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.io.BufferedReader;
25 import java.io.FileOutputStream;
26 import java.io.IOException;
27 import java.io.InputStreamReader;
28 import java.io.OutputStreamWriter;
29 import java.io.PrintWriter;
30 import java.net.BindException;
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;
42 import java.util.Vector;
43 import java.util.logging.ConsoleHandler;
44 import java.util.logging.Level;
45 import java.util.logging.Logger;
47 import javax.swing.UIManager;
48 import javax.swing.UIManager.LookAndFeelInfo;
50 import com.threerings.getdown.util.LaunchUtil;
52 import groovy.lang.Binding;
53 import groovy.util.GroovyScriptEngine;
54 import jalview.ext.so.SequenceOntology;
55 import jalview.gui.AlignFrame;
56 import jalview.gui.Desktop;
57 import jalview.gui.PromptUserConfig;
58 import jalview.httpserver.HttpServer;
59 import jalview.io.AppletFormatAdapter;
60 import jalview.io.BioJsHTMLOutput;
61 import jalview.io.DataSourceType;
62 import jalview.io.FileFormat;
63 import jalview.io.FileFormatException;
64 import jalview.io.FileFormatI;
65 import jalview.io.FileFormats;
66 import jalview.io.FileLoader;
67 import jalview.io.HtmlSvgOutput;
68 import jalview.io.IdentifyFile;
69 import jalview.io.NewickFile;
70 import jalview.io.gff.SequenceOntologyFactory;
71 import jalview.rest.API;
72 import jalview.schemes.ColourSchemeI;
73 import jalview.schemes.ColourSchemeProperty;
74 import jalview.util.ChannelProperties;
75 import jalview.util.HttpUtils;
76 import jalview.util.MessageManager;
77 import jalview.util.Platform;
78 import jalview.ws.jws2.Jws2Discoverer;
81 * Main class for Jalview Application <br>
83 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
86 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
87 * jalview.bin.Jalview jalview.bin.Jalview
89 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
90 * embellish '*' to e.g. '*.jar')
99 Platform.getURLCommandArguments();
103 * singleton instance of this class
105 private static Jalview instance;
107 private Desktop desktop;
109 public static AlignFrame currentAlignFrame;
113 if (!Platform.isJS())
120 // grab all the rights we can for the JVM
121 Policy.setPolicy(new Policy()
124 public PermissionCollection getPermissions(CodeSource codesource)
126 Permissions perms = new Permissions();
127 perms.add(new AllPermission());
132 public void refresh()
140 * keep track of feature fetching tasks.
148 * TODO: generalise to track all jalview events to orchestrate batch processing
152 private int queued = 0;
154 private int running = 0;
156 public FeatureFetcher()
161 public void addFetcher(final AlignFrame af,
162 final Vector<String> dasSources)
164 final long id = System.currentTimeMillis();
166 final FeatureFetcher us = this;
167 new Thread(new Runnable()
179 af.setProgressBar(MessageManager
180 .getString("status.das_features_being_retrived"), id);
181 af.featureSettings_actionPerformed(null);
182 af.setProgressBar(null, id);
191 public synchronized boolean allFinished()
193 return queued == 0 && running == 0;
198 public static Jalview getInstance()
204 * main class for Jalview application
207 * open <em>filename</em>
209 public static void main(String[] args)
211 // setLogging(); // BH - for event debugging in JavaScript
212 instance = new Jalview();
213 instance.doMain(args);
216 private static void logClass(String name)
218 // BH - for event debugging in JavaScript
219 ConsoleHandler consoleHandler = new ConsoleHandler();
220 consoleHandler.setLevel(Level.ALL);
221 Logger logger = Logger.getLogger(name);
222 logger.setLevel(Level.ALL);
223 logger.addHandler(consoleHandler);
226 @SuppressWarnings("unused")
227 private static void setLogging()
235 System.out.println("not in js");
238 // BH - for event debugging in JavaScript (Java mode only)
239 if (!Platform.isJS())
246 Logger.getLogger("").setLevel(Level.ALL);
247 logClass("java.awt.EventDispatchThread");
248 logClass("java.awt.EventQueue");
249 logClass("java.awt.Component");
250 logClass("java.awt.focus.Component");
251 logClass("java.awt.focus.DefaultKeyboardFocusManager");
259 void doMain(String[] args)
262 if (!Platform.isJS())
264 System.setSecurityManager(null);
268 .println("Java version: " + System.getProperty("java.version"));
269 System.out.println("Java Home: " + System.getProperty("java.home"));
270 System.out.println(System.getProperty("os.arch") + " "
