int length = seq1.length();
// match gap-residue, match gap-gap: 9/10 identical
+ // TODO should gap-gap be included in a PID score? JAL-791
assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
0.001f);
// overloaded version of the method signature above:
assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
// don't match gap-residue, match gap-gap: 7/10 identical
+ // TODO should gap-gap be included in a PID score?
assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
0.001f);
}