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.JvOptionPane;
80 import jalview.gui.PromptUserConfig;
81 import jalview.gui.QuitHandler;
82 import jalview.gui.QuitHandler.QResponse;
83 import jalview.gui.StructureViewerBase;
84 import jalview.io.AppletFormatAdapter;
85 import jalview.io.BioJsHTMLOutput;
86 import jalview.io.DataSourceType;
87 import jalview.io.FileFormat;
88 import jalview.io.FileFormatException;
89 import jalview.io.FileFormatI;
90 import jalview.io.FileFormats;
91 import jalview.io.FileLoader;
92 import jalview.io.HtmlSvgOutput;
93 import jalview.io.IdentifyFile;
94 import jalview.io.NewickFile;
95 import jalview.io.exceptions.ImageOutputException;
96 import jalview.io.gff.SequenceOntologyFactory;
97 import jalview.schemes.ColourSchemeI;
98 import jalview.schemes.ColourSchemeProperty;
99 import jalview.util.ChannelProperties;
100 import jalview.util.HttpUtils;
101 import jalview.util.LaunchUtils;
102 import jalview.util.MessageManager;
103 import jalview.util.Platform;
104 import jalview.ws.jws2.Jws2Discoverer;
107 * Main class for Jalview Application <br>
109 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
110 * jalview.bin.Jalview
112 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
113 * jalview.bin.Jalview jalview.bin.Jalview
115 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
116 * embellish '*' to e.g. '*.jar')
119 * @version $Revision$
125 Platform.getURLCommandArguments();
126 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
127 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
128 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
129 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
133 * singleton instance of this class
135 private static Jalview instance;
137 private Desktop desktop;
139 protected Commands cmds;
141 public static AlignFrame currentAlignFrame;
143 private ArgParser argparser = null;
145 private BootstrapArgs bootstrapArgs = null;
147 private boolean QUIET = false;
149 public static boolean quiet()
151 return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
156 if (!Platform.isJS())
163 // grab all the rights we can for the JVM
164 Policy.setPolicy(new Policy()
167 public PermissionCollection getPermissions(CodeSource codesource)
169 Permissions perms = new Permissions();
170 perms.add(new AllPermission());
175 public void refresh()
183 * keep track of feature fetching tasks.
191 * TODO: generalise to track all jalview events to orchestrate batch processing
195 private int queued = 0;
197 private int running = 0;
199 public FeatureFetcher()
204 public void addFetcher(final AlignFrame af,
205 final Vector<String> dasSources)
207 final long id = System.currentTimeMillis();
209 final FeatureFetcher us = this;
210 new Thread(new Runnable()
222 af.setProgressBar(MessageManager
223 .getString("status.das_features_being_retrived"), id);
224 af.featureSettings_actionPerformed(null);
225 af.setProgressBar(null, id);
234 public synchronized boolean allFinished()
236 return queued == 0 && running == 0;
241 public static Jalview getInstance()
247 * main class for Jalview application
250 * open <em>filename</em>
252 public static void main(String[] args)
254 // setLogging(); // BH - for event debugging in JavaScript
255 instance = new Jalview();
256 instance.doMain(args);
259 private static void logClass(String name)
261 // BH - for event debugging in JavaScript
262 ConsoleHandler consoleHandler = new ConsoleHandler();
263 consoleHandler.setLevel(Level.ALL);
264 Logger logger = Logger.getLogger(name);
265 logger.setLevel(Level.ALL);
266 logger.addHandler(consoleHandler);
269 @SuppressWarnings("unused")
270 private static void setLogging()
278 Console.outPrintln("not in js");
281 // BH - for event debugging in JavaScript (Java mode only)
282 if (!Platform.isJS())
289 Logger.getLogger("").setLevel(Level.ALL);
290 logClass("java.awt.EventDispatchThread");
291 logClass("java.awt.EventQueue");
292 logClass("java.awt.Component");
293 logClass("java.awt.focus.Component");
294 logClass("java.awt.focus.DefaultKeyboardFocusManager");
302 void doMain(String[] args)
304 if (!Platform.isJS())
306 System.setSecurityManager(null);
309 if (args == null || args.length == 0 || (args.length == 1
310 && (args[0] == null || args[0].length() == 0)))
312 args = new String[] {};
315 // get args needed before proper ArgParser
316 bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
318 if (!Platform.isJS())
320 // are we being --quiet ?
