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;
53 import javax.swing.JDialog;
54 import javax.swing.JFrame;
55 import javax.swing.JOptionPane;
56 import javax.swing.SwingUtilities;
57 import javax.swing.UIManager;
58 import javax.swing.UIManager.LookAndFeelInfo;
59 import javax.swing.UnsupportedLookAndFeelException;
61 import com.formdev.flatlaf.FlatLightLaf;
62 import com.formdev.flatlaf.themes.FlatMacLightLaf;
63 import com.formdev.flatlaf.util.SystemInfo;
64 import com.threerings.getdown.util.LaunchUtil;
66 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
67 import groovy.lang.Binding;
68 import groovy.util.GroovyScriptEngine;
69 import jalview.bin.argparser.Arg;
70 import jalview.bin.argparser.ArgParser;
71 import jalview.bin.argparser.BootstrapArgs;
72 import jalview.ext.so.SequenceOntology;
73 import jalview.gui.AlignFrame;
74 import jalview.gui.Desktop;
75 import jalview.gui.PromptUserConfig;
76 import jalview.gui.QuitHandler;
77 import jalview.gui.QuitHandler.QResponse;
78 import jalview.io.AppletFormatAdapter;
79 import jalview.io.BioJsHTMLOutput;
80 import jalview.io.DataSourceType;
81 import jalview.io.FileFormat;
82 import jalview.io.FileFormatException;
83 import jalview.io.FileFormatI;
84 import jalview.io.FileFormats;
85 import jalview.io.FileLoader;
86 import jalview.io.HtmlSvgOutput;
87 import jalview.io.IdentifyFile;
88 import jalview.io.NewickFile;
89 import jalview.io.gff.SequenceOntologyFactory;
90 import jalview.schemes.ColourSchemeI;
91 import jalview.schemes.ColourSchemeProperty;
92 import jalview.util.ChannelProperties;
93 import jalview.util.HttpUtils;
94 import jalview.util.LaunchUtils;
95 import jalview.util.MessageManager;
96 import jalview.util.Platform;
97 import jalview.ws.jws2.Jws2Discoverer;
100 * Main class for Jalview Application <br>
102 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
103 * jalview.bin.Jalview
105 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
106 * jalview.bin.Jalview jalview.bin.Jalview
108 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
109 * embellish '*' to e.g. '*.jar')
112 * @version $Revision$
118 Platform.getURLCommandArguments();
119 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
120 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
121 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
122 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
126 * singleton instance of this class
128 private static Jalview instance;
130 private Desktop desktop;
132 protected Commands cmds;
134 public static AlignFrame currentAlignFrame;
138 if (!Platform.isJS())
145 // grab all the rights we can for the JVM
146 Policy.setPolicy(new Policy()
149 public PermissionCollection getPermissions(CodeSource codesource)
151 Permissions perms = new Permissions();
152 perms.add(new AllPermission());
157 public void refresh()
165 * keep track of feature fetching tasks.
173 * TODO: generalise to track all jalview events to orchestrate batch processing
177 private int queued = 0;
179 private int running = 0;
181 public FeatureFetcher()
186 public void addFetcher(final AlignFrame af,
187 final Vector<String> dasSources)
189 final long id = System.currentTimeMillis();
191 final FeatureFetcher us = this;
192 new Thread(new Runnable()
204 af.setProgressBar(MessageManager
205 .getString("status.das_features_being_retrived"), id);
206 af.featureSettings_actionPerformed(null);
207 af.setProgressBar(null, id);
216 public synchronized boolean allFinished()
218 return queued == 0 && running == 0;
223 public static Jalview getInstance()
229 * main class for Jalview application
232 * open <em>filename</em>
234 public static void main(String[] args)
236 // setLogging(); // BH - for event debugging in JavaScript
237 instance = new Jalview();
238 instance.doMain(args);
241 private static void logClass(String name)
243 // BH - for event debugging in JavaScript
244 ConsoleHandler consoleHandler = new ConsoleHandler();
245 consoleHandler.setLevel(Level.ALL);
246 Logger logger = Logger.getLogger(name);
247 logger.setLevel(Level.ALL);
248 logger.addHandler(consoleHandler);
251 @SuppressWarnings("unused")
252 private static void setLogging()
260 System.out.println("not in js");
263 // BH - for event debugging in JavaScript (Java mode only)
264 if (!Platform.isJS())
271 Logger.getLogger("").setLevel(Level.ALL);
272 logClass("java.awt.EventDispatchThread");
273 logClass("java.awt.EventQueue");
274 logClass("java.awt.Component");
275 logClass("java.awt.focus.Component");
276 logClass("java.awt.focus.DefaultKeyboardFocusManager");
284 void doMain(String[] args)
287 if (!Platform.isJS())
289 System.setSecurityManager(null);
292 // Move any new getdown-launcher-new.jar into place over old
293 // getdown-launcher.jar
294 String appdirString = System.getProperty("getdownappdir");
295 if (appdirString != null && appdirString.length() > 0)
297 final File appdir = new File(appdirString);
303 LaunchUtil.upgradeGetdown(
304 new File(appdir, "getdown-launcher-old.jar"),
305 new File(appdir, "getdown-launcher.jar"),
306 new File(appdir, "getdown-launcher-new.jar"));
311 // get args needed before proper ArgParser
312 BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
314 if (!Platform.isJS())
316 // are we being --quiet ?
