-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
- *\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
-package jalview.bin;\r
-\r
-import jalview.gui.*;\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import java.applet.Applet;\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
-\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.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
- System.out.println("Goodbyeee");\r
-\r
- applet.stop();\r
- frame.setVisible(false);\r
-\r
- }\r
-\r
- public static void main(String[] args) {\r
- try{\r
- UIManager.setLookAndFeel(\r
- // "javax.swing.plaf.metal.MetalLookAndFeel"\r
- // "javax.swing.plaf.multi.MultiLookAndFeel"\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
-\r
- // JFrame.setDefaultLookAndFeelDecorated(true);\r
- Desktop frame = new Desktop();\r
- frame.setResizable(true);\r
- frame.setVisible(true);\r
-\r
-\r
- if(args!=null && args.length>0)\r
- {\r
- String file = args[0];\r
- jalview.bin.Cache.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
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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.util.Vector;
+
+
+/**
+ * Main class for Jalview Application
+ * <br>
+ * <br>start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview
+{
+
+ /**
+ * main class for Jalview application
+ *
+ * @param args open <em>filename</em>
+ */
+ public static void main(String[] args)
+ {
+ System.out.println("Java version: "+System.getProperty("java.version"));
+ System.out.println(System.getProperty("os.arch")+" "
+ +System.getProperty("os.name")+" "
+ +System.getProperty("os.version"));
+
+
+ ArgsParser aparser = new ArgsParser(args);
+ boolean headless = false;
+
+ 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"
+ +"-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+ +"-features FILE\tUse the given file to mark features on the alignment.\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."
+ +"\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ System.exit(0);
+ }
+
+ Cache.loadProperties(aparser.getValue("props")); // must do this before anything else!
+
+ if (aparser.contains("nodisplay"))
+ {
+ System.setProperty("java.awt.headless", "true");
+ }
+ if (System.getProperty("java.awt.headless") != null
+ && System.getProperty("java.awt.headless").equals("true"))
+ {
+ headless = true;
+ }
+
+ try
+ {
+ Cache.initLogger();
+ }
+ catch (java.lang.NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out.println(
+ "\nEssential logging libraries not found."
+ +"\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+ System.exit(0);
+ }
+
+ Desktop desktop = null;
+ if( !headless )
+ {
+ try
+ {
+ UIManager.setLookAndFeel(
+ UIManager.getSystemLookAndFeelClassName()
+ // UIManager.getCrossPlatformLookAndFeelClassName()
+//"com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
+//"javax.swing.plaf.metal.MetalLookAndFeel"
+//"com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
+//"com.sun.java.swing.plaf.motif.MotifLookAndFeel"
+
+ );
+ }
+ catch (Exception ex)
+ {
+ }
+
+ desktop = new Desktop();
+ desktop.setVisible(true);
+ desktop.discoverer.start();
+ }
+
+
+ String file = null, protocol = null, format = null, data=null;
+ jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
+
+ file = aparser.getValue("open");
+
+ if (file == null && desktop==null)
+ {
+ System.out.println("No files to open!");
+ System.exit(1);
+ }
+
+ if(file!=null)
+ {
+
+ if (!file.startsWith("http://"))
+ {
+ if (! (new java.io.File(file)).exists())
+ {
+ System.out.println("Can't find " + file);
+ if(headless)
+ System.exit(1);
+ }
+ }
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1)
+ {
+ protocol = "URL";
+ }
+
+ if (file.endsWith(".jar"))
+ format = "Jalview";
+ else
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+
+ System.out.println("Opening: " + format + " file " + file);
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+
+ data = aparser.getValue("colour");
+ if(data!=null)
+ {
+ data.replaceAll("%20", " ");
+
+ jalview.schemes.ColourSchemeI cs =
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().
+ getAlignment(), data);
+
+ if(cs == null)
+ {
+ jalview.schemes.UserColourScheme ucs
+ = new jalview.schemes.UserColourScheme("white");
+ ucs.parseAppletParameter(data);
+ cs = ucs;
+ }
+
+ System.out.println("colour is " + data);
+ af.changeColour( cs );
+ }
+
+
+ // Must maintain ability to use the groups flag
+ data = aparser.getValue("groups");
+ if (data != null)
+ {
+ af.parseFeaturesFile(data, protocol);
+ System.out.println("Added "+data);
+ }
+ data = aparser.getValue("features");
+ if (data != null)
+ {
+ af.parseFeaturesFile(data, protocol);
+ System.out.println("Added "+data);
+ }
+
+ data = aparser.getValue("annotations");
+ if (data != null)
+ {
+ af.loadJalviewDataFile(data);
+ System.out.println("Added "+data);
+ }
+
+
+ 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());
+ }
+ }
+
+ // We'll only open the default file if the desktop is visible.
+ // And the user
+ //////////////////////
+ if (
+ !headless
+ && file==null
+ && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
+ )
+ {
+
+ file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+ "http://www.jalview.org/examples/exampleFile.jar");
+
+ protocol = "File";
+
+ if (file.indexOf("http:") > -1)
+ {
+ protocol = "URL";
+ }
+
+ if (file.endsWith(".jar"))
+ {
+ new Jalview2XML().LoadJalviewAlign(file);
+ }
+ else
+ {
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ new jalview.io.FileLoader().LoadFile(file, protocol, format);
+ }
+ }
+ }
+}
+
+ class ArgsParser
+ {
+ Vector vargs = null;
+ public ArgsParser(String [] args)
+ {
+ vargs = new Vector();
+ for (int i = 0; i < args.length; i++)
+ {
+ String arg = args[i].trim();
+ if (arg.charAt(0) == '-')
+ arg = arg.substring(1);
+ vargs.addElement(arg);
+ }
+ }
+
+ 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;
+ }
+
+ 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();
+ }
+
+ }
git://source.jalview.org / jalview.git / blobdiff