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);
}
}
// print formatted info in no particular order
public String getInfoString() {
String s = "<HTML>";
// gene info
if (geneInfoSet) {
s += "<B>";
if (gene.getGeneType().equals(Gene.geneType.ENTREZ)) {
s += "Entrez Gene";
} else if (gene.getGeneType().equals(Gene.geneType.ENSEMBL)) {
s += "Ensembl Gene";
}
s += "</B><BR>";
String name = gene.getName();
if (name != null) s += "Name: " + name + "<BR>";
String description = gene.getDescription();
if (description != null) s += "Description: " + description + "<BR>";
String chromosome = gene.getChromosome();
if (chromosome != null) s += "Chromosome: " + chromosome + "<BR>";
s += "Start: " + gene.getStart() + "<BR>";
s += "End: " + gene.getEnd() + "<BR>";
s += "<BR>";
}
Iterator it = attributes.keySet().iterator();
while (it.hasNext()) {
String node = (String) it.next();
if (node.equals("Graphics")) continue;
s += "<B>" + node + "</B><BR>";
Iterator currentIt = attributes.get(node).keySet().iterator();
while (currentIt.hasNext()) {
String key = (String) currentIt.next();
s += key + ": " + attributes.get(node).get(key) + "<BR>";
}
s += "<BR>";
}
s += "</HTML>";
return s;
}