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.OutputStreamWriter;
30 import java.io.PrintWriter;
31 import java.net.MalformedURLException;
33 import java.net.URISyntaxException;
35 import java.security.AllPermission;
36 import java.security.CodeSource;
37 import java.security.PermissionCollection;
38 import java.security.Permissions;
39 import java.security.Policy;
40 import java.util.HashMap;
41 import java.util.Locale;
43 import java.util.Properties;
44 import java.util.Vector;
45 import java.util.logging.ConsoleHandler;
46 import java.util.logging.Level;
47 import java.util.logging.Logger;
49 import javax.swing.JDialog;
50 import javax.swing.JFrame;
51 import javax.swing.JOptionPane;
52 import javax.swing.SwingUtilities;
53 import javax.swing.UIManager;
54 import javax.swing.UIManager.LookAndFeelInfo;
55 import javax.swing.UnsupportedLookAndFeelException;
57 import com.formdev.flatlaf.FlatLightLaf;
58 import com.formdev.flatlaf.themes.FlatMacLightLaf;
59 import com.formdev.flatlaf.util.SystemInfo;
60 import com.threerings.getdown.util.LaunchUtil;
62 //import edu.stanford.ejalbert.launching.IBrowserLaunching;
63 import groovy.lang.Binding;
64 import groovy.util.GroovyScriptEngine;
65 import jalview.bin.ArgParser.Arg;
66 import jalview.ext.so.SequenceOntology;
67 import jalview.gui.AlignFrame;
68 import jalview.gui.Desktop;
69 import jalview.gui.PromptUserConfig;
70 import jalview.gui.QuitHandler;
71 import jalview.gui.QuitHandler.QResponse;
72 import jalview.io.AppletFormatAdapter;
73 import jalview.io.BioJsHTMLOutput;
74 import jalview.io.DataSourceType;
75 import jalview.io.FileFormat;
76 import jalview.io.FileFormatException;
77 import jalview.io.FileFormatI;
78 import jalview.io.FileFormats;
79 import jalview.io.FileLoader;
80 import jalview.io.HtmlSvgOutput;
81 import jalview.io.IdentifyFile;
82 import jalview.io.NewickFile;
83 import jalview.io.gff.SequenceOntologyFactory;
84 import jalview.schemes.ColourSchemeI;
85 import jalview.schemes.ColourSchemeProperty;
86 import jalview.util.ChannelProperties;
87 import jalview.util.HttpUtils;
88 import jalview.util.LaunchUtils;
89 import jalview.util.MessageManager;
90 import jalview.util.Platform;
91 import jalview.ws.jws2.Jws2Discoverer;
94 * Main class for Jalview Application <br>
96 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
99 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
100 * jalview.bin.Jalview jalview.bin.Jalview
102 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
103 * embellish '*' to e.g. '*.jar')
106 * @version $Revision$
112 Platform.getURLCommandArguments();
113 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
114 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
115 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
116 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
120 * singleton instance of this class
122 private static Jalview instance;
124 private Desktop desktop;
126 public static AlignFrame currentAlignFrame;
130 if (!Platform.isJS())
137 // grab all the rights we can for the JVM
138 Policy.setPolicy(new Policy()
141 public PermissionCollection getPermissions(CodeSource codesource)
143 Permissions perms = new Permissions();
144 perms.add(new AllPermission());
149 public void refresh()
157 * keep track of feature fetching tasks.
165 * TODO: generalise to track all jalview events to orchestrate batch processing
169 private int queued = 0;
171 private int running = 0;
173 public FeatureFetcher()
178 public void addFetcher(final AlignFrame af,
179 final Vector<String> dasSources)
181 final long id = System.currentTimeMillis();
183 final FeatureFetcher us = this;
184 new Thread(new Runnable()
196 af.setProgressBar(MessageManager
197 .getString("status.das_features_being_retrived"), id);
198 af.featureSettings_actionPerformed(null);
199 af.setProgressBar(null, id);
208 public synchronized boolean allFinished()
210 return queued == 0 && running == 0;
215 public static Jalview getInstance()
221 * main class for Jalview application
224 * open <em>filename</em>
226 public static void main(String[] args)
228 // setLogging(); // BH - for event debugging in JavaScript
229 instance = new Jalview();
230 instance.doMain(args);
233 private static void logClass(String name)
235 // BH - for event debugging in JavaScript
236 ConsoleHandler consoleHandler = new ConsoleHandler();
237 consoleHandler.setLevel(Level.ALL);
238 Logger logger = Logger.getLogger(name);
239 logger.setLevel(Level.ALL);
240 logger.addHandler(consoleHandler);
243 @SuppressWarnings("unused")
244 private static void setLogging()
252 System.out.println("not in js");
255 // BH - for event debugging in JavaScript (Java mode only)
256 if (!Platform.isJS())
263 Logger.getLogger("").setLevel(Level.ALL);
264 logClass("java.awt.EventDispatchThread");
265 logClass("java.awt.EventQueue");
266 logClass("java.awt.Component");
267 logClass("java.awt.focus.Component");
268 logClass("java.awt.focus.DefaultKeyboardFocusManager");
276 void doMain(String[] args)
279 if (!Platform.isJS())
281 System.setSecurityManager(null);
284 // get args needed before proper ArgParser
285 Map<String, String> bootstrapArgs = ArgParser.bootstrapArgs(args);
288 .println("Java version: " + System.getProperty("java.version"));
289 System.out.println("Java Home: " + System.getProperty("java.home"));
290 System.out.println(System.getProperty("os.arch") + " "
291 + System.getProperty("os.name") + " "
292 + System.getProperty("os.version"));
294 String val = System.getProperty("sys.install4jVersion");
297 System.out.println("Install4j version: " + val);
299 val = System.getProperty("installer_template_version");
302 System.out.println("Install4j template version: " + val);
304 val = System.getProperty("launcher_version");
307 System.out.println("Launcher version: " + val);
310 if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
312 System.setProperty("flatlaf.uiScale", "1");
315 // get bootstrap properties (mainly for the logger level)
316 Properties bootstrapProperties = Cache
317 .bootstrapProperties(bootstrapArgs.get("props"));
319 // report Jalview version
320 Cache.loadBuildProperties(true);
323 ArgsParser aparser = new ArgsParser(args);
325 boolean headless = false;
329 String logLevel = bootstrapArgs.containsKey("debug") ? "DEBUG" : null;
330 if (logLevel == null && !(bootstrapProperties == null))
332 logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
334 Console.initLogger(logLevel);
335 } catch (NoClassDefFoundError error)
337 error.printStackTrace();
338 System.out.println("\nEssential logging libraries not found."
339 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
343 // register SIGTERM listener
344 Runtime.getRuntime().addShutdownHook(new Thread()
348 Console.debug("Running shutdown hook");
349 if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
351 // Got to here by a SIGTERM signal.
352 // Note we will not actually cancel the quit from here -- it's too
353 // late -- but we can wait for saving files.
