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.Vector;
44 import java.util.logging.ConsoleHandler;
45 import java.util.logging.Level;
46 import java.util.logging.Logger;
48 import javax.swing.SwingUtilities;
49 import javax.swing.UIManager;
50 import javax.swing.UIManager.LookAndFeelInfo;
52 import com.formdev.flatlaf.FlatLightLaf;
53 import com.formdev.flatlaf.util.SystemInfo;
54 import com.threerings.getdown.util.LaunchUtil;
56 import groovy.lang.Binding;
57 import groovy.util.GroovyScriptEngine;
58 import jalview.ext.so.SequenceOntology;
59 import jalview.gui.AlignFrame;
60 import jalview.gui.Desktop;
61 import jalview.gui.PromptUserConfig;
62 import jalview.io.AppletFormatAdapter;
63 import jalview.io.BioJsHTMLOutput;
64 import jalview.io.DataSourceType;
65 import jalview.io.FileFormat;
66 import jalview.io.FileFormatException;
67 import jalview.io.FileFormatI;
68 import jalview.io.FileFormats;
69 import jalview.io.FileLoader;
70 import jalview.io.HtmlSvgOutput;
71 import jalview.io.IdentifyFile;
72 import jalview.io.NewickFile;
73 import jalview.io.gff.SequenceOntologyFactory;
74 import jalview.schemes.ColourSchemeI;
75 import jalview.schemes.ColourSchemeProperty;
76 import jalview.util.ChannelProperties;
77 import jalview.util.HttpUtils;
78 import jalview.util.MessageManager;
79 import jalview.util.Platform;
80 import jalview.ws.jws2.Jws2Discoverer;
83 * Main class for Jalview Application <br>
85 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
88 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
89 * jalview.bin.Jalview jalview.bin.Jalview
91 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
92 * embellish '*' to e.g. '*.jar')
101 Platform.getURLCommandArguments();
105 * singleton instance of this class
107 private static Jalview instance;
109 private Desktop desktop;
111 public static AlignFrame currentAlignFrame;
115 if (!Platform.isJS())
122 // grab all the rights we can for the JVM
123 Policy.setPolicy(new Policy()
126 public PermissionCollection getPermissions(CodeSource codesource)
128 Permissions perms = new Permissions();
129 perms.add(new AllPermission());
134 public void refresh()
142 * keep track of feature fetching tasks.
150 * TODO: generalise to track all jalview events to orchestrate batch processing
154 private int queued = 0;
156 private int running = 0;
158 public FeatureFetcher()
163 public void addFetcher(final AlignFrame af,
164 final Vector<String> dasSources)
166 final long id = System.currentTimeMillis();
168 final FeatureFetcher us = this;
169 new Thread(new Runnable()
181 af.setProgressBar(MessageManager
182 .getString("status.das_features_being_retrived"), id);
183 af.featureSettings_actionPerformed(null);
184 af.setProgressBar(null, id);
193 public synchronized boolean allFinished()
195 return queued == 0 && running == 0;
200 public static Jalview getInstance()
206 * main class for Jalview application
209 * open <em>filename</em>
211 public static void main(String[] args)
213 // setLogging(); // BH - for event debugging in JavaScript
214 instance = new Jalview();
215 instance.doMain(args);
218 private static void logClass(String name)
220 // BH - for event debugging in JavaScript
221 ConsoleHandler consoleHandler = new ConsoleHandler();
222 consoleHandler.setLevel(Level.ALL);
223 Logger logger = Logger.getLogger(name);
224 logger.setLevel(Level.ALL);
225 logger.addHandler(consoleHandler);
228 @SuppressWarnings("unused")
229 private static void setLogging()
237 System.out.println("not in js");
240 // BH - for event debugging in JavaScript (Java mode only)
241 if (!Platform.isJS())
248 Logger.getLogger("").setLevel(Level.ALL);
249 logClass("java.awt.EventDispatchThread");
250 logClass("java.awt.EventQueue");
251 logClass("java.awt.Component");
252 logClass("java.awt.focus.Component");
253 logClass("java.awt.focus.DefaultKeyboardFocusManager");
261 void doMain(String[] args)
264 if (!Platform.isJS())
266 System.setSecurityManager(null);
270 .println("Java version: " + System.getProperty("java.version"));
271 System.out.println("Java Home: " + System.getProperty("java.home"));
272 System.out.println(System.getProperty("os.arch") + " "
273 + System.getProperty("os.name") + " "
274 + System.getProperty("os.version"));
275 String val = System.getProperty("sys.install4jVersion");
278 System.out.println("Install4j version: " + val);
280 val = System.getProperty("installer_template_version");
283 System.out.println("Install4j template version: " + val);
285 val = System.getProperty("launcher_version");
288 System.out.println("Launcher version: " + val);
291 // report Jalview version
292 Cache.loadBuildProperties(true);
294 ArgsParser aparser = new ArgsParser(args);
295 boolean headless = false;
