From fb7845d8a5eb12e4e023d6df7f9f019c020fb8ca Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 8 Dec 2011 11:43:44 +0000
Subject: [PATCH] remove commented lines

---
 src/jalview/gui/AppJmol.java |   14 --------------
 1 file changed, 14 deletions(-)

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 2c0d7d6..0e00de4 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -321,7 +321,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
     openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
   }
   private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) {
-    boolean promptUser=pdbentrys.length==1;
     progressBar = ap.alignFrame;
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null, null);
     addAlignmentPanel(ap);
@@ -335,24 +334,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     worker=null;
-    String filelist="";
-//    for (PDBEntry pe: pdbentrys)
-//    {
-//      if (pe.getFile()==null)
       {
         addingStructures = false;
         worker = new Thread(this);
         worker.start();
-//        break;
       }
-//      filelist+=" \""+pe.getFile()+"\"";
-              
-/*    }
-    if (worker==null)
-    {
-      initJmol("load"+(pdbentrys.length>1 ? " APPEND" : "") + filelist);
-    }
-*/
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
-- 
1.7.10.2