X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1116fe404ec5733ba508dbdae70a5513b3b29d4f;hb=2d740577b9dda7b872d808e2419ca66e2ad0eb4b;hp=2899abb7f8c7b1eb985e110f700b0aeb76e5a9e7;hpb=6a9c2893f6ac47be883141c0a716d36f9dc67db1;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 2899abb..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 @@ -57,11 +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" @@ -72,10 +69,12 @@ 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")) { @@ -100,16 +99,14 @@ public class Jalview System.exit(0); } - Cache.loadProperties(aparser.getValue("props")); - Desktop desktop = null; if( !headless ) { try { UIManager.setLookAndFeel( - UIManager.getSystemLookAndFeelClassName() - // UIManager.getCrossPlatformLookAndFeelClassName() + UIManager.getSystemLookAndFeelClassName() + // UIManager.getCrossPlatformLookAndFeelClassName() //"com.sun.java.swing.plaf.gtk.GTKLookAndFeel" //"javax.swing.plaf.metal.MetalLookAndFeel" //"com.sun.java.swing.plaf.windows.WindowsLookAndFeel" @@ -127,7 +124,7 @@ public class Jalview } - 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"); @@ -140,6 +137,7 @@ public class Jalview if(file!=null) { + System.out.println("Opening file: " + file); if (!file.startsWith("http://")) { @@ -153,26 +151,72 @@ public class Jalview 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) { - af.parseGroupsFile(groups); + 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) { @@ -215,14 +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.getDefault("SHOW_STARTUP_FILE", true)) + !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) @@ -232,13 +280,15 @@ 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); + } } }