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.HashMap;
43 import java.util.Locale;
45 import java.util.Properties;
46 import java.util.Vector;
47 import java.util.logging.ConsoleHandler;
48 import java.util.logging.Level;
49 import java.util.logging.Logger;
51 import javax.swing.JDialog;
52 import javax.swing.JFrame;
53 import javax.swing.JOptionPane;
54 import javax.swing.SwingUtilities;
55 import javax.swing.UIManager;
56 import javax.swing.UIManager.LookAndFeelInfo;
57 import javax.swing.UnsupportedLookAndFeelException;
59 import com.formdev.flatlaf.FlatLightLaf;
60 import com.formdev.flatlaf.themes.FlatMacLightLaf;
61 import com.formdev.flatlaf.util.SystemInfo;
62 import com.threerings.getdown.util.LaunchUtil;
64 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
65 import groovy.lang.Binding;
66 import groovy.util.GroovyScriptEngine;
67 import jalview.bin.ArgParser.Arg;
68 import jalview.bin.ArgParser.BootstrapArgs;
69 import jalview.ext.so.SequenceOntology;
70 import jalview.gui.AlignFrame;
71 import jalview.gui.Desktop;
72 import jalview.gui.PromptUserConfig;
73 import jalview.gui.QuitHandler;
74 import jalview.gui.QuitHandler.QResponse;
75 import jalview.io.AppletFormatAdapter;
76 import jalview.io.BioJsHTMLOutput;
77 import jalview.io.DataSourceType;
78 import jalview.io.FileFormat;
79 import jalview.io.FileFormatException;
80 import jalview.io.FileFormatI;
81 import jalview.io.FileFormats;
82 import jalview.io.FileLoader;
83 import jalview.io.HtmlSvgOutput;
84 import jalview.io.IdentifyFile;
85 import jalview.io.NewickFile;
86 import jalview.io.gff.SequenceOntologyFactory;
87 import jalview.schemes.ColourSchemeI;
88 import jalview.schemes.ColourSchemeProperty;
89 import jalview.util.ChannelProperties;
90 import jalview.util.HttpUtils;
91 import jalview.util.LaunchUtils;
92 import jalview.util.MessageManager;
93 import jalview.util.Platform;
94 import jalview.ws.jws2.Jws2Discoverer;
97 * Main class for Jalview Application <br>
99 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
100 * jalview.bin.Jalview
102 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
103 * jalview.bin.Jalview jalview.bin.Jalview
105 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
106 * embellish '*' to e.g. '*.jar')
109 * @version $Revision$
115 Platform.getURLCommandArguments();
116 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
117 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
118 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
119 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
123 * singleton instance of this class
125 private static Jalview instance;
127 private Desktop desktop;
129 protected Commands cmds;
131 public static AlignFrame currentAlignFrame;
135 if (!Platform.isJS())
142 // grab all the rights we can for the JVM
143 Policy.setPolicy(new Policy()
146 public PermissionCollection getPermissions(CodeSource codesource)
148 Permissions perms = new Permissions();
149 perms.add(new AllPermission());
154 public void refresh()
162 * keep track of feature fetching tasks.
170 * TODO: generalise to track all jalview events to orchestrate batch processing
174 private int queued = 0;
176 private int running = 0;
178 public FeatureFetcher()
183 public void addFetcher(final AlignFrame af,
184 final Vector<String> dasSources)
186 final long id = System.currentTimeMillis();
188 final FeatureFetcher us = this;
189 new Thread(new Runnable()
201 af.setProgressBar(MessageManager
202 .getString("status.das_features_being_retrived"), id);
203 af.featureSettings_actionPerformed(null);
204 af.setProgressBar(null, id);
213 public synchronized boolean allFinished()
215 return queued == 0 && running == 0;
220 public static Jalview getInstance()
226 * main class for Jalview application
229 * open <em>filename</em>
231 public static void main(String[] args)
233 // setLogging(); // BH - for event debugging in JavaScript
234 instance = new Jalview();
235 instance.doMain(args);
238 private static void logClass(String name)
240 // BH - for event debugging in JavaScript
241 ConsoleHandler consoleHandler = new ConsoleHandler();
242 consoleHandler.setLevel(Level.ALL);
243 Logger logger = Logger.getLogger(name);
244 logger.setLevel(Level.ALL);
245 logger.addHandler(consoleHandler);
248 @SuppressWarnings("unused")
249 private static void setLogging()
257 System.out.println("not in js");
260 // BH - for event debugging in JavaScript (Java mode only)
261 if (!Platform.isJS())
268 Logger.getLogger("").setLevel(Level.ALL);
269 logClass("java.awt.EventDispatchThread");
270 logClass("java.awt.EventQueue");
271 logClass("java.awt.Component");
272 logClass("java.awt.focus.Component");
273 logClass("java.awt.focus.DefaultKeyboardFocusManager");
281 void doMain(String[] args)
284 if (!Platform.isJS())
286 System.setSecurityManager(null);
289 // get args needed before proper ArgParser
290 BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
292 if (!Platform.isJS())
294 // are we being --quiet ?
