X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1116fe404ec5733ba508dbdae70a5513b3b29d4f;hb=7f7fc2e5533f7b00c86465f964e37c55bcf12fd7;hp=ff2d06a86de195fa66503178e20552954bec0f0b;hpb=a109b496d2e0793d041fde50d1d3b50d3a58d271;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index ff2d06a..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 @@ -86,11 +57,8 @@ public class Jalview 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" + +"-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" @@ -101,31 +69,35 @@ public class Jalview +"-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."); + +"-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; } - Cache.loadProperties(aparser.getValue("props")); - - try - { - initLogger(); - } - catch (Exception e) - { - System.err.println("Problems initializing the log4j system\n"); - } - + 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 ) @@ -134,6 +106,12 @@ public class Jalview { 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) @@ -142,10 +120,11 @@ public class Jalview desktop = new Desktop(); desktop.setVisible(true); + desktop.discoverer.start(); } - String file = null, protocol = null, format = null, groups=null; + String file = null, protocol = null, format = null, data=null; jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); file = aparser.getValue("open"); @@ -158,38 +137,86 @@ public class Jalview 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); - System.exit(1); + if(headless) + System.exit(1); } } protocol = "File"; - if (file.indexOf("http:") > -1) + 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); + format = new jalview.io.IdentifyFile().Identify(file, protocol); + - System.out.println("Opening: " + format + " file " + file); AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); - groups = aparser.getValue("groups"); - if (groups != null) + 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.parseGroupsFile(groups); + af.loadJalviewDataFile(data); + System.out.println("Added "+data); } + String imageName = "unnamed.png"; while (aparser.getSize() > 1) { @@ -232,14 +259,18 @@ public class Jalview } // We'll only open the default file if the desktop is visible. + // And the user ////////////////////// if ( - !headless && - jalview.bin.Cache.getProperty("SHOW_STARTUP_FILE").equals("true") && - jalview.bin.Cache.getProperty("STARTUP_FILE") != null) + !headless + && file==null + && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) + ) { - file = jalview.bin.Cache.getProperty("STARTUP_FILE"); + file = jalview.bin.Cache.getDefault("STARTUP_FILE", + "http://www.jalview.org/examples/exampleFile.jar"); + protocol = "File"; if (file.indexOf("http:") > -1) @@ -249,18 +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); } - } + fileLoader.LoadFile(file, protocol, format); - if (desktop==null) - System.exit(0); + } } }