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();
101 * singleton instance of this class
103 private static Jalview instance;
105 private Desktop desktop;
107 public static AlignFrame currentAlignFrame;
111 if (!Platform.isJS())
118 // grab all the rights we can for the JVM
119 Policy.setPolicy(new Policy()
122 public PermissionCollection getPermissions(CodeSource codesource)
124 Permissions perms = new Permissions();
125 perms.add(new AllPermission());
130 public void refresh()
138 * keep track of feature fetching tasks.
146 * TODO: generalise to track all jalview events to orchestrate batch processing
150 private int queued = 0;
152 private int running = 0;
154 public FeatureFetcher()
159 public void addFetcher(final AlignFrame af,
160 final Vector<String> dasSources)
162 final long id = System.currentTimeMillis();
164 final FeatureFetcher us = this;
165 new Thread(new Runnable()
177 af.setProgressBar(MessageManager
178 .getString("status.das_features_being_retrived"), id);
179 af.featureSettings_actionPerformed(null);
180 af.setProgressBar(null, id);
189 public synchronized boolean allFinished()
191 return queued == 0 && running == 0;
196 public static Jalview getInstance()
202 * main class for Jalview application
205 * open <em>filename</em>
207 public static void main(String[] args)
209 // setLogging(); // BH - for event debugging in JavaScript
210 instance = new Jalview();
211 instance.doMain(args);
214 private static void logClass(String name)
216 // BH - for event debugging in JavaScript
217 ConsoleHandler consoleHandler = new ConsoleHandler();
218 consoleHandler.setLevel(Level.ALL);
219 Logger logger = Logger.getLogger(name);
220 logger.setLevel(Level.ALL);
221 logger.addHandler(consoleHandler);
224 @SuppressWarnings("unused")
225 private static void setLogging()
233 System.out.println("not in js");
236 // BH - for event debugging in JavaScript (Java mode only)
237 if (!Platform.isJS())
244 Logger.getLogger("").setLevel(Level.ALL);
245 logClass("java.awt.EventDispatchThread");
246 logClass("java.awt.EventQueue");
247 logClass("java.awt.Component");
248 logClass("java.awt.focus.Component");
249 logClass("java.awt.focus.DefaultKeyboardFocusManager");
257 void doMain(String[] args)
260 if (!Platform.isJS())
262 System.setSecurityManager(null);
266 .println("Java version: " + System.getProperty("java.version"));
267 System.out.println("Java Home: " + System.getProperty("java.home"));
268 System.out.println(System.getProperty("os.arch") + " "
269 + System.getProperty("os.name") + " "
270 + System.getProperty("os.version"));
271 String val = System.getProperty("sys.install4jVersion");
274 System.out.println("Install4j version: " + val);
276 val = System.getProperty("installer_template_version");
279 System.out.println("Install4j template version: " + val);
281 val = System.getProperty("launcher_version");
284 System.out.println("Launcher version: " + val);
287 // report Jalview version
288 Cache.loadBuildProperties(true);
290 ArgsParser aparser = new ArgsParser(args);
291 boolean headless = false;
293 String usrPropsFile = aparser.getValue("props");
294 Cache.loadProperties(usrPropsFile); // must do this before
295 if (usrPropsFile != null)
298 "CMD [-props " + usrPropsFile + "] executed successfully!");
301 if (!Platform.isJS())
308 if (aparser.contains("help") || aparser.contains("h"))
313 if (aparser.contains("nodisplay") || aparser.contains("nogui")
314 || aparser.contains("headless"))
316 System.setProperty("java.awt.headless", "true");
321 // allow https handshakes to download intermediate certs if necessary
322 System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
324 final String jabawsUrl = aparser.getValue("jabaws");
325 if (jabawsUrl != null)
329 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
331 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
332 } catch (MalformedURLException e)
335 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
340 String defs = aparser.getValue("setprop");
343 int p = defs.indexOf('=');
346 System.err.println("Ignoring invalid setprop argument : " + defs);
350 System.out.println("Executing setprop argument: " + defs);
353 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
355 // DISABLED FOR SECURITY REASONS
356 // TODO: add a property to allow properties to be overriden by cli args
357 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
359 defs = aparser.getValue("setprop");
361 if (System.getProperty("java.awt.headless") != null
362 && System.getProperty("java.awt.headless").equals("true"))
366 System.setProperty("http.agent",
367 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
371 Console.initLogger();
372 } catch (NoClassDefFoundError error)
374 error.printStackTrace();
