Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 0a23517..576f3b2 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -20,11 +20,28 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -32,6 +49,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ImageExporter.ImageWriterI;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.io.exceptions.ImageOutputException;
 import jalview.jbgui.GPCAPanel;
 import jalview.math.RotatableMatrix.Axis;
 import jalview.util.ImageMaker;
@@ -39,23 +57,6 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.PCAModel;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.print.PageFormat;
-import java.awt.print.Printable;
-import java.awt.print.PrinterException;
-import java.awt.print.PrinterJob;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
 /**
  * The panel holding the Principal Component Analysis 3-D visualisation
  */
@@ -92,6 +93,7 @@ public class PCAPanel extends GPCAPanel
           SimilarityParamsI params)
   {
     super();
+    this.setFrameIcon(null);
     this.av = alignPanel.av;
     this.ap = alignPanel;
     boolean nucleotide = av.getAlignment().isNucleotide();
@@ -122,8 +124,8 @@ public class PCAPanel extends GPCAPanel
 
     ScoreModelI scoreModel = ScoreModels.getInstance()
             .getScoreModel(modelName, ap);
-    setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
-            params));
+    setPcaModel(
+            new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
     PaintRefresher.Register(this, av.getSequenceSetId());
 
     setRotatableCanvas(new RotatableCanvas(alignPanel));
@@ -131,8 +133,6 @@ public class PCAPanel extends GPCAPanel
 
     addKeyListener(getRotatableCanvas());
     validate();
-
-    this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
   }
 
   /**
@@ -142,6 +142,12 @@ public class PCAPanel extends GPCAPanel
   protected void close_actionPerformed()
   {
     setPcaModel(null);
+    if (this.rc != null)
+    {
+      this.rc.sequencePoints = null;
+      this.rc.setAxisEndPoints(null);
+      this.rc = null;
+    }
   }
 
   @Override
@@ -206,6 +212,7 @@ public class PCAPanel extends GPCAPanel
               MessageManager.formatMessage("label.calc_title", "PCA",
                       getPcaModel().getScoreModelName()),
               475, 450);
+      this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
     working = false;
   }
@@ -292,7 +299,7 @@ public class PCAPanel extends GPCAPanel
     // JAL-2647 disabled after load from project (until save to project done)
     if (getPcaModel().getInputData() == null)
     {
-      Cache.log.info(
+      Console.info(
               "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -421,9 +428,9 @@ public class PCAPanel extends GPCAPanel
       @Override
       public void exportImage(Graphics g) throws Exception
       {
-       RotatableCanvas canvas = getRotatableCanvas();
-       canvas.drawBackground(g);
-       canvas.drawScene(g);
+        RotatableCanvas canvas = getRotatableCanvas();
+        canvas.drawBackground(g);
+        canvas.drawScene(g);
         if (canvas.drawAxes)
         {
           canvas.drawAxes(g);
@@ -432,7 +439,14 @@ public class PCAPanel extends GPCAPanel
     };
     String pca = MessageManager.getString("label.pca");
     ImageExporter exporter = new ImageExporter(writer, null, type, pca);
-    exporter.doExport(null, this, width, height, pca);
+    try
+    {
+      exporter.doExport(null, this, width, height, pca);
+    } catch (ImageOutputException ioex)
+    {
+      Console.error("Unexpected error whilst writing " + type.toString(),
+              ioex);
+    }
   }
 
   @Override
@@ -573,11 +587,11 @@ public class PCAPanel extends GPCAPanel
     // }
     //
     // JPanel progressPanel;
-    // Long lId = new Long(id);
+    // Long lId = Long.valueOf(id);
     // GridLayout layout = (GridLayout) statusPanel.getLayout();
     // if (progressBars.get(lId) != null)
     // {
-    // progressPanel = (JPanel) progressBars.get(new Long(id));
+    // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
     // statusPanel.remove(progressPanel);
     // progressBars.remove(lId);
     // progressPanel = null;
@@ -616,13 +630,14 @@ public class PCAPanel extends GPCAPanel
           final IProgressIndicatorHandler handler)
   {
     progressBar.registerHandler(id, handler);
-    // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+    // if (progressBarHandlers == null ||
+    // !progressBars.contains(Long.valueOf(id)))
     // {
     // throw new
     // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
     // }
-    // progressBarHandlers.put(new Long(id), handler);
-    // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    // progressBarHandlers.put(Long.valueOf(id), handler);
+    // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
     // if (handler.canCancel())
     // {
     // JButton cancel = new JButton(