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();
645 } catch (NoClassDefFoundError error)
647 error.printStackTrace();
648 String message = "\nEssential logging libraries not found."
649 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
650 Jalview.exit(message, ExitCode.NO_LOGGING);
654 if (!(headless || headlessArg))
658 * configure 'full' SO model if preferences say to, else use the default (full SO)
659 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
661 boolean soDefault = !Platform.isJS();
662 if (Cache.getDefault("USE_FULL_SO", soDefault))
664 SequenceOntologyFactory.setInstance(new SequenceOntology());
667 if (!(headless || headlessArg))
669 Desktop.nosplash = "false".equals(bootstrapArgs.getValue(Arg.SPLASH))
670 || aparser.contains("nosplash")
671 || Cache.getDefault("SPLASH", "true").equals("false");
672 desktop = new Desktop();
673 desktop.setInBatchMode(true); // indicate we are starting up
679 JalviewTaskbar.setTaskbar(this);
680 } catch (Exception e)
682 Console.info("Cannot set Taskbar");
683 Console.error(e.getMessage());
684 // e.printStackTrace();
685 } catch (Throwable t)
687 Console.info("Cannot set Taskbar");
688 Console.error(t.getMessage());
689 // t.printStackTrace();
692 // set Proxy settings before all the internet calls
693 Cache.setProxyPropertiesFromPreferences();
695 desktop.setVisible(true);
697 if (!Platform.isJS())
706 * Check to see that the JVM version being run is suitable for the Java
707 * version this Jalview was compiled for. Popup a warning if not.
709 if (!LaunchUtils.checkJavaVersion())
711 Console.warn("The Java version being used (Java "
712 + LaunchUtils.getJavaVersion()
713 + ") may lead to problems. This installation of Jalview should be used with Java "
714 + LaunchUtils.getJavaCompileVersion() + ".");
717 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
720 MessageManager.getString("label.continue") };
721 JOptionPane.showOptionDialog(null,
722 MessageManager.formatMessage(
723 "warning.wrong_jvm_version_message",
724 LaunchUtils.getJavaVersion(),
725 LaunchUtils.getJavaCompileVersion()),
727 .getString("warning.wrong_jvm_version_title"),
728 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
729 null, options, options[0]);
733 boolean webservicediscovery = bootstrapArgs
734 .getBoolean(Arg.WEBSERVICEDISCOVERY);
735 if (aparser.contains("nowebservicediscovery"))
736 webservicediscovery = false;
737 if (webservicediscovery)
739 desktop.startServiceDiscovery();
743 testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
746 boolean usagestats = !bootstrapArgs.getBoolean(Arg.NOUSAGESTATS);
747 if (aparser.contains("nousagestats"))
751 startUsageStats(desktop);
752 testoutput(argparser, Arg.NOUSAGESTATS);
756 Console.outPrintln("CMD [-nousagestats] executed successfully!");
757 testoutput(argparser, Arg.NOUSAGESTATS);
760 boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
761 if (aparser.contains("noquestionnaire"))
762 questionnaire = false;
765 String url = aparser.getValue("questionnaire");
768 // Start the desktop questionnaire prompter with the specified
770 Console.debug("Starting questionnaire url at " + url);
771 desktop.checkForQuestionnaire(url);
772 Console.outPrintln("CMD questionnaire[-" + url
773 + "] executed successfully!");
777 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
779 // Start the desktop questionnaire prompter with the specified
782 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
784 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
786 "Starting questionnaire with default url: " + defurl);
787 desktop.checkForQuestionnaire(defurl);
794 "CMD [-noquestionnaire] executed successfully!");
795 testoutput(argparser, Arg.QUESTIONNAIRE);
798 if ((!aparser.contains("nonews")
799 && Cache.getProperty("NONEWS") == null
800 && !"false".equals(bootstrapArgs.getValue(Arg.NEWS)))
801 || "true".equals(bootstrapArgs.getValue(Arg.NEWS)))
803 desktop.checkForNews();
