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 groovy.lang.Binding;
68 import groovy.util.GroovyScriptEngine;
71 * Main class for Jalview Application <br>
73 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
76 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
77 * jalview.bin.Jalview jalview.bin.Jalview
79 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
80 * embellish '*' to e.g. '*.jar')
88 * singleton instance of this class
90 private static Jalview instance;
92 private Desktop desktop;
94 public static AlignFrame currentAlignFrame;
98 // grab all the rights we can the JVM
99 Policy.setPolicy(new Policy()
102 public PermissionCollection getPermissions(CodeSource codesource)
104 Permissions perms = new Permissions();
105 perms.add(new AllPermission());
110 public void refresh()
117 * keep track of feature fetching tasks.
125 * TODO: generalise to track all jalview events to orchestrate batch
129 private int queued = 0;
131 private int running = 0;
133 public FeatureFetcher()
138 public void addFetcher(final AlignFrame af,
139 final Vector<String> dasSources)
141 final long id = System.currentTimeMillis();
143 final FeatureFetcher us = this;
144 new Thread(new Runnable()
156 af.setProgressBar(MessageManager
157 .getString("status.das_features_being_retrived"), id);
158 af.featureSettings_actionPerformed(null);
159 af.setProgressBar(null, id);
168 public synchronized boolean allFinished()
170 return queued == 0 && running == 0;
175 public static Jalview getInstance()
181 * main class for Jalview application
184 * open <em>filename</em>
186 public static void main(String[] args)
188 instance = new Jalview();
189 instance.doMain(args);
195 void doMain(String[] args)
197 System.setSecurityManager(null);
199 .println("Java version: " + System.getProperty("java.version"));
200 System.out.println(System.getProperty("os.arch") + " "
201 + System.getProperty("os.name") + " "
202 + System.getProperty("os.version"));
204 ArgsParser aparser = new ArgsParser(args);
205 boolean headless = false;
207 if (aparser.contains("help") || aparser.contains("h"))
212 if (aparser.contains("nodisplay") || aparser.contains("nogui")
213 || aparser.contains("headless"))
215 System.setProperty("java.awt.headless", "true");
218 String usrPropsFile = aparser.getValue("props");
219 Cache.loadProperties(usrPropsFile); // must do this before
220 if (usrPropsFile != null)
223 "CMD [-props " + usrPropsFile + "] executed successfully!");
228 final String jabawsUrl = aparser.getValue("jabaws");
229 if (jabawsUrl != null)
233 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
235 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
236 } catch (MalformedURLException e)
239 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
243 String defs = aparser.getValue("setprop");
246 int p = defs.indexOf('=');
249 System.err.println("Ignoring invalid setprop argument : " + defs);
253 System.out.println("Executing setprop argument: " + defs);
254 // DISABLED FOR SECURITY REASONS
255 // TODO: add a property to allow properties to be overriden by cli args
256 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
258 defs = aparser.getValue("setprop");
260 if (System.getProperty("java.awt.headless") != null
261 && System.getProperty("java.awt.headless").equals("true"))
265 System.setProperty("http.agent",
266 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
270 } catch (NoClassDefFoundError error)
272 error.printStackTrace();
273 System.out.println("\nEssential logging libraries not found."
274 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
282 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
283 } catch (Exception ex)
285 System.err.println("Unexpected Look and Feel Exception");
286 ex.printStackTrace();
288 if (Platform.isAMac())
291 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
293 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
295 System.setProperty("apple.laf.useScreenMenuBar", "true");
296 if (lookAndFeel != null)
300 UIManager.setLookAndFeel(lookAndFeel);
301 } catch (Throwable e)
304 "Failed to set QuaQua look and feel: " + e.toString());
307 if (lookAndFeel == null || !(lookAndFeel.getClass()
308 .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
309 || !UIManager.getLookAndFeel().getClass().toString()
310 .toLowerCase().contains("quaqua"))
315 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
316 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
317 } catch (Throwable e)
320 "Failed to reset look and feel: " + e.toString());
326 * configure 'full' SO model if preferences say to,
327 * else use the default (SO Lite)
329 if (Cache.getDefault("USE_FULL_SO", false))
331 SequenceOntologyFactory.setInstance(new SequenceOntology());
336 desktop = new Desktop();
337 desktop.setInBatchMode(true); // indicate we are starting up
338 desktop.setVisible(true);
339 desktop.startServiceDiscovery();
340 if (!aparser.contains("nousagestats"))
342 startUsageStats(desktop);
346 System.err.println("CMD [-nousagestats] executed successfully!");
349 if (!aparser.contains("noquestionnaire"))
351 String url = aparser.getValue("questionnaire");
354 // Start the desktop questionnaire prompter with the specified
356 Cache.log.debug("Starting questionnaire url at " + url);
357 desktop.checkForQuestionnaire(url);
359 "CMD questionnaire[-" + url + "] executed successfully!");
363 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
365 // Start the desktop questionnaire prompter with the specified
368 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
370 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
372 "Starting questionnaire with default url: " + defurl);
373 desktop.checkForQuestionnaire(defurl);
379 System.err.println("CMD [-noquestionnaire] executed successfully!");
382 if (!aparser.contains("nonews"))
384 desktop.checkForNews();
387 BioJsHTMLOutput.updateBioJS();
390 String file = null, data = null;
391 FileFormatI format = null;
392 DataSourceType protocol = null;
393 FileLoader fileLoader = new FileLoader(!headless);
395 String groovyscript = null; // script to execute after all loading is
396 // completed one way or another
397 // extract groovy argument and execute if necessary
398 groovyscript = aparser.getValue("groovy", true);
399 file = aparser.getValue("open", true);
401 if (file == null && desktop == null)
403 System.out.println("No files to open!");
406 String vamsasImport = aparser.getValue("vdoc");
407 String vamsasSession = aparser.getValue("vsess");
408 if (vamsasImport != null || vamsasSession != null)
410 if (desktop == null || headless)
413 "Headless vamsas sessions not yet supported. Sorry.");
416 // if we have a file, start a new session and import it.
417 boolean inSession = false;
418 if (vamsasImport != null)
422 DataSourceType viprotocol = AppletFormatAdapter
423 .checkProtocol(vamsasImport);
424 if (viprotocol == DataSourceType.FILE)
426 inSession = desktop.vamsasImport(new File(vamsasImport));
428 else if (viprotocol == DataSourceType.URL)
430 inSession = desktop.vamsasImport(new URL(vamsasImport));
433 } catch (Exception e)
435 System.err.println("Exeption when importing " + vamsasImport
436 + " as a vamsas document.");
441 System.err.println("Failed to import " + vamsasImport
442 + " as a vamsas document.");
446 System.out.println("Imported Successfully into new session "
447 + desktop.getVamsasApplication().getCurrentSession());
450 if (vamsasSession != null)
452 if (vamsasImport != null)
454 // close the newly imported session and import the Jalview specific
455 // remnants into the new session later on.
456 desktop.vamsasStop_actionPerformed(null);
458 // now join the new session
461 if (desktop.joinVamsasSession(vamsasSession))
464 "Successfully joined vamsas session " + vamsasSession);
468 System.err.println("WARNING: Failed to join vamsas session "
471 } catch (Exception e)
474 "ERROR: Failed to join vamsas session " + vamsasSession);
477 if (vamsasImport != null)
479 // the Jalview specific remnants can now be imported into the new
480 // session at the user's leisure.
482 "Skipping Push for import of data into existing vamsas session."); // TODO:
487 // desktop.getVamsasApplication().push_update();
492 // Finally, deal with the remaining input data.
497 desktop.setProgressBar(
499 .getString("status.processing_commandline_args"),
500 progress = System.currentTimeMillis());
502 System.out.println("CMD [-open " + file + "] executed successfully!");
504 if (!file.startsWith("http://"))
506 if (!(new File(file)).exists())
508 System.out.println("Can't find " + file);
516 protocol = AppletFormatAdapter.checkProtocol(file);
520 format = new IdentifyFile().identify(file, protocol);
521 } catch (FileFormatException e1)
526 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
530 System.out.println("error");
534 setCurrentAlignFrame(af);
535 data = aparser.getValue("colour", true);
538 data.replaceAll("%20", " ");
540 ColourSchemeI cs = ColourSchemeProperty
541 .getColourScheme(af.getViewport().getAlignment(), data);
546 "CMD [-color " + data + "] executed successfully!");
551 // Must maintain ability to use the groups flag
552 data = aparser.getValue("groups", true);
555 af.parseFeaturesFile(data,
556 AppletFormatAdapter.checkProtocol(data));
557 // System.out.println("Added " + data);
559 "CMD groups[-" + data + "] executed successfully!");
561 data = aparser.getValue("features", true);
564 af.parseFeaturesFile(data,
565 AppletFormatAdapter.checkProtocol(data));
566 // System.out.println("Added " + data);
568 "CMD [-features " + data + "] executed successfully!");
571 data = aparser.getValue("annotations", true);
574 af.loadJalviewDataFile(data, null, null, null);
575 // System.out.println("Added " + data);
577 "CMD [-annotations " + data + "] executed successfully!");
579 // set or clear the sortbytree flag.
