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);
382 if (!Platform.isJS())
389 if (argparser.isSet(Arg.HEADLESS))
391 headless = argparser.getBool(Arg.HEADLESS);
394 if (aparser.contains("help") || aparser.contains("h"))
399 if (headless || aparser.contains("nodisplay")
400 || aparser.contains("nogui") || aparser.contains("headless"))
402 System.setProperty("java.awt.headless", "true");
407 // allow https handshakes to download intermediate certs if necessary
408 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
410 final String jabawsUrl = aparser.getValue("jabaws");
411 if (jabawsUrl != null)
415 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
417 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
418 } catch (MalformedURLException e)
421 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
426 String defs = aparser.getValue("setprop");
429 int p = defs.indexOf('=');
432 System.err.println("Ignoring invalid setprop argument : " + defs);
436 System.out.println("Executing setprop argument: " + defs);
439 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
441 // DISABLED FOR SECURITY REASONS
442 // TODO: add a property to allow properties to be overriden by cli args
443 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
445 defs = aparser.getValue("setprop");
447 if (System.getProperty("java.awt.headless") != null
448 && System.getProperty("java.awt.headless").equals("true"))
452 System.setProperty("http.agent",
453 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
457 Console.initLogger();
460 NoClassDefFoundError error)
462 error.printStackTrace();
463 System.out.println("\nEssential logging libraries not found."
464 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
472 * configure 'full' SO model if preferences say to, else use the default (full SO)
473 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
475 boolean soDefault = !Platform.isJS();
476 if (Cache.getDefault("USE_FULL_SO", soDefault))
478 SequenceOntologyFactory.setInstance(new SequenceOntology());
483 Desktop.nosplash = aparser.contains("nosplash");
484 desktop = new Desktop();
485 desktop.setInBatchMode(true); // indicate we are starting up
489 JalviewTaskbar.setTaskbar(this);
490 } catch (Exception e)
492 Console.info("Cannot set Taskbar");
493 Console.error(e.getMessage());
494 // e.printStackTrace();
495 } catch (Throwable t)
497 Console.info("Cannot set Taskbar");
498 Console.error(t.getMessage());
499 // t.printStackTrace();
502 // set Proxy settings before all the internet calls
503 Cache.setProxyPropertiesFromPreferences();
505 desktop.setVisible(true);
507 if (!Platform.isJS())
516 * Check to see that the JVM version being run is suitable for the Java
517 * version this Jalview was compiled for. Popup a warning if not.
519 if (!LaunchUtils.checkJavaVersion())
521 Console.warn("The Java version being used (Java "
522 + LaunchUtils.getJavaVersion()
523 + ") may lead to problems. This installation of Jalview should be used with Java "
524 + LaunchUtils.getJavaCompileVersion() + ".");
527 .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
530 MessageManager.getString("label.continue") };
531 JOptionPane.showOptionDialog(null,
532 MessageManager.formatMessage(
533 "warning.wrong_jvm_version_message",
534 LaunchUtils.getJavaVersion(),
535 LaunchUtils.getJavaCompileVersion()),
537 .getString("warning.wrong_jvm_version_title"),
538 JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
539 null, options, options[0]);
543 if (!aparser.contains("nowebservicediscovery"))
545 desktop.startServiceDiscovery();
547 if (!aparser.contains("nousagestats"))
549 startUsageStats(desktop);
553 System.err.println("CMD [-nousagestats] executed successfully!");
556 if (!aparser.contains("noquestionnaire"))
558 String url = aparser.getValue("questionnaire");
561 // Start the desktop questionnaire prompter with the specified
563 Console.debug("Starting questionnaire url at " + url);
564 desktop.checkForQuestionnaire(url);
