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")
479 || Cache.getProperty("NONEWS") == null)
481 desktop.checkForNews();
484 if (!aparser.contains("nohtmltemplates")
485 || Cache.getProperty("NOHTMLTEMPLATES") == null)
487 BioJsHTMLOutput.updateBioJS();
492 // Move any new getdown-launcher-new.jar into place over old
493 // getdown-launcher.jar
494 String appdirString = System.getProperty("getdownappdir");
495 if (appdirString != null && appdirString.length() > 0)
497 final File appdir = new File(appdirString);
503 LaunchUtil.upgradeGetdown(
504 new File(appdir, "getdown-launcher-old.jar"),
505 new File(appdir, "getdown-launcher.jar"),
506 new File(appdir, "getdown-launcher-new.jar"));
511 String file = null, data = null;
512 FileFormatI format = null;
513 DataSourceType protocol = null;
514 FileLoader fileLoader = new FileLoader(!headless);
516 String groovyscript = null; // script to execute after all loading is
517 // completed one way or another
518 // extract groovy argument and execute if necessary
519 groovyscript = aparser.getValue("groovy", true);
520 file = aparser.getValue("open", true);
522 if (file == null && desktop == null)
524 System.out.println("No files to open!");
528 // Finally, deal with the remaining input data.
533 desktop.setProgressBar(
535 .getString("status.processing_commandline_args"),
536 progress = System.currentTimeMillis());
538 System.out.println("CMD [-open " + file + "] executed successfully!");
540 if (!Platform.isJS())
542 * ignore in JavaScript -- can't just file existence - could load it?
547 if (!HttpUtils.startsWithHttpOrHttps(file))
549 if (!(new File(file)).exists())
551 System.out.println("Can't find " + file);
560 protocol = AppletFormatAdapter.checkProtocol(file);
564 format = new IdentifyFile().identify(file, protocol);
565 } catch (FileFormatException e1)
570 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
574 System.out.println("error");
578 setCurrentAlignFrame(af);
579 data = aparser.getValue("colour", true);
582 data.replaceAll("%20", " ");
584 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
585 af.getViewport(), af.getViewport().getAlignment(), data);
590 "CMD [-color " + data + "] executed successfully!");
595 // Must maintain ability to use the groups flag
596 data = aparser.getValue("groups", true);
599 af.parseFeaturesFile(data,
600 AppletFormatAdapter.checkProtocol(data));
601 // System.out.println("Added " + data);
603 "CMD groups[-" + data + "] executed successfully!");
605 data = aparser.getValue("features", true);
608 af.parseFeaturesFile(data,
609 AppletFormatAdapter.checkProtocol(data));
610 // System.out.println("Added " + data);
612 "CMD [-features " + data + "] executed successfully!");
615 data = aparser.getValue("annotations", true);
618 af.loadJalviewDataFile(data, null, null, null);
619 // System.out.println("Added " + data);
621 "CMD [-annotations " + data + "] executed successfully!");
623 // set or clear the sortbytree flag.
624 if (aparser.contains("sortbytree"))
626 af.getViewport().setSortByTree(true);
627 if (af.getViewport().getSortByTree())
629 System.out.println("CMD [-sortbytree] executed successfully!");
632 if (aparser.contains("no-annotation"))
634 af.getViewport().setShowAnnotation(false);
635 if (!af.getViewport().isShowAnnotation())
637 System.out.println("CMD no-annotation executed successfully!");
640 if (aparser.contains("nosortbytree"))
642 af.getViewport().setSortByTree(false);
643 if (!af.getViewport().getSortByTree())
646 .println("CMD [-nosortbytree] executed successfully!");
649 data = aparser.getValue("tree", true);
655 "CMD [-tree " + data + "] executed successfully!");
656 NewickFile nf = new NewickFile(data,
657 AppletFormatAdapter.checkProtocol(data));
659 .setCurrentTree(af.showNewickTree(nf, data).getTree());
660 } catch (IOException ex)
662 System.err.println("Couldn't add tree " + data);
663 ex.printStackTrace(System.err);
666 // TODO - load PDB structure(s) to alignment JAL-629
667 // (associate with identical sequence in alignment, or a specified
669 if (groovyscript != null)
671 // Execute the groovy script after we've done all the rendering stuff
672 // and before any images or figures are generated.
673 System.out.println("Executing script " + groovyscript);
674 executeGroovyScript(groovyscript, af);
675 System.out.println("CMD groovy[" + groovyscript
676 + "] executed successfully!");
679 String imageName = "unnamed.png";
680 while (aparser.getSize() > 1)
682 String outputFormat = aparser.nextValue();
683 file = aparser.nextValue();
685 if (outputFormat.equalsIgnoreCase("png"))
687 af.createPNG(new File(file));
688 imageName = (new File(file)).getName();
689 System.out.println("Creating PNG image: " + file);
692 else if (outputFormat.equalsIgnoreCase("svg"))
694 File imageFile = new File(file);
695 imageName = imageFile.getName();
696 af.createSVG(imageFile);
697 System.out.println("Creating SVG image: " + file);
700 else if (outputFormat.equalsIgnoreCase("html"))
702 File imageFile = new File(file);
703 imageName = imageFile.getName();
704 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
705 htmlSVG.exportHTML(file);
707 System.out.println("Creating HTML image: " + file);
710 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
714 System.err.println("The output html file must not be null");
719 BioJsHTMLOutput.refreshVersionInfo(
720 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
721 } catch (URISyntaxException e)
725 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
726 bjs.exportHTML(file);
728 .println("Creating BioJS MSA Viwer HTML file: " + file);
731 else if (outputFormat.equalsIgnoreCase("imgMap"))
733 af.createImageMap(new File(file), imageName);
734 System.out.println("Creating image map: " + file);
737 else if (outputFormat.equalsIgnoreCase("eps"))
739 File outputFile = new File(file);
741 "Creating EPS file: " + outputFile.getAbsolutePath());
742 af.createEPS(outputFile);
745 FileFormatI outFormat = null;
748 outFormat = FileFormats.getInstance().forName(outputFormat);
749 } catch (Exception formatP)
751 System.out.println("Couldn't parse " + outFormat
752 + " as a valid Jalview format string.");
754 if (outFormat != null)
756 if (!outFormat.isWritable())
759 "This version of Jalview does not support alignment export as "
764 af.saveAlignment(file, outFormat);
765 if (af.isSaveAlignmentSuccessful())
767 System.out.println("Written alignment in "
768 + outFormat.getName() + " format to " + file);
772 System.out.println("Error writing file " + file + " in "
773 + outFormat.getName() + " format!!");
780 while (aparser.getSize() > 0)
782 System.out.println("Unknown arg: " + aparser.nextValue());
786 AlignFrame startUpAlframe = null;
787 // We'll only open the default file if the desktop is visible.
789 // ////////////////////
791 if (!Platform.isJS() && !headless && file == null
792 && Cache.getDefault("SHOW_STARTUP_FILE", true))
799 file = Cache.getDefault("STARTUP_FILE",
800 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
801 + "/examples/exampleFile_2_7.jvp");
802 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
804 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
806 file.replace("http:", "https:");
807 // hardwire upgrade of the startup file
808 file.replace("_2_3", "_2_7");
809 file.replace("2_7.jar", "2_7.jvp");
810 // and remove the stale setting
811 Cache.removeProperty("STARTUP_FILE");
814 protocol = AppletFormatAdapter.checkProtocol(file);
816 if (file.endsWith(".jar"))
818 format = FileFormat.Jalview;
824 format = new IdentifyFile().identify(file, protocol);
825 } catch (FileFormatException e)
831 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
833 // extract groovy arguments before anything else.
836 // Once all other stuff is done, execute any groovy scripts (in order)
837 if (groovyscript != null)
839 if (Cache.groovyJarsPresent())
841 System.out.println("Executing script " + groovyscript);
842 executeGroovyScript(groovyscript, startUpAlframe);
847 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
851 // and finally, turn off batch mode indicator - if the desktop still exists
856 desktop.setProgressBar(null, progress);
858 desktop.setInBatchMode(false);
862 private static void setLookAndFeel()
864 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
866 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
868 String lafProp = System.getProperty("laf");
869 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
875 else if (lafSetting != null)
879 boolean lafSet = false;
882 case "crossplatform":
883 lafSet = setCrossPlatformLookAndFeel();
886 Console.error("Could not set requested laf=" + laf);
890 lafSet = setSystemLookAndFeel();
893 Console.error("Could not set requested laf=" + laf);
897 lafSet = setGtkLookAndFeel();
900 Console.error("Could not set requested laf=" + laf);
904 lafSet = setMetalLookAndFeel();
907 Console.error("Could not set requested laf=" + laf);
911 lafSet = setNimbusLookAndFeel();
914 Console.error("Could not set requested laf=" + laf);
918 lafSet = setQuaquaLookAndFeel();
921 Console.error("Could not set requested laf=" + laf);
925 lafSet = setVaquaLookAndFeel();
928 Console.error("Could not set requested laf=" + laf);
932 lafSet = setMacLookAndFeel();
935 Console.error("Could not set requested laf=" + laf);
941 Console.error("Requested laf=" + laf + " not implemented");
945 setSystemLookAndFeel();
946 if (Platform.isLinux())
948 setMetalLookAndFeel();
950 if (Platform.isMac())
957 private static boolean setCrossPlatformLookAndFeel()
962 UIManager.setLookAndFeel(
963 UIManager.getCrossPlatformLookAndFeelClassName());
965 } catch (Exception ex)
967 Console.error("Unexpected Look and Feel Exception");
968 Console.error(ex.getMessage());
969 Console.debug(Cache.getStackTraceString(ex));
974 private static boolean setSystemLookAndFeel()
979 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
981 } catch (Exception ex)
983 Console.error("Unexpected Look and Feel Exception");
984 Console.error(ex.getMessage());
985 Console.debug(Cache.getStackTraceString(ex));
990 private static boolean setSpecificLookAndFeel(String name,
991 String className, boolean nameStartsWith)
996 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
998 if (info.getName() != null && nameStartsWith
999 ? info.getName().toLowerCase(Locale.ROOT)
1000 .startsWith(name.toLowerCase(Locale.ROOT))
1001 : info.getName().toLowerCase(Locale.ROOT)
1002 .equals(name.toLowerCase(Locale.ROOT)))
1004 className = info.getClassName();
1008 UIManager.setLookAndFeel(className);
1010 } catch (Exception ex)
1012 Console.error("Unexpected Look and Feel Exception");
1013 Console.error(ex.getMessage());
1014 Console.debug(Cache.getStackTraceString(ex));
1019 private static boolean setGtkLookAndFeel()
1021 return setSpecificLookAndFeel("gtk",
1022 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1025 private static boolean setMetalLookAndFeel()
1027 return setSpecificLookAndFeel("metal",
1028 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1031 private static boolean setNimbusLookAndFeel()
1033 return setSpecificLookAndFeel("nimbus",
1034 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1037 private static boolean setQuaquaLookAndFeel()
1039 return setSpecificLookAndFeel("quaqua",
1040 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
1045 private static boolean setVaquaLookAndFeel()
1047 return setSpecificLookAndFeel("vaqua",
1048 "org.violetlib.aqua.AquaLookAndFeel", false);
1051 private static boolean setMacLookAndFeel()
1053 boolean set = false;
1054 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1055 ChannelProperties.getProperty("app_name"));
1056 System.setProperty("apple.laf.useScreenMenuBar", "true");
1057 set = setQuaquaLookAndFeel();
1058 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1059 .toLowerCase(Locale.ROOT).contains("quaqua"))
1061 set = setVaquaLookAndFeel();
1066 private static void showUsage()
1069 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1070 + "-nodisplay\tRun Jalview without User Interface.\n"
1071 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1072 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1073 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1074 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1075 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1076 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1077 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1078 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1079 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1080 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1081 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1082 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1083 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1084 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1085 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1086 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1087 + "-html FILE\tCreate HTML file from alignment.\n"
1088 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1089 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1090 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1091 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1092 + "-noquestionnaire\tTurn off questionnaire check.\n"
1093 + "-nonews\tTurn off check for Jalview news.\n"
1094 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1095 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1097 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1098 // after all other properties files have been read\n\t
1099 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1100 // passed in correctly)"
1101 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1102 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1103 + "-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"
1104 + "-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"
1105 + "-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"
1106 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1109 private static void startUsageStats(final Desktop desktop)
1112 * start a User Config prompt asking if we can log usage statistics.
1114 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1115 "USAGESTATS", "Jalview Usage Statistics",
1116 "Do you want to help make Jalview better by enabling "
1117 + "the collection of usage statistics with Google Analytics ?"
1118 + "\n\n(you can enable or disable usage tracking in the preferences)",
1124 Console.debug("Initialising googletracker for usage stats.");
1125 Cache.initGoogleTracker();
1126 Console.debug("Tracking enabled.");
1133 Console.debug("Not enabling Google Tracking.");
1136 desktop.addDialogThread(prompter);
1140 * Locate the given string as a file and pass it to the groovy interpreter.
1142 * @param groovyscript
1143 * the script to execute
1144 * @param jalviewContext
1145 * the Jalview Desktop object passed in to the groovy binding as the
1148 private void executeGroovyScript(String groovyscript, AlignFrame af)
1151 * for scripts contained in files
1158 if (groovyscript.trim().equals("STDIN"))
1160 // read from stdin into a tempfile and execute it
1163 tfile = File.createTempFile("jalview", "groovy");
1164 PrintWriter outfile = new PrintWriter(
1165 new OutputStreamWriter(new FileOutputStream(tfile)));
1166 BufferedReader br = new BufferedReader(
1167 new InputStreamReader(System.in));
1169 while ((line = br.readLine()) != null)
1171 outfile.write(line + "\n");
1177 } catch (Exception ex)
1179 System.err.println("Failed to read from STDIN into tempfile "
1180 + ((tfile == null) ? "(tempfile wasn't created)"
1181 : tfile.toString()));
1182 ex.printStackTrace();
1187 sfile = tfile.toURI().toURL();
1188 } catch (Exception x)
1191 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1193 x.printStackTrace();
1201 sfile = new URI(groovyscript).toURL();
1202 } catch (Exception x)
1204 tfile = new File(groovyscript);
1205 if (!tfile.exists())
1207 System.err.println("File '" + groovyscript + "' does not exist.");
1210 if (!tfile.canRead())
1212 System.err.println("File '" + groovyscript + "' cannot be read.");
1215 if (tfile.length() < 1)
1217 System.err.println("File '" + groovyscript + "' is empty.");
1222 sfile = tfile.getAbsoluteFile().toURI().toURL();
1223 } catch (Exception ex)
1225 System.err.println("Failed to create a file URL for "
1226 + tfile.getAbsoluteFile());
1233 Map<String, java.lang.Object> vbinding = new HashMap<>();
1234 vbinding.put("Jalview", this);
1237 vbinding.put("currentAlFrame", af);
1239 Binding gbinding = new Binding(vbinding);
1240 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1241 gse.run(sfile.toString(), gbinding);
1242 if ("STDIN".equals(groovyscript))
1244 // delete temp file that we made -
1245 // only if it was successfully executed
1248 } catch (Exception e)
1250 System.err.println("Exception Whilst trying to execute file " + sfile
1251 + " as a groovy script.");
1252 e.printStackTrace(System.err);
1257 public static boolean isHeadlessMode()
1259 String isheadless = System.getProperty("java.awt.headless");
1260 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1267 public AlignFrame[] getAlignFrames()
1269 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1270 : Desktop.getAlignFrames();
1275 * Quit method delegates to Desktop.quit - unless running in headless mode
1276 * when it just ends the JVM
1280 if (desktop != null)
1290 public static AlignFrame getCurrentAlignFrame()
1292 return Jalview.currentAlignFrame;
1295 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1297 Jalview.currentAlignFrame = currentAlignFrame;