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 5ad4901..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 2.9.0b1)
- * 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.
  * 
@@ -20,13 +20,16 @@
  */
 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;
 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;
@@ -45,8 +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!
@@ -80,6 +84,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public PCAPanel(AlignmentPanel ap)
   {
+    super();
     this.av = ap.av;
     this.ap = ap;
 
@@ -113,13 +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());
 
@@ -129,34 +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())
+        jm.setText(MessageManager.getStringOrReturn("label.score_model_",
+                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();
               }
             }
@@ -167,10 +189,11 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
+  @Override
   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)
@@ -183,6 +206,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     long progId = System.currentTimeMillis();
@@ -288,6 +312,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void xCombobox_actionPerformed(ActionEvent e)
   {
     doDimensionChange();
@@ -299,6 +324,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void yCombobox_actionPerformed(ActionEvent e)
   {
     doDimensionChange();
@@ -310,11 +336,13 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   protected void zCombobox_actionPerformed(ActionEvent e)
   {
     doDimensionChange();
   }
 
+  @Override
   public void outputValues_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -330,17 +358,20 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
+  @Override
   public void showLabels_actionPerformed(ActionEvent e)
   {
     rc.showLabels(showLabels.getState());
   }
 
+  @Override
   public void print_actionPerformed(ActionEvent e)
   {
     PCAPrinter printer = new PCAPrinter();
     printer.start();
   }
 
+  @Override
   public void originalSeqData_actionPerformed(ActionEvent e)
   {
     // this was cut'n'pasted from the equivalent TreePanel method - we should
@@ -374,8 +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)
       {
@@ -414,6 +445,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
 
   class PCAPrinter extends Thread implements Printable
   {
+    @Override
     public void run()
     {
       PrinterJob printJob = PrinterJob.getPrinterJob();
@@ -433,6 +465,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       }
     }
 
+    @Override
     public int print(Graphics pg, PageFormat pf, int pi)
             throws PrinterException
     {
@@ -462,6 +495,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void eps_actionPerformed(ActionEvent e)
   {
     makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
@@ -473,6 +507,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void png_actionPerformed(ActionEvent e)
   {
     makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
@@ -489,19 +524,19 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     {
       im = new jalview.util.ImageMaker(this,
               jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from PCA",
-              width, height, null, null);
+              width, height, null, null, null, 0, false);
     }
     else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
       im = new jalview.util.ImageMaker(this,
               jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from PCA",
-              width, height, null, this.getTitle());
+              width, height, null, this.getTitle(), null, 0, false);
     }
     else
     {
       im = new jalview.util.ImageMaker(this,
               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
-              width, height, null, this.getTitle());
+              width, height, null, this.getTitle(), null, 0, false);
 
     }
 
@@ -517,6 +552,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     }
   }
 
+  @Override
   public void viewMenu_menuSelected()
   {
     buildAssociatedViewMenu();
@@ -552,6 +588,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
       buttonGroup.add(item);
       item.addActionListener(new ActionListener()
       {
+        @Override
         public void actionPerformed(ActionEvent evt)
         {
           rc.applyToAllViews = false;
@@ -571,6 +608,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     itemf.setSelected(rc.applyToAllViews);
     itemf.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         rc.applyToAllViews = itemf.isSelected();
@@ -587,6 +625,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * jalview.jbgui.GPCAPanel#outputPoints_actionPerformed(java.awt.event.ActionEvent
    * )
    */
+  @Override
   protected void outputPoints_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
@@ -612,6 +651,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    * jalview.jbgui.GPCAPanel#outputProjPoints_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void outputProjPoints_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();