2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.awt.Color;
24 import java.io.BufferedReader;
26 import java.io.FileOutputStream;
27 import java.io.IOException;
28 import java.io.InputStreamReader;
29 import java.io.OutputStream;
30 import java.io.OutputStreamWriter;
31 import java.io.PrintStream;
32 import java.io.PrintWriter;
33 import java.net.MalformedURLException;
35 import java.net.URISyntaxException;
37 import java.security.AllPermission;
38 import java.security.CodeSource;
39 import java.security.PermissionCollection;
40 import java.security.Permissions;
41 import java.security.Policy;
42 import java.util.ArrayList;
43 import java.util.HashMap;
44 import java.util.List;
45 import java.util.Locale;
47 import java.util.Properties;
48 import java.util.Vector;
49 import java.util.logging.ConsoleHandler;
50 import java.util.logging.Level;
51 import java.util.logging.Logger;
52 import java.util.stream.Collectors;
54 import javax.swing.JDialog;
55 import javax.swing.JFrame;
56 import javax.swing.JInternalFrame;
57 import javax.swing.JOptionPane;
58 import javax.swing.SwingUtilities;
59 import javax.swing.UIManager;
60 import javax.swing.UIManager.LookAndFeelInfo;
61 import javax.swing.UnsupportedLookAndFeelException;
63 import com.formdev.flatlaf.FlatLightLaf;
64 import com.formdev.flatlaf.themes.FlatMacLightLaf;
65 import com.formdev.flatlaf.util.SystemInfo;
66 import com.threerings.getdown.util.LaunchUtil;
68 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
69 import groovy.lang.Binding;
70 import groovy.util.GroovyScriptEngine;
71 import jalview.bin.argparser.Arg;
72 import jalview.bin.argparser.Arg.Opt;
73 import jalview.bin.argparser.Arg.Type;
74 import jalview.bin.argparser.ArgParser;
75 import jalview.bin.argparser.BootstrapArgs;
76 import jalview.ext.so.SequenceOntology;
77 import jalview.gui.AlignFrame;
78 import jalview.gui.Desktop;
79 import jalview.gui.PromptUserConfig;
80 import jalview.gui.QuitHandler;
81 import jalview.gui.QuitHandler.QResponse;
82 import jalview.gui.StructureViewerBase;
83 import jalview.io.AppletFormatAdapter;
84 import jalview.io.BioJsHTMLOutput;
85 import jalview.io.DataSourceType;
86 import jalview.io.FileFormat;
87 import jalview.io.FileFormatException;
88 import jalview.io.FileFormatI;
89 import jalview.io.FileFormats;
90 import jalview.io.FileLoader;
91 import jalview.io.HtmlSvgOutput;
92 import jalview.io.IdentifyFile;
93 import jalview.io.NewickFile;
94 import jalview.io.gff.SequenceOntologyFactory;
95 import jalview.schemes.ColourSchemeI;
96 import jalview.schemes.ColourSchemeProperty;
97 import jalview.util.ChannelProperties;
98 import jalview.util.HttpUtils;
99 import jalview.util.LaunchUtils;
100 import jalview.util.MessageManager;
101 import jalview.util.Platform;
102 import jalview.ws.jws2.Jws2Discoverer;
105 * Main class for Jalview Application <br>
107 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
108 * jalview.bin.Jalview
110 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
111 * jalview.bin.Jalview jalview.bin.Jalview
113 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
114 * embellish '*' to e.g. '*.jar')
117 * @version $Revision$
123 Platform.getURLCommandArguments();
124 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
125 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
126 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
127 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
131 * singleton instance of this class
133 private static Jalview instance;
135 private Desktop desktop;
137 protected Commands cmds;
139 public static AlignFrame currentAlignFrame;
141 public ArgParser argparser = null;
143 public BootstrapArgs bootstrapArgs = null;
145 private boolean QUIET = false;
147 public static boolean quiet()
149 return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
154 if (!Platform.isJS())
161 // grab all the rights we can for the JVM
162 Policy.setPolicy(new Policy()
165 public PermissionCollection getPermissions(CodeSource codesource)
167 Permissions perms = new Permissions();
168 perms.add(new AllPermission());
173 public void refresh()
181 * keep track of feature fetching tasks.
