@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 int getOverlap(HmmerDomain one, HmmerDomain other) {
int xs = one.getSqFrom();
int ys = one.getSqTo();
int as = other.getSqFrom();
int bs = other.getSqTo();
int overlap = 0;
// 1:
if (((xs < as) && (as < ys)) || ((xs < bs) && (bs <= ys)) || (as < xs && ys < bs)) {
// 2:
if (xs < as) {
if (ys < bs) overlap = ys - as;
else overlap = bs - as;
} else {
if (ys < bs) overlap = ys - xs;
else overlap = bs - xs;
}
}
return overlap;
}