remove system.out

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index e0f0910..df11327 100755 (executable)
--- 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)
@@ -582,8 +590,6 @@ public class JalviewLite
                                                  protocol);
                 lastFrameX += 40;
                 lastFrameY+=40;
-
-                System.out.println(lastFrameX+" "+lastFrameY);
               }
               else
                     new MCview.AppletPDBViewer(pdb,