<No Comment Entered>

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

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