354 Console.debug("Checking for saving files");
355 QuitHandler.getQuitResponse(false);
359 Console.debug("Nothing more to do");
361 Console.debug("Exiting, bye!");
362 // shutdownHook cannot be cancelled, JVM will now halt
366 String usrPropsFile = bootstrapArgs.containsKey("props")
367 ? bootstrapArgs.get("props")
368 : aparser.getValue("props");
369 Cache.loadProperties(usrPropsFile);
370 if (usrPropsFile != null)
373 "CMD [-props " + usrPropsFile + "] executed successfully!");
377 ArgParser argparser = new ArgParser(args);
379 if (argparser.isSet(Arg.HEADLESS))
380 headless = argparser.getBool(Arg.HEADLESS);
381 boolean commandsSuccess = Commands.processArgs(argparser, headless);
384 Console.info("Successfully completed commands");
390 Console.warn("Error when running commands");
395 if (!Platform.isJS())
402 if (argparser.isSet(Arg.HEADLESS))
404 headless = argparser.getBool(Arg.HEADLESS);
407 if (aparser.contains("help") || aparser.contains("h"))
412 if (headless || aparser.contains("nodisplay")
413 || aparser.contains("nogui") || aparser.contains("headless"))
415 System.setProperty("java.awt.headless", "true");
420 // allow https handshakes to download intermediate certs if necessary
421 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
423 final String jabawsUrl = aparser.getValue("jabaws");
424 if (jabawsUrl != null)
428 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
430 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
431 } catch (MalformedURLException e)
434 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
439 String defs = aparser.getValue("setprop");
442 int p = defs.indexOf('=');
445 System.err.println("Ignoring invalid setprop argument : " + defs);
449 System.out.println("Executing setprop argument: " + defs);
452 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
454 // DISABLED FOR SECURITY REASONS
455 // TODO: add a property to allow properties to be overriden by cli args
456 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
458 defs = aparser.getValue("setprop");
460 if (System.getProperty("java.awt.headless") != null
461 && System.getProperty("java.awt.headless").equals("true"))
465 System.setProperty("http.agent",
466 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
470 Console.initLogger();
473 NoClassDefFoundError error)
475 error.printStackTrace();
476 System.out.println("\nEssential logging libraries not found."
477 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
485 * configure 'full' SO model if preferences say to, else use the default (full SO)
486 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
488 boolean soDefault = !Platform.isJS();
489 if (Cache.getDefault("USE_FULL_SO", soDefault))
491 SequenceOntologyFactory.setInstance(new SequenceOntology());
496 Desktop.nosplash = aparser.contains("nosplash");
497 desktop = new Desktop();
498 desktop.setInBatchMode(true); // indicate we are starting up
502 JalviewTaskbar.setTaskbar(this);
503 } catch (Exception e)
505 Console.info("Cannot set Taskbar");
506 Console.error(e.getMessage());
507 // e.printStackTrace();
508 } catch (Throwable t)
510 Console.info("Cannot set Taskbar");
511 Console.error(t.getMessage());
512 // t.printStackTrace();
515 // set Proxy settings before all the internet calls
516 Cache.setProxyPropertiesFromPreferences();
518 desktop.setVisible(true);
520 if (!Platform.isJS())
529 * Check to see that the JVM version being run is suitable for the Java
530 * version this Jalview was compiled for. Popup a warning if not.
532 if (!LaunchUtils.checkJavaVersion())
534 Console.warn("The Java version being used (Java "
535 + LaunchUtils.getJavaVersion()
536 + ") may lead to problems. This installation of Jalview should be used with Java "
537 + LaunchUtils.getJavaCompileVersion() + ".");
540 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
543 MessageManager.getString("label.continue") };
544 JOptionPane.showOptionDialog(null,
545 MessageManager.formatMessage(
546 "warning.wrong_jvm_version_message",
547 LaunchUtils.getJavaVersion(),
548 LaunchUtils.getJavaCompileVersion()),
550 .getString("warning.wrong_jvm_version_title"),
551 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
552 null, options, options[0]);
556 if (!aparser.contains("nowebservicediscovery"))
558 desktop.startServiceDiscovery();
560 if (!aparser.contains("nousagestats"))
562 startUsageStats(desktop);
566 System.err.println("CMD [-nousagestats] executed successfully!");
569 if (!aparser.contains("noquestionnaire"))
571 String url = aparser.getValue("questionnaire");
574 // Start the desktop questionnaire prompter with the specified
576 Console.debug("Starting questionnaire url at " + url);
577 desktop.checkForQuestionnaire(url);
578 System.out.println("CMD questionnaire[-" + url
579 + "] executed successfully!");
583 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
585 // Start the desktop questionnaire prompter with the specified
588 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
590 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
592 "Starting questionnaire with default url: " + defurl);
593 desktop.checkForQuestionnaire(defurl);
600 .println("CMD [-noquestionnaire] executed successfully!");
603 if (!aparser.contains("nonews")
604 || Cache.getProperty("NONEWS") == null)
606 desktop.checkForNews();
609 if (!aparser.contains("nohtmltemplates")
610 || Cache.getProperty("NOHTMLTEMPLATES") == null)
612 BioJsHTMLOutput.updateBioJS();
617 // Check if JVM and compile version might cause problems and log if it
619 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
621 Console.warn("The Java version being used (Java "
622 + LaunchUtils.getJavaVersion()
623 + ") may lead to problems. This installation of Jalview should be used with Java "
624 + LaunchUtils.getJavaCompileVersion() + ".");
627 // Move any new getdown-launcher-new.jar into place over old
628 // getdown-launcher.jar
629 String appdirString = System.getProperty("getdownappdir");
630 if (appdirString != null && appdirString.length() > 0)
632 final File appdir = new File(appdirString);
638 LaunchUtil.upgradeGetdown(
639 new File(appdir, "getdown-launcher-old.jar"),
640 new File(appdir, "getdown-launcher.jar"),
641 new File(appdir, "getdown-launcher-new.jar"));
646 String file = null, data = null;
648 FileFormatI format = null;
650 DataSourceType protocol = null;
652 FileLoader fileLoader = new FileLoader(!headless);
654 String groovyscript = null; // script to execute after all loading is
655 // completed one way or another
656 // extract groovy argument and execute if necessary
657 groovyscript = aparser.getValue("groovy", true);
658 file = aparser.getValue("open", true);
660 if (file == null && desktop == null)
662 System.out.println("No files to open!");
667 // Finally, deal with the remaining input data.
672 desktop.setProgressBar(
674 .getString("status.processing_commandline_args"),
675 progress = System.currentTimeMillis());
677 System.out.println("CMD [-open " + file + "] executed successfully!");
679 if (!Platform.isJS())
681 * ignore in JavaScript -- can't just file existence - could load it?
686 if (!HttpUtils.startsWithHttpOrHttps(file))
688 if (!(new File(file)).exists())
690 System.out.println("Can't find " + file);
699 protocol = AppletFormatAdapter.checkProtocol(file);
703 format = new IdentifyFile().identify(file, protocol);
704 } catch (FileFormatException e1)
709 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
713 System.out.println("error");
717 setCurrentAlignFrame(af);
718 data = aparser.getValue("colour", true);
721 data.replaceAll("%20", " ");
723 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
724 af.getViewport(), af.getViewport().getAlignment(), data);
729 "CMD [-color " + data + "] executed successfully!");
734 // Must maintain ability to use the groups flag
735 data = aparser.getValue("groups", true);
738 af.parseFeaturesFile(data,
739 AppletFormatAdapter.checkProtocol(data));
740 // System.out.println("Added " + data);
742 "CMD groups[-" + data + "] executed successfully!");
744 data = aparser.getValue("features", true);
747 af.parseFeaturesFile(data,
748 AppletFormatAdapter.checkProtocol(data));
749 // System.out.println("Added " + data);
751 "CMD [-features " + data + "] executed successfully!");
754 data = aparser.getValue("annotations", true);
757 af.loadJalviewDataFile(data, null, null, null);
758 // System.out.println("Added " + data);
760 "CMD [-annotations " + data + "] executed successfully!");
762 // set or clear the sortbytree flag.
763 if (aparser.contains("sortbytree"))
765 af.getViewport().setSortByTree(true);
766 if (af.getViewport().getSortByTree())
768 System.out.println("CMD [-sortbytree] executed successfully!");
771 if (aparser.contains("no-annotation"))
773 af.getViewport().setShowAnnotation(false);
774 if (!af.getViewport().isShowAnnotation())
776 System.out.println("CMD no-annotation executed successfully!");
779 if (aparser.contains("nosortbytree"))
781 af.getViewport().setSortByTree(false);
782 if (!af.getViewport().getSortByTree())
785 .println("CMD [-nosortbytree] executed successfully!");
788 data = aparser.getValue("tree", true);
794 "CMD [-tree " + data + "] executed successfully!");
795 NewickFile nf = new NewickFile(data,
796 AppletFormatAdapter.checkProtocol(data));
798 .setCurrentTree(af.showNewickTree(nf, data).getTree());
799 } catch (IOException ex)
801 System.err.println("Couldn't add tree " + data);
802 ex.printStackTrace(System.err);
805 // TODO - load PDB structure(s) to alignment JAL-629
806 // (associate with identical sequence in alignment, or a specified
808 if (groovyscript != null)
810 // Execute the groovy script after we've done all the rendering stuff
811 // and before any images or figures are generated.
