Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 0a23517..000dd76 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -24,7 +24,7 @@ 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;
@@ -36,6 +36,7 @@ import jalview.jbgui.GPCAPanel;
 import jalview.math.RotatableMatrix.Axis;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.PCAModel;
 
@@ -122,8 +123,8 @@ 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 +132,6 @@ public class PCAPanel extends GPCAPanel
 
     addKeyListener(getRotatableCanvas());
     validate();
-
-    this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
   }
 
   /**
@@ -142,6 +141,12 @@ 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
@@ -202,10 +207,8 @@ public class PCAPanel extends GPCAPanel
     repaint();
     if (getParent() == null)
     {
-      Desktop.addInternalFrame(this,
-              MessageManager.formatMessage("label.calc_title", "PCA",
-                      getPcaModel().getScoreModelName()),
-              475, 450);
+      addToDesktop(this, getPcaModel().getScoreModelName());
+      this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     }
     working = false;
   }
@@ -292,7 +295,7 @@ 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 +424,9 @@ 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);
@@ -573,11 +576,11 @@ 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;
@@ -610,19 +613,26 @@ public class PCAPanel extends GPCAPanel
     // // setMenusForViewport();
     // validate();
   }
+  
+  @Override
+  public void removeProgressBar(long id)
+  {
+    progressBar.removeProgressBar(id);
+  }
 
   @Override
   public void registerHandler(final long id,
           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(
@@ -763,4 +773,12 @@ public class PCAPanel extends GPCAPanel
     getRotatableCanvas().ap = panel;
     PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId());
   }
+
+  public static void addToDesktop(PCAPanel panel, String modelName)
+  {
+    Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
+    Desktop.addInternalFrame(panel, MessageManager.formatMessage(
+            "label.calc_title", "PCA", modelName), dim.width,
+            dim.height);
+  }
 }