317 if (bootstrapArgs.contains(Arg.QUIET))
319 OutputStream devNull = new OutputStream()
322 public void write(int b)
327 System.setOut(new PrintStream(devNull));
328 // redirecting stderr not working
329 if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
331 System.setErr(new PrintStream(devNull));
337 .println("Java version: " + System.getProperty("java.version"));
338 System.out.println("Java Home: " + System.getProperty("java.home"));
339 System.out.println(System.getProperty("os.arch") + " "
340 + System.getProperty("os.name") + " "
341 + System.getProperty("os.version"));
343 String val = System.getProperty("sys.install4jVersion");
346 System.out.println("Install4j version: " + val);
348 val = System.getProperty("installer_template_version");
351 System.out.println("Install4j template version: " + val);
353 val = System.getProperty("launcher_version");
356 System.out.println("Launcher version: " + val);
359 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
361 System.setProperty("flatlaf.uiScale", "1");
364 // get bootstrap properties (mainly for the logger level)
365 Properties bootstrapProperties = Cache
366 .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
368 // report Jalview version
369 Cache.loadBuildProperties(true);
372 ArgsParser aparser = new ArgsParser(args);
375 boolean headless = false;
377 boolean headlessArg = false;
381 String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
382 if (logLevel == null && !(bootstrapProperties == null))
384 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
386 Console.initLogger(logLevel);
387 } catch (NoClassDefFoundError error)
389 error.printStackTrace();
390 String message = "\nEssential logging libraries not found."
391 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
392 Jalview.exit(message, 0);
395 // register SIGTERM listener
396 Runtime.getRuntime().addShutdownHook(new Thread()
400 Console.debug("Running shutdown hook");
401 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
403 // Got to here by a SIGTERM signal.
404 // Note we will not actually cancel the quit from here -- it's too
405 // late -- but we can wait for saving files.
