X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPaintRefresher.java;h=4e1bfaf2c86649ade08baeeefc98fac3194c6635;hb=45ce9dae1ec917b16d753b664ff804c9f6f84f02;hp=e5e9e89a8a2bdd54627e460c52b9ff3619d54ee2;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index e5e9e89..4e1bfaf 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/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.appletgui;
 
 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)
   {
@@ -123,8 +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)
@@ -184,7 +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
         {
@@ -226,4 +230,25 @@ public class PaintRefresher
       }
     }
   }
+
+  public static AlignmentPanel[] getAssociatedPanels(String id)
+  {
+    Vector comps = (Vector) components.get(id);
+    Vector tmp = new Vector();
+    int i, iSize = comps.size();
+    for (i = 0; i < iSize; i++)
+    {
+      if (comps.elementAt(i) instanceof AlignmentPanel)
+      {
+        tmp.addElement(comps.elementAt(i));
+      }
+    }
+    AlignmentPanel[] result = new AlignmentPanel[tmp.size()];
+    for (int ix=0;ix<result.length;ix++) {
+      result[ix] = (AlignmentPanel) tmp.elementAt(ix);
+    }
+
+    return result;
+  }
+
 }