X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=ef16e5553ac3eea7e7ad7c25d0a3bb3be04714e5;hb=2b08c849bd54a0799ddf251f602a421d4696005e;hp=5d0b9d674227137e562cf80cdad707684bf79648;hpb=013c39d4eaab0ed509d21e83676fa4da284d7fde;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 5d0b9d6..07fd4d6 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,614 +1,1369 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; +import jalview.api.AlignViewportI; +import jalview.api.JalviewApp; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.ext.so.SequenceOntology; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.Desktop; +import jalview.gui.Preferences; +import jalview.gui.PromptUserConfig; +import jalview.gui.StructureViewer; +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.FileFormats; +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.lang.reflect.Constructor; -import java.util.*; +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.*; +import javax.swing.LookAndFeel; +import javax.swing.UIManager; -import jalview.gui.*; -import jalview.io.AppletFormatAdapter; +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 + * 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 Jalview +public class Jalview implements ApplicationSingletonI { + public static Jalview getInstance() + { + return (Jalview) ApplicationSingletonProvider + .getInstance(Jalview.class); + } + + private Jalview() + { + } + + static + { + Platform.getURLCommandArguments(); + } + + private boolean headless; + + public static boolean isHeadlessMode() + { + return getInstance().headless; + } + + private Desktop desktop; + + private AlignFrame currentAlignFrame; + + public boolean isJavaAppletTag; + + public String appletResourcePath; + + public static AlignFrame getCurrentAlignFrame() + { + return getInstance().currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + getInstance().currentAlignFrame = currentAlignFrame; + } + + static + { + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + // grab all the rights we can for 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; + } + + } + /** * main class for Jalview application * * @param args - * open filename + * open filename */ public static void main(String[] args) { - System.out.println("Java version: " - + System.getProperty("java.version")); + // setLogging(); // BH - for event debugging in JavaScript + getInstance().doMain(args); + } + + 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() + { + + /** + * @j2sIgnore + * + */ + { + System.out.println("not in js"); + } + + // BH - for event debugging in JavaScript (Java mode only) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ + { + 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) + { + + boolean isJS = Platform.isJS(); + 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; - - if (aparser.contains("help") || aparser.contains("h")) - { - System.out - .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" - + "-nodisplay\tRun Jalview without User Interface.\n" - + "-props FILE\tUse the given Jalview properties file instead of users default.\n" - + "-annotations FILE\tAdd precalculated annotations to the alignment.\n" - + "-tree FILE\tLoad the given newick format tree file onto the alignment\n" - + "-features FILE\tUse the given file to mark features on the alignment.\n" - + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n" - + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n" - + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n" - + "-msf FILE\tCreate alignment file FILE in MSF format.\n" - + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" - + "-pir FILE\tCreate alignment file FILE in PIR format.\n" - + "-blc FILE\tCreate alignment file FILE in BLC format.\n" - + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" - + "-png FILE\tCreate PNG image FILE from alignment.\n" - + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n" - + "-eps FILE\tCreate EPS file FILE from alignment." - + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires." - + "-noquestionnaire\tTurn off questionnaire check." - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments." - + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them." - + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed." - + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); - System.exit(0); + + String usrPropsFile = aparser.getValue(ArgsParser.PROPS); + Cache.loadProperties(usrPropsFile); + if (isJS) + { + isJavaAppletTag = aparser.isApplet(); + if (isJavaAppletTag) + { + Preferences.setAppletDefaults(); + Cache.loadProperties(usrPropsFile); // again, because we + // might be changing defaults here? + } + System.out.println( + " found: " + aparser.getValue("Info.j2sAppletID")); + appletResourcePath = aparser.getValue("Info.resourcePath"); } + else + /** + * Java only + * + * @j2sIgnore + */ + { + if (usrPropsFile != null) + { + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); + } - Cache.loadProperties(aparser.getValue("props")); // must do this before - // anything else! + if (aparser.contains("help") || aparser.contains("h")) + { + showUsage(); + System.exit(0); + } + if (aparser.contains(ArgsParser.NODISPLAY) + || aparser.contains(ArgsParser.NOGUI) + || aparser.contains(ArgsParser.HEADLESS) + || "true".equals(System.getProperty("java.awt.headless"))) + { + headless = true; + } + + // anything else! + + final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS); + if (jabawsUrl != null) + { + try + { + Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl); + System.out.println( + "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); + } catch (MalformedURLException e) + { + System.err.println( + "Invalid jabaws parameter: " + jabawsUrl + " ignored"); + } + } - if (aparser.contains("nodisplay")) - { - System.setProperty("java.awt.headless", "true"); } - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + // check for property setting + String defs = aparser.getValue(ArgsParser.SETPROP); + while (defs != null) { - headless = true; + int p = defs.indexOf('='); + if (p == -1) + { + System.err.println("Ignoring invalid setprop argument : " + defs); + } + else + { + System.out.println("Executing setprop argument: " + defs); + if (isJS) + { + Cache.setProperty(defs.substring(0, p), defs.substring(p + 1)); + } + } + defs = aparser.getValue(ArgsParser.SETPROP); } - + System.setProperty("http.agent", + "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); try { Cache.initLogger(); - } catch (java.lang.NoClassDefFoundError error) + } 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.out.println("\nEssential logging libraries not found." + + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"); System.exit(0); } - Desktop desktop = null; + desktop = null; try { - UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName() - // UIManager.getCrossPlatformLookAndFeelClassName() - // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel" - // "javax.swing.plaf.metal.MetalLookAndFeel" - // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel" - // "com.sun.java.swing.plaf.motif.MotifLookAndFeel" - - ); + 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.setSequenceOntology(new SequenceOntology()); + } + if (!headless) { - desktop = new Desktop(); + desktop = Desktop.getInstance(); + desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); - desktop.discoverer.start(); - if (!aparser.contains("noquestionnaire")) + + if (!isJS) + /** + * Java only + * + * @j2sIgnore + */ { - String url = aparser.getValue("questionnaire"); - if (url != null) + desktop.startServiceDiscovery(); + if (!aparser.contains(ArgsParser.NOUSAGESTATS)) { - // Start the desktop questionnaire prompter with the specified - // questionnaire - Cache.log.debug("Starting questionnaire url at " + url); - desktop.checkForQuestionnaire(url); + startUsageStats(desktop); } else { - if (Cache.getProperty("NOQUESTIONNAIRES") == null) + System.err.println("CMD [-nousagestats] executed successfully!"); + } + + if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE)) + { + String url = aparser.getValue(ArgsParser.QUESTIONNAIRE); + if (url != 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); - + Cache.log.debug("Starting questionnaire url at " + url); + desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); } + else + { + if (Cache.getProperty(Preferences.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(ArgsParser.NONEWS)) + { + desktop.checkForNews(); + } + + BioJsHTMLOutput.updateBioJS(); } } - String file = null, protocol = null, format = null, data = null; - jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); - Vector getFeatures = null; // vector of das source nicknames to fetch features from - // loading is done. - String groovyscript = null; // script to execute after all loading is completed one way or another + + // script to execute after all loading is + // completed one way or another // extract groovy argument and execute if necessary - groovyscript = aparser.getValue("groovy"); - file = aparser.getValue("open"); + String groovyscript = (isJS ? null + : aparser.getValue(ArgsParser.GROOVY, true)); + String file = aparser.getValue(ArgsParser.OPEN, true); + String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null) + : null); + String fileFormat = (isJavaAppletTag + ? aparser.getAppletValue("format", null) + : null); + FileFormatI format = null; + DataSourceType protocol = null; if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } - + boolean haveImport = checkStartVamas(aparser); + // Finally, deal with the remaining input data. + long progress = -1; if (file != null) { - System.out.println("Opening file: " + file); + if (!headless) + { + desktop.setProgressBar( + MessageManager + .getString("status.processing_commandline_args"), + progress = System.currentTimeMillis()); + } - if (!file.startsWith("http://")) + if (!isJS) + /** + * ignore in JavaScript -- can't just check file existence - could load + * it? + * + * @j2sIgnore + */ { - if (!