X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=395875c82addd4e300b3b610ba864f79692bc937;hb=b8d09897dacc7b0ad203982b4578e2c1d8929142;hp=e1137286523f292ae2fddf743116ba1d451699fd;hpb=8ba4a1459e6fa628d4988da2897232cd00c912e4;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e113728..395875c 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1,102 +1,294 @@
-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
- * AM Waterhouse
- *******************/
-
-
+ * 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 org.apache.log4j.*;
+
import javax.swing.*;
-import java.awt.event.*;
-import jalview.io.*;
+import java.util.Vector;
-public class Jalview extends JApplet
+
+/**
+ * Main class for Jalview Application
+ *
+ *
start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview
{
- public static JApplet applet;
- Desktop frame;
- public void init()
- {
- applet = this;
-
- frame = new Desktop();
- frame.setResizable(true);
- frame.setVisible(true);
- frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
- frame.addWindowListener(new WindowAdapter()
+ /**
+ * Initialises the Apache Axis logger
+ */
+ private static void initLogger()
{
- public void windowClosing(WindowEvent e)
- {
- applet.stop();
- applet.destroy();
- }
- });
+ Logger laxis = Logger.getLogger("org.apache.axis");
+ Logger lcastor = Logger.getLogger("org.exolab.castor");
- String file = getParameter("alignment");
+ if (Cache.getProperty("logs.Axis.Level") == null)
+ {
+ Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
+ }
- if(file!=null)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);
- String protocol = "File";
- if (file.indexOf("http:") > -1)
- protocol = "URL";
+ if (Cache.getProperty("logs.Castor.Level") == null)
+ {
+ Cache.setProperty("logs.Castor.Level", Level.INFO.toString());
+ }
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
+ laxis.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
+ lcastor.setLevel(Level.toLevel(Cache.getProperty("logs.Castor.Level")));
- frame.LoadFile(file, protocol, format);
+ ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
+ "System.err");
+ ap.setName("JalviewLogger");
+ laxis.addAppender(ap);
+ lcastor.addAppender(ap);
}
- }
-
- public void destroy()
- {
- if(applet!=null)
- applet.stop();
- else
- System.exit(0);
- frame.setVisible(false);
- }
-
- public static void main(String[] args) {
-
- Cache.loadProperties();
-
- try{
- UIManager.setLookAndFeel(
- // "javax.swing.plaf.metal.MetalLookAndFeel"
- // "javax.swing.plaf.multi.MultiLookAndFeel"
- UIManager.getSystemLookAndFeelClassName()
- //.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)
- {}
- // JFrame.setDefaultLookAndFeelDecorated(true);
- Desktop frame = new Desktop();
- frame.setResizable(true);
- frame.setVisible(true);
+ /**
+ * main class for Jalview application
+ *
+ * @param args open filename
+ */
+ public static void main(String[] args)
+ {
+ ArgsParser aparser = new ArgsParser(args);
+
+ try
+ {
+ UIManager.setLookAndFeel(
+ // "javax.swing.plaf.metal.MetalLookAndFeel"
+ // "javax.swing.plaf.multi.MultiLookAndFeel"
+ UIManager.getSystemLookAndFeelClassName());
+ }
+ catch (Exception ex)
+ {
+ }
+
+ Cache.loadProperties(aparser.getValue("props"));
+ jalview.gui.Preferences.initPreferences();
+ try
+ {
+ initLogger();
+ }
+ catch (Exception e)
+ {
+ System.err.println("Problems initializing the log4j system\n");
+ }
+
+
+ String file = null, protocol = null, format = null, groups=null;
+ Desktop desktop = new Desktop();
+
+
+ if(args==null || args.length==0)
+ {
+ desktop.setVisible(true);
+ }
+ else
+ {
+ if( aparser.contains("help") || aparser.contains("h") )
+ {
+ System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+ +"-nodisplay\tRun Jalview without User Interface.\n"
+ +"-props FILE\tUse the given Jalview properties file instead of users default.\n"
+ +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"
+ +"TEXTSEQUENCE_IDSEQUENCE_INDEXSTART_RESIDUEEND_RESIDUECOLOUR\n"
+ +"SequenceID is used in preference to SequenceIndex if both are provided.\n"
