/**
* Adds a GenomeLoc to the collection, merging it if it overlaps another region. If it's not
* overlapping then we add it in sorted order.
*
* @param e the GenomeLoc to add to the collection
* @return true, if the GenomeLoc could be added to the collection
*/
public boolean addRegion(GenomeLoc e) {
if (e == null) {
return false;
}
// have we added it to the collection?
boolean haveAdded = false;
/**
* check if the specified element overlaps any current locations, if so we should merge the two.
*/
for (GenomeLoc g : mArray) {
if (g.contiguousP(e)) {
GenomeLoc c = g.merge(e);
mArray.set(mArray.indexOf(g), c);
haveAdded = true;
} else if ((g.getContigIndex() == e.getContigIndex())
&& (e.getStart() < g.getStart())
&& !haveAdded) {
mArray.add(mArray.indexOf(g), e);
return true;
} else if (haveAdded
&& ((e.getContigIndex() > e.getContigIndex())
|| (g.getContigIndex() == e.getContigIndex() && e.getStart() > g.getStart()))) {
return true;
}
}
/**
* we're at the end and we haven't found locations that should fall after it, so we'll put it at
* the end
*/
if (!haveAdded) {
mArray.add(e);
}
return true;
}
