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.exceptions.ImageOutputException;
95 import jalview.io.gff.SequenceOntologyFactory;
96 import jalview.schemes.ColourSchemeI;
97 import jalview.schemes.ColourSchemeProperty;
98 import jalview.util.ChannelProperties;
99 import jalview.util.HttpUtils;
100 import jalview.util.LaunchUtils;
101 import jalview.util.MessageManager;
102 import jalview.util.Platform;
103 import jalview.ws.jws2.Jws2Discoverer;
106 * Main class for Jalview Application <br>
108 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
109 * jalview.bin.Jalview
111 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
112 * jalview.bin.Jalview jalview.bin.Jalview
114 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
115 * embellish '*' to e.g. '*.jar')
118 * @version $Revision$
124 Platform.getURLCommandArguments();
125 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
126 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
127 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
128 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
132 * singleton instance of this class
134 private static Jalview instance;
136 private Desktop desktop;
138 protected Commands cmds;
140 public static AlignFrame currentAlignFrame;
142 public ArgParser argparser = null;
144 public BootstrapArgs bootstrapArgs = null;
146 private boolean QUIET = false;
148 public static boolean quiet()
150 return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
155 if (!Platform.isJS())
162 // grab all the rights we can for the JVM
163 Policy.setPolicy(new Policy()
166 public PermissionCollection getPermissions(CodeSource codesource)
168 Permissions perms = new Permissions();
169 perms.add(new AllPermission());
174 public void refresh()
182 * keep track of feature fetching tasks.
190 * TODO: generalise to track all jalview events to orchestrate batch processing
194 private int queued = 0;
196 private int running = 0;
198 public FeatureFetcher()
203 public void addFetcher(final AlignFrame af,
204 final Vector<String> dasSources)
206 final long id = System.currentTimeMillis();
208 final FeatureFetcher us = this;
209 new Thread(new Runnable()
221 af.setProgressBar(MessageManager
222 .getString("status.das_features_being_retrived"), id);
223 af.featureSettings_actionPerformed(null);
224 af.setProgressBar(null, id);
233 public synchronized boolean allFinished()
235 return queued == 0 && running == 0;
240 public static Jalview getInstance()
246 * main class for Jalview application
249 * open <em>filename</em>
251 public static void main(String[] args)
253 // setLogging(); // BH - for event debugging in JavaScript
254 instance = new Jalview();
255 instance.doMain(args);
258 private static void logClass(String name)
260 // BH - for event debugging in JavaScript
261 ConsoleHandler consoleHandler = new ConsoleHandler();
262 consoleHandler.setLevel(Level.ALL);
263 Logger logger = Logger.getLogger(name);
264 logger.setLevel(Level.ALL);
265 logger.addHandler(consoleHandler);
268 @SuppressWarnings("unused")
269 private static void setLogging()
277 Console.outputMessage("not in js");
280 // BH - for event debugging in JavaScript (Java mode only)
281 if (!Platform.isJS())
288 Logger.getLogger("").setLevel(Level.ALL);
289 logClass("java.awt.EventDispatchThread");
290 logClass("java.awt.EventQueue");
291 logClass("java.awt.Component");
292 logClass("java.awt.focus.Component");
293 logClass("java.awt.focus.DefaultKeyboardFocusManager");
301 void doMain(String[] args)
303 if (!Platform.isJS())
305 System.setSecurityManager(null);
308 if (args == null || args.length == 0 || (args.length == 1
309 && (args[0] == null || args[0].length() == 0)))
311 args = new String[] {};
314 // get args needed before proper ArgParser
315 bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
317 if (!Platform.isJS())
319 // are we being --quiet ?