375 System.out.println("\nEssential logging libraries not found."
376 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
385 * configure 'full' SO model if preferences say to, else use the default (full SO)
386 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
388 boolean soDefault = !Platform.isJS();
389 if (Cache.getDefault("USE_FULL_SO", soDefault))
391 SequenceOntologyFactory.setInstance(new SequenceOntology());
396 Desktop.nosplash = aparser.contains("nosplash");
397 desktop = new Desktop();
398 desktop.setInBatchMode(true); // indicate we are starting up
402 JalviewTaskbar.setTaskbar(this);
403 } catch (Exception e)
405 Console.info("Cannot set Taskbar");
406 Console.error(e.getMessage());
407 // e.printStackTrace();
408 } catch (Throwable t)
410 Console.info("Cannot set Taskbar");
411 Console.error(t.getMessage());
412 // t.printStackTrace();
415 // set Proxy settings before all the internet calls
416 Cache.setProxyPropertiesFromPreferences();
418 desktop.setVisible(true);
420 if (!Platform.isJS())
427 if (!aparser.contains("nowebservicediscovery"))
429 desktop.startServiceDiscovery();
431 if (!aparser.contains("nousagestats"))
433 startUsageStats(desktop);
437 System.err.println("CMD [-nousagestats] executed successfully!");
440 if (!aparser.contains("noquestionnaire"))
442 String url = aparser.getValue("questionnaire");
445 // Start the desktop questionnaire prompter with the specified
447 Console.debug("Starting questionnaire url at " + url);
448 desktop.checkForQuestionnaire(url);
449 System.out.println("CMD questionnaire[-" + url
450 + "] executed successfully!");
454 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
456 // Start the desktop questionnaire prompter with the specified
459 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
461 String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
463 "Starting questionnaire with default url: " + defurl);
464 desktop.checkForQuestionnaire(defurl);
471 .println("CMD [-noquestionnaire] executed successfully!");
474 if (!aparser.contains("nonews"))
476 desktop.checkForNews();
479 BioJsHTMLOutput.updateBioJS();
483 // Move any new getdown-launcher-new.jar into place over old
484 // getdown-launcher.jar
485 String appdirString = System.getProperty("getdownappdir");
486 if (appdirString != null && appdirString.length() > 0)
488 final File appdir = new File(appdirString);
494 LaunchUtil.upgradeGetdown(
495 new File(appdir, "getdown-launcher-old.jar"),
496 new File(appdir, "getdown-launcher.jar"),
497 new File(appdir, "getdown-launcher-new.jar"));
502 String file = null, data = null;
503 FileFormatI format = null;
504 DataSourceType protocol = null;
505 FileLoader fileLoader = new FileLoader(!headless);
507 String groovyscript = null; // script to execute after all loading is
508 // completed one way or another
509 // extract groovy argument and execute if necessary
510 groovyscript = aparser.getValue("groovy", true);
511 file = aparser.getValue("open", true);
513 if (file == null && desktop == null)
515 System.out.println("No files to open!");
519 // Finally, deal with the remaining input data.
524 desktop.setProgressBar(
526 .getString("status.processing_commandline_args"),
527 progress = System.currentTimeMillis());
529 System.out.println("CMD [-open " + file + "] executed successfully!");
531 if (!Platform.isJS())
533 * ignore in JavaScript -- can't just file existence - could load it?
538 if (!HttpUtils.startsWithHttpOrHttps(file))
540 if (!(new File(file)).exists())
542 System.out.println("Can't find " + file);
551 protocol = AppletFormatAdapter.checkProtocol(file);
555 format = new IdentifyFile().identify(file, protocol);
556 } catch (FileFormatException e1)
561 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
565 System.out.println("error");
569 setCurrentAlignFrame(af);
570 data = aparser.getValue("colour", true);
573 data.replaceAll("%20", " ");
575 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
576 af.getViewport(), af.getViewport().getAlignment(), data);
581 "CMD [-color " + data + "] executed successfully!");
586 // Must maintain ability to use the groups flag
587 data = aparser.getValue("groups", true);
590 af.parseFeaturesFile(data,
591 AppletFormatAdapter.checkProtocol(data));
592 // System.out.println("Added " + data);
594 "CMD groups[-" + data + "] executed successfully!");
596 data = aparser.getValue("features", true);
599 af.parseFeaturesFile(data,
600 AppletFormatAdapter.checkProtocol(data));
601 // System.out.println("Added " + data);
603 "CMD [-features " + data + "] executed successfully!");
606 data = aparser.getValue("annotations", true);
609 af.loadJalviewDataFile(data, null, null, null);
610 // System.out.println("Added " + data);
612 "CMD [-annotations " + data + "] executed successfully!");
614 // set or clear the sortbytree flag.
