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>
187 * @throws InterruptedException
188 * @throws IOException
190 public static void main(String[] args)
192 instance = new Jalview();
193 instance.doMain(args);
198 * @throws InterruptedException
199 * @throws IOException
201 void doMain(String[] args)
203 System.setSecurityManager(null);
205 .println("Java version: " + System.getProperty("java.version"));
206 System.out.println(System.getProperty("os.arch") + " "
207 + System.getProperty("os.name") + " "
208 + System.getProperty("os.version"));
210 String appdirString = System.getProperty("getdownappdir");
211 if (appdirString != null && appdirString.length() > 0)
213 final File appdir = new File(appdirString);
219 LaunchUtil.upgradeGetdown(
220 new File(appdir, "getdown-launcher-old.jar"),
221 new File(appdir, "getdown-launcher.jar"),
222 new File(appdir, "getdown-launcher-new.jar"));
227 ArgsParser aparser = new ArgsParser(args);
228 boolean headless = false;
230 if (aparser.contains("help") || aparser.contains("h"))
235 if (aparser.contains("nodisplay") || aparser.contains("nogui")
236 || aparser.contains("headless"))
238 System.setProperty("java.awt.headless", "true");
241 String usrPropsFile = aparser.getValue("props");
242 Cache.loadProperties(usrPropsFile); // must do this before
243 if (usrPropsFile != null)
246 "CMD [-props " + usrPropsFile + "] executed successfully!");
251 final String jabawsUrl = aparser.getValue("jabaws");
252 if (jabawsUrl != null)
256 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
258 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
259 } catch (MalformedURLException e)
262 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
266 String defs = aparser.getValue("setprop");
269 int p = defs.indexOf('=');
272 System.err.println("Ignoring invalid setprop argument : " + defs);
276 System.out.println("Executing setprop argument: " + defs);
277 // DISABLED FOR SECURITY REASONS
278 // TODO: add a property to allow properties to be overriden by cli args
279 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
281 defs = aparser.getValue("setprop");
283 if (System.getProperty("java.awt.headless") != null
284 && System.getProperty("java.awt.headless").equals("true"))
288 System.setProperty("http.agent",
289 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
293 } catch (NoClassDefFoundError error)
295 error.printStackTrace();
296 System.out.println("\nEssential logging libraries not found."
297 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
305 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
306 } catch (Exception ex)
308 System.err.println("Unexpected Look and Feel Exception");
309 ex.printStackTrace();
311 if (Platform.isAMac())
314 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
316 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
318 System.setProperty("apple.laf.useScreenMenuBar", "true");
319 if (lookAndFeel != null)
323 UIManager.setLookAndFeel(lookAndFeel);
324 } catch (Throwable e)
327 "Failed to set QuaQua look and feel: " + e.toString());
330 if (lookAndFeel == null || !(lookAndFeel.getClass()
331 .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
332 || !UIManager.getLookAndFeel().getClass().toString()
333 .toLowerCase().contains("quaqua"))
338 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
339 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
340 } catch (Throwable e)
343 "Failed to reset look and feel: " + e.toString());
349 * configure 'full' SO model if preferences say to,
350 * else use the default (SO Lite)
352 if (Cache.getDefault("USE_FULL_SO", false))
354 SequenceOntologyFactory.setInstance(new SequenceOntology());
359 desktop = new Desktop();
360 desktop.setInBatchMode(true); // indicate we are starting up
364 JalviewTaskbar.setTaskbar(this);
365 } catch (Exception e)
367 System.out.println("Cannot set Taskbar");
368 // e.printStackTrace();
369 } catch (Throwable t)
371 System.out.println("Cannot set Taskbar");
372 // t.printStackTrace();
375 desktop.setVisible(true);
376 desktop.startServiceDiscovery();
377 if (!aparser.contains("nousagestats"))
379 startUsageStats(desktop);
383 System.err.println("CMD [-nousagestats] executed successfully!");
386 if (!aparser.contains("noquestionnaire"))
388 String url = aparser.getValue("questionnaire");
391 // Start the desktop questionnaire prompter with the specified
393 Cache.log.debug("Starting questionnaire url at " + url);
394 desktop.checkForQuestionnaire(url);
396 "CMD questionnaire[-" + url + "] executed successfully!");
400 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
402 // Start the desktop questionnaire prompter with the specified
405 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
407 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
409 "Starting questionnaire with default url: " + defurl);
410 desktop.checkForQuestionnaire(defurl);
416 System.err.println("CMD [-noquestionnaire] executed successfully!");
419 if (!aparser.contains("nonews"))
421 desktop.checkForNews();
424 BioJsHTMLOutput.updateBioJS();
427 String file = null, data = null;
428 FileFormatI format = null;
429 DataSourceType protocol = null;
430 FileLoader fileLoader = new FileLoader(!headless);
432 String groovyscript = null; // script to execute after all loading is
433 // completed one way or another
434 // extract groovy argument and execute if necessary
435 groovyscript = aparser.getValue("groovy", true);
436 file = aparser.getValue("open", true);
438 if (file == null && desktop == null)
440 System.out.println("No files to open!");
443 String vamsasImport = aparser.getValue("vdoc");
444 String vamsasSession = aparser.getValue("vsess");
445 if (vamsasImport != null || vamsasSession != null)
447 if (desktop == null || headless)
450 "Headless vamsas sessions not yet supported. Sorry.");
453 // if we have a file, start a new session and import it.
454 boolean inSession = false;
455 if (vamsasImport != null)
459 DataSourceType viprotocol = AppletFormatAdapter
460 .checkProtocol(vamsasImport);
461 if (viprotocol == DataSourceType.FILE)
463 inSession = desktop.vamsasImport(new File(vamsasImport));
465 else if (viprotocol == DataSourceType.URL)
467 inSession = desktop.vamsasImport(new URL(vamsasImport));
470 } catch (Exception e)
472 System.err.println("Exeption when importing " + vamsasImport
473 + " as a vamsas document.");
478 System.err.println("Failed to import " + vamsasImport
479 + " as a vamsas document.");
483 System.out.println("Imported Successfully into new session "
484 + desktop.getVamsasApplication().getCurrentSession());
487 if (vamsasSession != null)
489 if (vamsasImport != null)
491 // close the newly imported session and import the Jalview specific
492 // remnants into the new session later on.
493 desktop.vamsasStop_actionPerformed(null);
495 // now join the new session
498 if (desktop.joinVamsasSession(vamsasSession))
501 "Successfully joined vamsas session " + vamsasSession);
505 System.err.println("WARNING: Failed to join vamsas session "
508 } catch (Exception e)
511 "ERROR: Failed to join vamsas session " + vamsasSession);
514 if (vamsasImport != null)
516 // the Jalview specific remnants can now be imported into the new
517 // session at the user's leisure.
519 "Skipping Push for import of data into existing vamsas session."); // TODO:
524 // desktop.getVamsasApplication().push_update();
529 // Finally, deal with the remaining input data.
534 desktop.setProgressBar(
536 .getString("status.processing_commandline_args"),
537 progress = System.currentTimeMillis());
539 System.out.println("CMD [-open " + file + "] executed successfully!");
541 if (!file.startsWith("http://"))
543 if (!(new File(file)).exists())
545 System.out.println("Can't find " + file);
553 protocol = AppletFormatAdapter.checkProtocol(file);
557 format = new IdentifyFile().identify(file, protocol);
558 } catch (FileFormatException e1)
563 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
567 System.out.println("error");
571 setCurrentAlignFrame(af);
572 data = aparser.getValue("colour", true);
575 data.replaceAll("%20", " ");
577 ColourSchemeI cs = ColourSchemeProperty
578 .getColourScheme(af.getViewport(),
579 af.getViewport().getAlignment(), data);
584 "CMD [-color " + data + "] executed successfully!");
589 // Must maintain ability to use the groups flag
590 data = aparser.getValue("groups", true);
593 af.parseFeaturesFile(data,
594 AppletFormatAdapter.checkProtocol(data));
595 // System.out.println("Added " + data);
597 "CMD groups[-" + data + "] executed successfully!");
599 data = aparser.getValue("features", true);
602 af.parseFeaturesFile(data,
603 AppletFormatAdapter.checkProtocol(data));
604 // System.out.println("Added " + data);
606 "CMD [-features " + data + "] executed successfully!");
609 data = aparser.getValue("annotations", true);
612 af.loadJalviewDataFile(data, null, null, null);
613 // System.out.println("Added " + data);
615 "CMD [-annotations " + data + "] executed successfully!");
617 // set or clear the sortbytree flag.