320 if (bootstrapArgs.contains(Arg.QUIET))
323 OutputStream devNull = new OutputStream()
327 public void write(int b)
332 System.setOut(new PrintStream(devNull));
333 // redirecting stderr not working
334 if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
336 System.setErr(new PrintStream(devNull));
340 if (bootstrapArgs.contains(Arg.HELP)
341 || bootstrapArgs.contains(Arg.VERSION))
347 // set individual session preferences
348 if (bootstrapArgs.contains(Arg.P))
350 for (String kev : bootstrapArgs.getValueList(Arg.P))
356 int equalsIndex = kev.indexOf(ArgParser.EQUALS);
357 if (equalsIndex > -1)
359 String key = kev.substring(0, equalsIndex);
360 String val = kev.substring(equalsIndex + 1);
361 Cache.setSessionProperty(key, val);
366 // Move any new getdown-launcher-new.jar into place over old
367 // getdown-launcher.jar
368 String appdirString = System.getProperty("getdownappdir");
369 if (appdirString != null && appdirString.length() > 0)
371 final File appdir = new File(appdirString);
378 LaunchUtil.upgradeGetdown(
379 new File(appdir, "getdown-launcher-old.jar"),
380 new File(appdir, "getdown-launcher.jar"),
381 new File(appdir, "getdown-launcher-new.jar"));
386 if (!quiet() || !bootstrapArgs.outputToStdout()
387 || bootstrapArgs.contains(Arg.VERSION))
389 Console.outputMessage(
390 "Java version: " + System.getProperty("java.version"));
391 Console.outputMessage(
392 "Java home: " + System.getProperty("java.home"));
393 Console.outputMessage("Java arch: " + System.getProperty("os.arch")
394 + " " + System.getProperty("os.name") + " "
395 + System.getProperty("os.version"));
397 String val = System.getProperty("sys.install4jVersion");
400 Console.outputMessage("Install4j version: " + val);
402 val = System.getProperty("installer_template_version");
405 Console.outputMessage("Install4j template version: " + val);
407 val = System.getProperty("launcher_version");
410 Console.outputMessage("Launcher version: " + val);
414 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
416 System.setProperty("flatlaf.uiScale", "1");
419 // get bootstrap properties (mainly for the logger level)
420 Properties bootstrapProperties = Cache
421 .bootstrapProperties(bootstrapArgs.getValue(Arg.PROPS));
423 // report Jalview version
424 Cache.loadBuildProperties(
425 !quiet() || bootstrapArgs.contains(Arg.VERSION));
427 // stop now if only after --version
428 if (bootstrapArgs.contains(Arg.VERSION))
430 Jalview.exit(null, 0);
434 ArgsParser aparser = new ArgsParser(args);
437 boolean headless = false;
439 boolean headlessArg = false;
443 String logLevel = null;
444 if (bootstrapArgs.contains(Arg.TRACE))
448 else if (bootstrapArgs.contains(Arg.DEBUG))
452 if (logLevel == null && !(bootstrapProperties == null))
454 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
456 Console.initLogger(logLevel);
457 } catch (NoClassDefFoundError error)
459 error.printStackTrace();
460 String message = "\nEssential logging libraries not found."
461 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
462 Jalview.exit(message, 0);
465 // register SIGTERM listener
466 Runtime.getRuntime().addShutdownHook(new Thread()
471 Console.debug("Running shutdown hook");
472 QuitHandler.startForceQuit();
473 boolean closeExternal = Cache
474 .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false)
475 || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false);
476 StructureViewerBase.setQuitClose(closeExternal);
479 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
481 if (frame instanceof StructureViewerBase)
483 ((StructureViewerBase) frame).closeViewer(closeExternal);
488 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
490 // Got to here by a SIGTERM signal.
491 // Note we will not actually cancel the quit from here -- it's too
492 // late -- but we can wait for saving files and close external viewers
494 // Close viewers/Leave viewers open
495 Console.debug("Checking for saving files");
496 QuitHandler.getQuitResponse(false);
500 Console.debug("Nothing more to do");
502 Console.debug("Exiting, bye!");
503 // shutdownHook cannot be cancelled, JVM will now halt
507 String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
508 ? bootstrapArgs.getValue(Arg.PROPS)
509 : aparser.getValue("props");
510 // if usrPropsFile == null, loadProperties will use the Channel
512 Cache.loadProperties(usrPropsFile);
513 if (usrPropsFile != null)
515 Console.outputMessage(
516 "CMD [-props " + usrPropsFile + "] executed successfully!");
517 testoutput(bootstrapArgs, Arg.PROPS,
518 "test/jalview/bin/testProps.jvprops", usrPropsFile);
521 // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
522 if (bootstrapArgs.contains(Arg.ARGFILE))
524 argparser = ArgParser.parseArgFiles(
525 bootstrapArgs.getValueList(Arg.ARGFILE),
526 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
531 argparser = new ArgParser(args,
532 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
536 if (!Platform.isJS())
543 if (bootstrapArgs.contains(Arg.HELP))
545 List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
547 Console.outputMessage(Arg.usage(helpArgs.stream()
548 .map(e -> e.getKey()).collect(Collectors.toList())));
549 Jalview.exit(null, 0);
551 if (aparser.contains("help") || aparser.contains("h"))
554 * Now using new usage statement.
