Alignment of node labels modified

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ff2d06a..9a85471 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -37,33 +37,6 @@ import java.util.Vector;
  */\r
 public class Jalview\r
 {\r
-    /**\r
-     * Initialises the Apache Axis logger\r
-     */\r
-    private static void initLogger()\r
-    {\r
-        Logger laxis = Logger.getLogger("org.apache.axis");\r
-        Logger lcastor = Logger.getLogger("org.exolab.castor");\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
-\r
-        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
-                "System.err");\r
-        ap.setName("JalviewLogger");\r
-        laxis.addAppender(ap);\r
-        lcastor.addAppender(ap);\r
-    }\r
 \r
     /**\r
      * main class for Jalview application\r
@@ -115,17 +88,20 @@ public class Jalview
             headless = true;\r
           }\r
 \r
-        Cache.loadProperties(aparser.getValue("props"));\r
-\r
-        try\r
-        {\r
-          initLogger();\r
-        }\r
-        catch (Exception e)\r
-        {\r
-          System.err.println("Problems initializing the log4j system\n");\r
-        }\r
+          try\r
+          {\r
+            Cache.initLogger();\r
+          }\r
+          catch (java.lang.NoClassDefFoundError error)\r
+          {\r
+            error.printStackTrace();\r
+            System.out.println(\r
+                "\nEssential logging libraries not found."\r
+                +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");\r
+            System.exit(0);\r
+          }\r
 \r
+        Cache.loadProperties(aparser.getValue("props"));\r
 \r
         Desktop desktop = null;\r
         if( !headless )\r
@@ -133,7 +109,13 @@ 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 +124,7 @@ public class Jalview
 \r
           desktop = new Desktop();\r
           desktop.setVisible(true);\r
+          desktop.discoverer.start();\r
         }\r
 \r
 \r
@@ -235,11 +218,11 @@ 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