615 if (aparser.contains("sortbytree"))
617 af.getViewport().setSortByTree(true);
618 if (af.getViewport().getSortByTree())
620 System.out.println("CMD [-sortbytree] executed successfully!");
623 if (aparser.contains("no-annotation"))
625 af.getViewport().setShowAnnotation(false);
626 if (!af.getViewport().isShowAnnotation())
628 System.out.println("CMD no-annotation executed successfully!");
631 if (aparser.contains("nosortbytree"))
633 af.getViewport().setSortByTree(false);
634 if (!af.getViewport().getSortByTree())
637 .println("CMD [-nosortbytree] executed successfully!");
640 data = aparser.getValue("tree", true);
646 "CMD [-tree " + data + "] executed successfully!");
647 NewickFile nf = new NewickFile(data,
648 AppletFormatAdapter.checkProtocol(data));
650 .setCurrentTree(af.showNewickTree(nf, data).getTree());
651 } catch (IOException ex)
653 System.err.println("Couldn't add tree " + data);
654 ex.printStackTrace(System.err);
657 // TODO - load PDB structure(s) to alignment JAL-629
658 // (associate with identical sequence in alignment, or a specified
660 if (groovyscript != null)
662 // Execute the groovy script after we've done all the rendering stuff
663 // and before any images or figures are generated.
664 System.out.println("Executing script " + groovyscript);
665 executeGroovyScript(groovyscript, af);
666 System.out.println("CMD groovy[" + groovyscript
667 + "] executed successfully!");
670 String imageName = "unnamed.png";
671 while (aparser.getSize() > 1)
673 String outputFormat = aparser.nextValue();
674 file = aparser.nextValue();
676 if (outputFormat.equalsIgnoreCase("png"))
678 af.createPNG(new File(file));
679 imageName = (new File(file)).getName();
680 System.out.println("Creating PNG image: " + file);
683 else if (outputFormat.equalsIgnoreCase("svg"))
685 File imageFile = new File(file);
686 imageName = imageFile.getName();
687 af.createSVG(imageFile);
688 System.out.println("Creating SVG image: " + file);
691 else if (outputFormat.equalsIgnoreCase("html"))
693 File imageFile = new File(file);
694 imageName = imageFile.getName();
695 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
696 htmlSVG.exportHTML(file);
698 System.out.println("Creating HTML image: " + file);
701 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
705 System.err.println("The output html file must not be null");
710 BioJsHTMLOutput.refreshVersionInfo(
711 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
712 } catch (URISyntaxException e)
716 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
717 bjs.exportHTML(file);
719 .println("Creating BioJS MSA Viwer HTML file: " + file);
722 else if (outputFormat.equalsIgnoreCase("imgMap"))
724 af.createImageMap(new File(file), imageName);
725 System.out.println("Creating image map: " + file);
728 else if (outputFormat.equalsIgnoreCase("eps"))
730 File outputFile = new File(file);
732 "Creating EPS file: " + outputFile.getAbsolutePath());
733 af.createEPS(outputFile);
736 FileFormatI outFormat = null;
739 outFormat = FileFormats.getInstance().forName(outputFormat);
740 } catch (Exception formatP)
742 System.out.println("Couldn't parse " + outFormat
743 + " as a valid Jalview format string.");
745 if (outFormat != null)
747 if (!outFormat.isWritable())
750 "This version of Jalview does not support alignment export as "
755 af.saveAlignment(file, outFormat);
756 if (af.isSaveAlignmentSuccessful())
758 System.out.println("Written alignment in "
759 + outFormat.getName() + " format to " + file);
763 System.out.println("Error writing file " + file + " in "
764 + outFormat.getName() + " format!!");
771 while (aparser.getSize() > 0)
773 System.out.println("Unknown arg: " + aparser.nextValue());
777 AlignFrame startUpAlframe = null;
778 // We'll only open the default file if the desktop is visible.
780 // ////////////////////
782 if (!Platform.isJS() && !headless && file == null
783 && Cache.getDefault("SHOW_STARTUP_FILE", true))
790 file = Cache.getDefault("STARTUP_FILE",
791 Cache.getDefault("www.jalview.org", "https://www.jalview.org")
792 + "/examples/exampleFile_2_7.jvp");
793 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
795 "http://www.jalview.org/examples/exampleFile_2_7.jar"))
797 file.replace("http:", "https:");
798 // hardwire upgrade of the startup file
799 file.replace("_2_3", "_2_7");
800 file.replace("2_7.jar", "2_7.jvp");
801 // and remove the stale setting
802 Cache.removeProperty("STARTUP_FILE");
805 protocol = AppletFormatAdapter.checkProtocol(file);
807 if (file.endsWith(".jar"))
809 format = FileFormat.Jalview;
815 format = new IdentifyFile().identify(file, protocol);
816 } catch (FileFormatException e)
822 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
824 // extract groovy arguments before anything else.
