X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=f96d4643d1135a8947f7e6dff1cd5cf8cc0186d5;hb=ff8c06845590fd9fd423aa59809dcce9610ab295;hp=58ed0080d5ebd87d0f587b04da2b19aee1c73ac8;hpb=ca0a70b02a67f842a195319414d241ffa336656b;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 58ed008..f96d464 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -20,6 +20,9 @@
  */
 package jalview.gui;
 
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -27,7 +30,6 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.PCAModel;
@@ -155,30 +157,28 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   protected void scoreMatrix_menuSelected()
   {
     scoreMatrixMenu.removeAll();
-    for (final String sm : ResidueProperties.scoreMatrices.keySet())
+    for (ScoreModelI sm : ScoreModels.getInstance().getModels())
     {
-      if (ResidueProperties.getScoreMatrix(sm) != null)
+      if (sm instanceof ScoreMatrix)
       {
+        final String name = sm.getName();
         // create an entry for this score matrix for use in PCA
         JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
         jm.setText(MessageManager.getStringOrReturn("label.score_model_",
-                sm));
-        jm.setSelected(pcaModel.getScore_matrix().equals(sm));
-        if ((ResidueProperties.scoreMatrices.get(sm).isDNA() && ResidueProperties.scoreMatrices
-                .get(sm).isProtein())
-                || pcaModel.isNucleotide() == ResidueProperties.scoreMatrices
-                        .get(sm).isDNA())
+                name));
+        jm.setSelected(pcaModel.getScore_matrix().equals(name));
+        if ((!pcaModel.isNucleotide() && !sm.isDNA())
+                || (pcaModel.isNucleotide() && sm.isDNA()))
         {
-          final PCAPanel us = this;
           jm.addActionListener(new ActionListener()
           {
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              if (!pcaModel.getScore_matrix().equals(sm))
+              if (!pcaModel.getScore_matrix().equals(name))
               {
-                pcaModel.setScore_matrix(sm);
-                Thread worker = new Thread(us);
+                pcaModel.setScore_matrix(name);
+                Thread worker = new Thread(PCAPanel.this);
                 worker.start();
               }
             }