295 if (bootstrapArgs.contains(Arg.QUIET))
297 OutputStream devNull = new OutputStream()
300 public void write(int b)
305 System.setOut(new PrintStream(devNull));
306 // redirecting stderr not working
307 if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
309 System.setErr(new PrintStream(devNull));
315 .println("Java version: " + System.getProperty("java.version"));
316 System.out.println("Java Home: " + System.getProperty("java.home"));
317 System.out.println(System.getProperty("os.arch") + " "
318 + System.getProperty("os.name") + " "
319 + System.getProperty("os.version"));
321 String val = System.getProperty("sys.install4jVersion");
324 System.out.println("Install4j version: " + val);
326 val = System.getProperty("installer_template_version");
329 System.out.println("Install4j template version: " + val);
331 val = System.getProperty("launcher_version");
334 System.out.println("Launcher version: " + val);
337 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
339 System.setProperty("flatlaf.uiScale", "1");
342 // get bootstrap properties (mainly for the logger level)
343 Properties bootstrapProperties = Cache
344 .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
346 // report Jalview version
347 Cache.loadBuildProperties(true);
350 ArgsParser aparser = new ArgsParser(args);
353 boolean headless = false;
355 boolean headlessArg = false;
359 String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
360 if (logLevel == null && !(bootstrapProperties == null))
362 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
364 Console.initLogger(logLevel);
365 } catch (NoClassDefFoundError error)
367 error.printStackTrace();
368 String message = "\nEssential logging libraries not found."
369 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
370 Jalview.exit(message, 0);
373 // register SIGTERM listener
374 Runtime.getRuntime().addShutdownHook(new Thread()
378 Console.debug("Running shutdown hook");
379 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
381 // Got to here by a SIGTERM signal.
382 // Note we will not actually cancel the quit from here -- it's too
383 // late -- but we can wait for saving files.
384 Console.debug("Checking for saving files");
385 QuitHandler.getQuitResponse(false);
389 Console.debug("Nothing more to do");
391 Console.debug("Exiting, bye!");
392 // shutdownHook cannot be cancelled, JVM will now halt
396 String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
397 ? bootstrapArgs.get(Arg.PROPS)
398 : aparser.getValue("props");
399 Cache.loadProperties(usrPropsFile);
400 if (usrPropsFile != null)
403 "CMD [-props " + usrPropsFile + "] executed successfully!");
408 // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
409 if (bootstrapArgs.contains(Arg.ARGFILE))
411 argparser = ArgParser
412 .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
416 argparser = new ArgParser(args);
419 if (!Platform.isJS())
426 if (aparser.contains("help") || aparser.contains("h")
427 || argparser.getBool(Arg.HELP))
430 Jalview.exit(null, 0);
433 if (bootstrapArgs.contains(Arg.HEADLESS))
435 System.setProperty("java.awt.headless", "true");
437 headlessArg = argparser.getBool(Arg.HEADLESS);
439 if (aparser.contains("nodisplay") || aparser.contains("nogui")
440 || aparser.contains("headless"))
442 System.setProperty("java.awt.headless", "true");
448 // allow https handshakes to download intermediate certs if necessary
449 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
451 final String jabawsUrl = aparser.getValue("jabaws");
452 if (jabawsUrl != null)
456 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
458 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
459 } catch (MalformedURLException e)
462 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
467 String defs = aparser.getValue("setprop");
470 int p = defs.indexOf('=');
473 System.err.println("Ignoring invalid setprop argument : " + defs);
477 System.out.println("Executing setprop argument: " + defs);
480 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
482 // DISABLED FOR SECURITY REASONS
483 // TODO: add a property to allow properties to be overriden by cli args
484 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
486 defs = aparser.getValue("setprop");
488 if (System.getProperty("java.awt.headless") != null
489 && System.getProperty("java.awt.headless").equals("true"))
493 System.setProperty("http.agent",
494 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
498 Console.initLogger();
501 NoClassDefFoundError error)
503 error.printStackTrace();
