/**
* 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);
}
