JAL-1432 updated copyright notices

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

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 41a0da9..dabf8db 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,30 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
 import jalview.datamodel.*;
 
 /**
- * DOCUMENT ME!
+ * Route datamodel/view update events for a sequence set to any display components involved
+ * TODO: JV3 refactor to abstract gui/view package
  * 
  * @author $author$
  * @version $Revision$
@@ -118,8 +121,8 @@ 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 +182,20 @@ 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
         {
@@ -224,16 +240,24 @@ public class PaintRefresher
 
   static AlignmentPanel[] getAssociatedPanels(String id)
   {
-    if (components==null) { return new AlignmentPanel[0]; };
+    if (components == null)
+    {
+      return new AlignmentPanel[0];
+    }
+    ;
     Vector comps = (Vector) components.get(id);
-    if (comps==null) { return new AlignmentPanel[0]; };
+    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()];