504 String message = "\nEssential logging libraries not found."
505 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
506 Jalview.exit(message, 0);
510 if (!(headless || headlessArg))
514 * configure 'full' SO model if preferences say to, else use the default (full SO)
515 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
517 boolean soDefault = !Platform.isJS();
518 if (Cache.getDefault("USE_FULL_SO", soDefault))
520 SequenceOntologyFactory.setInstance(new SequenceOntology());
523 if (!(headless || headlessArg))
525 Desktop.nosplash = aparser.contains("nosplash");
526 desktop = new Desktop();
527 desktop.setInBatchMode(true); // indicate we are starting up
531 JalviewTaskbar.setTaskbar(this);
532 } catch (Exception e)
534 Console.info("Cannot set Taskbar");
535 Console.error(e.getMessage());
536 // e.printStackTrace();
537 } catch (Throwable t)
539 Console.info("Cannot set Taskbar");
540 Console.error(t.getMessage());
541 // t.printStackTrace();
544 // set Proxy settings before all the internet calls
545 Cache.setProxyPropertiesFromPreferences();
547 desktop.setVisible(true);
549 if (!Platform.isJS())
558 * Check to see that the JVM version being run is suitable for the Java
559 * version this Jalview was compiled for. Popup a warning if not.
561 if (!LaunchUtils.checkJavaVersion())
563 Console.warn("The Java version being used (Java "
564 + LaunchUtils.getJavaVersion()
565 + ") may lead to problems. This installation of Jalview should be used with Java "
566 + LaunchUtils.getJavaCompileVersion() + ".");
569 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
572 MessageManager.getString("label.continue") };
573 JOptionPane.showOptionDialog(null,
574 MessageManager.formatMessage(
575 "warning.wrong_jvm_version_message",
576 LaunchUtils.getJavaVersion(),
577 LaunchUtils.getJavaCompileVersion()),
579 .getString("warning.wrong_jvm_version_title"),
580 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
581 null, options, options[0]);
585 if (!aparser.contains("nowebservicediscovery"))
587 desktop.startServiceDiscovery();
589 if (!aparser.contains("nousagestats"))
591 startUsageStats(desktop);
595 System.err.println("CMD [-nousagestats] executed successfully!");
598 if (!aparser.contains("noquestionnaire"))
600 String url = aparser.getValue("questionnaire");
603 // Start the desktop questionnaire prompter with the specified
605 Console.debug("Starting questionnaire url at " + url);
606 desktop.checkForQuestionnaire(url);
607 System.out.println("CMD questionnaire[-" + url
608 + "] executed successfully!");
612 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
614 // Start the desktop questionnaire prompter with the specified
617 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
619 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
621 "Starting questionnaire with default url: " + defurl);
622 desktop.checkForQuestionnaire(defurl);
629 .println("CMD [-noquestionnaire] executed successfully!");
632 if (!aparser.contains("nonews")
633 || Cache.getProperty("NONEWS") == null)
635 desktop.checkForNews();
638 if (!aparser.contains("nohtmltemplates")
639 || Cache.getProperty("NOHTMLTEMPLATES") == null)
641 BioJsHTMLOutput.updateBioJS();
645 // Run Commands from cli
646 cmds = new Commands(argparser, headlessArg);
647 boolean commandsSuccess = cmds.argsWereParsed();
652 Jalview.exit("Successfully completed commands in headless mode", 0);
654 Console.info("Successfully completed commands");
660 Jalview.exit("Error when running Commands in headless mode", 1);
662 Console.warn("Error when running commands");
665 // Check if JVM and compile version might cause problems and log if it
667 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
669 Console.warn("The Java version being used (Java "
670 + LaunchUtils.getJavaVersion()
671 + ") may lead to problems. This installation of Jalview should be used with Java "
672 + LaunchUtils.getJavaCompileVersion() + ".");
675 // Move any new getdown-launcher-new.jar into place over old
