Jalview 2.6 source licence

[jalview.git] / src / jalview / appletgui / ExtJmol.java

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 2c5da17..a854c6c 100644 (file)
--- 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;
@@ -22,14 +41,14 @@ 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;
@@ -86,7 +105,7 @@ public class ExtJmol extends JalviewJmolBinding
     ap.alignFrame.showURL(url, target);
   }
 
-  public void updateUI()
+  public void refreshGUI()
   {
     // ignore
   }
@@ -121,4 +140,32 @@ public class ExtJmol extends JalviewJmolBinding
       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;
+    }
+    
+  }
+
 }