- System.out.println(mapping[m].getSequence().getName()+" "+sequence[s].getName()+" "
- +((mapping[m].getSequence() == sequence[s])
- +" "+(ap.av.alignment.findIndex(sequence[s]))));
-
- if (mapping[m].getSequence() == sequence[s]
- && ap.av.alignment.findIndex(sequence[s])>-1)