806 if (!aparser.contains("nohtmltemplates")
807 && Cache.getProperty("NOHTMLTEMPLATES") == null)
809 BioJsHTMLOutput.updateBioJS();
816 if (getArgParser().isMixedStyle())
818 String warning = MessageManager.formatMessage(
819 "warning.using_mixed_command_line_arguments",
820 getArgParser().getMixedExamples());
821 Console.warn(warning);
823 "Exiting due to mixed old and new command line arguments",
824 ExitCode.INVALID_ARGUMENT);
826 if (getArgParser().isOldStyle())
828 String warning = MessageManager
829 .getString("warning.using_old_command_line_arguments")
831 + "https://www.jalview.org/help/html/features/commandline.html";
832 Console.warn(warning);
837 // Run Commands from cli
838 cmds = new Commands(argparser, headlessArg);
840 boolean commandsSuccess = cmds.argsWereParsed();
846 if (argparser.getBoolean(Arg.NOQUIT))
849 "Completed " + Arg.HEADLESS.getName() + " commands, but "
850 + Arg.NOQUIT + " is set so not quitting!");
854 Jalview.exit("Successfully completed commands in headless mode",
858 Console.info("Successfully completed commands");
864 Jalview.exit("Error when running Commands in headless mode",
865 ExitCode.ERROR_RUNNING_COMMANDS);
867 Console.warn("Error when running commands");
870 // Check if JVM and compile version might cause problems and log if it
872 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
874 Console.warn("The Java version being used (Java "
875 + LaunchUtils.getJavaVersion()
876 + ") may lead to problems. This installation of Jalview should be used with Java "
877 + LaunchUtils.getJavaCompileVersion() + ".");
880 String file = null, data = null;
882 FileFormatI format = null;
884 DataSourceType protocol = null;
886 FileLoader fileLoader = new FileLoader(!headless);
888 String groovyscript = null; // script to execute after all loading is
889 // completed one way or another
890 // extract groovy argument and execute if necessary
891 groovyscript = aparser.getValue("groovy", true);
892 file = aparser.getValue("open", true);
894 if (file == null && desktop == null && !commandsSuccess)
896 Jalview.exit("No files to open!", ExitCode.NO_FILES);
900 // Finally, deal with the remaining input data.
905 desktop.setProgressBar(
907 .getString("status.processing_commandline_args"),
908 progress = System.currentTimeMillis());
910 Console.outPrintln("CMD [-open " + file + "] executed successfully!");
912 if (!Platform.isJS())
914 * ignore in JavaScript -- can't just file existence - could load it?
919 if (!HttpUtils.startsWithHttpOrHttps(file))
921 if (!(new File(file)).exists())
926 "Can't find file '" + file + "' in headless mode",
927 ExitCode.FILE_NOT_FOUND);
929 Console.warn("Can't find file'" + file + "'");
934 protocol = AppletFormatAdapter.checkProtocol(file);
938 format = new IdentifyFile().identify(file, protocol);
939 } catch (FileFormatException e1)
944 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
948 Console.outPrintln("error");
952 setCurrentAlignFrame(af);
953 data = aparser.getValue("colour", true);
956 data.replaceAll("%20", " ");
958 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
959 af.getViewport(), af.getViewport().getAlignment(), data);
964 "CMD [-colour " + data + "] executed successfully!");
969 // Must maintain ability to use the groups flag
970 data = aparser.getValue("groups", true);
973 af.parseFeaturesFile(data,
974 AppletFormatAdapter.checkProtocol(data));
975 // Console.outPrintln("Added " + data);
977 "CMD groups[-" + data + "] executed successfully!");
979 data = aparser.getValue("features", true);
982 af.parseFeaturesFile(data,
983 AppletFormatAdapter.checkProtocol(data));
984 // Console.outPrintln("Added " + data);
986 "CMD [-features " + data + "] executed successfully!");
989 data = aparser.getValue("annotations", true);
992 af.loadJalviewDataFile(data, null, null, null);
993 // Console.outPrintln("Added " + data);
995 "CMD [-annotations " + data + "] executed successfully!");
997 // set or clear the sortbytree flag.
