X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;fp=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;h=ddfa1b056195dc6d68dcd512c6ecceee3d7706f7;hb=231e656ad21658b53eda2237b61547db74894e51;hp=cb197693e1a34cf1bb50d60f7abda52faf057c47;hpb=d8d49ee2a757173fa4417af5e42cc16023e0ae09;p=jalview.git

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index cb19769..ddfa1b0 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -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
   }
 
   /**
@@ -84,18 +79,11 @@ 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()}),