X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=3e8018bfc44d155f5a50bb1d0d791d8c6904b898;hb=46bcdb06851cdf7800d74d720d49cf6960cd0c55;hp=e780f78cc12371231b4b052afc2f024f16372f97;hpb=bb6cfec0589998373f5542e630660b06485a7569;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index e780f78..3e8018b 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,8 +20,6 @@ package jalview.bin; import jalview.gui.*; -import org.apache.log4j.*; - import javax.swing.*; import java.util.Vector; @@ -37,28 +35,6 @@ import java.util.Vector; */ public class Jalview { - /** - * Initialises the Apache Axis logger - */ - public static Logger log; - private static void initLogger() - { - Logger laxis = Logger.getLogger("org.apache.axis"); - Logger lcastor = Logger.getLogger("org.exolab.castor"); - log = Logger.getLogger("jalview.bin.Jalview"); - - laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", Level.INFO.toString()))); - lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", Level.INFO.toString()))); - log.setLevel(Level.toLevel(Cache.getDefault("logs.Jalview.level", Level.INFO.toString()))); - - ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), - "System.err"); - ap.setName("JalviewLogger"); - - laxis.addAppender(ap); - lcastor.addAppender(ap); - log.addAppender(ap); - } /** * main class for Jalview application @@ -81,11 +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" @@ -96,31 +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 ) @@ -147,7 +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"); @@ -166,7 +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); } } @@ -180,18 +158,34 @@ 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) + // Must maintain ability to use the groups flag + data = aparser.getValue("groups"); + if (data != null) + { + af.parseGroupsFile(data); + System.out.println("Added "+data); + } + data = aparser.getValue("features"); + if (data != null) + { + af.parseGroupsFile(data); + 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) { @@ -236,12 +230,14 @@ public class Jalview // We'll only open the default file if the desktop is visible. ////////////////////// if ( - !headless && - jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + !headless + && 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) @@ -251,18 +247,14 @@ public class Jalview if (file.endsWith(".jar")) { - Jalview2XML.LoadJalviewAlign(file); + new Jalview2XML().LoadJalviewAlign(file); } else { - format = jalview.io.IdentifyFile.Identify(file, protocol); + format = new jalview.io.IdentifyFile().Identify(file, protocol); desktop.LoadFile(file, protocol, format); } } - - - if (desktop==null) - System.exit(0); } }