297 String usrPropsFile = aparser.getValue("props");
298 Cache.loadProperties(usrPropsFile); // must do this before
299 if (usrPropsFile != null)
302 "CMD [-props " + usrPropsFile + "] executed successfully!");
305 if (!Platform.isJS())
312 if (aparser.contains("help") || aparser.contains("h"))
317 if (aparser.contains("nodisplay") || aparser.contains("nogui")
318 || aparser.contains("headless"))
320 System.setProperty("java.awt.headless", "true");
325 // allow https handshakes to download intermediate certs if necessary
326 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
328 final String jabawsUrl = aparser.getValue("jabaws");
329 if (jabawsUrl != null)
333 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
335 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
336 } catch (MalformedURLException e)
339 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
344 String defs = aparser.getValue("setprop");
347 int p = defs.indexOf('=');
350 System.err.println("Ignoring invalid setprop argument : " + defs);
354 System.out.println("Executing setprop argument: " + defs);
357 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
359 // DISABLED FOR SECURITY REASONS
360 // TODO: add a property to allow properties to be overriden by cli args
361 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
363 defs = aparser.getValue("setprop");
365 if (System.getProperty("java.awt.headless") != null
366 && System.getProperty("java.awt.headless").equals("true"))
370 System.setProperty("http.agent",
371 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
375 } catch (NoClassDefFoundError error)
377 error.printStackTrace();
378 System.out.println("\nEssential logging libraries not found."
379 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
388 * configure 'full' SO model if preferences say to, else use the default (full SO)
389 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
391 boolean soDefault = !Platform.isJS();
392 if (Cache.getDefault("USE_FULL_SO", soDefault))
394 SequenceOntologyFactory.setInstance(new SequenceOntology());
399 Desktop.nosplash = aparser.contains("nosplash");
400 desktop = new Desktop();
401 desktop.setInBatchMode(true); // indicate we are starting up
405 JalviewTaskbar.setTaskbar(this);
406 } catch (Exception e)
408 Cache.log.info("Cannot set Taskbar");
409 Cache.log.error(e.getMessage());
410 // e.printStackTrace();
411 } catch (Throwable t)
413 Cache.log.info("Cannot set Taskbar");
414 Cache.log.error(t.getMessage());
415 // t.printStackTrace();
418 // set Proxy settings before all the internet calls
419 Cache.setProxyPropertiesFromPreferences();
421 desktop.setVisible(true);
423 if (!Platform.isJS())
430 if (!aparser.contains("nowebservicediscovery"))
432 desktop.startServiceDiscovery();
434 if (!aparser.contains("nousagestats"))
436 startUsageStats(desktop);
440 System.err.println("CMD [-nousagestats] executed successfully!");
443 if (!aparser.contains("noquestionnaire"))
445 String url = aparser.getValue("questionnaire");
448 // Start the desktop questionnaire prompter with the specified
450 Cache.log.debug("Starting questionnaire url at " + url);
451 desktop.checkForQuestionnaire(url);
452 System.out.println("CMD questionnaire[-" + url
453 + "] executed successfully!");
457 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
459 // Start the desktop questionnaire prompter with the specified
462 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
464 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
466 "Starting questionnaire with default url: " + defurl);
467 desktop.checkForQuestionnaire(defurl);
474 .println("CMD [-noquestionnaire] executed successfully!");
477 if (!aparser.contains("nonews"))
479 desktop.checkForNews();
482 BioJsHTMLOutput.updateBioJS();
486 // Move any new getdown-launcher-new.jar into place over old
487 // getdown-launcher.jar
488 String appdirString = System.getProperty("getdownappdir");
489 if (appdirString != null && appdirString.length() > 0)
491 final File appdir = new File(appdirString);
497 LaunchUtil.upgradeGetdown(
498 new File(appdir, "getdown-launcher-old.jar"),
499 new File(appdir, "getdown-launcher.jar"),
500 new File(appdir, "getdown-launcher-new.jar"));
505 String file = null, data = null;
506 FileFormatI format = null;
507 DataSourceType protocol = null;
508 FileLoader fileLoader = new FileLoader(!headless);
510 String groovyscript = null; // script to execute after all loading is
511 // completed one way or another
512 // extract groovy argument and execute if necessary
513 groovyscript = aparser.getValue("groovy", true);
514 file = aparser.getValue("open", true);
516 if (file == null && desktop == null)
518 System.out.println("No files to open!");
522 // Finally, deal with the remaining input data.