998 if (aparser.contains("sortbytree"))
1000 af.getViewport().setSortByTree(true);
1001 if (af.getViewport().getSortByTree())
1003 Console.outPrintln("CMD [-sortbytree] executed successfully!");
1006 if (aparser.contains("no-annotation"))
1008 af.getViewport().setShowAnnotation(false);
1009 if (!af.getViewport().isShowAnnotation())
1011 Console.outPrintln("CMD no-annotation executed successfully!");
1014 if (aparser.contains("nosortbytree"))
1016 af.getViewport().setSortByTree(false);
1017 if (!af.getViewport().getSortByTree())
1020 "CMD [-nosortbytree] executed successfully!");
1023 data = aparser.getValue("tree", true);
1029 "CMD [-tree " + data + "] executed successfully!");
1030 NewickFile nf = new NewickFile(data,
1031 AppletFormatAdapter.checkProtocol(data));
1033 .setCurrentTree(af.showNewickTree(nf, data).getTree());
1034 } catch (IOException ex)
1036 jalview.bin.Console.errPrintln("Couldn't add tree " + data);
1037 ex.printStackTrace(System.err);
1041 if (groovyscript != null)
1043 // Execute the groovy script after we've done all the rendering stuff
1044 // and before any images or figures are generated.
1045 Console.outPrintln("Executing script " + groovyscript);
1046 executeGroovyScript(groovyscript, af);
1047 Console.outPrintln("CMD groovy[" + groovyscript
1048 + "] executed successfully!");
1049 groovyscript = null;
1051 String imageName = "unnamed.png";
1052 while (aparser.getSize() > 1)
1056 String outputFormat = aparser.nextValue();
1057 file = aparser.nextValue();
1059 if (outputFormat.equalsIgnoreCase("png"))
1061 Console.outPrintln("Creating PNG image: " + file);
1062 af.createPNG(new File(file));
1063 imageName = (new File(file)).getName();
1066 else if (outputFormat.equalsIgnoreCase("svg"))
1068 Console.outPrintln("Creating SVG image: " + file);
1069 File imageFile = new File(file);
1070 imageName = imageFile.getName();
1071 af.createSVG(imageFile);
1074 else if (outputFormat.equalsIgnoreCase("html"))
1076 File imageFile = new File(file);
1077 imageName = imageFile.getName();
1078 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
1080 Console.outPrintln("Creating HTML image: " + file);
1081 htmlSVG.exportHTML(file);
1084 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
1088 jalview.bin.Console.errPrintln(
1089 "The output html file must not be null");
1094 BioJsHTMLOutput.refreshVersionInfo(
1095 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
1096 } catch (URISyntaxException e)
1098 e.printStackTrace();
1100 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
1102 "Creating BioJS MSA Viwer HTML file: " + file);
1103 bjs.exportHTML(file);
1106 else if (outputFormat.equalsIgnoreCase("imgMap"))
1108 Console.outPrintln("Creating image map: " + file);
1109 af.createImageMap(new File(file), imageName);
1112 else if (outputFormat.equalsIgnoreCase("eps"))
1114 File outputFile = new File(file);
1116 "Creating EPS file: " + outputFile.getAbsolutePath());
1117 af.createEPS(outputFile);
1121 FileFormatI outFormat = null;
1124 outFormat = FileFormats.getInstance().forName(outputFormat);
1125 } catch (Exception formatP)
1127 Console.outPrintln("Couldn't parse " + outFormat
1128 + " as a valid Jalview format string.");
1130 if (outFormat != null)
1132 if (!outFormat.isWritable())
1135 "This version of Jalview does not support alignment export as "
1140 af.saveAlignment(file, outFormat);
1141 if (af.isSaveAlignmentSuccessful())
1143 Console.outPrintln("Written alignment in "
1144 + outFormat.getName() + " format to " + file);
1148 Console.outPrintln("Error writing file " + file + " in "
1149 + outFormat.getName() + " format!!");
1153 } catch (ImageOutputException ioexc)
1156 "Unexpected error whilst exporting image to " + file);
1157 ioexc.printStackTrace();
1162 while (aparser.getSize() > 0)
1164 Console.outPrintln("Unknown arg: " + aparser.nextValue());
1169 AlignFrame startUpAlframe = null;
1170 // We'll only open the default file if the desktop is visible.