406 Console.debug("Checking for saving files");
407 QuitHandler.getQuitResponse(false);
411 Console.debug("Nothing more to do");
413 Console.debug("Exiting, bye!");
414 // shutdownHook cannot be cancelled, JVM will now halt
418 String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
419 ? bootstrapArgs.get(Arg.PROPS)
420 : aparser.getValue("props");
421 // if usrPropsFile == null, loadProperties will use the Channel
423 Cache.loadProperties(usrPropsFile);
424 if (usrPropsFile != null)
427 "CMD [-props " + usrPropsFile + "] executed successfully!");
432 // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
433 if (bootstrapArgs.contains(Arg.ARGFILE))
435 argparser = ArgParser.parseArgFiles(
436 bootstrapArgs.getList(Arg.ARGFILE),
437 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
441 argparser = new ArgParser(args,
442 bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
445 if (!Platform.isJS())
452 if (bootstrapArgs.contains(Arg.HELP))
454 System.out.println(Arg.usage());
455 Jalview.exit(null, 0);
457 if (aparser.contains("help") || aparser.contains("h"))
460 Jalview.exit(null, 0);
463 if (bootstrapArgs.contains(Arg.HEADLESS))
465 System.setProperty("java.awt.headless", "true");
467 headlessArg = argparser.getBool(Arg.HEADLESS);
469 if (aparser.contains("nodisplay") || aparser.contains("nogui")
470 || aparser.contains("headless"))
472 System.setProperty("java.awt.headless", "true");
478 // allow https handshakes to download intermediate certs if necessary
479 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
481 final String jabawsUrl = aparser.getValue("jabaws");
482 if (jabawsUrl != null)
486 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
488 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
489 } catch (MalformedURLException e)
492 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
497 List<String> setprops = new ArrayList<>();
498 if (bootstrapArgs.contains(Arg.SETPROP))
500 setprops = bootstrapArgs.getList(Arg.SETPROP);
504 String sp = aparser.getValue("setprop");
508 sp = aparser.getValue("setprop");
511 for (String setprop : setprops)
513 int p = setprop.indexOf('=');
517 .println("Ignoring invalid setprop argument : " + setprop);
521 System.out.println("Executing setprop argument: " + setprop);
524 Cache.setProperty(setprop.substring(0, p),
525 setprop.substring(p + 1));
527 // DISABLED FOR SECURITY REASONS
528 // TODO: add a property to allow properties to be overriden by cli args
529 // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
532 if (System.getProperty("java.awt.headless") != null
533 && System.getProperty("java.awt.headless").equals("true"))
537 System.setProperty("http.agent",
538 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
542 Console.initLogger();
545 NoClassDefFoundError error)
547 error.printStackTrace();
548 String message = "\nEssential logging libraries not found."
549 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
550 Jalview.exit(message, 0);
554 if (!(headless || headlessArg))
558 * configure 'full' SO model if preferences say to, else use the default (full SO)
559 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
561 boolean soDefault = !Platform.isJS();
562 if (Cache.getDefault("USE_FULL_SO", soDefault))
564 SequenceOntologyFactory.setInstance(new SequenceOntology());
567 if (!(headless || headlessArg))
569 Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
570 || aparser.contains("nosplash")
571 || Cache.getDefault("SPLASH", "true").equals("false");
572 desktop = new Desktop();
573 desktop.setInBatchMode(true); // indicate we are starting up
577 JalviewTaskbar.setTaskbar(this);
578 } catch (Exception e)
580 Console.info("Cannot set Taskbar");
581 Console.error(e.getMessage());
582 // e.printStackTrace();
583 } catch (Throwable t)
585 Console.info("Cannot set Taskbar");
586 Console.error(t.getMessage());
587 // t.printStackTrace();
590 // set Proxy settings before all the internet calls
591 Cache.setProxyPropertiesFromPreferences();
593 desktop.setVisible(true);
595 if (!Platform.isJS())
604 * Check to see that the JVM version being run is suitable for the Java
605 * version this Jalview was compiled for. Popup a warning if not.
607 if (!LaunchUtils.checkJavaVersion())
609 Console.warn("The Java version being used (Java "
610 + LaunchUtils.getJavaVersion()
611 + ") may lead to problems. This installation of Jalview should be used with Java "
612 + LaunchUtils.getJavaCompileVersion() + ".");
615 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
618 MessageManager.getString("label.continue") };
619 JOptionPane.showOptionDialog(null,
620 MessageManager.formatMessage(
