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 jalview.ext.so.SequenceOntology;
24 import jalview.gui.AlignFrame;
25 import jalview.gui.Desktop;
26 import jalview.gui.PromptUserConfig;
27 import jalview.io.AppletFormatAdapter;
28 import jalview.io.BioJsHTMLOutput;
29 import jalview.io.DataSourceType;
30 import jalview.io.FileFormat;
31 import jalview.io.FileFormatException;
32 import jalview.io.FileFormatI;
33 import jalview.io.FileLoader;
34 import jalview.io.HtmlSvgOutput;
35 import jalview.io.IdentifyFile;
36 import jalview.io.NewickFile;
37 import jalview.io.gff.SequenceOntologyFactory;
38 import jalview.schemes.ColourSchemeI;
39 import jalview.schemes.ColourSchemeProperty;
40 import jalview.util.MessageManager;
41 import jalview.util.Platform;
42 import jalview.ws.jws2.Jws2Discoverer;
44 import java.io.BufferedReader;
46 import java.io.FileOutputStream;
47 import java.io.IOException;
48 import java.io.InputStreamReader;
49 import java.io.OutputStreamWriter;
50 import java.io.PrintWriter;
51 import java.net.MalformedURLException;
53 import java.net.URISyntaxException;
55 import java.security.AllPermission;
56 import java.security.CodeSource;
57 import java.security.PermissionCollection;
58 import java.security.Permissions;
59 import java.security.Policy;
60 import java.util.HashMap;
62 import java.util.Vector;
63 import java.util.logging.ConsoleHandler;
64 import java.util.logging.Level;
65 import java.util.logging.Logger;
67 import javax.swing.LookAndFeel;
68 import javax.swing.UIManager;
70 import com.threerings.getdown.util.LaunchUtil;
72 import groovy.lang.Binding;
73 import groovy.util.GroovyScriptEngine;
76 * Main class for Jalview Application <br>
78 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
81 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
82 * jalview.bin.Jalview jalview.bin.Jalview
84 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
85 * embellish '*' to e.g. '*.jar')
94 Platform.getURLCommandArguments();
97 // singleton instance of this class
99 private static Jalview instance;
101 private Desktop desktop;
103 public static AlignFrame currentAlignFrame;
107 if (!Platform.isJS())
114 // grab all the rights we can for the JVM
115 Policy.setPolicy(new Policy()
118 public PermissionCollection getPermissions(CodeSource codesource)
120 Permissions perms = new Permissions();
121 perms.add(new AllPermission());
126 public void refresh()
134 * keep track of feature fetching tasks.
142 * TODO: generalise to track all jalview events to orchestrate batch processing
146 private int queued = 0;
148 private int running = 0;
150 public FeatureFetcher()
155 public void addFetcher(final AlignFrame af,
156 final Vector<String> dasSources)
158 final long id = System.currentTimeMillis();
160 final FeatureFetcher us = this;
161 new Thread(new Runnable()
173 af.setProgressBar(MessageManager
174 .getString("status.das_features_being_retrived"), id);
175 af.featureSettings_actionPerformed(null);
176 af.setProgressBar(null, id);
185 public synchronized boolean allFinished()
187 return queued == 0 && running == 0;
192 public static Jalview getInstance()
198 * main class for Jalview application
201 * open <em>filename</em>
203 public static void main(String[] args)
205 // setLogging(); // BH - for event debugging in JavaScript
206 instance = new Jalview();
207 instance.doMain(args);
210 private static void logClass(String name)
212 // BH - for event debugging in JavaScript
213 ConsoleHandler consoleHandler = new ConsoleHandler();
214 consoleHandler.setLevel(Level.ALL);
215 Logger logger = Logger.getLogger(name);
216 logger.setLevel(Level.ALL);
217 logger.addHandler(consoleHandler);
220 @SuppressWarnings("unused")
221 private static void setLogging()
229 System.out.println("not in js");
232 // BH - for event debugging in JavaScript (Java mode only)
233 if (!Platform.isJS())