812 System.out.println("Executing script " + groovyscript);
813 executeGroovyScript(groovyscript, af);
814 System.out.println("CMD groovy[" + groovyscript
815 + "] executed successfully!");
818 String imageName = "unnamed.png";
819 while (aparser.getSize() > 1)
821 String outputFormat = aparser.nextValue();
822 file = aparser.nextValue();
824 if (outputFormat.equalsIgnoreCase("png"))
826 af.createPNG(new File(file));
827 imageName = (new File(file)).getName();
828 System.out.println("Creating PNG image: " + file);
831 else if (outputFormat.equalsIgnoreCase("svg"))
833 File imageFile = new File(file);
834 imageName = imageFile.getName();
835 af.createSVG(imageFile);
836 System.out.println("Creating SVG image: " + file);
839 else if (outputFormat.equalsIgnoreCase("html"))
841 File imageFile = new File(file);
842 imageName = imageFile.getName();
843 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
844 htmlSVG.exportHTML(file);
846 System.out.println("Creating HTML image: " + file);
849 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
853 System.err.println("The output html file must not be null");
858 BioJsHTMLOutput.refreshVersionInfo(
859 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
860 } catch (URISyntaxException e)
864 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
865 bjs.exportHTML(file);
867 .println("Creating BioJS MSA Viwer HTML file: " + file);
870 else if (outputFormat.equalsIgnoreCase("imgMap"))
872 af.createImageMap(new File(file), imageName);
873 System.out.println("Creating image map: " + file);
876 else if (outputFormat.equalsIgnoreCase("eps"))
878 File outputFile = new File(file);
880 "Creating EPS file: " + outputFile.getAbsolutePath());
881 af.createEPS(outputFile);
884 FileFormatI outFormat = null;
887 outFormat = FileFormats.getInstance().forName(outputFormat);
888 } catch (Exception formatP)
890 System.out.println("Couldn't parse " + outFormat
891 + " as a valid Jalview format string.");
893 if (outFormat != null)
895 if (!outFormat.isWritable())
898 "This version of Jalview does not support alignment export as "
903 af.saveAlignment(file, outFormat);
904 if (af.isSaveAlignmentSuccessful())
906 System.out.println("Written alignment in "
907 + outFormat.getName() + " format to " + file);
911 System.out.println("Error writing file " + file + " in "
912 + outFormat.getName() + " format!!");
919 while (aparser.getSize() > 0)
921 System.out.println("Unknown arg: " + aparser.nextValue());
926 AlignFrame startUpAlframe = null;
927 // We'll only open the default file if the desktop is visible.
929 // ////////////////////
931 if (!Platform.isJS() && !headless && file == null
932 && Cache.getDefault("SHOW_STARTUP_FILE", true))
939 file = Cache.getDefault("STARTUP_FILE",
940 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
941 + "/examples/exampleFile_2_7.jvp");
942 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
944 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
946 file.replace("http:", "https:");
947 // hardwire upgrade of the startup file
948 file.replace("_2_3", "_2_7");
949 file.replace("2_7.jar", "2_7.jvp");
950 // and remove the stale setting
951 Cache.removeProperty("STARTUP_FILE");
954 protocol = AppletFormatAdapter.checkProtocol(file);
956 if (file.endsWith(".jar"))
958 format = FileFormat.Jalview;
964 format = new IdentifyFile().identify(file, protocol);
965 } catch (FileFormatException e)
971 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
973 // don't ask to save when quitting if only the startup file has been
975 Console.debug("Resetting up-to-date flag for startup file");
976 startUpAlframe.getViewport().setSavedUpToDate(true);
977 // extract groovy arguments before anything else.