321 if (bootstrapArgs.contains(Arg.QUIET))
324 OutputStream devNull = new OutputStream()
328 public void write(int b)
333 System.setOut(new PrintStream(devNull));
334 // redirecting stderr not working
335 if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
337 System.setErr(new PrintStream(devNull));
341 if (bootstrapArgs.contains(Arg.HELP)
342 || bootstrapArgs.contains(Arg.VERSION))
348 // set individual session preferences
349 if (bootstrapArgs.contains(Arg.P))
351 for (String kev : bootstrapArgs.getValueList(Arg.P))
357 int equalsIndex = kev.indexOf(ArgParser.EQUALS);
358 if (equalsIndex > -1)
360 String key = kev.substring(0, equalsIndex);
361 String val = kev.substring(equalsIndex + 1);
362 Cache.setSessionProperty(key, val);
367 // Move any new getdown-launcher-new.jar into place over old
368 // getdown-launcher.jar
369 String appdirString = System.getProperty("getdownappdir");
370 if (appdirString != null && appdirString.length() > 0)
372 final File appdir = new File(appdirString);
379 LaunchUtil.upgradeGetdown(
380 new File(appdir, "getdown-launcher-old.jar"),
381 new File(appdir, "getdown-launcher.jar"),
382 new File(appdir, "getdown-launcher-new.jar"));
387 if (!quiet() || !bootstrapArgs.outputToStdout()
388 || bootstrapArgs.contains(Arg.VERSION))
391 "Java version: " + System.getProperty("java.version"));
392 Console.outPrintln("Java home: " + System.getProperty("java.home"));
393 Console.outPrintln("Java arch: " + System.getProperty("os.arch") + " "
394 + System.getProperty("os.name") + " "
395 + System.getProperty("os.version"));
397 String val = System.getProperty("sys.install4jVersion");
400 Console.outPrintln("Install4j version: " + val);
402 val = System.getProperty("installer_template_version");
405 Console.outPrintln("Install4j template version: " + val);
407 val = System.getProperty("launcher_version");
410 Console.outPrintln("Launcher version: " + val);
414 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
416 System.setProperty("flatlaf.uiScale", "1");
419 // get bootstrap properties (mainly for the logger level)
420 Properties bootstrapProperties = Cache
421 .bootstrapProperties(bootstrapArgs.getValue(Arg.PROPS));
423 // report Jalview version
424 Cache.loadBuildProperties(
425 !quiet() || bootstrapArgs.contains(Arg.VERSION));
427 // stop now if only after --version
428 if (bootstrapArgs.contains(Arg.VERSION))
430 Jalview.exit(null, ExitCode.OK);
434 ArgsParser aparser = new ArgsParser(args);
437 boolean headless = false;
439 boolean headlessArg = false;
443 String logLevel = null;
444 if (bootstrapArgs.contains(Arg.TRACE))
448 else if (bootstrapArgs.contains(Arg.DEBUG))
452 if (logLevel == null && !(bootstrapProperties == null))
454 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
456 Console.initLogger(logLevel);
457 } catch (NoClassDefFoundError error)
459 error.printStackTrace();
460 String message = "\nEssential logging libraries not found."
461 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
462 Jalview.exit(message, ExitCode.OK);
465 // register SIGTERM listener
466 Runtime.getRuntime().addShutdownHook(new Thread()
471 Console.debug("Running shutdown hook");
472 QuitHandler.startForceQuit();
473 boolean closeExternal = Cache
474 .getDefault("DEFAULT_CLOSE_EXTERNAL_VIEWERS", false)
475 || Cache.getDefault("ALWAYS_CLOSE_EXTERNAL_VIEWERS", false);
476 StructureViewerBase.setQuitClose(closeExternal);
479 for (JInternalFrame frame : Desktop.desktop.getAllFrames())
481 if (frame instanceof StructureViewerBase)
483 ((StructureViewerBase) frame).closeViewer(closeExternal);
488 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
490 // Got to here by a SIGTERM signal.
491 // Note we will not actually cancel the quit from here -- it's too
492 // late -- but we can wait for saving files and close external viewers
494 // Close viewers/Leave viewers open
495 Console.debug("Checking for saving files");
496 QuitHandler.getQuitResponse(false);
500 Console.debug("Nothing more to do");
502 Console.debug("Exiting, bye!");
503 // shutdownHook cannot be cancelled, JVM will now halt
507 String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
508 ? bootstrapArgs.getValue(Arg.PROPS)
509 : aparser.getValue("props");
510 // if usrPropsFile == null, loadProperties will use the Channel
512 Cache.loadProperties(usrPropsFile);
513 if (usrPropsFile != null)
516 "CMD [-props " + usrPropsFile + "] executed successfully!");
517 testoutput(bootstrapArgs, Arg.PROPS,
518 "test/jalview/bin/testProps.jvprops", usrPropsFile);
521 // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
522 if (bootstrapArgs.contains(Arg.ARGFILE))
524 argparser = ArgParser.parseArgFiles(
525 bootstrapArgs.getValueList(Arg.ARGFILE),
526 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
531 argparser = new ArgParser(args,
532 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
536 if (!Platform.isJS())
543 if (bootstrapArgs.contains(Arg.HELP))
545 List<Map.Entry<Type, String>> helpArgs = bootstrapArgs
547 Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey())
548 .collect(Collectors.toList())));
549 Jalview.exit(null, ExitCode.OK);
551 if (aparser.contains("help") || aparser.contains("h"))
554 * Now using new usage statement.
