Check startup file is not null

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

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index c54a347..88e6236 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,8 @@ public class Jalview extends JApplet
   public void init()\r
   {\r
     applet = this;\r
+    Cache.loadProperties();\r
+    jalview.gui.Preferences.initPreferences();\r
 \r
     frame = new Desktop();\r
     frame.setResizable(true);\r
@@ -63,7 +65,11 @@ public class Jalview extends JApplet
 \r
   private static void initLogger() {\r
     Logger l = Logger.getLogger("org.apache.axis");\r
-    l.setLevel(Level.INFO);\r
+    if (Cache.getProperty("logs.Axis.Level")==null) {\r
+      Cache.setProperty("logs.Axis.Level", Level.INFO.toString());\r
+    }\r
+\r
+    l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));\r
     ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");\r
     ap.setName("Axis");\r
     l.addAppender(ap);\r
@@ -71,10 +77,12 @@ public class Jalview extends JApplet
    public static void main(String[] args) {\r
 \r
     Cache.loadProperties();\r
+    jalview.gui.Preferences.initPreferences();\r
     try {\r
       initLogger();\r
     } catch (Exception e) {\r
-      System.out.println("Failed to initialise the log4j system for axis\n"+e);\r
+      System.err.println("Problems initializing the log4j system\n");\r
+      e.printStackTrace();\r
     }\r
     try{\r
        UIManager.setLookAndFeel(\r
@@ -90,15 +98,20 @@ public class Jalview extends JApplet
      catch (Exception ex)\r
      {}\r
 \r
-    // JFrame.setDefaultLookAndFeelDecorated(true);\r
      Desktop frame = new Desktop();\r
      frame.setResizable(true);\r
      frame.setVisible(true);\r
 \r
 \r
+\r
      if(args!=null && args.length>0)\r
      {\r
-         String file = args[0];\r
+         String file=null;\r
+         if(args[0].equals("-open"))\r
+           file = args[1];\r
+         else\r
+           file = args[0];\r
+\r
          String protocol = "File";\r
          if(file.indexOf("http:")>-1)\r
            protocol = "URL";\r
@@ -108,6 +121,25 @@ public class Jalview extends JApplet
          frame.LoadFile(file, protocol, format);\r
      }\r
 \r
+     if(jalview.gui.Preferences.showStartupFile &&\r
+         jalview.gui.Preferences.startupFile!=null)\r
+     {\r
+       String file = jalview.gui.Preferences.startupFile;\r
+       String protocol = "File";\r
+       if (file.indexOf("http:") > -1)\r
+         protocol = "URL";\r
+\r
+       if(file.endsWith(".jar"))\r
+         Jalview2XML.LoadJalviewAlign(file);\r
+       else\r
+       {\r
+         String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+         frame.LoadFile(file, protocol, format);\r
+       }\r
+     }\r
+\r
+\r
+\r
    }\r
 \r
 }\r