527 desktop.setProgressBar(
529 .getString("status.processing_commandline_args"),
530 progress = System.currentTimeMillis());
532 System.out.println("CMD [-open " + file + "] executed successfully!");
534 if (!Platform.isJS())
536 * ignore in JavaScript -- can't just file existence - could load it?
541 if (!HttpUtils.startsWithHttpOrHttps(file))
543 if (!(new File(file)).exists())
545 System.out.println("Can't find " + file);
554 protocol = AppletFormatAdapter.checkProtocol(file);
558 format = new IdentifyFile().identify(file, protocol);
559 } catch (FileFormatException e1)
564 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
568 System.out.println("error");
572 setCurrentAlignFrame(af);
573 data = aparser.getValue("colour", true);
576 data.replaceAll("%20", " ");
578 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
579 af.getViewport(), af.getViewport().getAlignment(), data);
584 "CMD [-color " + data + "] executed successfully!");
589 // Must maintain ability to use the groups flag
590 data = aparser.getValue("groups", true);
593 af.parseFeaturesFile(data,
594 AppletFormatAdapter.checkProtocol(data));
595 // System.out.println("Added " + data);
597 "CMD groups[-" + data + "] executed successfully!");
599 data = aparser.getValue("features", true);
602 af.parseFeaturesFile(data,
603 AppletFormatAdapter.checkProtocol(data));
604 // System.out.println("Added " + data);
606 "CMD [-features " + data + "] executed successfully!");
609 data = aparser.getValue("annotations", true);
612 af.loadJalviewDataFile(data, null, null, null);
613 // System.out.println("Added " + data);
615 "CMD [-annotations " + data + "] executed successfully!");
617 // set or clear the sortbytree flag.
618 if (aparser.contains("sortbytree"))
620 af.getViewport().setSortByTree(true);
621 if (af.getViewport().getSortByTree())
623 System.out.println("CMD [-sortbytree] executed successfully!");
626 if (aparser.contains("no-annotation"))
628 af.getViewport().setShowAnnotation(false);
629 if (!af.getViewport().isShowAnnotation())
631 System.out.println("CMD no-annotation executed successfully!");
634 if (aparser.contains("nosortbytree"))
636 af.getViewport().setSortByTree(false);
637 if (!af.getViewport().getSortByTree())
640 .println("CMD [-nosortbytree] executed successfully!");
643 data = aparser.getValue("tree", true);
649 "CMD [-tree " + data + "] executed successfully!");
650 NewickFile nf = new NewickFile(data,
651 AppletFormatAdapter.checkProtocol(data));
653 .setCurrentTree(af.showNewickTree(nf, data).getTree());
654 } catch (IOException ex)
656 System.err.println("Couldn't add tree " + data);
657 ex.printStackTrace(System.err);
660 // TODO - load PDB structure(s) to alignment JAL-629
661 // (associate with identical sequence in alignment, or a specified
663 if (groovyscript != null)
665 // Execute the groovy script after we've done all the rendering stuff
666 // and before any images or figures are generated.