271 + System.getProperty("os.name") + " "
272 + System.getProperty("os.version"));
273 String val = System.getProperty("sys.install4jVersion");
276 System.out.println("Install4j version: " + val);
278 val = System.getProperty("installer_template_version");
281 System.out.println("Install4j template version: " + val);
283 val = System.getProperty("launcher_version");
286 System.out.println("Launcher version: " + val);
289 // report Jalview version
290 Cache.loadBuildProperties(true);
292 ArgsParser aparser = new ArgsParser(args);
293 boolean headless = false;
295 String usrPropsFile = aparser.getValue("props");
296 Cache.loadProperties(usrPropsFile); // must do this before
297 if (usrPropsFile != null)
300 "CMD [-props " + usrPropsFile + "] executed successfully!");
303 if (!Platform.isJS())
310 if (aparser.contains("help") || aparser.contains("h"))
315 if (aparser.contains("nodisplay") || aparser.contains("nogui")
316 || aparser.contains("headless"))
318 System.setProperty("java.awt.headless", "true");
323 final String jabawsUrl = aparser.getValue("jabaws");
324 if (jabawsUrl != null)
328 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
330 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
331 } catch (MalformedURLException e)
334 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
339 String defs = aparser.getValue("setprop");
342 int p = defs.indexOf('=');
345 System.err.println("Ignoring invalid setprop argument : " + defs);
349 System.out.println("Executing setprop argument: " + defs);
352 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
354 // DISABLED FOR SECURITY REASONS
355 // TODO: add a property to allow properties to be overriden by cli args
356 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
358 defs = aparser.getValue("setprop");
360 if (System.getProperty("java.awt.headless") != null
361 && System.getProperty("java.awt.headless").equals("true"))
365 System.setProperty("http.agent",
366 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
370 } catch (NoClassDefFoundError error)
372 error.printStackTrace();
373 System.out.println("\nEssential logging libraries not found."
374 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
383 * configure 'full' SO model if preferences say to, else use the default (full SO)
384 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
386 boolean soDefault = !Platform.isJS();
387 if (Cache.getDefault("USE_FULL_SO", soDefault))
389 SequenceOntologyFactory.setInstance(new SequenceOntology());
394 Desktop.nosplash = aparser.contains("nosplash");
395 desktop = new Desktop();
396 desktop.setInBatchMode(true); // indicate we are starting up
400 JalviewTaskbar.setTaskbar(this);
401 } catch (Exception e)
403 Cache.log.info("Cannot set Taskbar");
404 Cache.log.error(e.getMessage());
405 // e.printStackTrace();
406 } catch (Throwable t)
408 Cache.log.info("Cannot set Taskbar");
409 Cache.log.error(t.getMessage());
410 // t.printStackTrace();
413 // set Proxy settings before all the internet calls
414 Cache.setProxyPropertiesFromPreferences();
416 desktop.setVisible(true);
418 if (!Platform.isJS())
425 if (!aparser.contains("nowebservicediscovery"))
427 desktop.startServiceDiscovery();
429 if (!aparser.contains("nousagestats"))
431 startUsageStats(desktop);
435 System.err.println("CMD [-nousagestats] executed successfully!");
438 if (!aparser.contains("noquestionnaire"))
440 String url = aparser.getValue("questionnaire");
443 // Start the desktop questionnaire prompter with the specified
445 Cache.log.debug("Starting questionnaire url at " + url);
446 desktop.checkForQuestionnaire(url);
447 System.out.println("CMD questionnaire[-" + url
448 + "] executed successfully!");
452 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
454 // Start the desktop questionnaire prompter with the specified
457 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
459 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
461 "Starting questionnaire with default url: " + defurl);
462 desktop.checkForQuestionnaire(defurl);
469 .println("CMD [-noquestionnaire] executed successfully!");
472 if (!aparser.contains("nonews"))
474 desktop.checkForNews();
477 BioJsHTMLOutput.updateBioJS();
481 // set the jetty port if suggested
482 String sPort = aparser.getValue("serverport");
488 port = Integer.parseInt(sPort);
489 HttpServer.setSuggestedPort(port);