1172 // ////////////////////
1174 if (!Platform.isJS() && !headless && file == null
1175 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1176 && !cmds.commandArgsProvided()
1177 && !bootstrapArgs.getBoolean(Arg.NOSTARTUPFILE))
1178 // don't open the startup file if command line args have been processed
1179 // (&& !Commands.commandArgsProvided())
1186 file = Cache.getDefault("STARTUP_FILE",
1187 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1188 + "/examples/exampleFile_2_7.jvp");
1189 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1191 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1193 file.replace("http:", "https:");
1194 // hardwire upgrade of the startup file
1195 file.replace("_2_3", "_2_7");
1196 file.replace("2_7.jar", "2_7.jvp");
1197 // and remove the stale setting
1198 Cache.removeProperty("STARTUP_FILE");
1201 protocol = AppletFormatAdapter.checkProtocol(file);
1203 if (file.endsWith(".jar"))
1205 format = FileFormat.Jalview;
1211 format = new IdentifyFile().identify(file, protocol);
1212 } catch (FileFormatException e)
1218 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1220 // don't ask to save when quitting if only the startup file has been
1222 Console.debug("Resetting up-to-date flag for startup file");
1223 startUpAlframe.getViewport().setSavedUpToDate(true);
1224 // extract groovy arguments before anything else.
1227 // Once all other stuff is done, execute any groovy scripts (in order)
1228 if (groovyscript != null)
1230 if (Cache.groovyJarsPresent())
1232 Console.outPrintln("Executing script " + groovyscript);
1233 executeGroovyScript(groovyscript, startUpAlframe);
1237 jalview.bin.Console.errPrintln(
1238 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1242 // and finally, turn off batch mode indicator - if the desktop still exists
1243 if (desktop != null)
1247 desktop.setProgressBar(null, progress);
1249 desktop.setInBatchMode(false);
1255 private static void setLookAndFeel()
1257 if (!Platform.isJS())
1264 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1266 // If not set (or chosen laf fails), use the normal SystemLaF and if on
1268 // try Quaqua/Vaqua.
1269 String lafProp = System.getProperty("laf");
1270 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1271 String laf = "none";
1272 if (lafProp != null)
1276 else if (lafSetting != null)
1280 boolean lafSet = false;
1283 case "crossplatform":
1284 lafSet = setCrossPlatformLookAndFeel();
1287 Console.error("Could not set requested laf=" + laf);
1291 lafSet = setSystemLookAndFeel();
1294 Console.error("Could not set requested laf=" + laf);
1298 lafSet = setGtkLookAndFeel();
1301 Console.error("Could not set requested laf=" + laf);
1305 lafSet = setMetalLookAndFeel();
1308 Console.error("Could not set requested laf=" + laf);
1312 lafSet = setNimbusLookAndFeel();
1315 Console.error("Could not set requested laf=" + laf);
1319 lafSet = setFlatLookAndFeel();
1322 Console.error("Could not set requested laf=" + laf);
1326 lafSet = setMacLookAndFeel();
1329 Console.error("Could not set requested laf=" + laf);
1335 Console.error("Requested laf=" + laf + " not implemented");
1339 // Flatlaf default for everyone!
