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;
64 import javax.swing.LookAndFeel;
65 import javax.swing.UIManager;
67 import com.threerings.getdown.util.LaunchUtil;
69 import groovy.lang.Binding;
70 import groovy.util.GroovyScriptEngine;
73 * Main class for Jalview Application <br>
75 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
78 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
79 * jalview.bin.Jalview jalview.bin.Jalview
81 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
82 * embellish '*' to e.g. '*.jar')
90 * singleton instance of this class
92 private static Jalview instance;
94 private Desktop desktop;
96 public static AlignFrame currentAlignFrame;
100 // grab all the rights we can the JVM
101 Policy.setPolicy(new Policy()
104 public PermissionCollection getPermissions(CodeSource codesource)
106 Permissions perms = new Permissions();
107 perms.add(new AllPermission());
112 public void refresh()
119 * keep track of feature fetching tasks.
127 * TODO: generalise to track all jalview events to orchestrate batch
131 private int queued = 0;
133 private int running = 0;
135 public FeatureFetcher()
140 public void addFetcher(final AlignFrame af,
141 final Vector<String> dasSources)
143 final long id = System.currentTimeMillis();
145 final FeatureFetcher us = this;
146 new Thread(new Runnable()
158 af.setProgressBar(MessageManager
159 .getString("status.das_features_being_retrived"), id);
160 af.featureSettings_actionPerformed(null);
161 af.setProgressBar(null, id);
170 public synchronized boolean allFinished()
172 return queued == 0 && running == 0;
177 public static Jalview getInstance()
183 * main class for Jalview application
186 * open <em>filename</em>
188 public static void main(String[] args)
190 instance = new Jalview();
191 instance.doMain(args);
197 void doMain(String[] args)
199 System.setSecurityManager(null);
201 .println("Java version: " + System.getProperty("java.version"));
202 System.out.println(System.getProperty("os.arch") + " "
203 + System.getProperty("os.name") + " "
204 + System.getProperty("os.version"));
206 String appdirString = System.getProperty("getdownappdir");
207 if (appdirString != null && appdirString.length() > 0)
209 final File appdir = new File(appdirString);
215 LaunchUtil.upgradeGetdown(
216 new File(appdir, "getdown-launcher-old.jar"),
217 new File(appdir, "getdown-launcher.jar"),
218 new File(appdir, "getdown-launcher-new.jar"));
223 ArgsParser aparser = new ArgsParser(args);
224 boolean headless = false;
226 if (aparser.contains("help") || aparser.contains("h"))
231 if (aparser.contains("nodisplay") || aparser.contains("nogui")
232 || aparser.contains("headless"))
234 System.setProperty("java.awt.headless", "true");
237 String usrPropsFile = aparser.getValue("props");
238 Cache.loadProperties(usrPropsFile); // must do this before
239 if (usrPropsFile != null)
242 "CMD [-props " + usrPropsFile + "] executed successfully!");
247 final String jabawsUrl = aparser.getValue("jabaws");
248 if (jabawsUrl != null)
252 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
254 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
255 } catch (MalformedURLException e)
258 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
262 String defs = aparser.getValue("setprop");
265 int p = defs.indexOf('=');
268 System.err.println("Ignoring invalid setprop argument : " + defs);
272 System.out.println("Executing setprop argument: " + defs);
273 // DISABLED FOR SECURITY REASONS
274 // TODO: add a property to allow properties to be overriden by cli args
275 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
277 defs = aparser.getValue("setprop");
279 if (System.getProperty("java.awt.headless") != null
280 && System.getProperty("java.awt.headless").equals("true"))
284 System.setProperty("http.agent",
285 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
289 } catch (NoClassDefFoundError error)
291 error.printStackTrace();