557 Console.outPrintln(Arg.usage());
558 Jalview.exit(null, ExitCode.OK);
562 headlessArg = bootstrapArgs.isHeadless();
565 System.setProperty("java.awt.headless", "true");
568 if (aparser.contains("nodisplay") || aparser.contains("nogui")
569 || aparser.contains("headless"))
571 System.setProperty("java.awt.headless", "true");
576 // allow https handshakes to download intermediate certs if necessary
577 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
579 String jabawsUrl = bootstrapArgs.getValue(Arg.JABAWS);
580 if (jabawsUrl == null)
581 jabawsUrl = aparser.getValue("jabaws");
582 if (jabawsUrl != null)
586 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
588 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
589 testoutput(bootstrapArgs, Arg.JABAWS,
590 "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
591 } catch (MalformedURLException e)
593 jalview.bin.Console.errPrintln(
594 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
599 List<String> setprops = new ArrayList<>();
600 if (bootstrapArgs.contains(Arg.SETPROP))
602 setprops = bootstrapArgs.getValueList(Arg.SETPROP);
606 String sp = aparser.getValue("setprop");
610 sp = aparser.getValue("setprop");
613 for (String setprop : setprops)
615 int p = setprop.indexOf('=');
619 .println("Ignoring invalid setprop argument : " + setprop);
624 .errPrintln("Executing setprop argument: " + setprop);
627 Cache.setProperty(setprop.substring(0, p),
628 setprop.substring(p + 1));
630 // DISABLED FOR SECURITY REASONS
631 // TODO: add a property to allow properties to be overriden by cli args
632 // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
635 if (System.getProperty("java.awt.headless") != null
636 && System.getProperty("java.awt.headless").equals("true"))
640 System.setProperty("http.agent", HttpUtils.getUserAgent());
644 Console.initLogger();
647 NoClassDefFoundError error)
649 error.printStackTrace();
650 String message = "\nEssential logging libraries not found."
651 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
652 Jalview.exit(message, ExitCode.OK);
656 if (!(headless || headlessArg))
660 * configure 'full' SO model if preferences say to, else use the default (full SO)
661 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
663 boolean soDefault = !Platform.isJS();
664 if (Cache.getDefault("USE_FULL_SO", soDefault))
666 SequenceOntologyFactory.setInstance(new SequenceOntology());
669 if (!(headless || headlessArg))
671 Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
672 || aparser.contains("nosplash")
673 || Cache.getDefault("SPLASH", "true").equals("false");
674 desktop = new Desktop();
675 desktop.setInBatchMode(true); // indicate we are starting up
681 JalviewTaskbar.setTaskbar(this);
682 } catch (Exception e)
684 Console.info("Cannot set Taskbar");
685 Console.error(e.getMessage());
686 // e.printStackTrace();
687 } catch (Throwable t)
689 Console.info("Cannot set Taskbar");
690 Console.error(t.getMessage());
691 // t.printStackTrace();
694 // set Proxy settings before all the internet calls
695 Cache.setProxyPropertiesFromPreferences();
697 desktop.setVisible(true);
699 if (!Platform.isJS())
708 * Check to see that the JVM version being run is suitable for the Java
709 * version this Jalview was compiled for. Popup a warning if not.
711 if (!LaunchUtils.checkJavaVersion())
713 Console.warn("The Java version being used (Java "
714 + LaunchUtils.getJavaVersion()
715 + ") may lead to problems. This installation of Jalview should be used with Java "
716 + LaunchUtils.getJavaCompileVersion() + ".");
719 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
722 MessageManager.getString("label.continue") };
723 JOptionPane.showOptionDialog(null,
724 MessageManager.formatMessage(
725 "warning.wrong_jvm_version_message",
726 LaunchUtils.getJavaVersion(),
727 LaunchUtils.getJavaCompileVersion()),
729 .getString("warning.wrong_jvm_version_title"),
730 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
731 null, options, options[0]);
735 boolean webservicediscovery = bootstrapArgs
736 .getBoolean(Arg.WEBSERVICEDISCOVERY);
737 if (aparser.contains("nowebservicediscovery"))
738 webservicediscovery = false;
739 if (webservicediscovery)
741 desktop.startServiceDiscovery();
745 testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
748 boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
749 if (aparser.contains("nousagestats"))
753 startUsageStats(desktop);
754 testoutput(argparser, Arg.NOUSAGESTATS);
758 Console.outPrintln("CMD [-nousagestats] executed successfully!");
759 testoutput(argparser, Arg.NOUSAGESTATS);
762 boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
763 if (aparser.contains("noquestionnaire"))
764 questionnaire = false;
767 String url = aparser.getValue("questionnaire");
770 // Start the desktop questionnaire prompter with the specified
772 Console.debug("Starting questionnaire url at " + url);
773 desktop.checkForQuestionnaire(url);
774 Console.outPrintln("CMD questionnaire[-" + url
775 + "] executed successfully!");
779 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
781 // Start the desktop questionnaire prompter with the specified
784 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
786 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
788 "Starting questionnaire with default url: " + defurl);
789 desktop.checkForQuestionnaire(defurl);
796 "CMD [-noquestionnaire] executed successfully!");
797 testoutput(argparser, Arg.QUESTIONNAIRE);
800 if ((!aparser.contains("nonews")
801 && Cache.getProperty("NONEWS") == null
802 && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
803 || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
805 desktop.checkForNews();
808 if (!aparser.contains("nohtmltemplates")
809 && Cache.getProperty("NOHTMLTEMPLATES") == null)
811 BioJsHTMLOutput.updateBioJS();
818 if (getArgParser().isMixedStyle())
820 String warning = MessageManager.formatMessage(
821 "warning.using_mixed_command_line_arguments",
822 getArgParser().getMixedExamples());
823 Console.warn(warning);
825 "Exiting due to mixed old and new command line arguments",
826 ExitCode.INVALID_ARGUMENT);
828 if (getArgParser().isOldStyle())
830 String warning = MessageManager
831 .getString("warning.using_old_command_line_arguments")
833 + "https://www.jalview.org/help/html/features/commandline.html";
834 Console.warn(warning);
839 // Run Commands from cli
840 cmds = new Commands(argparser, headlessArg);
842 boolean commandsSuccess = cmds.argsWereParsed();
848 if (argparser.getBoolean(Arg.NOQUIT))
851 "Completed " + Arg.HEADLESS.getName() + " commands, but "
852 + Arg.NOQUIT + " is set so not quitting!");
856 Jalview.exit("Successfully completed commands in headless mode",
860 Console.info("Successfully completed commands");
866 Jalview.exit("Error when running Commands in headless mode",
867 ExitCode.ERROR_RUNNING_COMMANDS);
869 Console.warn("Error when running commands");
872 // Check if JVM and compile version might cause problems and log if it
874 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
876 Console.warn("The Java version being used (Java "
877 + LaunchUtils.getJavaVersion()
878 + ") may lead to problems. This installation of Jalview should be used with Java "
879 + LaunchUtils.getJavaCompileVersion() + ".");
882 String file = null, data = null;
884 FileFormatI format = null;
886 DataSourceType protocol = null;
888 FileLoader fileLoader = new FileLoader(!headless);
890 String groovyscript = null; // script to execute after all loading is
891 // completed one way or another
892 // extract groovy argument and execute if necessary
893 groovyscript = aparser.getValue("groovy", true);
894 file = aparser.getValue("open", true);
896 if (file == null && desktop == null && !commandsSuccess)
898 Jalview.exit("No files to open!", ExitCode.NO_FILES);
902 // Finally, deal with the remaining input data.