1340 lafSet = setFlatLookAndFeel();
1343 setSystemLookAndFeel();
1345 if (Platform.isLinux())
1347 setLinuxLookAndFeel();
1349 if (Platform.isMac())
1351 setMacLookAndFeel();
1357 private static boolean setCrossPlatformLookAndFeel()
1359 boolean set = false;
1362 UIManager.setLookAndFeel(
1363 UIManager.getCrossPlatformLookAndFeelClassName());
1365 } catch (Exception ex)
1367 Console.error("Unexpected Look and Feel Exception");
1368 Console.error(ex.getMessage());
1369 Console.debug(Cache.getStackTraceString(ex));
1374 private static boolean setSystemLookAndFeel()
1376 boolean set = false;
1379 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1381 } catch (Exception ex)
1383 Console.error("Unexpected Look and Feel Exception");
1384 Console.error(ex.getMessage());
1385 Console.debug(Cache.getStackTraceString(ex));
1390 private static boolean setSpecificLookAndFeel(String name,
1391 String className, boolean nameStartsWith)
1393 boolean set = false;
1396 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1398 if (info.getName() != null && nameStartsWith
1399 ? info.getName().toLowerCase(Locale.ROOT)
1400 .startsWith(name.toLowerCase(Locale.ROOT))
1401 : info.getName().toLowerCase(Locale.ROOT)
1402 .equals(name.toLowerCase(Locale.ROOT)))
1404 className = info.getClassName();
1408 UIManager.setLookAndFeel(className);
1410 } catch (Exception ex)
1412 Console.error("Unexpected Look and Feel Exception");
1413 Console.error(ex.getMessage());
1414 Console.debug(Cache.getStackTraceString(ex));
1419 private static boolean setGtkLookAndFeel()
1421 return setSpecificLookAndFeel("gtk",
1422 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1425 private static boolean setMetalLookAndFeel()
1427 return setSpecificLookAndFeel("metal",
1428 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1431 private static boolean setNimbusLookAndFeel()
1433 return setSpecificLookAndFeel("nimbus",
1434 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1437 private static boolean setFlatLookAndFeel()
1439 boolean set = false;
1440 if (SystemInfo.isMacOS)
1444 UIManager.setLookAndFeel(
1445 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1447 Console.debug("Using FlatMacLightLaf");
1448 } catch (ClassNotFoundException | InstantiationException
1449 | IllegalAccessException | UnsupportedLookAndFeelException e)
1451 Console.debug("Exception loading FlatLightLaf", e);
1453 System.setProperty("apple.laf.useScreenMenuBar", "true");
1454 System.setProperty("apple.awt.application.name",
1455 ChannelProperties.getProperty("app_name"));
1456 System.setProperty("apple.awt.application.appearance", "system");
1457 if (SystemInfo.isMacFullWindowContentSupported
1458 && Desktop.desktop != null)
1460 Console.debug("Setting transparent title bar");
1461 Desktop.desktop.getRootPane()
1462 .putClientProperty("apple.awt.fullWindowContent", true);
1463 Desktop.desktop.getRootPane()
1464 .putClientProperty("apple.awt.transparentTitleBar", true);
1465 Desktop.desktop.getRootPane()
1466 .putClientProperty("apple.awt.fullscreenable", true);
1468 SwingUtilities.invokeLater(() -> {
1469 FlatMacLightLaf.setup();
1471 Console.debug("Using FlatMacLightLaf");
1478 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1480 Console.debug("Using FlatLightLaf");
1481 } catch (ClassNotFoundException | InstantiationException
1482 | IllegalAccessException | UnsupportedLookAndFeelException e)
1484 Console.debug("Exception loading FlatLightLaf", e);
1486 // Windows specific properties here
1487 SwingUtilities.invokeLater(() -> {
1488 FlatLightLaf.setup();
1490 Console.debug("Using FlatLightLaf");
1493 else if (SystemInfo.isLinux)
1497 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1499 Console.debug("Using FlatLightLaf");
1500 } catch (ClassNotFoundException | InstantiationException
1501 | IllegalAccessException | UnsupportedLookAndFeelException e)
1503 Console.debug("Exception loading FlatLightLaf", e);
1505 // enable custom window decorations
1506 JFrame.setDefaultLookAndFeelDecorated(true);
1507 JDialog.setDefaultLookAndFeelDecorated(true);
1508 SwingUtilities.invokeLater(() -> {
1509 FlatLightLaf.setup();
1511 Console.debug("Using FlatLightLaf");
1519 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1521 Console.debug("Using FlatLightLaf");
1522 } catch (ClassNotFoundException | InstantiationException
