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 boolean commandsSuccess = false;
841 if (!(argparser.isMixedStyle() || argparser.isOldStyle()))
843 cmds = new Commands(argparser, headlessArg);
845 commandsSuccess = cmds.argsWereParsed();
851 if (argparser.getBoolean(Arg.NOQUIT))
853 Console.warn("Completed " + Arg.HEADLESS.getName()
854 + " commands, but " + Arg.NOQUIT
855 + " is set so not quitting!");
859 Jalview.exit("Successfully completed commands in headless mode",
863 Console.info("Successfully completed commands");
869 Jalview.exit("Error when running Commands in headless mode",
870 ExitCode.ERROR_RUNNING_COMMANDS);
872 Console.warn("Error when running commands");
876 // Check if JVM and compile version might cause problems and log if it
878 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
880 Console.warn("The Java version being used (Java "
881 + LaunchUtils.getJavaVersion()
882 + ") may lead to problems. This installation of Jalview should be used with Java "
883 + LaunchUtils.getJavaCompileVersion() + ".");
886 String file = null, data = null;
888 FileFormatI format = null;
890 DataSourceType protocol = null;
892 FileLoader fileLoader = new FileLoader(!headless);
894 String groovyscript = null; // script to execute after all loading is
895 // completed one way or another
896 // extract groovy argument and execute if necessary
897 groovyscript = aparser.getValue("groovy", true);
898 file = aparser.getValue("open", true);
900 if (file == null && desktop == null && !commandsSuccess)
902 Jalview.exit("No files to open!", ExitCode.NO_FILES);
906 // Finally, deal with the remaining input data.
911 desktop.setProgressBar(
913 .getString("status.processing_commandline_args"),
914 progress = System.currentTimeMillis());
916 Console.outPrintln("CMD [-open " + file + "] executed successfully!");
918 if (!Platform.isJS())
920 * ignore in JavaScript -- can't just file existence - could load it?
925 if (!HttpUtils.startsWithHttpOrHttps(file))
927 if (!(new File(file)).exists())
932 "Can't find file '" + file + "' in headless mode",
933 ExitCode.FILE_NOT_FOUND);
935 Console.warn("Can't find file'" + file + "'");
940 protocol = AppletFormatAdapter.checkProtocol(file);
944 format = new IdentifyFile().identify(file, protocol);
945 } catch (FileFormatException e1)
950 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
954 Console.outPrintln("error");
958 setCurrentAlignFrame(af);
959 data = aparser.getValue("colour", true);
962 data.replaceAll("%20", " ");
964 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
965 af.getViewport(), af.getViewport().getAlignment(), data);
970 "CMD [-colour " + data + "] executed successfully!");
975 // Must maintain ability to use the groups flag
976 data = aparser.getValue("groups", true);
979 af.parseFeaturesFile(data,
980 AppletFormatAdapter.checkProtocol(data));
981 // Console.outPrintln("Added " + data);
983 "CMD groups[-" + data + "] executed successfully!");
985 data = aparser.getValue("features", true);
988 af.parseFeaturesFile(data,
989 AppletFormatAdapter.checkProtocol(data));
990 // Console.outPrintln("Added " + data);
992 "CMD [-features " + data + "] executed successfully!");
995 data = aparser.getValue("annotations", true);
998 af.loadJalviewDataFile(data, null, null, null);
999 // Console.outPrintln("Added " + data);
1001 "CMD [-annotations " + data + "] executed successfully!");
1003 // set or clear the sortbytree flag.
