JAL-1432 updated copyright notices

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

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 89d053b..edf2d45 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,13 +1,33 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.BitSet;
-
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
 
+import java.awt.Container;
+import java.util.BitSet;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
 import org.jmol.popup.JmolPopup;
 
 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
@@ -18,31 +38,38 @@ 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,
+          StructureSelectionManager sSm, PDBEntry[] pdbentry,
+          SequenceI[][] seq, String[][] chains, String protocol)
   {
-    super(pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, chains, protocol);
     appletJmolBinding = appletJmol;
   }
 
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
   {
+    AlignmentPanel ap = (AlignmentPanel) alignment;
     if (appletJmolBinding.ap.av.showSequenceFeatures)
     {
       if (appletJmolBinding.fr == null)
       {
-        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
+        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
+                appletJmolBinding.ap.av);
       }
 
-      appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
+      appletJmolBinding.fr
+              .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
+                      .getFeatureRenderer());
     }
 
     return appletJmolBinding.fr;
   }
 
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public jalview.api.SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appletJmolBinding.ap.av);
+    return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -68,32 +95,34 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
-  public void updateUI()
+  public void refreshGUI()
   {
     appletJmolBinding.updateTitleAndMenus();
   }
-  
+
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   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)
     {
     }
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
+  public void newJmolPopup(boolean translateLocale, String menuName,
+          boolean asPopup)
   {
-    
-    jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
+
+    jmolpopup = new JmolPopup();
+    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -104,13 +133,60 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void selectionChanged(BitSet arg0)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   public void refreshPdbEntries()
   {
     // TODO Auto-generated method stub
-    
+
+  }
+
+  @Override
+  public void showConsole(boolean show)
+  {
+    appletJmolBinding.showConsole(show);
   }
 
-}
\ No newline at end of file
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    // return new org.jmol.console.AppletConsole(viewer2, consolePanel);
+    JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole()
+            .getAppConsole(viewer2);
+    return appc;
+  }
+
+  @Override
+  protected void releaseUIResources()
+  {
+    appletJmolBinding = null;
+    if (console != null)
+    {
+      try
+      {
+        console.setVisible(false);
+      } catch (Error e)
+      {
+      } catch (Exception x)
+      {
+      }
+      ;
+      console = null;
+    }
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+  }
+
+  @Override
+  public void resizeInnerPanel(String data)
+  {
+    // TODO Auto-generated method stub
+
+  }
+}