490 Cache.info("Set suggested server port to " + port);
491 } catch (NumberFormatException e)
493 Cache.warn("server_port '" + sPort + "' not parseable as Integer");
496 // Start a TestListener
497 if (aparser.contains("genomeapi"))
501 API gb = API.getInstance();
502 Cache.info(gb.getName() + " started at "
503 + HttpServer.getInstance().getUri().toString());
504 } catch (BindException e)
506 Cache.warn("Could not open a genomeapi");
511 // Move any new getdown-launcher-new.jar into place over old
512 // getdown-launcher.jar
513 String appdirString = System.getProperty("getdownappdir");
514 if (appdirString != null && appdirString.length() > 0)
516 final File appdir = new File(appdirString);
522 LaunchUtil.upgradeGetdown(
523 new File(appdir, "getdown-launcher-old.jar"),
524 new File(appdir, "getdown-launcher.jar"),
525 new File(appdir, "getdown-launcher-new.jar"));
530 String file = null, data = null;
531 FileFormatI format = null;
532 DataSourceType protocol = null;
533 FileLoader fileLoader = new FileLoader(!headless);
535 String groovyscript = null; // script to execute after all loading is
536 // completed one way or another
537 // extract groovy argument and execute if necessary
538 groovyscript = aparser.getValue("groovy", true);
539 file = aparser.getValue("open", true);
541 if (file == null && desktop == null)
543 System.out.println("No files to open!");
547 // Finally, deal with the remaining input data.
552 desktop.setProgressBar(
554 .getString("status.processing_commandline_args"),
555 progress = System.currentTimeMillis());
557 System.out.println("CMD [-open " + file + "] executed successfully!");
559 if (!Platform.isJS())
561 * ignore in JavaScript -- can't just file existence - could load it?
566 if (!HttpUtils.startsWithHttpOrHttps(file))
568 if (!(new File(file)).exists())
570 System.out.println("Can't find " + file);
579 protocol = AppletFormatAdapter.checkProtocol(file);
583 format = new IdentifyFile().identify(file, protocol);
584 } catch (FileFormatException e1)
589 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
593 System.out.println("error");
597 setCurrentAlignFrame(af);
598 data = aparser.getValue("colour", true);
601 data.replaceAll("%20", " ");
603 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
604 af.getViewport(), af.getViewport().getAlignment(), data);
609 "CMD [-color " + data + "] executed successfully!");
614 // Must maintain ability to use the groups flag
615 data = aparser.getValue("groups", true);
618 af.parseFeaturesFile(data,
619 AppletFormatAdapter.checkProtocol(data));
620 // System.out.println("Added " + data);
622 "CMD groups[-" + data + "] executed successfully!");
624 data = aparser.getValue("features", true);
627 af.parseFeaturesFile(data,
628 AppletFormatAdapter.checkProtocol(data));
629 // System.out.println("Added " + data);
631 "CMD [-features " + data + "] executed successfully!");
634 data = aparser.getValue("annotations", true);
637 af.loadJalviewDataFile(data, null, null, null);
638 // System.out.println("Added " + data);
640 "CMD [-annotations " + data + "] executed successfully!");
642 // set or clear the sortbytree flag.
643 if (aparser.contains("sortbytree"))
645 af.getViewport().setSortByTree(true);
646 if (af.getViewport().getSortByTree())
648 System.out.println("CMD [-sortbytree] executed successfully!");
651 if (aparser.contains("no-annotation"))
653 af.getViewport().setShowAnnotation(false);
654 if (!af.getViewport().isShowAnnotation())
656 System.out.println("CMD no-annotation executed successfully!");
659 if (aparser.contains("nosortbytree"))
661 af.getViewport().setSortByTree(false);
662 if (!af.getViewport().getSortByTree())
665 .println("CMD [-nosortbytree] executed successfully!");
668 data = aparser.getValue("tree", true);
674 "CMD [-tree " + data + "] executed successfully!");
675 NewickFile nf = new NewickFile(data,
676 AppletFormatAdapter.checkProtocol(data));
678 .setCurrentTree(af.showNewickTree(nf, data).getTree());
679 } catch (IOException ex)
681 System.err.println("Couldn't add tree " + data);
682 ex.printStackTrace(System.err);
685 // TODO - load PDB structure(s) to alignment JAL-629
686 // (associate with identical sequence in alignment, or a specified
688 if (groovyscript != null)
690 // Execute the groovy script after we've done all the rendering stuff
691 // and before any images or figures are generated.
