/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.bin; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.lang.reflect.Constructor; import java.net.URL; import java.net.URLDecoder; import java.security.AllPermission; import java.security.CodeSource; import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; import java.util.*; import javax.swing.*; import jalview.gui.*; import jalview.util.Platform; /** * Main class for Jalview Application
*
* start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview * * @author $author$ * @version $Revision$ */ public class Jalview { static { // grab all the rights we can the JVM Policy.setPolicy(new Policy() { public PermissionCollection getPermissions(CodeSource codesource) { Permissions perms = new Permissions(); perms.add(new AllPermission()); return (perms); } public void refresh() { } }); } /** * main class for Jalview application * * @param args * open filename */ 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")); 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"); System.exit(0); } Cache.loadProperties(aparser.getValue("props")); // must do this before // anything else! String defs = aparser.getValue("setprop"); while (defs != null) { int p = defs.indexOf('='); if (p == -1) { System.err.println("Ignoring invalid setprop argument : " + defs); } else { System.out.println("Executing setprop argument: " + defs); // DISABLED FOR SECURITY REASONS // TODO: add a property to allow properties to be overriden by cli args // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); } defs = aparser.getValue("setprop"); } 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; try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception ex) { } if (!headless) { desktop = new Desktop(); desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); desktop.startServiceDiscovery(); if (!aparser.contains("nousagestats")) { startUsageStats(desktop); } if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); if (url != null) { // Start the desktop questionnaire prompter with the specified // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); } else { if (Cache.getProperty("NOQUESTIONNAIRES") == null) { // Start the desktop questionnaire prompter with the specified // questionnaire // String defurl = // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // // String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; Cache.log.debug("Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); } } } } String file = null, protocol = null, format = null, data = null; jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); Vector getFeatures = null; // vector of das source nicknames to fetch // features from // loading is done. String groovyscript = null; // script to execute after all loading is // completed one way or another // extract groovy argument and execute if necessary groovyscript = aparser.getValue("groovy", true); file = aparser.getValue("open", true); if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser .getValue("vsess"); if (vamsasImport != null || vamsasSession != null) { if (desktop == null || headless) { System.out .println("Headless vamsas sessions not yet supported. Sorry."); System.exit(1); } // if we have a file, start a new session and import it. boolean inSession = false; if (vamsasImport != null) { try { String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport); if (viprotocol == jalview.io.FormatAdapter.FILE) { inSession = desktop.vamsasImport(new File(vamsasImport)); } else if (viprotocol == jalview.io.FormatAdapter.URL) { inSession = desktop.vamsasImport(new URL(vamsasImport)); } } catch (Exception e) { System.err.println("Exeption when importing " + vamsasImport + " as a vamsas document."); e.printStackTrace(); } if (!inSession) { System.err.println("Failed to import " + vamsasImport + " as a vamsas document."); } else { System.out.println("Imported Successfully into new session " + desktop.getVamsasApplication().getCurrentSession()); } } if (vamsasSession != null) { if (vamsasImport != null) { // close the newly imported session and import the Jalview specific // remnants into the new session later on. desktop.vamsasStop_actionPerformed(null); } // now join the new session try { if (desktop.joinVamsasSession(vamsasSession)) { System.out.println("Successfully joined vamsas session " + vamsasSession); } else { System.err.println("WARNING: Failed to join vamsas session " + vamsasSession); } } catch (Exception e) { System.err.println("ERROR: Failed to join vamsas session " + vamsasSession); e.printStackTrace(); } if (vamsasImport != null) { // the Jalview specific remnants can now be imported into the new // session at the user's leisure. Cache.log .info("Skipping Push for import of data into existing vamsas session."); // TODO: // enable // this // when // debugged // desktop.getVamsasApplication().push_update(); } } } // Finally, deal with the remaining input data. if (file != null) { System.out.println("Opening file: " + file); if (!file.startsWith("http://")) { if (!