X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=d3dad58f982edccc05f422578f0e94b0eae4b445;hb=6b71746c98f7c1118b474b0b920db3bd7b2a15c0;hp=8e42f2a6ebe8a3c487984674403942b77372b164;hpb=8449a33e712dfec13771d4e1b8be20bf625f190b;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 8e42f2a..d3dad58 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,9 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 
+ * 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/>.
+ */
 package jalview.appletgui;
 
+import java.awt.Container;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Vector;
 
+import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 
 import jalview.api.FeatureRenderer;
@@ -14,22 +33,24 @@ import jalview.ext.jmol.JalviewJmolBinding;
 
 /**
  * bind an alignment view to an external Jmol instance.
+ * 
  * @author JimP
- *
+ * 
  */
 public class ExtJmol extends JalviewJmolBinding
 {
 
   private AlignmentPanel ap;
 
-  protected ExtJmol(jalview.appletgui.AlignFrame alframe, PDBEntry[] pdbentry, SequenceI[] seq, String[] chains,
+  protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+          PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
           String protocol)
   {
     super(pdbentry, seq, chains, protocol);
   }
 
   public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
-          SequenceI[] seqs)
+          SequenceI[][] seqs)
   {
     super(viewer);
     ap = alignPanel;
@@ -39,7 +60,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    
+
     // TODO Auto-generated method stub
 
   }
@@ -101,24 +122,64 @@ public class ExtJmol extends JalviewJmolBinding
     Vector pdbe = new Vector();
     Hashtable fileids = new Hashtable();
     SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
-    for (int s=0;s<sq.length;s++)
+    for (int s = 0; s < sq.length; s++)
     {
       Vector pdbids = sq[s].getPDBId();
-      if (pdbids!=null)
+      if (pdbids != null)
       {
-        for (int pe=0,peSize=pdbids.size(); pe<peSize; pe++)
+        for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
         {
           PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
-          if (!fileids.containsKey(pentry.getId())) {
+          if (!fileids.containsKey(pentry.getId()))
+          {
             pdbe.addElement(pentry);
           }
         }
       }
     }
     pdbentry = new PDBEntry[pdbe.size()];
-    for (int pe=0;pe<pdbe.size(); pe++)
+    for (int pe = 0; pe < pdbe.size(); pe++)
     {
       pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
     }
   }
+
+  @Override
+  public void showConsole(boolean show)
+  {
+    // This never gets called because we haven't overriden the associated Jmol's
+    // console
+    System.err
+            .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+                    + show);
+  }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  protected void releaseUIResources()
+  {
+    ap = null;
+    if (console != null)
+    {
+      try
+      {
+        console.setVisible(false);
+      } catch (Error e)
+      {
+      } catch (Exception x)
+      {
+      }
+      ;
+      console = null;
+    }
+
+  }
+
 }