JAL-2397 scale PCA by PID to alignment width to match SeqSpace

[jalview.git] / src / jalview / analysis / PCA.java

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index b481e89..5d2e7e7 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PIDModel;
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -235,6 +236,14 @@ public class PCA implements Runnable
     {
       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)
     {