1004 if (aparser.contains("sortbytree"))
1006 af.getViewport().setSortByTree(true);
1007 if (af.getViewport().getSortByTree())
1009 Console.outPrintln("CMD [-sortbytree] executed successfully!");
1012 if (aparser.contains("no-annotation"))
1014 af.getViewport().setShowAnnotation(false);
1015 if (!af.getViewport().isShowAnnotation())
1017 Console.outPrintln("CMD no-annotation executed successfully!");
1020 if (aparser.contains("nosortbytree"))
1022 af.getViewport().setSortByTree(false);
1023 if (!af.getViewport().getSortByTree())
1026 "CMD [-nosortbytree] executed successfully!");
1029 data = aparser.getValue("tree", true);
1035 "CMD [-tree " + data + "] executed successfully!");
1036 NewickFile nf = new NewickFile(data,
1037 AppletFormatAdapter.checkProtocol(data));
1039 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1040 } catch (IOException ex)
1042 jalview.bin.Console.errPrintln("Couldn't add tree " + data);
1043 ex.printStackTrace(System.err);
1047 if (groovyscript != null)
1049 // Execute the groovy script after we've done all the rendering stuff
1050 // and before any images or figures are generated.
1051 Console.outPrintln("Executing script " + groovyscript);
1052 executeGroovyScript(groovyscript, af);
1053 Console.outPrintln("CMD groovy[" + groovyscript
1054 + "] executed successfully!");
1055 groovyscript = null;
1057 String imageName = "unnamed.png";
1058 while (aparser.getSize() > 1)
1062 String outputFormat = aparser.nextValue();
1063 file = aparser.nextValue();
1065 if (outputFormat.equalsIgnoreCase("png"))
1067 Console.outPrintln("Creating PNG image: " + file);
1068 af.createPNG(new File(file));
1069 imageName = (new File(file)).getName();
1072 else if (outputFormat.equalsIgnoreCase("svg"))
1074 Console.outPrintln("Creating SVG image: " + file);
1075 File imageFile = new File(file);
1076 imageName = imageFile.getName();
1077 af.createSVG(imageFile);
1080 else if (outputFormat.equalsIgnoreCase("html"))
1082 File imageFile = new File(file);
1083 imageName = imageFile.getName();
1084 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1086 Console.outPrintln("Creating HTML image: " + file);
1087 htmlSVG.exportHTML(file);
1090 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1094 jalview.bin.Console.errPrintln(
1095 "The output html file must not be null");
1100 BioJsHTMLOutput.refreshVersionInfo(
1101 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1102 } catch (URISyntaxException e)
1104 e.printStackTrace();
1106 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1108 "Creating BioJS MSA Viwer HTML file: " + file);
1109 bjs.exportHTML(file);
1112 else if (outputFormat.equalsIgnoreCase("imgMap"))
1114 Console.outPrintln("Creating image map: " + file);
1115 af.createImageMap(new File(file), imageName);
1118 else if (outputFormat.equalsIgnoreCase("eps"))
1120 File outputFile = new File(file);
1122 "Creating EPS file: " + outputFile.getAbsolutePath());
1123 af.createEPS(outputFile);
1127 FileFormatI outFormat = null;
1130 outFormat = FileFormats.getInstance().forName(outputFormat);
1131 } catch (Exception formatP)
1133 Console.outPrintln("Couldn't parse " + outFormat
1134 + " as a valid Jalview format string.");
1136 if (outFormat != null)
1138 if (!outFormat.isWritable())
1141 "This version of Jalview does not support alignment export as "
1146 af.saveAlignment(file, outFormat);
1147 if (af.isSaveAlignmentSuccessful())
1149 Console.outPrintln("Written alignment in "
1150 + outFormat.getName() + " format to " + file);
1154 Console.outPrintln("Error writing file " + file + " in "
1155 + outFormat.getName() + " format!!");
1159 } catch (ImageOutputException ioexc)
1162 "Unexpected error whilst exporting image to " + file);
1163 ioexc.printStackTrace();
1168 while (aparser.getSize() > 0)
1170 Console.outPrintln("Unknown arg: " + aparser.nextValue());
1175 AlignFrame startUpAlframe = null;
1176 // We'll only open the default file if the desktop is visible.