621 "warning.wrong_jvm_version_message",
622 LaunchUtils.getJavaVersion(),
623 LaunchUtils.getJavaCompileVersion()),
625 .getString("warning.wrong_jvm_version_title"),
626 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
627 null, options, options[0]);
631 if (!aparser.contains("nowebservicediscovery"))
633 desktop.startServiceDiscovery();
635 if (!aparser.contains("nousagestats"))
637 startUsageStats(desktop);
641 System.err.println("CMD [-nousagestats] executed successfully!");
644 if (!aparser.contains("noquestionnaire"))
646 String url = aparser.getValue("questionnaire");
649 // Start the desktop questionnaire prompter with the specified
651 Console.debug("Starting questionnaire url at " + url);
652 desktop.checkForQuestionnaire(url);
653 System.out.println("CMD questionnaire[-" + url
654 + "] executed successfully!");
658 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
660 // Start the desktop questionnaire prompter with the specified
663 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
665 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
667 "Starting questionnaire with default url: " + defurl);
668 desktop.checkForQuestionnaire(defurl);
675 .println("CMD [-noquestionnaire] executed successfully!");
678 if ((!aparser.contains("nonews")
679 && Cache.getProperty("NONEWS") == null
680 && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
681 || "true".equals(bootstrapArgs.get(Arg.NEWS)))
683 desktop.checkForNews();
686 if (!aparser.contains("nohtmltemplates")
687 && Cache.getProperty("NOHTMLTEMPLATES") == null)
689 BioJsHTMLOutput.updateBioJS();
693 // Run Commands from cli
694 cmds = new Commands(argparser, headlessArg);
695 boolean commandsSuccess = cmds.argsWereParsed();
700 Jalview.exit("Successfully completed commands in headless mode", 0);
702 Console.info("Successfully completed commands");
708 Jalview.exit("Error when running Commands in headless mode", 1);
710 Console.warn("Error when running commands");
713 // Check if JVM and compile version might cause problems and log if it
715 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
717 Console.warn("The Java version being used (Java "
718 + LaunchUtils.getJavaVersion()
719 + ") may lead to problems. This installation of Jalview should be used with Java "
720 + LaunchUtils.getJavaCompileVersion() + ".");
723 String file = null, data = null;
725 FileFormatI format = null;
727 DataSourceType protocol = null;
729 FileLoader fileLoader = new FileLoader(!headless);
731 String groovyscript = null; // script to execute after all loading is
732 // completed one way or another
733 // extract groovy argument and execute if necessary
734 groovyscript = aparser.getValue("groovy", true);
735 file = aparser.getValue("open", true);
737 if (file == null && desktop == null && !commandsSuccess)
739 Jalview.exit("No files to open!", 1);
743 // Finally, deal with the remaining input data.
748 desktop.setProgressBar(
750 .getString("status.processing_commandline_args"),
751 progress = System.currentTimeMillis());
753 System.out.println("CMD [-open " + file + "] executed successfully!");
755 if (!Platform.isJS())
757 * ignore in JavaScript -- can't just file existence - could load it?
762 if (!HttpUtils.startsWithHttpOrHttps(file))
764 if (!(new File(file)).exists())
769 "Can't find file '" + file + "' in headless mode", 1);
771 Console.warn("Can't find file'" + file + "'");
776 protocol = AppletFormatAdapter.checkProtocol(file);
780 format = new IdentifyFile().identify(file, protocol);
781 } catch (FileFormatException e1)
786 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
790 System.out.println("error");
794 setCurrentAlignFrame(af);
795 data = aparser.getValue("colour", true);
798 data.replaceAll("%20", " ");
800 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
801 af.getViewport(), af.getViewport().getAlignment(), data);
806 "CMD [-colour " + data + "] executed successfully!");
811 // Must maintain ability to use the groups flag
812 data = aparser.getValue("groups", true);
815 af.parseFeaturesFile(data,
816 AppletFormatAdapter.checkProtocol(data));
817 // System.out.println("Added " + data);
819 "CMD groups[-" + data + "] executed successfully!");
821 data = aparser.getValue("features", true);
824 af.parseFeaturesFile(data,
825 AppletFormatAdapter.checkProtocol(data));
826 // System.out.println("Added " + data);
828 "CMD [-features " + data + "] executed successfully!");
831 data = aparser.getValue("annotations", true);
834 af.loadJalviewDataFile(data, null, null, null);
835 // System.out.println("Added " + data);
837 "CMD [-annotations " + data + "] executed successfully!");
839 // set or clear the sortbytree flag.
