X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=df11327c055dc66112b34ecbe5ee9170606f2f02;hb=83f6c6309e9705037a0853a26da74821c9d4fd12;hp=292c6592a18a232204982b8fe7c45458378a5e64;hpb=04fe5ab63df768c865eb40c9300b52239fbe8746;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 292c659..df11327 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -321,7 +321,6 @@ public class JalviewLite
         {
           Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
           jmolAvailable = true;
-          System.out.println("JMOL FOUND");
         }
       }
       catch (java.lang.ClassNotFoundException ex)
@@ -563,7 +562,16 @@ public class JalviewLite
               }
             }
 
-            param = addProtocol(param);
+            if (inArchive(param) && !jmolAvailable)
+            {
+              protocol = AppletFormatAdapter.CLASSLOADER;
+            }
+            else
+            {
+              protocol = AppletFormatAdapter.URL;
+              param = addProtocol(param);
+            }
+
             pdb.setFile(param);
 
             if(seqs!=null)