618 if (aparser.contains("sortbytree"))
620 af.getViewport().setSortByTree(true);
621 if (af.getViewport().getSortByTree())
623 System.out.println("CMD [-sortbytree] executed successfully!");
626 if (aparser.contains("no-annotation"))
628 af.getViewport().setShowAnnotation(false);
629 if (!af.getViewport().isShowAnnotation())
631 System.out.println("CMD no-annotation executed successfully!");
634 if (aparser.contains("nosortbytree"))
636 af.getViewport().setSortByTree(false);
637 if (!af.getViewport().getSortByTree())
640 .println("CMD [-nosortbytree] executed successfully!");
643 data = aparser.getValue("tree", true);
649 "CMD [-tree " + data + "] executed successfully!");
650 NewickFile nf = new NewickFile(data,
651 AppletFormatAdapter.checkProtocol(data));
653 .setCurrentTree(af.showNewickTree(nf, data).getTree());
654 } catch (IOException ex)
656 System.err.println("Couldn't add tree " + data);
657 ex.printStackTrace(System.err);
660 // TODO - load PDB structure(s) to alignment JAL-629
661 // (associate with identical sequence in alignment, or a specified
663 if (groovyscript != null)
665 // Execute the groovy script after we've done all the rendering stuff
666 // and before any images or figures are generated.
667 System.out.println("Executing script " + groovyscript);
668 executeGroovyScript(groovyscript, af);
669 System.out.println("CMD groovy[" + groovyscript
670 + "] executed successfully!");
673 String imageName = "unnamed.png";
674 while (aparser.getSize() > 1)
676 String outputFormat = aparser.nextValue();
677 file = aparser.nextValue();
679 if (outputFormat.equalsIgnoreCase("png"))
681 af.createPNG(new File(file));
682 imageName = (new File(file)).getName();
683 System.out.println("Creating PNG image: " + file);
686 else if (outputFormat.equalsIgnoreCase("svg"))
688 File imageFile = new File(file);
689 imageName = imageFile.getName();
690 af.createSVG(imageFile);
691 System.out.println("Creating SVG image: " + file);
694 else if (outputFormat.equalsIgnoreCase("html"))
696 File imageFile = new File(file);
697 imageName = imageFile.getName();
698 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
699 htmlSVG.exportHTML(file);
701 System.out.println("Creating HTML image: " + file);
704 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
708 System.err.println("The output html file must not be null");
713 BioJsHTMLOutput.refreshVersionInfo(
714 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
715 } catch (URISyntaxException e)
719 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
720 bjs.exportHTML(file);
722 .println("Creating BioJS MSA Viwer HTML file: " + file);
725 else if (outputFormat.equalsIgnoreCase("imgMap"))
727 af.createImageMap(new File(file), imageName);
728 System.out.println("Creating image map: " + file);
731 else if (outputFormat.equalsIgnoreCase("eps"))
733 File outputFile = new File(file);
735 "Creating EPS file: " + outputFile.getAbsolutePath());
736 af.createEPS(outputFile);
740 if (af.saveAlignment(file, format))
742 System.out.println("Written alignment in " + format
743 + " format to " + file);
747 System.out.println("Error writing file " + file + " in "
748 + format + " format!!");
753 while (aparser.getSize() > 0)
755 System.out.println("Unknown arg: " + aparser.nextValue());
759 AlignFrame startUpAlframe = null;
760 // We'll only open the default file if the desktop is visible.
762 // ////////////////////
764 if (!headless && file == null && vamsasImport == null
765 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
767 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
768 jalview.bin.Cache.getDefault("www.jalview.org",
769 "http://www.jalview.org")
770 + "/examples/exampleFile_2_7.jar");
772 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
774 // hardwire upgrade of the startup file
775 file.replace("_2_3.jar", "_2_7.jar");
776 // and remove the stale setting
777 jalview.bin.Cache.removeProperty("STARTUP_FILE");
780 protocol = DataSourceType.FILE;
782 if (file.indexOf("http:") > -1)
784 protocol = DataSourceType.URL;
787 if (file.endsWith(".jar"))
789 format = FileFormat.Jalview;
795 format = new IdentifyFile().identify(file, protocol);
796 } catch (FileFormatException e)
802 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
804 // extract groovy arguments before anything else.
