JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 4746932..6479296 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,6 @@
  */
 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;
@@ -35,6 +27,16 @@ 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.
  * 
@@ -54,12 +56,11 @@ public class ExtJmol extends JalviewJmolBinding
             chains, protocol);
   }
 
-  public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
+  public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
           SequenceI[][] seqs)
   {
-    super(alignPanel.getStructureSelectionManager(), viewer);
+    super(alignPanel.getStructureSelectionManager(), seqs, viewer);
     ap = alignPanel;
-    this.sequence = seqs;
     notifyFileLoaded(null, null, null, null, 0);
   }
 
@@ -75,10 +76,11 @@ public class ExtJmol extends JalviewJmolBinding
     showUrl(arg0, "jmol");
   }
 
+  @Override
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       return ap.getFeatureRenderer();
     }
@@ -88,66 +90,78 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
+  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     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);
   }
 
+  @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++)
     {
-      Vector pdbids = sq[s].getPDBId();
+      Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
       if (pdbids != null)
       {
         for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
         {
-          PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
-          if (!fileids.containsKey(pentry.getId()))
+          PDBEntry pentry = pdbids.elementAt(pe);
+          if (!fileids.contains(pentry.getId()))
+          {
+            pdbe.add(pentry);
+          }
+          else
           {
-            pdbe.addElement(pentry);
+            fileids.add(pentry.getId());
           }
         }
       }
     }
-    pdbentry = new PDBEntry[pdbe.size()];
+    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
@@ -161,7 +175,7 @@ public class ExtJmol extends JalviewJmolBinding
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
     // TODO Auto-generated method stub
@@ -172,19 +186,7 @@ public class ExtJmol extends JalviewJmolBinding
   protected void releaseUIResources()
   {
     ap = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
+    closeConsole();
 
   }
 
@@ -195,4 +197,11 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }