/**
* Valid values for <tt>s1</tt> and <tt>s2</tt> are [0, ordering.size()-1]
*
* @param s1 The serial number of the sequence (<tt>s1</tt>) whose coordinate we wish to map
* against that of (<tt>s2</tt>)
* @param s2 The other sequence
* @param ugidx The ungapped coordinate of (<tt>s1</tt>)
* @return The ungapped coordinate of (<tt>s2</tt>) corresponding to <tt>ugidx</tt>
* @see GappedAlignmentString
*/
public int mapUngapped(int s1, int s2, int ugidx) throws IndexOutOfBoundsException {
if ((s1 < 0 || s1 >= ordering.size()) || (s2 < 0 || s2 >= ordering.size()))
throw new IndexOutOfBoundsException("Valid values for s1 and s2 are [0, ordering.size()-1]");
GappedAlignmentString str1 = gappedAlignments.get(ordering.get(s1));
GappedAlignmentString str2 = gappedAlignments.get(ordering.get(s2));
int gidx = str1.ungappedToGapped(ugidx);
int ugidx2 = str2.gappedToUngapped(gidx);
if (str2.isGap(gidx)) {
return -1;
}
return ugidx2;
}