840 if (aparser.contains("sortbytree"))
842 af.getViewport().setSortByTree(true);
843 if (af.getViewport().getSortByTree())
845 System.out.println("CMD [-sortbytree] executed successfully!");
848 if (aparser.contains("no-annotation"))
850 af.getViewport().setShowAnnotation(false);
851 if (!af.getViewport().isShowAnnotation())
853 System.out.println("CMD no-annotation executed successfully!");
856 if (aparser.contains("nosortbytree"))
858 af.getViewport().setSortByTree(false);
859 if (!af.getViewport().getSortByTree())
862 .println("CMD [-nosortbytree] executed successfully!");
865 data = aparser.getValue("tree", true);
871 "CMD [-tree " + data + "] executed successfully!");
872 NewickFile nf = new NewickFile(data,
873 AppletFormatAdapter.checkProtocol(data));
875 .setCurrentTree(af.showNewickTree(nf, data).getTree());
876 } catch (IOException ex)
878 System.err.println("Couldn't add tree " + data);
879 ex.printStackTrace(System.err);
882 // TODO - load PDB structure(s) to alignment JAL-629
883 // (associate with identical sequence in alignment, or a specified
885 if (groovyscript != null)
887 // Execute the groovy script after we've done all the rendering stuff
888 // and before any images or figures are generated.
889 System.out.println("Executing script " + groovyscript);
890 executeGroovyScript(groovyscript, af);
891 System.out.println("CMD groovy[" + groovyscript
892 + "] executed successfully!");
895 String imageName = "unnamed.png";
896 while (aparser.getSize() > 1)
898 String outputFormat = aparser.nextValue();
899 file = aparser.nextValue();
901 if (outputFormat.equalsIgnoreCase("png"))
903 af.createPNG(new File(file));
904 imageName = (new File(file)).getName();
905 System.out.println("Creating PNG image: " + file);
908 else if (outputFormat.equalsIgnoreCase("svg"))
910 File imageFile = new File(file);
911 imageName = imageFile.getName();
912 af.createSVG(imageFile);
913 System.out.println("Creating SVG image: " + file);
916 else if (outputFormat.equalsIgnoreCase("html"))
918 File imageFile = new File(file);
919 imageName = imageFile.getName();
920 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
921 htmlSVG.exportHTML(file);
923 System.out.println("Creating HTML image: " + file);
926 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
930 System.err.println("The output html file must not be null");
935 BioJsHTMLOutput.refreshVersionInfo(
936 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
937 } catch (URISyntaxException e)
941 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
942 bjs.exportHTML(file);
944 .println("Creating BioJS MSA Viwer HTML file: " + file);
947 else if (outputFormat.equalsIgnoreCase("imgMap"))
949 af.createImageMap(new File(file), imageName);
950 System.out.println("Creating image map: " + file);
953 else if (outputFormat.equalsIgnoreCase("eps"))
955 File outputFile = new File(file);
957 "Creating EPS file: " + outputFile.getAbsolutePath());
958 af.createEPS(outputFile);
961 FileFormatI outFormat = null;
964 outFormat = FileFormats.getInstance().forName(outputFormat);
965 } catch (Exception formatP)
967 System.out.println("Couldn't parse " + outFormat
968 + " as a valid Jalview format string.");
970 if (outFormat != null)
972 if (!outFormat.isWritable())
975 "This version of Jalview does not support alignment export as "
980 af.saveAlignment(file, outFormat);
981 if (af.isSaveAlignmentSuccessful())
983 System.out.println("Written alignment in "
984 + outFormat.getName() + " format to " + file);
988 System.out.println("Error writing file " + file + " in "
989 + outFormat.getName() + " format!!");
996 while (aparser.getSize() > 0)
998 System.out.println("Unknown arg: " + aparser.nextValue());
1003 AlignFrame startUpAlframe = null;
1004 // We'll only open the default file if the desktop is visible.
1006 // ////////////////////
1008 if (!Platform.isJS() && !headless && file == null
1009 && Cache.getDefault("SHOW_STARTUP_FILE", true)
1010 && !cmds.commandArgsProvided())
1011 // don't open the startup file if command line args have been processed
1012 // (&& !Commands.commandArgsProvided())
1019 file = Cache.getDefault("STARTUP_FILE",
1020 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
1021 + "/examples/exampleFile_2_7.jvp");
1022 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
1024 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
1026 file.replace("http:", "https:");
1027 // hardwire upgrade of the startup file
1028 file.replace("_2_3", "_2_7");
1029 file.replace("2_7.jar", "2_7.jvp");
1030 // and remove the stale setting
1031 Cache.removeProperty("STARTUP_FILE");
1034 protocol = AppletFormatAdapter.checkProtocol(file);
1036 if (file.endsWith(".jar"))
1038 format = FileFormat.Jalview;
1044 format = new IdentifyFile().identify(file, protocol);
1045 } catch (FileFormatException e)
1051 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
1053 // don't ask to save when quitting if only the startup file has been
1055 Console.debug("Resetting up-to-date flag for startup file");
1056 startUpAlframe.getViewport().setSavedUpToDate(true);
1057 // extract groovy arguments before anything else.
