JAL-838 added 'SeqSpace' PID mode, added parameters to findDistances and

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

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 1797296..1f923b1 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.SimilarityParams;
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityScoreModelI;
@@ -228,13 +229,16 @@ public class PCA implements Runnable
   MatrixI computeSimilarity(AlignmentView av)
   {
     MatrixI result = null;
+    // TODO pass choice of params from GUI in constructo
     if (scoreModel instanceof SimilarityScoreModelI)
     {
-      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av);
+      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
+              SimilarityParams.SeqSpace);
     }
     else if (scoreModel instanceof DistanceScoreModelI)
     {
-      result = ((DistanceScoreModelI) scoreModel).findDistances(av);
+      result = ((DistanceScoreModelI) scoreModel).findDistances(av,
+              SimilarityParams.SeqSpace);
       result.reverseRange(false);
     }
     else