1178 // ////////////////////
1180 if (!Platform.isJS() && !headless && file == null
1181 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1182 && !cmds.commandArgsProvided()
1183 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1184 // don't open the startup file if command line args have been processed
1185 // (&& !Commands.commandArgsProvided())
1192 file = Cache.getDefault("STARTUP_FILE",
1193 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1194 + "/examples/exampleFile_2_7.jvp");
1195 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1197 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1199 file.replace("http:", "https:");
1200 // hardwire upgrade of the startup file
1201 file.replace("_2_3", "_2_7");
1202 file.replace("2_7.jar", "2_7.jvp");
1203 // and remove the stale setting
1204 Cache.removeProperty("STARTUP_FILE");
1207 protocol = AppletFormatAdapter.checkProtocol(file);
1209 if (file.endsWith(".jar"))
1211 format = FileFormat.Jalview;
1217 format = new IdentifyFile().identify(file, protocol);
1218 } catch (FileFormatException e)
1224 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1226 // don't ask to save when quitting if only the startup file has been
1228 Console.debug("Resetting up-to-date flag for startup file");
1229 startUpAlframe.getViewport().setSavedUpToDate(true);
1230 // extract groovy arguments before anything else.
1233 // Once all other stuff is done, execute any groovy scripts (in order)
1234 if (groovyscript != null)
1236 if (Cache.groovyJarsPresent())
1238 Console.outPrintln("Executing script " + groovyscript);
1239 executeGroovyScript(groovyscript, startUpAlframe);
1243 jalview.bin.Console.errPrintln(
1244 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1248 // and finally, turn off batch mode indicator - if the desktop still exists
1249 if (desktop != null)
1253 desktop.setProgressBar(null, progress);
1255 desktop.setInBatchMode(false);
1261 private static void setLookAndFeel()
1263 if (!Platform.isJS())
1270 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1272 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1274 // try Quaqua/Vaqua.
1275 String lafProp = System.getProperty("laf");
1276 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1277 String laf = "none";
1278 if (lafProp != null)
1282 else if (lafSetting != null)
1286 boolean lafSet = false;
1289 case "crossplatform":
1290 lafSet = setCrossPlatformLookAndFeel();
1293 Console.error("Could not set requested laf=" + laf);
1297 lafSet = setSystemLookAndFeel();
1300 Console.error("Could not set requested laf=" + laf);
1304 lafSet = setGtkLookAndFeel();
1307 Console.error("Could not set requested laf=" + laf);
1311 lafSet = setMetalLookAndFeel();
1314 Console.error("Could not set requested laf=" + laf);
1318 lafSet = setNimbusLookAndFeel();
1321 Console.error("Could not set requested laf=" + laf);
1325 lafSet = setFlatLookAndFeel();
1328 Console.error("Could not set requested laf=" + laf);
1332 lafSet = setMacLookAndFeel();
1335 Console.error("Could not set requested laf=" + laf);
1341 Console.error("Requested laf=" + laf + " not implemented");
1345 // Flatlaf default for everyone!