676 // getdown-launcher.jar
677 String appdirString = System.getProperty("getdownappdir");
678 if (appdirString != null && appdirString.length() > 0)
680 final File appdir = new File(appdirString);
686 LaunchUtil.upgradeGetdown(
687 new File(appdir, "getdown-launcher-old.jar"),
688 new File(appdir, "getdown-launcher.jar"),
689 new File(appdir, "getdown-launcher-new.jar"));
694 String file = null, data = null;
696 FileFormatI format = null;
698 DataSourceType protocol = null;
700 FileLoader fileLoader = new FileLoader(!headless);
702 String groovyscript = null; // script to execute after all loading is
703 // completed one way or another
704 // extract groovy argument and execute if necessary
705 groovyscript = aparser.getValue("groovy", true);
706 file = aparser.getValue("open", true);
708 if (file == null && desktop == null)
710 Jalview.exit("No files to open!", 1);
714 // Finally, deal with the remaining input data.
719 desktop.setProgressBar(
721 .getString("status.processing_commandline_args"),
722 progress = System.currentTimeMillis());
724 System.out.println("CMD [-open " + file + "] executed successfully!");
726 if (!Platform.isJS())
728 * ignore in JavaScript -- can't just file existence - could load it?
733 if (!HttpUtils.startsWithHttpOrHttps(file))
735 if (!(new File(file)).exists())
740 "Can't find file '" + file + "' in headless mode", 1);
742 Console.warn("Can't find file'" + file + "'");
747 protocol = AppletFormatAdapter.checkProtocol(file);
751 format = new IdentifyFile().identify(file, protocol);
752 } catch (FileFormatException e1)
757 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
761 System.out.println("error");
765 setCurrentAlignFrame(af);
766 data = aparser.getValue("colour", true);
769 data.replaceAll("%20", " ");
771 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
772 af.getViewport(), af.getViewport().getAlignment(), data);
777 "CMD [-colour " + data + "] executed successfully!");
782 // Must maintain ability to use the groups flag
783 data = aparser.getValue("groups", true);
786 af.parseFeaturesFile(data,
787 AppletFormatAdapter.checkProtocol(data));
788 // System.out.println("Added " + data);
790 "CMD groups[-" + data + "] executed successfully!");
792 data = aparser.getValue("features", true);
795 af.parseFeaturesFile(data,
796 AppletFormatAdapter.checkProtocol(data));
797 // System.out.println("Added " + data);
799 "CMD [-features " + data + "] executed successfully!");
802 data = aparser.getValue("annotations", true);
805 af.loadJalviewDataFile(data, null, null, null);
806 // System.out.println("Added " + data);
808 "CMD [-annotations " + data + "] executed successfully!");
810 // set or clear the sortbytree flag.
811 if (aparser.contains("sortbytree"))
813 af.getViewport().setSortByTree(true);
814 if (af.getViewport().getSortByTree())
816 System.out.println("CMD [-sortbytree] executed successfully!");
819 if (aparser.contains("no-annotation"))
821 af.getViewport().setShowAnnotation(false);
822 if (!af.getViewport().isShowAnnotation())
824 System.out.println("CMD no-annotation executed successfully!");
827 if (aparser.contains("nosortbytree"))
829 af.getViewport().setSortByTree(false);
830 if (!af.getViewport().getSortByTree())
833 .println("CMD [-nosortbytree] executed successfully!");
836 data = aparser.getValue("tree", true);
842 "CMD [-tree " + data + "] executed successfully!");
843 NewickFile nf = new NewickFile(data,
844 AppletFormatAdapter.checkProtocol(data));
846 .setCurrentTree(af.showNewickTree(nf, data).getTree());
847 } catch (IOException ex)
849 System.err.println("Couldn't add tree " + data);
850 ex.printStackTrace(System.err);
853 // TODO - load PDB structure(s) to alignment JAL-629
854 // (associate with identical sequence in alignment, or a specified
856 if (groovyscript != null)
858 // Execute the groovy script after we've done all the rendering stuff
859 // and before any images or figures are generated.