907 desktop.setProgressBar(
909 .getString("status.processing_commandline_args"),
910 progress = System.currentTimeMillis());
912 Console.outPrintln("CMD [-open " + file + "] executed successfully!");
914 if (!Platform.isJS())
916 * ignore in JavaScript -- can't just file existence - could load it?
921 if (!HttpUtils.startsWithHttpOrHttps(file))
923 if (!(new File(file)).exists())
928 "Can't find file '" + file + "' in headless mode",
929 ExitCode.FILE_NOT_FOUND);
931 Console.warn("Can't find file'" + file + "'");
936 protocol = AppletFormatAdapter.checkProtocol(file);
940 format = new IdentifyFile().identify(file, protocol);
941 } catch (FileFormatException e1)
946 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
950 Console.outPrintln("error");
954 setCurrentAlignFrame(af);
955 data = aparser.getValue("colour", true);
958 data.replaceAll("%20", " ");
960 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
961 af.getViewport(), af.getViewport().getAlignment(), data);
966 "CMD [-colour " + data + "] executed successfully!");
971 // Must maintain ability to use the groups flag
972 data = aparser.getValue("groups", true);
975 af.parseFeaturesFile(data,
976 AppletFormatAdapter.checkProtocol(data));
977 // Console.outPrintln("Added " + data);
979 "CMD groups[-" + data + "] executed successfully!");
981 data = aparser.getValue("features", true);
984 af.parseFeaturesFile(data,
985 AppletFormatAdapter.checkProtocol(data));
986 // Console.outPrintln("Added " + data);
988 "CMD [-features " + data + "] executed successfully!");
991 data = aparser.getValue("annotations", true);
994 af.loadJalviewDataFile(data, null, null, null);
995 // Console.outPrintln("Added " + data);
997 "CMD [-annotations " + data + "] executed successfully!");
999 // set or clear the sortbytree flag.
1000 if (aparser.contains("sortbytree"))
1002 af.getViewport().setSortByTree(true);
1003 if (af.getViewport().getSortByTree())
1005 Console.outPrintln("CMD [-sortbytree] executed successfully!");
1008 if (aparser.contains("no-annotation"))
1010 af.getViewport().setShowAnnotation(false);
1011 if (!af.getViewport().isShowAnnotation())
1013 Console.outPrintln("CMD no-annotation executed successfully!");
1016 if (aparser.contains("nosortbytree"))
1018 af.getViewport().setSortByTree(false);
1019 if (!af.getViewport().getSortByTree())
1022 "CMD [-nosortbytree] executed successfully!");
1025 data = aparser.getValue("tree", true);
1031 "CMD [-tree " + data + "] executed successfully!");
1032 NewickFile nf = new NewickFile(data,
1033 AppletFormatAdapter.checkProtocol(data));
1035 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1036 } catch (IOException ex)
1038 jalview.bin.Console.errPrintln("Couldn't add tree " + data);
1039 ex.printStackTrace(System.err);
1043 if (groovyscript != null)
1045 // Execute the groovy script after we've done all the rendering stuff
1046 // and before any images or figures are generated.