692 System.out.println("Executing script " + groovyscript);
693 executeGroovyScript(groovyscript, af);
694 System.out.println("CMD groovy[" + groovyscript
695 + "] executed successfully!");
698 String imageName = "unnamed.png";
699 while (aparser.getSize() > 1)
701 String outputFormat = aparser.nextValue();
702 file = aparser.nextValue();
704 if (outputFormat.equalsIgnoreCase("png"))
706 af.createPNG(new File(file));
707 imageName = (new File(file)).getName();
708 System.out.println("Creating PNG image: " + file);
711 else if (outputFormat.equalsIgnoreCase("svg"))
713 File imageFile = new File(file);
714 imageName = imageFile.getName();
715 af.createSVG(imageFile);
716 System.out.println("Creating SVG image: " + file);
719 else if (outputFormat.equalsIgnoreCase("html"))
721 File imageFile = new File(file);
722 imageName = imageFile.getName();
723 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
724 htmlSVG.exportHTML(file);
726 System.out.println("Creating HTML image: " + file);
729 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
733 System.err.println("The output html file must not be null");
738 BioJsHTMLOutput.refreshVersionInfo(
739 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
740 } catch (URISyntaxException e)
744 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
745 bjs.exportHTML(file);
747 .println("Creating BioJS MSA Viwer HTML file: " + file);
750 else if (outputFormat.equalsIgnoreCase("imgMap"))
752 af.createImageMap(new File(file), imageName);
753 System.out.println("Creating image map: " + file);
756 else if (outputFormat.equalsIgnoreCase("eps"))
758 File outputFile = new File(file);
760 "Creating EPS file: " + outputFile.getAbsolutePath());
761 af.createEPS(outputFile);
764 FileFormatI outFormat = null;
767 outFormat = FileFormats.getInstance().forName(outputFormat);
768 } catch (Exception formatP)
770 System.out.println("Couldn't parse " + outFormat
771 + " as a valid Jalview format string.");
773 if (outFormat != null)
775 if (!outFormat.isWritable())
778 "This version of Jalview does not support alignment export as "
783 af.saveAlignment(file, outFormat);
784 if (af.isSaveAlignmentSuccessful())
786 System.out.println("Written alignment in "
787 + outFormat.getName() + " format to " + file);
791 System.out.println("Error writing file " + file + " in "
792 + outFormat.getName() + " format!!");
799 while (aparser.getSize() > 0)
801 System.out.println("Unknown arg: " + aparser.nextValue());
805 AlignFrame startUpAlframe = null;
806 // We'll only open the default file if the desktop is visible.
808 // ////////////////////
810 if (!Platform.isJS() && !headless && file == null
811 && Cache.getDefault("SHOW_STARTUP_FILE", true))
818 file = Cache.getDefault("STARTUP_FILE",
819 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
820 + "/examples/exampleFile_2_7.jar");
822 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
824 // hardwire upgrade of the startup file
825 file.replace("_2_3.jar", "_2_7.jar");
826 // and remove the stale setting
827 Cache.removeProperty("STARTUP_FILE");
830 protocol = AppletFormatAdapter.checkProtocol(file);
832 if (file.endsWith(".jar"))
834 format = FileFormat.Jalview;
840 format = new IdentifyFile().identify(file, protocol);
841 } catch (FileFormatException e)
847 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
849 // extract groovy arguments before anything else.
