X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e780f78cc12371231b4b052afc2f024f16372f97;hb=bb6cfec0589998373f5542e630660b06485a7569;hp=e8e66d8250bfd01bf7fe397d25998eaa6a982e03;hpb=bf702237a1f0b07104d976ee43270711b9e66a4d;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e8e66d8..e780f78 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -40,29 +40,24 @@ public class Jalview
     /**
      * Initialises the Apache Axis logger
      */
+    public static Logger log;
     private static void initLogger()
     {
         Logger laxis = Logger.getLogger("org.apache.axis");
         Logger lcastor = Logger.getLogger("org.exolab.castor");
+        log = Logger.getLogger("jalview.bin.Jalview");
 
-        if (Cache.getProperty("logs.Axis.Level") == null)
-        {
-            Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
-        }
-
-        if (Cache.getProperty("logs.Castor.Level") == null)
-        {
-            Cache.setProperty("logs.Castor.Level", Level.INFO.toString());
-        }
-
-        laxis.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
-        lcastor.setLevel(Level.toLevel(Cache.getProperty("logs.Castor.Level")));
+        laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
+        lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", Level.INFO.toString())));
+        log.setLevel(Level.toLevel(Cache.getDefault("logs.Jalview.level", Level.INFO.toString())));
 
         ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
                 "System.err");
         ap.setName("JalviewLogger");
+
         laxis.addAppender(ap);
         lcastor.addAppender(ap);
+        log.addAppender(ap);
     }
 
     /**
@@ -148,6 +143,7 @@ public class Jalview
 
           desktop = new Desktop();
           desktop.setVisible(true);
+          desktop.discoverer.start();
         }
 
 
@@ -241,9 +237,7 @@ public class Jalview
         //////////////////////
           if (
               !headless &&
-              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) &&
-              jalview.bin.Cache.getDefault("STARTUP_FILE",
-                                         "http://www.jalview.org/examples/exampleFile.jar")!= null)
+              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
           {
 
             file = jalview.bin.Cache.getDefault("STARTUP_FILE",