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 System.out.println("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.contains(Arg.VERSION))
389 "Java version: " + System.getProperty("java.version"));
390 System.out.println("Java home: " + System.getProperty("java.home"));
391 System.out.println("Java arch: " + System.getProperty("os.arch") + " "
392 + System.getProperty("os.name") + " "
393 + System.getProperty("os.version"));
395 String val = System.getProperty("sys.install4jVersion");
398 System.out.println("Install4j version: " + val);
400 val = System.getProperty("installer_template_version");
403 System.out.println("Install4j template version: " + val);
405 val = System.getProperty("launcher_version");
408 System.out.println("Launcher version: " + val);
412 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
414 System.setProperty("flatlaf.uiScale", "1");
417 // get bootstrap properties (mainly for the logger level)
418 Properties bootstrapProperties = Cache
419 .bootstrapProperties(bootstrapArgs.getValue(Arg.PROPS));
421 // report Jalview version
422 Cache.loadBuildProperties(
423 !quiet() || bootstrapArgs.contains(Arg.VERSION));
425 // stop now if only after --version
426 if (bootstrapArgs.contains(Arg.VERSION))
428 Jalview.exit(null, 0);
432 ArgsParser aparser = new ArgsParser(args);
435 boolean headless = false;
437 boolean headlessArg = false;
441 String logLevel = null;
442 if (bootstrapArgs.contains(Arg.TRACE))
446 else if (bootstrapArgs.contains(Arg.DEBUG))
450 if (logLevel == null && !(bootstrapProperties == null))
452 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
454 Console.initLogger(logLevel);
455 } catch (NoClassDefFoundError error)
457 error.printStackTrace();
458 String message = "\nEssential logging libraries not found."
459 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
460 Jalview.exit(message, 0);
463 // register SIGTERM listener
464 Runtime.getRuntime().addShutdownHook(new Thread()
468 Console.debug("Running shutdown hook");
469 QuitHandler.startForceQuit();
470 boolean closeExternal = Cache
471 .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false)
472 || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false);
473 StructureViewerBase.setQuitClose(closeExternal);
476 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
478 if (frame instanceof StructureViewerBase)
480 ((StructureViewerBase) frame).closeViewer(closeExternal);
485 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
487 // Got to here by a SIGTERM signal.
488 // Note we will not actually cancel the quit from here -- it's too
489 // late -- but we can wait for saving files and close external viewers
491 // Close viewers/Leave viewers open
492 Console.debug("Checking for saving files");
493 QuitHandler.getQuitResponse(false);
497 Console.debug("Nothing more to do");
499 Console.debug("Exiting, bye!");
500 // shutdownHook cannot be cancelled, JVM will now halt
504 String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
505 ? bootstrapArgs.getValue(Arg.PROPS)
506 : aparser.getValue("props");
507 // if usrPropsFile == null, loadProperties will use the Channel
509 Cache.loadProperties(usrPropsFile);
510 if (usrPropsFile != null)
513 "CMD [-props " + usrPropsFile + "] executed successfully!");
514 testoutput(bootstrapArgs, Arg.PROPS,
515 "test/jalview/bin/testProps.jvprops", usrPropsFile);
518 // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
519 if (bootstrapArgs.contains(Arg.ARGFILE))
521 argparser = ArgParser.parseArgFiles(
522 bootstrapArgs.getValueList(Arg.ARGFILE),
523 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
528 argparser = new ArgParser(args,
529 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
533 if (!Platform.isJS())
540 if (bootstrapArgs.contains(Arg.HELP))
542 List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
544 System.out.println(Arg.usage(helpArgs.stream().map(e -> e.getKey())
545 .collect(Collectors.toList())));
546 Jalview.exit(null, 0);
548 if (aparser.contains("help") || aparser.contains("h"))
551 * Now using new usage statement.
554 System.out.println(Arg.usage());
555 Jalview.exit(null, 0);
559 headlessArg = bootstrapArgs.isHeadless();
562 System.setProperty("java.awt.headless", "true");
565 if (aparser.contains("nodisplay") || aparser.contains("nogui")
566 || aparser.contains("headless"))
568 System.setProperty("java.awt.headless", "true");
573 // allow https handshakes to download intermediate certs if necessary
574 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
576 String jabawsUrl = bootstrapArgs.getValue(Arg.JABAWS);
577 if (jabawsUrl == null)
578 jabawsUrl = aparser.getValue("jabaws");
579 if (jabawsUrl != null)
583 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
585 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
586 testoutput(bootstrapArgs, Arg.JABAWS,
587 "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
588 } catch (MalformedURLException e)
591 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
596 List<String> setprops = new ArrayList<>();
597 if (bootstrapArgs.contains(Arg.SETPROP))
599 setprops = bootstrapArgs.getValueList(Arg.SETPROP);
603 String sp = aparser.getValue("setprop");
607 sp = aparser.getValue("setprop");
610 for (String setprop : setprops)
612 int p = setprop.indexOf('=');
616 .println("Ignoring invalid setprop argument : " + setprop);
620 System.out.println("Executing setprop argument: " + setprop);
623 Cache.setProperty(setprop.substring(0, p),
624 setprop.substring(p + 1));
626 // DISABLED FOR SECURITY REASONS
627 // TODO: add a property to allow properties to be overriden by cli args
628 // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
631 if (System.getProperty("java.awt.headless") != null
632 && System.getProperty("java.awt.headless").equals("true"))
636 System.setProperty("http.agent", HttpUtils.getUserAgent());
640 Console.initLogger();
643 NoClassDefFoundError error)
645 error.printStackTrace();
646 String message = "\nEssential logging libraries not found."
647 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
648 Jalview.exit(message, 0);
652 if (!(headless || headlessArg))
656 * configure 'full' SO model if preferences say to, else use the default (full SO)
657 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
659 boolean soDefault = !Platform.isJS();
660 if (Cache.getDefault("USE_FULL_SO", soDefault))
662 SequenceOntologyFactory.setInstance(new SequenceOntology());
665 if (!(headless || headlessArg))
667 Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
668 || aparser.contains("nosplash")
669 || Cache.getDefault("SPLASH", "true").equals("false");
670 desktop = new Desktop();
671 desktop.setInBatchMode(true); // indicate we are starting up
675 JalviewTaskbar.setTaskbar(this);
676 } catch (Exception e)
678 Console.info("Cannot set Taskbar");
679 Console.error(e.getMessage());
680 // e.printStackTrace();
681 } catch (Throwable t)
683 Console.info("Cannot set Taskbar");
684 Console.error(t.getMessage());
685 // t.printStackTrace();
688 // set Proxy settings before all the internet calls
689 Cache.setProxyPropertiesFromPreferences();
691 desktop.setVisible(true);
693 if (!Platform.isJS())
702 * Check to see that the JVM version being run is suitable for the Java
703 * version this Jalview was compiled for. Popup a warning if not.
705 if (!LaunchUtils.checkJavaVersion())
707 Console.warn("The Java version being used (Java "
708 + LaunchUtils.getJavaVersion()
709 + ") may lead to problems. This installation of Jalview should be used with Java "
710 + LaunchUtils.getJavaCompileVersion() + ".");
713 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
716 MessageManager.getString("label.continue") };
717 JOptionPane.showOptionDialog(null,
718 MessageManager.formatMessage(
719 "warning.wrong_jvm_version_message",
720 LaunchUtils.getJavaVersion(),
721 LaunchUtils.getJavaCompileVersion()),
723 .getString("warning.wrong_jvm_version_title"),
724 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
725 null, options, options[0]);
729 boolean webservicediscovery = bootstrapArgs
730 .getBoolean(Arg.WEBSERVICEDISCOVERY);
731 if (aparser.contains("nowebservicediscovery"))
732 webservicediscovery = false;
733 if (webservicediscovery)
735 desktop.startServiceDiscovery();
739 testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
742 boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
743 if (aparser.contains("nousagestats"))
747 startUsageStats(desktop);
748 testoutput(argparser, Arg.NOUSAGESTATS);
752 System.out.println("CMD [-nousagestats] executed successfully!");
753 testoutput(argparser, Arg.NOUSAGESTATS);
756 boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
757 if (aparser.contains("noquestionnaire"))
758 questionnaire = false;
761 String url = aparser.getValue("questionnaire");
764 // Start the desktop questionnaire prompter with the specified
766 Console.debug("Starting questionnaire url at " + url);
767 desktop.checkForQuestionnaire(url);
768 System.out.println("CMD questionnaire[-" + url
769 + "] executed successfully!");
773 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
775 // Start the desktop questionnaire prompter with the specified
778 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
780 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
782 "Starting questionnaire with default url: " + defurl);
783 desktop.checkForQuestionnaire(defurl);
790 .println("CMD [-noquestionnaire] executed successfully!");
791 testoutput(argparser, Arg.QUESTIONNAIRE);
794 if ((!aparser.contains("nonews")
795 && Cache.getProperty("NONEWS") == null
796 && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
797 || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
799 desktop.checkForNews();
802 if (!aparser.contains("nohtmltemplates")
803 && Cache.getProperty("NOHTMLTEMPLATES") == null)
805 BioJsHTMLOutput.updateBioJS();
809 // Run Commands from cli
810 cmds = new Commands(argparser, headlessArg);
811 boolean commandsSuccess = cmds.argsWereParsed();
817 if (argparser.getBoolean(Arg.NOQUIT))
820 "Completed " + Arg.HEADLESS.getName() + " commands, but "
821 + Arg.NOQUIT + " is set so not quitting!");
825 // record usage stats if in headless mode
826 if (Cache.getDefault("USAGESTATS", false))
828 Cache.initGoogleTracker(headlessArg);
830 Jalview.exit("Successfully completed commands in headless mode",
834 Console.info("Successfully completed commands");
840 Jalview.exit("Error when running Commands in headless mode", 1);
842 Console.warn("Error when running commands");
845 // Check if JVM and compile version might cause problems and log if it
847 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
849 Console.warn("The Java version being used (Java "
850 + LaunchUtils.getJavaVersion()
851 + ") may lead to problems. This installation of Jalview should be used with Java "
852 + LaunchUtils.getJavaCompileVersion() + ".");
855 String file = null, data = null;
857 FileFormatI format = null;
859 DataSourceType protocol = null;
861 FileLoader fileLoader = new FileLoader(!headless);
863 String groovyscript = null; // script to execute after all loading is
864 // completed one way or another
865 // extract groovy argument and execute if necessary
866 groovyscript = aparser.getValue("groovy", true);
867 file = aparser.getValue("open", true);
869 if (file == null && desktop == null && !commandsSuccess)
871 Jalview.exit("No files to open!", 1);
875 // Finally, deal with the remaining input data.
880 desktop.setProgressBar(
882 .getString("status.processing_commandline_args"),
883 progress = System.currentTimeMillis());
885 System.out.println("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 System.out.println("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);
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 // System.out.println("Added " + data);
951 "CMD groups[-" + data + "] executed successfully!");
953 data = aparser.getValue("features", true);
956 af.parseFeaturesFile(data,
957 AppletFormatAdapter.checkProtocol(data));
958 // System.out.println("Added " + data);
960 "CMD [-features " + data + "] executed successfully!");
963 data = aparser.getValue("annotations", true);
966 af.loadJalviewDataFile(data, null, null, null);
967 // System.out.println("Added " + data);
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 System.out.println("CMD [-sortbytree] executed successfully!");
980 if (aparser.contains("no-annotation"))
982 af.getViewport().setShowAnnotation(false);
983 if (!af.getViewport().isShowAnnotation())
985 System.out.println("CMD no-annotation executed successfully!");
988 if (aparser.contains("nosortbytree"))
990 af.getViewport().setSortByTree(false);
991 if (!af.getViewport().getSortByTree())
994 .println("CMD [-nosortbytree] executed successfully!");
997 data = aparser.getValue("tree", true);
1003 "CMD [-tree " + data + "] executed successfully!");
1004 NewickFile nf = new NewickFile(data,
1005 AppletFormatAdapter.checkProtocol(data));
1007 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1008 } catch (IOException ex)
1010 System.err.println("Couldn't add tree " + data);
1011 ex.printStackTrace(System.err);
1015 if (groovyscript != null)
1017 // Execute the groovy script after we've done all the rendering stuff
1018 // and before any images or figures are generated.
1019 System.out.println("Executing script " + groovyscript);
1020 executeGroovyScript(groovyscript, af);
1021 System.out.println("CMD groovy[" + groovyscript
1022 + "] executed successfully!");
1023 groovyscript = null;
1025 String imageName = "unnamed.png";
1026 while (aparser.getSize() > 1)
1030 String outputFormat = aparser.nextValue();
1031 file = aparser.nextValue();
1033 if (outputFormat.equalsIgnoreCase("png"))
1035 System.out.println("Creating PNG image: " + file);
1036 af.createPNG(new File(file));
1037 imageName = (new File(file)).getName();
1040 else if (outputFormat.equalsIgnoreCase("svg"))
1042 System.out.println("Creating SVG image: " + file);
1043 File imageFile = new File(file);
1044 imageName = imageFile.getName();
1045 af.createSVG(imageFile);
1048 else if (outputFormat.equalsIgnoreCase("html"))
1050 File imageFile = new File(file);
1051 imageName = imageFile.getName();
1052 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1054 System.out.println("Creating HTML image: " + file);
1055 htmlSVG.exportHTML(file);
1058 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1062 System.err.println("The output html file must not be null");
1067 BioJsHTMLOutput.refreshVersionInfo(
1068 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1069 } catch (URISyntaxException e)
1071 e.printStackTrace();
1073 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1075 "Creating BioJS MSA Viwer HTML file: " + file);
1076 bjs.exportHTML(file);
1079 else if (outputFormat.equalsIgnoreCase("imgMap"))
1081 System.out.println("Creating image map: " + file);
1082 af.createImageMap(new File(file), imageName);
1085 else if (outputFormat.equalsIgnoreCase("eps"))
1087 File outputFile = new File(file);
1089 "Creating EPS file: " + outputFile.getAbsolutePath());
1090 af.createEPS(outputFile);
1094 FileFormatI outFormat = null;
1097 outFormat = FileFormats.getInstance().forName(outputFormat);
1098 } catch (Exception formatP)
1100 System.out.println("Couldn't parse " + outFormat
1101 + " as a valid Jalview format string.");
1103 if (outFormat != null)
1105 if (!outFormat.isWritable())
1108 "This version of Jalview does not support alignment export as "
1113 af.saveAlignment(file, outFormat);
1114 if (af.isSaveAlignmentSuccessful())
1116 System.out.println("Written alignment in "
1117 + outFormat.getName() + " format to " + file);
1121 System.out.println("Error writing file " + file + " in "
1122 + outFormat.getName() + " format!!");
1126 } catch (ImageOutputException ioexc)
1129 "Unexpected error whilst exporting image to " + file);
1130 ioexc.printStackTrace();
1135 while (aparser.getSize() > 0)
1137 System.out.println("Unknown arg: " + aparser.nextValue());
1142 AlignFrame startUpAlframe = null;
1143 // We'll only open the default file if the desktop is visible.
1145 // ////////////////////
1147 if (!Platform.isJS() && !headless && file == null
1148 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1149 && !cmds.commandArgsProvided()
1150 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1151 // don't open the startup file if command line args have been processed
1152 // (&& !Commands.commandArgsProvided())
1159 file = Cache.getDefault("STARTUP_FILE",
1160 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1161 + "/examples/exampleFile_2_7.jvp");
1162 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1164 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1166 file.replace("http:", "https:");
1167 // hardwire upgrade of the startup file
1168 file.replace("_2_3", "_2_7");
1169 file.replace("2_7.jar", "2_7.jvp");
1170 // and remove the stale setting
1171 Cache.removeProperty("STARTUP_FILE");
1174 protocol = AppletFormatAdapter.checkProtocol(file);
1176 if (file.endsWith(".jar"))
1178 format = FileFormat.Jalview;
1184 format = new IdentifyFile().identify(file, protocol);
1185 } catch (FileFormatException e)
1191 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1193 // don't ask to save when quitting if only the startup file has been
1195 Console.debug("Resetting up-to-date flag for startup file");
1196 startUpAlframe.getViewport().setSavedUpToDate(true);
1197 // extract groovy arguments before anything else.
1200 // Once all other stuff is done, execute any groovy scripts (in order)
1201 if (groovyscript != null)
1203 if (Cache.groovyJarsPresent())
1205 System.out.println("Executing script " + groovyscript);
1206 executeGroovyScript(groovyscript, startUpAlframe);
1211 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1215 // and finally, turn off batch mode indicator - if the desktop still exists
1216 if (desktop != null)
1220 desktop.setProgressBar(null, progress);
1222 desktop.setInBatchMode(false);
1226 private static void setLookAndFeel()
1228 if (!Platform.isJS())
1235 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1237 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1239 // try Quaqua/Vaqua.
1240 String lafProp = System.getProperty("laf");
1241 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1242 String laf = "none";
1243 if (lafProp != null)
1247 else if (lafSetting != null)
1251 boolean lafSet = false;
1254 case "crossplatform":
1255 lafSet = setCrossPlatformLookAndFeel();
1258 Console.error("Could not set requested laf=" + laf);
1262 lafSet = setSystemLookAndFeel();
1265 Console.error("Could not set requested laf=" + laf);
1269 lafSet = setGtkLookAndFeel();
1272 Console.error("Could not set requested laf=" + laf);
1276 lafSet = setMetalLookAndFeel();
1279 Console.error("Could not set requested laf=" + laf);
1283 lafSet = setNimbusLookAndFeel();
1286 Console.error("Could not set requested laf=" + laf);
1290 lafSet = setFlatLookAndFeel();
1293 Console.error("Could not set requested laf=" + laf);
1297 lafSet = setMacLookAndFeel();
1300 Console.error("Could not set requested laf=" + laf);
1306 Console.error("Requested laf=" + laf + " not implemented");
1310 // Flatlaf default for everyone!
1311 lafSet = setFlatLookAndFeel();
1314 setSystemLookAndFeel();
1316 if (Platform.isLinux())
1318 setLinuxLookAndFeel();
1320 if (Platform.isMac())
1322 setMacLookAndFeel();
1328 private static boolean setCrossPlatformLookAndFeel()
1330 boolean set = false;
1333 UIManager.setLookAndFeel(
1334 UIManager.getCrossPlatformLookAndFeelClassName());
1336 } catch (Exception ex)
1338 Console.error("Unexpected Look and Feel Exception");
1339 Console.error(ex.getMessage());
1340 Console.debug(Cache.getStackTraceString(ex));
1345 private static boolean setSystemLookAndFeel()
1347 boolean set = false;
1350 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1352 } catch (Exception ex)
1354 Console.error("Unexpected Look and Feel Exception");
1355 Console.error(ex.getMessage());
1356 Console.debug(Cache.getStackTraceString(ex));
1361 private static boolean setSpecificLookAndFeel(String name,
1362 String className, boolean nameStartsWith)
1364 boolean set = false;
1367 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1369 if (info.getName() != null && nameStartsWith
1370 ? info.getName().toLowerCase(Locale.ROOT)
1371 .startsWith(name.toLowerCase(Locale.ROOT))
1372 : info.getName().toLowerCase(Locale.ROOT)
1373 .equals(name.toLowerCase(Locale.ROOT)))
1375 className = info.getClassName();
1379 UIManager.setLookAndFeel(className);
1381 } catch (Exception ex)
1383 Console.error("Unexpected Look and Feel Exception");
1384 Console.error(ex.getMessage());
1385 Console.debug(Cache.getStackTraceString(ex));
1390 private static boolean setGtkLookAndFeel()
1392 return setSpecificLookAndFeel("gtk",
1393 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1396 private static boolean setMetalLookAndFeel()
1398 return setSpecificLookAndFeel("metal",
1399 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1402 private static boolean setNimbusLookAndFeel()
1404 return setSpecificLookAndFeel("nimbus",
1405 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1408 private static boolean setFlatLookAndFeel()
1410 boolean set = false;
1411 if (SystemInfo.isMacOS)
1415 UIManager.setLookAndFeel(
1416 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1418 Console.debug("Using FlatMacLightLaf");
1419 } catch (ClassNotFoundException | InstantiationException
1420 | IllegalAccessException | UnsupportedLookAndFeelException e)
1422 Console.debug("Exception loading FlatLightLaf", e);
1424 System.setProperty("apple.laf.useScreenMenuBar", "true");
1425 System.setProperty("apple.awt.application.name",
1426 ChannelProperties.getProperty("app_name"));
1427 System.setProperty("apple.awt.application.appearance", "system");
1428 if (SystemInfo.isMacFullWindowContentSupported
1429 && Desktop.desktop != null)
1431 Console.debug("Setting transparent title bar");
1432 Desktop.desktop.getRootPane()
1433 .putClientProperty("apple.awt.fullWindowContent", true);
1434 Desktop.desktop.getRootPane()
1435 .putClientProperty("apple.awt.transparentTitleBar", true);
1436 Desktop.desktop.getRootPane()
1437 .putClientProperty("apple.awt.fullscreenable", true);
1439 SwingUtilities.invokeLater(() -> {
1440 FlatMacLightLaf.setup();
1442 Console.debug("Using FlatMacLightLaf");
1449 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1451 Console.debug("Using FlatLightLaf");
1452 } catch (ClassNotFoundException | InstantiationException
1453 | IllegalAccessException | UnsupportedLookAndFeelException e)
1455 Console.debug("Exception loading FlatLightLaf", e);
1457 // Windows specific properties here
1458 SwingUtilities.invokeLater(() -> {
1459 FlatLightLaf.setup();
1461 Console.debug("Using FlatLightLaf");
1464 else if (SystemInfo.isLinux)
1468 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1470 Console.debug("Using FlatLightLaf");
1471 } catch (ClassNotFoundException | InstantiationException
1472 | IllegalAccessException | UnsupportedLookAndFeelException e)
1474 Console.debug("Exception loading FlatLightLaf", e);
1476 // enable custom window decorations
1477 JFrame.setDefaultLookAndFeelDecorated(true);
1478 JDialog.setDefaultLookAndFeelDecorated(true);
1479 SwingUtilities.invokeLater(() -> {
1480 FlatLightLaf.setup();
1482 Console.debug("Using FlatLightLaf");
1490 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1492 Console.debug("Using FlatLightLaf");
1493 } catch (ClassNotFoundException | InstantiationException
1494 | IllegalAccessException | UnsupportedLookAndFeelException e)
1496 Console.debug("Exception loading FlatLightLaf", e);
1502 UIManager.put("TabbedPane.tabType", "card");
1503 UIManager.put("TabbedPane.showTabSeparators", true);
1504 UIManager.put("TabbedPane.showContentSeparator", true);
1505 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1506 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1507 UIManager.put("TabbedPane.hasFullBorder", true);
1508 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1509 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1510 UIManager.put("TabbedPane.smoothScrolling", true);
1511 UIManager.put("TabbedPane.tabWidthMode", "compact");
1512 UIManager.put("TabbedPane.selectedBackground", Color.white);
1513 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1514 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1517 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1521 private static boolean setMacLookAndFeel()
1523 boolean set = false;
1524 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1525 ChannelProperties.getProperty("app_name"));
1526 System.setProperty("apple.laf.useScreenMenuBar", "true");
1528 * broken native LAFs on (ARM?) macbooks
1529 set = setQuaquaLookAndFeel();
1530 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1531 .toLowerCase(Locale.ROOT).contains("quaqua"))
1533 set = setVaquaLookAndFeel();
1536 set = setFlatLookAndFeel();
1540 private static boolean setLinuxLookAndFeel()
1542 boolean set = false;
1543 set = setFlatLookAndFeel();
1545 set = setMetalLookAndFeel();
1546 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1548 set = setNimbusLookAndFeel();
1553 private static void showUsage()
1556 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1557 + "-nodisplay\tRun Jalview without User Interface.\n"
1558 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1559 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1560 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1561 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1562 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1563 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1564 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1565 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1566 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1567 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1568 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1569 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1570 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1571 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1572 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1573 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1574 + "-html FILE\tCreate HTML file from alignment.\n"
1575 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1576 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1577 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1578 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1579 + "-noquestionnaire\tTurn off questionnaire check.\n"
1580 + "-nonews\tTurn off check for Jalview news.\n"
1581 + "-nousagestats\tTurn off analytics tracking for this session.\n"
1582 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1584 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1585 // after all other properties files have been read\n\t
1586 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1587 // passed in correctly)"
1588 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1589 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1590 + "-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"
1591 + "-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"
1592 + "-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"
1593 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1597 private static void startUsageStats(final Desktop desktop)
1600 * start a User Config prompt asking if we can log usage statistics.
1602 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1604 MessageManager.getString("prompt.plausible_analytics_title"),
1605 MessageManager.getString("prompt.plausible_analytics"),
1611 Console.debug("Initialising analytics for usage stats.");
1612 Cache.initAnalytics();
1613 Console.debug("Tracking enabled.");
1620 Console.debug("Not enabling analytics.");
1623 desktop.addDialogThread(prompter);
1627 * Locate the given string as a file and pass it to the groovy interpreter.
1629 * @param groovyscript
1630 * the script to execute
1631 * @param jalviewContext
1632 * the Jalview Desktop object passed in to the groovy binding as the
1635 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1638 * for scripts contained in files
1645 if (groovyscript.trim().equals("STDIN"))
1647 // read from stdin into a tempfile and execute it
1650 tfile = File.createTempFile("jalview", "groovy");
1651 PrintWriter outfile = new PrintWriter(
1652 new OutputStreamWriter(new FileOutputStream(tfile)));
1653 BufferedReader br = new BufferedReader(
1654 new InputStreamReader(System.in));
1656 while ((line = br.readLine()) != null)
1658 outfile.write(line + "\n");
1664 } catch (Exception ex)
1666 System.err.println("Failed to read from STDIN into tempfile "
1667 + ((tfile == null) ? "(tempfile wasn't created)"
1668 : tfile.toString()));
1669 ex.printStackTrace();
1674 sfile = tfile.toURI().toURL();
1675 } catch (Exception x)
1678 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1680 x.printStackTrace();
1688 sfile = new URI(groovyscript).toURL();
1689 } catch (Exception x)
1691 tfile = new File(groovyscript);
1692 if (!tfile.exists())
1694 System.err.println("File '" + groovyscript + "' does not exist.");
1697 if (!tfile.canRead())
1699 System.err.println("File '" + groovyscript + "' cannot be read.");
1702 if (tfile.length() < 1)
1704 System.err.println("File '" + groovyscript + "' is empty.");
1709 sfile = tfile.getAbsoluteFile().toURI().toURL();
1710 } catch (Exception ex)
1712 System.err.println("Failed to create a file URL for "
1713 + tfile.getAbsoluteFile());
1720 Map<String, java.lang.Object> vbinding = new HashMap<>();
1721 vbinding.put("Jalview", this);
1724 vbinding.put("currentAlFrame", af);
1726 Binding gbinding = new Binding(vbinding);
1727 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1728 gse.run(sfile.toString(), gbinding);
1729 if ("STDIN".equals(groovyscript))
1731 // delete temp file that we made -
1732 // only if it was successfully executed
1735 } catch (Exception e)
1737 System.err.println("Exception Whilst trying to execute file " + sfile
1738 + " as a groovy script.");
1739 e.printStackTrace(System.err);
1744 public static boolean isHeadlessMode()
1746 String isheadless = System.getProperty("java.awt.headless");
1747 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1754 public AlignFrame[] getAlignFrames()
1756 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1757 : Desktop.getAlignFrames();
1762 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1766 // System.exit will run the shutdownHook first
1767 Jalview.exit("Quitting now. Bye!", 0);
1770 public static AlignFrame getCurrentAlignFrame()
1772 return Jalview.currentAlignFrame;
1775 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1777 Jalview.currentAlignFrame = currentAlignFrame;
1780 protected Commands getCommands()
1785 public static void exit(String message, int exitcode)
1787 if (Console.log == null)
1789 // Don't start the logger just to exit!
1790 if (message != null)
1794 System.out.println(message);
1798 System.err.println(message);
1804 Console.debug("Using Jalview.exit");
1805 if (message != null)
1809 Console.info(message);
1813 Console.error(message);
1819 System.exit(exitcode);
1823 /******************************
1825 * TEST OUTPUT METHODS
1827 ******************************/
1829 * method for reporting string values parsed/processed during tests
1832 protected static void testoutput(ArgParser ap, Arg a, String s1,
1835 BootstrapArgs bsa = ap.getBootstrapArgs();
1836 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1838 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1840 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1841 + s2 + "' for arg " + a.argString());
1844 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1848 Console.warn("Arg '" + a.getName() + "' not set at all");
1851 testoutput(true, a, s1, s2);
1855 * method for reporting string values parsed/processed during tests
1858 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1861 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1863 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1865 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1866 + s2 + "' for arg " + a.argString());
1869 if (!a.hasOption(Opt.BOOTSTRAP))
1871 Console.error("Non-bootstrap Arg '" + a.getName()
1872 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1874 if (!bsa.contains(a))
1876 Console.warn("Arg '" + a.getName() + "' not set at all");
1879 testoutput(true, a, s1, s2);
1883 * report value set for string values parsed/processed during tests
1885 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1887 if (yes && ((s1 == null && s2 == null)
1888 || (s1 != null && s1.equals(s2))))
1890 System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1896 * testoutput for boolean and unary values
1898 protected static void testoutput(ArgParser ap, Arg a)
1902 BootstrapArgs bsa = ap.getBootstrapArgs();
1905 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1907 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1909 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1913 Console.warn("Arg '" + a.getName() + "' not set at all");
1919 protected static void testoutput(BootstrapArgs bsa, Arg a)
1921 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1923 if (!a.hasOption(Opt.BOOTSTRAP))
1925 Console.warn("Non-bootstrap Arg '" + a.getName()
1926 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1929 if (!bsa.contains(a))
1931 Console.warn("Arg '" + a.getName() + "' not set at all");
1934 testoutput(bsa.getBoolean(a), a);
1937 private static void testoutput(boolean yes, Arg a)
1939 String message = null;
1940 if (a.hasOption(Opt.BOOLEAN))
1942 message = (yes ? a.argString() : a.negateArgString()) + " was set";
1944 else if (a.hasOption(Opt.UNARY))
1946 message = a.argString() + (yes ? " was set" : " was not set");
1948 System.out.println("[TESTOUTPUT] arg " + message);