JAL-1115 refactor base collection for Alignment from Vector to locally synchronized...

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

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index f08bd66..fbdea9d 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -18,6 +18,7 @@
 package jalview.appletgui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
@@ -122,8 +123,8 @@ public class PaintRefresher
       else 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)
@@ -183,7 +184,11 @@ 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
+          List<SequenceI> alsq;
+          synchronized (alsq=comp.getSequences()) {
+            alsq.add(i, a1[i]);
+          }
         }
         else
         {
@@ -239,7 +244,9 @@ public class PaintRefresher
       }
     }
     AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
-    tmp.toArray(result);
+    for (int ix=0;ix<result.length;ix++) {
+      result[ix] = (AlignmentPanel) tmp.elementAt(ix);
+    }
 
     return result;
   }