1047 Console.outPrintln("Executing script " + groovyscript);
1048 executeGroovyScript(groovyscript, af);
1049 Console.outPrintln("CMD groovy[" + groovyscript
1050 + "] executed successfully!");
1051 groovyscript = null;
1053 String imageName = "unnamed.png";
1054 while (aparser.getSize() > 1)
1058 String outputFormat = aparser.nextValue();
1059 file = aparser.nextValue();
1061 if (outputFormat.equalsIgnoreCase("png"))
1063 Console.outPrintln("Creating PNG image: " + file);
1064 af.createPNG(new File(file));
1065 imageName = (new File(file)).getName();
1068 else if (outputFormat.equalsIgnoreCase("svg"))
1070 Console.outPrintln("Creating SVG image: " + file);
1071 File imageFile = new File(file);
1072 imageName = imageFile.getName();
1073 af.createSVG(imageFile);
1076 else if (outputFormat.equalsIgnoreCase("html"))
1078 File imageFile = new File(file);
1079 imageName = imageFile.getName();
1080 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1082 Console.outPrintln("Creating HTML image: " + file);
1083 htmlSVG.exportHTML(file);
1086 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1090 jalview.bin.Console.errPrintln(
1091 "The output html file must not be null");
1096 BioJsHTMLOutput.refreshVersionInfo(
1097 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1098 } catch (URISyntaxException e)
1100 e.printStackTrace();
1102 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1104 "Creating BioJS MSA Viwer HTML file: " + file);
1105 bjs.exportHTML(file);
1108 else if (outputFormat.equalsIgnoreCase("imgMap"))
1110 Console.outPrintln("Creating image map: " + file);
1111 af.createImageMap(new File(file), imageName);
1114 else if (outputFormat.equalsIgnoreCase("eps"))
1116 File outputFile = new File(file);
1118 "Creating EPS file: " + outputFile.getAbsolutePath());
1119 af.createEPS(outputFile);
1123 FileFormatI outFormat = null;
1126 outFormat = FileFormats.getInstance().forName(outputFormat);
1127 } catch (Exception formatP)
1129 Console.outPrintln("Couldn't parse " + outFormat
1130 + " as a valid Jalview format string.");
1132 if (outFormat != null)
1134 if (!outFormat.isWritable())
1137 "This version of Jalview does not support alignment export as "
1142 af.saveAlignment(file, outFormat);
1143 if (af.isSaveAlignmentSuccessful())
1145 Console.outPrintln("Written alignment in "
1146 + outFormat.getName() + " format to " + file);
1150 Console.outPrintln("Error writing file " + file + " in "
1151 + outFormat.getName() + " format!!");
1155 } catch (ImageOutputException ioexc)
1158 "Unexpected error whilst exporting image to " + file);
1159 ioexc.printStackTrace();
1164 while (aparser.getSize() > 0)
1166 Console.outPrintln("Unknown arg: " + aparser.nextValue());
1171 AlignFrame startUpAlframe = null;
1172 // We'll only open the default file if the desktop is visible.
1174 // ////////////////////
1176 if (!Platform.isJS() && !headless && file == null
1177 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1178 && !cmds.commandArgsProvided()
1179 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1180 // don't open the startup file if command line args have been processed
1181 // (&& !Commands.commandArgsProvided())
1188 file = Cache.getDefault("STARTUP_FILE",
1189 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1190 + "/examples/exampleFile_2_7.jvp");
1191 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1193 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1195 file.replace("http:", "https:");
1196 // hardwire upgrade of the startup file
1197 file.replace("_2_3", "_2_7");
1198 file.replace("2_7.jar", "2_7.jvp");
1199 // and remove the stale setting
1200 Cache.removeProperty("STARTUP_FILE");
1203 protocol = AppletFormatAdapter.checkProtocol(file);
1205 if (file.endsWith(".jar"))
1207 format = FileFormat.Jalview;
1213 format = new IdentifyFile().identify(file, protocol);
1214 } catch (FileFormatException e)
1220 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1222 // don't ask to save when quitting if only the startup file has been
1224 Console.debug("Resetting up-to-date flag for startup file");
1225 startUpAlframe.getViewport().setSavedUpToDate(true);
1226 // extract groovy arguments before anything else.
1229 // Once all other stuff is done, execute any groovy scripts (in order)
1230 if (groovyscript != null)
1232 if (Cache.groovyJarsPresent())
1234 Console.outPrintln("Executing script " + groovyscript);
1235 executeGroovyScript(groovyscript, startUpAlframe);
1239 jalview.bin.Console.errPrintln(
1240 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1244 // and finally, turn off batch mode indicator - if the desktop still exists
1245 if (desktop != null)
1249 desktop.setProgressBar(null, progress);
1251 desktop.setInBatchMode(false);
1257 private static void setLookAndFeel()
1259 if (!Platform.isJS())
1266 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1268 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1270 // try Quaqua/Vaqua.
1271 String lafProp = System.getProperty("laf");
1272 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1273 String laf = "none";
1274 if (lafProp != null)
1278 else if (lafSetting != null)
1282 boolean lafSet = false;
1285 case "crossplatform":
1286 lafSet = setCrossPlatformLookAndFeel();
1289 Console.error("Could not set requested laf=" + laf);
1293 lafSet = setSystemLookAndFeel();
1296 Console.error("Could not set requested laf=" + laf);
1300 lafSet = setGtkLookAndFeel();
1303 Console.error("Could not set requested laf=" + laf);
1307 lafSet = setMetalLookAndFeel();
1310 Console.error("Could not set requested laf=" + laf);
1314 lafSet = setNimbusLookAndFeel();
1317 Console.error("Could not set requested laf=" + laf);
1321 lafSet = setFlatLookAndFeel();
1324 Console.error("Could not set requested laf=" + laf);
1328 lafSet = setMacLookAndFeel();
1331 Console.error("Could not set requested laf=" + laf);
1337 Console.error("Requested laf=" + laf + " not implemented");
1341 // Flatlaf default for everyone!
