formatting

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 22776f2..14beaf8 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -46,8 +46,9 @@ 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 +57,31 @@ 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 +131,12 @@ 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 +158,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           boolean asPopup)
   {
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+    jmolpopup = new JmolPopup();
+    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
 
   public void selectionChanged(BitSet arg0)
@@ -222,9 +228,11 @@ 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);
-      
-    };
+
+    }
+    ;
   }
 }