X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=c7ce9945777ec67adcb2a65626a35ac414687515;hb=4f30214e8098748469c6a4269ac2ed6c5750e4b0;hp=f7a121c518b98e75da846417abf4e0bba77b3654;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index f7a121c..c7ce994 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -24,16 +24,15 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Container;
 import java.util.Map;
 
-import javajs.awt.Dimension;
-
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.console.AppletConsole;
-import org.jmol.java.BS;
+import javajs.util.BS;
 
 class AppletJmolBinding extends JalviewJmolBinding
 {
@@ -45,34 +44,13 @@ class AppletJmolBinding extends JalviewJmolBinding
 
   public AppletJmolBinding(AppletJmol appletJmol,
           StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] seq, String[][] chains, String protocol)
+          SequenceI[][] seq, DataSourceType protocol)
   {
-    super(sSm, pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, protocol);
     appletJmolBinding = appletJmol;
   }
 
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (appletJmolBinding.ap.av.isShowSequenceFeatures())
-    {
-      if (appletJmolBinding.fr == null)
-      {
-        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
-                appletJmolBinding.ap.av);
-      }
-
-      appletJmolBinding.fr
-              .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
-    }
-
-    return appletJmolBinding.fr;
-  }
-
-  @Override
   public jalview.api.SequenceRenderer getSequenceRenderer(
           AlignmentViewPanel alignment)
   {
@@ -113,18 +91,20 @@ class AppletJmolBinding extends JalviewJmolBinding
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
     colourBySequence(ap);
   }
 
+  @Override
   public void showUrl(String url)
   {
     try
     {
-      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
-              new java.net.URL(url), "jmol");
+      appletJmolBinding.ap.av.applet.getAppletContext()
+              .showDocument(new java.net.URL(url), "jmol");
     } catch (java.net.MalformedURLException ex)
     {
     }
@@ -143,6 +123,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     // do nothing.
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
@@ -166,7 +147,7 @@ class AppletJmolBinding extends JalviewJmolBinding
           Container consolePanel, String buttonsToShow)
   {
     JmolAppConsoleInterface appc = new AppletConsole();
-    appc.start(viewer);
+    appc.start(jmolViewer);
     return appc;
   }
 
@@ -183,16 +164,14 @@ class AppletJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
   @Override
   public Map<String, Object> getJSpecViewProperty(String arg0)
   {
-    // TODO Auto-generated method stub
     return null;
   }
 }