(new java.io.File(file)).exists()) + if (!file.startsWith("http://") && !file.startsWith("https://")) + // BH 2019 added https check for Java { - System.out.println("Can't find " + file); - if (headless) + if (!(new File(file)).exists()) { - System.exit(1); + System.out.println("Can't find " + file); + if (headless) + { + System.exit(1); + } } } } - protocol = checkProtocol(file); + protocol = AppletFormatAdapter.checkProtocol(file); - format = new jalview.io.IdentifyFile().Identify(file, protocol); + try + { + format = (isJavaAppletTag && fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } + } catch (FileFormatException e1) + { + // TODO ? + } - AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, + AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file, + protocol, format); - if (af == null) { System.out.println("error"); - return; } - - data = aparser.getValue("colour"); - if (data != null) + else { - data.replaceAll("%20", " "); - - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); - - if (cs == null) + System.out + .println("CMD [-open " + file + "] executed successfully!"); + if (file2 != null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(data); - cs = ucs; + protocol = AppletFormatAdapter.checkProtocol(file2); + try + { + format = new IdentifyFile().identify(file2, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } + AlignFrame af2 = new FileLoader(!headless).loadFileWaitTillLoaded( + file2, + protocol, format); + if (af2 == null) + { + System.out.println("error"); + } + else + { + AlignViewport.openLinkedAlignmentAs(af, + af.getViewport().getAlignment(), + af2.getViewport().getAlignment(), "", + AlignViewport.SPLIT_FRAME); + } } - System.out.println("colour is " + data); - af.changeColour(cs); - } + setCurrentAlignFrame(af); - // Must maintain ability to use the groups flag - data = aparser.getValue("groups"); - if (data != null) - { - af.parseFeaturesFile(data, checkProtocol(data)); - System.out.println("Added " + data); - } - data = aparser.getValue("features"); - if (data != null) - { - af.parseFeaturesFile(data, checkProtocol(data)); - System.out.println("Added " + data); - } + // TODO: file2 How to implement file2 for the applet spit screen? - data = aparser.getValue("annotations"); - if (data != null) - { - af.loadJalviewDataFile(data); - System.out.println("Added " + data); - } - data = aparser.getValue("tree"); - if (data != null) - { - jalview.io.NewickFile fin = null; - try + String data = aparser.getValue(ArgsParser.COLOUR, true); + if (data != null) { - fin = new jalview.io.NewickFile(data, checkProtocol(data)); - if (fin != null) + data.replaceAll("%20", " "); + + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); + + if (cs != null) { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } - } catch (IOException ex) - { - System.err.println("Couldn't add tree " + data); - ex.printStackTrace(System.err); + af.changeColour(cs); } - } - getFeatures = checkDasArguments(aparser); - if (af != null && getFeatures!=null) - { - startFeatureFetching(getFeatures); - // need to block until fetching is complete. - while (af.operationInProgress()) + + // Must maintain ability to use the groups flag + data = aparser.getValue(ArgsParser.GROUPS, true); + if (data != null) { - // wait around until fetching is finished. - try { - Thread.sleep(10); - } catch (Exception e) - { - - } + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD groups[-" + data + "] executed successfully!"); } - } - if (groovyscript!