+ /**
+ * 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.
+ *
+ * @param av
+ * @return
+ */
+ MatrixI computeSimilarity(AlignmentView av)
+ {
+ MatrixI result = null;
+ if (scoreModel instanceof SimilarityScoreModelI)
+ {
+ result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
+ similarityParams);
+ if (scoreModel instanceof PIDModel)
+ {
+ /*
+ * scale % identities to width of alignment for backwards
+ * compatibility with Jalview 2.10.1 SeqSpace PCA calculation
+ */
+ result.multiply(av.getWidth() / 100d);
+ }
+ }
+ 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);
+ }
+ else
+ {
+ System.err
+ .println("Unexpected type of score model, cannot calculate similarity");
+ }
+
+ return result;
+ }