240 Logger.getLogger("").setLevel(Level.ALL);
241 logClass("java.awt.EventDispatchThread");
242 logClass("java.awt.EventQueue");
243 logClass("java.awt.Component");
244 logClass("java.awt.focus.Component");
245 logClass("java.awt.focus.DefaultKeyboardFocusManager");
256 void doMain(String[] args)
259 if (!Platform.isJS())
261 System.setSecurityManager(null);
265 .println("Java version: "
266 + 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");
273 System.out.println("Install4j version: " + val);
275 val = System.getProperty("installer_template_version");
277 System.out.println("Install4j template version: " + val);
279 val = System.getProperty("launcher_version");
281 System.out.println("Launcher version: " + val);
284 // report Jalview version
285 Cache.loadBuildProperties(true);
287 ArgsParser aparser = new ArgsParser(args);
288 boolean headless = false;
290 String usrPropsFile = aparser.getValue("props");
291 Cache.loadProperties(usrPropsFile); // must do this before
292 if (usrPropsFile != null)
295 "CMD [-props " + usrPropsFile + "] executed successfully!");
298 if (!Platform.isJS())
305 if (aparser.contains("help") || aparser.contains("h"))
310 if (aparser.contains("nodisplay") || aparser.contains("nogui")
311 || aparser.contains("headless"))
313 System.setProperty("java.awt.headless", "true");
318 final String jabawsUrl = aparser.getValue("jabaws");
319 if (jabawsUrl != null)
323 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
325 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
326 } catch (MalformedURLException e)
329 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
334 String defs = aparser.getValue("setprop");
337 int p = defs.indexOf('=');
340 System.err.println("Ignoring invalid setprop argument : " + defs);
344 System.out.println("Executing setprop argument: " + defs);
347 Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
350 defs = aparser.getValue("setprop");
352 if (System.getProperty("java.awt.headless") != null
353 && System.getProperty("java.awt.headless").equals("true"))
357 System.setProperty("http.agent",
358 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
362 } catch (NoClassDefFoundError error)
364 error.printStackTrace();
365 System.out.println("\nEssential logging libraries not found."
366 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
374 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
375 } catch (Exception ex)
377 System.err.println("Unexpected Look and Feel Exception");
378 ex.printStackTrace();
380 if (Platform.isAMacAndNotJS())
383 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
385 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
387 System.setProperty("apple.laf.useScreenMenuBar", "true");
388 if (lookAndFeel != null)
392 UIManager.setLookAndFeel(lookAndFeel);
393 } catch (Throwable e)
396 "Failed to set QuaQua look and feel: " + e.toString());
399 if (lookAndFeel == null
400 || !(lookAndFeel.getClass().isAssignableFrom(
401 UIManager.getLookAndFeel().getClass()))
402 || !UIManager.getLookAndFeel().getClass().toString()
403 .toLowerCase().contains("quaqua"))
408 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
409 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
410 } catch (Throwable e)
413 "Failed to reset look and feel: " + e.toString());
419 * configure 'full' SO model if preferences say to, else use the default (full SO)
420 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
422 boolean soDefault = !Platform.isJS();
423 if (Cache.getDefault("USE_FULL_SO", soDefault))
425 SequenceOntologyFactory.setInstance(new SequenceOntology());
430 desktop = new Desktop();
431 desktop.setInBatchMode(true); // indicate we are starting up
435 JalviewTaskbar.setTaskbar(this);
436 } catch (Throwable t)
438 System.out.println("Error setting Taskbar: " + t.getMessage());