1342 lafSet = setFlatLookAndFeel();
1345 setSystemLookAndFeel();
1347 if (Platform.isLinux())
1349 setLinuxLookAndFeel();
1351 if (Platform.isMac())
1353 setMacLookAndFeel();
1359 private static boolean setCrossPlatformLookAndFeel()
1361 boolean set = false;
1364 UIManager.setLookAndFeel(
1365 UIManager.getCrossPlatformLookAndFeelClassName());
1367 } catch (Exception ex)
1369 Console.error("Unexpected Look and Feel Exception");
1370 Console.error(ex.getMessage());
1371 Console.debug(Cache.getStackTraceString(ex));
1376 private static boolean setSystemLookAndFeel()
1378 boolean set = false;
1381 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1383 } catch (Exception ex)
1385 Console.error("Unexpected Look and Feel Exception");
1386 Console.error(ex.getMessage());
1387 Console.debug(Cache.getStackTraceString(ex));
1392 private static boolean setSpecificLookAndFeel(String name,
1393 String className, boolean nameStartsWith)
1395 boolean set = false;
1398 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1400 if (info.getName() != null && nameStartsWith
1401 ? info.getName().toLowerCase(Locale.ROOT)
1402 .startsWith(name.toLowerCase(Locale.ROOT))
1403 : info.getName().toLowerCase(Locale.ROOT)
1404 .equals(name.toLowerCase(Locale.ROOT)))
1406 className = info.getClassName();
1410 UIManager.setLookAndFeel(className);
1412 } catch (Exception ex)
1414 Console.error("Unexpected Look and Feel Exception");
1415 Console.error(ex.getMessage());
1416 Console.debug(Cache.getStackTraceString(ex));
1421 private static boolean setGtkLookAndFeel()
1423 return setSpecificLookAndFeel("gtk",
1424 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1427 private static boolean setMetalLookAndFeel()
1429 return setSpecificLookAndFeel("metal",
1430 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1433 private static boolean setNimbusLookAndFeel()
1435 return setSpecificLookAndFeel("nimbus",
1436 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1439 private static boolean setFlatLookAndFeel()
1441 boolean set = false;
1442 if (SystemInfo.isMacOS)
1446 UIManager.setLookAndFeel(
1447 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1449 Console.debug("Using FlatMacLightLaf");
1450 } catch (ClassNotFoundException | InstantiationException
1451 | IllegalAccessException | UnsupportedLookAndFeelException e)
1453 Console.debug("Exception loading FlatLightLaf", e);
1455 System.setProperty("apple.laf.useScreenMenuBar", "true");
1456 System.setProperty("apple.awt.application.name",
1457 ChannelProperties.getProperty("app_name"));
1458 System.setProperty("apple.awt.application.appearance", "system");
1459 if (SystemInfo.isMacFullWindowContentSupported
1460 && Desktop.desktop != null)
1462 Console.debug("Setting transparent title bar");
1463 Desktop.desktop.getRootPane()
1464 .putClientProperty("apple.awt.fullWindowContent", true);
1465 Desktop.desktop.getRootPane()
1466 .putClientProperty("apple.awt.transparentTitleBar", true);
1467 Desktop.desktop.getRootPane()
1468 .putClientProperty("apple.awt.fullscreenable", true);
1470 SwingUtilities.invokeLater(() -> {
1471 FlatMacLightLaf.setup();
1473 Console.debug("Using FlatMacLightLaf");
1480 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1482 Console.debug("Using FlatLightLaf");
1483 } catch (ClassNotFoundException | InstantiationException
1484 | IllegalAccessException | UnsupportedLookAndFeelException e)
1486 Console.debug("Exception loading FlatLightLaf", e);
1488 // Windows specific properties here
1489 SwingUtilities.invokeLater(() -> {
1490 FlatLightLaf.setup();
1492 Console.debug("Using FlatLightLaf");
1495 else if (SystemInfo.isLinux)
1499 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1501 Console.debug("Using FlatLightLaf");
1502 } catch (ClassNotFoundException | InstantiationException
1503 | IllegalAccessException | UnsupportedLookAndFeelException e)
1505 Console.debug("Exception loading FlatLightLaf", e);
1507 // enable custom window decorations
1508 JFrame.setDefaultLookAndFeelDecorated(true);
1509 JDialog.setDefaultLookAndFeelDecorated(true);
1510 SwingUtilities.invokeLater(() -> {
1511 FlatLightLaf.setup();
1513 Console.debug("Using FlatLightLaf");
1521 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1523 Console.debug("Using FlatLightLaf");
1524 } catch (ClassNotFoundException | InstantiationException
1525 | IllegalAccessException | UnsupportedLookAndFeelException e)
1527 Console.debug("Exception loading FlatLightLaf", e);
1533 UIManager.put("TabbedPane.tabType", "card");
1534 UIManager.put("TabbedPane.showTabSeparators", true);
1535 UIManager.put("TabbedPane.showContentSeparator", true);
1536 // UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1537 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1538 UIManager.put("TabbedPane.hasFullBorder", true);
1539 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1540 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1541 UIManager.put("TabbedPane.smoothScrolling", true);
1542 UIManager.put("TabbedPane.tabWidthMode", "compact");
1543 UIManager.put("TabbedPane.selectedBackground", Color.white);
1544 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1545 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1548 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1552 private static boolean setMacLookAndFeel()
1554 boolean set = false;
1555 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1556 ChannelProperties.getProperty("app_name"));
1557 System.setProperty("apple.laf.useScreenMenuBar", "true");
1559 * broken native LAFs on (ARM?) macbooks
1560 set = setQuaquaLookAndFeel();
1561 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1562 .toLowerCase(Locale.ROOT).contains("quaqua"))
1564 set = setVaquaLookAndFeel();
1567 set = setFlatLookAndFeel();
1571 private static boolean setLinuxLookAndFeel()
1573 boolean set = false;
1574 set = setFlatLookAndFeel();
1576 set = setMetalLookAndFeel();
1577 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1579 set = setNimbusLookAndFeel();
1584 private static void showUsage()
1586 jalview.bin.Console.outPrintln(
1587 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1588 + "-nodisplay\tRun Jalview without User Interface.\n"
1589 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1590 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1591 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1592 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1593 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1594 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1595 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1596 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1597 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1598 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1599 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1600 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1601 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1602 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1603 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1604 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1605 + "-html FILE\tCreate HTML file from alignment.\n"
1606 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1607 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1608 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1609 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1610 + "-noquestionnaire\tTurn off questionnaire check.\n"
1611 + "-nonews\tTurn off check for Jalview news.\n"
1612 + "-nousagestats\tTurn off analytics tracking for this session.\n"
1613 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1615 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1616 // after all other properties files have been read\n\t
1617 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1618 // passed in correctly)"
1619 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1620 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1621 + "-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"
1622 + "-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"
1623 + "-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"
1624 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1628 private static void startUsageStats(final Desktop desktop)
1631 * start a User Config prompt asking if we can log usage statistics.