827 // Once all other stuff is done, execute any groovy scripts (in order)
828 if (groovyscript != null)
830 if (Cache.groovyJarsPresent())
832 System.out.println("Executing script " + groovyscript);
833 executeGroovyScript(groovyscript, startUpAlframe);
838 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
842 // and finally, turn off batch mode indicator - if the desktop still exists
847 desktop.setProgressBar(null, progress);
849 desktop.setInBatchMode(false);
853 private static void setLookAndFeel()
855 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
857 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
859 String lafProp = System.getProperty("laf");
860 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
866 else if (lafSetting != null)
870 boolean lafSet = false;
873 case "crossplatform":
874 lafSet = setCrossPlatformLookAndFeel();
877 Console.error("Could not set requested laf=" + laf);
881 lafSet = setSystemLookAndFeel();
884 Console.error("Could not set requested laf=" + laf);
888 lafSet = setGtkLookAndFeel();
891 Console.error("Could not set requested laf=" + laf);
895 lafSet = setMetalLookAndFeel();
898 Console.error("Could not set requested laf=" + laf);
902 lafSet = setNimbusLookAndFeel();
905 Console.error("Could not set requested laf=" + laf);
909 lafSet = setQuaquaLookAndFeel();
912 Console.error("Could not set requested laf=" + laf);
916 lafSet = setVaquaLookAndFeel();
919 Console.error("Could not set requested laf=" + laf);
923 lafSet = setMacLookAndFeel();
926 Console.error("Could not set requested laf=" + laf);
932 Console.error("Requested laf=" + laf + " not implemented");
936 setSystemLookAndFeel();
937 if (Platform.isLinux())
939 setMetalLookAndFeel();
941 if (Platform.isMac())
948 private static boolean setCrossPlatformLookAndFeel()
953 UIManager.setLookAndFeel(
954 UIManager.getCrossPlatformLookAndFeelClassName());
956 } catch (Exception ex)
958 Console.error("Unexpected Look and Feel Exception");
959 Console.error(ex.getMessage());
960 Console.debug(Cache.getStackTraceString(ex));
965 private static boolean setSystemLookAndFeel()
970 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
972 } catch (Exception ex)
974 Console.error("Unexpected Look and Feel Exception");
975 Console.error(ex.getMessage());
976 Console.debug(Cache.getStackTraceString(ex));
981 private static boolean setSpecificLookAndFeel(String name,
982 String className, boolean nameStartsWith)
987 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
989 if (info.getName() != null && nameStartsWith
990 ? info.getName().toLowerCase(Locale.ROOT)
991 .startsWith(name.toLowerCase(Locale.ROOT))
992 : info.getName().toLowerCase(Locale.ROOT)
993 .equals(name.toLowerCase(Locale.ROOT)))
995 className = info.getClassName();
999 UIManager.setLookAndFeel(className);
1001 } catch (Exception ex)
1003 Console.error("Unexpected Look and Feel Exception");
1004 Console.error(ex.getMessage());
1005 Console.debug(Cache.getStackTraceString(ex));
1010 private static boolean setGtkLookAndFeel()
1012 return setSpecificLookAndFeel("gtk",
1013 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
1016 private static boolean setMetalLookAndFeel()
1018 return setSpecificLookAndFeel("metal",
1019 "javax.swing.plaf.metal.MetalLookAndFeel", false);
1022 private static boolean setNimbusLookAndFeel()
1024 return setSpecificLookAndFeel("nimbus",
1025 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
1028 private static boolean setQuaquaLookAndFeel()
1030 return setSpecificLookAndFeel("quaqua",
1031 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
1036 private static boolean setVaquaLookAndFeel()
1038 return setSpecificLookAndFeel("vaqua",
1039 "org.violetlib.aqua.AquaLookAndFeel", false);
1042 private static boolean setMacLookAndFeel()
1044 boolean set = false;
1045 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
1046 ChannelProperties.getProperty("app_name"));
1047 System.setProperty("apple.laf.useScreenMenuBar", "true");
1048 set = setQuaquaLookAndFeel();
1049 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
1050 .toLowerCase(Locale.ROOT).contains("quaqua"))
1052 set = setVaquaLookAndFeel();
1057 private static void showUsage()
1060 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
1061 + "-nodisplay\tRun Jalview without User Interface.\n"
1062 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1063 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1064 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1065 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1066 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1067 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1068 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1069 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1070 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1071 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1072 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1073 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1074 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1075 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1076 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1077 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1078 + "-html FILE\tCreate HTML file from alignment.\n"
1079 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1080 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1081 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1082 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1083 + "-noquestionnaire\tTurn off questionnaire check.\n"
1084 + "-nonews\tTurn off check for Jalview news.\n"
1085 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1086 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1088 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1089 // after all other properties files have been read\n\t
1090 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1091 // passed in correctly)"
1092 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1093 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1094 + "-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"
1095 + "-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"
1096 + "-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"
1097 + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
1100 private static void startUsageStats(final Desktop desktop)
1103 * start a User Config prompt asking if we can log usage statistics.