860 System.out.println("Executing script " + groovyscript);
861 executeGroovyScript(groovyscript, af);
862 System.out.println("CMD groovy[" + groovyscript
863 + "] executed successfully!");
866 String imageName = "unnamed.png";
867 while (aparser.getSize() > 1)
869 String outputFormat = aparser.nextValue();
870 file = aparser.nextValue();
872 if (outputFormat.equalsIgnoreCase("png"))
874 af.createPNG(new File(file));
875 imageName = (new File(file)).getName();
876 System.out.println("Creating PNG image: " + file);
879 else if (outputFormat.equalsIgnoreCase("svg"))
881 File imageFile = new File(file);
882 imageName = imageFile.getName();
883 af.createSVG(imageFile);
884 System.out.println("Creating SVG image: " + file);
887 else if (outputFormat.equalsIgnoreCase("html"))
889 File imageFile = new File(file);
890 imageName = imageFile.getName();
891 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
892 htmlSVG.exportHTML(file);
894 System.out.println("Creating HTML image: " + file);
897 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
901 System.err.println("The output html file must not be null");
906 BioJsHTMLOutput.refreshVersionInfo(
907 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
908 } catch (URISyntaxException e)
912 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
913 bjs.exportHTML(file);
915 .println("Creating BioJS MSA Viwer HTML file: " + file);
918 else if (outputFormat.equalsIgnoreCase("imgMap"))
920 af.createImageMap(new File(file), imageName);
921 System.out.println("Creating image map: " + file);
924 else if (outputFormat.equalsIgnoreCase("eps"))
926 File outputFile = new File(file);
928 "Creating EPS file: " + outputFile.getAbsolutePath());
929 af.createEPS(outputFile);
932 FileFormatI outFormat = null;
935 outFormat = FileFormats.getInstance().forName(outputFormat);
936 } catch (Exception formatP)
938 System.out.println("Couldn't parse " + outFormat
939 + " as a valid Jalview format string.");
941 if (outFormat != null)
943 if (!outFormat.isWritable())
946 "This version of Jalview does not support alignment export as "
951 af.saveAlignment(file, outFormat);
952 if (af.isSaveAlignmentSuccessful())
954 System.out.println("Written alignment in "
955 + outFormat.getName() + " format to " + file);
959 System.out.println("Error writing file " + file + " in "
960 + outFormat.getName() + " format!!");
967 while (aparser.getSize() > 0)
969 System.out.println("Unknown arg: " + aparser.nextValue());
974 AlignFrame startUpAlframe = null;
975 // We'll only open the default file if the desktop is visible.
977 // ////////////////////
979 if (!Platform.isJS() && !headless && file == null
980 && Cache.getDefault("SHOW_STARTUP_FILE", true)
981 && !cmds.commandArgsProvided())
982 // don't open the startup file if command line args have been processed
983 // (&& !Commands.commandArgsProvided())
990 file = Cache.getDefault("STARTUP_FILE",
991 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
992 + "/examples/exampleFile_2_7.jvp");
993 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
995 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
997 file.replace("http:", "https:");
998 // hardwire upgrade of the startup file
999 file.replace("_2_3", "_2_7");
1000 file.replace("2_7.jar", "2_7.jvp");
1001 // and remove the stale setting
1002 Cache.removeProperty("STARTUP_FILE");
1005 protocol = AppletFormatAdapter.checkProtocol(file);
1007 if (file.endsWith(".jar"))
1009 format = FileFormat.Jalview;
1015 format = new IdentifyFile().identify(file, protocol);
1016 } catch (FileFormatException e)
1022 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1024 // don't ask to save when quitting if only the startup file has been
1026 Console.debug("Resetting up-to-date flag for startup file");
1027 startUpAlframe.getViewport().setSavedUpToDate(true);
1028 // extract groovy arguments before anything else.