1523 | IllegalAccessException | UnsupportedLookAndFeelException e)
1525 Console.debug("Exception loading FlatLightLaf", e);
1531 UIManager.put("TabbedPane.tabType", "card");
1532 UIManager.put("TabbedPane.showTabSeparators", true);
1533 UIManager.put("TabbedPane.showContentSeparator", true);
1534 // UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1535 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1536 UIManager.put("TabbedPane.hasFullBorder", true);
1537 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1538 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1539 UIManager.put("TabbedPane.smoothScrolling", true);
1540 UIManager.put("TabbedPane.tabWidthMode", "compact");
1541 UIManager.put("TabbedPane.selectedBackground", Color.white);
1542 UIManager.put("TabbedPane.background", new Color(236, 236, 236));
1543 UIManager.put("TabbedPane.hoverColor", Color.lightGray);
1546 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1550 private static boolean setMacLookAndFeel()
1552 boolean set = false;
1553 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1554 ChannelProperties.getProperty("app_name"));
1555 System.setProperty("apple.laf.useScreenMenuBar", "true");
1557 * broken native LAFs on (ARM?) macbooks
1558 set = setQuaquaLookAndFeel();
1559 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1560 .toLowerCase(Locale.ROOT).contains("quaqua"))
1562 set = setVaquaLookAndFeel();
1565 set = setFlatLookAndFeel();
1569 private static boolean setLinuxLookAndFeel()
1571 boolean set = false;
1572 set = setFlatLookAndFeel();
1574 set = setMetalLookAndFeel();
1575 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1577 set = setNimbusLookAndFeel();
1582 private static void showUsage()
1584 jalview.bin.Console.outPrintln(
1585 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1586 + "-nodisplay\tRun Jalview without User Interface.\n"
1587 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1588 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1589 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1590 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1591 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1592 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1593 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1594 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1595 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1596 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1597 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1598 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1599 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1600 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1601 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1602 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1603 + "-html FILE\tCreate HTML file from alignment.\n"
1604 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1605 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1606 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1607 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1608 + "-noquestionnaire\tTurn off questionnaire check.\n"
1609 + "-nonews\tTurn off check for Jalview news.\n"
1610 + "-nousagestats\tTurn off analytics tracking for this session.\n"
1611 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1613 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1614 // after all other properties files have been read\n\t
1615 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1616 // passed in correctly)"
1617 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1618 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1619 + "-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"
1620 + "-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"
1621 + "-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"
1622 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1626 private static void startUsageStats(final Desktop desktop)
1629 * start a User Config prompt asking if we can log usage statistics.
1631 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1633 MessageManager.getString("prompt.analytics_title"),
1634 MessageManager.getString("prompt.analytics"), new Runnable()
1639 Console.debug("Initialising analytics for usage stats.");
1640 Cache.initAnalytics();
1641 Console.debug("Tracking enabled.");
1648 Console.debug("Not enabling analytics.");