441 desktop.setVisible(true);
443 if (!Platform.isJS())
450 desktop.startServiceDiscovery();
451 if (!aparser.contains("nousagestats"))
453 startUsageStats(desktop);
457 System.err.println("CMD [-nousagestats] executed successfully!");
460 if (!aparser.contains("noquestionnaire"))
462 String url = aparser.getValue("questionnaire");
465 // Start the desktop questionnaire prompter with the specified
467 Cache.log.debug("Starting questionnaire url at " + url);
468 desktop.checkForQuestionnaire(url);
469 System.out.println("CMD questionnaire[-" + url
470 + "] executed successfully!");
474 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
476 // Start the desktop questionnaire prompter with the specified
479 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
481 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
483 "Starting questionnaire with default url: " + defurl);
484 desktop.checkForQuestionnaire(defurl);
491 .println("CMD [-noquestionnaire] executed successfully!");
494 if (!aparser.contains("nonews"))
496 desktop.checkForNews();
499 BioJsHTMLOutput.updateBioJS();
503 // Move any new getdown-launcher-new.jar into place over old
504 // getdown-launcher.jar
505 String appdirString = System.getProperty("getdownappdir");
506 if (appdirString != null && appdirString.length() > 0)
508 final File appdir = new File(appdirString);
514 LaunchUtil.upgradeGetdown(
515 new File(appdir, "getdown-launcher-old.jar"),
516 new File(appdir, "getdown-launcher.jar"),
517 new File(appdir, "getdown-launcher-new.jar"));
522 String file = null, data = null;
523 FileFormatI format = null;
524 DataSourceType protocol = null;
525 FileLoader fileLoader = new FileLoader(!headless);
527 String groovyscript = null; // script to execute after all loading is
528 // completed one way or another
529 // extract groovy argument and execute if necessary
530 groovyscript = aparser.getValue("groovy", true);
531 file = aparser.getValue("open", true);
533 if (file == null && desktop == null)
535 System.out.println("No files to open!");
539 // Finally, deal with the remaining input data.
544 desktop.setProgressBar(
546 .getString("status.processing_commandline_args"),
547 progress = System.currentTimeMillis());
549 System.out.println("CMD [-open " + file + "] executed successfully!");
551 if (!Platform.isJS())
553 * ignore in JavaScript -- can't just file existence - could load it?
558 if (!file.startsWith("http://") && !file.startsWith("https://"))
559 // BH 2019 added https check for Java
561 if (!(new File(file)).exists())
563 System.out.println("Can't find " + file);
572 protocol = AppletFormatAdapter.checkProtocol(file);
576 format = new IdentifyFile().identify(file, protocol);
577 } catch (FileFormatException e1)
582 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
586 System.out.println("error");
590 setCurrentAlignFrame(af);
591 data = aparser.getValue("colour", true);
594 data.replaceAll("%20", " ");
596 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
597 af.getViewport(), af.getViewport().getAlignment(), data);
602 "CMD [-color " + data + "] executed successfully!");
607 // Must maintain ability to use the groups flag
608 data = aparser.getValue("groups", true);
611 af.parseFeaturesFile(data,
612 AppletFormatAdapter.checkProtocol(data));
613 // System.out.println("Added " + data);
615 "CMD groups[-" + data + "] executed successfully!");
617 data = aparser.getValue("features", true);
620 af.parseFeaturesFile(data,
621 AppletFormatAdapter.checkProtocol(data));
622 // System.out.println("Added " + data);
624 "CMD [-features " + data + "] executed successfully!");
627 data = aparser.getValue("annotations", true);
630 af.loadJalviewDataFile(data, null, null, null);
631 // System.out.println("Added " + data);
633 "CMD [-annotations " + data + "] executed successfully!");
635 // set or clear the sortbytree flag.
