*/
package jalview.analysis;
+import jalview.analysis.scoremodels.PIDModel;
import jalview.api.analysis.DistanceScoreModelI;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
{
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)
{