From: Ben Soares Date: Wed, 19 Jun 2019 11:50:36 +0000 (+0100) Subject: JAL-3321 Last pieces of the getdown-launcher.jar upgrade puzzle X-Git-Tag: Release_2_11_0~6^2^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a84906104415e9e65713af39a225090ebd7beff0;p=jalview.git JAL-3321 Last pieces of the getdown-launcher.jar upgrade puzzle --- diff --git a/build.gradle b/build.gradle index af9a26f..84d5f73 100644 --- a/build.gradle +++ b/build.gradle @@ -819,9 +819,8 @@ task getdownWebsite() { } copy { - from project.ext.getdownWebsiteDir + from getdownLauncher into project.ext.getdownWebsiteDir - include(file(getdownLauncher).getName()) rename(file(getdownLauncher).getName(), getdown_launcher_new) } diff --git a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar index 8828380..965e75d 100644 Binary files a/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar and b/getdown/lib/getdown-core-1.8.3-SNAPSHOT.jar differ diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar index 1efee70..dcede78 100644 Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java index f2cd573..ae493bb 100644 --- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java +++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/util/LaunchUtil.java @@ -9,8 +9,14 @@ import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.PrintStream; +import java.nio.file.Files; +import java.nio.file.Paths; import java.util.Locale; +import javax.xml.bind.DatatypeConverter; + +import java.security.MessageDigest; + import static com.threerings.getdown.Log.log; /** @@ -125,6 +131,21 @@ public class LaunchUtil return vmpath; } + private static String _getMD5FileChecksum (File file) { + // check md5 digest + String algo = "MD5"; + String checksum = ""; + try { + MessageDigest md = MessageDigest.getInstance(algo); + md.update(Files.readAllBytes(Paths.get(file.getAbsolutePath()))); + byte[] digest = md.digest(); + checksum = DatatypeConverter.printHexBinary(digest).toUpperCase(); + } catch (Exception e) { + System.out.println("Couldn't create "+algo+" digest of "+file.getPath()); + } + return checksum; + } + /** * Upgrades Getdown by moving an installation managed copy of the Getdown jar file over the * non-managed copy (which would be used to run Getdown itself). @@ -137,9 +158,17 @@ public class LaunchUtil // we assume getdown's jar file size changes with every upgrade, this is not guaranteed, // but in reality it will, and it allows us to avoid pointlessly upgrading getdown every // time the client is updated which is unnecessarily flirting with danger - if (!newgd.exists() || newgd.length() == curgd.length()) { + if (!newgd.exists()) + { return; } + + if (newgd.length() == curgd.length()) { + if (_getMD5FileChecksum(newgd).equals(_getMD5FileChecksum(curgd))) + { + return; + } + } log.info("Updating Getdown with " + newgd + "..."); diff --git a/getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java b/getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java index eaf9f2e..fd83de3 100644 --- a/getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java +++ b/getdown/src/getdown/launcher/src/main/java/com/threerings/getdown/launcher/GetdownApp.java @@ -92,7 +92,7 @@ public class GetdownApp } if (abort) System.exit(-1); - log.info("Starting...."); + log.info("Starting ...."); try { jalview.bin.StartupNotificationListener.setListener(); diff --git a/gradle.properties b/gradle.properties index 9ec5511..b483978 100644 --- a/gradle.properties +++ b/gradle.properties @@ -59,7 +59,7 @@ getdown_channel_base = http://www.jalview.org/getdown/jalview getdown_channel_name = TEST getdown_txt_allow_offline = true getdown_txt_jalview.jvmmempc = 90 -getdown_txt_multi_jvmarg = -Dgetdownappdir="%APPDIR%" +getdown_txt_multi_jvmarg = -Dgetdownappdir=%APPDIR% getdown_txt_strict_comments = true getdown_txt_title = Jalview getdown_txt_ui.name = Jalview diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar index 8828380..965e75d 100644 Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar index 8828380..965e75d 100644 Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index f4b4aac..8418d68 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1094,12 +1094,12 @@ public class Cache + System.getProperty("os.version") + (jalview.bin.Cache.getDefault("VERSION", "TEST") .equals("DEVELOPMENT") - ? "\nJava path:" + ? "\nGetdown appdir: " + System.getProperty("getdownappdir") + "\nJava path: " + System.getProperty( "java.home") + File.separator + "bin" + File.separator + "java" - : ""); + : ""); } /** diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 74889d7..c1354c7 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -86,982 +86,749 @@ import groovy.util.GroovyScriptEngine; */ 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.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 - */ - public static void main(String[] args) - { - instance = new Jalview(); - instance.doMain(args); - } - - /** - * @param args - */ - 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")); - // report Jalview version - Cache.loadBuildProperties(true); - - String appdirString = System.getProperty("getdownappdir"); - if (appdirString != null && appdirString.length() > 0) - { - final File appdir = new File(appdirString); - new Thread() - { - @Override - public void run() - { - LaunchUtil.upgradeGetdown( - new File(appdir, "getdown-launcher-old.jar"), - new File(appdir, "getdown-launcher.jar"), - new File(appdir, "getdown-launcher-new.jar")); - } - }.start(); - - } - 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 -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.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 - - try - { - JalviewTaskbar.setTaskbar(this); - } catch (Exception e) - { - System.out.println("Cannot set Taskbar"); - // e.printStackTrace(); - } catch (Throwable t) - { - System.out.println("Cannot set Taskbar"); - // t.printStackTrace(); - } - - 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); - - 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(), - 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) - 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); - // extract groovy arguments before anything else. - } - - // 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" - + "-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); - - } - } - - 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; - } + /* + * 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.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 + */ + public static void main(String[] args) { + instance = new Jalview(); + instance.doMain(args); + } + + /** + * @param args + */ + 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")); + // report Jalview version + Cache.loadBuildProperties(true); + + 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 -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.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 + + try { + JalviewTaskbar.setTaskbar(this); + } catch (Exception e) { + System.out.println("Cannot set Taskbar"); + // e.printStackTrace(); + } catch (Throwable t) { + System.out.println("Cannot set Taskbar"); + // t.printStackTrace(); + } + + 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(); + } + + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 0) { + final File appdir = new File(appdirString); + new Thread() { + @Override + public void run() { + LaunchUtil.upgradeGetdown(new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); + } + + String file = null, data = null; + FileFormatI format = null; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + + 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(), + 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) + 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); + // extract groovy arguments before anything else. + } + + // 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" + + "-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); + + } + } + + 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; + } }