1060 // Once all other stuff is done, execute any groovy scripts (in order)
1061 if (groovyscript != null)
1063 if (Cache.groovyJarsPresent())
1065 System.out.println("Executing script " + groovyscript);
1066 executeGroovyScript(groovyscript, startUpAlframe);
1071 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
1075 // and finally, turn off batch mode indicator - if the desktop still exists
1076 if (desktop != null)
1080 desktop.setProgressBar(null, progress);
1082 desktop.setInBatchMode(false);
1086 private static void setLookAndFeel()
1088 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1090 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
1091 // try Quaqua/Vaqua.
1092 String lafProp = System.getProperty("laf");
1093 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1094 String laf = "none";
1095 if (lafProp != null)
1099 else if (lafSetting != null)
1103 boolean lafSet = false;
1106 case "crossplatform":
1107 lafSet = setCrossPlatformLookAndFeel();
1110 Console.error("Could not set requested laf=" + laf);
1114 lafSet = setSystemLookAndFeel();
1117 Console.error("Could not set requested laf=" + laf);
1121 lafSet = setGtkLookAndFeel();
1124 Console.error("Could not set requested laf=" + laf);
1128 lafSet = setMetalLookAndFeel();
1131 Console.error("Could not set requested laf=" + laf);
1135 lafSet = setNimbusLookAndFeel();
1138 Console.error("Could not set requested laf=" + laf);
1142 lafSet = setFlatLookAndFeel();
1145 Console.error("Could not set requested laf=" + laf);
1149 lafSet = setMacLookAndFeel();
1152 Console.error("Could not set requested laf=" + laf);
1158 Console.error("Requested laf=" + laf + " not implemented");
1162 setSystemLookAndFeel();
1163 if (Platform.isLinux())
1165 setLinuxLookAndFeel();
1167 if (Platform.isMac())
1169 setMacLookAndFeel();
1174 private static boolean setCrossPlatformLookAndFeel()
1176 boolean set = false;
1179 UIManager.setLookAndFeel(
1180 UIManager.getCrossPlatformLookAndFeelClassName());
1182 } catch (Exception ex)
1184 Console.error("Unexpected Look and Feel Exception");
1185 Console.error(ex.getMessage());
1186 Console.debug(Cache.getStackTraceString(ex));
1191 private static boolean setSystemLookAndFeel()
1193 boolean set = false;
1196 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
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 setSpecificLookAndFeel(String name,
1208 String className, boolean nameStartsWith)
1210 boolean set = false;
1213 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1215 if (info.getName() != null && nameStartsWith
1216 ? info.getName().toLowerCase(Locale.ROOT)
1217 .startsWith(name.toLowerCase(Locale.ROOT))
1218 : info.getName().toLowerCase(Locale.ROOT)
1219 .equals(name.toLowerCase(Locale.ROOT)))
1221 className = info.getClassName();
1225 UIManager.setLookAndFeel(className);
1227 } catch (Exception ex)
1229 Console.error("Unexpected Look and Feel Exception");
1230 Console.error(ex.getMessage());
1231 Console.debug(Cache.getStackTraceString(ex));
1236 private static boolean setGtkLookAndFeel()
1238 return setSpecificLookAndFeel("gtk",
1239 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1242 private static boolean setMetalLookAndFeel()
1244 return setSpecificLookAndFeel("metal",
1245 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1248 private static boolean setNimbusLookAndFeel()
1250 return setSpecificLookAndFeel("nimbus",
1251 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1254 private static boolean setFlatLookAndFeel()
1256 boolean set = false;
1257 if (SystemInfo.isMacOS)
1261 UIManager.setLookAndFeel(
1262 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1264 Console.debug("Using FlatMacLightLaf");
1265 } catch (ClassNotFoundException | InstantiationException
1266 | IllegalAccessException | UnsupportedLookAndFeelException e)
1268 Console.debug("Exception loading FlatLightLaf", e);
1270 System.setProperty("apple.laf.useScreenMenuBar", "true");
1271 System.setProperty("apple.awt.application.name",
1272 ChannelProperties.getProperty("app_name"));
1273 System.setProperty("apple.awt.application.appearance", "system");
1274 if (SystemInfo.isMacFullWindowContentSupported
1275 && Desktop.desktop != null)
1277 Console.debug("Setting transparent title bar");
1278 Desktop.desktop.getRootPane()
1279 .putClientProperty("apple.awt.fullWindowContent", true);
1280 Desktop.desktop.getRootPane()
1281 .putClientProperty("apple.awt.transparentTitleBar", true);
1282 Desktop.desktop.getRootPane()
1283 .putClientProperty("apple.awt.fullscreenable", true);
1285 SwingUtilities.invokeLater(() -> {
1286 FlatMacLightLaf.setup();
1288 Console.debug("Using FlatMacLightLaf");
1295 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1297 Console.debug("Using FlatLightLaf");
1298 } catch (ClassNotFoundException | InstantiationException
