+
+ MatrixI result = findSimilarities(seqs, options);
+
+ result.multiply(seqData.getWidth() / 100d);
+
+ return result;
+ }
+
+ /**
+ * A distance score is computed in the usual way (by reversing the range of
+ * the similarity score results), and then rescaled to percentage values
+ * (reversing the rescaling to count values done in findSimilarities). This
+ * method is thread-safe.
+ */
+ @Override
+ public MatrixI findDistances(AlignmentView seqData,
+ SimilarityParamsI options)
+ {
+ MatrixI result = super.findDistances(seqData, options);
+
+ if (seqData.getWidth() != 0)
+ {
+ result.multiply(100d / seqData.getWidth());
+ }
+
+ return result;