189 * TODO: generalise to track all jalview events to orchestrate batch processing
193 private int queued = 0;
195 private int running = 0;
197 public FeatureFetcher()
202 public void addFetcher(final AlignFrame af,
203 final Vector<String> dasSources)
205 final long id = System.currentTimeMillis();
207 final FeatureFetcher us = this;
208 new Thread(new Runnable()
220 af.setProgressBar(MessageManager
221 .getString("status.das_features_being_retrived"), id);
222 af.featureSettings_actionPerformed(null);
223 af.setProgressBar(null, id);
232 public synchronized boolean allFinished()
234 return queued == 0 && running == 0;
239 public static Jalview getInstance()
245 * main class for Jalview application
248 * open <em>filename</em>
250 public static void main(String[] args)
252 // setLogging(); // BH - for event debugging in JavaScript
253 instance = new Jalview();
254 instance.doMain(args);
257 private static void logClass(String name)
259 // BH - for event debugging in JavaScript
260 ConsoleHandler consoleHandler = new ConsoleHandler();
261 consoleHandler.setLevel(Level.ALL);
262 Logger logger = Logger.getLogger(name);
263 logger.setLevel(Level.ALL);
264 logger.addHandler(consoleHandler);
267 @SuppressWarnings("unused")
268 private static void setLogging()
276 System.out.println("not in js");
279 // BH - for event debugging in JavaScript (Java mode only)
280 if (!Platform.isJS())
287 Logger.getLogger("").setLevel(Level.ALL);
288 logClass("java.awt.EventDispatchThread");
289 logClass("java.awt.EventQueue");
290 logClass("java.awt.Component");
291 logClass("java.awt.focus.Component");
292 logClass("java.awt.focus.DefaultKeyboardFocusManager");
300 void doMain(String[] args)
302 if (!Platform.isJS())
304 System.setSecurityManager(null);
307 if (args == null || args.length == 0 || (args.length == 1
308 && (args[0] == null || args[0].length() == 0)))
310 args = new String[] {};
313 // get args needed before proper ArgParser
314 bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
316 if (!Platform.isJS())
318 // are we being --quiet ?
319 if (bootstrapArgs.contains(Arg.QUIET))
322 OutputStream devNull = new OutputStream()
326 public void write(int b)
331 System.setOut(new PrintStream(devNull));
332 // redirecting stderr not working
333 if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
335 System.setErr(new PrintStream(devNull));
339 if (bootstrapArgs.contains(Arg.HELP)
340 || bootstrapArgs.contains(Arg.VERSION))
346 // Move any new getdown-launcher-new.jar into place over old
347 // getdown-launcher.jar
348 String appdirString = System.getProperty("getdownappdir");
349 if (appdirString != null && appdirString.length() > 0)
351 final File appdir = new File(appdirString);
358 LaunchUtil.upgradeGetdown(
359 new File(appdir, "getdown-launcher-old.jar"),
360 new File(appdir, "getdown-launcher.jar"),
361 new File(appdir, "getdown-launcher-new.jar"));
366 if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
369 "Java version: " + System.getProperty("java.version"));
370 System.out.println("Java home: " + System.getProperty("java.home"));
371 System.out.println("Java arch: " + System.getProperty("os.arch") + " "
372 + System.getProperty("os.name") + " "
373 + System.getProperty("os.version"));
375 String val = System.getProperty("sys.install4jVersion");
378 System.out.println("Install4j version: " + val);
380 val = System.getProperty("installer_template_version");
383 System.out.println("Install4j template version: " + val);
385 val = System.getProperty("launcher_version");
388 System.out.println("Launcher version: " + val);
392 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
394 System.setProperty("flatlaf.uiScale", "1");
397 // get bootstrap properties (mainly for the logger level)
398 Properties bootstrapProperties = Cache
399 .bootstrapProperties(bootstrapArgs.getValue(Arg.PROPS));
401 // report Jalview version
402 Cache.loadBuildProperties(
403 !quiet() || bootstrapArgs.contains(Arg.VERSION));
405 // stop now if only after --version
406 if (bootstrapArgs.contains(Arg.VERSION))
408 Jalview.exit(null, 0);
412 ArgsParser aparser = new ArgsParser(args);
415 boolean headless = false;
417 boolean headlessArg = false;
421 String logLevel = null;
422 if (bootstrapArgs.contains(Arg.TRACE))
426 else if (bootstrapArgs.contains(Arg.DEBUG))
430 if (logLevel == null && !(bootstrapProperties == null))
432 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
434 Console.initLogger(logLevel);
435 } catch (NoClassDefFoundError error)
437 error.printStackTrace();
438 String message = "\nEssential logging libraries not found."
439 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
440 Jalview.exit(message, 0);
443 // register SIGTERM listener
444 Runtime.getRuntime().addShutdownHook(new Thread()
448 Console.debug("Running shutdown hook");
449 QuitHandler.startForceQuit();
450 boolean closeExternal = Cache
451 .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false)
452 || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false);
453 StructureViewerBase.setQuitClose(closeExternal);
456 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
458 if (frame instanceof StructureViewerBase)
460 ((StructureViewerBase) frame).closeViewer(closeExternal);
465 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
467 // Got to here by a SIGTERM signal.
468 // Note we will not actually cancel the quit from here -- it's too
469 // late -- but we can wait for saving files and close external viewers
471 // Close viewers/Leave viewers open
472 Console.debug("Checking for saving files");
473 QuitHandler.getQuitResponse(false);
477 Console.debug("Nothing more to do");
479 Console.debug("Exiting, bye!");
480 // shutdownHook cannot be cancelled, JVM will now halt
484 String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
485 ? bootstrapArgs.getValue(Arg.PROPS)
486 : aparser.getValue("props");
487 // if usrPropsFile == null, loadProperties will use the Channel
489 Cache.loadProperties(usrPropsFile);
490 if (usrPropsFile != null)
493 "CMD [-props " + usrPropsFile + "] executed successfully!");
494 testoutput(bootstrapArgs, Arg.PROPS,
495 "test/jalview/bin/testProps.jvprops", usrPropsFile);
498 // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
499 if (bootstrapArgs.contains(Arg.ARGFILE))
501 argparser = ArgParser.parseArgFiles(
502 bootstrapArgs.getValueList(Arg.ARGFILE),
503 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
508 argparser = new ArgParser(args,
509 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
513 if (!Platform.isJS())
520 if (bootstrapArgs.contains(Arg.HELP))
522 List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
524 System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
525 .collect(Collectors.toList())));
526 Jalview.exit(null, 0);
528 if (aparser.contains("help") || aparser.contains("h"))
531 * Now using new usage statement.
534 System.out.println(Arg.usage());
535 Jalview.exit(null, 0);
539 headlessArg = bootstrapArgs.isHeadless();
542 System.setProperty("java.awt.headless", "true");
545 if (aparser.contains("nodisplay") || aparser.contains("nogui")
546 || aparser.contains("headless"))
548 System.setProperty("java.awt.headless", "true");
553 // allow https handshakes to download intermediate certs if necessary
554 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
556 String jabawsUrl = bootstrapArgs.getValue(Arg.JABAWS);
557 if (jabawsUrl == null)
558 jabawsUrl = aparser.getValue("jabaws");
559 if (jabawsUrl != null)
563 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
565 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
566 testoutput(bootstrapArgs, Arg.JABAWS,
567 "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
568 } catch (MalformedURLException e)
571 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
576 List<String> setprops = new ArrayList<>();
577 if (bootstrapArgs.contains(Arg.SETPROP))
579 setprops = bootstrapArgs.getValueList(Arg.SETPROP);
583 String sp = aparser.getValue("setprop");
587 sp = aparser.getValue("setprop");
590 for (String setprop : setprops)
592 int p = setprop.indexOf('=');
596 .println("Ignoring invalid setprop argument : " + setprop);
600 System.out.println("Executing setprop argument: " + setprop);
603 Cache.setProperty(setprop.substring(0, p),
604 setprop.substring(p + 1));
606 // DISABLED FOR SECURITY REASONS
607 // TODO: add a property to allow properties to be overriden by cli args
608 // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
611 if (System.getProperty("java.awt.headless") != null
612 && System.getProperty("java.awt.headless").equals("true"))
616 System.setProperty("http.agent",
617 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
621 Console.initLogger();
624 NoClassDefFoundError error)
626 error.printStackTrace();
627 String message = "\nEssential logging libraries not found."
628 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
629 Jalview.exit(message, 0);
633 if (!(headless || headlessArg))
637 * configure 'full' SO model if preferences say to, else use the default (full SO)
638 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
640 boolean soDefault = !Platform.isJS();
641 if (Cache.getDefault("USE_FULL_SO", soDefault))
643 SequenceOntologyFactory.setInstance(new SequenceOntology());
646 if (!(headless || headlessArg))
648 Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
649 || aparser.contains("nosplash")
650 || Cache.getDefault("SPLASH", "true").equals("false");
651 desktop = new Desktop();
652 desktop.setInBatchMode(true); // indicate we are starting up
656 JalviewTaskbar.setTaskbar(this);
657 } catch (Exception e)
659 Console.info("Cannot set Taskbar");
660 Console.error(e.getMessage());
661 // e.printStackTrace();
662 } catch (Throwable t)
664 Console.info("Cannot set Taskbar");
665 Console.error(t.getMessage());
666 // t.printStackTrace();
669 // set Proxy settings before all the internet calls
670 Cache.setProxyPropertiesFromPreferences();
672 desktop.setVisible(true);
674 if (!Platform.isJS())
683 * Check to see that the JVM version being run is suitable for the Java
684 * version this Jalview was compiled for. Popup a warning if not.