292 System.out.println("\nEssential logging libraries not found."
293 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
301 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
302 } catch (Exception ex)
304 System.err.println("Unexpected Look and Feel Exception");
305 ex.printStackTrace();
307 if (Platform.isAMac())
310 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
312 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
314 System.setProperty("apple.laf.useScreenMenuBar", "true");
315 if (lookAndFeel != null)
319 UIManager.setLookAndFeel(lookAndFeel);
320 } catch (Throwable e)
323 "Failed to set QuaQua look and feel: " + e.toString());
326 if (lookAndFeel == null || !(lookAndFeel.getClass()
327 .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
328 || !UIManager.getLookAndFeel().getClass().toString()
329 .toLowerCase().contains("quaqua"))
334 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
335 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
336 } catch (Throwable e)
339 "Failed to reset look and feel: " + e.toString());
345 * configure 'full' SO model if preferences say to,
346 * else use the default (SO Lite)
348 if (Cache.getDefault("USE_FULL_SO", false))
350 SequenceOntologyFactory.setInstance(new SequenceOntology());
355 desktop = new Desktop();
356 desktop.setInBatchMode(true); // indicate we are starting up
360 JalviewTaskbar.setTaskbar(this);
361 } catch (Exception e)
363 System.out.println("Cannot set Taskbar");
364 // e.printStackTrace();
365 } catch (Throwable t)
367 System.out.println("Cannot set Taskbar");
368 // t.printStackTrace();
371 desktop.setVisible(true);
372 desktop.startServiceDiscovery();
373 if (!aparser.contains("nousagestats"))
375 startUsageStats(desktop);
379 System.err.println("CMD [-nousagestats] executed successfully!");
382 if (!aparser.contains("noquestionnaire"))
384 String url = aparser.getValue("questionnaire");
387 // Start the desktop questionnaire prompter with the specified
389 Cache.log.debug("Starting questionnaire url at " + url);
390 desktop.checkForQuestionnaire(url);
392 "CMD questionnaire[-" + url + "] executed successfully!");
396 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
398 // Start the desktop questionnaire prompter with the specified
401 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
403 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
405 "Starting questionnaire with default url: " + defurl);
406 desktop.checkForQuestionnaire(defurl);
412 System.err.println("CMD [-noquestionnaire] executed successfully!");
415 if (!aparser.contains("nonews"))
417 desktop.checkForNews();
420 BioJsHTMLOutput.updateBioJS();
423 String file = null, data = null;
424 FileFormatI format = null;
425 DataSourceType protocol = null;
426 FileLoader fileLoader = new FileLoader(!headless);
428 String groovyscript = null; // script to execute after all loading is
429 // completed one way or another
430 // extract groovy argument and execute if necessary
431 groovyscript = aparser.getValue("groovy", true);
432 file = aparser.getValue("open", true);
434 if (file == null && desktop == null)
436 System.out.println("No files to open!");
439 String vamsasImport = aparser.getValue("vdoc");
440 String vamsasSession = aparser.getValue("vsess");
441 if (vamsasImport != null || vamsasSession != null)
443 if (desktop == null || headless)
446 "Headless vamsas sessions not yet supported. Sorry.");
449 // if we have a file, start a new session and import it.
450 boolean inSession = false;
451 if (vamsasImport != null)
455 DataSourceType viprotocol = AppletFormatAdapter
456 .checkProtocol(vamsasImport);
457 if (viprotocol == DataSourceType.FILE)
459 inSession = desktop.vamsasImport(new File(vamsasImport));
461 else if (viprotocol == DataSourceType.URL)
463 inSession = desktop.vamsasImport(new URL(vamsasImport));
466 } catch (Exception e)
468 System.err.println("Exeption when importing " + vamsasImport
469 + " as a vamsas document.");
474 System.err.println("Failed to import " + vamsasImport
475 + " as a vamsas document.");
479 System.out.println("Imported Successfully into new session "
480 + desktop.getVamsasApplication().getCurrentSession());
483 if (vamsasSession != null)
485 if (vamsasImport != null)
487 // close the newly imported session and import the Jalview specific
488 // remnants into the new session later on.
489 desktop.vamsasStop_actionPerformed(null);
491 // now join the new session
494 if (desktop.joinVamsasSession(vamsasSession))
497 "Successfully joined vamsas session " + vamsasSession);
501 System.err.println("WARNING: Failed to join vamsas session "
504 } catch (Exception e)
507 "ERROR: Failed to join vamsas session " + vamsasSession);
510 if (vamsasImport != null)
512 // the Jalview specific remnants can now be imported into the new
513 // session at the user's leisure.
515 "Skipping Push for import of data into existing vamsas session."); // TODO:
520 // desktop.getVamsasApplication().push_update();
525 // Finally, deal with the remaining input data.
530 desktop.setProgressBar(
532 .getString("status.processing_commandline_args"),
533 progress = System.currentTimeMillis());
535 System.out.println("CMD [-open " + file + "] executed successfully!");
537 if (!file.startsWith("http://"))
539 if (!(new File(file)).exists())
541 System.out.println("Can't find " + file);
549 protocol = AppletFormatAdapter.checkProtocol(file);
553 format = new IdentifyFile().identify(file, protocol);
554 } catch (FileFormatException e1)
559 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
563 System.out.println("error");
567 setCurrentAlignFrame(af);
568 data = aparser.getValue("colour", true);
571 data.replaceAll("%20", " ");
573 ColourSchemeI cs = ColourSchemeProperty
574 .getColourScheme(af.getViewport(),
575 af.getViewport().getAlignment(), data);
580 "CMD [-color " + data + "] executed successfully!");
585 // Must maintain ability to use the groups flag
586 data = aparser.getValue("groups", true);
589 af.parseFeaturesFile(data,
590 AppletFormatAdapter.checkProtocol(data));
591 // System.out.println("Added " + data);
593 "CMD groups[-" + data + "] executed successfully!");
595 data = aparser.getValue("features", true);
598 af.parseFeaturesFile(data,
599 AppletFormatAdapter.checkProtocol(data));
600 // System.out.println("Added " + data);
602 "CMD [-features " + data + "] executed successfully!");
605 data = aparser.getValue("annotations", true);
608 af.loadJalviewDataFile(data, null, null, null);
609 // System.out.println("Added " + data);
611 "CMD [-annotations " + data + "] executed successfully!");
613 // set or clear the sortbytree flag.
