From 8ff6ad0a4030c6e8d816cb086aababfce4eaeb17 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 23 Jan 2019 15:00:25 +0000 Subject: [PATCH] JalviewJS pre-configured entry point for demos --- src/jalview/bin/JalviewJS.java | 1244 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 1244 insertions(+) create mode 100644 src/jalview/bin/JalviewJS.java diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java new file mode 100644 index 0000000..d7c4d19 --- /dev/null +++ b/src/jalview/bin/JalviewJS.java @@ -0,0 +1,1244 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.bin; + +import jalview.ext.so.SequenceOntology; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.PromptUserConfig; +import jalview.io.AppletFormatAdapter; +import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileLoader; +import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.NewickFile; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; + +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.net.MalformedURLException; +import java.net.URI; +import java.net.URISyntaxException; +import java.net.URL; +import java.security.AllPermission; +import java.security.CodeSource; +import java.security.PermissionCollection; +import java.security.Permissions; +import java.security.Policy; +import java.util.HashMap; +import java.util.Map; +import java.util.Vector; +import java.util.logging.ConsoleHandler; +import java.util.logging.Level; +import java.util.logging.Logger; + +import javax.swing.LookAndFeel; +import javax.swing.Timer; +import javax.swing.UIManager; + +import groovy.lang.Binding; +import groovy.util.GroovyScriptEngine; + +/** + * Main class for Jalview Application
+ *
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \ + * jalview.bin.Jalview + * + * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \ + * jalview.bin.Jalview jalview.bin.Jalview + * + * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not + * embellish '*' to e.g. '*.jar') + * + * @author $author$ + * @version $Revision$ + */ +public class JalviewJS +{ + + // BH 6/19/2018 starting to work on JS version - just discovering issues + + /* + * singleton instance of this class + */ + private static JalviewJS instance; + + private Desktop desktop; + + public static AlignFrame currentAlignFrame; + + /** + * Answers true if Jalview is running as Javascript, else false. The value is + * set at compile time. + * + * @return + */ + public static boolean isJS() + { + return /** @j2sNative true || */ + false; + } + + static + { + if (!isJS()) + { // BH 2018 + // grab all the rights we can the JVM + Policy.setPolicy(new Policy() + { + @Override + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + @Override + public void refresh() + { + } + }); + + } + } + + /** + * 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() + { + + @Override + public void run() + { + synchronized (us) + { + queued--; + running++; + } + + af.setProgressBar(MessageManager + .getString("status.das_features_being_retrived"), id); + af.featureSettings_actionPerformed(null); + af.setProgressBar(null, id); + synchronized (us) + { + running--; + } + } + }).start(); + } + + public synchronized boolean allFinished() + { + return queued == 0 && running == 0; + } + + } + + public static JalviewJS getInstance() + { + return instance; + } + + /** + * main class for Jalview application + * + * @param args + * open filename + */ + public static void main(String[] args) + { + instance = new JalviewJS(); + instance.doMain(new String[] {"open","http://www.jalview.org/examples/uniref50.fa", "-features","http://www.jalview.org/examples/exampleFeatures.txt"}); +} + + private static void logClass(String name) + { + // BH - for event debugging in JavaScript + ConsoleHandler consoleHandler = new ConsoleHandler(); + consoleHandler.setLevel(Level.ALL); + Logger logger = Logger.getLogger(name); + logger.setLevel(Level.ALL); + logger.addHandler(consoleHandler); + } + + @SuppressWarnings("unused") + private static void setLogging() + { + // BH - for event debugging in JavaScript (Java mode only) + if (!(/** @j2sNative true ||*/false)) + { + Logger.getLogger("").setLevel(Level.ALL); + logClass("java.awt.EventDispatchThread"); + logClass("java.awt.EventQueue"); + logClass("java.awt.Component"); + logClass("java.awt.focus.Component"); + logClass("java.awt.focus.DefaultKeyboardFocusManager"); + } + + } + + + + + /** + * @param args + */ + void doMain(String[] args) + { + + if (!isJS()) + { + System.setSecurityManager(null); + } + + System.out + .println("Java version: " + System.getProperty("java.version")); + System.out.println(System.getProperty("os.arch") + " " + + System.getProperty("os.name") + " " + + System.getProperty("os.version")); + + ArgsParser aparser = new ArgsParser(args); + boolean headless = false; + + String usrPropsFile = aparser.getValue("props"); + Cache.loadProperties(usrPropsFile); // must do this before + if (usrPropsFile != null) + { + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); + } + + /** + * BH 2018 ignoring this section for JS + * + * @j2sNative + */ + { + if (aparser.contains("help") || aparser.contains("h")) + { + showUsage(); + System.exit(0); + } + if (aparser.contains("nodisplay") || aparser.contains("nogui") + || aparser.contains("headless")) + { + System.setProperty("java.awt.headless", "true"); + headless = true; + } + // 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) + { + 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 (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + headless = true; + } + System.setProperty("http.agent", + "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); + try + { + Cache.initLogger(); + } catch (NoClassDefFoundError error) + { + error.printStackTrace(); + System.out.println("\nEssential logging libraries not found." + + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"); + System.exit(0); + } + + desktop = null; + + try + { + UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); + } catch (Exception ex) + { + System.err.println("Unexpected Look and Feel Exception"); + ex.printStackTrace(); + } + if (Platform.isAMacAndNotJS()) + { + + LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel(); + System.setProperty("com.apple.mrj.application.apple.menu.about.name", + "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); + if (lookAndFeel != null) + { + try + { + UIManager.setLookAndFeel(lookAndFeel); + } catch (Throwable e) + { + System.err.println( + "Failed to set QuaQua look and feel: " + e.toString()); + } + } + if (lookAndFeel == null || !