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 e20b7cb..d053468 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -46,8 +48,9 @@ import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 
 /**
  * DOCUMENT ME!
@@ -81,6 +84,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public PCAPanel(AlignmentPanel ap)
   {
+    super();
     this.av = ap.av;
     this.ap = ap;
 
@@ -114,13 +118,23 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
     if (!sameLength)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
+      JvOptionPane.showMessageDialog(Desktop.desktop,
               MessageManager.getString("label.pca_sequences_not_aligned"),
               MessageManager.getString("label.sequences_not_aligned"),
-              JOptionPane.WARNING_MESSAGE);
+              JvOptionPane.WARNING_MESSAGE);
 
       return;
     }
+
+    addInternalFrameListener(new InternalFrameAdapter()
+    {
+      @Override
+      public void internalFrameClosed(InternalFrameEvent e)
+      {
+        close_actionPerformed();
+      }
+    });
+
     pcaModel = new PCAModel(seqstrings, seqs, nucleotide);
     PaintRefresher.Register(this, av.getSequenceSetId());
 
@@ -130,34 +144,41 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     worker.start();
   }
 
+  /**
+   * Ensure references to potentially very large objects (the PCA matrices) are
+   * nulled when the frame is closed
+   */
+  protected void close_actionPerformed()
+  {
+    pcaModel = null;
+  }
+
   @Override
   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();
               }
             }
@@ -172,7 +193,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   public void bgcolour_actionPerformed(ActionEvent e)
   {
     Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_backgroud_colour"),
+            MessageManager.getString("label.select_background_colour"),
             rc.bgColour);
 
     if (col != null)