- if (sm instanceof DistanceScoreModelI)
- {
- distances = ((DistanceScoreModelI) sm).findDistances(seqData,
- scoreOptions);
- }
- else if (sm instanceof SimilarityScoreModelI)
- {
- /*
- * compute similarity and invert it to give a distance measure
- * reverseRange(true) converts maximum similarity to zero distance
- */
- MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
- seqData, scoreOptions);
- result.reverseRange(true);
- distances = result;
- }