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",
637 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
641 Console.initLogger();
644 NoClassDefFoundError error)
646 error.printStackTrace();
647 String message = "\nEssential logging libraries not found."
648 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
649 Jalview.exit(message, 0);
653 if (!(headless || headlessArg))
657 * configure 'full' SO model if preferences say to, else use the default (full SO)
658 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
660 boolean soDefault = !Platform.isJS();
661 if (Cache.getDefault("USE_FULL_SO", soDefault))
663 SequenceOntologyFactory.setInstance(new SequenceOntology());
666 if (!(headless || headlessArg))
668 Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
669 || aparser.contains("nosplash")
670 || Cache.getDefault("SPLASH", "true").equals("false");
671 desktop = new Desktop();
672 desktop.setInBatchMode(true); // indicate we are starting up
676 JalviewTaskbar.setTaskbar(this);
677 } catch (Exception e)
679 Console.info("Cannot set Taskbar");
680 Console.error(e.getMessage());
681 // e.printStackTrace();
682 } catch (Throwable t)
684 Console.info("Cannot set Taskbar");
685 Console.error(t.getMessage());
686 // t.printStackTrace();
689 // set Proxy settings before all the internet calls
690 Cache.setProxyPropertiesFromPreferences();
692 desktop.setVisible(true);
694 if (!Platform.isJS())
703 * Check to see that the JVM version being run is suitable for the Java
704 * version this Jalview was compiled for. Popup a warning if not.
706 if (!LaunchUtils.checkJavaVersion())
708 Console.warn("The Java version being used (Java "
709 + LaunchUtils.getJavaVersion()
710 + ") may lead to problems. This installation of Jalview should be used with Java "
711 + LaunchUtils.getJavaCompileVersion() + ".");
714 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
717 MessageManager.getString("label.continue") };
718 JOptionPane.showOptionDialog(null,
719 MessageManager.formatMessage(
720 "warning.wrong_jvm_version_message",
721 LaunchUtils.getJavaVersion(),
722 LaunchUtils.getJavaCompileVersion()),
724 .getString("warning.wrong_jvm_version_title"),
725 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
726 null, options, options[0]);
730 boolean webservicediscovery = bootstrapArgs
731 .getBoolean(Arg.WEBSERVICEDISCOVERY);
732 if (aparser.contains("nowebservicediscovery"))
733 webservicediscovery = false;
734 if (webservicediscovery)
736 desktop.startServiceDiscovery();
740 testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
743 boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
744 if (aparser.contains("nousagestats"))
748 startUsageStats(desktop);
749 testoutput(argparser, Arg.NOUSAGESTATS);
753 System.out.println("CMD [-nousagestats] executed successfully!");
754 testoutput(argparser, Arg.NOUSAGESTATS);
757 boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
758 if (aparser.contains("noquestionnaire"))
759 questionnaire = false;
762 String url = aparser.getValue("questionnaire");
765 // Start the desktop questionnaire prompter with the specified
767 Console.debug("Starting questionnaire url at " + url);
768 desktop.checkForQuestionnaire(url);
769 System.out.println("CMD questionnaire[-" + url
770 + "] executed successfully!");
774 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
776 // Start the desktop questionnaire prompter with the specified
779 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
781 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
783 "Starting questionnaire with default url: " + defurl);
784 desktop.checkForQuestionnaire(defurl);
791 .println("CMD [-noquestionnaire] executed successfully!");
792 testoutput(argparser, Arg.QUESTIONNAIRE);
795 if ((!aparser.contains("nonews")
796 && Cache.getProperty("NONEWS") == null
797 && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
798 || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
800 desktop.checkForNews();
803 if (!aparser.contains("nohtmltemplates")
804 && Cache.getProperty("NOHTMLTEMPLATES") == null)
806 BioJsHTMLOutput.updateBioJS();
810 // Run Commands from cli
811 cmds = new Commands(argparser, headlessArg);
812 boolean commandsSuccess = cmds.argsWereParsed();
818 if (argparser.getBoolean(Arg.NOQUIT))
821 "Completed " + Arg.HEADLESS.getName() + " commands, but "
822 + Arg.NOQUIT + " is set so not quitting!");
826 // record usage stats if in headless mode
827 if (Cache.getDefault("USAGESTATS", false))
829 Cache.initGoogleTracker(headlessArg);
831 Jalview.exit("Successfully completed commands in headless mode",
835 Console.info("Successfully completed commands");
841 Jalview.exit("Error when running Commands in headless mode", 1);
843 Console.warn("Error when running commands");
846 // Check if JVM and compile version might cause problems and log if it
848 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
850 Console.warn("The Java version being used (Java "
851 + LaunchUtils.getJavaVersion()
852 + ") may lead to problems. This installation of Jalview should be used with Java "
853 + LaunchUtils.getJavaCompileVersion() + ".");
856 String file = null, data = null;
858 FileFormatI format = null;
860 DataSourceType protocol = null;
862 FileLoader fileLoader = new FileLoader(!headless);
864 String groovyscript = null; // script to execute after all loading is
865 // completed one way or another
866 // extract groovy argument and execute if necessary
867 groovyscript = aparser.getValue("groovy", true);
868 file = aparser.getValue("open", true);
870 if (file == null && desktop == null && !commandsSuccess)
872 Jalview.exit("No files to open!", 1);
876 // Finally, deal with the remaining input data.
881 desktop.setProgressBar(
883 .getString("status.processing_commandline_args"),
884 progress = System.currentTimeMillis());
886 System.out.println("CMD [-open " + file + "] executed successfully!");
888 if (!Platform.isJS())
890 * ignore in JavaScript -- can't just file existence - could load it?
895 if (!HttpUtils.startsWithHttpOrHttps(file))
897 if (!(new File(file)).exists())
902 "Can't find file '" + file + "' in headless mode", 1);
904 Console.warn("Can't find file'" + file + "'");
909 protocol = AppletFormatAdapter.checkProtocol(file);
913 format = new IdentifyFile().identify(file, protocol);
914 } catch (FileFormatException e1)
919 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
923 System.out.println("error");
927 setCurrentAlignFrame(af);
928 data = aparser.getValue("colour", true);
931 data.replaceAll("%20", " ");
933 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
934 af.getViewport(), af.getViewport().getAlignment(), data);
939 "CMD [-colour " + data + "] executed successfully!");
944 // Must maintain ability to use the groups flag
945 data = aparser.getValue("groups", true);
948 af.parseFeaturesFile(data,
949 AppletFormatAdapter.checkProtocol(data));
950 // System.out.println("Added " + data);
952 "CMD groups[-" + data + "] executed successfully!");
954 data = aparser.getValue("features", true);
957 af.parseFeaturesFile(data,
958 AppletFormatAdapter.checkProtocol(data));
959 // System.out.println("Added " + data);
961 "CMD [-features " + data + "] executed successfully!");
964 data = aparser.getValue("annotations", true);
967 af.loadJalviewDataFile(data, null, null, null);
968 // System.out.println("Added " + data);
970 "CMD [-annotations " + data + "] executed successfully!");
972 // set or clear the sortbytree flag.
973 if (aparser.contains("sortbytree"))
975 af.getViewport().setSortByTree(true);
976 if (af.getViewport().getSortByTree())
978 System.out.println("CMD [-sortbytree] executed successfully!");
981 if (aparser.contains("no-annotation"))
983 af.getViewport().setShowAnnotation(false);
984 if (!af.getViewport().isShowAnnotation())
986 System.out.println("CMD no-annotation executed successfully!");
989 if (aparser.contains("nosortbytree"))
991 af.getViewport().setSortByTree(false);
992 if (!af.getViewport().getSortByTree())
995 .println("CMD [-nosortbytree] executed successfully!");
998 data = aparser.getValue("tree", true);
1004 "CMD [-tree " + data + "] executed successfully!");
1005 NewickFile nf = new NewickFile(data,
1006 AppletFormatAdapter.checkProtocol(data));
1008 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1009 } catch (IOException ex)
1011 System.err.println("Couldn't add tree " + data);
1012 ex.printStackTrace(System.err);
1016 if (groovyscript != null)
1018 // Execute the groovy script after we've done all the rendering stuff
1019 // and before any images or figures are generated.
1020 System.out.println("Executing script " + groovyscript);
1021 executeGroovyScript(groovyscript, af);
1022 System.out.println("CMD groovy[" + groovyscript
1023 + "] executed successfully!");
1024 groovyscript = null;
1026 String imageName = "unnamed.png";
1027 while (aparser.getSize() > 1)
1031 String outputFormat = aparser.nextValue();
1032 file = aparser.nextValue();
1034 if (outputFormat.equalsIgnoreCase("png"))
1036 System.out.println("Creating PNG image: " + file);
1037 af.createPNG(new File(file));
1038 imageName = (new File(file)).getName();
1041 else if (outputFormat.equalsIgnoreCase("svg"))
1043 System.out.println("Creating SVG image: " + file);
1044 File imageFile = new File(file);
1045 imageName = imageFile.getName();
1046 af.createSVG(imageFile);
1049 else if (outputFormat.equalsIgnoreCase("html"))
1051 File imageFile = new File(file);
1052 imageName = imageFile.getName();
1053 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1055 System.out.println("Creating HTML image: " + file);
1056 htmlSVG.exportHTML(file);
1059 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1063 System.err.println("The output html file must not be null");
1068 BioJsHTMLOutput.refreshVersionInfo(
1069 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1070 } catch (URISyntaxException e)
1072 e.printStackTrace();
1074 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1076 "Creating BioJS MSA Viwer HTML file: " + file);
1077 bjs.exportHTML(file);
1080 else if (outputFormat.equalsIgnoreCase("imgMap"))
1082 System.out.println("Creating image map: " + file);
1083 af.createImageMap(new File(file), imageName);
1086 else if (outputFormat.equalsIgnoreCase("eps"))
1088 File outputFile = new File(file);
1090 "Creating EPS file: " + outputFile.getAbsolutePath());
1091 af.createEPS(outputFile);
1095 FileFormatI outFormat = null;
1098 outFormat = FileFormats.getInstance().forName(outputFormat);
1099 } catch (Exception formatP)
1101 System.out.println("Couldn't parse " + outFormat
1102 + " as a valid Jalview format string.");
1104 if (outFormat != null)
1106 if (!outFormat.isWritable())
1109 "This version of Jalview does not support alignment export as "
1114 af.saveAlignment(file, outFormat);
1115 if (af.isSaveAlignmentSuccessful())
1117 System.out.println("Written alignment in "
1118 + outFormat.getName() + " format to " + file);
1122 System.out.println("Error writing file " + file + " in "
1123 + outFormat.getName() + " format!!");
1127 } catch (ImageOutputException ioexc)
1130 "Unexpected error whilst exporting image to " + file);
1131 ioexc.printStackTrace();
1136 while (aparser.getSize() > 0)
1138 System.out.println("Unknown arg: " + aparser.nextValue());
1143 AlignFrame startUpAlframe = null;
1144 // We'll only open the default file if the desktop is visible.
1146 // ////////////////////
1148 if (!Platform.isJS() && !headless && file == null
1149 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1150 && !cmds.commandArgsProvided()
1151 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1152 // don't open the startup file if command line args have been processed
1153 // (&& !Commands.commandArgsProvided())
1160 file = Cache.getDefault("STARTUP_FILE",
1161 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1162 + "/examples/exampleFile_2_7.jvp");
1163 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1165 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1167 file.replace("http:", "https:");
1168 // hardwire upgrade of the startup file
1169 file.replace("_2_3", "_2_7");
1170 file.replace("2_7.jar", "2_7.jvp");
1171 // and remove the stale setting
1172 Cache.removeProperty("STARTUP_FILE");
1175 protocol = AppletFormatAdapter.checkProtocol(file);
1177 if (file.endsWith(".jar"))
1179 format = FileFormat.Jalview;
1185 format = new IdentifyFile().identify(file, protocol);
1186 } catch (FileFormatException e)
1192 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1194 // don't ask to save when quitting if only the startup file has been
1196 Console.debug("Resetting up-to-date flag for startup file");
1197 startUpAlframe.getViewport().setSavedUpToDate(true);
1198 // extract groovy arguments before anything else.
1201 // Once all other stuff is done, execute any groovy scripts (in order)
1202 if (groovyscript != null)
1204 if (Cache.groovyJarsPresent())
1206 System.out.println("Executing script " + groovyscript);
1207 executeGroovyScript(groovyscript, startUpAlframe);
1212 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1216 // and finally, turn off batch mode indicator - if the desktop still exists
1217 if (desktop != null)
1221 desktop.setProgressBar(null, progress);
1223 desktop.setInBatchMode(false);
1227 private static void setLookAndFeel()
1229 if (!Platform.isJS())
1236 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1238 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1240 // try Quaqua/Vaqua.
1241 String lafProp = System.getProperty("laf");
1242 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1243 String laf = "none";
1244 if (lafProp != null)
1248 else if (lafSetting != null)
1252 boolean lafSet = false;
1255 case "crossplatform":
1256 lafSet = setCrossPlatformLookAndFeel();
1259 Console.error("Could not set requested laf=" + laf);
1263 lafSet = setSystemLookAndFeel();
1266 Console.error("Could not set requested laf=" + laf);
1270 lafSet = setGtkLookAndFeel();
1273 Console.error("Could not set requested laf=" + laf);
1277 lafSet = setMetalLookAndFeel();
1280 Console.error("Could not set requested laf=" + laf);
1284 lafSet = setNimbusLookAndFeel();
1287 Console.error("Could not set requested laf=" + laf);
1291 lafSet = setFlatLookAndFeel();
1294 Console.error("Could not set requested laf=" + laf);
1298 lafSet = setMacLookAndFeel();
1301 Console.error("Could not set requested laf=" + laf);
1307 Console.error("Requested laf=" + laf + " not implemented");
1311 // Flatlaf default for everyone!
1312 lafSet = setFlatLookAndFeel();
1315 setSystemLookAndFeel();
1317 if (Platform.isLinux())
1319 setLinuxLookAndFeel();
1321 if (Platform.isMac())
1323 setMacLookAndFeel();
1329 private static boolean setCrossPlatformLookAndFeel()
1331 boolean set = false;
1334 UIManager.setLookAndFeel(
1335 UIManager.getCrossPlatformLookAndFeelClassName());
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 setSystemLookAndFeel()
1348 boolean set = false;
1351 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1353 } catch (Exception ex)
1355 Console.error("Unexpected Look and Feel Exception");
1356 Console.error(ex.getMessage());
1357 Console.debug(Cache.getStackTraceString(ex));
1362 private static boolean setSpecificLookAndFeel(String name,
1363 String className, boolean nameStartsWith)
1365 boolean set = false;
1368 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1370 if (info.getName() != null && nameStartsWith
1371 ? info.getName().toLowerCase(Locale.ROOT)
1372 .startsWith(name.toLowerCase(Locale.ROOT))
1373 : info.getName().toLowerCase(Locale.ROOT)
1374 .equals(name.toLowerCase(Locale.ROOT)))
1376 className = info.getClassName();
1380 UIManager.setLookAndFeel(className);
1382 } catch (Exception ex)
1384 Console.error("Unexpected Look and Feel Exception");
1385 Console.error(ex.getMessage());
1386 Console.debug(Cache.getStackTraceString(ex));
1391 private static boolean setGtkLookAndFeel()
1393 return setSpecificLookAndFeel("gtk",
1394 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1397 private static boolean setMetalLookAndFeel()
1399 return setSpecificLookAndFeel("metal",
1400 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1403 private static boolean setNimbusLookAndFeel()
1405 return setSpecificLookAndFeel("nimbus",
1406 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1409 private static boolean setFlatLookAndFeel()
1411 boolean set = false;
1412 if (SystemInfo.isMacOS)
1416 UIManager.setLookAndFeel(
1417 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1419 Console.debug("Using FlatMacLightLaf");
1420 } catch (ClassNotFoundException | InstantiationException
1421 | IllegalAccessException | UnsupportedLookAndFeelException e)
1423 Console.debug("Exception loading FlatLightLaf", e);
1425 System.setProperty("apple.laf.useScreenMenuBar", "true");
1426 System.setProperty("apple.awt.application.name",
1427 ChannelProperties.getProperty("app_name"));
1428 System.setProperty("apple.awt.application.appearance", "system");
1429 if (SystemInfo.isMacFullWindowContentSupported
1430 && Desktop.desktop != null)
1432 Console.debug("Setting transparent title bar");
1433 Desktop.desktop.getRootPane()
1434 .putClientProperty("apple.awt.fullWindowContent", true);
1435 Desktop.desktop.getRootPane()
1436 .putClientProperty("apple.awt.transparentTitleBar", true);
1437 Desktop.desktop.getRootPane()
1438 .putClientProperty("apple.awt.fullscreenable", true);
1440 SwingUtilities.invokeLater(() -> {
1441 FlatMacLightLaf.setup();
1443 Console.debug("Using FlatMacLightLaf");
1450 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1452 Console.debug("Using FlatLightLaf");
1453 } catch (ClassNotFoundException | InstantiationException
1454 | IllegalAccessException | UnsupportedLookAndFeelException e)
1456 Console.debug("Exception loading FlatLightLaf", e);
1458 // Windows specific properties here
1459 SwingUtilities.invokeLater(() -> {
1460 FlatLightLaf.setup();
1462 Console.debug("Using FlatLightLaf");
1465 else if (SystemInfo.isLinux)
1469 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1471 Console.debug("Using FlatLightLaf");
1472 } catch (ClassNotFoundException | InstantiationException
1473 | IllegalAccessException | UnsupportedLookAndFeelException e)
1475 Console.debug("Exception loading FlatLightLaf", e);
1477 // enable custom window decorations
1478 JFrame.setDefaultLookAndFeelDecorated(true);
1479 JDialog.setDefaultLookAndFeelDecorated(true);
1480 SwingUtilities.invokeLater(() -> {
1481 FlatLightLaf.setup();
1483 Console.debug("Using FlatLightLaf");
1491 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1493 Console.debug("Using FlatLightLaf");
1494 } catch (ClassNotFoundException | InstantiationException
1495 | IllegalAccessException | UnsupportedLookAndFeelException e)
1497 Console.debug("Exception loading FlatLightLaf", e);
1503 UIManager.put("TabbedPane.tabType", "card");
1504 UIManager.put("TabbedPane.showTabSeparators", true);
1505 UIManager.put("TabbedPane.showContentSeparator", true);
1506 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1507 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1508 UIManager.put("TabbedPane.hasFullBorder", true);
1509 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1510 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1511 UIManager.put("TabbedPane.smoothScrolling", true);
1512 UIManager.put("TabbedPane.tabWidthMode", "compact");
1513 UIManager.put("TabbedPane.selectedBackground", Color.white);
1514 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1515 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1518 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1522 private static boolean setMacLookAndFeel()
1524 boolean set = false;
1525 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1526 ChannelProperties.getProperty("app_name"));
1527 System.setProperty("apple.laf.useScreenMenuBar", "true");
1529 * broken native LAFs on (ARM?) macbooks
1530 set = setQuaquaLookAndFeel();
1531 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1532 .toLowerCase(Locale.ROOT).contains("quaqua"))
1534 set = setVaquaLookAndFeel();
1537 set = setFlatLookAndFeel();
1541 private static boolean setLinuxLookAndFeel()
1543 boolean set = false;
1544 set = setFlatLookAndFeel();
1546 set = setMetalLookAndFeel();
1547 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1549 set = setNimbusLookAndFeel();
1554 private static void showUsage()
1557 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1558 + "-nodisplay\tRun Jalview without User Interface.\n"
1559 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1560 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1561 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1562 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1563 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1564 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1565 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1566 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1567 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1568 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1569 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1570 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1571 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1572 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1573 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1574 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1575 + "-html FILE\tCreate HTML file from alignment.\n"
1576 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1577 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1578 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1579 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1580 + "-noquestionnaire\tTurn off questionnaire check.\n"
1581 + "-nonews\tTurn off check for Jalview news.\n"
1582 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1583 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1585 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1586 // after all other properties files have been read\n\t
1587 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1588 // passed in correctly)"
1589 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1590 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1591 + "-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"
1592 + "-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"
1593 + "-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"
1594 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1598 private static void startUsageStats(final Desktop desktop)
1601 * start a User Config prompt asking if we can log usage statistics.
1603 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1605 MessageManager.getString("prompt.google_analytics_title"),
1606 MessageManager.getString("prompt.google_analytics"),
1613 "Initialising googletracker for usage stats.");
1614 Cache.initGoogleTracker();
1615 Console.debug("Tracking enabled.");
1622 Console.debug("Not enabling Google Tracking.");
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 System.out.println(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 System.out.println("[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 System.out.println("[TESTOUTPUT] arg " + message);