+ +"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"
+ +"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"
+ +"-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+ +"-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+ +"-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+ +"-msf FILE\tCreate alignment file FILE in MSF format.\n"
+ +"-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+ +"-pir FILE\tCreate alignment file FILE in PIR format.\n"
+ +"-blc FILE\tCreate alignment file FILE in BLC format.\n"
+ +"-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+ +"-png FILE\tCreate PNG image FILE from alignment.\n"
+ +"-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+ +"-eps FILE\tCreate EPS file FILE from alignment.");
+ System.exit(0);
+
+ }
+
+ if (!aparser.contains("nodisplay"))
+ desktop.setVisible(true);
+
+ file = aparser.getValue("open");
+
+ if (file == null && !desktop.isVisible())
+ {
+ System.out.println("No files to open!");
+ System.exit(1);
+ }
+ else if(!file.startsWith("http://"))
+ {
+ if (!(new java.io.File(file)).exists())
+ {
+ System.out.println("Can't find " + file);
+ System.exit(1);
+ }
+ }
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ if(file.endsWith(".jar"))
+ format = "Jalview";
+ else
+ format = jalview.io.IdentifyFile.Identify(file, protocol);
+ System.out.println("Opening: " + format + " file " + file);
- if(args!=null && args.length>0)
+ AlignFrame af = desktop.LoadFileWaitTillLoaded(file, protocol, format);
+
+ groups = aparser.getValue("groups");
+ if(groups!=null)
+ {
+ af.parseGroupsFile(groups);
+ }
+
+ String imageName = "unnamed.png";
+ while (aparser.getSize() > 1)
+ {
+ format = aparser.nextValue();
+ file = aparser.nextValue();
+
+ if (format.equalsIgnoreCase("png"))
+ {
+ af.createPNG(new java.io.File(file));
+ imageName = (new java.io.File(file)).getName();
+ System.out.println("Creating PNG image: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("imgMap"))
+ {
+ af.createImageMap(new java.io.File(file), imageName);
+ System.out.println("Creating image map: " + file);
+ continue;
+ }
+ else if (format.equalsIgnoreCase("eps"))
+ {
+ System.out.println("Creating EPS file: " + file);
+ af.createEPS(new java.io.File(file));
+ continue;
+ }
+
+ if (af.saveAlignment(file, format))
+ System.out.println("Written alignment in " + format +
+ " format to " + file);
+ else
+ System.out.println("Error writing file " + file + " in " + format +
+ " format!!");
+
+ }
+
+ while (aparser.getSize() > 0)
+ {
+ System.out.println("Unknown arg: " + aparser.nextValue());
+ }
+ }
+
+ if (jalview.gui.Preferences.showStartupFile &&
+ (jalview.gui.Preferences.startupFile != null))
+ {
+
+ file = jalview.gui.Preferences.startupFile;
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ Jalview2XML.LoadJalviewAlign(file);
+ }
+ else
+ {
+ format = jalview.io.IdentifyFile.Identify(file, protocol);
+ desktop.LoadFile(file, protocol, format);
+ }
+ }
+
+ if (!desktop.isVisible())
+ System.exit(0);
+ }
+}
+
+ class ArgsParser
+ {
+ Vector vargs = null;
+ public ArgsParser(String [] args)
+ {
+ vargs = new Vector();
+ for (int i = 0; i < args.length; i++)
{
- String file = args[0];
- String protocol = "File";
- if(file.indexOf("http:")>-1)
- protocol = "URL";
+ String arg = args[i].trim();
+ if (arg.charAt(0) == '-')
+ arg = arg.substring(1);
+ vargs.addElement(arg);
+ }
+ }
- String format = jalview.io.IdentifyFile.Identify(file, protocol);
+ public String getValue(String arg)
+ {
+ int index = vargs.indexOf(arg);
+ String ret = null;
+ if (index != -1)
+ {
+ ret = vargs.elementAt(index + 1).toString();
+ vargs.removeElementAt(index);
+ vargs.removeElementAt(index);
+ }
+ return ret;
+ }
- frame.LoadFile(file, protocol, format);
+ public boolean contains(String arg)
+ {
+ if(vargs.contains(arg))
+ {
+ vargs.removeElement(arg);
+ return true;
}
+ else
+ return false;
+ }
+ public String nextValue()
+ {
+ return vargs.remove(0).toString();
}
-}
+ public int getSize()
+ {
+ return vargs.size();
+ }
+ }