return ""; StringBuilder builder = new StringBuilder(); if (strand.equals(Strand.NEGATIVE)) {
@Override public String toString() { String circ = (isCircular()) ? " - circular" : ""; String between = (isBetweenCompounds()) ? "^" : ".."; return format("%d%s%d(%s%s)", getStart().getPosition(), between, getEnd().getPosition(), getStrand().getStringRepresentation(), circ); }
@Override public String toString() { String circ = (isCircular()) ? " - circular" : ""; String between = (isBetweenCompounds()) ? "^" : ".."; return format("%d%s%d(%s%s)", getStart().getPosition(), between, getEnd().getPosition(), getStrand().getStringRepresentation(), circ); }
String line = scaffold + "\t" + geneSequence.getSource() + "_" + "UNIPROT\tmatch\t" + dnaBeginIndex + "\t" + dnaEndIndex + "\t.\t" + transcriptSequence.getStrand().getStringRepresentation() + "\t.\t"; if (gff3Index == 0) { FeaturesKeyWordInterface featureKeyWords = proteinSequence.getFeaturesKeyWord();
return ""; StringBuilder builder = new StringBuilder(); if (strand.equals(Strand.NEGATIVE)) {
gff3line = gff3line + score + "\t"; gff3line = gff3line + geneSequence.getStrand().getStringRepresentation() + "\t"; gff3line = gff3line + ".\t"; gff3line = gff3line + "ID=" + geneSequence.getAccession().getID() + ";Name=" + geneSequence.getAccession().getID(); gff3line = gff3line + score + "\t"; gff3line = gff3line + transcriptSequence.getStrand().getStringRepresentation() + "\t"; gff3line = gff3line + ".\t"; String id = geneSequence.getAccession().getID() + "." + transcriptIndex; gff3line = gff3line + score + "\t"; gff3line = gff3line + cdsSequence.getStrand().getStringRepresentation() + "\t"; gff3line = gff3line + cdsSequence.getPhase() + "\t"; gff3line = gff3line + "ID=" + cdsSequence.getAccession().getID() + ";Parent=" + transcriptParentName;