1651 desktop.addDialogThread(prompter);
1655 * Locate the given string as a file and pass it to the groovy interpreter.
1657 * @param groovyscript
1658 * the script to execute
1659 * @param jalviewContext
1660 * the Jalview Desktop object passed in to the groovy binding as the
1663 protected void executeGroovyScript(String groovyscript, AlignFrame af)
1666 * for scripts contained in files
1673 if (groovyscript.trim().equals("STDIN"))
1675 // read from stdin into a tempfile and execute it
1678 tfile = File.createTempFile("jalview", "groovy");
1679 PrintWriter outfile = new PrintWriter(
1680 new OutputStreamWriter(new FileOutputStream(tfile)));
1681 BufferedReader br = new BufferedReader(
1682 new InputStreamReader(System.in));
1684 while ((line = br.readLine()) != null)
1686 outfile.write(line + "\n");
1692 } catch (Exception ex)
1695 .errPrintln("Failed to read from STDIN into tempfile "
1696 + ((tfile == null) ? "(tempfile wasn't created)"
1697 : tfile.toString()));
1698 ex.printStackTrace();
1703 sfile = tfile.toURI().toURL();
1704 } catch (Exception x)
1706 jalview.bin.Console.errPrintln(
1707 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1709 x.printStackTrace();
1717 sfile = new URI(groovyscript).toURL();
1718 } catch (Exception x)
1720 tfile = new File(groovyscript);
1721 if (!tfile.exists())
1723 jalview.bin.Console.errPrintln(
1724 "File '" + groovyscript + "' does not exist.");
1727 if (!tfile.canRead())
1729 jalview.bin.Console.errPrintln(
1730 "File '" + groovyscript + "' cannot be read.");
1733 if (tfile.length() < 1)
1736 .errPrintln("File '" + groovyscript + "' is empty.");
1741 sfile = tfile.getAbsoluteFile().toURI().toURL();
1742 } catch (Exception ex)
1744 jalview.bin.Console.errPrintln("Failed to create a file URL for "
1745 + tfile.getAbsoluteFile());
1752 Map<String, java.lang.Object> vbinding = new HashMap<>();
1753 vbinding.put("Jalview", this);
1756 vbinding.put("currentAlFrame", af);
1758 Binding gbinding = new Binding(vbinding);
1759 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1760 gse.run(sfile.toString(), gbinding);
1761 if ("STDIN".equals(groovyscript))
1763 // delete temp file that we made -
1764 // only if it was successfully executed
1767 } catch (Exception e)
1770 .errPrintln("Exception Whilst trying to execute file " + sfile
1771 + " as a groovy script.");
1772 e.printStackTrace(System.err);
1777 public static boolean isHeadlessMode()
1779 String isheadless = System.getProperty("java.awt.headless");
1780 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1787 public AlignFrame[] getAlignFrames()
1789 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1790 : Desktop.getAlignFrames();
1795 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1799 // System.exit will run the shutdownHook first
1800 Jalview.exit("Quitting now. Bye!", ExitCode.OK);
1803 public static AlignFrame getCurrentAlignFrame()
1805 return Jalview.currentAlignFrame;
1808 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1810 Jalview.currentAlignFrame = currentAlignFrame;
1813 public Commands getCommands()
1818 public static void exit(String message, ExitCode ec)
1820 int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1;
1821 if (Console.log == null)
1823 // Don't start the logger just to exit!
1824 if (message != null)
1828 Console.outPrintln(message);
1832 jalview.bin.Console.errPrintln(message);
1838 Console.debug("Using Jalview.exit");
1839 if (message != null)
1843 Console.info(message);
1847 Console.error(message);
1853 System.exit(exitcode);
1857 public enum ExitCode
1859 // only add new ones to the end of the list (to preserve ordinal values)
1860 OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
1861 INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
1862 ERROR_RUNNING_COMMANDS, NO_LOGGING;
1865 /******************************
1867 * TEST OUTPUT METHODS
1869 * these operate only when Arg.TESTOUTPUT has been passed, and variously check
1870 * if an expected value / arg was set and report it to the test framework.
1872 ******************************/
1874 * report string values parsed/processed during tests When the Bootstrap
1875 * argument Arg.TESTOUTPUT is present - reports on debug if given s1 is not
1876 * null and not equals s2, warns if given argument is not set, and calls
1877 * testoutput(true,a,s1,s2) to report processing progress.