667 System.out.println("Executing script " + groovyscript);
668 executeGroovyScript(groovyscript, af);
669 System.out.println("CMD groovy[" + groovyscript
670 + "] executed successfully!");
673 String imageName = "unnamed.png";
674 while (aparser.getSize() > 1)
676 String outputFormat = aparser.nextValue();
677 file = aparser.nextValue();
679 if (outputFormat.equalsIgnoreCase("png"))
681 af.createPNG(new File(file));
682 imageName = (new File(file)).getName();
683 System.out.println("Creating PNG image: " + file);
686 else if (outputFormat.equalsIgnoreCase("svg"))
688 File imageFile = new File(file);
689 imageName = imageFile.getName();
690 af.createSVG(imageFile);
691 System.out.println("Creating SVG image: " + file);
694 else if (outputFormat.equalsIgnoreCase("html"))
696 File imageFile = new File(file);
697 imageName = imageFile.getName();
698 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
699 htmlSVG.exportHTML(file);
701 System.out.println("Creating HTML image: " + file);
704 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
708 System.err.println("The output html file must not be null");
713 BioJsHTMLOutput.refreshVersionInfo(
714 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
715 } catch (URISyntaxException e)
719 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
720 bjs.exportHTML(file);
722 .println("Creating BioJS MSA Viwer HTML file: " + file);
725 else if (outputFormat.equalsIgnoreCase("imgMap"))
727 af.createImageMap(new File(file), imageName);
728 System.out.println("Creating image map: " + file);
731 else if (outputFormat.equalsIgnoreCase("eps"))
733 File outputFile = new File(file);
735 "Creating EPS file: " + outputFile.getAbsolutePath());
736 af.createEPS(outputFile);
739 FileFormatI outFormat = null;
742 outFormat = FileFormats.getInstance().forName(outputFormat);
743 } catch (Exception formatP)
745 System.out.println("Couldn't parse " + outFormat
746 + " as a valid Jalview format string.");
748 if (outFormat != null)
750 if (!outFormat.isWritable())
753 "This version of Jalview does not support alignment export as "
758 af.saveAlignment(file, outFormat);
759 if (af.isSaveAlignmentSuccessful())
761 System.out.println("Written alignment in "
762 + outFormat.getName() + " format to " + file);
766 System.out.println("Error writing file " + file + " in "
767 + outFormat.getName() + " format!!");
774 while (aparser.getSize() > 0)
776 System.out.println("Unknown arg: " + aparser.nextValue());
780 AlignFrame startUpAlframe = null;
781 // We'll only open the default file if the desktop is visible.
783 // ////////////////////
785 if (!Platform.isJS() && !headless && file == null
786 && Cache.getDefault("SHOW_STARTUP_FILE", true))
793 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
794 jalview.bin.Cache.getDefault("www.jalview.org",
795 "https://www.jalview.org")
796 + "/examples/exampleFile_2_7.jvp");
797 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
799 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
801 file.replace("http:", "https:");
802 // hardwire upgrade of the startup file
803 file.replace("_2_3", "_2_7");
804 file.replace("2_7.jar", "2_7.jvp");
805 // and remove the stale setting
806 Cache.removeProperty("STARTUP_FILE");
809 protocol = AppletFormatAdapter.checkProtocol(file);
811 if (file.endsWith(".jar"))
813 format = FileFormat.Jalview;
819 format = new IdentifyFile().identify(file, protocol);
820 } catch (FileFormatException e)
826 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
828 // extract groovy arguments before anything else.
831 // Once all other stuff is done, execute any groovy scripts (in order)
832 if (groovyscript != null)
834 if (Cache.groovyJarsPresent())
836 System.out.println("Executing script " + groovyscript);
837 executeGroovyScript(groovyscript, startUpAlframe);
842 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
846 // and finally, turn off batch mode indicator - if the desktop still exists
851 desktop.setProgressBar(null, progress);
853 desktop.setInBatchMode(false);
857 private static void setLookAndFeel()
859 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
861 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
863 String lafProp = System.getProperty("laf");
864 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
870 else if (lafSetting != null)
874 boolean lafSet = false;
877 case "crossplatform":
878 lafSet = setCrossPlatformLookAndFeel();
881 Cache.log.error("Could not set requested laf=" + laf);
885 lafSet = setSystemLookAndFeel();
888 Cache.log.error("Could not set requested laf=" + laf);
892 lafSet = setGtkLookAndFeel();
895 Cache.log.error("Could not set requested laf=" + laf);
899 lafSet = setMetalLookAndFeel();
902 Cache.log.error("Could not set requested laf=" + laf);
906 lafSet = setNimbusLookAndFeel();
909 Cache.log.error("Could not set requested laf=" + laf);
913 lafSet = setFlatLookAndFeel();
916 Cache.log.error("Could not set requested laf=" + laf);
920 lafSet = setQuaquaLookAndFeel();
923 Cache.log.error("Could not set requested laf=" + laf);
927 lafSet = setVaquaLookAndFeel();
930 Cache.log.error("Could not set requested laf=" + laf);
934 lafSet = setMacLookAndFeel();
937 Cache.log.error("Could not set requested laf=" + laf);
943 Cache.log.error("Requested laf=" + laf + " not implemented");
947 setSystemLookAndFeel();
948 if (Platform.isLinux())
950 setFlatLookAndFeel();
952 if (Platform.isMac())
959 private static boolean setCrossPlatformLookAndFeel()
964 UIManager.setLookAndFeel(
965 UIManager.getCrossPlatformLookAndFeelClassName());
967 } catch (Exception ex)
969 Cache.log.error("Unexpected Look and Feel Exception");
970 Cache.log.error(ex.getMessage());
971 Cache.log.debug(Cache.getStackTraceString(ex));
