public void setEntrezGeneInfo(Element node) {
// check to make sure ids match
NodeList idList = node.getElementsByTagName("Id");
if (!idList.item(0).getTextContent().equals(this.getAttribute("Xref", "ID"))) return;
gene = new Gene(Gene.geneType.ENTREZ, this.getAttribute("Xref", "ID"));
NodeList items = node.getElementsByTagName("Item");
for (int i = 0; i < items.getLength(); i++) {
Node n = items.item(i);
String name = ((Element) n).getAttribute("Name");
if (name.equals("GenomicInfo")) {
NodeList subItems = ((Element) n).getElementsByTagName("Item");
for (int j = 0; j < subItems.getLength(); j++) {
Node m = subItems.item(j);
String subName = ((Element) m).getAttribute("Name");
if (subName.equals("ChrStart")) {
gene.setStart(m.getTextContent());
} else if (subName.equals("ChrStop")) {
gene.setEnd(m.getTextContent());
}
}
} else if (name.equals("Chromosome")) {
gene.setChromosome(n.getTextContent());
} else if (name.equals("Name")) {
gene.setName(n.getTextContent());
} else if (name.equals("Description")) {
gene.setDescription(n.getTextContent());
}
}
geneInfoSet = true;
}
public void setEnsemblGeneInfo(String id, String chrom, String start, String end) {
gene = new Gene(Gene.geneType.ENSEMBL, id);
gene.setChromosome(chrom);
gene.setStart(start);
gene.setEnd(end);
geneInfoSet = true;
}
private void addGene(
Map<String, Gene> map, String gene, String chr, long start, long end, long len) {
if (map.containsKey(gene)) {
Gene geneObj = map.get(gene);
// move start
if (geneObj.getStart() > start) {
geneObj.setStart(start);
}
// move end
if (geneObj.getEnd() < end) {
geneObj.setEnd(end);
}
// update length
geneObj.setLen(geneObj.getLen() + len);
} else {
Gene geneObj = new Gene(gene, chr, start, end, len);
map.put(gene, geneObj);
}
}