JAL-1683 replace year/version strings with tokens in source

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

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index aaab8bd..cec77d2 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,30 +1,25 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 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;
@@ -32,6 +27,15 @@ 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.List;
+import java.util.Vector;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
+
 /**
  * bind an alignment view to an external Jmol instance.
  * 
@@ -54,9 +58,8 @@ public class ExtJmol extends JalviewJmolBinding
   public ExtJmol(JmolViewer 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);
   }
 
@@ -75,7 +78,7 @@ public class ExtJmol extends JalviewJmolBinding
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
+    if (ap.av.isShowSequenceFeatures())
     {
       return ap.getFeatureRenderer();
     }
@@ -122,8 +125,8 @@ 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++)
     {
@@ -133,18 +136,23 @@ public class ExtJmol extends JalviewJmolBinding
         for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
         {
           PDBEntry pentry = (PDBEntry) pdbids.elementAt(pe);
-          if (!fileids.containsKey(pentry.getId()))
+          if (!fileids.contains(pentry.getId()))
           {
-            pdbe.addElement(pentry);
+            pdbe.add(pentry);
+          }
+          else
+          {
+            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
@@ -169,19 +177,7 @@ 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();
 
   }