From d982e0264da4cd35cb993144754e797db11c8c48 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 27 Feb 2007 13:39:49 +0000
Subject: [PATCH] Launch applet jmol

---
 src/jalview/bin/JalviewLite.java |   52 +++++++++++++++++++++++++++++---------
 1 file changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index e6bb685..0623193 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -37,6 +37,8 @@ public class JalviewLite
     extends Applet
 {
 
+
+
   ///////////////////////////////////////////
   //The following public methods maybe called
   //externally, eg via javascript in HTML page
@@ -147,11 +149,25 @@ public class JalviewLite
 
   boolean embedded = false;
 
+  public boolean jmolAvailable = false;
+
   /**
    * init method for Jalview Applet
    */
   public void init()
   {
+    try
+    {
+      Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter",
+                    true, Thread.currentThread().getContextClassLoader());
+
+      jmolAvailable = true;
+    }
+    catch (java.lang.ClassNotFoundException ex)
+    {
+      System.out.println("Jmol not found - Use MCview for structures");
+    }
+
     int r = 255;
     int g = 255;
     int b = 255;
@@ -489,28 +505,41 @@ public class JalviewLite
           }
         }
 
+
         param = getParameter("PDBFILE");
         if (param != null)
         {
-          if (inArchive(param))
-          {
-            protocol = AppletFormatAdapter.CLASSLOADER;
-          }
-          else
+
+          PDBEntry pdb = new PDBEntry();
+
+          if (!inArchive(param) || jmolAvailable)
           {
-            protocol = AppletFormatAdapter.URL;
             param = addProtocol(param);
           }
 
+          pdb.setFile(param);
+
           String sequence = applet.getParameter("PDBSEQ");
 
           if (sequence != null)
           {
-            new MCview.AppletPDBViewer(param, protocol,
-                                       (Sequence) currentAlignFrame.
-                                       getAlignViewport().getAlignment().
-                                       findName(sequence),
-                                       currentAlignFrame.getSeqcanvas());
+            if (jmolAvailable)
+              new jalview.appletgui.AppletJmol(pdb,
+                                               new SequenceI[]
+                                               { (Sequence) currentAlignFrame.
+                                               getAlignViewport().getAlignment().
+                                               findName(sequence)},
+                                               currentAlignFrame.alignPanel,
+                                               protocol);
+            else
+
+              new MCview.AppletPDBViewer(pdb,
+                                         new SequenceI[]
+                                         { (Sequence) currentAlignFrame.
+                                         getAlignViewport().getAlignment().
+                                         findName(sequence)},
+                                         currentAlignFrame.alignPanel,
+                                         protocol);
           }
 
         }
@@ -552,6 +581,5 @@ public class JalviewLite
 
       return file;
     }
-
   }
 }
-- 
1.7.10.2