980 // Once all other stuff is done, execute any groovy scripts (in order)
981 if (groovyscript != null)
983 if (Cache.groovyJarsPresent())
985 System.out.println("Executing script " + groovyscript);
986 executeGroovyScript(groovyscript, startUpAlframe);
991 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
995 // and finally, turn off batch mode indicator - if the desktop still exists
1000 desktop.setProgressBar(null, progress);
1002 desktop.setInBatchMode(false);
1006 private static void setLookAndFeel()
1008 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1010 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
1011 // try Quaqua/Vaqua.
1012 String lafProp = System.getProperty("laf");
1013 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1014 String laf = "none";
1015 if (lafProp != null)
1019 else if (lafSetting != null)
1023 boolean lafSet = false;
1026 case "crossplatform":
1027 lafSet = setCrossPlatformLookAndFeel();
1030 Console.error("Could not set requested laf=" + laf);
1034 lafSet = setSystemLookAndFeel();
1037 Console.error("Could not set requested laf=" + laf);
1041 lafSet = setGtkLookAndFeel();
1044 Console.error("Could not set requested laf=" + laf);
1048 lafSet = setMetalLookAndFeel();
1051 Console.error("Could not set requested laf=" + laf);
1055 lafSet = setNimbusLookAndFeel();
1058 Console.error("Could not set requested laf=" + laf);
1062 lafSet = setFlatLookAndFeel();
1065 Console.error("Could not set requested laf=" + laf);
1069 lafSet = setMacLookAndFeel();
1072 Console.error("Could not set requested laf=" + laf);
1078 Console.error("Requested laf=" + laf + " not implemented");
1082 setSystemLookAndFeel();
1083 if (Platform.isLinux())
1085 setLinuxLookAndFeel();
1087 if (Platform.isMac())
1089 setMacLookAndFeel();
1094 private static boolean setCrossPlatformLookAndFeel()
1096 boolean set = false;
1099 UIManager.setLookAndFeel(
1100 UIManager.getCrossPlatformLookAndFeelClassName());
1102 } catch (Exception ex)
1104 Console.error("Unexpected Look and Feel Exception");
1105 Console.error(ex.getMessage());
1106 Console.debug(Cache.getStackTraceString(ex));
1111 private static boolean setSystemLookAndFeel()
1113 boolean set = false;
1116 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1118 } catch (Exception ex)
1120 Console.error("Unexpected Look and Feel Exception");
1121 Console.error(ex.getMessage());
1122 Console.debug(Cache.getStackTraceString(ex));
1127 private static boolean setSpecificLookAndFeel(String name,
1128 String className, boolean nameStartsWith)
1130 boolean set = false;
1133 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1135 if (info.getName() != null && nameStartsWith
1136 ? info.getName().toLowerCase(Locale.ROOT)
1137 .startsWith(name.toLowerCase(Locale.ROOT))
1138 : info.getName().toLowerCase(Locale.ROOT)
1139 .equals(name.toLowerCase(Locale.ROOT)))
1141 className = info.getClassName();
1145 UIManager.setLookAndFeel(className);
1147 } catch (Exception ex)
1149 Console.error("Unexpected Look and Feel Exception");
1150 Console.error(ex.getMessage());
1151 Console.debug(Cache.getStackTraceString(ex));
1156 private static boolean setGtkLookAndFeel()
1158 return setSpecificLookAndFeel("gtk",
1159 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1162 private static boolean setMetalLookAndFeel()
1164 return setSpecificLookAndFeel("metal",
1165 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1168 private static boolean setNimbusLookAndFeel()
1170 return setSpecificLookAndFeel("nimbus",
1171 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1174 private static boolean setFlatLookAndFeel()
1176 boolean set = false;
1177 if (SystemInfo.isMacOS)
1181 UIManager.setLookAndFeel(
1182 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1184 Console.debug("Using FlatMacLightLaf");
1185 } catch (ClassNotFoundException | InstantiationException
1186 | IllegalAccessException | UnsupportedLookAndFeelException e)
1188 Console.debug("Exception loading FlatLightLaf", e);
1190 System.setProperty("apple.laf.useScreenMenuBar", "true");
1191 System.setProperty("apple.awt.application.name",
1192 ChannelProperties.getProperty("app_name"));
1193 System.setProperty("apple.awt.application.appearance", "system");
1194 if (SystemInfo.isMacFullWindowContentSupported
1195 && Desktop.desktop != null)
1197 Console.debug("Setting transparent title bar");
1198 Desktop.desktop.getRootPane()
1199 .putClientProperty("apple.awt.fullWindowContent", true);
1200 Desktop.desktop.getRootPane()
1201 .putClientProperty("apple.awt.transparentTitleBar", true);
1202 Desktop.desktop.getRootPane()
1203 .putClientProperty("apple.awt.fullscreenable", true);
1205 SwingUtilities.invokeLater(() -> {
1206 FlatMacLightLaf.setup();
1208 Console.debug("Using FlatMacLightLaf");
1215 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1217 Console.debug("Using FlatLightLaf");