565 System.out.println("CMD questionnaire[-" + url
566 + "] executed successfully!");
570 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
572 // Start the desktop questionnaire prompter with the specified
575 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
577 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
579 "Starting questionnaire with default url: " + defurl);
580 desktop.checkForQuestionnaire(defurl);
587 .println("CMD [-noquestionnaire] executed successfully!");
590 if (!aparser.contains("nonews")
591 || Cache.getProperty("NONEWS") == null)
593 desktop.checkForNews();
596 if (!aparser.contains("nohtmltemplates")
597 || Cache.getProperty("NOHTMLTEMPLATES") == null)
599 BioJsHTMLOutput.updateBioJS();
603 // Run Commands from cli
604 boolean commandsSuccess = Commands.processArgs(argparser, headless);
607 Console.info("Successfully completed commands");
613 Console.warn("Error when running commands");
618 // Check if JVM and compile version might cause problems and log if it
620 if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
622 Console.warn("The Java version being used (Java "
623 + LaunchUtils.getJavaVersion()
624 + ") may lead to problems. This installation of Jalview should be used with Java "
625 + LaunchUtils.getJavaCompileVersion() + ".");
628 // Move any new getdown-launcher-new.jar into place over old
629 // getdown-launcher.jar
630 String appdirString = System.getProperty("getdownappdir");
631 if (appdirString != null && appdirString.length() > 0)
633 final File appdir = new File(appdirString);
639 LaunchUtil.upgradeGetdown(
640 new File(appdir, "getdown-launcher-old.jar"),
641 new File(appdir, "getdown-launcher.jar"),
642 new File(appdir, "getdown-launcher-new.jar"));
647 String file = null, data = null;
649 FileFormatI format = null;
651 DataSourceType protocol = null;
653 FileLoader fileLoader = new FileLoader(!headless);
655 String groovyscript = null; // script to execute after all loading is
656 // completed one way or another
657 // extract groovy argument and execute if necessary
658 groovyscript = aparser.getValue("groovy", true);
659 file = aparser.getValue("open", true);
661 if (file == null && desktop == null)
663 System.out.println("No files to open!");
668 // Finally, deal with the remaining input data.
673 desktop.setProgressBar(
675 .getString("status.processing_commandline_args"),
676 progress = System.currentTimeMillis());
678 System.out.println("CMD [-open " + file + "] executed successfully!");
680 if (!Platform.isJS())
682 * ignore in JavaScript -- can't just file existence - could load it?
687 if (!HttpUtils.startsWithHttpOrHttps(file))
689 if (!(new File(file)).exists())
691 System.out.println("Can't find " + file);
700 protocol = AppletFormatAdapter.checkProtocol(file);
704 format = new IdentifyFile().identify(file, protocol);
705 } catch (FileFormatException e1)
710 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
714 System.out.println("error");
718 setCurrentAlignFrame(af);
719 data = aparser.getValue("colour", true);
722 data.replaceAll("%20", " ");
724 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
725 af.getViewport(), af.getViewport().getAlignment(), data);
730 "CMD [-color " + data + "] executed successfully!");
735 // Must maintain ability to use the groups flag
736 data = aparser.getValue("groups", true);
739 af.parseFeaturesFile(data,
740 AppletFormatAdapter.checkProtocol(data));
741 // System.out.println("Added " + data);
743 "CMD groups[-" + data + "] executed successfully!");
745 data = aparser.getValue("features", true);
748 af.parseFeaturesFile(data,
749 AppletFormatAdapter.checkProtocol(data));
750 // System.out.println("Added " + data);
752 "CMD [-features " + data + "] executed successfully!");
755 data = aparser.getValue("annotations", true);
758 af.loadJalviewDataFile(data, null, null, null);
759 // System.out.println("Added " + data);
761 "CMD [-annotations " + data + "] executed successfully!");
763 // set or clear the sortbytree flag.