1105 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1106 "USAGESTATS", "Jalview Usage Statistics",
1107 "Do you want to help make Jalview better by enabling "
1108 + "the collection of usage statistics with Google Analytics ?"
1109 + "\n\n(you can enable or disable usage tracking in the preferences)",
1115 Console.debug("Initialising googletracker for usage stats.");
1116 Cache.initGoogleTracker();
1117 Console.debug("Tracking enabled.");
1124 Console.debug("Not enabling Google Tracking.");
1127 desktop.addDialogThread(prompter);
1131 * Locate the given string as a file and pass it to the groovy interpreter.
1133 * @param groovyscript
1134 * the script to execute
1135 * @param jalviewContext
1136 * the Jalview Desktop object passed in to the groovy binding as the
1139 private void executeGroovyScript(String groovyscript, AlignFrame af)
1142 * for scripts contained in files
1149 if (groovyscript.trim().equals("STDIN"))
1151 // read from stdin into a tempfile and execute it
1154 tfile = File.createTempFile("jalview", "groovy");
1155 PrintWriter outfile = new PrintWriter(
1156 new OutputStreamWriter(new FileOutputStream(tfile)));
1157 BufferedReader br = new BufferedReader(
1158 new InputStreamReader(System.in));
1160 while ((line = br.readLine()) != null)
1162 outfile.write(line + "\n");
1168 } catch (Exception ex)
1170 System.err.println("Failed to read from STDIN into tempfile "
1171 + ((tfile == null) ? "(tempfile wasn't created)"
1172 : tfile.toString()));
1173 ex.printStackTrace();
1178 sfile = tfile.toURI().toURL();
1179 } catch (Exception x)
1182 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1184 x.printStackTrace();
1192 sfile = new URI(groovyscript).toURL();
1193 } catch (Exception x)
1195 tfile = new File(groovyscript);
1196 if (!tfile.exists())
1198 System.err.println("File '" + groovyscript + "' does not exist.");
1201 if (!tfile.canRead())
1203 System.err.println("File '" + groovyscript + "' cannot be read.");
1206 if (tfile.length() < 1)
1208 System.err.println("File '" + groovyscript + "' is empty.");
1213 sfile = tfile.getAbsoluteFile().toURI().toURL();
1214 } catch (Exception ex)
1216 System.err.println("Failed to create a file URL for "
1217 + tfile.getAbsoluteFile());
1224 Map<String, java.lang.Object> vbinding = new HashMap<>();
1225 vbinding.put("Jalview", this);
1228 vbinding.put("currentAlFrame", af);
1230 Binding gbinding = new Binding(vbinding);
1231 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1232 gse.run(sfile.toString(), gbinding);
1233 if ("STDIN".equals(groovyscript))
1235 // delete temp file that we made -
1236 // only if it was successfully executed
1239 } catch (Exception e)
1241 System.err.println("Exception Whilst trying to execute file " + sfile
1242 + " as a groovy script.");
1243 e.printStackTrace(System.err);
1248 public static boolean isHeadlessMode()
1250 String isheadless = System.getProperty("java.awt.headless");
1251 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1258 public AlignFrame[] getAlignFrames()
1260 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1261 : Desktop.getAlignFrames();
1266 * Quit method delegates to Desktop.quit - unless running in headless mode
1267 * when it just ends the JVM
1271 if (desktop != null)
1281 public static AlignFrame getCurrentAlignFrame()
1283 return Jalview.currentAlignFrame;
1286 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1288 Jalview.currentAlignFrame = currentAlignFrame;