X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=929a871106b9c3c4888212175405efac1d13cc9f;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=2c5da174bb38c206e0e1bd589da1d7027867e85b;hpb=cdb2c3afc153577cceb0d5c6a4b12532f6dde601;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 2c5da17..929a871 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,45 +1,72 @@
+/*
+ * 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.
+ *  
+ * 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 java.util.Hashtable;
-import java.util.Vector;
-
-import org.jmol.api.JmolViewer;
-
+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.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.java.BS;
+import org.jmol.viewer.Viewer;
+
 /**
  * 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)
+  public ExtJmol(Viewer 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
 
   }
@@ -49,9 +76,11 @@ public class ExtJmol extends JalviewJmolBinding
     showUrl(arg0, "jmol");
   }
 
-  public FeatureRenderer getFeatureRenderer()
+  @Override
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    if (ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (AlignmentPanel) alignment;
+    if (ap.av.isShowSequenceFeatures())
     {
       return ap.getFeatureRenderer();
     }
@@ -61,64 +90,118 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
-  public SequenceRenderer getSequenceRenderer()
+  @Override
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return ap.getSequenceRenderer();
+    return ((AlignmentPanel) alignment).getSequenceRenderer();
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // ignore
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     // ignore
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     // ignore
   }
 
+  @Override
   public void showUrl(String url, String target)
   {
     ap.alignFrame.showURL(url, target);
   }
 
-  public void updateUI()
+  @Override
+  public void refreshGUI()
   {
     // ignore
   }
 
-  public void selectionChanged(BitSet arg0)
+  public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);
   }
 
+  @Override
   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)
+      Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
+      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);
+          PDBEntry pentry = pdbids.elementAt(pe);
+          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);
+  }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(
+          Container consolePanel, String buttonsToShow)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  protected void releaseUIResources()
+  {
+    ap = null;
+    closeConsole();
+
   }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }