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.MalformedURLException;
32 import java.net.URISyntaxException;
34 import java.security.AllPermission;
35 import java.security.CodeSource;
36 import java.security.PermissionCollection;
37 import java.security.Permissions;
38 import java.security.Policy;
39 import java.util.HashMap;
40 import java.util.Locale;
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.io.AppletFormatAdapter;
59 import jalview.io.BioJsHTMLOutput;
60 import jalview.io.DataSourceType;
61 import jalview.io.FileFormat;
62 import jalview.io.FileFormatException;
63 import jalview.io.FileFormatI;
64 import jalview.io.FileFormats;
65 import jalview.io.FileLoader;
66 import jalview.io.HtmlSvgOutput;
67 import jalview.io.IdentifyFile;
68 import jalview.io.NewickFile;
69 import jalview.io.gff.SequenceOntologyFactory;
70 import jalview.schemes.ColourSchemeI;
71 import jalview.schemes.ColourSchemeProperty;
72 import jalview.util.ChannelProperties;
73 import jalview.util.HttpUtils;
74 import jalview.util.MessageManager;
75 import jalview.util.Platform;
76 import jalview.ws.jws2.Jws2Discoverer;
79 * Main class for Jalview Application <br>
81 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
84 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
85 * jalview.bin.Jalview jalview.bin.Jalview
87 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
88 * embellish '*' to e.g. '*.jar')
97 Platform.getURLCommandArguments();
98 Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
99 Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
100 Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
101 Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
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 Console.initLogger();
376 } catch (NoClassDefFoundError error)
378 error.printStackTrace();
379 System.out.println("\nEssential logging libraries not found."
380 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
389 * configure 'full' SO model if preferences say to, else use the default (full SO)
390 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
392 boolean soDefault = !Platform.isJS();
393 if (Cache.getDefault("USE_FULL_SO", soDefault))
395 SequenceOntologyFactory.setInstance(new SequenceOntology());
400 Desktop.nosplash = aparser.contains("nosplash");
401 desktop = new Desktop();
402 desktop.setInBatchMode(true); // indicate we are starting up
406 JalviewTaskbar.setTaskbar(this);
407 } catch (Exception e)
409 Console.info("Cannot set Taskbar");
410 Console.error(e.getMessage());
411 // e.printStackTrace();
412 } catch (Throwable t)
414 Console.info("Cannot set Taskbar");
415 Console.error(t.getMessage());
416 // t.printStackTrace();
419 // set Proxy settings before all the internet calls
420 Cache.setProxyPropertiesFromPreferences();
422 desktop.setVisible(true);
424 if (!Platform.isJS())
431 if (!aparser.contains("nowebservicediscovery"))
433 desktop.startServiceDiscovery();
435 if (!aparser.contains("nousagestats"))
437 startUsageStats(desktop);
441 System.err.println("CMD [-nousagestats] executed successfully!");
444 if (!aparser.contains("noquestionnaire"))
446 String url = aparser.getValue("questionnaire");
449 // Start the desktop questionnaire prompter with the specified
451 Console.debug("Starting questionnaire url at " + url);
452 desktop.checkForQuestionnaire(url);
453 System.out.println("CMD questionnaire[-" + url
454 + "] executed successfully!");
458 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
460 // Start the desktop questionnaire prompter with the specified
463 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
465 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
467 "Starting questionnaire with default url: " + defurl);
468 desktop.checkForQuestionnaire(defurl);
475 .println("CMD [-noquestionnaire] executed successfully!");
478 if (!aparser.contains("nonews"))
480 desktop.checkForNews();
483 BioJsHTMLOutput.updateBioJS();
487 // Move any new getdown-launcher-new.jar into place over old
488 // getdown-launcher.jar
489 String appdirString = System.getProperty("getdownappdir");
490 if (appdirString != null && appdirString.length() > 0)
492 final File appdir = new File(appdirString);
498 LaunchUtil.upgradeGetdown(
499 new File(appdir, "getdown-launcher-old.jar"),
500 new File(appdir, "getdown-launcher.jar"),
501 new File(appdir, "getdown-launcher-new.jar"));
506 String file = null, data = null;
507 FileFormatI format = null;
508 DataSourceType protocol = null;
509 FileLoader fileLoader = new FileLoader(!headless);
511 String groovyscript = null; // script to execute after all loading is
512 // completed one way or another
513 // extract groovy argument and execute if necessary
514 groovyscript = aparser.getValue("groovy", true);
515 file = aparser.getValue("open", true);
517 if (file == null && desktop == null)
519 System.out.println("No files to open!");
523 // Finally, deal with the remaining input data.
528 desktop.setProgressBar(
530 .getString("status.processing_commandline_args"),
531 progress = System.currentTimeMillis());
533 System.out.println("CMD [-open " + file + "] executed successfully!");
535 if (!Platform.isJS())
537 * ignore in JavaScript -- can't just file existence - could load it?
542 if (!HttpUtils.startsWithHttpOrHttps(file))
544 if (!(new File(file)).exists())
546 System.out.println("Can't find " + file);
555 protocol = AppletFormatAdapter.checkProtocol(file);
559 format = new IdentifyFile().identify(file, protocol);
560 } catch (FileFormatException e1)
565 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
569 System.out.println("error");
573 setCurrentAlignFrame(af);
574 data = aparser.getValue("colour", true);
577 data.replaceAll("%20", " ");
579 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
580 af.getViewport(), af.getViewport().getAlignment(), data);
585 "CMD [-color " + data + "] executed successfully!");
590 // Must maintain ability to use the groups flag
591 data = aparser.getValue("groups", true);
594 af.parseFeaturesFile(data,
595 AppletFormatAdapter.checkProtocol(data));
596 // System.out.println("Added " + data);
598 "CMD groups[-" + data + "] executed successfully!");
600 data = aparser.getValue("features", true);
603 af.parseFeaturesFile(data,
604 AppletFormatAdapter.checkProtocol(data));
605 // System.out.println("Added " + data);
607 "CMD [-features " + data + "] executed successfully!");
610 data = aparser.getValue("annotations", true);
613 af.loadJalviewDataFile(data, null, null, null);
614 // System.out.println("Added " + data);
616 "CMD [-annotations " + data + "] executed successfully!");
618 // set or clear the sortbytree flag.
619 if (aparser.contains("sortbytree"))
621 af.getViewport().setSortByTree(true);
622 if (af.getViewport().getSortByTree())
624 System.out.println("CMD [-sortbytree] executed successfully!");
627 if (aparser.contains("no-annotation"))
629 af.getViewport().setShowAnnotation(false);
630 if (!af.getViewport().isShowAnnotation())
632 System.out.println("CMD no-annotation executed successfully!");
635 if (aparser.contains("nosortbytree"))
637 af.getViewport().setSortByTree(false);
638 if (!af.getViewport().getSortByTree())
641 .println("CMD [-nosortbytree] executed successfully!");
644 data = aparser.getValue("tree", true);
650 "CMD [-tree " + data + "] executed successfully!");
651 NewickFile nf = new NewickFile(data,
652 AppletFormatAdapter.checkProtocol(data));
654 .setCurrentTree(af.showNewickTree(nf, data).getTree());
655 } catch (IOException ex)
657 System.err.println("Couldn't add tree " + data);
658 ex.printStackTrace(System.err);
661 // TODO - load PDB structure(s) to alignment JAL-629
662 // (associate with identical sequence in alignment, or a specified
664 if (groovyscript != null)
666 // Execute the groovy script after we've done all the rendering stuff
667 // and before any images or figures are generated.
668 System.out.println("Executing script " + groovyscript);
669 executeGroovyScript(groovyscript, af);
670 System.out.println("CMD groovy[" + groovyscript
671 + "] executed successfully!");
674 String imageName = "unnamed.png";
675 while (aparser.getSize() > 1)
677 String outputFormat = aparser.nextValue();
678 file = aparser.nextValue();
680 if (outputFormat.equalsIgnoreCase("png"))
682 af.createPNG(new File(file));
683 imageName = (new File(file)).getName();
684 System.out.println("Creating PNG image: " + file);
687 else if (outputFormat.equalsIgnoreCase("svg"))
689 File imageFile = new File(file);
690 imageName = imageFile.getName();
691 af.createSVG(imageFile);
692 System.out.println("Creating SVG image: " + file);
695 else if (outputFormat.equalsIgnoreCase("html"))
697 File imageFile = new File(file);
698 imageName = imageFile.getName();
699 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
700 htmlSVG.exportHTML(file);
702 System.out.println("Creating HTML image: " + file);
705 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
709 System.err.println("The output html file must not be null");
714 BioJsHTMLOutput.refreshVersionInfo(
715 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
716 } catch (URISyntaxException e)
720 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
721 bjs.exportHTML(file);
723 .println("Creating BioJS MSA Viwer HTML file: " + file);
726 else if (outputFormat.equalsIgnoreCase("imgMap"))
728 af.createImageMap(new File(file), imageName);
729 System.out.println("Creating image map: " + file);
732 else if (outputFormat.equalsIgnoreCase("eps"))
734 File outputFile = new File(file);
736 "Creating EPS file: " + outputFile.getAbsolutePath());
737 af.createEPS(outputFile);
740 FileFormatI outFormat = null;
743 outFormat = FileFormats.getInstance().forName(outputFormat);
744 } catch (Exception formatP)
746 System.out.println("Couldn't parse " + outFormat
747 + " as a valid Jalview format string.");
749 if (outFormat != null)
751 if (!outFormat.isWritable())
754 "This version of Jalview does not support alignment export as "
759 af.saveAlignment(file, outFormat);
760 if (af.isSaveAlignmentSuccessful())
762 System.out.println("Written alignment in "
763 + outFormat.getName() + " format to " + file);
767 System.out.println("Error writing file " + file + " in "
768 + outFormat.getName() + " format!!");
775 while (aparser.getSize() > 0)
777 System.out.println("Unknown arg: " + aparser.nextValue());
781 AlignFrame startUpAlframe = null;
782 // We'll only open the default file if the desktop is visible.
784 // ////////////////////
786 if (!Platform.isJS() && !headless && file == null
787 && Cache.getDefault("SHOW_STARTUP_FILE", true))
794 file = Cache.getDefault("STARTUP_FILE",
795 Cache.getDefault("www.jalview.org", "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" or
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 Console.error("Could not set requested laf=" + laf);
885 lafSet = setSystemLookAndFeel();
888 Console.error("Could not set requested laf=" + laf);
892 lafSet = setGtkLookAndFeel();
895 Console.error("Could not set requested laf=" + laf);
899 lafSet = setMetalLookAndFeel();
902 Console.error("Could not set requested laf=" + laf);
906 lafSet = setNimbusLookAndFeel();
909 Console.error("Could not set requested laf=" + laf);
913 lafSet = setQuaquaLookAndFeel();
916 Console.error("Could not set requested laf=" + laf);
920 lafSet = setVaquaLookAndFeel();
923 Console.error("Could not set requested laf=" + laf);
927 lafSet = setMacLookAndFeel();
930 Console.error("Could not set requested laf=" + laf);
936 Console.error("Requested laf=" + laf + " not implemented");
940 setSystemLookAndFeel();
941 if (Platform.isLinux())
943 setMetalLookAndFeel();
945 if (Platform.isMac())
952 private static boolean setCrossPlatformLookAndFeel()
957 UIManager.setLookAndFeel(
958 UIManager.getCrossPlatformLookAndFeelClassName());
960 } catch (Exception ex)
962 Console.error("Unexpected Look and Feel Exception");
963 Console.error(ex.getMessage());
964 Console.debug(Cache.getStackTraceString(ex));
969 private static boolean setSystemLookAndFeel()
974 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
976 } catch (Exception ex)
978 Console.error("Unexpected Look and Feel Exception");
979 Console.error(ex.getMessage());
980 Console.debug(Cache.getStackTraceString(ex));
985 private static boolean setSpecificLookAndFeel(String name,
986 String className, boolean nameStartsWith)
991 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
993 if (info.getName() != null && nameStartsWith
994 ? info.getName().toLowerCase(Locale.ROOT)
995 .startsWith(name.toLowerCase(Locale.ROOT))
996 : info.getName().toLowerCase(Locale.ROOT)
997 .equals(name.toLowerCase(Locale.ROOT)))
999 className = info.getClassName();
1003 UIManager.setLookAndFeel(className);
1005 } catch (Exception ex)
1007 Console.error("Unexpected Look and Feel Exception");
1008 Console.error(ex.getMessage());
1009 Console.debug(Cache.getStackTraceString(ex));
1014 private static boolean setGtkLookAndFeel()
1016 return setSpecificLookAndFeel("gtk",
1017 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1020 private static boolean setMetalLookAndFeel()
1022 return setSpecificLookAndFeel("metal",
1023 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1026 private static boolean setNimbusLookAndFeel()
1028 return setSpecificLookAndFeel("nimbus",
1029 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1032 private static boolean setQuaquaLookAndFeel()
1034 return setSpecificLookAndFeel("quaqua",
1035 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
1040 private static boolean setVaquaLookAndFeel()
1042 return setSpecificLookAndFeel("vaqua",
1043 "org.violetlib.aqua.AquaLookAndFeel", false);
1046 private static boolean setMacLookAndFeel()
1048 boolean set = false;
1049 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1050 ChannelProperties.getProperty("app_name"));
1051 System.setProperty("apple.laf.useScreenMenuBar", "true");
1052 set = setQuaquaLookAndFeel();
1053 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1054 .toLowerCase(Locale.ROOT).contains("quaqua"))
1056 set = setVaquaLookAndFeel();
1061 private static void showUsage()
1064 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1065 + "-nodisplay\tRun Jalview without User Interface.\n"
1066 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1067 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1068 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1069 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1070 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1071 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1072 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1073 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1074 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1075 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1076 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1077 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1078 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1079 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1080 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1081 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1082 + "-html FILE\tCreate HTML file from alignment.\n"
1083 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1084 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1085 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1086 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1087 + "-noquestionnaire\tTurn off questionnaire check.\n"
1088 + "-nonews\tTurn off check for Jalview news.\n"
1089 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1090 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1092 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1093 // after all other properties files have been read\n\t
1094 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1095 // passed in correctly)"
1096 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1097 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1098 + "-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"
1099 + "-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"
1100 + "-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"
1101 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1104 private static void startUsageStats(final Desktop desktop)
1107 * start a User Config prompt asking if we can log usage statistics.
1109 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1110 "USAGESTATS", "Jalview Usage Statistics",
1111 "Do you want to help make Jalview better by enabling "
1112 + "the collection of usage statistics with Google Analytics ?"
1113 + "\n\n(you can enable or disable usage tracking in the preferences)",
1119 Console.debug("Initialising googletracker for usage stats.");
1120 Cache.initGoogleTracker();
1121 Console.debug("Tracking enabled.");
1128 Console.debug("Not enabling Google Tracking.");
1131 desktop.addDialogThread(prompter);
1135 * Locate the given string as a file and pass it to the groovy interpreter.
1137 * @param groovyscript
1138 * the script to execute
1139 * @param jalviewContext
1140 * the Jalview Desktop object passed in to the groovy binding as the
1143 private void executeGroovyScript(String groovyscript, AlignFrame af)
1146 * for scripts contained in files
1153 if (groovyscript.trim().equals("STDIN"))
1155 // read from stdin into a tempfile and execute it
1158 tfile = File.createTempFile("jalview", "groovy");
1159 PrintWriter outfile = new PrintWriter(
1160 new OutputStreamWriter(new FileOutputStream(tfile)));
1161 BufferedReader br = new BufferedReader(
1162 new InputStreamReader(System.in));
1164 while ((line = br.readLine()) != null)
1166 outfile.write(line + "\n");
1172 } catch (Exception ex)
1174 System.err.println("Failed to read from STDIN into tempfile "
1175 + ((tfile == null) ? "(tempfile wasn't created)"
1176 : tfile.toString()));
1177 ex.printStackTrace();
1182 sfile = tfile.toURI().toURL();
1183 } catch (Exception x)
1186 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1188 x.printStackTrace();
1196 sfile = new URI(groovyscript).toURL();
1197 } catch (Exception x)
1199 tfile = new File(groovyscript);
1200 if (!tfile.exists())
1202 System.err.println("File '" + groovyscript + "' does not exist.");
1205 if (!tfile.canRead())
1207 System.err.println("File '" + groovyscript + "' cannot be read.");
1210 if (tfile.length() < 1)
1212 System.err.println("File '" + groovyscript + "' is empty.");
1217 sfile = tfile.getAbsoluteFile().toURI().toURL();
1218 } catch (Exception ex)
1220 System.err.println("Failed to create a file URL for "
1221 + tfile.getAbsoluteFile());
1228 Map<String, java.lang.Object> vbinding = new HashMap<>();
1229 vbinding.put("Jalview", this);
1232 vbinding.put("currentAlFrame", af);
1234 Binding gbinding = new Binding(vbinding);
1235 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1236 gse.run(sfile.toString(), gbinding);
1237 if ("STDIN".equals(groovyscript))
1239 // delete temp file that we made -
1240 // only if it was successfully executed
1243 } catch (Exception e)
1245 System.err.println("Exception Whilst trying to execute file " + sfile
1246 + " as a groovy script.");
1247 e.printStackTrace(System.err);
1252 public static boolean isHeadlessMode()
1254 String isheadless = System.getProperty("java.awt.headless");
1255 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1262 public AlignFrame[] getAlignFrames()
1264 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1265 : Desktop.getAlignFrames();
1270 * Quit method delegates to Desktop.quit - unless running in headless mode
1271 * when it just ends the JVM
1275 if (desktop != null)
1285 public static AlignFrame getCurrentAlignFrame()
1287 return Jalview.currentAlignFrame;
1290 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1292 Jalview.currentAlignFrame = currentAlignFrame;