807 // Once all other stuff is done, execute any groovy scripts (in order)
808 if (groovyscript != null)
810 if (Cache.groovyJarsPresent())
812 System.out.println("Executing script " + groovyscript);
813 executeGroovyScript(groovyscript, startUpAlframe);
818 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
822 // and finally, turn off batch mode indicator - if the desktop still exists
827 desktop.setProgressBar(null, progress);
829 desktop.setInBatchMode(false);
833 private static void showUsage()
836 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
837 + "-nodisplay\tRun Jalview without User Interface.\n"
838 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
839 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
840 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
841 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
842 + "-features FILE\tUse the given file to mark features on the alignment.\n"
843 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
844 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
845 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
846 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
847 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
848 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
849 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
850 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
851 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
852 + "-png FILE\tCreate PNG image FILE from alignment.\n"
853 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
854 + "-html FILE\tCreate HTML file from alignment.\n"
855 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
856 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
857 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
858 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
859 + "-noquestionnaire\tTurn off questionnaire check.\n"
860 + "-nonews\tTurn off check for Jalview news.\n"
861 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
862 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
864 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
865 // after all other properties files have been read\n\t
866 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
867 // passed in correctly)"
868 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
869 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
871 // "-vdoc vamsas-document\tImport vamsas document into new
872 // session or join existing session with same URN\n"
873 // + "-vses vamsas-session\tJoin session with given URN\n"
874 + "-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"
875 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
878 private static void startUsageStats(final Desktop desktop)
881 * start a User Config prompt asking if we can log usage statistics.
883 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
884 "USAGESTATS", "Jalview Usage Statistics",
885 "Do you want to help make Jalview better by enabling "
886 + "the collection of usage statistics with Google Analytics ?"
887 + "\n\n(you can enable or disable usage tracking in the preferences)",
894 "Initialising googletracker for usage stats.");
895 Cache.initGoogleTracker();
896 Cache.log.debug("Tracking enabled.");
903 Cache.log.debug("Not enabling Google Tracking.");
906 desktop.addDialogThread(prompter);
910 * Locate the given string as a file and pass it to the groovy interpreter.
912 * @param groovyscript
913 * the script to execute
914 * @param jalviewContext
915 * the Jalview Desktop object passed in to the groovy binding as the
918 private void executeGroovyScript(String groovyscript, AlignFrame af)
921 * for scripts contained in files
928 if (groovyscript.trim().equals("STDIN"))
930 // read from stdin into a tempfile and execute it
933 tfile = File.createTempFile("jalview", "groovy");
934 PrintWriter outfile = new PrintWriter(
935 new OutputStreamWriter(new FileOutputStream(tfile)));
936 BufferedReader br = new BufferedReader(
937 new InputStreamReader(System.in));
939 while ((line = br.readLine()) != null)
941 outfile.write(line + "\n");
947 } catch (Exception ex)
949 System.err.println("Failed to read from STDIN into tempfile "
950 + ((tfile == null) ? "(tempfile wasn't created)"
951 : tfile.toString()));
952 ex.printStackTrace();
957 sfile = tfile.toURI().toURL();
958 } catch (Exception x)
961 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
971 sfile = new URI(groovyscript).toURL();
972 } catch (Exception x)
974 tfile = new File(groovyscript);
977 System.err.println("File '" + groovyscript + "' does not exist.");
980 if (!tfile.canRead())
982 System.err.println("File '" + groovyscript + "' cannot be read.");
985 if (tfile.length() < 1)
987 System.err.println("File '" + groovyscript + "' is empty.");
992 sfile = tfile.getAbsoluteFile().toURI().toURL();
993 } catch (Exception ex)
995 System.err.println("Failed to create a file URL for "
996 + tfile.getAbsoluteFile());
1003 Map<String, java.lang.Object> vbinding = new HashMap<>();
1004 vbinding.put("Jalview", this);
1007 vbinding.put("currentAlFrame", af);
1009 Binding gbinding = new Binding(vbinding);
1010 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1011 gse.run(sfile.toString(), gbinding);
1012 if ("STDIN".equals(groovyscript))
1014 // delete temp file that we made -
1015 // only if it was successfully executed
1018 } catch (Exception e)
1020 System.err.println("Exception Whilst trying to execute file " + sfile
1021 + " as a groovy script.");
1022 e.printStackTrace(System.err);
1027 public static boolean isHeadlessMode()
1029 String isheadless = System.getProperty("java.awt.headless");
1030 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1037 public AlignFrame[] getAlignFrames()
1039 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1040 : Desktop.getAlignFrames();
1045 * Quit method delegates to Desktop.quit - unless running in headless mode
1046 * when it just ends the JVM
1050 if (desktop != null)
1060 public static AlignFrame getCurrentAlignFrame()
1062 return Jalview.currentAlignFrame;
1065 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1067 Jalview.currentAlignFrame = currentAlignFrame;