1633 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1635 MessageManager.getString("prompt.analytics_title"),
1636 MessageManager.getString("prompt.analytics"),
1642 Console.debug("Initialising analytics for usage stats.");
1643 Cache.initAnalytics();
1644 Console.debug("Tracking enabled.");
1651 Console.debug("Not enabling analytics.");
1654 desktop.addDialogThread(prompter);
1658 * Locate the given string as a file and pass it to the groovy interpreter.
1660 * @param groovyscript
1661 * the script to execute
1662 * @param jalviewContext
1663 * the Jalview Desktop object passed in to the groovy binding as the
1666 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1669 * for scripts contained in files
1676 if (groovyscript.trim().equals("STDIN"))
1678 // read from stdin into a tempfile and execute it
1681 tfile = File.createTempFile("jalview", "groovy");
1682 PrintWriter outfile = new PrintWriter(
1683 new OutputStreamWriter(new FileOutputStream(tfile)));
1684 BufferedReader br = new BufferedReader(
1685 new InputStreamReader(System.in));
1687 while ((line = br.readLine()) != null)
1689 outfile.write(line + "\n");
1695 } catch (Exception ex)
1698 .errPrintln("Failed to read from STDIN into tempfile "
1699 + ((tfile == null) ? "(tempfile wasn't created)"
1700 : tfile.toString()));
1701 ex.printStackTrace();
1706 sfile = tfile.toURI().toURL();
1707 } catch (Exception x)
1709 jalview.bin.Console.errPrintln(
1710 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1712 x.printStackTrace();
1720 sfile = new URI(groovyscript).toURL();
1721 } catch (Exception x)
1723 tfile = new File(groovyscript);
1724 if (!tfile.exists())
1726 jalview.bin.Console.errPrintln(
1727 "File '" + groovyscript + "' does not exist.");
1730 if (!tfile.canRead())
1732 jalview.bin.Console.errPrintln(
1733 "File '" + groovyscript + "' cannot be read.");
1736 if (tfile.length() < 1)
1739 .errPrintln("File '" + groovyscript + "' is empty.");
1744 sfile = tfile.getAbsoluteFile().toURI().toURL();
1745 } catch (Exception ex)
1747 jalview.bin.Console.errPrintln("Failed to create a file URL for "
1748 + tfile.getAbsoluteFile());
1755 Map<String, java.lang.Object> vbinding = new HashMap<>();
1756 vbinding.put("Jalview", this);
1759 vbinding.put("currentAlFrame", af);
1761 Binding gbinding = new Binding(vbinding);
1762 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1763 gse.run(sfile.toString(), gbinding);
1764 if ("STDIN".equals(groovyscript))
1766 // delete temp file that we made -
1767 // only if it was successfully executed
1770 } catch (Exception e)
1773 .errPrintln("Exception Whilst trying to execute file " + sfile
1774 + " as a groovy script.");
1775 e.printStackTrace(System.err);
1780 public static boolean isHeadlessMode()
1782 String isheadless = System.getProperty("java.awt.headless");
1783 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1790 public AlignFrame[] getAlignFrames()
1792 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1793 : Desktop.getAlignFrames();
1798 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1802 // System.exit will run the shutdownHook first
1803 Jalview.exit("Quitting now. Bye!", ExitCode.OK);
1806 public static AlignFrame getCurrentAlignFrame()
1808 return Jalview.currentAlignFrame;
1811 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1813 Jalview.currentAlignFrame = currentAlignFrame;
1816 public Commands getCommands()
1821 public static void exit(String message, ExitCode ec)
1823 int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1;
1824 if (Console.log == null)
1826 // Don't start the logger just to exit!
