JAL-1925 update source version in license

[jalview.git] / src / jalview / ext / jmol / PDBFileWithJmol.java

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index cb19769..8171f9d 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -45,7 +45,6 @@ import org.jmol.modelset.ModelSet;
 import org.jmol.modelsetbio.BioModel;
 import org.jmol.modelsetbio.BioPolymer;
 import org.jmol.viewer.Viewer;
-import org.openscience.jmol.app.JmolApp;
 
 /**
  * Import and process PDB files with Jmol
@@ -56,9 +55,6 @@ import org.openscience.jmol.app.JmolApp;
 public class PDBFileWithJmol extends AlignFile implements
         JmolStatusListener
 {
-
-  JmolApp jmolApp = null;
-
   Viewer viewer = null;
 
   public PDBFileWithJmol(String inFile, String type) throws IOException
@@ -73,7 +69,6 @@ public class PDBFileWithJmol extends AlignFile implements
 
   public PDBFileWithJmol()
   {
-    // TODO Auto-generated constructor stub
   }
 
   /**
@@ -84,22 +79,16 @@ public class PDBFileWithJmol extends AlignFile implements
   private Viewer getJmolData()
   {
     if (viewer == null)
-    { // note that -o -n -x are all implied // TODO check for Jmol 14.2
-      jmolApp = new JmolApp();
-      jmolApp.isDataOnly = true;
-      jmolApp.haveConsole = false;
-      jmolApp.haveDisplay = false;
+    {
       try
       {
         viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
                 null, "-x -o -n", this);
-        viewer.setScreenDimension(jmolApp.startupWidth,
-                jmolApp.startupHeight);
-        jmolApp.startViewer(viewer, null, false);
       } catch (ClassCastException x)
       {
-        throw new Error(MessageManager.formatMessage("error.jmol_version_not_compatible_with_jalview_version", new String[]{JmolViewer.getJmolVersion()}),
-                x);
+        throw new Error(MessageManager.formatMessage(
+                "error.jmol_version_not_compatible_with_jalview_version",
+                new String[] { JmolViewer.getJmolVersion() }), x);
       }
     }
     return viewer;
@@ -248,7 +237,8 @@ public class PDBFileWithJmol extends AlignFile implements
                * equivalent (e.g. MSE with MET->M) to maximise sequence matching
                */
               String threeLetterCode = group.getGroup3();
-              String canonical = ResidueProperties.getCanonicalAminoAcid(threeLetterCode);
+              String canonical = ResidueProperties
+                      .getCanonicalAminoAcid(threeLetterCode);
               if (canonical != null
                       && !canonical.equalsIgnoreCase(threeLetterCode))
               {