/**
* Get the overlap between two HmmerResult objects
*
* @param other
* @return 0 if no overlap, otherwise the length of the overlap
*/
public int getOverlapLength(HmmerResult other) {
int overlap = 0;
for (HmmerDomain d1 : getDomains()) {
for (HmmerDomain d2 : other.getDomains()) {
overlap += getOverlap(d1, d2);
}
}
return overlap;
}
@Override
public int compareTo(HmmerResult o) {
// sort by the start position of the first domain
if (emptyDomains(this) && emptyDomains(o)) {
return 0;
}
if (!emptyDomains(this) && emptyDomains(o)) return -1;
if (emptyDomains(this) && (!emptyDomains(o))) return 1;
// ok when we are here, both domains are not empty
HmmerDomain me = this.getDomains().first();
HmmerDomain other = o.getDomains().first();
// System.out.println(" domains: " + me.getHmmAcc() + " " + other.getHmmAcc()+ " " +
// me.getSqFrom().compareTo(other.getSqFrom()));
return (me.getSqFrom().compareTo(other.getSqFrom()));
}
private boolean emptyDomains(HmmerResult o) {
if (o.getDomains() == null || o.getDomains().size() == 0) return true;
return false;
}