- int seqDistance = SetUtils.countDisjunction(sfap.get(seqs[i]),
- sfap.get(seqs[j]));
- distances[i][j] += seqDistance;
+ SeqCigar sc1 = seqs[i];
+ SeqCigar sc2 = seqs[j];
+ Set<String> set1 = sfap.get(sc1);
+ Set<String> set2 = sfap.get(sc2);
+ boolean gap1 = set1 == null;
+ boolean gap2 = set2 == null;
+
+ /*
+ * gap-gap always scores zero
+ * residue-residue is always scored
+ * include gap-residue score if params say to do so
+ */
+ if ((!gap1 && !gap2) || params.includeGaps())
+ {
+ int seqDistance = SetUtils.countDisjunction(set1, set2);
+ distances[i][j] += seqDistance;
+ }