JAL-1620 version bump and release notes

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

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 4bee84c..4746932 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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;
@@ -8,6 +28,7 @@ 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;
@@ -16,24 +37,27 @@ 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);
@@ -41,7 +65,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    
+
     // TODO Auto-generated method stub
 
   }
@@ -51,8 +75,9 @@ 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();
@@ -63,9 +88,9 @@ 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)
@@ -103,22 +128,23 @@ 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);
     }
@@ -127,8 +153,11 @@ public class ExtJmol extends JalviewJmolBinding
   @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);
+    // 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
@@ -138,17 +167,32 @@ public class ExtJmol extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
   @Override
   protected void releaseUIResources()
   {
     ap = null;
-    if (console!=null) {
-      try {
+    if (console != null)
+    {
+      try
+      {
         console.setVisible(false);
-      } catch (Error e) {} catch (Exception x) {};
-      console=null;
+      } catch (Error e)
+      {
+      } catch (Exception x)
+      {
+      }
+      ;
+      console = null;
     }
-    
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
   }
 
 }