976 private static boolean setSystemLookAndFeel()
981 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
983 } catch (Exception ex)
985 Cache.log.error("Unexpected Look and Feel Exception");
986 Cache.log.error(ex.getMessage());
987 Cache.log.debug(Cache.getStackTraceString(ex));
992 private static boolean setSpecificLookAndFeel(String name,
993 String className, boolean nameStartsWith)
998 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1000 if (info.getName() != null && nameStartsWith
1001 ? info.getName().toLowerCase(Locale.ROOT)
1002 .startsWith(name.toLowerCase(Locale.ROOT))
1003 : info.getName().toLowerCase(Locale.ROOT)
1004 .equals(name.toLowerCase(Locale.ROOT)))
1006 className = info.getClassName();
1010 UIManager.setLookAndFeel(className);
1012 } catch (Exception ex)
1014 Cache.log.error("Unexpected Look and Feel Exception");
1015 Cache.log.error(ex.getMessage());
1016 Cache.log.debug(Cache.getStackTraceString(ex));
1021 private static boolean setGtkLookAndFeel()
1023 return setSpecificLookAndFeel("gtk",
1024 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1027 private static boolean setMetalLookAndFeel()
1029 return setSpecificLookAndFeel("metal",
1030 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1033 private static boolean setNimbusLookAndFeel()
1035 return setSpecificLookAndFeel("nimbus",
1036 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1039 private static boolean setFlatLookAndFeel()
1041 boolean set = setSpecificLookAndFeel("flatlaf light",
1042 "com.formdev.flatlaf.FlatLightLaf", false);
1045 if (Platform.isMac())
1047 System.setProperty("apple.laf.useScreenMenuBar", "true");
1048 System.setProperty("apple.awt.application.name",
1049 ChannelProperties.getProperty("app_name"));
1050 System.setProperty("apple.awt.application.appearance", "system");
1051 if (SystemInfo.isMacFullWindowContentSupported
1052 && Desktop.desktop != null)
1054 Desktop.desktop.getRootPane()
1055 .putClientProperty("apple.awt.fullWindowContent", true);
1056 Desktop.desktop.getRootPane()
1057 .putClientProperty("apple.awt.transparentTitleBar", true);
1060 SwingUtilities.invokeLater(() -> {
1061 FlatLightLaf.setup();
1065 UIManager.put("TabbedPane.showTabSeparators", true);
1066 UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
1067 UIManager.put("TabbedPane.tabsOverlapBorder", true);
1068 // UIManager.put("TabbedPane.hasFullBorder", true);
1069 UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
1070 UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
1071 UIManager.put("TabbedPane.smoothScrolling", true);
1072 UIManager.put("TabbedPane.tabWidthMode", "compact");
1073 UIManager.put("TabbedPane.selectedBackground", Color.white);
1078 private static boolean setQuaquaLookAndFeel()
1080 return setSpecificLookAndFeel("quaqua",
1081 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
1086 private static boolean setVaquaLookAndFeel()
1088 return setSpecificLookAndFeel("vaqua",
1089 "org.violetlib.aqua.AquaLookAndFeel", false);
1092 private static boolean setMacLookAndFeel()
1094 boolean set = false;
1095 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1096 ChannelProperties.getProperty("app_name"));
1097 System.setProperty("apple.laf.useScreenMenuBar", "true");
1098 set = setQuaquaLookAndFeel();
1099 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1100 .toLowerCase(Locale.ROOT).contains("quaqua"))
1102 set = setVaquaLookAndFeel();
1107 private static void showUsage()
1110 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1111 + "-nodisplay\tRun Jalview without User Interface.\n"
1112 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1113 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1114 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1115 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1116 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1117 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1118 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1119 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1120 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1121 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1122 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1123 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1124 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1125 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1126 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1127 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1128 + "-html FILE\tCreate HTML file from alignment.\n"
1129 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1130 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1131 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1132 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1133 + "-noquestionnaire\tTurn off questionnaire check.\n"
1134 + "-nonews\tTurn off check for Jalview news.\n"
1135 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1136 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1138 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1139 // after all other properties files have been read\n\t
1140 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1141 // passed in correctly)"
1142 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1143 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1144 + "-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"
1145 + "-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"
1146 + "-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"
1147 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1150 private static void startUsageStats(final Desktop desktop)
1153 * start a User Config prompt asking if we can log usage statistics.