764 if (aparser.contains("sortbytree"))
766 af.getViewport().setSortByTree(true);
767 if (af.getViewport().getSortByTree())
769 System.out.println("CMD [-sortbytree] executed successfully!");
772 if (aparser.contains("no-annotation"))
774 af.getViewport().setShowAnnotation(false);
775 if (!af.getViewport().isShowAnnotation())
777 System.out.println("CMD no-annotation executed successfully!");
780 if (aparser.contains("nosortbytree"))
782 af.getViewport().setSortByTree(false);
783 if (!af.getViewport().getSortByTree())
786 .println("CMD [-nosortbytree] executed successfully!");
789 data = aparser.getValue("tree", true);
795 "CMD [-tree " + data + "] executed successfully!");
796 NewickFile nf = new NewickFile(data,
797 AppletFormatAdapter.checkProtocol(data));
799 .setCurrentTree(af.showNewickTree(nf, data).getTree());
800 } catch (IOException ex)
802 System.err.println("Couldn't add tree " + data);
803 ex.printStackTrace(System.err);
806 // TODO - load PDB structure(s) to alignment JAL-629
807 // (associate with identical sequence in alignment, or a specified
809 if (groovyscript != null)
811 // Execute the groovy script after we've done all the rendering stuff
812 // and before any images or figures are generated.
813 System.out.println("Executing script " + groovyscript);
814 executeGroovyScript(groovyscript, af);
815 System.out.println("CMD groovy[" + groovyscript
816 + "] executed successfully!");
819 String imageName = "unnamed.png";
820 while (aparser.getSize() > 1)
822 String outputFormat = aparser.nextValue();
823 file = aparser.nextValue();
825 if (outputFormat.equalsIgnoreCase("png"))
827 af.createPNG(new File(file));
828 imageName = (new File(file)).getName();
829 System.out.println("Creating PNG image: " + file);
832 else if (outputFormat.equalsIgnoreCase("svg"))
834 File imageFile = new File(file);
835 imageName = imageFile.getName();
836 af.createSVG(imageFile);
837 System.out.println("Creating SVG image: " + file);
840 else if (outputFormat.equalsIgnoreCase("html"))
842 File imageFile = new File(file);
843 imageName = imageFile.getName();
844 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
845 htmlSVG.exportHTML(file);
847 System.out.println("Creating HTML image: " + file);
850 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
854 System.err.println("The output html file must not be null");
859 BioJsHTMLOutput.refreshVersionInfo(
860 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
861 } catch (URISyntaxException e)
865 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
866 bjs.exportHTML(file);
868 .println("Creating BioJS MSA Viwer HTML file: " + file);
871 else if (outputFormat.equalsIgnoreCase("imgMap"))
873 af.createImageMap(new File(file), imageName);
874 System.out.println("Creating image map: " + file);
877 else if (outputFormat.equalsIgnoreCase("eps"))
879 File outputFile = new File(file);
881 "Creating EPS file: " + outputFile.getAbsolutePath());
882 af.createEPS(outputFile);
885 FileFormatI outFormat = null;
888 outFormat = FileFormats.getInstance().forName(outputFormat);
889 } catch (Exception formatP)
891 System.out.println("Couldn't parse " + outFormat
892 + " as a valid Jalview format string.");
894 if (outFormat != null)
896 if (!outFormat.isWritable())
899 "This version of Jalview does not support alignment export as "
904 af.saveAlignment(file, outFormat);
905 if (af.isSaveAlignmentSuccessful())
907 System.out.println("Written alignment in "
908 + outFormat.getName() + " format to " + file);
912 System.out.println("Error writing file " + file + " in "
913 + outFormat.getName() + " format!!");
920 while (aparser.getSize() > 0)
922 System.out.println("Unknown arg: " + aparser.nextValue());
927 AlignFrame startUpAlframe = null;
928 // We'll only open the default file if the desktop is visible.
930 // ////////////////////
932 if (!Platform.isJS() && !headless && file == null
933 && Cache.getDefault("SHOW_STARTUP_FILE", true))
940 file = Cache.getDefault("STARTUP_FILE",
941 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
942 + "/examples/exampleFile_2_7.jvp");
943 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
945 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
947 file.replace("http:", "https:");
948 // hardwire upgrade of the startup file
949 file.replace("_2_3", "_2_7");
950 file.replace("2_7.jar", "2_7.jvp");
951 // and remove the stale setting
952 Cache.removeProperty("STARTUP_FILE");
955 protocol = AppletFormatAdapter.checkProtocol(file);
957 if (file.endsWith(".jar"))
959 format = FileFormat.Jalview;
965 format = new IdentifyFile().identify(file, protocol);
966 } catch (FileFormatException e)
972 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
974 // don't ask to save when quitting if only the startup file has been
976 Console.debug("Resetting up-to-date flag for startup file");
977 startUpAlframe.getViewport().setSavedUpToDate(true);
978 // extract groovy arguments before anything else.