686 if (!LaunchUtils.checkJavaVersion())
688 Console.warn("The Java version being used (Java "
689 + LaunchUtils.getJavaVersion()
690 + ") may lead to problems. This installation of Jalview should be used with Java "
691 + LaunchUtils.getJavaCompileVersion() + ".");
694 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
697 MessageManager.getString("label.continue") };
698 JOptionPane.showOptionDialog(null,
699 MessageManager.formatMessage(
700 "warning.wrong_jvm_version_message",
701 LaunchUtils.getJavaVersion(),
702 LaunchUtils.getJavaCompileVersion()),
704 .getString("warning.wrong_jvm_version_title"),
705 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
706 null, options, options[0]);
710 boolean webservicediscovery = bootstrapArgs
711 .getBoolean(Arg.WEBSERVICEDISCOVERY);
712 if (aparser.contains("nowebservicediscovery"))
713 webservicediscovery = false;
714 if (webservicediscovery)
716 desktop.startServiceDiscovery();
720 testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
723 boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
724 if (aparser.contains("nousagestats"))
728 startUsageStats(desktop);
729 testoutput(argparser, Arg.USAGESTATS);
733 System.out.println("CMD [-nousagestats] executed successfully!");
734 testoutput(argparser, Arg.USAGESTATS);
737 boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
738 if (aparser.contains("noquestionnaire"))
739 questionnaire = false;
742 String url = aparser.getValue("questionnaire");
745 // Start the desktop questionnaire prompter with the specified
747 Console.debug("Starting questionnaire url at " + url);
748 desktop.checkForQuestionnaire(url);
749 System.out.println("CMD questionnaire[-" + url
750 + "] executed successfully!");
754 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
756 // Start the desktop questionnaire prompter with the specified
759 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
761 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
763 "Starting questionnaire with default url: " + defurl);
764 desktop.checkForQuestionnaire(defurl);
771 .println("CMD [-noquestionnaire] executed successfully!");
772 testoutput(argparser, Arg.QUESTIONNAIRE);
775 if ((!aparser.contains("nonews")
776 && Cache.getProperty("NONEWS") == null
777 && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
778 || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
780 desktop.checkForNews();
783 if (!aparser.contains("nohtmltemplates")
784 && Cache.getProperty("NOHTMLTEMPLATES") == null)
786 BioJsHTMLOutput.updateBioJS();
790 // Run Commands from cli
791 cmds = new Commands(argparser, headlessArg);
792 boolean commandsSuccess = cmds.argsWereParsed();
797 if (argparser.getBoolean(Arg.NOQUIT))
800 "Completed " + Arg.HEADLESS.getName() + " commands, but "
801 + Arg.NOQUIT + " is set so not quitting!");
805 Jalview.exit("Successfully completed commands in headless mode",
809 Console.info("Successfully completed commands");
815 Jalview.exit("Error when running Commands in headless mode", 1);
817 Console.warn("Error when running commands");
820 // Check if JVM and compile version might cause problems and log if it
822 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
824 Console.warn("The Java version being used (Java "
825 + LaunchUtils.getJavaVersion()
826 + ") may lead to problems. This installation of Jalview should be used with Java "
827 + LaunchUtils.getJavaCompileVersion() + ".");
830 String file = null, data = null;
832 FileFormatI format = null;
834 DataSourceType protocol = null;
836 FileLoader fileLoader = new FileLoader(!headless);
838 String groovyscript = null; // script to execute after all loading is
839 // completed one way or another
840 // extract groovy argument and execute if necessary
841 groovyscript = aparser.getValue("groovy", true);
842 file = aparser.getValue("open", true);
844 if (file == null && desktop == null && !commandsSuccess)
846 Jalview.exit("No files to open!", 1);
850 // Finally, deal with the remaining input data.
855 desktop.setProgressBar(
857 .getString("status.processing_commandline_args"),
858 progress = System.currentTimeMillis());
860 System.out.println("CMD [-open " + file + "] executed successfully!");
862 if (!Platform.isJS())
864 * ignore in JavaScript -- can't just file existence - could load it?
869 if (!HttpUtils.startsWithHttpOrHttps(file))
871 if (!(new File(file)).exists())
876 "Can't find file '" + file + "' in headless mode", 1);
878 Console.warn("Can't find file'" + file + "'");
883 protocol = AppletFormatAdapter.checkProtocol(file);
887 format = new IdentifyFile().identify(file, protocol);
888 } catch (FileFormatException e1)
893 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
897 System.out.println("error");
901 setCurrentAlignFrame(af);
902 data = aparser.getValue("colour", true);
905 data.replaceAll("%20", " ");
907 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
908 af.getViewport(), af.getViewport().getAlignment(), data);
913 "CMD [-colour " + data + "] executed successfully!");
918 // Must maintain ability to use the groups flag
919 data = aparser.getValue("groups", true);
922 af.parseFeaturesFile(data,
923 AppletFormatAdapter.checkProtocol(data));
924 // System.out.println("Added " + data);
926 "CMD groups[-" + data + "] executed successfully!");
928 data = aparser.getValue("features", true);
931 af.parseFeaturesFile(data,
932 AppletFormatAdapter.checkProtocol(data));
933 // System.out.println("Added " + data);
935 "CMD [-features " + data + "] executed successfully!");
938 data = aparser.getValue("annotations", true);
941 af.loadJalviewDataFile(data, null, null, null);
942 // System.out.println("Added " + data);
944 "CMD [-annotations " + data + "] executed successfully!");
946 // set or clear the sortbytree flag.
