X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=1eeda9850f0f8db3d16df111d0aef88a6a2681be;hb=743a0473c959092ec7c80bdb8169a541d33657cd;hp=184c267c460399655968d975d88799141f1afff4;hpb=36c3d72e0344f1aaa2137dca8eba829e7395f05a;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 184c267..1eeda98 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. * @@ -22,8 +22,11 @@ package jalview.bin; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.io.BioJsHTMLOutput; +import jalview.io.HtmlSvgOutput; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; @@ -34,6 +37,7 @@ 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; @@ -42,7 +46,7 @@ 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; @@ -63,6 +67,7 @@ public class Jalview // grab all the rights we can the JVM Policy.setPolicy(new Policy() { + @Override public PermissionCollection getPermissions(CodeSource codesource) { Permissions perms = new Permissions(); @@ -70,6 +75,7 @@ public class Jalview return (perms); } + @Override public void refresh() { } @@ -77,11 +83,6 @@ 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 +95,13 @@ 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"); - } 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") @@ -148,8 +110,31 @@ public class Jalview System.setProperty("java.awt.headless", "true"); headless = true; } - Cache.loadProperties(aparser.getValue("props")); // must do this before + String usrPropsFile = aparser.getValue("props"); + Cache.loadProperties(usrPropsFile); // must do this before + if (usrPropsFile != null) + { + System.out.println("CMD [-props " + usrPropsFile + + "] executed successfully!"); + } + // anything else! + + final String jabawsUrl = aparser.getValue("jabaws"); + if (jabawsUrl != null) + { + try + { + Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + System.out.println("CMD [-jabaws " + jabawsUrl + + "] executed successfully!"); + } catch (MalformedURLException e) + { + System.err.println("Invalid jabaws parameter: " + jabawsUrl + + " ignored"); + } + } + String defs = aparser.getValue("setprop"); while (defs != null) { @@ -194,6 +179,21 @@ public class Jalview } catch (Exception ex) { } + if (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 (Throwable e) + { + System.err.println("Failed to set QuaQua look and feel: " + + e.toString()); + } + } if (!headless) { @@ -205,6 +205,11 @@ public class Jalview { startUsageStats(desktop); } + else + { + System.err.println("CMD [-nousagestats] executed successfully!"); + } + if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); @@ -214,6 +219,8 @@ public class Jalview // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); } else { @@ -232,11 +239,20 @@ public class Jalview } } } + else + { + System.err.println("CMD [-noquestionnaire] executed successfully!"); + } desktop.checkForNews(); } + if (!isHeadlessMode()) + { + BioJsHTMLOutput.updateBioJS(); + } + String file = null, protocol = null, format = null, data = null; - jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); + jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(!headless); Vector getFeatures = null; // vector of das source nicknames to fetch // features from // loading is done. @@ -342,10 +358,11 @@ public class Jalview { if (!headless) { - desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"), + desktop.setProgressBar(MessageManager + .getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } - System.out.println("Opening file: " + file); + System.out.println("CMD [-open " + file + "] executed successfully!"); if (!file.startsWith("http://")) { @@ -361,7 +378,7 @@ public class Jalview protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); - format = new jalview.io.IdentifyFile().Identify(file, protocol); + format = new jalview.io.IdentifyFile().identify(file, protocol); AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); @@ -371,7 +388,7 @@ public class Jalview } else { - + Desktop.setCurrentAlignFrame(af); data = aparser.getValue("colour", true); if (data != null) { @@ -387,8 +404,11 @@ public class Jalview ucs.parseAppletParameter(data); cs = ucs; } - - System.out.println("colour is " + data); + else + { + System.out.println("CMD [-color " + data + + "] executed successfully!"); + } af.changeColour(cs); } @@ -398,30 +418,53 @@ public class Jalview { af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD groups[-" + data + + "] executed successfully!"); } data = aparser.getValue("features", true); if (data != null) { af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD [-features " + data + + "] executed successfully!"); } data = aparser.getValue("annotations", true); if (data != null) { af.loadJalviewDataFile(data, null, null, null); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD [-annotations " + data + + "] executed successfully!"); } // set or clear the sortbytree flag. if (aparser.contains("sortbytree")) { af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } + } + if (aparser.contains("no-annotation")) + { + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + System.out.println("CMD no-annotation executed successfully!"); + } } if (aparser.contains("nosortbytree")) { af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } } data = aparser.getValue("tree", true); if (data != null) @@ -429,13 +472,14 @@ public class Jalview jalview.io.NewickFile fin = null; try { + System.out.println("CMD [-tree " + data + + "] executed successfully!"); fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); if (fin != null) { af.getViewport().setCurrentTree( af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); } } catch (IOException ex) { @@ -474,8 +518,10 @@ public class Jalview if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] - { desktop, af }); + executeGroovyScript(groovyscript, new Object[] { desktop, af }); + + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); } else { @@ -506,6 +552,14 @@ 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); @@ -514,8 +568,10 @@ public class Jalview } else if (format.equalsIgnoreCase("eps")) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); + File outputFile = new java.io.File(file); + System.out.println("Creating EPS file: " + + outputFile.getAbsolutePath()); + af.createEPS(outputFile); continue; } @@ -544,8 +600,7 @@ 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", @@ -573,7 +628,7 @@ public class Jalview } else { - format = new jalview.io.IdentifyFile().Identify(file, protocol); + format = new jalview.io.IdentifyFile().identify(file, protocol); } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, @@ -598,8 +653,8 @@ public class Jalview if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] - { desktop, startUpAlframe }); + executeGroovyScript(groovyscript, new Object[] { desktop, + startUpAlframe }); } else { @@ -619,6 +674,48 @@ 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" + + "-json FILE\tCreate alignment file FILE in JSON 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) { /** @@ -633,18 +730,20 @@ public class Jalview + "\n\n(you can enable or disable usage tracking in the preferences)", new Runnable() { + @Override public void run() { Cache.log - .info("Initialising googletracker for usage stats."); + .debug("Initialising googletracker for usage stats."); Cache.initGoogleTracker(); Cache.log.debug("Tracking enabled."); } }, new Runnable() { + @Override public void run() { - Cache.log.info("Not enabling Google Tracking."); + Cache.log.debug("Not enabling Google Tracking."); } }, null, true); desktop.addDialogThread(prompter); @@ -762,17 +861,16 @@ 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); - String cnames[] = new String[] - { "Jalview", "currentAlFrame" }; + String cnames[] = new String[] { "Jalview", "currentAlFrame" }; bspec = new Class[blen * 2]; 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 +887,8 @@ 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 { @@ -800,23 +898,23 @@ 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[] - { URL[].class }); // String[].class }); - Object gse = gseccons.newInstance(new Object[] - { new URL[] - { sfile } }); // .toString() } }); - java.lang.reflect.Method run = gsec.getMethod("run", new Class[] - { String.class, gbindingc }); - run.invoke(gse, new Object[] - { sfile.toString(), gbinding }); + + 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[] { sfile } }); // .toString() + // } }); + java.lang.reflect.Method run = gsec.getMethod("run", new Class[] { + String.class, gbindingc }); + run.invoke(gse, new Object[] { sfile.toString(), gbinding }); success = true; } catch (Exception e) { @@ -881,6 +979,8 @@ public class Jalview } source.addElement(nickname); } + System.out.println("CMD [-dasserver " + data + + "] executed successfully!"); } // loop until no more server entries are found. if (locsources != null && locsources.indexOf('|') > -1) { @@ -908,7 +1008,7 @@ 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; @@ -919,6 +1019,16 @@ public class Jalview } return ff; } + + public static boolean isHeadlessMode() + { + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) + { + return true; + } + return false; + } } /** @@ -933,6 +1043,7 @@ public class Jalview class rnabuttonlistener implements ActionListener { + @Override public void actionPerformed(ActionEvent arg0) { System.out.println("Good idea ! "); @@ -942,6 +1053,7 @@ class rnabuttonlistener implements ActionListener class pbuttonlistener implements ActionListener { + @Override public void actionPerformed(ActionEvent arg0) { @@ -1062,6 +1174,7 @@ class FeatureFetcher new Thread(new Runnable() { + @Override public void run() { synchronized (us) @@ -1070,7 +1183,8 @@ class FeatureFetcher running++; } - af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id); + af.setProgressBar(MessageManager + .getString("status.das_features_being_retrived"), id); af.featureSettings_actionPerformed(null); af.featureSettings.fetchDasFeatures(dasSources, true); af.setProgressBar(null, id); @@ -1087,4 +1201,4 @@ class FeatureFetcher return queued == 0 && running == 0; } -}; +}