1218 } catch (ClassNotFoundException | InstantiationException
1219 | IllegalAccessException | UnsupportedLookAndFeelException e)
1221 Console.debug("Exception loading FlatLightLaf", e);
1223 // Windows specific properties here
1224 SwingUtilities.invokeLater(() -> {
1225 FlatLightLaf.setup();
1227 Console.debug("Using FlatLightLaf");
1230 else if (SystemInfo.isLinux)
1234 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1236 Console.debug("Using FlatLightLaf");
1237 } catch (ClassNotFoundException | InstantiationException
1238 | IllegalAccessException | UnsupportedLookAndFeelException e)
1240 Console.debug("Exception loading FlatLightLaf", e);
1242 // enable custom window decorations
1243 JFrame.setDefaultLookAndFeelDecorated(true);
1244 JDialog.setDefaultLookAndFeelDecorated(true);
1245 SwingUtilities.invokeLater(() -> {
1246 FlatLightLaf.setup();
1248 Console.debug("Using FlatLightLaf");
1256 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1258 Console.debug("Using FlatLightLaf");
1259 } catch (ClassNotFoundException | InstantiationException
1260 | IllegalAccessException | UnsupportedLookAndFeelException e)
1262 Console.debug("Exception loading FlatLightLaf", e);
1268 UIManager.put("TabbedPane.tabType", "card");
1269 UIManager.put("TabbedPane.showTabSeparators", true);
1270 UIManager.put("TabbedPane.showContentSeparator", true);
1271 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1272 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1273 UIManager.put("TabbedPane.hasFullBorder", true);
1274 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1275 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1276 UIManager.put("TabbedPane.smoothScrolling", true);
1277 UIManager.put("TabbedPane.tabWidthMode", "compact");
1278 UIManager.put("TabbedPane.selectedBackground", Color.white);
1281 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1285 private static boolean setMacLookAndFeel()
1287 boolean set = false;
1288 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1289 ChannelProperties.getProperty("app_name"));
1290 System.setProperty("apple.laf.useScreenMenuBar", "true");
1292 * broken native LAFs on (ARM?) macbooks
1293 set = setQuaquaLookAndFeel();
1294 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1295 .toLowerCase(Locale.ROOT).contains("quaqua"))
1297 set = setVaquaLookAndFeel();
1300 set = setFlatLookAndFeel();
1304 private static boolean setLinuxLookAndFeel()
1306 boolean set = false;
1307 set = setFlatLookAndFeel();
1309 set = setMetalLookAndFeel();
1310 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1312 set = setNimbusLookAndFeel();
1316 private static void showUsage()
1319 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1320 + "-nodisplay\tRun Jalview without User Interface.\n"
1321 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1322 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1323 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1324 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1325 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1326 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1327 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1328 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1329 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1330 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1331 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1332 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1333 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1334 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1335 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1336 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1337 + "-html FILE\tCreate HTML file from alignment.\n"
1338 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1339 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1340 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1341 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1342 + "-noquestionnaire\tTurn off questionnaire check.\n"
1343 + "-nonews\tTurn off check for Jalview news.\n"
1344 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1345 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1347 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1348 // after all other properties files have been read\n\t
1349 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1350 // passed in correctly)"
1351 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1352 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1353 + "-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"
1354 + "-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"
1355 + "-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"
1356 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1359 private static void startUsageStats(final Desktop desktop)
1362 * start a User Config prompt asking if we can log usage statistics.
