Init PCA in thread

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

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