557 Console.outputMessage(Arg.usage());
558 Jalview.exit(null, 0);
562 headlessArg = bootstrapArgs.isHeadless();
565 System.setProperty("java.awt.headless", "true");
568 if (aparser.contains("nodisplay") || aparser.contains("nogui")
569 || aparser.contains("headless"))
571 System.setProperty("java.awt.headless", "true");
576 // allow https handshakes to download intermediate certs if necessary
577 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
579 String jabawsUrl = bootstrapArgs.getValue(Arg.JABAWS);
580 if (jabawsUrl == null)
581 jabawsUrl = aparser.getValue("jabaws");
582 if (jabawsUrl != null)
586 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
587 Console.outputMessage(
588 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
589 testoutput(bootstrapArgs, Arg.JABAWS,
590 "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
591 } catch (MalformedURLException e)
594 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
599 List<String> setprops = new ArrayList<>();
600 if (bootstrapArgs.contains(Arg.SETPROP))
602 setprops = bootstrapArgs.getValueList(Arg.SETPROP);
606 String sp = aparser.getValue("setprop");
610 sp = aparser.getValue("setprop");
613 for (String setprop : setprops)
615 int p = setprop.indexOf('=');
619 .println("Ignoring invalid setprop argument : " + setprop);
623 System.err.println("Executing setprop argument: " + setprop);
626 Cache.setProperty(setprop.substring(0, p),
627 setprop.substring(p + 1));
629 // DISABLED FOR SECURITY REASONS
630 // TODO: add a property to allow properties to be overriden by cli args
631 // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
634 if (System.getProperty("java.awt.headless") != null
635 && System.getProperty("java.awt.headless").equals("true"))
639 System.setProperty("http.agent", HttpUtils.getUserAgent());
643 Console.initLogger();
646 NoClassDefFoundError error)
648 error.printStackTrace();
649 String message = "\nEssential logging libraries not found."
650 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
651 Jalview.exit(message, 0);
655 if (!(headless || headlessArg))
659 * configure 'full' SO model if preferences say to, else use the default (full SO)
660 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
662 boolean soDefault = !Platform.isJS();
663 if (Cache.getDefault("USE_FULL_SO", soDefault))
665 SequenceOntologyFactory.setInstance(new SequenceOntology());
668 if (!(headless || headlessArg))
670 Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
671 || aparser.contains("nosplash")
672 || Cache.getDefault("SPLASH", "true").equals("false");
673 desktop = new Desktop();
674 desktop.setInBatchMode(true); // indicate we are starting up
678 JalviewTaskbar.setTaskbar(this);
679 } catch (Exception e)
681 Console.info("Cannot set Taskbar");
682 Console.error(e.getMessage());
683 // e.printStackTrace();
684 } catch (Throwable t)
686 Console.info("Cannot set Taskbar");
687 Console.error(t.getMessage());
688 // t.printStackTrace();
691 // set Proxy settings before all the internet calls
692 Cache.setProxyPropertiesFromPreferences();
694 desktop.setVisible(true);
696 if (!Platform.isJS())
705 * Check to see that the JVM version being run is suitable for the Java
706 * version this Jalview was compiled for. Popup a warning if not.
708 if (!LaunchUtils.checkJavaVersion())
710 Console.warn("The Java version being used (Java "
711 + LaunchUtils.getJavaVersion()
712 + ") may lead to problems. This installation of Jalview should be used with Java "
713 + LaunchUtils.getJavaCompileVersion() + ".");
716 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
719 MessageManager.getString("label.continue") };
720 JOptionPane.showOptionDialog(null,
721 MessageManager.formatMessage(
722 "warning.wrong_jvm_version_message",
723 LaunchUtils.getJavaVersion(),
724 LaunchUtils.getJavaCompileVersion()),
726 .getString("warning.wrong_jvm_version_title"),
727 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
728 null, options, options[0]);
732 boolean webservicediscovery = bootstrapArgs
733 .getBoolean(Arg.WEBSERVICEDISCOVERY);
734 if (aparser.contains("nowebservicediscovery"))
735 webservicediscovery = false;
736 if (webservicediscovery)
738 desktop.startServiceDiscovery();
742 testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
745 boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
746 if (aparser.contains("nousagestats"))
750 startUsageStats(desktop);
751 testoutput(argparser, Arg.NOUSAGESTATS);
755 Console.outputMessage(
756 "CMD [-nousagestats] executed successfully!");
757 testoutput(argparser, Arg.NOUSAGESTATS);
760 boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
761 if (aparser.contains("noquestionnaire"))
762 questionnaire = false;
765 String url = aparser.getValue("questionnaire");
768 // Start the desktop questionnaire prompter with the specified
770 Console.debug("Starting questionnaire url at " + url);
771 desktop.checkForQuestionnaire(url);
772 Console.outputMessage("CMD questionnaire[-" + url
773 + "] executed successfully!");
777 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
779 // Start the desktop questionnaire prompter with the specified
782 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
