X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e5ad207ecd5b77f53c32f2e368c344d59c4ab5d0;hb=521ce3c96d5977a9bd941894eda7a13dd09deea9;hp=3ab3bf467fbbda66378bbf5501c5295c1d64408e;hpb=c3ded07cf4a7708564e9878bf1763fe837e03ddc;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 3ab3bf4..e5ad207 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,14 +20,9 @@ package jalview.bin; import jalview.gui.*; -import org.apache.log4j.*; - import javax.swing.*; import java.util.Vector; -import jalview.datamodel.Alignment; -import jalview.io.FormatAdapter; -import jalview.datamodel.SequenceI; /** @@ -40,33 +35,6 @@ import jalview.datamodel.SequenceI; */ 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 @@ -75,6 +43,12 @@ public class Jalview */ 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; @@ -83,11 +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" @@ -98,32 +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")); - jalview.gui.Preferences.initPreferences(); - try - { - initLogger(); - } - catch (Exception e) - { - System.err.println("Problems initializing the log4j system\n"); - } + 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 ) @@ -131,9 +105,14 @@ public class Jalview try { UIManager.setLookAndFeel( - // "javax.swing.plaf.metal.MetalLookAndFeel" - // "javax.swing.plaf.multi.MultiLookAndFeel" - UIManager.getSystemLookAndFeelClassName()); + 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) { @@ -141,10 +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"); @@ -163,7 +143,8 @@ public class Jalview if (! (new java.io.File(file)).exists()) { System.out.println("Can't find " + file); - System.exit(1); + if(headless) + System.exit(1); } } @@ -177,18 +158,56 @@ public class Jalview 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) + 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.parseGroupsFile(groups); + 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) { @@ -231,14 +250,18 @@ public class Jalview } // We'll only open the default file if the desktop is visible. + // And the user ////////////////////// if ( - !headless && - jalview.gui.Preferences.showStartupFile && - jalview.gui.Preferences.startupFile != null) + !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) @@ -248,18 +271,14 @@ public class Jalview if (file.endsWith(".jar")) { - Jalview2XML.LoadJalviewAlign(file); + new Jalview2XML().LoadJalviewAlign(file); } else { - format = jalview.io.IdentifyFile.Identify(file, protocol); - desktop.LoadFile(file, protocol, format); + format = new jalview.io.IdentifyFile().Identify(file, protocol); + new jalview.io.FileLoader().LoadFile(file, protocol, format); } } - - - if (desktop==null) - System.exit(0); } }