=null) - { - // Execute the groovy script after we've done all the rendering stuff - // and before any images or figures are generated. - if (jalview.bin.Cache.groovyJarsPresent()) + data = aparser.getValue(ArgsParser.FEATURES, true); + if (data != null) { - System.out.println("Executing script "+groovyscript); - executeGroovyScript(groovyscript, desktop); - } else { - System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript); + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD [-features " + data + "] executed successfully!"); } - groovyscript = null; - } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - format = aparser.nextValue(); - file = aparser.nextValue(); - if (format.equalsIgnoreCase("png")) + data = aparser.getValue(ArgsParser.ANNOTATIONS, true); + if (data != null) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; + af.loadJalviewDataFile(data, null, null, null); + // System.out.println("Added " + data); + System.out.println( + "CMD [-annotations " + data + "] executed successfully!"); } - else if (format.equalsIgnoreCase("imgMap")) + // set or clear the sortbytree flag. + if (aparser.contains(ArgsParser.SORTBYTREE)) { - af.createImageMap(new java.io.File(file), imageName); - System.out.println("Creating image map: " + file); - continue; + af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } } - else if (format.equalsIgnoreCase("eps")) + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); - continue; + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + System.out.println("CMD no-annotation executed successfully!"); + } } - - if (af.saveAlignment(file, format)) + if (aparser.contains(ArgsParser.NOSORTBYTREE)) + { + af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } + } + data = aparser.getValue(ArgsParser.TREE, true); + if (data != null) { - System.out.println("Written alignment in " + format - + " format to " + file); + 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); + } } - else + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) + if (isJavaAppletTag) { - System.out.println("Error writing file " + file + " in " + format - + " format!!"); + loadAppletParams(aparser, af); + } + else if (!isJS) + /** + * Java only + * + * @j2sIgnore + */ + { + 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; + } + checkOutputFile(aparser, af, format); + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); + } } - - } - - 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 + + if (!isJS && !headless && file == null && !haveImport && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + /** + * Java only + * + * @j2sIgnore + */ { file = jalview.bin.Cache.getDefault("STARTUP_FILE", - "http://www.jalview.org/examples/exampleFile_2_3.jar"); + 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 = "File"; + protocol = DataSourceType.FILE; if (file.indexOf("http:") > -1) { - protocol = "URL"; + protocol = DataSourceType.URL; } if (file.endsWith(".jar")) { - format = "Jalview"; + format = FileFormat.Jalview; } else { - format = new jalview.io.IdentifyFile().Identify(file, protocol); + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e) + { + // TODO what? + } } - startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, + startUpAlframe = new FileLoader(!headless) + .loadFileWaitTillLoaded(file, protocol, format); - getFeatures = checkDasArguments(aparser); // extract groovy arguments before anything else. } - // Once all loading is done. Retrieve features. - if (getFeatures!=null) + + // Once all other stuff is done, execute any groovy scripts (in order) + if (groovyscript != null) { - if (startUpAlframe!=null) + if (Cache.groovyJarsPresent()) { - startFeatureFetching(getFeatures); + 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); } } - if (groovyscript!=null) + // and finally, turn off batch mode indicator - if the desktop still exists + if (desktop != null) { - if (jalview.bin.Cache.groovyJarsPresent()) + if (progress != -1) { - System.out.println("Executing script "+groovyscript); - executeGroovyScript(groovyscript, desktop); - } else { - System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript); + desktop.setProgressBar(null, progress); } + desktop.setInBatchMode(false); } - - // Once all other stuff is done, execute any groovy scripts (in order) } - /** - * Locate the given string as a file and pass it to the groovy interpreter. - * @param groovyscript the script to execute - * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object. - */ - private static void executeGroovyScript(String groovyscript, Object jalviewContext) + + private boolean checkStartVamas(ArgsParser aparser) { - if (jalviewContext==null) + String vamsasImport = aparser.getValue(ArgsParser.VDOC); + String vamsasSession = aparser.getValue(ArgsParser.VSESS); + if (vamsasImport == null && vamsasSession == null) { - System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); + return false; } - File sfile = new File(groovyscript); - if (!sfile.exists()) + if (desktop == null || headless) { - System.err.println("File '"+groovyscript+"' does not exist."); - return; + System.out.println( + "Headless vamsas sessions not yet supported. Sorry."); + System.exit(1); } - if (!sfile.canRead()) + boolean haveImport = (vamsasImport != null); + if (haveImport) { - System.err.println("File '"+groovyscript+"' cannot be read."); - return; + // if we have a file, start a new