X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=6734200f1ac4c82f2c42504b289ea171c886dd01;hb=dd3059c62cd80e712c0f6df866d6d69588e5f3eb;hp=df62eabe1b33c15475b192dd86e03c4784e883d6;hpb=7ef02aa7c7559f3a37f2f0524243c52b00335294;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index df62eab..6734200 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,13 +1,13 @@
 /*
- * 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 
  * 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 
@@ -18,17 +18,10 @@
 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 +39,9 @@ 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;
@@ -56,15 +50,19 @@ 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)
+      if (fr == null)
+      {
+        fr = ap.cloneFeatureRenderer();
+      }
+      else
       {
-        fr=ap.cloneFeatureRenderer();
-      } else {
         ap.updateFeatureRenderer(fr);
       }
     }
@@ -73,9 +71,10 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @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)
@@ -125,11 +124,12 @@ 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);
     }
   }
@@ -152,8 +152,7 @@ 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)
@@ -222,9 +221,11 @@ 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);
-      
-    };
+
+    }
+    ;
   }
 }