Merge branch 'develop' into features/JAL-2393customMatrices

[jalview.git] / src / jalview / appletgui / PCAPanel.java

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index efb204e..2d77c59 100644 (file)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -105,8 +105,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
 
     ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
             !nucleotide);
-    pcaModel = new PCAModel(seqstrings, seqs, nucleotide,
- scoreModel,
+    pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
             SimilarityParams.SeqSpace);
 
     rc = new RotatableCanvas(viewport);
@@ -217,6 +216,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (!pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(true);
+        ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+                false);
+        pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
     }
@@ -225,6 +227,9 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
       if (pcaModel.isNucleotide())
       {
         pcaModel.setNucleotide(false);
+        ScoreModelI scoreModel = ScoreModels.getInstance().getDefaultModel(
+                true);
+        pcaModel.setScoreModel(scoreModel);
         new Thread(this).start();
       }
     }