636 if (aparser.contains("sortbytree"))
638 af.getViewport().setSortByTree(true);
639 if (af.getViewport().getSortByTree())
641 System.out.println("CMD [-sortbytree] executed successfully!");
644 if (aparser.contains("no-annotation"))
646 af.getViewport().setShowAnnotation(false);
647 if (!af.getViewport().isShowAnnotation())
649 System.out.println("CMD no-annotation executed successfully!");
652 if (aparser.contains("nosortbytree"))
654 af.getViewport().setSortByTree(false);
655 if (!af.getViewport().getSortByTree())
658 .println("CMD [-nosortbytree] executed successfully!");
661 data = aparser.getValue("tree", true);
667 "CMD [-tree " + data + "] executed successfully!");
668 NewickFile nf = new NewickFile(data,
669 AppletFormatAdapter.checkProtocol(data));
671 .setCurrentTree(af.showNewickTree(nf, data).getTree());
672 } catch (IOException ex)
674 System.err.println("Couldn't add tree " + data);
675 ex.printStackTrace(System.err);
678 // TODO - load PDB structure(s) to alignment JAL-629
679 // (associate with identical sequence in alignment, or a specified
681 if (groovyscript != null)
683 // Execute the groovy script after we've done all the rendering stuff
684 // and before any images or figures are generated.
685 System.out.println("Executing script " + groovyscript);
686 executeGroovyScript(groovyscript, af);
687 System.out.println("CMD groovy[" + groovyscript
688 + "] executed successfully!");
691 String imageName = "unnamed.png";
692 while (aparser.getSize() > 1)
694 String outputFormat = aparser.nextValue();
695 file = aparser.nextValue();
697 if (outputFormat.equalsIgnoreCase("png"))
699 af.createPNG(new File(file));
700 imageName = (new File(file)).getName();
701 System.out.println("Creating PNG image: " + file);
704 else if (outputFormat.equalsIgnoreCase("svg"))
706 File imageFile = new File(file);
707 imageName = imageFile.getName();
708 af.createSVG(imageFile);
709 System.out.println("Creating SVG image: " + file);
712 else if (outputFormat.equalsIgnoreCase("html"))
714 File imageFile = new File(file);
715 imageName = imageFile.getName();
716 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
717 htmlSVG.exportHTML(file);
719 System.out.println("Creating HTML image: " + file);
722 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
726 System.err.println("The output html file must not be null");
731 BioJsHTMLOutput.refreshVersionInfo(
732 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
733 } catch (URISyntaxException e)
737 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
738 bjs.exportHTML(file);
740 .println("Creating BioJS MSA Viwer HTML file: " + file);
743 else if (outputFormat.equalsIgnoreCase("imgMap"))
745 af.createImageMap(new File(file), imageName);
746 System.out.println("Creating image map: " + file);
749 else if (outputFormat.equalsIgnoreCase("eps"))
751 File outputFile = new File(file);
753 "Creating EPS file: " + outputFile.getAbsolutePath());
754 af.createEPS(outputFile);
758 af.saveAlignment(file, format);
759 if (af.isSaveAlignmentSuccessful())
761 System.out.println("Written alignment in " + format
762 + " format to " + file);
766 System.out.println("Error writing file " + file + " in "
767 + format + " format!!");
772 while (aparser.getSize() > 0)
774 System.out.println("Unknown arg: " + aparser.nextValue());
778 AlignFrame startUpAlframe = null;
779 // We'll only open the default file if the desktop is visible.
781 // ////////////////////
783 if (!Platform.isJS() && !headless && file == null
784 && Cache.getDefault("SHOW_STARTUP_FILE", true))
791 file = Cache.getDefault("STARTUP_FILE",
792 Cache.getDefault("www.jalview.org",
793 "http://www.jalview.org")
794 + "/examples/exampleFile_2_7.jar");
796 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
798 // hardwire upgrade of the startup file
799 file.replace("_2_3.jar", "_2_7.jar");
800 // and remove the stale setting
801 Cache.removeProperty("STARTUP_FILE");
804 protocol = DataSourceType.FILE;
806 if (file.indexOf("http:") > -1)
808 protocol = DataSourceType.URL;
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 showUsage()
860 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
861 + "-nodisplay\tRun Jalview without User Interface.\n"
862 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
863 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
864 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
865 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
866 + "-features FILE\tUse the given file to mark features on the alignment.\n"
867 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
868 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
869 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
870 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
871 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
872 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
873 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
874 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
875 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
876 + "-png FILE\tCreate PNG image FILE from alignment.\n"
877 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
878 + "-html FILE\tCreate HTML file from alignment.\n"
879 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
880 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
881 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
882 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
883 + "-noquestionnaire\tTurn off questionnaire check.\n"
884 + "-nonews\tTurn off check for Jalview news.\n"
885 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
886 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
888 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
889 // after all other properties files have been read\n\t
890 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
891 // passed in correctly)"
892 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
893 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
894 + "-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"
895 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
898 private static void startUsageStats(final Desktop desktop)
901 * start a User Config prompt asking if we can log usage statistics.