852 // Once all other stuff is done, execute any groovy scripts (in order)
853 if (groovyscript != null)
855 if (Cache.groovyJarsPresent())
857 System.out.println("Executing script " + groovyscript);
858 executeGroovyScript(groovyscript, startUpAlframe);
863 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
867 // and finally, turn off batch mode indicator - if the desktop still exists
872 desktop.setProgressBar(null, progress);
874 desktop.setInBatchMode(false);
878 private static void setLookAndFeel()
880 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
882 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
884 String lafProp = System.getProperty("laf");
885 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
891 else if (lafSetting != null)
895 boolean lafSet = false;
898 case "crossplatform":
899 lafSet = setCrossPlatformLookAndFeel();
902 Cache.log.error("Could not set requested laf=" + laf);
906 lafSet = setSystemLookAndFeel();
909 Cache.log.error("Could not set requested laf=" + laf);
913 lafSet = setGtkLookAndFeel();
916 Cache.log.error("Could not set requested laf=" + laf);
920 lafSet = setMetalLookAndFeel();
923 Cache.log.error("Could not set requested laf=" + laf);
927 lafSet = setNimbusLookAndFeel();
930 Cache.log.error("Could not set requested laf=" + laf);
934 lafSet = setQuaquaLookAndFeel();
937 Cache.log.error("Could not set requested laf=" + laf);
941 lafSet = setVaquaLookAndFeel();
944 Cache.log.error("Could not set requested laf=" + laf);
948 lafSet = setMacLookAndFeel();
951 Cache.log.error("Could not set requested laf=" + laf);
957 Cache.log.error("Requested laf=" + laf + " not implemented");
961 setSystemLookAndFeel();
962 if (Platform.isLinux())
964 setMetalLookAndFeel();
966 if (Platform.isMac())
973 private static boolean setCrossPlatformLookAndFeel()
978 UIManager.setLookAndFeel(
979 UIManager.getCrossPlatformLookAndFeelClassName());
981 } catch (Exception ex)
983 Cache.log.error("Unexpected Look and Feel Exception");
984 Cache.log.error(ex.getMessage());
985 Cache.log.debug(Cache.getStackTraceString(ex));
990 private static boolean setSystemLookAndFeel()
995 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
997 } catch (Exception ex)
999 Cache.log.error("Unexpected Look and Feel Exception");
1000 Cache.log.error(ex.getMessage());
1001 Cache.log.debug(Cache.getStackTraceString(ex));
1006 private static boolean setSpecificLookAndFeel(String name,
1007 String className, boolean nameStartsWith)
1009 boolean set = false;
1012 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
1014 if (info.getName() != null && nameStartsWith
1015 ? info.getName().toLowerCase()
1016 .startsWith(name.toLowerCase())
1017 : info.getName().toLowerCase().equals(name.toLowerCase()))
1019 className = info.getClassName();
1023 UIManager.setLookAndFeel(className);
1025 } catch (Exception ex)
1027 Cache.log.error("Unexpected Look and Feel Exception");
1028 Cache.log.error(ex.getMessage());
1029 Cache.log.debug(Cache.getStackTraceString(ex));
1034 private static boolean setGtkLookAndFeel()
1036 return setSpecificLookAndFeel("gtk",
1037 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1040 private static boolean setMetalLookAndFeel()
1042 return setSpecificLookAndFeel("metal",
1043 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1046 private static boolean setNimbusLookAndFeel()
1048 return setSpecificLookAndFeel("nimbus",
1049 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1052 private static boolean setQuaquaLookAndFeel()
1054 return setSpecificLookAndFeel("quaqua",
1055 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
1060 private static boolean setVaquaLookAndFeel()
1062 return setSpecificLookAndFeel("vaqua",
1063 "org.violetlib.aqua.AquaLookAndFeel", false);
1066 private static boolean setMacLookAndFeel()
1068 boolean set = false;
1069 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1070 ChannelProperties.getProperty("app_name"));
1071 System.setProperty("apple.laf.useScreenMenuBar", "true");
1072 set = setQuaquaLookAndFeel();
1073 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1074 .toLowerCase().contains("quaqua"))
1076 set = setVaquaLookAndFeel();
1081 private static void showUsage()
1084 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1085 + "-nodisplay\tRun Jalview without User Interface.\n"
1086 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1087 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1088 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1089 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1090 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1091 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1092 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1093 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1094 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1095 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1096 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1097 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1098 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1099 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1100 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1101 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1102 + "-html FILE\tCreate HTML file from alignment.\n"
1103 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1104 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1105 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1106 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1107 + "-noquestionnaire\tTurn off questionnaire check.\n"
1108 + "-nonews\tTurn off check for Jalview news.\n"
1109 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1110 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1112 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1113 // after all other properties files have been read\n\t
1114 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1115 // passed in correctly)"
1116 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1117 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1118 + "-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"
1119 + "-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"
1120 + "-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"
1121 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
1124 private static void startUsageStats(final Desktop desktop)
1127 * start a User Config prompt asking if we can log usage statistics.