947 if (aparser.contains("sortbytree"))
949 af.getViewport().setSortByTree(true);
950 if (af.getViewport().getSortByTree())
952 System.out.println("CMD [-sortbytree] executed successfully!");
955 if (aparser.contains("no-annotation"))
957 af.getViewport().setShowAnnotation(false);
958 if (!af.getViewport().isShowAnnotation())
960 System.out.println("CMD no-annotation executed successfully!");
963 if (aparser.contains("nosortbytree"))
965 af.getViewport().setSortByTree(false);
966 if (!af.getViewport().getSortByTree())
969 .println("CMD [-nosortbytree] executed successfully!");
972 data = aparser.getValue("tree", true);
978 "CMD [-tree " + data + "] executed successfully!");
979 NewickFile nf = new NewickFile(data,
980 AppletFormatAdapter.checkProtocol(data));
982 .setCurrentTree(af.showNewickTree(nf, data).getTree());
983 } catch (IOException ex)
985 System.err.println("Couldn't add tree " + data);
986 ex.printStackTrace(System.err);
990 if (groovyscript != null)
992 // Execute the groovy script after we've done all the rendering stuff
993 // and before any images or figures are generated.
994 System.out.println("Executing script " + groovyscript);
995 executeGroovyScript(groovyscript, af);
996 System.out.println("CMD groovy[" + groovyscript
997 + "] executed successfully!");
1000 String imageName = "unnamed.png";
1001 while (aparser.getSize() > 1)
1003 String outputFormat = aparser.nextValue();
1004 file = aparser.nextValue();
1006 if (outputFormat.equalsIgnoreCase("png"))
1008 af.createPNG(new File(file));
1009 imageName = (new File(file)).getName();
1010 System.out.println("Creating PNG image: " + file);
1013 else if (outputFormat.equalsIgnoreCase("svg"))
1015 File imageFile = new File(file);
1016 imageName = imageFile.getName();
1017 af.createSVG(imageFile);
1018 System.out.println("Creating SVG image: " + file);
1021 else if (outputFormat.equalsIgnoreCase("html"))
1023 File imageFile = new File(file);
1024 imageName = imageFile.getName();
1025 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1026 htmlSVG.exportHTML(file);
1028 System.out.println("Creating HTML image: " + file);
1031 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1035 System.err.println("The output html file must not be null");
1040 BioJsHTMLOutput.refreshVersionInfo(
1041 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1042 } catch (URISyntaxException e)
1044 e.printStackTrace();
1046 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1047 bjs.exportHTML(file);
1049 .println("Creating BioJS MSA Viwer HTML file: " + file);
1052 else if (outputFormat.equalsIgnoreCase("imgMap"))
1054 af.createImageMap(new File(file), imageName);
1055 System.out.println("Creating image map: " + file);
1058 else if (outputFormat.equalsIgnoreCase("eps"))
1060 File outputFile = new File(file);
1062 "Creating EPS file: " + outputFile.getAbsolutePath());
1063 af.createEPS(outputFile);
1066 FileFormatI outFormat = null;
1069 outFormat = FileFormats.getInstance().forName(outputFormat);
1070 } catch (Exception formatP)
1072 System.out.println("Couldn't parse " + outFormat
1073 + " as a valid Jalview format string.");
1075 if (outFormat != null)
1077 if (!outFormat.isWritable())
1080 "This version of Jalview does not support alignment export as "
1085 af.saveAlignment(file, outFormat);
1086 if (af.isSaveAlignmentSuccessful())
1088 System.out.println("Written alignment in "
1089 + outFormat.getName() + " format to " + file);
1093 System.out.println("Error writing file " + file + " in "
1094 + outFormat.getName() + " format!!");
1101 while (aparser.getSize() > 0)
1103 System.out.println("Unknown arg: " + aparser.nextValue());
1108 AlignFrame startUpAlframe = null;
1109 // We'll only open the default file if the desktop is visible.
1111 // ////////////////////
1113 if (!Platform.isJS() && !headless && file == null
1114 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1115 && !cmds.commandArgsProvided())
1116 // don't open the startup file if command line args have been processed
1117 // (&& !Commands.commandArgsProvided())
1124 file = Cache.getDefault("STARTUP_FILE",
1125 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1126 + "/examples/exampleFile_2_7.jvp");
1127 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1129 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1131 file.replace("http:", "https:");
1132 // hardwire upgrade of the startup file
1133 file.replace("_2_3", "_2_7");
1134 file.replace("2_7.jar", "2_7.jvp");
1135 // and remove the stale setting
1136 Cache.removeProperty("STARTUP_FILE");
1139 protocol = AppletFormatAdapter.checkProtocol(file);
1141 if (file.endsWith(".jar"))
1143 format = FileFormat.Jalview;
1149 format = new IdentifyFile().identify(file, protocol);
1150 } catch (FileFormatException e)
1156 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1158 // don't ask to save when quitting if only the startup file has been
1160 Console.debug("Resetting up-to-date flag for startup file");
1161 startUpAlframe.getViewport().setSavedUpToDate(true);
1162 // extract groovy arguments before anything else.