1155 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1156 "USAGESTATS", "Jalview Usage Statistics",
1157 "Do you want to help make Jalview better by enabling "
1158 + "the collection of usage statistics with Google Analytics ?"
1159 + "\n\n(you can enable or disable usage tracking in the preferences)",
1166 "Initialising googletracker for usage stats.");
1167 Cache.initGoogleTracker();
1168 Cache.log.debug("Tracking enabled.");
1175 Cache.log.debug("Not enabling Google Tracking.");
1178 desktop.addDialogThread(prompter);
1182 * Locate the given string as a file and pass it to the groovy interpreter.
1184 * @param groovyscript
1185 * the script to execute
1186 * @param jalviewContext
1187 * the Jalview Desktop object passed in to the groovy binding as the
1190 private void executeGroovyScript(String groovyscript, AlignFrame af)
1193 * for scripts contained in files
1200 if (groovyscript.trim().equals("STDIN"))
1202 // read from stdin into a tempfile and execute it
1205 tfile = File.createTempFile("jalview", "groovy");
1206 PrintWriter outfile = new PrintWriter(
1207 new OutputStreamWriter(new FileOutputStream(tfile)));
1208 BufferedReader br = new BufferedReader(
1209 new InputStreamReader(System.in));
1211 while ((line = br.readLine()) != null)
1213 outfile.write(line + "\n");
1219 } catch (Exception ex)
1221 System.err.println("Failed to read from STDIN into tempfile "
1222 + ((tfile == null) ? "(tempfile wasn't created)"
1223 : tfile.toString()));
1224 ex.printStackTrace();
1229 sfile = tfile.toURI().toURL();
1230 } catch (Exception x)
1233 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1235 x.printStackTrace();
1243 sfile = new URI(groovyscript).toURL();
1244 } catch (Exception x)
1246 tfile = new File(groovyscript);
1247 if (!tfile.exists())
1249 System.err.println("File '" + groovyscript + "' does not exist.");
1252 if (!tfile.canRead())
1254 System.err.println("File '" + groovyscript + "' cannot be read.");
1257 if (tfile.length() < 1)
1259 System.err.println("File '" + groovyscript + "' is empty.");
1264 sfile = tfile.getAbsoluteFile().toURI().toURL();
1265 } catch (Exception ex)
1267 System.err.println("Failed to create a file URL for "
1268 + tfile.getAbsoluteFile());
1275 Map<String, java.lang.Object> vbinding = new HashMap<>();
1276 vbinding.put("Jalview", this);
1279 vbinding.put("currentAlFrame", af);
1281 Binding gbinding = new Binding(vbinding);
1282 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1283 gse.run(sfile.toString(), gbinding);
1284 if ("STDIN".equals(groovyscript))
1286 // delete temp file that we made -
1287 // only if it was successfully executed
1290 } catch (Exception e)
1292 System.err.println("Exception Whilst trying to execute file " + sfile
1293 + " as a groovy script.");
1294 e.printStackTrace(System.err);
1299 public static boolean isHeadlessMode()
1301 String isheadless = System.getProperty("java.awt.headless");
1302 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1309 public AlignFrame[] getAlignFrames()
1311 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1312 : Desktop.getAlignFrames();
1317 * Quit method delegates to Desktop.quit - unless running in headless mode
1318 * when it just ends the JVM
1322 if (desktop != null)
1332 public static AlignFrame getCurrentAlignFrame()
1334 return Jalview.currentAlignFrame;
1337 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1339 Jalview.currentAlignFrame = currentAlignFrame;