1364 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1365 "USAGESTATS", "Jalview Usage Statistics",
1366 "Do you want to help make Jalview better by enabling "
1367 + "the collection of usage statistics with Google Analytics ?"
1368 + "\n\n(you can enable or disable usage tracking in the preferences)",
1375 "Initialising googletracker for usage stats.");
1376 Cache.initGoogleTracker();
1377 Console.debug("Tracking enabled.");
1384 Console.debug("Not enabling Google Tracking.");
1387 desktop.addDialogThread(prompter);
1391 * Locate the given string as a file and pass it to the groovy interpreter.
1393 * @param groovyscript
1394 * the script to execute
1395 * @param jalviewContext
1396 * the Jalview Desktop object passed in to the groovy binding as the
1399 private void executeGroovyScript(String groovyscript, AlignFrame af)
1402 * for scripts contained in files
1409 if (groovyscript.trim().equals("STDIN"))
1411 // read from stdin into a tempfile and execute it
1414 tfile = File.createTempFile("jalview", "groovy");
1415 PrintWriter outfile = new PrintWriter(
1416 new OutputStreamWriter(new FileOutputStream(tfile)));
1417 BufferedReader br = new BufferedReader(
1418 new InputStreamReader(System.in));
1420 while ((line = br.readLine()) != null)
1422 outfile.write(line + "\n");
1428 } catch (Exception ex)
1430 System.err.println("Failed to read from STDIN into tempfile "
1431 + ((tfile == null) ? "(tempfile wasn't created)"
1432 : tfile.toString()));
1433 ex.printStackTrace();
1438 sfile = tfile.toURI().toURL();
1439 } catch (Exception x)
1442 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1444 x.printStackTrace();
1452 sfile = new URI(groovyscript).toURL();
1453 } catch (Exception x)
1455 tfile = new File(groovyscript);
1456 if (!tfile.exists())
1458 System.err.println("File '" + groovyscript + "' does not exist.");
1461 if (!tfile.canRead())
1463 System.err.println("File '" + groovyscript + "' cannot be read.");
1466 if (tfile.length() < 1)
1468 System.err.println("File '" + groovyscript + "' is empty.");
1473 sfile = tfile.getAbsoluteFile().toURI().toURL();
1474 } catch (Exception ex)
1476 System.err.println("Failed to create a file URL for "
1477 + tfile.getAbsoluteFile());
1484 Map<String, java.lang.Object> vbinding = new HashMap<>();
1485 vbinding.put("Jalview", this);
1488 vbinding.put("currentAlFrame", af);
1490 Binding gbinding = new Binding(vbinding);
1491 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1492 gse.run(sfile.toString(), gbinding);
1493 if ("STDIN".equals(groovyscript))
1495 // delete temp file that we made -
1496 // only if it was successfully executed
1499 } catch (Exception e)
1501 System.err.println("Exception Whilst trying to execute file " + sfile
1502 + " as a groovy script.");
1503 e.printStackTrace(System.err);
1508 public static boolean isHeadlessMode()
1510 String isheadless = System.getProperty("java.awt.headless");
1511 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1518 public AlignFrame[] getAlignFrames()
1520 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1521 : Desktop.getAlignFrames();
1526 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1530 // System.exit will run the shutdownHook first
1534 public static AlignFrame getCurrentAlignFrame()
1536 return Jalview.currentAlignFrame;
1539 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1541 Jalview.currentAlignFrame = currentAlignFrame;