1165 // Once all other stuff is done, execute any groovy scripts (in order)
1166 if (groovyscript != null)
1168 if (Cache.groovyJarsPresent())
1170 System.out.println("Executing script " + groovyscript);
1171 executeGroovyScript(groovyscript, startUpAlframe);
1176 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1180 // and finally, turn off batch mode indicator - if the desktop still exists
1181 if (desktop != null)
1185 desktop.setProgressBar(null, progress);
1187 desktop.setInBatchMode(false);
1191 private static void setLookAndFeel()
1193 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1195 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
1196 // try Quaqua/Vaqua.
1197 String lafProp = System.getProperty("laf");
1198 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1199 String laf = "none";
1200 if (lafProp != null)
1204 else if (lafSetting != null)
1208 boolean lafSet = false;
1211 case "crossplatform":
1212 lafSet = setCrossPlatformLookAndFeel();
1215 Console.error("Could not set requested laf=" + laf);
1219 lafSet = setSystemLookAndFeel();
1222 Console.error("Could not set requested laf=" + laf);
1226 lafSet = setGtkLookAndFeel();
1229 Console.error("Could not set requested laf=" + laf);
1233 lafSet = setMetalLookAndFeel();
1236 Console.error("Could not set requested laf=" + laf);
1240 lafSet = setNimbusLookAndFeel();
1243 Console.error("Could not set requested laf=" + laf);
1247 lafSet = setFlatLookAndFeel();
1250 Console.error("Could not set requested laf=" + laf);
1254 lafSet = setMacLookAndFeel();
1257 Console.error("Could not set requested laf=" + laf);
1263 Console.error("Requested laf=" + laf + " not implemented");
1267 // Flatlaf default for everyone!
1268 lafSet = setFlatLookAndFeel();
1271 setSystemLookAndFeel();
1273 if (Platform.isLinux())
1275 setLinuxLookAndFeel();
1277 if (Platform.isMac())
1279 setMacLookAndFeel();
1284 private static boolean setCrossPlatformLookAndFeel()
1286 boolean set = false;
1289 UIManager.setLookAndFeel(
1290 UIManager.getCrossPlatformLookAndFeelClassName());
1292 } catch (Exception ex)
1294 Console.error("Unexpected Look and Feel Exception");
1295 Console.error(ex.getMessage());
1296 Console.debug(Cache.getStackTraceString(ex));
1301 private static boolean setSystemLookAndFeel()
1303 boolean set = false;
1306 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1308 } catch (Exception ex)
1310 Console.error("Unexpected Look and Feel Exception");
1311 Console.error(ex.getMessage());
1312 Console.debug(Cache.getStackTraceString(ex));
1317 private static boolean setSpecificLookAndFeel(String name,
1318 String className, boolean nameStartsWith)
1320 boolean set = false;
1323 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1325 if (info.getName() != null && nameStartsWith
1326 ? info.getName().toLowerCase(Locale.ROOT)
1327 .startsWith(name.toLowerCase(Locale.ROOT))
1328 : info.getName().toLowerCase(Locale.ROOT)
1329 .equals(name.toLowerCase(Locale.ROOT)))
1331 className = info.getClassName();
1335 UIManager.setLookAndFeel(className);
1337 } catch (Exception ex)
1339 Console.error("Unexpected Look and Feel Exception");
1340 Console.error(ex.getMessage());
1341 Console.debug(Cache.getStackTraceString(ex));
1346 private static boolean setGtkLookAndFeel()
1348 return setSpecificLookAndFeel("gtk",
1349 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1352 private static boolean setMetalLookAndFeel()
1354 return setSpecificLookAndFeel("metal",
1355 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1358 private static boolean setNimbusLookAndFeel()
1360 return setSpecificLookAndFeel("nimbus",
1361 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1364 private static boolean setFlatLookAndFeel()
1366 boolean set = false;
1367 if (SystemInfo.isMacOS)
1371 UIManager.setLookAndFeel(
1372 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1374 Console.debug("Using FlatMacLightLaf");
1375 } catch (ClassNotFoundException | InstantiationException
1376 | IllegalAccessException | UnsupportedLookAndFeelException e)
1378 Console.debug("Exception loading FlatLightLaf", e);
1380 System.setProperty("apple.laf.useScreenMenuBar", "true");
1381 System.setProperty("apple.awt.application.name",
1382 ChannelProperties.getProperty("app_name"));
1383 System.setProperty("apple.awt.application.appearance", "system");
1384 if (SystemInfo.isMacFullWindowContentSupported
1385 && Desktop.desktop != null)
1387 Console.debug("Setting transparent title bar");
1388 Desktop.desktop.getRootPane()
1389 .putClientProperty("apple.awt.fullWindowContent", true);
1390 Desktop.desktop.getRootPane()
1391 .putClientProperty("apple.awt.transparentTitleBar", true);
1392 Desktop.desktop.getRootPane()
1393 .putClientProperty("apple.awt.fullscreenable", true);
1395 SwingUtilities.invokeLater(() -> {
1396 FlatMacLightLaf.setup();
1398 Console.debug("Using FlatMacLightLaf");
1405 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1407 Console.debug("Using FlatLightLaf");
1408 } catch (ClassNotFoundException | InstantiationException
1409 | IllegalAccessException | UnsupportedLookAndFeelException e)
1411 Console.debug("Exception loading FlatLightLaf", e);
1413 // Windows specific properties here
1414 SwingUtilities.invokeLater(() -> {
1415 FlatLightLaf.setup();
1417 Console.debug("Using FlatLightLaf");
