X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0fe16645fc85cd09e4c7b740d85fdb438cf7c9a0;hb=bc98852ff1a926cf7b11a92db96ff8fe308ceae0;hp=184c267c460399655968d975d88799141f1afff4;hpb=de1a68f7d6f2aeb9c46c8abe2ad8e824bf9d9fc3;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 184c267..0fe1664 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,11 +20,6 @@ */ package jalview.bin; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.util.MessageManager; -import jalview.util.Platform; - import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedReader; @@ -34,6 +29,7 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; +import java.net.MalformedURLException; import java.net.URI; import java.net.URL; import java.net.URLDecoder; @@ -42,11 +38,19 @@ import java.security.CodeSource; import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; -import java.util.Hashtable; +import java.util.HashMap; import java.util.Map; import java.util.Vector; import javax.swing.UIManager; +import javax.swing.UnsupportedLookAndFeelException; + +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.io.HtmlSvgOutput; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; /** * Main class for Jalview Application
@@ -77,11 +81,6 @@ public class Jalview } /** - * Put protein=true for get a protein example - */ - private static boolean protein = false; - - /** * main class for Jalview application * * @param args @@ -94,52 +93,30 @@ public class Jalview System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); - if (new Platform().isAMac()) - { - System.setProperty("com.apple.mrj.application.apple.menu.about.name", - "Jalview"); - System.setProperty("apple.laf.useScreenMenuBar", "true"); - } + // if (new Platform().isAMac()) + // { + // // System.setProperty("com.apple.mrj.application.apple.menu.about.name", + // // "Jalview"); + // // System.setProperty("apple.laf.useScreenMenuBar", "true"); + // try + // { + // UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager + // .getLookAndFeel()); + // System.out + // .println("--------------------------------------------> in here"); + // } catch (UnsupportedLookAndFeelException e) + // { + // // TODO Auto-generated catch block + // e.printStackTrace(); + // } + // } ArgsParser aparser = new ArgsParser(args); boolean headless = false; if (aparser.contains("help") || aparser.contains("h")) { - 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" - + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" - + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" - + "-tree FILE\tLoad the given newick format tree file onto 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" - + "-msf FILE\tCreate alignment file FILE in MSF format.\n" - + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" - + "-pir FILE\tCreate alignment file FILE in PIR format.\n" - + "-blc FILE\tCreate alignment file FILE in BLC format.\n" - + "-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.\n" - + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" - + "-noquestionnaire\tTurn off questionnaire check.\n" - + "-nousagestats\tTurn off google analytics tracking for this session.\n" - + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" - // + - // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" - + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" - + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" - + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" - // + - // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" - // + "-vses vamsas-session\tJoin session with given URN\n" - + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" - + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + showUsage(); System.exit(0); } if (aparser.contains("nodisplay") || aparser.contains("nogui") @@ -150,6 +127,20 @@ public class Jalview } Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! + + final String jabawsUrl = aparser.getValue("jabaws"); + if (jabawsUrl != null) + { + try + { + Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + } catch (MalformedURLException e) + { + System.err.println("Invalid jabaws parameter: " + jabawsUrl + + " ignored"); + } + } + String defs = aparser.getValue("setprop"); while (defs != null) { @@ -194,6 +185,21 @@ public class Jalview } catch (Exception ex) { } + if (new Platform().isAMac()) + { + System.setProperty("com.apple.mrj.application.apple.menu.about.name", + "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); + try + { + UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel()); + } catch (UnsupportedLookAndFeelException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } if (!headless) { @@ -419,6 +425,10 @@ public class Jalview { af.getViewport().setSortByTree(true); } + if (aparser.contains("no-annotation")) + { + af.getViewport().setShowAnnotation(false); + } if (aparser.contains("nosortbytree")) { af.getViewport().setSortByTree(false); @@ -506,6 +516,14 @@ public class Jalview System.out.println("Creating SVG image: " + file); continue; } + else if (format.equalsIgnoreCase("html")) + { + File imageFile = new java.io.File(file); + imageName = imageFile.getName(); + new HtmlSvgOutput(new java.io.File(file), af.alignPanel); + System.out.println("Creating HTML image: " + file); + continue; + } else if (format.equalsIgnoreCase("imgMap")) { af.createImageMap(new java.io.File(file), imageName); @@ -544,8 +562,7 @@ public class Jalview // //////////////////// if (!headless && file == null && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true) - && protein == true) + && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault( "STARTUP_FILE", @@ -619,6 +636,47 @@ public class Jalview } } + private static void showUsage() + { + 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" + + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" + + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" + + "-tree FILE\tLoad the given newick format tree file onto 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" + + "-msf FILE\tCreate alignment file FILE in MSF format.\n" + + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" + + "-pir FILE\tCreate alignment file FILE in PIR format.\n" + + "-blc FILE\tCreate alignment file FILE in BLC format.\n" + + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" + + "-png FILE\tCreate PNG image FILE from alignment.\n" + + "-svg FILE\tCreate SVG image FILE from alignment.\n" + + "-html FILE\tCreate HTML 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.\n" + + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" + + "-noquestionnaire\tTurn off questionnaire check.\n" + + "-nousagestats\tTurn off google analytics tracking for this session.\n" + + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" + // + + // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" + + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" + + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" + + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" + + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" + + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" + // + + // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" + // + "-vses vamsas-session\tJoin session with given URN\n" + + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n" + + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); + } + private static void startUsageStats(final Desktop desktop) { /** @@ -636,7 +694,7 @@ public class Jalview public void run() { Cache.log - .info("Initialising googletracker for usage stats."); + .debug("Initialising googletracker for usage stats."); Cache.initGoogleTracker(); Cache.log.debug("Tracking enabled."); } @@ -644,7 +702,7 @@ public class Jalview { public void run() { - Cache.log.info("Not enabling Google Tracking."); + Cache.log.debug("Not enabling Google Tracking."); } }, null, true); desktop.addDialogThread(prompter); @@ -762,7 +820,7 @@ public class Jalview * = new Binding(); binding.setVariable("input", "world"); * gse.run("hello.groovy", binding); */ - Class[] bspec; + Class[] bspec; Object[] binding; int blen = ((jalviewContext[0] == null) ? 0 : 1) + ((jalviewContext[1] == null) ? 0 : 1); @@ -772,7 +830,7 @@ public class Jalview binding = new Object[blen * 2]; blen = 0; ClassLoader cl = null; - Map vbinding = new Hashtable(); + Map vbinding = new HashMap(); for (int jc = 0; jc < jalviewContext.length; jc++) { if (jalviewContext[jc] != null) @@ -789,8 +847,8 @@ public class Jalview blen++; } } - Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons; + Class gbindingc = cl.loadClass("groovy.lang.Binding"); + Constructor gbcons; Object gbinding; try { @@ -800,15 +858,15 @@ public class Jalview { // old style binding config - using series of string/object values to // setVariable. - gbcons = gbindingc.getConstructor(null); - gbinding = gbcons.newInstance(null); + gbcons = gbindingc.getConstructor(); + gbinding = gbcons.newInstance(); java.lang.reflect.Method setvar = gbindingc.getMethod( "setVariable", bspec); setvar.invoke(gbinding, binding); } - ; - Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); - Constructor gseccons = gsec.getConstructor(new Class[] + + Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); + Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class }); // String[].class }); Object gse = gseccons.newInstance(new Object[] { new URL[] @@ -908,7 +966,7 @@ public class Jalview private static FeatureFetcher startFeatureFetching(final Vector dasSources) { FeatureFetcher ff = new FeatureFetcher(); - AlignFrame afs[] = Desktop.getAlignframes(); + AlignFrame afs[] = Desktop.getAlignFrames(); if (afs == null || afs.length == 0) { return null;