X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=cec77d2fb4e131d90eec93c0e2a9fa7626196d2c;hb=e6139c0f78da30cdf0dabb986706f3a2110c02fc;hp=a854c6c1cae9f76ae325d9d19ee464db328ea35f;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index a854c6c..cec77d2 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,64 +1,71 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- * 
+ * 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/>.
+ * 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 jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+
 import java.awt.Container;
+import java.util.ArrayList;
 import java.util.BitSet;
-import java.util.Hashtable;
+import java.util.List;
 import java.util.Vector;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-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(), seqs, viewer);
     ap = alignPanel;
-    this.sequence = seqs;
     notifyFileLoaded(null, null, null, null, 0);
   }
 
   public void updateColours(Object source)
   {
-    
+
     // TODO Auto-generated method stub
 
   }
@@ -68,9 +75,10 @@ public class ExtJmol extends JalviewJmolBinding
     showUrl(arg0, "jmol");
   }
 
-  public FeatureRenderer getFeatureRenderer()
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    if (ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (AlignmentPanel) alignment;
+    if (ap.av.isShowSequenceFeatures())
     {
       return ap.getFeatureRenderer();
     }
@@ -80,9 +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)
@@ -117,35 +125,44 @@ public class ExtJmol extends JalviewJmolBinding
 
   public void refreshPdbEntries()
   {
-    Vector pdbe = new Vector();
-    Hashtable fileids = new Hashtable();
+    List<PDBEntry> pdbe = new ArrayList<PDBEntry>();
+    List<String> fileids = new ArrayList<String>();
     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())) {
-            pdbe.addElement(pentry);
+          if (!fileids.contains(pentry.getId()))
+          {
+            pdbe.add(pentry);
+          }
+          else
+          {
+            fileids.add(pentry.getId());
           }
         }
       }
     }
-    pdbentry = new PDBEntry[pdbe.size()];
-    for (int pe=0;pe<pdbe.size(); pe++)
+    PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
+    for (int pe = 0; pe < pdbe.size(); pe++)
     {
-      pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe);
+      newEntries[pe] = pdbe.get(pe);
     }
+    setPdbentry(newEntries);
   }
 
   @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
@@ -155,17 +172,20 @@ public class ExtJmol extends JalviewJmolBinding
     // 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;
-    }
-    
+    closeConsole();
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
   }
 
 }