X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=21a222495efd79ec8dd8305af7946356fff40feb;hb=6235128370382f0fecdf3ba1cc683052c5aa11e7;hp=91a0978eacd4691272c1a1401e51a730aa34379b;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 91a0978..21a2224 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,18 +1,18 @@
 /*
- * 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
- *
+ * 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
+ * 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
+ *  
+ * 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/>.
  */
 package jalview.gui;
@@ -25,8 +25,9 @@ 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 $Revision$
  */
@@ -36,7 +37,7 @@ public class PaintRefresher
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param comp
    *          DOCUMENT ME!
    * @param al
@@ -180,14 +181,18 @@ public class PaintRefresher
       {
         if (i < comp.getHeight())
         {
-          // TODO: the following does not trigger any recalculation of height/etc, or maintain the dataset
-          if (comp.getDataset()!=source.getDataset())
+          // 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)");
+            // 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()) {
+          synchronized (alsq = comp.getSequences())
+          {
             alsq.add(i, a1[i]);
           }
         }
@@ -234,9 +239,17 @@ 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++)