X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=2524abd87dec2655613f3940b6cf23789c5b8506;hb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;hp=be0440a8ba6ab9d613a059613f059320f30aefcd;hpb=740623d8f15a4edaa7c1c6383c06cc6fc194a3c4;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index be0440a..2524abd 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,26 +1,105 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 
 package jalview.bin;
 
 import jalview.gui.*;
 import javax.swing.*;
+import java.awt.event.*;
+import jalview.io.*;
+
+import org.apache.log4j.*;
 
-public class Jalview
+public class Jalview extends JApplet
 {
+  public static JApplet applet;
+  Desktop frame;
+  public void init()
+  {
+    applet = this;
+    Cache.loadProperties();
+    jalview.gui.Preferences.initPreferences();
+
+    frame = new Desktop();
+    frame.setResizable(true);
+    frame.setVisible(true);
+    frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
+    frame.addWindowListener(new WindowAdapter()
+    {
+      public void windowClosing(WindowEvent e)
+      {
+          applet.stop();
+          applet.destroy();
+      }
+    });
+
+    String file = getParameter("alignment");
+
+    if(file!=null)
+    {
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);
+      String protocol = "File";
+      if (file.indexOf("http:") > -1)
+        protocol = "URL";
+
+      String format = jalview.io.IdentifyFile.Identify(file, protocol);
 
+      frame.LoadFile(file, protocol, format);
+    }
+  }
+
+  public void destroy()
+  {
+    if(applet!=null)
+      applet.stop();
+    else
+      System.exit(0);
+    frame.setVisible(false);
+  }
+
+  private static void initLogger() {
+    Logger l = Logger.getLogger("org.apache.axis");
+    if (Cache.getProperty("logs.Axis.Level")==null) {
+      Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
+    }
+
+    l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
+    ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");
+    ap.setName("Axis");
+    l.addAppender(ap);
+  }
    public static void main(String[] args) {
-     try{
+
+    Cache.loadProperties();
+    jalview.gui.Preferences.initPreferences();
+    try {
+      initLogger();
+    } catch (Exception e) {
+      System.err.println("Problems initializing the log4j system\n");
+      e.printStackTrace();
+    }
+    try{
        UIManager.setLookAndFeel(
    //   "javax.swing.plaf.metal.MetalLookAndFeel"
     //  "javax.swing.plaf.multi.MultiLookAndFeel"
-         UIManager.getCrossPlatformLookAndFeelClassName()
+         UIManager.getSystemLookAndFeelClassName()
+     //    UIManager.getCrossPlatformLookAndFeelClassName()
        // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
        //   "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
        //  "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
@@ -29,16 +108,20 @@ public class Jalview
      catch (Exception ex)
      {}
 
-    // JFrame.setDefaultLookAndFeelDecorated(true);
      Desktop frame = new Desktop();
      frame.setResizable(true);
      frame.setVisible(true);
 
 
+
      if(args!=null && args.length>0)
      {
-         String file = args[0];
-         jalview.bin.Cache.LAST_DIRECTORY = file;
+         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";
@@ -48,6 +131,26 @@ public class Jalview
          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);
+       }
+     }
+
+
+
    }
 
 }
+