange = consequenceType.getProteinVariantAnnotation().getReference() + "/" + consequenceType.getProteinVariantAnnotation().getAlternate();
putNotNull(ct, CT_AA_POSITION_FIELD, proteinVariantAnnotation.getPosition()); putNotNull(ct, CT_AA_REFERENCE_FIELD, proteinVariantAnnotation.getReference()); putNotNull(ct, CT_AA_ALTERNATE_FIELD, proteinVariantAnnotation.getAlternate()); putNotNull(ct, CT_PROTEIN_UNIPROT_ACCESSION, proteinVariantAnnotation.getUniprotAccession()); putNotNull(ct, CT_PROTEIN_UNIPROT_NAME, proteinVariantAnnotation.getUniprotName());
String inRef = inCT.getProteinVariantAnnotation().getReference() == null ? "" : inCT.getProteinVariantAnnotation().getReference(); String outRef = outCT.getProteinVariantAnnotation().getReference() == null ? "" : outCT.getProteinVariantAnnotation().getReference(); String inAlt = inCT.getProteinVariantAnnotation().getAlternate() == null ? "" : inCT.getProteinVariantAnnotation().getAlternate(); String outAlt = outCT.getProteinVariantAnnotation().getAlternate() == null ? "" : outCT.getProteinVariantAnnotation().getAlternate(); System.out.println(inPosition + " vs " + outPosition + " ; " + inRef + " vs " + outRef
.setPosition(proteinAnnotation.getPosition()) .setReference(proteinAnnotation.getReference()) .setAlternate(proteinAnnotation.getAlternate()) .setUniprotVariantId(proteinAnnotation.getUniprotVariantId()) .setFunctionalDescription(proteinAnnotation.getFunctionalDescription());