JAL-1620 version bump and release notes

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 3e243fc..2104399 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,34 +1,30 @@
 /*
- * 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 2.8.2b1)
+ * 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.
- * 
+ * 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/>.
+ * 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.awt.Container;
-import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
 import java.util.BitSet;
 
-import javax.swing.JPanel;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
@@ -46,8 +42,9 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppJmol appJmolWindow;
 
-  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          String protocol)
   {
     super(sSm, pdbentry, sequenceIs, chains, protocol);
     appJmolWindow = appJmol;
@@ -56,27 +53,31 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   FeatureRenderer fr = null;
 
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+            : (AlignmentPanel) alignment;
     if (ap.av.showSequenceFeatures)
     {
       if (fr == null)
       {
-        fr = new FeatureRenderer(ap);
+        fr = ap.cloneFeatureRenderer();
+      }
+      else
+      {
+        ap.updateFeatureRenderer(fr);
       }
-
-      fr.transferSettings(ap.
-              seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     return fr;
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+  public jalview.api.SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(((AlignmentPanel)alignment).av);
+    return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -126,11 +127,12 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source,topap;
+    AlignmentPanel ap = (AlignmentPanel) source, topap;
     // ignore events from panels not used to colour this view
     if (!appJmolWindow.isUsedforcolourby(ap))
       return;
-    if (!isLoadingFromArchive()) {
+    if (!isLoadingFromArchive())
+    {
       colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
   }
@@ -153,8 +155,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
 
     jmolpopup = new JmolPopup();
-    jmolpopup.initialize(viewer, translateLocale, menuName,
-            asPopup);
+    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
 
   public void selectionChanged(BitSet arg0)
@@ -223,9 +224,11 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   @Override
   public void releaseReferences(Object svl)
   {
-    if (svl instanceof SeqPanel) {
+    if (svl instanceof SeqPanel)
+    {
       appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-      
-    };
+
+    }
+    ;
   }
 }