* Computes a pairwise similarity matrix for the given sequence regions using
* the configured score model. If the score model is a similarity model, then
* it computes the result directly. If it is a distance model, then use it to
- * compute pairwise distances, and convert these to similarity scores by
- * substracting from the maximum value.
+ * compute pairwise distances, and convert these to similarity scores.
*
* @param av
* @return
}
else if (scoreModel instanceof DistanceScoreModelI)
{
+ /*
+ * find distances and convert to similarity scores
+ * reverseRange(false) preserves but reverses the min-max range
+ */
result = ((DistanceScoreModelI) scoreModel).findDistances(av,
similarityParams);
result.reverseRange(false);