/** * Updates the data list by adding oncotator data by using the given oncotator record. * * @param data data representing a single line in a MAF * @param oncotatorRecord record containing the oncotator data */ public void updateOncotatorData(List<String> data, OncotatorRecord oncotatorRecord) { if (oncotatorRecord == null) { oncotatorRecord = new OncotatorRecord("NA"); } String cosmicOverlapping = oncotatorRecord.getCosmicOverlappingMutations(); String dbSnpRs = oncotatorRecord.getDbSnpRs(); String dbSnpValStatus = oncotatorRecord.getDbSnpValStatus(); String proteinChange = oncotatorRecord.getBestCanonicalTranscript().getProteinChange(); String variantClassification = oncotatorRecord.getBestCanonicalTranscript().getVariantClassification(); String geneSymbol = oncotatorRecord.getBestCanonicalTranscript().getGene(); String refseqMrnaId = oncotatorRecord.getBestCanonicalTranscript().getRefseqMrnaId(); String refseqProtId = oncotatorRecord.getBestCanonicalTranscript().getRefseqProtId(); String uniprotName = oncotatorRecord.getBestCanonicalTranscript().getUniprotName(); String uniprotAccession = oncotatorRecord.getBestCanonicalTranscript().getUniprotAccession(); String codonChange = oncotatorRecord.getBestCanonicalTranscript().getCodonChange(); String transcriptChange = oncotatorRecord.getBestCanonicalTranscript().getTranscriptChange(); String exonAffected = (oncotatorRecord.getBestCanonicalTranscript().getExonAffected() == null) ? null : oncotatorRecord.getBestCanonicalTranscript().getExonAffected().toString(); String proteinChangeBe = oncotatorRecord.getBestEffectTranscript().getProteinChange(); String variantClassificationBe = oncotatorRecord.getBestEffectTranscript().getVariantClassification(); String geneSymbolBe = oncotatorRecord.getBestEffectTranscript().getGene(); String refseqMrnaIdBe = oncotatorRecord.getBestEffectTranscript().getRefseqMrnaId(); String refseqProtIdBe = oncotatorRecord.getBestEffectTranscript().getRefseqProtId(); String uniprotNameBe = oncotatorRecord.getBestEffectTranscript().getUniprotName(); String uniprotAccessionBe = oncotatorRecord.getBestEffectTranscript().getUniprotAccession(); String codonChangeBe = oncotatorRecord.getBestEffectTranscript().getCodonChange(); String transcriptChangeBe = oncotatorRecord.getBestEffectTranscript().getTranscriptChange(); String exonAffectedBe = (oncotatorRecord.getBestEffectTranscript().getExonAffected() == null) ? null : oncotatorRecord.getBestEffectTranscript().getExonAffected().toString(); // create a new maf util for the new header line to get new oncotator indices String newHeaderLine = this.newHeaderLineAsString(); MafUtil mafUtil = new MafUtil(newHeaderLine); // update oncotator values data.set(mafUtil.getOncoCosmicOverlappingIndex(), cosmicOverlapping); data.set(mafUtil.getOncoDbSnpRsIndex(), dbSnpRs); data.set(mafUtil.getOncoDbSnpValStatusIndex(), dbSnpValStatus); data.set(mafUtil.getOncoProteinChangeIndex(), proteinChange); data.set(mafUtil.getOncoVariantClassificationIndex(), variantClassification); data.set(mafUtil.getOncoGeneSymbolIndex(), geneSymbol); data.set(mafUtil.getOncoRefseqMrnaIdIndex(), refseqMrnaId); data.set(mafUtil.getOncoRefseqProtIdIndex(), refseqProtId); data.set(mafUtil.getOncoUniprotNameIndex(), uniprotName); data.set(mafUtil.getOncoUniprotAccessionIndex(), uniprotAccession); data.set(mafUtil.getOncoCodonChangeIndex(), codonChange); data.set(mafUtil.getOncoTranscriptChangeIndex(), transcriptChange); data.set(mafUtil.getOncoExonAffectedIndex(), exonAffected); data.set(mafUtil.getOncoProteinChangeBeIndex(), proteinChangeBe); data.set(mafUtil.getOncoVariantClassificationBeIndex(), variantClassificationBe); data.set(mafUtil.getOncoGeneSymbolBeIndex(), geneSymbolBe); data.set(mafUtil.getOncoRefseqMrnaIdBeIndex(), refseqMrnaIdBe); data.set(mafUtil.getOncoRefseqProtIdBeIndex(), refseqProtIdBe); data.set(mafUtil.getOncoUniprotNameBeIndex(), uniprotNameBe); data.set(mafUtil.getOncoUniprotAccessionBeIndex(), uniprotAccessionBe); data.set(mafUtil.getOncoCodonChangeBeIndex(), codonChangeBe); data.set(mafUtil.getOncoTranscriptChangeBeIndex(), transcriptChangeBe); data.set(mafUtil.getOncoExonAffectedBeIndex(), exonAffectedBe); }