(new java.io.File(file)).exists()) { System.out.println("Can't find " + file); if (headless) { System.exit(1); } } } protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); format = new jalview.io.IdentifyFile().Identify(file, protocol); AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); if (af == null) { System.out.println("error"); return; } data = aparser.getValue("colour", true); 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", true); if (data != null) { af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); System.out.println("Added " + data); } data = aparser.getValue("features", true); if (data != null) { af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data)); System.out.println("Added " + data); } data = aparser.getValue("annotations", true); if (data != null) { af.loadJalviewDataFile(data, null, null, null); System.out.println("Added " + data); } // set or clear the sortbytree flag. if (aparser.contains("sortbytree")) { af.getViewport().setSortByTree(true); } if (aparser.contains("nosortbytree")) { af.getViewport().setSortByTree(false); } data = aparser.getValue("tree", true); if (data != null) { jalview.io.NewickFile fin = null; try { 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) { System.err.println("Couldn't add tree " + data); ex.printStackTrace(System.err); } } // TODO - load PDB structure(s) to alignment JAL-629 // (associate with identical sequence in alignment, or a specified // sequence) getFeatures = checkDasArguments(aparser); if (af != null && getFeatures != null) { FeatureFetcher ff = startFeatureFetching(getFeatures); if (ff != null) while (!ff.allFinished() || af.operationInProgress()) { // wait around until fetching is finished. try { Thread.sleep(100); } catch (Exception e) { } } getFeatures = null; // have retrieved features - forget them now. } if (groovyscript != null) { // Execute the groovy script after we've done all the rendering stuff // and before any images or figures are generated. if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, new Object[] {desktop,af}); } else { System.err .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + groovyscript); } groovyscript = null; } String imageName = "unnamed.png"; while (aparser.getSize() > 1) { format = aparser.nextValue(); file = aparser.nextValue(); if (format.equalsIgnoreCase("png")) { af.createPNG(new java.io.File(file)); imageName = (new java.io.File(file)).getName(); System.out.println("Creating PNG image: " + file); continue; } else if (format.equalsIgnoreCase("imgMap")) { af.createImageMap(new java.io.File(file), imageName); System.out.println("Creating image map: " + file); continue; } else if (format.equalsIgnoreCase("eps")) { System.out.println("Creating EPS file: " + file); af.createEPS(new java.io.File(file)); continue; } if (af.saveAlignment(file, format)) { System.out.println("Written alignment in " + format + " format to " + file); } else { System.out.println("Error writing file " + file + " in " + format + " format!!"); } } while (aparser.getSize() > 0) { System.out.println("Unknown arg: " + aparser.nextValue()); } } AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user // //////////////////// if (!headless && file == null && vamsasImport == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) { file = jalview.bin.Cache.getDefault("STARTUP_FILE", "http://www.jalview.org/examples/exampleFile_2_3.jar"); protocol = "File"; if (file.indexOf("http:") > -1) { protocol = "URL"; } if (file.endsWith(".jar")) { format = "Jalview"; } else { format = new jalview.io.IdentifyFile().Identify(file, protocol); } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); getFeatures = checkDasArguments(aparser); // extract groovy arguments before anything else. } // If the user has specified features to be retrieved, // or a groovy script to be executed, do them if they // haven't been done already // fetch features for the default alignment if (getFeatures != null) { if (startUpAlframe != null) { startFeatureFetching(getFeatures); } } // Once all other stuff is done, execute any groovy scripts (in order) if (groovyscript != null) { if (jalview.bin.Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); executeGroovyScript(groovyscript, new Object[] { desktop, startUpAlframe}); } else { System.err .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + groovyscript); } } // and finally, turn off batch mode indicator - if the desktop still exists if (desktop != null) { desktop.setInBatchMode(false); } } private static void startUsageStats(final Desktop desktop) { /** * start a User Config prompt asking if we can log usage statistics. */ jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig( desktop.desktop, "USAGESTATS", "Jalview Usage Statistics", "Do you want to help make Jalview better by enabling " + "the collection of usage statistics with Google Analytics ?" + "\n\n(you can enable or disable usage tracking in the preferences)", new Runnable() { public void run() { Cache.log .info("Initialising googletracker for usage stats."); Cache.initGoogleTracker(); Cache.log.debug("Tracking enabled."); } }, new Runnable() { public void run() { Cache.log.info("Not enabling Google Tracking."); } }, null, true); SwingUtilities.invokeLater(prompter); } /** * Locate the given string as a file and pass it to the groovy interpreter. * * @param groovyscript * the script to execute * @param jalviewContext * the Jalview Desktop object passed in to the groovy binding as the * 'Jalview' object. */ private static void executeGroovyScript(String groovyscript, Object[] jalviewContext) { if (jalviewContext == null) { System.err .