X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e780f78cc12371231b4b052afc2f024f16372f97;hb=8c2ee75d86492f03e4c01404855f9ad2dd305719;hp=3ab3bf467fbbda66378bbf5501c5295c1d64408e;hpb=c3ded07cf4a7708564e9878bf1763fe837e03ddc;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 3ab3bf4..e780f78 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -25,9 +25,6 @@ import org.apache.log4j.*;
 import javax.swing.*;
 
 import java.util.Vector;
-import jalview.datamodel.Alignment;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.SequenceI;
 
 
 /**
@@ -43,29 +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);
     }
 
     /**
@@ -75,6 +67,12 @@ public class Jalview
      */
     public static void main(String[] args)
     {
+      System.out.println("Java version: "+System.getProperty("java.version"));
+      System.out.println(System.getProperty("os.arch")+" "
+                         +System.getProperty("os.name")+" "
+                         +System.getProperty("os.version"));
+
+
       ArgsParser aparser = new ArgsParser(args);
       boolean headless = false;
 
@@ -103,18 +101,17 @@ public class Jalview
           }
 
 
-     if (aparser.contains("nodisplay"))
-      System.setProperty("java.awt.headless", "true");
-
-    if(   System.getProperty("java.awt.headless") != null
-          && System.getProperty("java.awt.headless").equals("true"))
-      {
-        headless = true;
-      }
+          if (aparser.contains("nodisplay"))
+            System.setProperty("java.awt.headless", "true");
 
+          if (System.getProperty("java.awt.headless") != null
+              && System.getProperty("java.awt.headless").equals("true"))
+          {
+            headless = true;
+          }
 
         Cache.loadProperties(aparser.getValue("props"));
-        jalview.gui.Preferences.initPreferences();
+
         try
         {
           initLogger();
@@ -131,9 +128,14 @@ public class Jalview
           try
           {
             UIManager.setLookAndFeel(
-                //  "javax.swing.plaf.metal.MetalLookAndFeel"
-                //  "javax.swing.plaf.multi.MultiLookAndFeel"
-                UIManager.getSystemLookAndFeelClassName());
+                   UIManager.getSystemLookAndFeelClassName()
+            //        UIManager.getCrossPlatformLookAndFeelClassName()
+//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
+//"javax.swing.plaf.metal.MetalLookAndFeel"
+//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
+//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
+                );
           }
           catch (Exception ex)
           {
@@ -141,6 +143,7 @@ public class Jalview
 
           desktop = new Desktop();
           desktop.setVisible(true);
+          desktop.discoverer.start();
         }
 
 
@@ -234,11 +237,11 @@ public class Jalview
         //////////////////////
           if (
               !headless &&
-              jalview.gui.Preferences.showStartupFile &&
-              jalview.gui.Preferences.startupFile != null)
+              jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
           {
 
-            file = jalview.gui.Preferences.startupFile;
+            file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+                                                "http://www.jalview.org/examples/exampleFile.jar");
             protocol = "File";
 
             if (file.indexOf("http:") > -1)