X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=87bacc15af3fbf4c4d54002eecc0b2b1ab7bdadb;hb=37a5dfc3c72a42689e90ad8a0e118e8855d9868b;hp=9a854711ad0ce1597c5ef4a6432812b50c51b4d9;hpb=d16f364a9df0e2abe0d41889eb4b696bbeb3ca31;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 9a85471..87bacc1 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; @@ -59,11 +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" @@ -74,14 +69,17 @@ 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")) { @@ -101,16 +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" @@ -128,7 +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"); @@ -147,13 +143,14 @@ 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); } } protocol = "File"; - if (file.indexOf("http:") > -1) + if (file.indexOf("http:") > -1 || file.indexOf("file:") >-1) { protocol = "URL"; } @@ -161,18 +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) { - 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 +250,18 @@ 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) @@ -232,18 +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); } }