-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.bin;\r
\r
import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
+\r
import jalview.io.*;\r
\r
import org.apache.log4j.*;\r
\r
-public class Jalview extends JApplet\r
-{\r
- public static JApplet applet;\r
- Desktop frame;\r
- public void init()\r
- {\r
- applet = this;\r
- Cache.loadProperties();\r
-\r
- frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent e)\r
- {\r
- applet.stop();\r
- applet.destroy();\r
- }\r
- });\r
-\r
- String file = getParameter("alignment");\r
-\r
- if(file!=null)\r
- {\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
- String protocol = "File";\r
- if (file.indexOf("http:") > -1)\r
- protocol = "URL";\r
-\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
-\r
- frame.LoadFile(file, protocol, format);\r
- }\r
- }\r
-\r
- public void destroy()\r
- {\r
- if(applet!=null)\r
- applet.stop();\r
- else\r
- System.exit(0);\r
- frame.setVisible(false);\r
- }\r
-\r
- private static void initLogger() {\r
- Logger l = Logger.getLogger("org.apache.axis");\r
- if (Cache.getProperty("logs.Axis.Level")==null) {\r
- Cache.setProperty("logs.Axis.Level", Level.INFO.toString());\r
- }\r
+import java.awt.event.*;\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
- }\r
- public static void main(String[] args) {\r
-\r
- Cache.loadProperties();\r
- try {\r
- initLogger();\r
- } catch (Exception e) {\r
- System.out.println("Problems initializing the log4j system\n"+e);\r
- }\r
- try{\r
- UIManager.setLookAndFeel(\r
- // "javax.swing.plaf.metal.MetalLookAndFeel"\r
- // "javax.swing.plaf.multi.MultiLookAndFeel"\r
- UIManager.getSystemLookAndFeelClassName()\r
- // UIManager.getCrossPlatformLookAndFeelClassName()\r
- // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"\r
- // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"\r
- // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"\r
- );\r
- }\r
- catch (Exception ex)\r
- {}\r
+import javax.swing.*;\r
\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
\r
+public class Jalview extends JApplet {\r
+ public static JApplet applet;\r
+ Desktop frame;\r
\r
+ public void init() {\r
+ applet = this;\r
+ Cache.loadProperties();\r
+ jalview.gui.Preferences.initPreferences();\r
\r
- if(args!=null && args.length>0)\r
- {\r
- String file=null;\r
- if(args[0].equals("-open"))\r
- file = args[1];\r
- else\r
- file = args[0];\r
+ frame = new Desktop();\r
+ frame.setResizable(true);\r
+ frame.setVisible(true);\r
+ frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);\r
+ frame.addWindowListener(new WindowAdapter() {\r
+ public void windowClosing(WindowEvent e) {\r
+ applet.stop();\r
+ applet.destroy();\r
+ }\r
+ });\r
\r
- String protocol = "File";\r
- if(file.indexOf("http:")>-1)\r
- protocol = "URL";\r
+ String file = getParameter("alignment");\r
\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ if (file != null) {\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);\r
\r
- frame.LoadFile(file, protocol, format);\r
- }\r
+ String protocol = "File";\r
\r
- }\r
+ if (file.indexOf("http:") > -1) {\r
+ protocol = "URL";\r
+ }\r
\r
-}\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
\r
+ frame.LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+\r
+ public void destroy() {\r
+ if (applet != null) {\r
+ applet.stop();\r
+ } else {\r
+ System.exit(0);\r
+ }\r
+\r
+ frame.setVisible(false);\r
+ }\r
+\r
+ private static void initLogger() {\r
+ Logger l = Logger.getLogger("org.apache.axis");\r
+\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
+\r
+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),\r
+ "System.err");\r
+ ap.setName("Axis");\r
+ l.addAppender(ap);\r
+ }\r
+\r
+ public static void main(String[] args) {\r
+ Cache.loadProperties();\r
+ jalview.gui.Preferences.initPreferences();\r
+\r
+ try {\r
+ initLogger();\r
+ } catch (Exception e) {\r
+ System.err.println("Problems initializing the log4j system\n");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ try {\r
+ UIManager.setLookAndFeel(\r
+ // "javax.swing.plaf.metal.MetalLookAndFeel"\r
+ // "javax.swing.plaf.multi.MultiLookAndFeel"\r
+ UIManager.getSystemLookAndFeelClassName());\r
+ } catch (Exception ex) {\r
+ }\r
+\r
+ Desktop frame = new Desktop();\r
+ frame.setResizable(true);\r
+ frame.setVisible(true);\r
+\r
+ if ((args != null) && (args.length > 0)) {\r
+ String file = null;\r
+\r
+ if (args[0].equals("-open")) {\r
+ file = args[1];\r
+ } else {\r
+ file = args[0];\r
+ }\r
+\r
+ String protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1) {\r
+ protocol = "URL";\r
+ }\r
+\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+\r
+ frame.LoadFile(file, protocol, format);\r
+ }\r
+\r
+ if (jalview.gui.Preferences.showStartupFile &&\r
+ (jalview.gui.Preferences.startupFile != null)) {\r
+ String file = jalview.gui.Preferences.startupFile;\r
+ String protocol = "File";\r
+\r
+ if (file.indexOf("http:") > -1) {\r
+ protocol = "URL";\r
+ }\r
+\r
+ if (file.endsWith(".jar")) {\r
+ Jalview2XML.LoadJalviewAlign(file);\r
+ } else {\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ frame.LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff