/** Find (or create) a gene for this transcript */
Gene findOrCreateGene(
String geneName,
String trId,
Chromosome chromo,
int start,
int end,
boolean strandMinus,
boolean isCoding) {
Marker tr = new Marker(chromo, start, end, strandMinus, trId);
List<Gene> genes = genesByName.get(geneName);
int geneIndex = 0;
if (genes != null) {
for (Gene gene : genes) {
if (gene.intersects(tr)) {
// Do we need to update gene length?
if (start < gene.getStart()) gene.setStart(start);
if (gene.getEnd() < end) gene.setEnd(end);
return gene;
}
}
geneIndex = genes.size() + 1;
}
// Need to create a new gene
String geneId = geneName + (geneIndex > 0 ? "." + geneIndex : "");
Gene gene =
new Gene(chromo, start, end, strandMinus, geneId, geneName, BioType.coding(isCoding));
genesByName.add(geneName, gene);
add(gene);
return gene;
}