session and import it. + boolean inSession = false; + 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 (sfile.length()<1) + if (vamsasSession != null) { - System.err.println("File '"+groovyscript+"' is empty."); - return; - } - try { - /* The following code performs the GroovyScriptEngine invocation using reflection, - * and is equivalent to this fragment from the embedding groovy documentation on - * the groovy site: - * - import groovy.lang.Binding; - import groovy.util.GroovyScriptEngine; - - String[] roots = new String[] { "/my/groovy/script/path" }; - GroovyScriptEngine gse = new GroovyScriptEngine(roots); - Binding binding = new Binding(); - binding.setVariable("input", "world"); - gse.run("hello.groovy", binding); - * - */ - ClassLoader cl = jalviewContext.getClass().getClassLoader(); - Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons = gbindingc.getConstructor(null); - Object gbinding = gbcons.newInstance(null); - java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} ); - setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext}); - Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); - Constructor gseccons = gsec.getConstructor(new Class[] { String[].class }); - Object gse = gseccons.newInstance(new Object[] { new String[] { groovyscript } }); - java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc }); - run.invoke(gse, new Object[] { sfile.getName(), gbinding }); - } catch (Exception e) - { - System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script."); - e.printStackTrace(System.err); + 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(); + } } + return haveImport; } - /** - * 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) + + private void checkOutputFile(ArgsParser aparser, AlignFrame af, + FileFormatI format) { - Vector source=null; - String data; - String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); - while ((data = aparser.getValue("dasserver"))!=null) + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) { - String nickname = null; - String url = null; - int pos = data.indexOf('='); - if (pos > 0) + // PNG filename + // SVG filename + // HTML filename + // biojsmsa filename + String outputFormat = aparser.nextValue(); + String 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")) { - nickname = data.substring(0, pos); + File imageFile = new File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG image: " + file); + continue; } - url = data.substring(pos + 1); - if (url != null && url.startsWith("http:")) + else if (outputFormat.equalsIgnoreCase("html")) { - if (nickname == null) + 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) { - nickname = url; + System.err.println("The output html file must not be null"); + return; } - if (locsources==null) + try { - 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) + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) { - source = new Vector(); + e.printStackTrace(); } - source.addElement(nickname); + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(file); + System.out.println("Creating BioJS MSA Viwer HTML file: " + file); + continue; } - } // 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"))!=null) - { - System.out.println("adding source '"+data+"'"); - if (source==null) + 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()) { - source = new Vector(); + System.out.println( + "Written alignment in " + format + " format to " + file); } - source.addElement(data); + else + { + System.out.println("Error writing file " + file + " in " + format + + " format!!"); + } + } - return source; } + + 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.getDesktopPane(), "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); + } + /** - * start a feature fetcher for every alignment frame - * @param dasSources + * Locate the given string as a file and pass it to the groovy interpreter. + * + * @param groovyscript + * the script to execute + * @param jalviewContext + * the Jalview Desktop object passed in to the groovy binding as the + * 'Jalview' object. */ - private static void startFeatureFetching(final Vector dasSources) + private void executeGroovyScript(String groovyscript, AlignFrame af) { - AlignFrame afs[] = Desktop.getAlignframes(); - if (afs==null || afs.length==0) + /** + * 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 { - return; + 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; + } + } } - for (int i = 0; i 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 void run() - { - af.featureSettings_actionPerformed(null); - af.featureSettings.fetchDasFeatures(dasSources); - } - }); } } - private static String checkProtocol(String file) + public AlignFrame[] getAlignFrames() { - String