614 if (aparser.contains("sortbytree"))
616 af.getViewport().setSortByTree(true);
617 if (af.getViewport().getSortByTree())
619 System.out.println("CMD [-sortbytree] executed successfully!");
622 if (aparser.contains("no-annotation"))
624 af.getViewport().setShowAnnotation(false);
625 if (!af.getViewport().isShowAnnotation())
627 System.out.println("CMD no-annotation executed successfully!");
630 if (aparser.contains("nosortbytree"))
632 af.getViewport().setSortByTree(false);
633 if (!af.getViewport().getSortByTree())
636 .println("CMD [-nosortbytree] executed successfully!");
639 data = aparser.getValue("tree", true);
645 "CMD [-tree " + data + "] executed successfully!");
646 NewickFile nf = new NewickFile(data,
647 AppletFormatAdapter.checkProtocol(data));
649 .setCurrentTree(af.showNewickTree(nf, data).getTree());
650 } catch (IOException ex)
652 System.err.println("Couldn't add tree " + data);
653 ex.printStackTrace(System.err);
656 // TODO - load PDB structure(s) to alignment JAL-629
657 // (associate with identical sequence in alignment, or a specified
659 if (groovyscript != null)
661 // Execute the groovy script after we've done all the rendering stuff
662 // and before any images or figures are generated.
663 System.out.println("Executing script " + groovyscript);
664 executeGroovyScript(groovyscript, af);
665 System.out.println("CMD groovy[" + groovyscript
666 + "] executed successfully!");
669 String imageName = "unnamed.png";
670 while (aparser.getSize() > 1)
672 String outputFormat = aparser.nextValue();
673 file = aparser.nextValue();
675 if (outputFormat.equalsIgnoreCase("png"))
677 af.createPNG(new File(file));
678 imageName = (new File(file)).getName();
679 System.out.println("Creating PNG image: " + file);
682 else if (outputFormat.equalsIgnoreCase("svg"))
684 File imageFile = new File(file);
685 imageName = imageFile.getName();
686 af.createSVG(imageFile);
687 System.out.println("Creating SVG image: " + file);
690 else if (outputFormat.equalsIgnoreCase("html"))
692 File imageFile = new File(file);
693 imageName = imageFile.getName();
694 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
695 htmlSVG.exportHTML(file);
697 System.out.println("Creating HTML image: " + file);
700 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
704 System.err.println("The output html file must not be null");
709 BioJsHTMLOutput.refreshVersionInfo(
710 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
711 } catch (URISyntaxException e)
715 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
716 bjs.exportHTML(file);
718 .println("Creating BioJS MSA Viwer HTML file: " + file);
721 else if (outputFormat.equalsIgnoreCase("imgMap"))
723 af.createImageMap(new File(file), imageName);
724 System.out.println("Creating image map: " + file);
727 else if (outputFormat.equalsIgnoreCase("eps"))
729 File outputFile = new File(file);
731 "Creating EPS file: " + outputFile.getAbsolutePath());
732 af.createEPS(outputFile);
736 if (af.saveAlignment(file, format))
738 System.out.println("Written alignment in " + format
739 + " format to " + file);
743 System.out.println("Error writing file " + file + " in "
744 + format + " format!!");
749 while (aparser.getSize() > 0)
751 System.out.println("Unknown arg: " + aparser.nextValue());
755 AlignFrame startUpAlframe = null;
756 // We'll only open the default file if the desktop is visible.
758 // ////////////////////
760 if (!headless && file == null && vamsasImport == null
761 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
763 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
764 jalview.bin.Cache.getDefault("www.jalview.org",
765 "http://www.jalview.org")
766 + "/examples/exampleFile_2_7.jar");
768 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
770 // hardwire upgrade of the startup file
771 file.replace("_2_3.jar", "_2_7.jar");
772 // and remove the stale setting
773 jalview.bin.Cache.removeProperty("STARTUP_FILE");
776 protocol = DataSourceType.FILE;
778 if (file.indexOf("http:") > -1)
780 protocol = DataSourceType.URL;
783 if (file.endsWith(".jar"))
785 format = FileFormat.Jalview;
791 format = new IdentifyFile().identify(file, protocol);
792 } catch (FileFormatException e)
798 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
800 // extract groovy arguments before anything else.
