Jalview 2.6 source licence

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

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 89d053b..7490edc 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,13 +1,31 @@
-/**
+/*
+ * 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 jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
+import org.jmol.applet.AppletConsole;
 import org.jmol.popup.JmolPopup;
 
 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
@@ -18,8 +36,8 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[] seq,
-          String[] chains, String protocol)
+  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
+          String[][] chains, String protocol)
   {
     super(pdbentry, seq, chains, protocol);
     appletJmolBinding = appletJmol;
@@ -68,7 +86,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
-  public void updateUI()
+  public void refreshGUI()
   {
     appletJmolBinding.updateTitleAndMenus();
   }
@@ -113,4 +131,29 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     
   }
 
-}
\ No newline at end of file
+  @Override
+  public void showConsole(boolean show)
+  {
+    appletJmolBinding.showConsole(show);
+  }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    return new AppletConsole(viewer2, consolePanel);
+  }
+  @Override
+  protected void releaseUIResources()
+  {
+    appletJmolBinding = null;
+    if (console!=null) {
+      try {
+        console.setVisible(false);
+      } catch (Error e) {} catch (Exception x) {};
+      console=null;
+    }
+    
+  }
+
+}