903 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
904 "USAGESTATS", "Jalview Usage Statistics",
905 "Do you want to help make Jalview better by enabling "
906 + "the collection of usage statistics with Google Analytics ?"
907 + "\n\n(you can enable or disable usage tracking in the preferences)",
914 "Initialising googletracker for usage stats.");
915 Cache.initGoogleTracker();
916 Cache.log.debug("Tracking enabled.");
923 Cache.log.debug("Not enabling Google Tracking.");
926 desktop.addDialogThread(prompter);
930 * Locate the given string as a file and pass it to the groovy interpreter.
932 * @param groovyscript
933 * the script to execute
934 * @param jalviewContext
935 * the Jalview Desktop object passed in to the groovy
936 * binding as the 'Jalview' object.
938 private void executeGroovyScript(String groovyscript, AlignFrame af)
941 * for scripts contained in files
948 if (groovyscript.trim().equals("STDIN"))
950 // read from stdin into a tempfile and execute it
953 tfile = File.createTempFile("jalview", "groovy");
954 PrintWriter outfile = new PrintWriter(
955 new OutputStreamWriter(new FileOutputStream(tfile)));
956 BufferedReader br = new BufferedReader(
957 new InputStreamReader(System.in));
959 while ((line = br.readLine()) != null)
961 outfile.write(line + "\n");
967 } catch (Exception ex)
969 System.err.println("Failed to read from STDIN into tempfile "
970 + ((tfile == null) ? "(tempfile wasn't created)"
971 : tfile.toString()));
972 ex.printStackTrace();
977 sfile = tfile.toURI().toURL();
978 } catch (Exception x)
981 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
991 sfile = new URI(groovyscript).toURL();
992 } catch (Exception x)
994 tfile = new File(groovyscript);
997 System.err.println("File '" + groovyscript + "' does not exist.");
1000 if (!tfile.canRead())
1002 System.err.println("File '" + groovyscript + "' cannot be read.");
1005 if (tfile.length() < 1)
1007 System.err.println("File '" + groovyscript + "' is empty.");
1012 sfile = tfile.getAbsoluteFile().toURI().toURL();
1013 } catch (Exception ex)
1015 System.err.println("Failed to create a file URL for "
1016 + tfile.getAbsoluteFile());
1023 Map<String, java.lang.Object> vbinding = new HashMap<>();
1024 vbinding.put("Jalview", this);
1027 vbinding.put("currentAlFrame", af);
1029 Binding gbinding = new Binding(vbinding);
1030 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1031 gse.run(sfile.toString(), gbinding);
1032 if ("STDIN".equals(groovyscript))
1034 // delete temp file that we made -
1035 // only if it was successfully executed
1038 } catch (Exception e)
1040 System.err.println("Exception Whilst trying to execute file " + sfile
1041 + " as a groovy script.");
1042 e.printStackTrace(System.err);
1047 public static boolean isHeadlessMode()
1049 String isheadless = System.getProperty("java.awt.headless");
1050 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1057 public AlignFrame[] getAlignFrames()
1059 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1060 : Desktop.getAlignFrames();
1065 * Quit method delegates to Desktop.quit - unless running in headless mode when
1066 * it just ends the JVM
1070 if (desktop != null)
1080 public static AlignFrame getCurrentAlignFrame()
1082 return Jalview.currentAlignFrame;
1085 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1087 Jalview.currentAlignFrame = currentAlignFrame;