1827 if (message != null)
1831 Console.outPrintln(message);
1835 jalview.bin.Console.errPrintln(message);
1841 Console.debug("Using Jalview.exit");
1842 if (message != null)
1846 Console.info(message);
1850 Console.error(message);
1856 System.exit(exitcode);
1860 public enum ExitCode
1862 // only add new ones to the end of the list (to preserve ordinal values)
1863 OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
1864 INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
1865 ERROR_RUNNING_COMMANDS;
1868 /******************************
1870 * TEST OUTPUT METHODS
1872 * these operate only when Arg.TESTOUTPUT has been passed, and variously check
1873 * if an expected value / arg was set and report it to the test framework.
1875 ******************************/
1877 * report string values parsed/processed during tests When the Bootstrap
1878 * argument Arg.TESTOUTPUT is present - reports on debug if given s1 is not
1879 * null and not equals s2, warns if given argument is not set, and calls
1880 * testoutput(true,a,s1,s2) to report processing progress.
1883 * - ArgParser handling parsing
1885 * - Arg currently being processed
1890 protected static void testoutput(ArgParser ap, Arg a, String s1,
1893 BootstrapArgs bsa = ap.getBootstrapArgs();
1894 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1896 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1898 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1899 + s2 + "' for arg " + a.argString());
1902 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1906 Console.warn("Arg '" + a.getName() + "' not set at all");
1909 testoutput(true, a, s1, s2);
1913 * report values passed via bootstrap arguments
1915 * TODO: significant code duplication with testouput(Argparser...) - move it
1918 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1921 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1923 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1925 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1926 + s2 + "' for arg " + a.argString());
1929 if (!a.hasOption(Opt.BOOTSTRAP))
1931 Console.error("Non-bootstrap Arg '" + a.getName()
1932 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1934 if (!bsa.contains(a))
1936 Console.warn("Arg '" + a.getName() + "' not set at all");
1939 testoutput(true, a, s1, s2);
1943 * conditionally (on @param yes) report that expected value s1 was set during
1944 * CommandsTest tests
1946 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1948 if (yes && ((s1 == null && s2 == null)
1949 || (s1 != null && s1.equals(s2))))
1951 Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1957 * testoutput for boolean and unary values
1959 protected static void testoutput(ArgParser ap, Arg a)
1963 BootstrapArgs bsa = ap.getBootstrapArgs();
1966 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1968 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1970 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1974 Console.warn("Arg '" + a.getName() + "' not set at all");
1980 protected static void testoutput(BootstrapArgs bsa, Arg a)
1982 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1984 if (!a.hasOption(Opt.BOOTSTRAP))
1986 Console.warn("Non-bootstrap Arg '" + a.getName()
1987 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1990 if (!bsa.contains(a))
1992 Console.warn("Arg '" + a.getName() + "' not set at all");
1995 testoutput(bsa.getBoolean(a), a);
1998 private static void testoutput(boolean yes, Arg a)
2000 String message = null;
2001 if (a.hasOption(Opt.BOOLEAN))
2003 message = (yes ? a.argString() : a.negateArgString()) + " was set";
2005 else if (a.hasOption(Opt.UNARY))
2007 message = a.argString() + (yes ? " was set" : " was not set");
2009 Console.outPrintln("[TESTOUTPUT] arg " + message);
2012 public ArgParser getArgParser()
2017 public BootstrapArgs getBootstrapArgs()
2019 return bootstrapArgs;
2022 public static boolean isBatchMode()
2024 return getInstance() != null && (getInstance().desktop == null
2025 || getInstance().desktop.isInBatchMode());
2029 * Warning about old or mixed command line arguments
2031 private void mixedCliWarning()
2033 Jalview j = Jalview.getInstance();
2034 boolean mixedStyle = j.getArgParser() != null
2035 && j.getArgParser().isMixedStyle();
2036 String title = MessageManager.getString("label.command_line_arguments");
2039 String warning = MessageManager.formatMessage(
2040 "warning.using_mixed_command_line_arguments",
2041 j.getArgParser().getMixedExamples());
2042 String quit = MessageManager.getString("action.quit");
2044 Desktop.instance.nonBlockingDialog(title, warning, quit,
2045 JvOptionPane.WARNING_MESSAGE, false, true);
2048 "Exiting due to mixed old and new command line arguments.",
2049 ExitCode.MIXED_CLI_ARGUMENTS);
2053 private void cliWarning()
2055 Jalview j = Jalview.getInstance();
2056 Commands c = j.getCommands();
2057 boolean oldStyle = j.getArgParser() != null
2058 && j.getArgParser().isOldStyle();
2059 String title = MessageManager.getString("label.command_line_arguments");
2062 String warning = MessageManager
2063 .getString("warning.using_old_command_line_arguments");
2064 String url = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
2065 if (Desktop.instance != null)
2067 String cont = MessageManager.getString("label.continue");
2069 Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
2070 JvOptionPane.WARNING_MESSAGE, false, true, true);
2073 if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
2075 if (Desktop.instance != null)
2077 String message = MessageManager
2078 .getString("warning.the_following_errors");
2079 String ok = MessageManager.getString("action.ok");
2081 List<String> errors = j.getCommands().getErrors();
2082 for (int i = 0; i < errors.size(); i++)
2084 shortest = Math.min(shortest, errors.get(i).length());
2086 Desktop.instance.nonBlockingDialog(
2087 Math.max(message.length(), Math.min(60, shortest)),
2088 Math.min(errors.size(), 20), title, message,
2089 j.getCommands().errorsToString(), ok,
2090 JvOptionPane.WARNING_MESSAGE, true, false, true);