JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 58ed008..d053468 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -20,6 +20,9 @@
  */
 package jalview.gui;
 
+import jalview.analysis.scoremodels.PairwiseDistanceModel;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.DistanceModelI;
 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 (DistanceModelI sm : ScoreModels.getInstance().getModels())
     {
-      if (ResidueProperties.getScoreMatrix(sm) != null)
+      if (sm instanceof PairwiseDistanceModel)
       {
+        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.isProtein()))
         {
-          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();
               }
             }