protocol = jalview.io.FormatAdapter.FILE; + return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } + : Desktop.getAlignFrames(); - if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1) - { - protocol = jalview.io.FormatAdapter.URL; - } - return protocol; } -} - -/** - * Notes: this argParser does not distinguish between parameter switches, - * parameter values and argument text. If an argument happens to be identical - * to a parameter, it will be taken as such (even though it didn't have a '-' prefixing it). - * - * @author Andrew Waterhouse and JBP documented. - * - */ -class ArgsParser -{ - Vector vargs = null; - public ArgsParser(String[] args) + /** + * Quit method delegates to Desktop.quit - unless running in headless mode + * when it just ends the JVM + */ + public void quit() { - vargs = new Vector(); - for (int i = 0; i < args.length; i++) + if (desktop != null) { - String arg = args[i].trim(); - if (arg.charAt(0) == '-') - { - arg = arg.substring(1); - } - vargs.addElement(arg); + desktop.quit(); + } + else + { + System.exit(0); } } + /** - * check for and remove first occurence of arg+parameter in arglist. - * @param arg - * @return return the argument following the given arg if arg was in list. + * Get the SwingJS applet ID and combine that with the frameType + * + * @param frameType + * "alignment", "desktop", etc., or null + * @return */ - public String getValue(String arg) + public static String getAppID(String frameType) { - int index = vargs.indexOf(arg); - String ret = null; - if (index != -1) + String id = Cache.getProperty("Info.j2sAppletID"); + if (id == null) { - ret = vargs.elementAt(index + 1).toString(); - vargs.removeElementAt(index); - vargs.removeElementAt(index); + id = "jalview"; } - return ret; + return id + (frameType == null ? "" : "-" + frameType); } + /** - * check for and remove first occurence of arg in arglist. - * @param arg - * @return true if arg was present in argslist. + * Handle all JalviewLite applet parameters + * + * @param aparser + * @param af */ - public boolean contains(String arg) + private void loadAppletParams(ArgsParser aparser, AlignFrame af) { - if (vargs.contains(arg)) + JalviewApp app = new JalviewApp() { - vargs.removeElement(arg); - return true; - } - else - { - return false; - } - } - public String nextValue() - { - return vargs.remove(0).toString(); - } + private boolean alignPDBStructures; // From JalviewLite; not implemented - public int getSize() - { - return vargs.size(); + @Override + public String getParameter(String name) + { + return aparser.getAppletValue(name, null); + } + + @Override + public boolean getDefaultParameter(String name, boolean def) + { + String stn; + return ((stn = getParameter(name)) == null ? def + : "true".equalsIgnoreCase(stn)); + } + + /** + * Get the applet-like document base even though this is an application. + */ + @Override + public URL getDocumentBase() + { + return Platform.getDocumentBase(); + } + + /** + * Get the applet-like code base even though this is an application. + */ + @Override + public URL getCodeBase() + { + return Platform.getCodeBase(); + } + + @Override + public AlignViewportI getViewport() + { + return af.getViewport(); + } + + /** + * features + * + */ + @Override + public boolean parseFeaturesFile(String filename, + DataSourceType protocol) + { + return af.parseFeaturesFile(filename, protocol); + } + + /** + * scorefile + * + */ + @Override + public boolean loadScoreFile(String sScoreFile) throws IOException + { + af.loadJalviewDataFile(sScoreFile, null, null, null); + return true; + } + + /** + * annotations, jpredfile, jnetfile + * + */ + @Override + public void updateForAnnotations() + { + af.updateForAnnotations(); + } + + @Override + public void loadTree(NewickFile fin, String treeFile) + throws IOException + { + // n/a -- already done by standard Jalview command line processing + } + + @Override + public void setAlignPdbStructures(boolean defaultParameter) + { + alignPDBStructures = true; + } + + @Override + public void newStructureView(PDBEntry pdb, SequenceI[] seqs, + String[] chains, DataSourceType protocol) + { + StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs); + } + + @Override + public void setFeatureGroupState(String[] groups, boolean state) + { + af.setFeatureGroupState(groups, state); + } + + @Override + public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, + String[][] chains, String[] protocols) + { + System.err.println( + "Jalview applet interface alignedStructureView not implemented"); + } + + @Override + public void newFeatureSettings() + { + System.err.println( + "Jalview applet interface newFeatureSettings not implemented"); + } + + }; + + new JalviewAppLoader(true).load(app); } }