1346 lafSet = setFlatLookAndFeel();
1349 setSystemLookAndFeel();
1351 if (Platform.isLinux())
1353 setLinuxLookAndFeel();
1355 if (Platform.isMac())
1357 setMacLookAndFeel();
1363 private static boolean setCrossPlatformLookAndFeel()
1365 boolean set = false;
1368 UIManager.setLookAndFeel(
1369 UIManager.getCrossPlatformLookAndFeelClassName());
1371 } catch (Exception ex)
1373 Console.error("Unexpected Look and Feel Exception");
1374 Console.error(ex.getMessage());
1375 Console.debug(Cache.getStackTraceString(ex));
1380 private static boolean setSystemLookAndFeel()
1382 boolean set = false;
1385 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1387 } catch (Exception ex)
1389 Console.error("Unexpected Look and Feel Exception");
1390 Console.error(ex.getMessage());
1391 Console.debug(Cache.getStackTraceString(ex));
1396 private static boolean setSpecificLookAndFeel(String name,
1397 String className, boolean nameStartsWith)
1399 boolean set = false;
1402 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1404 if (info.getName() != null && nameStartsWith
1405 ? info.getName().toLowerCase(Locale.ROOT)
1406 .startsWith(name.toLowerCase(Locale.ROOT))
1407 : info.getName().toLowerCase(Locale.ROOT)
1408 .equals(name.toLowerCase(Locale.ROOT)))
1410 className = info.getClassName();
1414 UIManager.setLookAndFeel(className);
1416 } catch (Exception ex)
1418 Console.error("Unexpected Look and Feel Exception");
1419 Console.error(ex.getMessage());
1420 Console.debug(Cache.getStackTraceString(ex));
1425 private static boolean setGtkLookAndFeel()
1427 return setSpecificLookAndFeel("gtk",
1428 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1431 private static boolean setMetalLookAndFeel()
1433 return setSpecificLookAndFeel("metal",
1434 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1437 private static boolean setNimbusLookAndFeel()
1439 return setSpecificLookAndFeel("nimbus",
1440 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1443 private static boolean setFlatLookAndFeel()
1445 boolean set = false;
1446 if (SystemInfo.isMacOS)
1450 UIManager.setLookAndFeel(
1451 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1453 Console.debug("Using FlatMacLightLaf");
1454 } catch (ClassNotFoundException | InstantiationException
1455 | IllegalAccessException | UnsupportedLookAndFeelException e)
1457 Console.debug("Exception loading FlatLightLaf", e);
1459 System.setProperty("apple.laf.useScreenMenuBar", "true");
1460 System.setProperty("apple.awt.application.name",
1461 ChannelProperties.getProperty("app_name"));
1462 System.setProperty("apple.awt.application.appearance", "system");
1463 if (SystemInfo.isMacFullWindowContentSupported
1464 && Desktop.desktop != null)
1466 Console.debug("Setting transparent title bar");
1467 Desktop.desktop.getRootPane()
1468 .putClientProperty("apple.awt.fullWindowContent", true);
1469 Desktop.desktop.getRootPane()
1470 .putClientProperty("apple.awt.transparentTitleBar", true);
1471 Desktop.desktop.getRootPane()
1472 .putClientProperty("apple.awt.fullscreenable", true);
1474 SwingUtilities.invokeLater(() -> {
1475 FlatMacLightLaf.setup();
1477 Console.debug("Using FlatMacLightLaf");
1484 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1486 Console.debug("Using FlatLightLaf");
1487 } catch (ClassNotFoundException | InstantiationException
1488 | IllegalAccessException | UnsupportedLookAndFeelException e)
1490 Console.debug("Exception loading FlatLightLaf", e);
1492 // Windows specific properties here
1493 SwingUtilities.invokeLater(() -> {
1494 FlatLightLaf.setup();
1496 Console.debug("Using FlatLightLaf");
1499 else if (SystemInfo.isLinux)
1503 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1505 Console.debug("Using FlatLightLaf");
1506 } catch (ClassNotFoundException | InstantiationException
1507 | IllegalAccessException | UnsupportedLookAndFeelException e)
1509 Console.debug("Exception loading FlatLightLaf", e);
1511 // enable custom window decorations
1512 JFrame.setDefaultLookAndFeelDecorated(true);
1513 JDialog.setDefaultLookAndFeelDecorated(true);
1514 SwingUtilities.invokeLater(() -> {
1515 FlatLightLaf.setup();
1517 Console.debug("Using FlatLightLaf");
1525 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1527 Console.debug("Using FlatLightLaf");
1528 } catch (ClassNotFoundException | InstantiationException
1529 | IllegalAccessException | UnsupportedLookAndFeelException e)
