From bb6cfec0589998373f5542e630660b06485a7569 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 17 Aug 2005 16:24:08 +0000
Subject: [PATCH] <No Comment Entered>

---
 src/jalview/bin/Cache.java   |    3 +++
 src/jalview/bin/Jalview.java |   24 +++++++++---------------
 2 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 8fae6a9..7f714e5 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -30,6 +30,9 @@ import java.net.*;
  * <br><br>Current properties include:
  * <br>logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services)
  * <br>logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization)
+ * <br>logs.Jalview.Level - Jalview.log stringified level.
+ * <br>DISCOVERY_START - Boolean - controls if discovery services are queried on startup
+ * <br>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
  * <br>SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN
  * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR
  * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION,
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",
-- 
1.7.10.2