X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1116fe404ec5733ba508dbdae70a5513b3b29d4f;hb=bb52159f5a5a001b9450fa05f110cdb9411a3e9a;hp=395875c82addd4e300b3b610ba864f79692bc937;hpb=f4f2089f39304cb43e4a07e792aceecd80e7256c;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 395875c..1116fe4 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 @@ -20,8 +20,6 @@ package jalview.bin; import jalview.gui.*; -import org.apache.log4j.*; - import javax.swing.*; import java.util.Vector; @@ -37,33 +35,6 @@ import java.util.Vector; */ public class Jalview { - /** - * Initialises the Apache Axis logger - */ - 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); - } /** * main class for Jalview application @@ -72,153 +43,234 @@ public class Jalview */ public static void main(String[] args) { - ArgsParser aparser = new ArgsParser(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")); - 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"); - } + 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! - String file = null, protocol = null, format = null, groups=null; - Desktop desktop = new Desktop(); + 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); + } - if(args==null || args.length==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(); } - 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); + 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.isVisible()) + if (file == null && desktop==null) { System.out.println("No files to open!"); System.exit(1); } - else if(!file.startsWith("http://")) + + if(file!=null) { - if (!(new java.io.File(file)).exists()) + System.out.println("Opening file: " + file); + + if (!file.startsWith("http://")) { - System.out.println("Can't find " + file); - System.exit(1); + if (! (new java.io.File(file)).exists()) + { + System.out.println("Can't find " + file); + if(headless) + System.exit(1); + } } - } - protocol = "File"; + protocol = "File"; - if (file.indexOf("http:") > -1) - { - protocol = "URL"; - } + if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1) + { + protocol = "URL"; + } - if(file.endsWith(".jar")) - format = "Jalview"; - else - format = jalview.io.IdentifyFile.Identify(file, protocol); - System.out.println("Opening: " + format + " file " + file); - AlignFrame af = desktop.LoadFileWaitTillLoaded(file, protocol, format); + if (file.endsWith(".jar")) + format = "Jalview"; + else + format = new jalview.io.IdentifyFile().Identify(file, protocol); - 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")) + AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); + + if(af==null) + { + System.out.println("error"); + return; + } + + data = aparser.getValue("colour"); + if(data!=null) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; + 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 ); } - else if (format.equalsIgnoreCase("imgMap")) + + + // Must maintain ability to use the groups flag + data = aparser.getValue("groups"); + if (data != null) { - af.createImageMap(new java.io.File(file), imageName); - System.out.println("Creating image map: " + file); - continue; + af.parseFeaturesFile(data, protocol); + System.out.println("Added "+data); } - else if (format.equalsIgnoreCase("eps")) + data = aparser.getValue("features"); + if (data != null) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); - continue; + af.parseFeaturesFile(data, protocol); + System.out.println("Added "+data); } - 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!!"); + data = aparser.getValue("annotations"); + if (data != null) + { + af.loadJalviewDataFile(data); + System.out.println("Added "+data); + } - } - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); + 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)) + // 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.gui.Preferences.startupFile; + file = jalview.bin.Cache.getDefault("STARTUP_FILE", + "http://www.jalview.org/examples/exampleFile.jar"); + protocol = "File"; if (file.indexOf("http:") > -1) @@ -228,17 +280,16 @@ public class Jalview if (file.endsWith(".jar")) { - Jalview2XML.LoadJalviewAlign(file); + format = "Jalview"; } else { - format = jalview.io.IdentifyFile.Identify(file, protocol); - desktop.LoadFile(file, protocol, format); + format = new jalview.io.IdentifyFile().Identify(file, protocol); } - } - if (!desktop.isVisible()) - System.exit(0); + fileLoader.LoadFile(file, protocol, format); + + } } }