1531 Console.debug("Exception loading FlatLightLaf", e);
1537 UIManager.put("TabbedPane.tabType", "card");
1538 UIManager.put("TabbedPane.showTabSeparators", true);
1539 UIManager.put("TabbedPane.showContentSeparator", true);
1540 // UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1541 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1542 UIManager.put("TabbedPane.hasFullBorder", true);
1543 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1544 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1545 UIManager.put("TabbedPane.smoothScrolling", true);
1546 UIManager.put("TabbedPane.tabWidthMode", "compact");
1547 UIManager.put("TabbedPane.selectedBackground", Color.white);
1548 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1549 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1552 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1556 private static boolean setMacLookAndFeel()
1558 boolean set = false;
1559 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1560 ChannelProperties.getProperty("app_name"));
1561 System.setProperty("apple.laf.useScreenMenuBar", "true");
1563 * broken native LAFs on (ARM?) macbooks
1564 set = setQuaquaLookAndFeel();
1565 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1566 .toLowerCase(Locale.ROOT).contains("quaqua"))
1568 set = setVaquaLookAndFeel();
1571 set = setFlatLookAndFeel();
1575 private static boolean setLinuxLookAndFeel()
1577 boolean set = false;
1578 set = setFlatLookAndFeel();
1580 set = setMetalLookAndFeel();
1581 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1583 set = setNimbusLookAndFeel();
1588 private static void showUsage()
1590 jalview.bin.Console.outPrintln(
1591 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1592 + "-nodisplay\tRun Jalview without User Interface.\n"
1593 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1594 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1595 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1596 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1597 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1598 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1599 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1600 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1601 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1602 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1603 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1604 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1605 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1606 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1607 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1608 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1609 + "-html FILE\tCreate HTML file from alignment.\n"
1610 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1611 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1612 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1613 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1614 + "-noquestionnaire\tTurn off questionnaire check.\n"
1615 + "-nonews\tTurn off check for Jalview news.\n"
1616 + "-nousagestats\tTurn off analytics tracking for this session.\n"
1617 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1619 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1620 // after all other properties files have been read\n\t
1621 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1622 // passed in correctly)"
1623 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1624 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1625 + "-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"
1626 + "-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"
1627 + "-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"
1628 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1632 private static void startUsageStats(final Desktop desktop)
1635 * start a User Config prompt asking if we can log usage statistics.
1637 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1639 MessageManager.getString("prompt.analytics_title"),
1640 MessageManager.getString("prompt.analytics"), new Runnable()
1645 Console.debug("Initialising analytics for usage stats.");
1646 Cache.initAnalytics();
1647 Console.debug("Tracking enabled.");
1654 Console.debug("Not enabling analytics.");
1657 desktop.addDialogThread(prompter);
1661 * Locate the given string as a file and pass it to the groovy interpreter.