784 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
786 "Starting questionnaire with default url: " + defurl);
787 desktop.checkForQuestionnaire(defurl);
793 Console.outputMessage(
794 "CMD [-noquestionnaire] executed successfully!");
795 testoutput(argparser, Arg.QUESTIONNAIRE);
798 if ((!aparser.contains("nonews")
799 && Cache.getProperty("NONEWS") == null
800 && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
801 || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
803 desktop.checkForNews();
806 if (!aparser.contains("nohtmltemplates")
807 && Cache.getProperty("NOHTMLTEMPLATES") == null)
809 BioJsHTMLOutput.updateBioJS();
813 // Run Commands from cli
814 cmds = new Commands(argparser, headlessArg);
815 boolean commandsSuccess = cmds.argsWereParsed();
821 if (argparser.getBoolean(Arg.NOQUIT))
824 "Completed " + Arg.HEADLESS.getName() + " commands, but "
825 + Arg.NOQUIT + " is set so not quitting!");
829 Jalview.exit("Successfully completed commands in headless mode",
833 Console.info("Successfully completed commands");
839 Jalview.exit("Error when running Commands in headless mode", 1);
841 Console.warn("Error when running commands");
844 // Check if JVM and compile version might cause problems and log if it
846 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
848 Console.warn("The Java version being used (Java "
849 + LaunchUtils.getJavaVersion()
850 + ") may lead to problems. This installation of Jalview should be used with Java "
851 + LaunchUtils.getJavaCompileVersion() + ".");
854 String file = null, data = null;
856 FileFormatI format = null;
858 DataSourceType protocol = null;
860 FileLoader fileLoader = new FileLoader(!headless);
862 String groovyscript = null; // script to execute after all loading is
863 // completed one way or another
864 // extract groovy argument and execute if necessary
865 groovyscript = aparser.getValue("groovy", true);
866 file = aparser.getValue("open", true);
868 if (file == null && desktop == null && !commandsSuccess)
870 Jalview.exit("No files to open!", 1);
874 // Finally, deal with the remaining input data.
879 desktop.setProgressBar(
881 .getString("status.processing_commandline_args"),
882 progress = System.currentTimeMillis());
884 Console.outputMessage(
885 "CMD [-open " + file + "] executed successfully!");
887 if (!Platform.isJS())
889 * ignore in JavaScript -- can't just file existence - could load it?
894 if (!HttpUtils.startsWithHttpOrHttps(file))
896 if (!(new File(file)).exists())
901 "Can't find file '" + file + "' in headless mode", 1);
903 Console.warn("Can't find file'" + file + "'");
908 protocol = AppletFormatAdapter.checkProtocol(file);
912 format = new IdentifyFile().identify(file, protocol);
913 } catch (FileFormatException e1)
918 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
922 Console.outputMessage("error");
926 setCurrentAlignFrame(af);
927 data = aparser.getValue("colour", true);
930 data.replaceAll("%20", " ");
932 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
933 af.getViewport(), af.getViewport().getAlignment(), data);
937 Console.outputMessage(
938 "CMD [-colour " + data + "] executed successfully!");
943 // Must maintain ability to use the groups flag
944 data = aparser.getValue("groups", true);
947 af.parseFeaturesFile(data,
948 AppletFormatAdapter.checkProtocol(data));
949 // Console.outputMessage("Added " + data);
950 Console.outputMessage(
951 "CMD groups[-" + data + "] executed successfully!");
953 data = aparser.getValue("features", true);
956 af.parseFeaturesFile(data,
957 AppletFormatAdapter.checkProtocol(data));
958 // Console.outputMessage("Added " + data);
959 Console.outputMessage(
960 "CMD [-features " + data + "] executed successfully!");
963 data = aparser.getValue("annotations", true);
966 af.loadJalviewDataFile(data, null, null, null);
967 // Console.outputMessage("Added " + data);
968 Console.outputMessage(
969 "CMD [-annotations " + data + "] executed successfully!");
971 // set or clear the sortbytree flag.
972 if (aparser.contains("sortbytree"))
974 af.getViewport().setSortByTree(true);
975 if (af.getViewport().getSortByTree())
977 Console.outputMessage(
978 "CMD [-sortbytree] executed successfully!");
981 if (aparser.contains("no-annotation"))
983 af.getViewport().setShowAnnotation(false);
984 if (!af.getViewport().isShowAnnotation())
986 Console.outputMessage(
987 "CMD no-annotation executed successfully!");
990 if (aparser.contains("nosortbytree"))
992 af.getViewport().setSortByTree(false);
993 if (!af.getViewport().getSortByTree())
995 Console.outputMessage(
996 "CMD [-nosortbytree] executed successfully!");
999 data = aparser.getValue("tree", true);
1004 Console.outputMessage(
1005 "CMD [-tree " + data + "] executed successfully!");
1006 NewickFile nf = new NewickFile(data,
1007 AppletFormatAdapter.checkProtocol(data));
1009 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1010 } catch (IOException ex)
1012 System.err.println("Couldn't add tree " + data);
1013 ex.printStackTrace(System.err);
1017 if (groovyscript != null)
1019 // Execute the groovy script after we've done all the rendering stuff
1020 // and before any images or figures are generated.
