X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=88e6236faab154e6a6fe0fe7790e5ecb30821d68;hb=dd4cc875a15a345a7245083fba46ce6013d8cff9;hp=f7a2dcd70d3a36aaf695f89326d8e8efed68b50d;hpb=792e2bd7bfa0bb50682055537838275581284f9f;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f7a2dcd..88e6236 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -23,6 +23,8 @@ public class Jalview extends JApplet
   public void init()
   {
     applet = this;
+    Cache.loadProperties();
+    jalview.gui.Preferences.initPreferences();
 
     frame = new Desktop();
     frame.setResizable(true);
@@ -75,10 +77,12 @@ public class Jalview extends JApplet
    public static void main(String[] args) {
 
     Cache.loadProperties();
+    jalview.gui.Preferences.initPreferences();
     try {
       initLogger();
     } catch (Exception e) {
-      System.out.println("Problems initializing the log4j system\n"+e);
+      System.err.println("Problems initializing the log4j system\n");
+      e.printStackTrace();
     }
     try{
        UIManager.setLookAndFeel(
@@ -99,9 +103,15 @@ public class Jalview extends JApplet
      frame.setVisible(true);
 
 
+
      if(args!=null && args.length>0)
      {
-         String file = args[0];
+         String file=null;
+         if(args[0].equals("-open"))
+           file = args[1];
+         else
+           file = args[0];
+
          String protocol = "File";
          if(file.indexOf("http:")>-1)
            protocol = "URL";
@@ -111,6 +121,25 @@ public class Jalview extends JApplet
          frame.LoadFile(file, protocol, format);
      }
 
+     if(jalview.gui.Preferences.showStartupFile &&
+         jalview.gui.Preferences.startupFile!=null)
+     {
+       String file = jalview.gui.Preferences.startupFile;
+       String protocol = "File";
+       if (file.indexOf("http:") > -1)
+         protocol = "URL";
+
+       if(file.endsWith(".jar"))
+         Jalview2XML.LoadJalviewAlign(file);
+       else
+       {
+         String format = jalview.io.IdentifyFile.Identify(file, protocol);
+         frame.LoadFile(file, protocol, format);
+       }
+     }
+
+
+
    }
 
 }