Must update globalColourScheme with new consensus

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ff2d06a..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
@@ -133,7 +128,13 @@ public class Jalview
           try\r
           {\r
             UIManager.setLookAndFeel(\r
-                UIManager.getSystemLookAndFeelClassName()\r
+                   UIManager.getSystemLookAndFeelClassName()\r
+            //        UIManager.getCrossPlatformLookAndFeelClassName()\r
+//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
+//"javax.swing.plaf.metal.MetalLookAndFeel"\r
+//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
+//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
+\r
                 );\r
           }\r
           catch (Exception ex)\r
@@ -142,6 +143,7 @@ public class Jalview
 \r
           desktop = new Desktop();\r
           desktop.setVisible(true);\r
+          desktop.discoverer.start();\r
         }\r
 \r
 \r
@@ -235,11 +237,11 @@ public class Jalview
         //////////////////////\r
           if (\r
               !headless &&\r
-              jalview.bin.Cache.getProperty("SHOW_STARTUP_FILE").equals("true") &&\r
-              jalview.bin.Cache.getProperty("STARTUP_FILE") != null)\r
+              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))\r
           {\r
 \r
-            file = jalview.bin.Cache.getProperty("STARTUP_FILE");\r
+            file = jalview.bin.Cache.getDefault("STARTUP_FILE",\r
+                                                "http://www.jalview.org/examples/exampleFile.jar");\r
             protocol = "File";\r
 \r
             if (file.indexOf("http:") > -1)\r