1021 Console.outputMessage("Executing script " + groovyscript);
1022 executeGroovyScript(groovyscript, af);
1023 Console.outputMessage("CMD groovy[" + groovyscript
1024 + "] executed successfully!");
1025 groovyscript = null;
1027 String imageName = "unnamed.png";
1028 while (aparser.getSize() > 1)
1032 String outputFormat = aparser.nextValue();
1033 file = aparser.nextValue();
1035 if (outputFormat.equalsIgnoreCase("png"))
1037 Console.outputMessage("Creating PNG image: " + file);
1038 af.createPNG(new File(file));
1039 imageName = (new File(file)).getName();
1042 else if (outputFormat.equalsIgnoreCase("svg"))
1044 Console.outputMessage("Creating SVG image: " + file);
1045 File imageFile = new File(file);
1046 imageName = imageFile.getName();
1047 af.createSVG(imageFile);
1050 else if (outputFormat.equalsIgnoreCase("html"))
1052 File imageFile = new File(file);
1053 imageName = imageFile.getName();
1054 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1056 Console.outputMessage("Creating HTML image: " + file);
1057 htmlSVG.exportHTML(file);
1060 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1064 System.err.println("The output html file must not be null");
1069 BioJsHTMLOutput.refreshVersionInfo(
1070 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1071 } catch (URISyntaxException e)
1073 e.printStackTrace();
1075 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1076 Console.outputMessage(
1077 "Creating BioJS MSA Viwer HTML file: " + file);
1078 bjs.exportHTML(file);
1081 else if (outputFormat.equalsIgnoreCase("imgMap"))
1083 Console.outputMessage("Creating image map: " + file);
1084 af.createImageMap(new File(file), imageName);
1087 else if (outputFormat.equalsIgnoreCase("eps"))
1089 File outputFile = new File(file);
1090 Console.outputMessage(
1091 "Creating EPS file: " + outputFile.getAbsolutePath());
1092 af.createEPS(outputFile);
1096 FileFormatI outFormat = null;
1099 outFormat = FileFormats.getInstance().forName(outputFormat);
1100 } catch (Exception formatP)
1102 Console.outputMessage("Couldn't parse " + outFormat
1103 + " as a valid Jalview format string.");
1105 if (outFormat != null)
1107 if (!outFormat.isWritable())
1109 Console.outputMessage(
1110 "This version of Jalview does not support alignment export as "
1115 af.saveAlignment(file, outFormat);
1116 if (af.isSaveAlignmentSuccessful())
1118 Console.outputMessage("Written alignment in "
1119 + outFormat.getName() + " format to " + file);
1123 Console.outputMessage("Error writing file " + file
1124 + " in " + outFormat.getName() + " format!!");
1128 } catch (ImageOutputException ioexc)
1130 Console.outputMessage(
1131 "Unexpected error whilst exporting image to " + file);
1132 ioexc.printStackTrace();
1137 while (aparser.getSize() > 0)
1139 Console.outputMessage("Unknown arg: " + aparser.nextValue());
1144 AlignFrame startUpAlframe = null;
1145 // We'll only open the default file if the desktop is visible.
1147 // ////////////////////
1149 if (!Platform.isJS() && !headless && file == null
1150 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1151 && !cmds.commandArgsProvided()
1152 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1153 // don't open the startup file if command line args have been processed
1154 // (&& !Commands.commandArgsProvided())
1161 file = Cache.getDefault("STARTUP_FILE",
1162 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1163 + "/examples/exampleFile_2_7.jvp");
1164 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1166 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1168 file.replace("http:", "https:");
1169 // hardwire upgrade of the startup file
1170 file.replace("_2_3", "_2_7");
1171 file.replace("2_7.jar", "2_7.jvp");
1172 // and remove the stale setting
1173 Cache.removeProperty("STARTUP_FILE");
1176 protocol = AppletFormatAdapter.checkProtocol(file);
1178 if (file.endsWith(".jar"))
1180 format = FileFormat.Jalview;
1186 format = new IdentifyFile().identify(file, protocol);
1187 } catch (FileFormatException e)
1193 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1195 // don't ask to save when quitting if only the startup file has been
1197 Console.debug("Resetting up-to-date flag for startup file");
1198 startUpAlframe.getViewport().setSavedUpToDate(true);
1199 // extract groovy arguments before anything else.
1202 // Once all other stuff is done, execute any groovy scripts (in order)
1203 if (groovyscript != null)
1205 if (Cache.groovyJarsPresent())
1207 Console.outputMessage("Executing script " + groovyscript);
1208 executeGroovyScript(groovyscript, startUpAlframe);
1213 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1217 // and finally, turn off batch mode indicator - if the desktop still exists
1218 if (desktop != null)
1222 desktop.setProgressBar(null, progress);
1224 desktop.setInBatchMode(false);
1228 private static void setLookAndFeel()
1230 if (!Platform.isJS())
1237 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1239 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1241 // try Quaqua/Vaqua.
1242 String lafProp = System.getProperty("laf");
1243 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1244 String laf = "none";
1245 if (lafProp != null)
1249 else if (lafSetting != null)
1253 boolean lafSet = false;
1256 case "crossplatform":
1257 lafSet = setCrossPlatformLookAndFeel();
1260 Console.error("Could not set requested laf=" + laf);
1264 lafSet = setSystemLookAndFeel();
1267 Console.error("Could not set requested laf=" + laf);
1271 lafSet = setGtkLookAndFeel();
1274 Console.error("Could not set requested laf=" + laf);
1278 lafSet = setMetalLookAndFeel();
1281 Console.error("Could not set requested laf=" + laf);
1285 lafSet = setNimbusLookAndFeel();
1288 Console.error("Could not set requested laf=" + laf);
1292 lafSet = setFlatLookAndFeel();
1295 Console.error("Could not set requested laf=" + laf);
1299 lafSet = setMacLookAndFeel();
1302 Console.error("Could not set requested laf=" + laf);
1308 Console.error("Requested laf=" + laf + " not implemented");
1312 // Flatlaf default for everyone!
1313 lafSet = setFlatLookAndFeel();
1316 setSystemLookAndFeel();
1318 if (Platform.isLinux())
1320 setLinuxLookAndFeel();
1322 if (Platform.isMac())
1324 setMacLookAndFeel();
1330 private static boolean setCrossPlatformLookAndFeel()
1332 boolean set = false;
1335 UIManager.setLookAndFeel(
1336 UIManager.getCrossPlatformLookAndFeelClassName());
1338 } catch (Exception ex)
1340 Console.error("Unexpected Look and Feel Exception");
1341 Console.error(ex.getMessage());
1342 Console.debug(Cache.getStackTraceString(ex));
1347 private static boolean setSystemLookAndFeel()
1349 boolean set = false;
1352 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1354 } catch (Exception ex)
1356 Console.error("Unexpected Look and Feel Exception");
1357 Console.error(ex.getMessage());
1358 Console.debug(Cache.getStackTraceString(ex));
1363 private static boolean setSpecificLookAndFeel(String name,
1364 String className, boolean nameStartsWith)
1366 boolean set = false;
1369 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1371 if (info.getName() != null && nameStartsWith
1372 ? info.getName().toLowerCase(Locale.ROOT)
1373 .startsWith(name.toLowerCase(Locale.ROOT))
1374 : info.getName().toLowerCase(Locale.ROOT)
1375 .equals(name.toLowerCase(Locale.ROOT)))
1377 className = info.getClassName();
1381 UIManager.setLookAndFeel(className);
1383 } catch (Exception ex)
1385 Console.error("Unexpected Look and Feel Exception");
1386 Console.error(ex.getMessage());
1387 Console.debug(Cache.getStackTraceString(ex));
1392 private static boolean setGtkLookAndFeel()
1394 return setSpecificLookAndFeel("gtk",
1395 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1398 private static boolean setMetalLookAndFeel()
1400 return setSpecificLookAndFeel("metal",
1401 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1404 private static boolean setNimbusLookAndFeel()
1406 return setSpecificLookAndFeel("nimbus",
1407 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1410 private static boolean setFlatLookAndFeel()
1412 boolean set = false;
1413 if (SystemInfo.isMacOS)
1417 UIManager.setLookAndFeel(
1418 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1420 Console.debug("Using FlatMacLightLaf");
1421 } catch (ClassNotFoundException | InstantiationException
1422 | IllegalAccessException | UnsupportedLookAndFeelException e)
1424 Console.debug("Exception loading FlatLightLaf", e);
1426 System.setProperty("apple.laf.useScreenMenuBar", "true");
1427 System.setProperty("apple.awt.application.name",
1428 ChannelProperties.getProperty("app_name"));
1429 System.setProperty("apple.awt.application.appearance", "system");
1430 if (SystemInfo.isMacFullWindowContentSupported
1431 && Desktop.desktop != null)
1433 Console.debug("Setting transparent title bar");
1434 Desktop.desktop.getRootPane()
1435 .putClientProperty("apple.awt.fullWindowContent", true);
1436 Desktop.desktop.getRootPane()
1437 .putClientProperty("apple.awt.transparentTitleBar", true);
1438 Desktop.desktop.getRootPane()
1439 .putClientProperty("apple.awt.fullscreenable", true);
1441 SwingUtilities.invokeLater(() -> {
1442 FlatMacLightLaf.setup();
1444 Console.debug("Using FlatMacLightLaf");
1451 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1453 Console.debug("Using FlatLightLaf");
1454 } catch (ClassNotFoundException | InstantiationException
1455 | IllegalAccessException | UnsupportedLookAndFeelException e)
1457 Console.debug("Exception loading FlatLightLaf", e);
1459 // Windows specific properties here
1460 SwingUtilities.invokeLater(() -> {
1461 FlatLightLaf.setup();
1463 Console.debug("Using FlatLightLaf");
1466 else if (SystemInfo.isLinux)
1470 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1472 Console.debug("Using FlatLightLaf");
1473 } catch (ClassNotFoundException | InstantiationException
1474 | IllegalAccessException | UnsupportedLookAndFeelException e)
1476 Console.debug("Exception loading FlatLightLaf", e);
1478 // enable custom window decorations
1479 JFrame.setDefaultLookAndFeelDecorated(true);
1480 JDialog.setDefaultLookAndFeelDecorated(true);
1481 SwingUtilities.invokeLater(() -> {
1482 FlatLightLaf.setup();
1484 Console.debug("Using FlatLightLaf");
1492 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1494 Console.debug("Using FlatLightLaf");
1495 } catch (ClassNotFoundException | InstantiationException
1496 | IllegalAccessException | UnsupportedLookAndFeelException e)
1498 Console.debug("Exception loading FlatLightLaf", e);
1504 UIManager.put("TabbedPane.tabType", "card");
1505 UIManager.put("TabbedPane.showTabSeparators", true);
1506 UIManager.put("TabbedPane.showContentSeparator", true);
1507 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1508 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1509 UIManager.put("TabbedPane.hasFullBorder", true);
1510 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1511 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1512 UIManager.put("TabbedPane.smoothScrolling", true);
1513 UIManager.put("TabbedPane.tabWidthMode", "compact");
1514 UIManager.put("TabbedPane.selectedBackground", Color.white);
1515 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1516 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1519 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1523 private static boolean setMacLookAndFeel()
1525 boolean set = false;
1526 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1527 ChannelProperties.getProperty("app_name"));
1528 System.setProperty("apple.laf.useScreenMenuBar", "true");
1530 * broken native LAFs on (ARM?) macbooks
1531 set = setQuaquaLookAndFeel();
1532 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1533 .toLowerCase(Locale.ROOT).contains("quaqua"))
1535 set = setVaquaLookAndFeel();
1538 set = setFlatLookAndFeel();
1542 private static boolean setLinuxLookAndFeel()
1544 boolean set = false;
1545 set = setFlatLookAndFeel();
1547 set = setMetalLookAndFeel();
1548 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1550 set = setNimbusLookAndFeel();
1555 private static void showUsage()
1558 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1559 + "-nodisplay\tRun Jalview without User Interface.\n"
1560 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1561 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1562 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1563 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1564 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1565 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1566 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1567 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1568 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1569 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1570 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1571 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1572 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1573 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1574 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1575 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1576 + "-html FILE\tCreate HTML file from alignment.\n"
1577 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1578 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1579 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1580 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1581 + "-noquestionnaire\tTurn off questionnaire check.\n"
1582 + "-nonews\tTurn off check for Jalview news.\n"
1583 + "-nousagestats\tTurn off analytics tracking for this session.\n"
1584 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1586 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1587 // after all other properties files have been read\n\t
1588 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1589 // passed in correctly)"
1590 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1591 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1592 + "-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"
1593 + "-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"
1594 + "-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"
1595 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1599 private static void startUsageStats(final Desktop desktop)
1602 * start a User Config prompt asking if we can log usage statistics.
1604 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1606 MessageManager.getString("prompt.plausible_analytics_title"),
1607 MessageManager.getString("prompt.plausible_analytics"),
1613 Console.debug("Initialising analytics for usage stats.");
1614 Cache.initAnalytics();
1615 Console.debug("Tracking enabled.");
1622 Console.debug("Not enabling analytics.");
1625 desktop.addDialogThread(prompter);
1629 * Locate the given string as a file and pass it to the groovy interpreter.
1631 * @param groovyscript
1632 * the script to execute
1633 * @param jalviewContext
1634 * the Jalview Desktop object passed in to the groovy binding as the
1637 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1640 * for scripts contained in files
1647 if (groovyscript.trim().equals("STDIN"))
1649 // read from stdin into a tempfile and execute it
1652 tfile = File.createTempFile("jalview", "groovy");
1653 PrintWriter outfile = new PrintWriter(
1654 new OutputStreamWriter(new FileOutputStream(tfile)));
1655 BufferedReader br = new BufferedReader(
1656 new InputStreamReader(System.in));
1658 while ((line = br.readLine()) != null)
1660 outfile.write(line + "\n");
1666 } catch (Exception ex)
1668 System.err.println("Failed to read from STDIN into tempfile "
1669 + ((tfile == null) ? "(tempfile wasn't created)"
1670 : tfile.toString()));
1671 ex.printStackTrace();
1676 sfile = tfile.toURI().toURL();
1677 } catch (Exception x)
1680 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1682 x.printStackTrace();
1690 sfile = new URI(groovyscript).toURL();
1691 } catch (Exception x)
1693 tfile = new File(groovyscript);
1694 if (!tfile.exists())
1696 System.err.println("File '" + groovyscript + "' does not exist.");
1699 if (!tfile.canRead())
1701 System.err.println("File '" + groovyscript + "' cannot be read.");
1704 if (tfile.length() < 1)
1706 System.err.println("File '" + groovyscript + "' is empty.");
1711 sfile = tfile.getAbsoluteFile().toURI().toURL();
1712 } catch (Exception ex)
1714 System.err.println("Failed to create a file URL for "
1715 + tfile.getAbsoluteFile());
1722 Map<String, java.lang.Object> vbinding = new HashMap<>();
1723 vbinding.put("Jalview", this);
1726 vbinding.put("currentAlFrame", af);
1728 Binding gbinding = new Binding(vbinding);
1729 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1730 gse.run(sfile.toString(), gbinding);
1731 if ("STDIN".equals(groovyscript))
1733 // delete temp file that we made -
1734 // only if it was successfully executed
1737 } catch (Exception e)
1739 System.err.println("Exception Whilst trying to execute file " + sfile
1740 + " as a groovy script.");
1741 e.printStackTrace(System.err);
1746 public static boolean isHeadlessMode()
1748 String isheadless = System.getProperty("java.awt.headless");
1749 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1756 public AlignFrame[] getAlignFrames()
1758 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1759 : Desktop.getAlignFrames();
1764 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1768 // System.exit will run the shutdownHook first
1769 Jalview.exit("Quitting now. Bye!", 0);
1772 public static AlignFrame getCurrentAlignFrame()
1774 return Jalview.currentAlignFrame;
1777 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1779 Jalview.currentAlignFrame = currentAlignFrame;
1782 protected Commands getCommands()
1787 public static void exit(String message, int exitcode)
1789 if (Console.log == null)
1791 // Don't start the logger just to exit!
1792 if (message != null)
1796 Console.outputMessage(message);
1800 System.err.println(message);
1806 Console.debug("Using Jalview.exit");
1807 if (message != null)
1811 Console.info(message);
1815 Console.error(message);
1821 System.exit(exitcode);
1825 /******************************
1827 * TEST OUTPUT METHODS
1829 ******************************/
1831 * method for reporting string values parsed/processed during tests
1834 protected static void testoutput(ArgParser ap, Arg a, String s1,
1837 BootstrapArgs bsa = ap.getBootstrapArgs();
1838 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1840 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1842 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1843 + s2 + "' for arg " + a.argString());
1846 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1850 Console.warn("Arg '" + a.getName() + "' not set at all");
1853 testoutput(true, a, s1, s2);
1857 * method for reporting string values parsed/processed during tests
1860 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1863 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1865 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1867 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1868 + s2 + "' for arg " + a.argString());
1871 if (!a.hasOption(Opt.BOOTSTRAP))
1873 Console.error("Non-bootstrap Arg '" + a.getName()
1874 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1876 if (!bsa.contains(a))
1878 Console.warn("Arg '" + a.getName() + "' not set at all");
1881 testoutput(true, a, s1, s2);
1885 * report value set for string values parsed/processed during tests
1887 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1889 if (yes && ((s1 == null && s2 == null)
1890 || (s1 != null && s1.equals(s2))))
1892 Console.outputMessage("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1898 * testoutput for boolean and unary values
1900 protected static void testoutput(ArgParser ap, Arg a)
1904 BootstrapArgs bsa = ap.getBootstrapArgs();
1907 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1909 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1911 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1915 Console.warn("Arg '" + a.getName() + "' not set at all");
1921 protected static void testoutput(BootstrapArgs bsa, Arg a)
1923 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1925 if (!a.hasOption(Opt.BOOTSTRAP))
1927 Console.warn("Non-bootstrap Arg '" + a.getName()
1928 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1931 if (!bsa.contains(a))
1933 Console.warn("Arg '" + a.getName() + "' not set at all");
1936 testoutput(bsa.getBoolean(a), a);
1939 private static void testoutput(boolean yes, Arg a)
1941 String message = null;
1942 if (a.hasOption(Opt.BOOLEAN))
1944 message = (yes ? a.argString() : a.negateArgString()) + " was set";
1946 else if (a.hasOption(Opt.UNARY))
1948 message = a.argString() + (yes ? " was set" : " was not set");
1950 Console.outputMessage("[TESTOUTPUT] arg " + message);