1880 * - ArgParser handling parsing
1882 * - Arg currently being processed
1887 protected static void testoutput(ArgParser ap, Arg a, String s1,
1890 BootstrapArgs bsa = ap.getBootstrapArgs();
1891 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1893 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1895 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1896 + s2 + "' for arg " + a.argString());
1899 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1903 Console.warn("Arg '" + a.getName() + "' not set at all");
1906 testoutput(true, a, s1, s2);
1910 * report values passed via bootstrap arguments
1912 * TODO: significant code duplication with testouput(Argparser...) - move it
1915 protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
1918 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1920 if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
1922 Console.debug("testoutput with unmatching values '" + s1 + "' and '"
1923 + s2 + "' for arg " + a.argString());
1926 if (!a.hasOption(Opt.BOOTSTRAP))
1928 Console.error("Non-bootstrap Arg '" + a.getName()
1929 + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
1931 if (!bsa.contains(a))
1933 Console.warn("Arg '" + a.getName() + "' not set at all");
1936 testoutput(true, a, s1, s2);
1940 * conditionally (on @param yes) report that expected value s1 was set during
1941 * CommandsTest tests
1943 private static void testoutput(boolean yes, Arg a, String s1, String s2)
1945 if (yes && ((s1 == null && s2 == null)
1946 || (s1 != null && s1.equals(s2))))
1948 Console.outPrintln("[TESTOUTPUT] arg " + a.argString() + "='" + s1
1954 * testoutput for boolean and unary values
1956 protected static void testoutput(ArgParser ap, Arg a)
1960 BootstrapArgs bsa = ap.getBootstrapArgs();
1963 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1965 boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
1967 boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
1971 Console.warn("Arg '" + a.getName() + "' not set at all");
1977 protected static void testoutput(BootstrapArgs bsa, Arg a)
1979 if (!bsa.getBoolean(Arg.TESTOUTPUT))
1981 if (!a.hasOption(Opt.BOOTSTRAP))
1983 Console.warn("Non-bootstrap Arg '" + a.getName()
1984 + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
1987 if (!bsa.contains(a))
1989 Console.warn("Arg '" + a.getName() + "' not set at all");
1992 testoutput(bsa.getBoolean(a), a);
1995 private static void testoutput(boolean yes, Arg a)
1997 String message = null;
1998 if (a.hasOption(Opt.BOOLEAN))
2000 message = (yes ? a.argString() : a.negateArgString()) + " was set";
2002 else if (a.hasOption(Opt.UNARY))
2004 message = a.argString() + (yes ? " was set" : " was not set");
2006 Console.outPrintln("[TESTOUTPUT] arg " + message);
2009 public ArgParser getArgParser()
2014 public BootstrapArgs getBootstrapArgs()
2016 return bootstrapArgs;
2019 public static boolean isBatchMode()
2021 return getInstance() != null && (getInstance().desktop == null
2022 || getInstance().desktop.isInBatchMode());
2026 * Warning about old or mixed command line arguments
2028 private void mixedCliWarning()
2030 Jalview j = Jalview.getInstance();
2031 boolean mixedStyle = j.getArgParser() != null
2032 && j.getArgParser().isMixedStyle();
2033 String title = MessageManager.getString("label.command_line_arguments");
2036 String warning = MessageManager.formatMessage(
2037 "warning.using_mixed_command_line_arguments",
2038 j.getArgParser().getMixedExamples());
2039 String quit = MessageManager.getString("action.quit");
2041 Desktop.instance.nonBlockingDialog(title, warning, null, quit,
2042 JvOptionPane.WARNING_MESSAGE, false, false, true, 30000);
2045 "Exiting due to mixed old and new command line arguments.",
2046 ExitCode.MIXED_CLI_ARGUMENTS);
2050 private void cliWarning()
2052 Jalview j = Jalview.getInstance();
2053 Commands c = j.getCommands();
2054 boolean oldStyle = j.getArgParser() != null
2055 && j.getArgParser().isOldStyle();
2056 String title = MessageManager.getString("label.command_line_arguments");
2059 String warning = MessageManager
2060 .getString("warning.using_old_command_line_arguments");
2061 String url = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
2062 if (Desktop.instance != null)
2064 String cont = MessageManager.getString("label.continue");
2066 Desktop.instance.nonBlockingDialog(title, warning, url, cont,
2067 JvOptionPane.WARNING_MESSAGE, false, true, true, 30000);
2070 if (j.getCommands() != null && j.getCommands().getErrors().size() > 0)
2072 if (Desktop.instance != null)
2074 String message = MessageManager
2075 .getString("warning.the_following_errors");
2076 String ok = MessageManager.getString("action.ok");
2078 List<String> errors = j.getCommands().getErrors();
2079 for (int i = 0; i < errors.size(); i++)
2081 shortest = Math.min(shortest, errors.get(i).length());
2083 Desktop.instance.nonBlockingDialog(
2084 Math.max(message.length(), Math.min(60, shortest)),
2085 Math.min(errors.size(), 20), title, message,
2086 j.getCommands().errorsToString(), ok,
2087 JvOptionPane.WARNING_MESSAGE, true, false, true, -1);