981 // Once all other stuff is done, execute any groovy scripts (in order)
982 if (groovyscript != null)
984 if (Cache.groovyJarsPresent())
986 System.out.println("Executing script " + groovyscript);
987 executeGroovyScript(groovyscript, startUpAlframe);
992 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
996 // and finally, turn off batch mode indicator - if the desktop still exists
1001 desktop.setProgressBar(null, progress);
1003 desktop.setInBatchMode(false);
1007 private static void setLookAndFeel()
1009 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
1011 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
1012 // try Quaqua/Vaqua.
1013 String lafProp = System.getProperty("laf");
1014 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
1015 String laf = "none";
1016 if (lafProp != null)
1020 else if (lafSetting != null)
1024 boolean lafSet = false;
1027 case "crossplatform":
1028 lafSet = setCrossPlatformLookAndFeel();
1031 Console.error("Could not set requested laf=" + laf);
1035 lafSet = setSystemLookAndFeel();
1038 Console.error("Could not set requested laf=" + laf);
1042 lafSet = setGtkLookAndFeel();
1045 Console.error("Could not set requested laf=" + laf);
1049 lafSet = setMetalLookAndFeel();
1052 Console.error("Could not set requested laf=" + laf);
1056 lafSet = setNimbusLookAndFeel();
1059 Console.error("Could not set requested laf=" + laf);
1063 lafSet = setFlatLookAndFeel();
1066 Console.error("Could not set requested laf=" + laf);
1070 lafSet = setMacLookAndFeel();
1073 Console.error("Could not set requested laf=" + laf);
1079 Console.error("Requested laf=" + laf + " not implemented");
1083 setSystemLookAndFeel();
1084 if (Platform.isLinux())
1086 setLinuxLookAndFeel();
1088 if (Platform.isMac())
1090 setMacLookAndFeel();
1095 private static boolean setCrossPlatformLookAndFeel()
1097 boolean set = false;
1100 UIManager.setLookAndFeel(
1101 UIManager.getCrossPlatformLookAndFeelClassName());
1103 } catch (Exception ex)
1105 Console.error("Unexpected Look and Feel Exception");
1106 Console.error(ex.getMessage());
1107 Console.debug(Cache.getStackTraceString(ex));
1112 private static boolean setSystemLookAndFeel()
1114 boolean set = false;
1117 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
1119 } catch (Exception ex)
1121 Console.error("Unexpected Look and Feel Exception");
1122 Console.error(ex.getMessage());
1123 Console.debug(Cache.getStackTraceString(ex));
1128 private static boolean setSpecificLookAndFeel(String name,
1129 String className, boolean nameStartsWith)
1131 boolean set = false;
1134 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1136 if (info.getName() != null && nameStartsWith
1137 ? info.getName().toLowerCase(Locale.ROOT)
1138 .startsWith(name.toLowerCase(Locale.ROOT))
1139 : info.getName().toLowerCase(Locale.ROOT)
1140 .equals(name.toLowerCase(Locale.ROOT)))
1142 className = info.getClassName();
1146 UIManager.setLookAndFeel(className);
1148 } catch (Exception ex)
1150 Console.error("Unexpected Look and Feel Exception");
1151 Console.error(ex.getMessage());
1152 Console.debug(Cache.getStackTraceString(ex));
1157 private static boolean setGtkLookAndFeel()
1159 return setSpecificLookAndFeel("gtk",
1160 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1163 private static boolean setMetalLookAndFeel()
1165 return setSpecificLookAndFeel("metal",
1166 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1169 private static boolean setNimbusLookAndFeel()
1171 return setSpecificLookAndFeel("nimbus",
1172 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1175 private static boolean setFlatLookAndFeel()
1177 boolean set = false;
1178 if (SystemInfo.isMacOS)
1182 UIManager.setLookAndFeel(
1183 "com.formdev.flatlaf.themes.FlatMacLightLaf");
1185 Console.debug("Using FlatMacLightLaf");
1186 } catch (ClassNotFoundException | InstantiationException
1187 | IllegalAccessException | UnsupportedLookAndFeelException e)
1189 Console.debug("Exception loading FlatLightLaf", e);
1191 System.setProperty("apple.laf.useScreenMenuBar", "true");
1192 System.setProperty("apple.awt.application.name",
1193 ChannelProperties.getProperty("app_name"));
1194 System.setProperty("apple.awt.application.appearance", "system");
1195 if (SystemInfo.isMacFullWindowContentSupported
1196 && Desktop.desktop != null)
1198 Console.debug("Setting transparent title bar");
1199 Desktop.desktop.getRootPane()
1200 .putClientProperty("apple.awt.fullWindowContent", true);
1201 Desktop.desktop.getRootPane()
1202 .putClientProperty("apple.awt.transparentTitleBar", true);
1203 Desktop.desktop.getRootPane()
1204 .putClientProperty("apple.awt.fullscreenable", true);
1206 SwingUtilities.invokeLater(() -> {
1207 FlatMacLightLaf.setup();
1209 Console.debug("Using FlatMacLightLaf");
1216 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1218 Console.debug("Using FlatLightLaf");
1219 } catch (ClassNotFoundException | InstantiationException