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); } File sfile = null; if (groovyscript.trim().equals("STDIN")) { // read from stdin into a tempfile and execute it try { sfile = File.createTempFile("jalview", "groovy"); PrintWriter outfile = new PrintWriter(new OutputStreamWriter( new FileOutputStream(sfile))); BufferedReader br = new BufferedReader( new java.io.InputStreamReader(System.in)); String line = null; while ((line = br.readLine()) != null) { outfile.write(line + "\n"); } br.close(); outfile.flush(); outfile.close(); } catch (Exception ex) { System.err.println("Failed to read from STDIN into tempfile " + ((sfile == null) ? "(tempfile wasn't created)" : sfile .toString())); ex.printStackTrace(); return; } } else { sfile = new File(groovyscript); } if (!sfile.exists()) { System.err.println("File '" + groovyscript + "' does not exist."); return; } if (!sfile.canRead()) { System.err.println("File '" + groovyscript + "' cannot be read."); return; } if (sfile.length() < 1) { System.err.println("File '" + groovyscript + "' is empty."); return; } boolean success = false; try { /* * The following code performs the GroovyScriptEngine invocation using * reflection, and is equivalent to this fragment from the embedding * groovy documentation on the groovy site: import * groovy.lang.Binding; import groovy.util.GroovyScriptEngine; * * String[] roots = new String[] { "/my/groovy/script/path" }; * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding * = new Binding(); binding.setVariable("input", "world"); * gse.run("hello.groovy", binding); */ Class[] bspec; Object[] binding; int blen=((jalviewContext[0]==null) ? 0 : 1) + ((jalviewContext[1]==null) ? 0 : 1); String cnames[] = new String[] { "Jalview", "currentAlFrame"}; bspec=new Class[blen*2]; binding=new Object[blen*2]; blen=0; ClassLoader cl=null; for (int jc=0;jc 0) { nickname = data.substring(0, pos); } url = data.substring(pos + 1); if (url != null && (url.startsWith("http:") || url .startsWith("sequence:http:"))) { if (nickname == null) { nickname = url; } if (locsources == null) { locsources = ""; } else { locsources += "\t"; } locsources = locsources + nickname + "|" + url; System.err .println("NOTE! dasserver parameter not yet really supported (got args of " + nickname + "|" + url); if (source == null) { source = new Vector(); } source.addElement(nickname); } } // loop until no more server entries are found. if (locsources != null && locsources.indexOf('|') > -1) { Cache.log.debug("Setting local source list in properties file to:\n" + locsources); Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources); } while ((data = aparser.getValue("fetchfrom", true)) != null) { System.out.println("adding source '" + data + "'"); if (source == null) { source = new Vector(); } source.addElement(data); } return source; } /** * start a feature fetcher for every alignment frame * * @param dasSources */ private static FeatureFetcher startFeatureFetching(final Vector dasSources) { FeatureFetcher ff = new FeatureFetcher(); AlignFrame afs[] = Desktop.getAlignframes(); if (afs == null || afs.length == 0) { return null; } for (int i = 0; i < afs.length; i++) { ff.addFetcher(afs[i], dasSources); } return ff; } } /** * Notes: this argParser does not distinguish between parameter switches, * parameter values and argument text. If an argument happens to be identical to * a parameter, it will be taken as such (even though it didn't have a '-' * prefixing it). * * @author Andrew Waterhouse and JBP documented. * */ class ArgsParser { Vector vargs = null; public ArgsParser(String[] args) { vargs = new Vector(); for (int i = 0; i < args.length; i++) { String arg = args[i].trim(); if (arg.charAt(0) == '-') { arg = arg.substring(1); } vargs.addElement(arg); } } /** * check for and remove first occurence of arg+parameter in arglist. * * @param arg * @return return the argument following the given arg if arg was in list. */ public String getValue(String arg) { return getValue(arg, false); } public String getValue(String arg, boolean utf8decode) { int index = vargs.indexOf(arg); String dc = null, ret = null; if (index != -1) { ret = vargs.elementAt(index + 1).toString(); vargs.removeElementAt(index); vargs.removeElementAt(index); if (utf8decode && ret != null) { try { dc = URLDecoder.decode(ret, "UTF-8"); ret = dc; } catch (Exception e) { // TODO: log failure to decode } } } return ret; } /** * check for and remove first occurence of arg in arglist. * * @param arg * @return true if arg was present in argslist. */ public boolean contains(String arg) { if (vargs.contains(arg)) { vargs.removeElement(arg); return true; } else { return false; } } public String nextValue() { return vargs.remove(0).toString(); } public int getSize() { return vargs.size(); } } /** * keep track of feature fetching tasks. * * @author JimP * */ class FeatureFetcher { /* * TODO: generalise to track all jalview events to orchestrate batch * processing events. */ private int queued = 0; private int running = 0; public FeatureFetcher() { } public void addFetcher(final AlignFrame af, final Vector dasSources) { final long id = System.currentTimeMillis(); queued++; final FeatureFetcher us = this; new Thread(new Runnable() { public void run() { synchronized (us) { queued--; running++; } af.setProgressBar("DAS features being retrieved...", id); af.featureSettings_actionPerformed(null); af.featureSettings.fetchDasFeatures(dasSources, true); af.setProgressBar(null, id); synchronized (us) { running--; } } }).start(); } public synchronized boolean allFinished() { return queued == 0 && running == 0; } };