1031 // Once all other stuff is done, execute any groovy scripts (in order)
1032 if (groovyscript != null)
1034 if (Cache.groovyJarsPresent())
1036 System.out.println("Executing script " + groovyscript);
1037 executeGroovyScript(groovyscript, startUpAlframe);
1042 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1046 // and finally, turn off batch mode indicator - if the desktop still exists
1047 if (desktop != null)
1051 desktop.setProgressBar(null, progress);
1053 desktop.setInBatchMode(false);
1057 private static void setLookAndFeel()
1059 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1061 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
1062 // try Quaqua/Vaqua.
1063 String lafProp = System.getProperty("laf");
1064 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1065 String laf = "none";
1066 if (lafProp != null)
1070 else if (lafSetting != null)
1074 boolean lafSet = false;
1077 case "crossplatform":
1078 lafSet = setCrossPlatformLookAndFeel();
1081 Console.error("Could not set requested laf=" + laf);
1085 lafSet = setSystemLookAndFeel();
1088 Console.error("Could not set requested laf=" + laf);
1092 lafSet = setGtkLookAndFeel();
1095 Console.error("Could not set requested laf=" + laf);
1099 lafSet = setMetalLookAndFeel();
1102 Console.error("Could not set requested laf=" + laf);
1106 lafSet = setNimbusLookAndFeel();
1109 Console.error("Could not set requested laf=" + laf);
1113 lafSet = setFlatLookAndFeel();
1116 Console.error("Could not set requested laf=" + laf);
1120 lafSet = setMacLookAndFeel();
1123 Console.error("Could not set requested laf=" + laf);
1129 Console.error("Requested laf=" + laf + " not implemented");
1133 setSystemLookAndFeel();
1134 if (Platform.isLinux())
1136 setLinuxLookAndFeel();
1138 if (Platform.isMac())
1140 setMacLookAndFeel();
1145 private static boolean setCrossPlatformLookAndFeel()
1147 boolean set = false;
1150 UIManager.setLookAndFeel(
1151 UIManager.getCrossPlatformLookAndFeelClassName());
1153 } catch (Exception ex)
1155 Console.error("Unexpected Look and Feel Exception");
1156 Console.error(ex.getMessage());
1157 Console.debug(Cache.getStackTraceString(ex));
1162 private static boolean setSystemLookAndFeel()
1164 boolean set = false;
1167 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1169 } catch (Exception ex)
1171 Console.error("Unexpected Look and Feel Exception");
1172 Console.error(ex.getMessage());
1173 Console.debug(Cache.getStackTraceString(ex));
1178 private static boolean setSpecificLookAndFeel(String name,
1179 String className, boolean nameStartsWith)
1181 boolean set = false;
1184 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1186 if (info.getName() != null && nameStartsWith
1187 ? info.getName().toLowerCase(Locale.ROOT)
1188 .startsWith(name.toLowerCase(Locale.ROOT))
1189 : info.getName().toLowerCase(Locale.ROOT)
1190 .equals(name.toLowerCase(Locale.ROOT)))
1192 className = info.getClassName();
1196 UIManager.setLookAndFeel(className);
1198 } catch (Exception ex)
1200 Console.error("Unexpected Look and Feel Exception");
1201 Console.error(ex.getMessage());
1202 Console.debug(Cache.getStackTraceString(ex));
1207 private static boolean setGtkLookAndFeel()
1209 return setSpecificLookAndFeel("gtk",
1210 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1213 private static boolean setMetalLookAndFeel()
1215 return setSpecificLookAndFeel("metal",
1216 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1219 private static boolean setNimbusLookAndFeel()
1221 return setSpecificLookAndFeel("nimbus",
1222 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1225 private static boolean setFlatLookAndFeel()
1227 boolean set = false;
1228 if (SystemInfo.isMacOS)
1232 UIManager.setLookAndFeel(
1233 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1235 Console.debug("Using FlatMacLightLaf");
1236 } catch (ClassNotFoundException | InstantiationException
1237 | IllegalAccessException | UnsupportedLookAndFeelException e)
1239 Console.debug("Exception loading FlatLightLaf", e);
1241 System.setProperty("apple.laf.useScreenMenuBar", "true");
1242 System.setProperty("apple.awt.application.name",
1243 ChannelProperties.getProperty("app_name"));
1244 System.setProperty("apple.awt.application.appearance", "system");
1245 if (SystemInfo.isMacFullWindowContentSupported
1246 && Desktop.desktop != null)
1248 Console.debug("Setting transparent title bar");
1249 Desktop.desktop.getRootPane()
1250 .putClientProperty("apple.awt.fullWindowContent", true);
1251 Desktop.desktop.getRootPane()
1252 .putClientProperty("apple.awt.transparentTitleBar", true);
1253 Desktop.desktop.getRootPane()
1254 .putClientProperty("apple.awt.fullscreenable", true);
1256 SwingUtilities.invokeLater(() -> {
1257 FlatMacLightLaf.setup();
1259 Console.debug("Using FlatMacLightLaf");
1266 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1268 Console.debug("Using FlatLightLaf");
