X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;fp=src%2Fjalview%2Fanalysis%2FPCA.java;h=1f923b1822fa54848904df05ad90c24109fee000;hp=179729634a45306dd909ec7aacac2594deb057fd;hb=8717834368bd00d8adfa47ee099288acd34363ef;hpb=70af62ad365829d2fc430db10336cf13c4d4ce1a

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 1797296..1f923b1 100755
--- 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