/** Get the simplest string describing the effect (this is mostly used for testcases) */
public String toStringSimple(boolean shortFormat) {
String transcriptId = "";
Transcript tr = getTranscript();
if (tr != null) transcriptId = tr.getId();
String exonId = "";
Exon exon = getExon();
if (exon != null) exonId = exon.getId();
String eff = effect(shortFormat, true, true, false);
if (!eff.isEmpty()) return eff;
if (!exonId.isEmpty()) return exonId;
if (!transcriptId.isEmpty()) return transcriptId;
return "NO EFFECT";
}
public String toString(boolean useSeqOntology, boolean useHgvs) {
// Get data to show
String geneId = "", geneName = "", bioType = "", transcriptId = "", exonId = "", customId = "";
int exonRank = -1;
if (marker != null) {
// Gene Id, name and biotype
Gene gene = getGene();
Transcript tr = getTranscript();
// CDS size info
if (gene != null) {
geneId = gene.getId();
geneName = gene.getGeneName();
bioType = getBiotype();
}
// Update trId
if (tr != null) transcriptId = tr.getId();
// Exon rank information
Exon exon = getExon();
if (exon != null) {
exonId = exon.getId();
exonRank = exon.getRank();
}
// Regulation
if (isRegulation()) bioType = ((Regulation) marker).getCellType();
}
// Add seqChage's ID
if (!variant.getId().isEmpty()) customId += variant.getId();
// Add custom markers
if ((marker != null) && (marker instanceof Custom))
customId += (customId.isEmpty() ? "" : ";") + marker.getId();
// CDS length
int cdsSize = getCdsLength();
String errWarn = error + (error.isEmpty() ? "" : "|") + warning;
String aaChange = "";
if (useHgvs) aaChange = getHgvs();
else aaChange = ((aaRef.length() + aaAlt.length()) > 0 ? aaRef + "/" + aaAlt : "");
return errWarn //
+ "\t"
+ geneId //
+ "\t"
+ geneName //
+ "\t"
+ bioType //
+ "\t"
+ transcriptId //
+ "\t"
+ exonId //
+ "\t"
+ (exonRank >= 0 ? exonRank : "") //
+ "\t"
+ effect(false, false, false, useSeqOntology) //
+ "\t"
+ aaChange //
+ "\t"
+ ((codonsRef.length() + codonsAlt.length()) > 0 ? codonsRef + "/" + codonsAlt : "") //
+ "\t"
+ (codonNum >= 0 ? (codonNum + 1) : "") //
+ "\t"
+ (codonDegeneracy >= 0 ? codonDegeneracy + "" : "") //
+ "\t"
+ (cdsSize >= 0 ? cdsSize : "") //
+ "\t"
+ (codonsAroundOld.length() > 0 ? codonsAroundOld + " / " + codonsAroundNew : "") //
+ "\t"
+ (aasAroundOld.length() > 0 ? aasAroundOld + " / " + aasAroundNew : "") //
+ "\t"
+ customId //
;
}