(lookAndFeel.getClass() + .isAssignableFrom(UIManager.getLookAndFeel().getClass())) + || !UIManager.getLookAndFeel().getClass().toString() + .toLowerCase().contains("quaqua")) + { + try + { + System.err.println( + "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976"); + UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel"); + } catch (Throwable e) + { + System.err.println( + "Failed to reset look and feel: " + e.toString()); + } + } + } + + /* + * configure 'full' SO model if preferences say to, + * else use the default (SO Lite) + */ + if (Cache.getDefault("USE_FULL_SO", false)) + { + SequenceOntologyFactory.setInstance(new SequenceOntology()); + } + + if (!headless) + { + desktop = new Desktop() +// { +// // BH testing +// @Override +// protected void processEvent(AWTEvent e) { +// System.out.println("Jalview.java " + e); +// super.processEvent(e); +// } +// } + ; + desktop.setInBatchMode(true); // indicate we are starting up + desktop.setVisible(true); + + /** + * BH 2018 JS bypass this section + * + * @j2sNative + * + */ + { + desktop.startServiceDiscovery(); + if (!aparser.contains("nousagestats")) + { + startUsageStats(desktop); + } + else + { + System.err.println("CMD [-nousagestats] executed successfully!"); + } + + 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); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); + } + 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); + } + } + } + else + { + System.err + .println("CMD [-noquestionnaire] executed successfully!"); + } + + if (!aparser.contains("nonews")) + { + desktop.checkForNews(); + } + + BioJsHTMLOutput.updateBioJS(); + } + } + + String file = null, data = null; + FileFormatI format = null; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + 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"); + String 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 + { + DataSourceType viprotocol = AppletFormatAdapter + .checkProtocol(vamsasImport); + if (viprotocol == DataSourceType.FILE) + { + inSession = desktop.vamsasImport(new File(vamsasImport)); + } + else if (viprotocol == DataSourceType.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(); + } + } + } + long progress = -1; + // Finally, deal with the remaining input data. + if (file != null) + { + if (!headless) + { + desktop.setProgressBar( + MessageManager + .getString("status.processing_commandline_args"), + progress = System.currentTimeMillis()); + } + System.out.println("CMD [-open " + file + "] executed successfully!"); + + if (!isJS() && !file.startsWith("http://")) + { + if (!(new File(file)).exists()) + { + System.out.println("Can't find " + file); + if (headless) + { + System.exit(1); + } + } + } + + protocol = AppletFormatAdapter.checkProtocol(file); + + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } + + AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, + format); + if (af == null) + { + System.out.println("error"); + } + else + { + setCurrentAlignFrame(af); + data = aparser.getValue("colour", true); + if (data != null) + { + data.replaceAll("%20", " "); + + ColourSchemeI cs = ColourSchemeProperty + .getColourScheme(af.getViewport().getAlignment(), data); + + if (cs != null) + { + System.out.println( + "CMD [-color " + data + "] executed successfully!"); + } + af.changeColour(cs); + } + + // Must maintain ability to use the groups flag + data = aparser.getValue("groups", true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(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, + AppletFormatAdapter.checkProtocol(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( + "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) + { + try + { + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + NewickFile nf = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); + } 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. + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + groovyscript = null; + } + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + String outputFormat = aparser.nextValue(); + file = aparser.nextValue(); + + if (outputFormat.equalsIgnoreCase("png")) + { + af.createPNG(new File(file)); + imageName = (new File(file)).getName(); + System.out.println("Creating PNG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("svg")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("html")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(file); + + System.out.println("Creating HTML image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("biojsmsa")) + { + if (file == null) + { + System.err.println("The output html file must not be null"); + return; + } + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(file); + System.out + .println("Creating BioJS MSA Viwer HTML file: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("imgMap")) + { + af.createImageMap(new File(file), imageName); + System.out.println("Creating image map: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("eps")) + { + File outputFile = new File(file); + System.out.println( + "Creating EPS file: " + outputFile.getAbsolutePath()); + af.createEPS(outputFile); + continue; + } + + af.saveAlignment(file, format); + if (af.isSaveAlignmentSuccessful()) + { + 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 (/** @j2sNative false && */ // BH 2018 + !headless && file == null && vamsasImport == null + && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + { + file = jalview.bin.Cache.getDefault("STARTUP_FILE", + jalview.bin.Cache.getDefault("www.jalview.org", + "http://www.jalview.org") + + "/examples/exampleFile_2_7.jar"); + if (file.equals( + "http://www.jalview.org/examples/exampleFile_2_3.jar")) + { + // hardwire upgrade of the startup file + file.replace("_2_3.jar", "_2_7.jar"); + // and remove the stale setting + jalview.bin.Cache.removeProperty("STARTUP_FILE"); + } + + protocol = DataSourceType.FILE; + + if (file.indexOf("http:") > -1) + { + protocol = DataSourceType.URL; + } + + if (file.endsWith(".jar")) + { + format = FileFormat.Jalview; + } + else + { + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e) + { + // TODO what? + } + } + + 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 (Cache.groovyJarsPresent()) + { + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, 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) + { + if (progress != -1) + { + desktop.setProgressBar(null, progress); + } + desktop.setInBatchMode(false); + } + } + + 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" + + "-biojsMSA FILE\tCreate BioJS MSA Viewer 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" + + "-nonews\tTurn off check for Jalview news.\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) + { + /** + * start a User Config prompt asking if we can log usage statistics. + */ + PromptUserConfig prompter = new 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() + { + @Override + public void run() + { + Cache.log.debug( + "Initialising googletracker for usage stats."); + Cache.initGoogleTracker(); + Cache.log.debug("Tracking enabled."); + } + }, new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Not enabling Google Tracking."); + } + }, null, true); + desktop.addDialogThread(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 void executeGroovyScript(String groovyscript, AlignFrame af) + { + /** + * for scripts contained in files + */ + File tfile = null; + /** + * script's URI + */ + URL sfile = null; + if (groovyscript.trim().equals("STDIN")) + { + // read from stdin into a tempfile and execute it + try + { + tfile = File.createTempFile("jalview", "groovy"); + PrintWriter outfile = new PrintWriter( + new OutputStreamWriter(new FileOutputStream(tfile))); + BufferedReader br = new BufferedReader( + new 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 " + + ((tfile == null) ? "(tempfile wasn't created)" + : tfile.toString())); + ex.printStackTrace(); + return; + } + try + { + sfile = tfile.toURI().toURL(); + } catch (Exception x) + { + System.err.println( + "Unexpected Malformed URL Exception for temporary file created from STDIN: " + + tfile.toURI()); + x.printStackTrace(); + return; + } + } + else + { + try + { + sfile = new URI(groovyscript).toURL(); + } catch (Exception x) + { + tfile = new File(groovyscript); + if (!tfile.exists()) + { + System.err.println("File '" + groovyscript + "' does not exist."); + return; + } + if (!tfile.canRead()) + { + System.err.println("File '" + groovyscript + "' cannot be read."); + return; + } + if (tfile.length() < 1) + { + System.err.println("File '" + groovyscript + "' is empty."); + return; + } + try + { + sfile = tfile.getAbsoluteFile().toURI().toURL(); + } catch (Exception ex) + { + System.err.println("Failed to create a file URL for " + + tfile.getAbsoluteFile()); + return; + } + } + } + try + { + Map vbinding = new HashMap<>(); + vbinding.put("Jalview", this); + if (af != null) + { + vbinding.put("currentAlFrame", af); + } + Binding gbinding = new Binding(vbinding); + GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile }); + gse.run(sfile.toString(), gbinding); + if ("STDIN".equals(groovyscript)) + { + // delete temp file that we made - + // only if it was successfully executed + tfile.delete(); + } + } catch (Exception e) + { + System.err.println("Exception Whilst trying to execute file " + sfile + + " as a groovy script."); + e.printStackTrace(System.err); + + } + } + + /** + * Check commandline for any das server definitions or any fetchfrom switches + * + * @return vector of DAS source nicknames to retrieve from + */ + private static Vector checkDasArguments(ArgsParser aparser) + { + Vector source = null; + String data; + String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); + while ((data = aparser.getValue("dasserver", true)) != null) + { + String nickname = null; + String url = null; + int pos = data.indexOf('='); + // determine capabilities + if (pos > 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); + } + System.out.println( + "CMD [-dasserver " + data + "] executed successfully!"); + } // 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 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; + } + + public static boolean isHeadlessMode() + { + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) + { + return true; + } + return false; + } + + public AlignFrame[] getAlignFrames() + { + return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } + : Desktop.getAlignFrames(); + + } + + /** + * Quit method delegates to Desktop.quit - unless running in headless mode + * when it just ends the JVM + */ + public void quit() + { + if (desktop != null) + { + desktop.quit(); + } + else + { + System.exit(0); + } + } + + public static AlignFrame getCurrentAlignFrame() + { + return JalviewJS.currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + JalviewJS.currentAlignFrame = currentAlignFrame; + } +} -- 1.7.10.2