1299 | IllegalAccessException | UnsupportedLookAndFeelException e)
1301 Console.debug("Exception loading FlatLightLaf", e);
1303 // Windows specific properties here
1304 SwingUtilities.invokeLater(() -> {
1305 FlatLightLaf.setup();
1307 Console.debug("Using FlatLightLaf");
1310 else if (SystemInfo.isLinux)
1314 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1316 Console.debug("Using FlatLightLaf");
1317 } catch (ClassNotFoundException | InstantiationException
1318 | IllegalAccessException | UnsupportedLookAndFeelException e)
1320 Console.debug("Exception loading FlatLightLaf", e);
1322 // enable custom window decorations
1323 JFrame.setDefaultLookAndFeelDecorated(true);
1324 JDialog.setDefaultLookAndFeelDecorated(true);
1325 SwingUtilities.invokeLater(() -> {
1326 FlatLightLaf.setup();
1328 Console.debug("Using FlatLightLaf");
1336 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1338 Console.debug("Using FlatLightLaf");
1339 } catch (ClassNotFoundException | InstantiationException
1340 | IllegalAccessException | UnsupportedLookAndFeelException e)
1342 Console.debug("Exception loading FlatLightLaf", e);
1348 UIManager.put("TabbedPane.tabType", "card");
1349 UIManager.put("TabbedPane.showTabSeparators", true);
1350 UIManager.put("TabbedPane.showContentSeparator", true);
1351 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1352 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1353 UIManager.put("TabbedPane.hasFullBorder", true);
1354 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1355 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1356 UIManager.put("TabbedPane.smoothScrolling", true);
1357 UIManager.put("TabbedPane.tabWidthMode", "compact");
1358 UIManager.put("TabbedPane.selectedBackground", Color.white);
1361 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1365 private static boolean setMacLookAndFeel()
1367 boolean set = false;
1368 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1369 ChannelProperties.getProperty("app_name"));
1370 System.setProperty("apple.laf.useScreenMenuBar", "true");
1372 * broken native LAFs on (ARM?) macbooks
1373 set = setQuaquaLookAndFeel();
1374 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1375 .toLowerCase(Locale.ROOT).contains("quaqua"))
1377 set = setVaquaLookAndFeel();
1380 set = setFlatLookAndFeel();
1384 private static boolean setLinuxLookAndFeel()
1386 boolean set = false;
1387 set = setFlatLookAndFeel();
1389 set = setMetalLookAndFeel();
1390 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1392 set = setNimbusLookAndFeel();
1396 private static void showUsage()
1399 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1400 + "-nodisplay\tRun Jalview without User Interface.\n"
1401 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1402 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1403 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1404 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1405 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1406 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1407 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1408 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1409 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1410 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1411 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1412 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1413 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1414 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1415 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1416 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1417 + "-html FILE\tCreate HTML file from alignment.\n"
1418 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1419 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1420 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1421 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1422 + "-noquestionnaire\tTurn off questionnaire check.\n"
1423 + "-nonews\tTurn off check for Jalview news.\n"
1424 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1425 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1427 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1428 // after all other properties files have been read\n\t
1429 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1430 // passed in correctly)"
1431 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1432 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1433 + "-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"
1434 + "-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"
1435 + "-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"
1436 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1439 private static void startUsageStats(final Desktop desktop)
1442 * start a User Config prompt asking if we can log usage statistics.