1663 * @param groovyscript
1664 * the script to execute
1665 * @param jalviewContext
1666 * the Jalview Desktop object passed in to the groovy binding as the
1669 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1672 * for scripts contained in files
1679 if (groovyscript.trim().equals("STDIN"))
1681 // read from stdin into a tempfile and execute it
1684 tfile = File.createTempFile("jalview", "groovy");
1685 PrintWriter outfile = new PrintWriter(
1686 new OutputStreamWriter(new FileOutputStream(tfile)));
1687 BufferedReader br = new BufferedReader(
1688 new InputStreamReader(System.in));
1690 while ((line = br.readLine()) != null)
1692 outfile.write(line + "\n");
1698 } catch (Exception ex)
1701 .errPrintln("Failed to read from STDIN into tempfile "
1702 + ((tfile == null) ? "(tempfile wasn't created)"
1703 : tfile.toString()));
1704 ex.printStackTrace();
1709 sfile = tfile.toURI().toURL();
1710 } catch (Exception x)
1712 jalview.bin.Console.errPrintln(
1713 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1715 x.printStackTrace();
1723 sfile = new URI(groovyscript).toURL();
1724 } catch (Exception x)
1726 tfile = new File(groovyscript);
1727 if (!tfile.exists())
1729 jalview.bin.Console.errPrintln(
1730 "File '" + groovyscript + "' does not exist.");
1733 if (!tfile.canRead())
1735 jalview.bin.Console.errPrintln(
1736 "File '" + groovyscript + "' cannot be read.");
1739 if (tfile.length() < 1)
1742 .errPrintln("File '" + groovyscript + "' is empty.");
1747 sfile = tfile.getAbsoluteFile().toURI().toURL();
1748 } catch (Exception ex)
1750 jalview.bin.Console.errPrintln("Failed to create a file URL for "
1751 + tfile.getAbsoluteFile());
1758 Map<String, java.lang.Object> vbinding = new HashMap<>();
1759 vbinding.put("Jalview", this);
1762 vbinding.put("currentAlFrame", af);
1764 Binding gbinding = new Binding(vbinding);
1765 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1766 gse.run(sfile.toString(), gbinding);
1767 if ("STDIN".equals(groovyscript))
1769 // delete temp file that we made -
1770 // only if it was successfully executed
1773 } catch (Exception e)
1776 .errPrintln("Exception Whilst trying to execute file " + sfile
1777 + " as a groovy script.");
1778 e.printStackTrace(System.err);
1783 public static boolean isHeadlessMode()
1785 String isheadless = System.getProperty("java.awt.headless");
1786 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1793 public AlignFrame[] getAlignFrames()
1795 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1796 : Desktop.getAlignFrames();
1801 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1805 // System.exit will run the shutdownHook first
1806 Jalview.exit("Quitting now. Bye!", ExitCode.OK);
1809 public static AlignFrame getCurrentAlignFrame()
1811 return Jalview.currentAlignFrame;
1814 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1816 Jalview.currentAlignFrame = currentAlignFrame;
1819 public Commands getCommands()
1824 public static void exit(String message, ExitCode ec)
1826 int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1;
1827 if (Console.log == null)
1829 // Don't start the logger just to exit!
1830 if (message != null)
1834 Console.outPrintln(message);
1838 jalview.bin.Console.errPrintln(message);
1844 Console.debug("Using Jalview.exit");
1845 if (message != null)
1849 Console.info(message);
1853 Console.error(message);
1859 System.exit(exitcode);
1863 public enum ExitCode
1865 // only add new ones to the end of the list (to preserve ordinal values)
1866 OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
1867 INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
1868 ERROR_RUNNING_COMMANDS;
1871 /******************************
1873 * TEST OUTPUT METHODS
1875 * these operate only when Arg.TESTOUTPUT has been passed, and variously check
1876 * if an expected value / arg was set and report it to the test framework.
1878 ******************************/
1880 * report string values parsed/processed during tests When the Bootstrap
1881 * argument Arg.TESTOUTPUT is present - reports on debug if given s1 is not
1882 * null and not equals s2, warns if given argument is not set, and calls
1883 * testoutput(true,a,s1,s2) to report processing progress.