803 // Once all other stuff is done, execute any groovy scripts (in order)
804 if (groovyscript != null)
806 if (Cache.groovyJarsPresent())
808 System.out.println("Executing script " + groovyscript);
809 executeGroovyScript(groovyscript, startUpAlframe);
814 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
818 // and finally, turn off batch mode indicator - if the desktop still exists
823 desktop.setProgressBar(null, progress);
825 desktop.setInBatchMode(false);
829 private static void showUsage()
832 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
833 + "-nodisplay\tRun Jalview without User Interface.\n"
834 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
835 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
836 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
837 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
838 + "-features FILE\tUse the given file to mark features on the alignment.\n"
839 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
840 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
841 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
842 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
843 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
844 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
845 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
846 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
847 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
848 + "-png FILE\tCreate PNG image FILE from alignment.\n"
849 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
850 + "-html FILE\tCreate HTML file from alignment.\n"
851 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
852 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
853 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
854 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
855 + "-noquestionnaire\tTurn off questionnaire check.\n"
856 + "-nonews\tTurn off check for Jalview news.\n"
857 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
858 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
860 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
861 // after all other properties files have been read\n\t
862 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
863 // passed in correctly)"
864 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
865 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
867 // "-vdoc vamsas-document\tImport vamsas document into new
868 // session or join existing session with same URN\n"
869 // + "-vses vamsas-session\tJoin session with given URN\n"
870 + "-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"
871 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
874 private static void startUsageStats(final Desktop desktop)
877 * start a User Config prompt asking if we can log usage statistics.
879 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
880 "USAGESTATS", "Jalview Usage Statistics",
881 "Do you want to help make Jalview better by enabling "
882 + "the collection of usage statistics with Google Analytics ?"
883 + "\n\n(you can enable or disable usage tracking in the preferences)",
890 "Initialising googletracker for usage stats.");
891 Cache.initGoogleTracker();
892 Cache.log.debug("Tracking enabled.");
899 Cache.log.debug("Not enabling Google Tracking.");
902 desktop.addDialogThread(prompter);
906 * Locate the given string as a file and pass it to the groovy interpreter.
908 * @param groovyscript
909 * the script to execute
910 * @param jalviewContext
911 * the Jalview Desktop object passed in to the groovy binding as the
914 private void executeGroovyScript(String groovyscript, AlignFrame af)
917 * for scripts contained in files
924 if (groovyscript.trim().equals("STDIN"))
926 // read from stdin into a tempfile and execute it
929 tfile = File.createTempFile("jalview", "groovy");
930 PrintWriter outfile = new PrintWriter(
931 new OutputStreamWriter(new FileOutputStream(tfile)));
932 BufferedReader br = new BufferedReader(
933 new InputStreamReader(System.in));
935 while ((line = br.readLine()) != null)
937 outfile.write(line + "\n");
943 } catch (Exception ex)
945 System.err.println("Failed to read from STDIN into tempfile "
946 + ((tfile == null) ? "(tempfile wasn't created)"
947 : tfile.toString()));
948 ex.printStackTrace();
953 sfile = tfile.toURI().toURL();
954 } catch (Exception x)
957 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
967 sfile = new URI(groovyscript).toURL();
968 } catch (Exception x)
970 tfile = new File(groovyscript);
973 System.err.println("File '" + groovyscript + "' does not exist.");
976 if (!tfile.canRead())
978 System.err.println("File '" + groovyscript + "' cannot be read.");
981 if (tfile.length() < 1)
983 System.err.println("File '" + groovyscript + "' is empty.");
988 sfile = tfile.getAbsoluteFile().toURI().toURL();
989 } catch (Exception ex)
991 System.err.println("Failed to create a file URL for "
992 + tfile.getAbsoluteFile());
999 Map<String, java.lang.Object> vbinding = new HashMap<>();
1000 vbinding.put("Jalview", this);
1003 vbinding.put("currentAlFrame", af);
1005 Binding gbinding = new Binding(vbinding);
1006 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1007 gse.run(sfile.toString(), gbinding);
1008 if ("STDIN".equals(groovyscript))
1010 // delete temp file that we made -
1011 // only if it was successfully executed
1014 } catch (Exception e)
1016 System.err.println("Exception Whilst trying to execute file " + sfile
1017 + " as a groovy script.");
1018 e.printStackTrace(System.err);
1023 public static boolean isHeadlessMode()
1025 String isheadless = System.getProperty("java.awt.headless");
1026 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1033 public AlignFrame[] getAlignFrames()
1035 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1036 : Desktop.getAlignFrames();
1041 * Quit method delegates to Desktop.quit - unless running in headless mode
1042 * when it just ends the JVM
1046 if (desktop != null)
1056 public static AlignFrame getCurrentAlignFrame()
1058 return Jalview.currentAlignFrame;
1061 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1063 Jalview.currentAlignFrame = currentAlignFrame;