Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 47add28..58ed008 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SeqCigar;
@@ -45,8 +46,9 @@ 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!
@@ -80,6 +82,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public PCAPanel(AlignmentPanel ap)
   {
+    super();
     this.av = ap.av;
     this.ap = ap;
 
@@ -113,13 +116,23 @@ 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());
 
@@ -129,6 +142,15 @@ 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()
   {
@@ -139,8 +161,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       {
         // create an entry for this score matrix for use in PCA
         JCheckBoxMenuItem jm = new JCheckBoxMenuItem();
-        jm.setText(MessageManager
-                .getStringOrReturn("label.score_model", sm));
+        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())
@@ -171,7 +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)
@@ -383,8 +405,8 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     {
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
-      Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
-      Alignment dataset = (av != null && av.getAlignment() != null) ? av
+      AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
               .getAlignment().getDataset() : null;
       if (dataset != null)
       {