X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=6638718281828c80a9164d0008fa1428077b3145;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=c0d57a6bdb93d3317566bf484bf9e3ac77be1974;hpb=586ade46bdcd05ff028a1cff82c3c527326d28ec;p=jalview.git

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index c0d57a6..6638718 100644
--- 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;
@@ -123,8 +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));
@@ -141,6 +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
@@ -289,7 +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;
     }
@@ -418,9 +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);
@@ -609,6 +615,12 @@ public class PCAPanel extends GPCAPanel
   }
   
   @Override
+  public void addProgressBar(long id, String message)
+  {
+    progressBar.addProgressBar(id, message);
+  }
+
+  @Override
   public void removeProgressBar(long id)
   {
     progressBar.removeProgressBar(id);
@@ -619,7 +631,8 @@ public class PCAPanel extends GPCAPanel
           final IProgressIndicatorHandler handler)
   {
     progressBar.registerHandler(id, handler);
-    // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
+    // if (progressBarHandlers == null ||
+    // !progressBars.contains(Long.valueOf(id)))
     // {
     // throw new
     // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));