X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=1a23f019d097735eae166de0de8f1c728c3bfa45;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=1f0686e667702d8bb4776f36443eb539a10b07fa;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 1f0686e..1a23f01 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -29,12 +29,13 @@ import jalview.ext.jmol.JalviewJmolBinding;
 
 import java.awt.Container;
 import java.util.ArrayList;
-import java.util.BitSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
+import org.jmol.java.BS;
+import org.jmol.viewer.Viewer;
 
 /**
  * bind an alignment view to an external Jmol instance.
@@ -55,7 +56,7 @@ public class ExtJmol extends JalviewJmolBinding
             chains, protocol);
   }
 
-  public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
+  public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
           SequenceI[][] seqs)
   {
     super(alignPanel.getStructureSelectionManager(), seqs, viewer);
@@ -75,6 +76,7 @@ public class ExtJmol extends JalviewJmolBinding
     showUrl(arg0, "jmol");
   }
 
+  @Override
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (AlignmentPanel) alignment;
@@ -88,41 +90,48 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return ((AlignmentPanel) alignment).getSequenceRenderer();
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // ignore
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     // ignore
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     // ignore
   }
 
+  @Override
   public void showUrl(String url, String target)
   {
     ap.alignFrame.showURL(url, target);
   }
 
+  @Override
   public void refreshGUI()
   {
     // ignore
   }
 
-  public void selectionChanged(BitSet arg0)
+  public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);
   }
 
+  @Override
   public void refreshPdbEntries()
   {
     List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
@@ -130,12 +139,12 @@ public class ExtJmol extends JalviewJmolBinding
     SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
     for (int s = 0; s < sq.length; s++)
     {
-      Vector pdbids = sq[s].getPDBId();
+      Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
       if (pdbids != null)
       {
         for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
         {
-          PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
+          PDBEntry pentry = pdbids.elementAt(pe);
           if (!fileids.contains(pentry.getId()))
           {
             pdbe.add(pentry);
@@ -166,7 +175,7 @@ public class ExtJmol extends JalviewJmolBinding
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
     // TODO Auto-generated method stub
@@ -188,4 +197,11 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }