JAL-976 test if the sliders have been modified from the service default (where no...

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

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index f505453..91a0978 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -1,24 +1,24 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program is free software; you can redistribute it and/or
+ * 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.
+ *
+ * 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 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
@@ -26,7 +26,7 @@ import jalview.datamodel.*;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -36,11 +36,11 @@ public class PaintRefresher
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param comp
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param al
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public static void Register(Component comp, String seqSetId)
   {
@@ -119,8 +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)
@@ -180,7 +180,16 @@ 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
         {
@@ -225,14 +234,16 @@ 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()];