1420 else if (SystemInfo.isLinux)
1424 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1426 Console.debug("Using FlatLightLaf");
1427 } catch (ClassNotFoundException | InstantiationException
1428 | IllegalAccessException | UnsupportedLookAndFeelException e)
1430 Console.debug("Exception loading FlatLightLaf", e);
1432 // enable custom window decorations
1433 JFrame.setDefaultLookAndFeelDecorated(true);
1434 JDialog.setDefaultLookAndFeelDecorated(true);
1435 SwingUtilities.invokeLater(() -> {
1436 FlatLightLaf.setup();
1438 Console.debug("Using FlatLightLaf");
1446 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1448 Console.debug("Using FlatLightLaf");
1449 } catch (ClassNotFoundException | InstantiationException
1450 | IllegalAccessException | UnsupportedLookAndFeelException e)
1452 Console.debug("Exception loading FlatLightLaf", e);
1458 UIManager.put("TabbedPane.tabType", "card");
1459 UIManager.put("TabbedPane.showTabSeparators", true);
1460 UIManager.put("TabbedPane.showContentSeparator", true);
1461 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1462 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1463 UIManager.put("TabbedPane.hasFullBorder", true);
1464 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1465 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1466 UIManager.put("TabbedPane.smoothScrolling", true);
1467 UIManager.put("TabbedPane.tabWidthMode", "compact");
1468 UIManager.put("TabbedPane.selectedBackground", Color.white);
1469 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1470 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1473 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1477 private static boolean setMacLookAndFeel()
1479 boolean set = false;
1480 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1481 ChannelProperties.getProperty("app_name"));
1482 System.setProperty("apple.laf.useScreenMenuBar", "true");
1484 * broken native LAFs on (ARM?) macbooks
1485 set = setQuaquaLookAndFeel();
1486 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1487 .toLowerCase(Locale.ROOT).contains("quaqua"))
1489 set = setVaquaLookAndFeel();
1492 set = setFlatLookAndFeel();
1496 private static boolean setLinuxLookAndFeel()
1498 boolean set = false;
1499 set = setFlatLookAndFeel();
1501 set = setMetalLookAndFeel();
1502 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1504 set = setNimbusLookAndFeel();
1509 private static void showUsage()
1512 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1513 + "-nodisplay\tRun Jalview without User Interface.\n"
1514 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1515 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1516 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1517 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1518 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1519 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1520 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1521 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1522 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1523 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1524 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1525 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1526 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1527 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1528 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1529 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1530 + "-html FILE\tCreate HTML file from alignment.\n"
1531 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1532 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1533 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1534 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1535 + "-noquestionnaire\tTurn off questionnaire check.\n"
1536 + "-nonews\tTurn off check for Jalview news.\n"
1537 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1538 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1540 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1541 // after all other properties files have been read\n\t
1542 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1543 // passed in correctly)"
1544 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1545 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1546 + "-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"
1547 + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
1548 + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
1549 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1553 private static void startUsageStats(final Desktop desktop)
1556 * start a User Config prompt asking if we can log usage statistics.
1558 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1559 "USAGESTATS", "Jalview Usage Statistics",
1560 "Do you want to help make Jalview better by enabling "
1561 + "the collection of usage statistics with Google Analytics ?"
1562 + "\n\n(you can enable or disable usage tracking in the preferences)",
1569 "Initialising googletracker for usage stats.");
1570 Cache.initGoogleTracker();
1571 Console.debug("Tracking enabled.");
1578 Console.debug("Not enabling Google Tracking.");
1581 desktop.addDialogThread(prompter);
1585 * Locate the given string as a file and pass it to the groovy interpreter.
