{
lastmatch = true;
// extend mapping interval.
- if (lp1 + 1 != alignpos)
+ if (lp1 + 1 != alignpos || lp2+1 !=pdbpos)
{
as1.add(Integer.valueOf(alignpos));
- lp1 = alignpos;
- }
-
- if (lp2 + 1 != pdbpos)
- {
as2.add(Integer.valueOf(pdbpos));
- lp2 = pdbpos;
}
+ lp1 = alignpos;
+ lp2 = pdbpos;
}
else
{