1269 } catch (ClassNotFoundException | InstantiationException
1270 | IllegalAccessException | UnsupportedLookAndFeelException e)
1272 Console.debug("Exception loading FlatLightLaf", e);
1274 // Windows specific properties here
1275 SwingUtilities.invokeLater(() -> {
1276 FlatLightLaf.setup();
1278 Console.debug("Using FlatLightLaf");
1281 else if (SystemInfo.isLinux)
1285 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1287 Console.debug("Using FlatLightLaf");
1288 } catch (ClassNotFoundException | InstantiationException
1289 | IllegalAccessException | UnsupportedLookAndFeelException e)
1291 Console.debug("Exception loading FlatLightLaf", e);
1293 // enable custom window decorations
1294 JFrame.setDefaultLookAndFeelDecorated(true);
1295 JDialog.setDefaultLookAndFeelDecorated(true);
1296 SwingUtilities.invokeLater(() -> {
1297 FlatLightLaf.setup();
1299 Console.debug("Using FlatLightLaf");
1307 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1309 Console.debug("Using FlatLightLaf");
1310 } catch (ClassNotFoundException | InstantiationException
1311 | IllegalAccessException | UnsupportedLookAndFeelException e)
1313 Console.debug("Exception loading FlatLightLaf", e);
1319 UIManager.put("TabbedPane.tabType", "card");
1320 UIManager.put("TabbedPane.showTabSeparators", true);
1321 UIManager.put("TabbedPane.showContentSeparator", true);
1322 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1323 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1324 UIManager.put("TabbedPane.hasFullBorder", true);
1325 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1326 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1327 UIManager.put("TabbedPane.smoothScrolling", true);
1328 UIManager.put("TabbedPane.tabWidthMode", "compact");
1329 UIManager.put("TabbedPane.selectedBackground", Color.white);
1332 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1336 private static boolean setMacLookAndFeel()
1338 boolean set = false;
1339 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1340 ChannelProperties.getProperty("app_name"));
1341 System.setProperty("apple.laf.useScreenMenuBar", "true");
1343 * broken native LAFs on (ARM?) macbooks
1344 set = setQuaquaLookAndFeel();
1345 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1346 .toLowerCase(Locale.ROOT).contains("quaqua"))
1348 set = setVaquaLookAndFeel();
1351 set = setFlatLookAndFeel();
1355 private static boolean setLinuxLookAndFeel()
1357 boolean set = false;
1358 set = setFlatLookAndFeel();
1360 set = setMetalLookAndFeel();
1361 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1363 set = setNimbusLookAndFeel();
1367 private static void showUsage()
1370 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1371 + "-nodisplay\tRun Jalview without User Interface.\n"
1372 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1373 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1374 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1375 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1376 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1377 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1378 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1379 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1380 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1381 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1382 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1383 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1384 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1385 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1386 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1387 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1388 + "-html FILE\tCreate HTML file from alignment.\n"
1389 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1390 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1391 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1392 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1393 + "-noquestionnaire\tTurn off questionnaire check.\n"
1394 + "-nonews\tTurn off check for Jalview news.\n"
1395 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1396 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1398 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1399 // after all other properties files have been read\n\t
1400 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1401 // passed in correctly)"
1402 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1403 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1404 + "-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"
1405 + "-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"
1406 + "-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"
1407 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1410 private static void startUsageStats(final Desktop desktop)
1413 * start a User Config prompt asking if we can log usage statistics.
