tidy imports

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

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index f974f0a..014f076 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
@@ -118,8 +119,8 @@ public class PaintRefresher
       if (validateSequences && comp instanceof AlignmentPanel
               && source instanceof AlignmentPanel)
       {
-        validateSequences(((AlignmentPanel) source).av.alignment,
-                ((AlignmentPanel) comp).av.alignment);
+        validateSequences(((AlignmentPanel) source).av.getAlignment(),
+                ((AlignmentPanel) comp).av.getAlignment());
       }
 
       if (comp instanceof AlignmentPanel && alignmentChanged)
@@ -179,7 +180,20 @@ public class PaintRefresher
       {
         if (i < comp.getHeight())
         {
-          comp.getSequences().insertElementAt(a1[i], i);
+          // TODO: the following does not trigger any recalculation of
+          // height/etc, or maintain the dataset
+          if (comp.getDataset() != source.getDataset())
+          {
+            // raise an implementation warning here - not sure if this situation
+            // will ever occur
+            System.err
+                    .println("IMPLEMENTATION PROBLEM: DATASET out of sync due to an insert whilst calling PaintRefresher.validateSequences(AlignmentI, ALignmentI)");
+          }
+          List<SequenceI> alsq;
+          synchronized (alsq = comp.getSequences())
+          {
+            alsq.add(i, a1[i]);
+          }
         }
         else
         {
@@ -224,14 +238,24 @@ public class PaintRefresher
 
   static AlignmentPanel[] getAssociatedPanels(String id)
   {
+    if (components == null)
+    {
+      return new AlignmentPanel[0];
+    }
+    ;
     Vector comps = (Vector) components.get(id);
+    if (comps == null)
+    {
+      return new AlignmentPanel[0];
+    }
+    ;
     Vector tmp = new Vector();
     int i, iSize = comps.size();
     for (i = 0; i < iSize; i++)
     {
       if (comps.elementAt(i) instanceof AlignmentPanel)
       {
-        tmp.addElement(((AlignmentPanel) comps.elementAt(i)));
+        tmp.addElement(comps.elementAt(i));
       }
     }
     AlignmentPanel[] result = new AlignmentPanel[tmp.size()];