1886 * - ArgParser handling parsing
1888 * - Arg currently being processed
1893 protected static void testoutput(ArgParser ap, Arg a, String s1,
1896 BootstrapArgs bsa = ap.getBootstrapArgs();
1897 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1899 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1901 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1902 + s2 + "' for arg " + a.argString());
1905 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1909 Console.warn("Arg '" + a.getName() + "' not set at all");
1912 testoutput(true, a, s1, s2);
1916 * report values passed via bootstrap arguments
1918 * TODO: significant code duplication with testouput(Argparser...) - move it
1921 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1924 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1926 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1928 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1929 + s2 + "' for arg " + a.argString());
1932 if (!a.hasOption(Opt.BOOTSTRAP))
1934 Console.error("Non-bootstrap Arg '" + a.getName()
1935 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1937 if (!bsa.contains(a))
1939 Console.warn("Arg '" + a.getName() + "' not set at all");
1942 testoutput(true, a, s1, s2);
1946 * conditionally (on @param yes) report that expected value s1 was set during
1947 * CommandsTest tests
1949 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1951 if (yes && ((s1 == null && s2 == null)
1952 || (s1 != null && s1.equals(s2))))
1954 Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1960 * testoutput for boolean and unary values
1962 protected static void testoutput(ArgParser ap, Arg a)
1966 BootstrapArgs bsa = ap.getBootstrapArgs();
1969 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1971 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1973 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1977 Console.warn("Arg '" + a.getName() + "' not set at all");
1983 protected static void testoutput(BootstrapArgs bsa, Arg a)
1985 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1987 if (!a.hasOption(Opt.BOOTSTRAP))
1989 Console.warn("Non-bootstrap Arg '" + a.getName()
1990 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1993 if (!bsa.contains(a))
1995 Console.warn("Arg '" + a.getName() + "' not set at all");
1998 testoutput(bsa.getBoolean(a), a);
2001 private static void testoutput(boolean yes, Arg a)
2003 String message = null;
2004 if (a.hasOption(Opt.BOOLEAN))
2006 message = (yes ? a.argString() : a.negateArgString()) + " was set";
2008 else if (a.hasOption(Opt.UNARY))
2010 message = a.argString() + (yes ? " was set" : " was not set");
2012 Console.outPrintln("[TESTOUTPUT] arg " + message);
2015 public ArgParser getArgParser()
2020 public BootstrapArgs getBootstrapArgs()
2022 return bootstrapArgs;
2025 public static boolean isBatchMode()
2027 return getInstance() != null && (getInstance().desktop == null
2028 || getInstance().desktop.isInBatchMode());
2032 * Warning about old or mixed command line arguments
2034 private void mixedCliWarning()
2036 Jalview j = Jalview.getInstance();
2037 boolean mixedStyle = j.getArgParser() != null
2038 && j.getArgParser().isMixedStyle();
2039 String title = MessageManager.getString("label.command_line_arguments");
2042 String warning = MessageManager.formatMessage(
2043 "warning.using_mixed_command_line_arguments",
2044 j.getArgParser().getMixedExamples());
2045 String quit = MessageManager.getString("action.quit");
2047 Desktop.instance.nonBlockingDialog(title, warning, quit,
2048 JvOptionPane.WARNING_MESSAGE, false, true);
2051 "Exiting due to mixed old and new command line arguments.",
2052 ExitCode.MIXED_CLI_ARGUMENTS);
2056 private void cliWarning()
2058 Jalview j = Jalview.getInstance();
2059 Commands c = j.getCommands();
2060 boolean oldStyle = j.getArgParser() != null
2061 && j.getArgParser().isOldStyle();
2062 String title = MessageManager.getString("label.command_line_arguments");
2065 String warning = MessageManager
2066 .getString("warning.using_old_command_line_arguments");
2067 String url = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
2068 if (Desktop.instance != null)
2070 String cont = MessageManager.getString("label.continue");
2072 Desktop.instance.nonBlockingDialog(32, 2, title, warning, url, cont,
2073 JvOptionPane.WARNING_MESSAGE, false, true, true);
2076 if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
2078 if (Desktop.instance != null)
2080 String message = MessageManager
2081 .getString("warning.the_following_errors");
2082 String ok = MessageManager.getString("action.ok");
2084 List<String> errors = j.getCommands().getErrors();
2085 for (int i = 0; i < errors.size(); i++)
2087 shortest = Math.min(shortest, errors.get(i).length());
2089 Desktop.instance.nonBlockingDialog(
2090 Math.max(message.length(), Math.min(60, shortest)),
2091 Math.min(errors.size(), 20), title, message,
2092 j.getCommands().errorsToString(), ok,
2093 JvOptionPane.WARNING_MESSAGE, true, false, true);