/* * Jalview - A Sequence Alignment Editor and Viewer * Copyright (C) 2007 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 java.util.*; import javax.swing.*; import jalview.gui.*; /** * Main class for Jalview Application *
*
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 filename */ 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." + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires." + "\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; 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) {} if (!headless) { desktop = new Desktop(); desktop.setVisible(true); desktop.discoverer.start(); String url = aparser.getValue("questionnaire"); if (url != null) { // Start the desktop questionnaire prompter with the specified questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); } else { if (Cache.getProperty("NOQUESTIONNAIRES") == null) { // Start the desktop questionnaire prompter with the specified questionnaire // String defurl = "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; Cache.log.debug("Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); } } } 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) { System.out.println("Opening file: " + file); 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); } AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); if (af == null) { System.out.println("error"); return; } 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_2_3.jar"); protocol = "File"; if (file.indexOf("http:") > -1) { protocol = "URL"; } if (file.endsWith(".jar")) { format = "Jalview"; } else { format = new jalview.io.IdentifyFile().Identify(file, protocol); } 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(); } }