1129 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1130 "USAGESTATS", "Jalview Usage Statistics",
1131 "Do you want to help make Jalview better by enabling "
1132 + "the collection of usage statistics with Google Analytics ?"
1133 + "\n\n(you can enable or disable usage tracking in the preferences)",
1140 "Initialising googletracker for usage stats.");
1141 Cache.initGoogleTracker();
1142 Cache.log.debug("Tracking enabled.");
1149 Cache.log.debug("Not enabling Google Tracking.");
1152 desktop.addDialogThread(prompter);
1156 * Locate the given string as a file and pass it to the groovy interpreter.
1158 * @param groovyscript
1159 * the script to execute
1160 * @param jalviewContext
1161 * the Jalview Desktop object passed in to the groovy binding as the
1164 private void executeGroovyScript(String groovyscript, AlignFrame af)
1167 * for scripts contained in files
1174 if (groovyscript.trim().equals("STDIN"))
1176 // read from stdin into a tempfile and execute it
1179 tfile = File.createTempFile("jalview", "groovy");
1180 PrintWriter outfile = new PrintWriter(
1181 new OutputStreamWriter(new FileOutputStream(tfile)));
1182 BufferedReader br = new BufferedReader(
1183 new InputStreamReader(System.in));
1185 while ((line = br.readLine()) != null)
1187 outfile.write(line + "\n");
1193 } catch (Exception ex)
1195 System.err.println("Failed to read from STDIN into tempfile "
1196 + ((tfile == null) ? "(tempfile wasn't created)"
1197 : tfile.toString()));
1198 ex.printStackTrace();
1203 sfile = tfile.toURI().toURL();
1204 } catch (Exception x)
1207 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1209 x.printStackTrace();
1217 sfile = new URI(groovyscript).toURL();
1218 } catch (Exception x)
1220 tfile = new File(groovyscript);
1221 if (!tfile.exists())
1223 System.err.println("File '" + groovyscript + "' does not exist.");
1226 if (!tfile.canRead())
1228 System.err.println("File '" + groovyscript + "' cannot be read.");
1231 if (tfile.length() < 1)
1233 System.err.println("File '" + groovyscript + "' is empty.");
1238 sfile = tfile.getAbsoluteFile().toURI().toURL();
1239 } catch (Exception ex)
1241 System.err.println("Failed to create a file URL for "
1242 + tfile.getAbsoluteFile());
1249 Map<String, java.lang.Object> vbinding = new HashMap<>();
1250 vbinding.put("Jalview", this);
1253 vbinding.put("currentAlFrame", af);
1255 Binding gbinding = new Binding(vbinding);
1256 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1257 gse.run(sfile.toString(), gbinding);
1258 if ("STDIN".equals(groovyscript))
1260 // delete temp file that we made -
1261 // only if it was successfully executed
1264 } catch (Exception e)
1266 System.err.println("Exception Whilst trying to execute file " + sfile
1267 + " as a groovy script.");
1268 e.printStackTrace(System.err);
1273 public static boolean isHeadlessMode()
1275 String isheadless = System.getProperty("java.awt.headless");
1276 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1283 public AlignFrame[] getAlignFrames()
1285 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1286 : Desktop.getAlignFrames();
1291 * Quit method delegates to Desktop.quit - unless running in headless mode
1292 * when it just ends the JVM
1296 if (desktop != null)
1306 public static AlignFrame getCurrentAlignFrame()
1308 return Jalview.currentAlignFrame;
1311 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1313 Jalview.currentAlignFrame = currentAlignFrame;