1220 | IllegalAccessException | UnsupportedLookAndFeelException e)
1222 Console.debug("Exception loading FlatLightLaf", e);
1224 // Windows specific properties here
1225 SwingUtilities.invokeLater(() -> {
1226 FlatLightLaf.setup();
1228 Console.debug("Using FlatLightLaf");
1231 else if (SystemInfo.isLinux)
1235 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1237 Console.debug("Using FlatLightLaf");
1238 } catch (ClassNotFoundException | InstantiationException
1239 | IllegalAccessException | UnsupportedLookAndFeelException e)
1241 Console.debug("Exception loading FlatLightLaf", e);
1243 // enable custom window decorations
1244 JFrame.setDefaultLookAndFeelDecorated(true);
1245 JDialog.setDefaultLookAndFeelDecorated(true);
1246 SwingUtilities.invokeLater(() -> {
1247 FlatLightLaf.setup();
1249 Console.debug("Using FlatLightLaf");
1257 UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
1259 Console.debug("Using FlatLightLaf");
1260 } catch (ClassNotFoundException | InstantiationException
1261 | IllegalAccessException | UnsupportedLookAndFeelException e)
1263 Console.debug("Exception loading FlatLightLaf", e);
1269 UIManager.put("TabbedPane.tabType", "card");
1270 UIManager.put("TabbedPane.showTabSeparators", true);
1271 UIManager.put("TabbedPane.showContentSeparator", true);
1272 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1273 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1274 UIManager.put("TabbedPane.hasFullBorder", true);
1275 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1276 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1277 UIManager.put("TabbedPane.smoothScrolling", true);
1278 UIManager.put("TabbedPane.tabWidthMode", "compact");
1279 UIManager.put("TabbedPane.selectedBackground", Color.white);
1282 Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
1286 private static boolean setMacLookAndFeel()
1288 boolean set = false;
1289 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1290 ChannelProperties.getProperty("app_name"));
1291 System.setProperty("apple.laf.useScreenMenuBar", "true");
1293 * broken native LAFs on (ARM?) macbooks
1294 set = setQuaquaLookAndFeel();
1295 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1296 .toLowerCase(Locale.ROOT).contains("quaqua"))
1298 set = setVaquaLookAndFeel();
1301 set = setFlatLookAndFeel();
1305 private static boolean setLinuxLookAndFeel()
1307 boolean set = false;
1308 set = setFlatLookAndFeel();
1310 set = setMetalLookAndFeel();
1311 // avoid GtkLookAndFeel -- not good results especially on HiDPI
1313 set = setNimbusLookAndFeel();
1317 private static void showUsage()
1320 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1321 + "-nodisplay\tRun Jalview without User Interface.\n"
1322 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1323 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1324 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1325 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1326 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1327 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1328 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1329 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1330 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1331 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1332 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1333 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1334 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1335 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1336 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1337 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1338 + "-html FILE\tCreate HTML file from alignment.\n"
1339 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1340 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1341 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1342 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1343 + "-noquestionnaire\tTurn off questionnaire check.\n"
1344 + "-nonews\tTurn off check for Jalview news.\n"
1345 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1346 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1348 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1349 // after all other properties files have been read\n\t
1350 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1351 // passed in correctly)"
1352 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1353 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1354 + "-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"
1355 + "-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"
1356 + "-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"
1357 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1360 private static void startUsageStats(final Desktop desktop)
1363 * start a User Config prompt asking if we can log usage statistics.
1365 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1366 "USAGESTATS", "Jalview Usage Statistics",
1367 "Do you want to help make Jalview better by enabling "
1368 + "the collection of usage statistics with Google Analytics ?"
1369 + "\n\n(you can enable or disable usage tracking in the preferences)",
1376 "Initialising googletracker for usage stats.");
1377 Cache.initGoogleTracker();
1378 Console.debug("Tracking enabled.");
1385 Console.debug("Not enabling Google Tracking.");
1388 desktop.addDialogThread(prompter);
1392 * Locate the given string as a file and pass it to the groovy interpreter.
1394 * @param groovyscript
1395 * the script to execute
1396 * @param jalviewContext
1397 * the Jalview Desktop object passed in to the groovy binding as the
1400 private void executeGroovyScript(String groovyscript, AlignFrame af)
1403 * for scripts contained in files
1410 if (groovyscript.trim().equals("STDIN"))
1412 // read from stdin into a tempfile and execute it
1415 tfile = File.createTempFile("jalview", "groovy");
1416 PrintWriter outfile = new PrintWriter(
1417 new OutputStreamWriter(new FileOutputStream(tfile)));
1418 BufferedReader br = new BufferedReader(
1419 new InputStreamReader(System.in));
1421 while ((line = br.readLine()) != null)
1423 outfile.write(line + "\n");
1429 } catch (Exception ex)
1431 System.err.println("Failed to read from STDIN into tempfile "
1432 + ((tfile == null) ? "(tempfile wasn't created)"
1433 : tfile.toString()));
1434 ex.printStackTrace();
1439 sfile = tfile.toURI().toURL();
1440 } catch (Exception x)
1443 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1445 x.printStackTrace();
1453 sfile = new URI(groovyscript).toURL();
1454 } catch (Exception x)
1456 tfile = new File(groovyscript);
1457 if (!tfile.exists())
1459 System.err.println("File '" + groovyscript + "' does not exist.");
1462 if (!tfile.canRead())
1464 System.err.println("File '" + groovyscript + "' cannot be read.");
1467 if (tfile.length() < 1)
1469 System.err.println("File '" + groovyscript + "' is empty.");
1474 sfile = tfile.getAbsoluteFile().toURI().toURL();
1475 } catch (Exception ex)
1477 System.err.println("Failed to create a file URL for "
1478 + tfile.getAbsoluteFile());
1485 Map<String, java.lang.Object> vbinding = new HashMap<>();
1486 vbinding.put("Jalview", this);
1489 vbinding.put("currentAlFrame", af);
1491 Binding gbinding = new Binding(vbinding);
1492 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1493 gse.run(sfile.toString(), gbinding);
1494 if ("STDIN".equals(groovyscript))
1496 // delete temp file that we made -
1497 // only if it was successfully executed
1500 } catch (Exception e)
1502 System.err.println("Exception Whilst trying to execute file " + sfile
1503 + " as a groovy script.");
1504 e.printStackTrace(System.err);
1509 public static boolean isHeadlessMode()
1511 String isheadless = System.getProperty("java.awt.headless");
1512 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1519 public AlignFrame[] getAlignFrames()
1521 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1522 : Desktop.getAlignFrames();
1527 * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
1531 // System.exit will run the shutdownHook first
1535 public static AlignFrame getCurrentAlignFrame()
1537 return Jalview.currentAlignFrame;
1540 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1542 Jalview.currentAlignFrame = currentAlignFrame;