1587 * @param groovyscript
1588 * the script to execute
1589 * @param jalviewContext
1590 * the Jalview Desktop object passed in to the groovy binding as the
1593 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1596 * for scripts contained in files
1603 if (groovyscript.trim().equals("STDIN"))
1605 // read from stdin into a tempfile and execute it
1608 tfile = File.createTempFile("jalview", "groovy");
1609 PrintWriter outfile = new PrintWriter(
1610 new OutputStreamWriter(new FileOutputStream(tfile)));
1611 BufferedReader br = new BufferedReader(
1612 new InputStreamReader(System.in));
1614 while ((line = br.readLine()) != null)
1616 outfile.write(line + "\n");
1622 } catch (Exception ex)
1624 System.err.println("Failed to read from STDIN into tempfile "
1625 + ((tfile == null) ? "(tempfile wasn't created)"
1626 : tfile.toString()));
1627 ex.printStackTrace();
1632 sfile = tfile.toURI().toURL();
1633 } catch (Exception x)
1636 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1638 x.printStackTrace();
1646 sfile = new URI(groovyscript).toURL();
1647 } catch (Exception x)
1649 tfile = new File(groovyscript);
1650 if (!tfile.exists())
1652 System.err.println("File '" + groovyscript + "' does not exist.");
1655 if (!tfile.canRead())
1657 System.err.println("File '" + groovyscript + "' cannot be read.");
1660 if (tfile.length() < 1)
1662 System.err.println("File '" + groovyscript + "' is empty.");
1667 sfile = tfile.getAbsoluteFile().toURI().toURL();
1668 } catch (Exception ex)
1670 System.err.println("Failed to create a file URL for "
1671 + tfile.getAbsoluteFile());
1678 Map<String, java.lang.Object> vbinding = new HashMap<>();
1679 vbinding.put("Jalview", this);
1682 vbinding.put("currentAlFrame", af);
1684 Binding gbinding = new Binding(vbinding);
1685 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1686 gse.run(sfile.toString(), gbinding);
1687 if ("STDIN".equals(groovyscript))
1689 // delete temp file that we made -
1690 // only if it was successfully executed
1693 } catch (Exception e)
1695 System.err.println("Exception Whilst trying to execute file " + sfile
1696 + " as a groovy script.");
1697 e.printStackTrace(System.err);
1702 public static boolean isHeadlessMode()
1704 String isheadless = System.getProperty("java.awt.headless");
1705 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1712 public AlignFrame[] getAlignFrames()
1714 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1715 : Desktop.getAlignFrames();
1720 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1724 // System.exit will run the shutdownHook first
1725 Jalview.exit("Quitting now. Bye!", 0);
1728 public static AlignFrame getCurrentAlignFrame()
1730 return Jalview.currentAlignFrame;
1733 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1735 Jalview.currentAlignFrame = currentAlignFrame;
1738 protected Commands getCommands()
1743 public static void exit(String message, int exitcode)
1745 if (Console.log == null)
1747 // Don't start the logger just to exit!
1748 if (message != null)
1752 System.out.println(message);
1756 System.err.println(message);
1762 Console.debug("Using Jalview.exit");
1763 if (message != null)
1767 Console.info(message);
1771 Console.error(message);
1777 System.exit(exitcode);
1781 /******************************
1783 * TEST OUTPUT METHODS
1785 ******************************/
1787 * method for reporting string values parsed/processed during tests
1790 protected static void testoutput(ArgParser ap, Arg a, String s1,
1793 BootstrapArgs bsa = ap.getBootstrapArgs();
1794 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1796 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1798 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1799 + s2 + "' for arg " + a.argString());
1802 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1806 Console.warn("Arg '" + a.getName() + "' not set at all");
1809 testoutput(true, a, s1, s2);
1813 * method for reporting string values parsed/processed during tests
1816 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1819 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1821 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1823 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1824 + s2 + "' for arg " + a.argString());
1827 if (!a.hasOption(Opt.BOOTSTRAP))
1829 Console.error("Non-bootstrap Arg '" + a.getName()
1830 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1832 if (!bsa.contains(a))
1834 Console.warn("Arg '" + a.getName() + "' not set at all");
1837 testoutput(true, a, s1, s2);
1841 * report value set for string values parsed/processed during tests
1843 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1845 if (yes && ((s1 == null && s2 == null)
1846 || (s1 != null && s1.equals(s2))))
1848 System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1854 * testoutput for boolean values
1856 protected static void testoutput(ArgParser ap, Arg a)
1860 BootstrapArgs bsa = ap.getBootstrapArgs();
1863 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1865 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1867 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1871 Console.warn("Arg '" + a.getName() + "' not set at all");
1877 protected static void testoutput(BootstrapArgs bsa, Arg a)
1879 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1881 if (!a.hasOption(Opt.BOOTSTRAP))
1883 Console.warn("Non-bootstrap Arg '" + a.getName()
1884 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1887 if (!bsa.contains(a))
1889 Console.warn("Arg '" + a.getName() + "' not set at all");
1892 testoutput(bsa.getBoolean(a), a);
1895 private static void testoutput(boolean yes, Arg a)
1897 System.out.println("[TESTOUTPUT] arg "
1898 + (yes ? a.argString() : a.negateArgString()) + " was set");