X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fbin%2FJalview.java;h=c11d051a49d4daef9f8343b0246e4fb98221ff70;hb=6e71f42b0a3713ddbc3054e7ea9d8f5088130ec9;hp=56c923ac6ae31a06dff694552745f8010d51f2c2;hpb=6128e84256007e63797e8b51ff24fe7165129653;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 56c923a..c11d051 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,124 +1,159 @@
-/********************
- * 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 extends JApplet
-{
-  public static JApplet applet;
-  Desktop frame;
-  public void init()
-  {
-    applet = this;
-    Cache.loadProperties();
-
-    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());
-    }
+import java.awt.event.*;
 
-    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) {
-
-    Cache.loadProperties();
-    try {
-      initLogger();
-    } catch (Exception e) {
-      System.out.println("Problems initializing the log4j system\n"+e);
-    }
-    try{
-       UIManager.setLookAndFeel(
-   //   "javax.swing.plaf.metal.MetalLookAndFeel"
-    //  "javax.swing.plaf.multi.MultiLookAndFeel"
-         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"
-     );
-     }
-     catch (Exception ex)
-     {}
+import javax.swing.*;
 
-     Desktop frame = new Desktop();
-     frame.setResizable(true);
-     frame.setVisible(true);
 
+public class Jalview extends JApplet {
+    public static JApplet applet;
+    Desktop frame;
 
+    public void init() {
+        applet = this;
+        Cache.loadProperties();
+        jalview.gui.Preferences.initPreferences();
 
-     if(args!=null && args.length>0)
-     {
-         String file=null;
-         if(args[0].equals("-open"))
-           file = args[1];
-         else
-           file = args[0];
+        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 protocol = "File";
-         if(file.indexOf("http:")>-1)
-           protocol = "URL";
+        String file = getParameter("alignment");
 
-         String format = jalview.io.IdentifyFile.Identify(file, protocol);
+        if (file != null) {
+            jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);
 
-         frame.LoadFile(file, protocol, format);
-     }
+            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 laxis = Logger.getLogger("org.apache.axis");
+        Logger lcastor = Logger.getLogger("org.exolab.castor");
+        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")));
+
+        ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+                "System.err");
+        ap.setName("JalviewLogger");
+        laxis.addAppender(ap);
+        lcastor.addAppender(ap);
+    }
 
+    public static void main(String[] args) {
+        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.getSystemLookAndFeelClassName());
+        } catch (Exception ex) {
+        }
+
+        Desktop frame = new Desktop();
+        frame.setResizable(true);
+        frame.setVisible(true);
+
+        if ((args != null) && (args.length > 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";
+            }
+
+            String format = jalview.io.IdentifyFile.Identify(file, protocol);
+
+            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);
+            }
+        }
+    }
+}