1415 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1416 "USAGESTATS", "Jalview Usage Statistics",
1417 "Do you want to help make Jalview better by enabling "
1418 + "the collection of usage statistics with Google Analytics ?"
1419 + "\n\n(you can enable or disable usage tracking in the preferences)",
1426 "Initialising googletracker for usage stats.");
1427 Cache.initGoogleTracker();
1428 Console.debug("Tracking enabled.");
1435 Console.debug("Not enabling Google Tracking.");
1438 desktop.addDialogThread(prompter);
1442 * Locate the given string as a file and pass it to the groovy interpreter.
1444 * @param groovyscript
1445 * the script to execute
1446 * @param jalviewContext
1447 * the Jalview Desktop object passed in to the groovy binding as the
1450 private void executeGroovyScript(String groovyscript, AlignFrame af)
1453 * for scripts contained in files
1460 if (groovyscript.trim().equals("STDIN"))
1462 // read from stdin into a tempfile and execute it
1465 tfile = File.createTempFile("jalview", "groovy");
1466 PrintWriter outfile = new PrintWriter(
1467 new OutputStreamWriter(new FileOutputStream(tfile)));
1468 BufferedReader br = new BufferedReader(
1469 new InputStreamReader(System.in));
1471 while ((line = br.readLine()) != null)
1473 outfile.write(line + "\n");
1479 } catch (Exception ex)
1481 System.err.println("Failed to read from STDIN into tempfile "
1482 + ((tfile == null) ? "(tempfile wasn't created)"
1483 : tfile.toString()));
1484 ex.printStackTrace();
1489 sfile = tfile.toURI().toURL();
1490 } catch (Exception x)
1493 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1495 x.printStackTrace();
1503 sfile = new URI(groovyscript).toURL();
1504 } catch (Exception x)
1506 tfile = new File(groovyscript);
1507 if (!tfile.exists())
1509 System.err.println("File '" + groovyscript + "' does not exist.");
1512 if (!tfile.canRead())
1514 System.err.println("File '" + groovyscript + "' cannot be read.");
1517 if (tfile.length() < 1)
1519 System.err.println("File '" + groovyscript + "' is empty.");
1524 sfile = tfile.getAbsoluteFile().toURI().toURL();
1525 } catch (Exception ex)
1527 System.err.println("Failed to create a file URL for "
1528 + tfile.getAbsoluteFile());
1535 Map<String, java.lang.Object> vbinding = new HashMap<>();
1536 vbinding.put("Jalview", this);
1539 vbinding.put("currentAlFrame", af);
1541 Binding gbinding = new Binding(vbinding);
1542 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1543 gse.run(sfile.toString(), gbinding);
1544 if ("STDIN".equals(groovyscript))
1546 // delete temp file that we made -
1547 // only if it was successfully executed
1550 } catch (Exception e)
1552 System.err.println("Exception Whilst trying to execute file " + sfile
1553 + " as a groovy script.");
1554 e.printStackTrace(System.err);
1559 public static boolean isHeadlessMode()
1561 String isheadless = System.getProperty("java.awt.headless");
1562 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1569 public AlignFrame[] getAlignFrames()
1571 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1572 : Desktop.getAlignFrames();
1577 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1581 // System.exit will run the shutdownHook first
1582 Jalview.exit("Quitting now. Bye!", 0);
1585 public static AlignFrame getCurrentAlignFrame()
1587 return Jalview.currentAlignFrame;
1590 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1592 Jalview.currentAlignFrame = currentAlignFrame;
1595 protected Commands getCommands()
1600 public static void exit(String message, int exitcode)
1602 System.err.println("####### EXITING HERE!");
1603 Console.debug("Using Jalview.exit");
1604 if (message != null)
1606 Console.info(message);
1608 Console.error(message);
1610 System.exit(exitcode);