public String toString() {
StringBuilder s = new StringBuilder();
s.append("[");
for (GenomeLoc e : this) {
s.append(" ");
s.append(e.toString());
}
s.append("]");
return s.toString();
}
/**
* add a genomeLoc to the collection, simply inserting in order into the set
*
* @param e the GenomeLoc to add
* @return true
*/
public boolean add(GenomeLoc e) {
// assuming that the intervals coming arrive in order saves us a fair amount of time (and it's
// most likely true)
if (mArray.size() > 0 && e.isPast(mArray.get(mArray.size() - 1))) {
mArray.add(e);
return true;
} else {
int loc = Collections.binarySearch(mArray, e);
if (loc >= 0) {
throw new ReviewedStingException(
"Genome Loc Sorted Set already contains the GenomicLoc " + e.toString());
} else {
mArray.add((loc + 1) * -1, e);
return true;
}
}
}