1444 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1445 "USAGESTATS", "Jalview Usage Statistics",
1446 "Do you want to help make Jalview better by enabling "
1447 + "the collection of usage statistics with Google Analytics ?"
1448 + "\n\n(you can enable or disable usage tracking in the preferences)",
1455 "Initialising googletracker for usage stats.");
1456 Cache.initGoogleTracker();
1457 Console.debug("Tracking enabled.");
1464 Console.debug("Not enabling Google Tracking.");
1467 desktop.addDialogThread(prompter);
1471 * Locate the given string as a file and pass it to the groovy interpreter.
1473 * @param groovyscript
1474 * the script to execute
1475 * @param jalviewContext
1476 * the Jalview Desktop object passed in to the groovy binding as the
1479 private void executeGroovyScript(String groovyscript, AlignFrame af)
1482 * for scripts contained in files
1489 if (groovyscript.trim().equals("STDIN"))
1491 // read from stdin into a tempfile and execute it
1494 tfile = File.createTempFile("jalview", "groovy");
1495 PrintWriter outfile = new PrintWriter(
1496 new OutputStreamWriter(new FileOutputStream(tfile)));
1497 BufferedReader br = new BufferedReader(
1498 new InputStreamReader(System.in));
1500 while ((line = br.readLine()) != null)
1502 outfile.write(line + "\n");
1508 } catch (Exception ex)
1510 System.err.println("Failed to read from STDIN into tempfile "
1511 + ((tfile == null) ? "(tempfile wasn't created)"
1512 : tfile.toString()));
1513 ex.printStackTrace();
1518 sfile = tfile.toURI().toURL();
1519 } catch (Exception x)
1522 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1524 x.printStackTrace();
1532 sfile = new URI(groovyscript).toURL();
1533 } catch (Exception x)
1535 tfile = new File(groovyscript);
1536 if (!tfile.exists())
1538 System.err.println("File '" + groovyscript + "' does not exist.");
1541 if (!tfile.canRead())
1543 System.err.println("File '" + groovyscript + "' cannot be read.");
1546 if (tfile.length() < 1)
1548 System.err.println("File '" + groovyscript + "' is empty.");
1553 sfile = tfile.getAbsoluteFile().toURI().toURL();
1554 } catch (Exception ex)
1556 System.err.println("Failed to create a file URL for "
1557 + tfile.getAbsoluteFile());
1564 Map<String, java.lang.Object> vbinding = new HashMap<>();
1565 vbinding.put("Jalview", this);
1568 vbinding.put("currentAlFrame", af);
1570 Binding gbinding = new Binding(vbinding);
1571 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1572 gse.run(sfile.toString(), gbinding);
1573 if ("STDIN".equals(groovyscript))
1575 // delete temp file that we made -
1576 // only if it was successfully executed
1579 } catch (Exception e)
1581 System.err.println("Exception Whilst trying to execute file " + sfile
1582 + " as a groovy script.");
1583 e.printStackTrace(System.err);
1588 public static boolean isHeadlessMode()
1590 String isheadless = System.getProperty("java.awt.headless");
1591 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1598 public AlignFrame[] getAlignFrames()
1600 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1601 : Desktop.getAlignFrames();
1606 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1610 // System.exit will run the shutdownHook first
1611 Jalview.exit("Quitting now. Bye!", 0);
1614 public static AlignFrame getCurrentAlignFrame()
1616 return Jalview.currentAlignFrame;
1619 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1621 Jalview.currentAlignFrame = currentAlignFrame;
1624 protected Commands getCommands()
1629 public static void exit(String message, int exitcode)
1631 Console.debug("Using Jalview.exit");
1632 if (message != null)
1634 Console.info(message);
1636 Console.error(message);
1638 System.exit(exitcode);