JAL-1503 update version in GPL header

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

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 53c2f1c..ae6b5ab 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,11 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.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.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
@@ -14,24 +35,27 @@ 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);
+    super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+            chains, protocol);
   }
 
   public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
           SequenceI[][] seqs)
   {
-    super(viewer);
+    super(alignPanel.getStructureSelectionManager(), viewer);
     ap = alignPanel;
     this.sequence = seqs;
     notifyFileLoaded(null, null, null, null, 0);
@@ -39,7 +63,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    
+
     // TODO Auto-generated method stub
 
   }
@@ -49,8 +73,9 @@ public class ExtJmol extends JalviewJmolBinding
     showUrl(arg0, "jmol");
   }
 
-  public FeatureRenderer getFeatureRenderer()
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
+    AlignmentPanel ap = (AlignmentPanel) alignment;
     if (ap.av.showSequenceFeatures)
     {
       return ap.getFeatureRenderer();
@@ -61,9 +86,9 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
-  public SequenceRenderer getSequenceRenderer()
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return ap.getSequenceRenderer();
+    return ((AlignmentPanel) alignment).getSequenceRenderer();
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -101,24 +126,71 @@ 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;
+    }
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }