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();
817 if (argparser.getBoolean(Arg.NOQUIT))
820 "Completed " + Arg.HEADLESS.getName() + " commands, but "
821 + Arg.NOQUIT + " is set so not quitting!");
825 Jalview.exit("Successfully completed commands in headless mode",
829 Console.info("Successfully completed commands");
835 Jalview.exit("Error when running Commands in headless mode", 1);
837 Console.warn("Error when running commands");
840 // Check if JVM and compile version might cause problems and log if it
842 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
844 Console.warn("The Java version being used (Java "
845 + LaunchUtils.getJavaVersion()
846 + ") may lead to problems. This installation of Jalview should be used with Java "
847 + LaunchUtils.getJavaCompileVersion() + ".");
850 String file = null, data = null;
852 FileFormatI format = null;
854 DataSourceType protocol = null;
856 FileLoader fileLoader = new FileLoader(!headless);
858 String groovyscript = null; // script to execute after all loading is
859 // completed one way or another
860 // extract groovy argument and execute if necessary
861 groovyscript = aparser.getValue("groovy", true);
862 file = aparser.getValue("open", true);
864 if (file == null && desktop == null && !commandsSuccess)
866 Jalview.exit("No files to open!", 1);
870 // Finally, deal with the remaining input data.
875 desktop.setProgressBar(
877 .getString("status.processing_commandline_args"),
878 progress = System.currentTimeMillis());
880 System.out.println("CMD [-open " + file + "] executed successfully!");
882 if (!Platform.isJS())
884 * ignore in JavaScript -- can't just file existence - could load it?
889 if (!HttpUtils.startsWithHttpOrHttps(file))
891 if (!(new File(file)).exists())
896 "Can't find file '" + file + "' in headless mode", 1);
898 Console.warn("Can't find file'" + file + "'");
903 protocol = AppletFormatAdapter.checkProtocol(file);
907 format = new IdentifyFile().identify(file, protocol);
908 } catch (FileFormatException e1)
913 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
917 System.out.println("error");
921 setCurrentAlignFrame(af);
922 data = aparser.getValue("colour", true);
925 data.replaceAll("%20", " ");
927 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
928 af.getViewport(), af.getViewport().getAlignment(), data);
933 "CMD [-colour " + data + "] executed successfully!");
938 // Must maintain ability to use the groups flag
939 data = aparser.getValue("groups", true);
942 af.parseFeaturesFile(data,
943 AppletFormatAdapter.checkProtocol(data));
944 // System.out.println("Added " + data);
946 "CMD groups[-" + data + "] executed successfully!");
948 data = aparser.getValue("features", true);
951 af.parseFeaturesFile(data,
952 AppletFormatAdapter.checkProtocol(data));
953 // System.out.println("Added " + data);
955 "CMD [-features " + data + "] executed successfully!");
958 data = aparser.getValue("annotations", true);
961 af.loadJalviewDataFile(data, null, null, null);
962 // System.out.println("Added " + data);
964 "CMD [-annotations " + data + "] executed successfully!");
966 // set or clear the sortbytree flag.
967 if (aparser.contains("sortbytree"))
969 af.getViewport().setSortByTree(true);
970 if (af.getViewport().getSortByTree())
972 System.out.println("CMD [-sortbytree] executed successfully!");
975 if (aparser.contains("no-annotation"))
977 af.getViewport().setShowAnnotation(false);
978 if (!af.getViewport().isShowAnnotation())
980 System.out.println("CMD no-annotation executed successfully!");
983 if (aparser.contains("nosortbytree"))
985 af.getViewport().setSortByTree(false);
986 if (!af.getViewport().getSortByTree())
989 .println("CMD [-nosortbytree] executed successfully!");
992 data = aparser.getValue("tree", true);
998 "CMD [-tree " + data + "] executed successfully!");
999 NewickFile nf = new NewickFile(data,
1000 AppletFormatAdapter.checkProtocol(data));
1002 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1003 } catch (IOException ex)
1005 System.err.println("Couldn't add tree " + data);
1006 ex.printStackTrace(System.err);
1010 if (groovyscript != null)
1012 // Execute the groovy script after we've done all the rendering stuff
1013 // and before any images or figures are generated.
1014 System.out.println("Executing script " + groovyscript);
1015 executeGroovyScript(groovyscript, af);
1016 System.out.println("CMD groovy[" + groovyscript
1017 + "] executed successfully!");
1018 groovyscript = null;
1020 String imageName = "unnamed.png";
1021 while (aparser.getSize() > 1)
1025 String outputFormat = aparser.nextValue();
1026 file = aparser.nextValue();
1028 if (outputFormat.equalsIgnoreCase("png"))
1030 System.out.println("Creating PNG image: " + file);
1031 af.createPNG(new File(file));
1032 imageName = (new File(file)).getName();
1035 else if (outputFormat.equalsIgnoreCase("svg"))
1037 System.out.println("Creating SVG image: " + file);
1038 File imageFile = new File(file);
1039 imageName = imageFile.getName();
1040 af.createSVG(imageFile);
1043 else if (outputFormat.equalsIgnoreCase("html"))
1045 File imageFile = new File(file);
1046 imageName = imageFile.getName();
1047 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1049 System.out.println("Creating HTML image: " + file);
1050 htmlSVG.exportHTML(file);
1053 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1057 System.err.println("The output html file must not be null");
1062 BioJsHTMLOutput.refreshVersionInfo(
1063 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1064 } catch (URISyntaxException e)
1066 e.printStackTrace();
1068 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1070 "Creating BioJS MSA Viwer HTML file: " + file);
1071 bjs.exportHTML(file);
1074 else if (outputFormat.equalsIgnoreCase("imgMap"))
1076 System.out.println("Creating image map: " + file);
1077 af.createImageMap(new File(file), imageName);
1080 else if (outputFormat.equalsIgnoreCase("eps"))
1082 File outputFile = new File(file);
1084 "Creating EPS file: " + outputFile.getAbsolutePath());
1085 af.createEPS(outputFile);
1089 FileFormatI outFormat = null;
1092 outFormat = FileFormats.getInstance().forName(outputFormat);
1093 } catch (Exception formatP)
1095 System.out.println("Couldn't parse " + outFormat
1096 + " as a valid Jalview format string.");
1098 if (outFormat != null)
1100 if (!outFormat.isWritable())
1103 "This version of Jalview does not support alignment export as "
1108 af.saveAlignment(file, outFormat);
1109 if (af.isSaveAlignmentSuccessful())
1111 System.out.println("Written alignment in "
1112 + outFormat.getName() + " format to " + file);
1116 System.out.println("Error writing file " + file + " in "
1117 + outFormat.getName() + " format!!");
1121 } catch (ImageOutputException ioexc)
1124 "Unexpected error whilst exporting image to " + file);
1125 ioexc.printStackTrace();
1130 while (aparser.getSize() > 0)
1132 System.out.println("Unknown arg: " + aparser.nextValue());
1137 AlignFrame startUpAlframe = null;
1138 // We'll only open the default file if the desktop is visible.
1140 // ////////////////////
1142 if (!Platform.isJS() && !headless && file == null
1143 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1144 && !cmds.commandArgsProvided()
1145 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1146 // don't open the startup file if command line args have been processed
1147 // (&& !Commands.commandArgsProvided())
1154 file = Cache.getDefault("STARTUP_FILE",
1155 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1156 + "/examples/exampleFile_2_7.jvp");
1157 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1159 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1161 file.replace("http:", "https:");
1162 // hardwire upgrade of the startup file
1163 file.replace("_2_3", "_2_7");
1164 file.replace("2_7.jar", "2_7.jvp");
1165 // and remove the stale setting
1166 Cache.removeProperty("STARTUP_FILE");
1169 protocol = AppletFormatAdapter.checkProtocol(file);
1171 if (file.endsWith(".jar"))
1173 format = FileFormat.Jalview;
1179 format = new IdentifyFile().identify(file, protocol);
1180 } catch (FileFormatException e)
1186 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1188 // don't ask to save when quitting if only the startup file has been
1190 Console.debug("Resetting up-to-date flag for startup file");
1191 startUpAlframe.getViewport().setSavedUpToDate(true);
1192 // extract groovy arguments before anything else.
1195 // Once all other stuff is done, execute any groovy scripts (in order)
1196 if (groovyscript != null)
1198 if (Cache.groovyJarsPresent())
1200 System.out.println("Executing script " + groovyscript);
1201 executeGroovyScript(groovyscript, startUpAlframe);
1206 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1210 // and finally, turn off batch mode indicator - if the desktop still exists
1211 if (desktop != null)
1215 desktop.setProgressBar(null, progress);
1217 desktop.setInBatchMode(false);
1221 private static void setLookAndFeel()
1223 if (!Platform.isJS())
1230 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1232 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1234 // try Quaqua/Vaqua.
1235 String lafProp = System.getProperty("laf");
1236 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1237 String laf = "none";
1238 if (lafProp != null)
1242 else if (lafSetting != null)
1246 boolean lafSet = false;
1249 case "crossplatform":
1250 lafSet = setCrossPlatformLookAndFeel();
1253 Console.error("Could not set requested laf=" + laf);
1257 lafSet = setSystemLookAndFeel();
1260 Console.error("Could not set requested laf=" + laf);
1264 lafSet = setGtkLookAndFeel();
1267 Console.error("Could not set requested laf=" + laf);
1271 lafSet = setMetalLookAndFeel();
1274 Console.error("Could not set requested laf=" + laf);
1278 lafSet = setNimbusLookAndFeel();
1281 Console.error("Could not set requested laf=" + laf);
1285 lafSet = setFlatLookAndFeel();
1288 Console.error("Could not set requested laf=" + laf);
1292 lafSet = setMacLookAndFeel();
1295 Console.error("Could not set requested laf=" + laf);
1301 Console.error("Requested laf=" + laf + " not implemented");
1305 // Flatlaf default for everyone!
1306 lafSet = setFlatLookAndFeel();
1309 setSystemLookAndFeel();
1311 if (Platform.isLinux())
1313 setLinuxLookAndFeel();
1315 if (Platform.isMac())
1317 setMacLookAndFeel();
1323 private static boolean setCrossPlatformLookAndFeel()
1325 boolean set = false;
1328 UIManager.setLookAndFeel(
1329 UIManager.getCrossPlatformLookAndFeelClassName());
1331 } catch (Exception ex)
1333 Console.error("Unexpected Look and Feel Exception");
1334 Console.error(ex.getMessage());
1335 Console.debug(Cache.getStackTraceString(ex));
1340 private static boolean setSystemLookAndFeel()
1342 boolean set = false;
1345 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1347 } catch (Exception ex)
1349 Console.error("Unexpected Look and Feel Exception");
1350 Console.error(ex.getMessage());
1351 Console.debug(Cache.getStackTraceString(ex));
1356 private static boolean setSpecificLookAndFeel(String name,
1357 String className, boolean nameStartsWith)
1359 boolean set = false;
1362 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1364 if (info.getName() != null && nameStartsWith
1365 ? info.getName().toLowerCase(Locale.ROOT)
1366 .startsWith(name.toLowerCase(Locale.ROOT))
1367 : info.getName().toLowerCase(Locale.ROOT)
1368 .equals(name.toLowerCase(Locale.ROOT)))
1370 className = info.getClassName();
1374 UIManager.setLookAndFeel(className);
1376 } catch (Exception ex)
1378 Console.error("Unexpected Look and Feel Exception");
1379 Console.error(ex.getMessage());
1380 Console.debug(Cache.getStackTraceString(ex));
1385 private static boolean setGtkLookAndFeel()
1387 return setSpecificLookAndFeel("gtk",
1388 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1391 private static boolean setMetalLookAndFeel()
1393 return setSpecificLookAndFeel("metal",
1394 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1397 private static boolean setNimbusLookAndFeel()
1399 return setSpecificLookAndFeel("nimbus",
1400 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1403 private static boolean setFlatLookAndFeel()
1405 boolean set = false;
1406 UIManager.put("InternalFrame.dropShadowPainted", false);
1407 if (SystemInfo.isMacOS)
1411 UIManager.setLookAndFeel(
1412 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1414 Console.debug("Using FlatMacLightLaf");
1415 } catch (ClassNotFoundException | InstantiationException
1416 | IllegalAccessException | UnsupportedLookAndFeelException e)
1418 Console.debug("Exception loading FlatLightLaf", e);
1420 System.setProperty("apple.laf.useScreenMenuBar", "true");
1421 System.setProperty("apple.awt.application.name",
1422 ChannelProperties.getProperty("app_name"));
1423 System.setProperty("apple.awt.application.appearance", "system");
1424 if (SystemInfo.isMacFullWindowContentSupported
1425 && Desktop.desktop != null)
1427 Console.debug("Setting transparent title bar");
1428 Desktop.desktop.getRootPane()
1429 .putClientProperty("apple.awt.fullWindowContent", true);
1430 Desktop.desktop.getRootPane()
1431 .putClientProperty("apple.awt.transparentTitleBar", true);
1432 Desktop.desktop.getRootPane()
1433 .putClientProperty("apple.awt.fullscreenable", true);
1435 SwingUtilities.invokeLater(() -> {
1436 FlatMacLightLaf.setup();
1438 Console.debug("Using FlatMacLightLaf");
1445 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1447 Console.debug("Using FlatLightLaf");
1448 } catch (ClassNotFoundException | InstantiationException
1449 | IllegalAccessException | UnsupportedLookAndFeelException e)
1451 Console.debug("Exception loading FlatLightLaf", e);
1453 // Windows specific properties here
1454 SwingUtilities.invokeLater(() -> {
1455 FlatLightLaf.setup();
1457 Console.debug("Using FlatLightLaf");
1460 else if (SystemInfo.isLinux)
1464 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1466 Console.debug("Using FlatLightLaf");
1467 } catch (ClassNotFoundException | InstantiationException
1468 | IllegalAccessException | UnsupportedLookAndFeelException e)
1470 Console.debug("Exception loading FlatLightLaf", e);
1472 // enable custom window decorations
1473 JFrame.setDefaultLookAndFeelDecorated(true);
1474 JDialog.setDefaultLookAndFeelDecorated(true);
1475 SwingUtilities.invokeLater(() -> {
1476 FlatLightLaf.setup();
1478 Console.debug("Using FlatLightLaf");
1486 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1488 Console.debug("Using FlatLightLaf");
1489 } catch (ClassNotFoundException | InstantiationException
1490 | IllegalAccessException | UnsupportedLookAndFeelException e)
1492 Console.debug("Exception loading FlatLightLaf", e);
1498 UIManager.put("TabbedPane.tabType", "card");
1499 UIManager.put("TabbedPane.showTabSeparators", true);
1500 UIManager.put("TabbedPane.showContentSeparator", true);
1501 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1502 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1503 UIManager.put("TabbedPane.hasFullBorder", true);
1504 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1505 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1506 UIManager.put("TabbedPane.smoothScrolling", true);
1507 UIManager.put("TabbedPane.tabWidthMode", "compact");
1508 UIManager.put("TabbedPane.selectedBackground", Color.white);
1509 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1510 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1513 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1517 private static boolean setMacLookAndFeel()
1519 boolean set = false;
1520 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1521 ChannelProperties.getProperty("app_name"));
1522 System.setProperty("apple.laf.useScreenMenuBar", "true");
1524 * broken native LAFs on (ARM?) macbooks
1525 set = setQuaquaLookAndFeel();
1526 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1527 .toLowerCase(Locale.ROOT).contains("quaqua"))
1529 set = setVaquaLookAndFeel();
1532 set = setFlatLookAndFeel();
1536 private static boolean setLinuxLookAndFeel()
1538 boolean set = false;
1539 set = setFlatLookAndFeel();
1541 set = setMetalLookAndFeel();
1542 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1544 set = setNimbusLookAndFeel();
1549 private static void showUsage()
1552 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1553 + "-nodisplay\tRun Jalview without User Interface.\n"
1554 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1555 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1556 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1557 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1558 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1559 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1560 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1561 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1562 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1563 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1564 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1565 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1566 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1567 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1568 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1569 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1570 + "-html FILE\tCreate HTML file from alignment.\n"
1571 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1572 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1573 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1574 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1575 + "-noquestionnaire\tTurn off questionnaire check.\n"
1576 + "-nonews\tTurn off check for Jalview news.\n"
1577 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1578 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1580 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1581 // after all other properties files have been read\n\t
1582 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1583 // passed in correctly)"
1584 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1585 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1586 + "-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"
1587 + "-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"
1588 + "-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"
1589 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1593 private static void startUsageStats(final Desktop desktop)
1596 * start a User Config prompt asking if we can log usage statistics.
1598 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1599 "USAGESTATS", "Jalview Usage Statistics",
1600 "Do you want to help make Jalview better by enabling "
1601 + "the collection of usage statistics with Google Analytics ?"
1602 + "\n\n(you can enable or disable usage tracking in the preferences)",
1609 "Initialising googletracker for usage stats.");
1610 Cache.initGoogleTracker();
1611 Console.debug("Tracking enabled.");
1618 Console.debug("Not enabling Google Tracking.");
1621 desktop.addDialogThread(prompter);
1625 * Locate the given string as a file and pass it to the groovy interpreter.
1627 * @param groovyscript
1628 * the script to execute
1629 * @param jalviewContext
1630 * the Jalview Desktop object passed in to the groovy binding as the
1633 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1636 * for scripts contained in files
1643 if (groovyscript.trim().equals("STDIN"))
1645 // read from stdin into a tempfile and execute it
1648 tfile = File.createTempFile("jalview", "groovy");
1649 PrintWriter outfile = new PrintWriter(
1650 new OutputStreamWriter(new FileOutputStream(tfile)));
1651 BufferedReader br = new BufferedReader(
1652 new InputStreamReader(System.in));
1654 while ((line = br.readLine()) != null)
1656 outfile.write(line + "\n");
1662 } catch (Exception ex)
1664 System.err.println("Failed to read from STDIN into tempfile "
1665 + ((tfile == null) ? "(tempfile wasn't created)"
1666 : tfile.toString()));
1667 ex.printStackTrace();
1672 sfile = tfile.toURI().toURL();
1673 } catch (Exception x)
1676 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1678 x.printStackTrace();
1686 sfile = new URI(groovyscript).toURL();
1687 } catch (Exception x)
1689 tfile = new File(groovyscript);
1690 if (!tfile.exists())
1692 System.err.println("File '" + groovyscript + "' does not exist.");
1695 if (!tfile.canRead())
1697 System.err.println("File '" + groovyscript + "' cannot be read.");
1700 if (tfile.length() < 1)
1702 System.err.println("File '" + groovyscript + "' is empty.");
1707 sfile = tfile.getAbsoluteFile().toURI().toURL();
1708 } catch (Exception ex)
1710 System.err.println("Failed to create a file URL for "
1711 + tfile.getAbsoluteFile());
1718 Map<String, java.lang.Object> vbinding = new HashMap<>();
1719 vbinding.put("Jalview", this);
1722 vbinding.put("currentAlFrame", af);
1724 Binding gbinding = new Binding(vbinding);
1725 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1726 gse.run(sfile.toString(), gbinding);
1727 if ("STDIN".equals(groovyscript))
1729 // delete temp file that we made -
1730 // only if it was successfully executed
1733 } catch (Exception e)
1735 System.err.println("Exception Whilst trying to execute file " + sfile
1736 + " as a groovy script.");
1737 e.printStackTrace(System.err);
1742 public static boolean isHeadlessMode()
1744 String isheadless = System.getProperty("java.awt.headless");
1745 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1752 public AlignFrame[] getAlignFrames()
1754 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1755 : Desktop.getAlignFrames();
1760 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1764 // System.exit will run the shutdownHook first
1765 Jalview.exit("Quitting now. Bye!", 0);
1768 public static AlignFrame getCurrentAlignFrame()
1770 return Jalview.currentAlignFrame;
1773 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1775 Jalview.currentAlignFrame = currentAlignFrame;
1778 protected Commands getCommands()
1783 public static void exit(String message, int exitcode)
1785 if (Console.log == null)
1787 // Don't start the logger just to exit!
1788 if (message != null)
1792 System.out.println(message);
1796 System.err.println(message);
1802 Console.debug("Using Jalview.exit");
1803 if (message != null)
1807 Console.info(message);
1811 Console.error(message);
1817 System.exit(exitcode);
1821 /******************************
1823 * TEST OUTPUT METHODS
1825 ******************************/
1827 * method for reporting string values parsed/processed during tests
1830 protected static void testoutput(ArgParser ap, Arg a, String s1,
1833 BootstrapArgs bsa = ap.getBootstrapArgs();
1834 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1836 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1838 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1839 + s2 + "' for arg " + a.argString());
1842 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1846 Console.warn("Arg '" + a.getName() + "' not set at all");
1849 testoutput(true, a, s1, s2);
1853 * method for reporting string values parsed/processed during tests
1856 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1859 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1861 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1863 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1864 + s2 + "' for arg " + a.argString());
1867 if (!a.hasOption(Opt.BOOTSTRAP))
1869 Console.error("Non-bootstrap Arg '" + a.getName()
1870 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1872 if (!bsa.contains(a))
1874 Console.warn("Arg '" + a.getName() + "' not set at all");
1877 testoutput(true, a, s1, s2);
1881 * report value set for string values parsed/processed during tests
1883 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1885 if (yes && ((s1 == null && s2 == null)
1886 || (s1 != null && s1.equals(s2))))
1888 System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1894 * testoutput for boolean and unary values
1896 protected static void testoutput(ArgParser ap, Arg a)
1900 BootstrapArgs bsa = ap.getBootstrapArgs();
1903 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1905 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1907 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1911 Console.warn("Arg '" + a.getName() + "' not set at all");
1917 protected static void testoutput(BootstrapArgs bsa, Arg a)
1919 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1921 if (!a.hasOption(Opt.BOOTSTRAP))
1923 Console.warn("Non-bootstrap Arg '" + a.getName()
1924 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1927 if (!bsa.contains(a))
1929 Console.warn("Arg '" + a.getName() + "' not set at all");
1932 testoutput(bsa.getBoolean(a), a);
1935 private static void testoutput(boolean yes, Arg a)
1937 String message = null;
1938 if (a.hasOption(Opt.BOOLEAN))
1940 message = (yes ? a.argString() : a.negateArgString()) + " was set";
1942 else if (a.hasOption(Opt.UNARY))
1944 message = a.argString() + (yes ? " was set" : " was not set");
1946 System.out.println("[TESTOUTPUT] arg " + message);