/* * 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.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 javax.swing.LookAndFeel; import javax.swing.UIManager; import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; /** * Main class for Jalview Application
*
* start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview * * @author $author$ * @version $Revision$ */ public class Jalview { /* * singleton instance of this class */ private static Jalview instance; private Desktop desktop; public static AlignFrame currentAlignFrame; static { // 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.featureSettings.fetchDasFeatures(dasSources, true); af.setProgressBar(null, id); synchronized (us) { running--; } } }).start(); } public synchronized boolean allFinished() { return queued == 0 && running == 0; } } public static Jalview getInstance() { return instance; } /** * main class for Jalview application * * @param args * open filename * @throws InterruptedException * @throws IOException */ public static void main(String[] args) { instance = new Jalview(); instance.doMain(args); } /** * @param args * @throws InterruptedException * @throws IOException */ void doMain(String[] args) { 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; 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; } 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) { 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 -Djava.ext.dirs=$PATH_TO_LIB$ 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.isAMac()) { 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(); desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); 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 (!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; } 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", 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 Jalview.currentAlignFrame; } public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) { Jalview.currentAlignFrame = currentAlignFrame; } }