580 if (aparser.contains("sortbytree"))
582 af.getViewport().setSortByTree(true);
583 if (af.getViewport().getSortByTree())
585 System.out.println("CMD [-sortbytree] executed successfully!");
588 if (aparser.contains("no-annotation"))
590 af.getViewport().setShowAnnotation(false);
591 if (!af.getViewport().isShowAnnotation())
593 System.out.println("CMD no-annotation executed successfully!");
596 if (aparser.contains("nosortbytree"))
598 af.getViewport().setSortByTree(false);
599 if (!af.getViewport().getSortByTree())
602 .println("CMD [-nosortbytree] executed successfully!");
605 data = aparser.getValue("tree", true);
611 "CMD [-tree " + data + "] executed successfully!");
612 NewickFile nf = new NewickFile(data,
613 AppletFormatAdapter.checkProtocol(data));
615 .setCurrentTree(af.showNewickTree(nf, data).getTree());
616 } catch (IOException ex)
618 System.err.println("Couldn't add tree " + data);
619 ex.printStackTrace(System.err);
622 // TODO - load PDB structure(s) to alignment JAL-629
623 // (associate with identical sequence in alignment, or a specified
625 if (groovyscript != null)
627 // Execute the groovy script after we've done all the rendering stuff
628 // and before any images or figures are generated.
629 System.out.println("Executing script " + groovyscript);
630 executeGroovyScript(groovyscript, af);
631 System.out.println("CMD groovy[" + groovyscript
632 + "] executed successfully!");
635 String imageName = "unnamed.png";
636 while (aparser.getSize() > 1)
638 String outputFormat = aparser.nextValue();
639 file = aparser.nextValue();
641 if (outputFormat.equalsIgnoreCase("png"))
643 af.createPNG(new File(file));
644 imageName = (new File(file)).getName();
645 System.out.println("Creating PNG image: " + file);
648 else if (outputFormat.equalsIgnoreCase("svg"))
650 File imageFile = new File(file);
651 imageName = imageFile.getName();
652 af.createSVG(imageFile);
653 System.out.println("Creating SVG image: " + file);
656 else if (outputFormat.equalsIgnoreCase("html"))
658 File imageFile = new File(file);
659 imageName = imageFile.getName();
660 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
661 htmlSVG.exportHTML(file);
663 System.out.println("Creating HTML image: " + file);
666 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
670 System.err.println("The output html file must not be null");
675 BioJsHTMLOutput.refreshVersionInfo(
676 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
677 } catch (URISyntaxException e)
681 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
682 bjs.exportHTML(file);
684 .println("Creating BioJS MSA Viwer HTML file: " + file);
687 else if (outputFormat.equalsIgnoreCase("imgMap"))
689 af.createImageMap(new File(file), imageName);
690 System.out.println("Creating image map: " + file);
693 else if (outputFormat.equalsIgnoreCase("eps"))
695 File outputFile = new File(file);
697 "Creating EPS file: " + outputFile.getAbsolutePath());
698 af.createEPS(outputFile);
702 if (af.saveAlignment(file, format))
704 System.out.println("Written alignment in " + format
705 + " format to " + file);
709 System.out.println("Error writing file " + file + " in "
710 + format + " format!!");
715 while (aparser.getSize() > 0)
717 System.out.println("Unknown arg: " + aparser.nextValue());
721 AlignFrame startUpAlframe = null;
722 // We'll only open the default file if the desktop is visible.
724 // ////////////////////
726 if (!headless && file == null && vamsasImport == null
727 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
729 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
730 jalview.bin.Cache.getDefault("www.jalview.org",
731 "http://www.jalview.org")
732 + "/examples/exampleFile_2_7.jar");
734 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
736 // hardwire upgrade of the startup file
737 file.replace("_2_3.jar", "_2_7.jar");
738 // and remove the stale setting
739 jalview.bin.Cache.removeProperty("STARTUP_FILE");
742 protocol = DataSourceType.FILE;
744 if (file.indexOf("http:") > -1)
746 protocol = DataSourceType.URL;
749 if (file.endsWith(".jar"))
751 format = FileFormat.Jalview;
757 format = new IdentifyFile().identify(file, protocol);
758 } catch (FileFormatException e)
764 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
766 // extract groovy arguments before anything else.
769 // Once all other stuff is done, execute any groovy scripts (in order)
770 if (groovyscript != null)
772 if (Cache.groovyJarsPresent())
774 System.out.println("Executing script " + groovyscript);
775 executeGroovyScript(groovyscript, startUpAlframe);
780 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
784 // and finally, turn off batch mode indicator - if the desktop still exists
789 desktop.setProgressBar(null, progress);
791 desktop.setInBatchMode(false);
795 private static void showUsage()
798 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
799 + "-nodisplay\tRun Jalview without User Interface.\n"
800 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
801 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
802 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
803 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
804 + "-features FILE\tUse the given file to mark features on the alignment.\n"
805 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
806 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
807 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
808 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
809 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
810 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
811 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
812 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
813 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
814 + "-png FILE\tCreate PNG image FILE from alignment.\n"
815 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
816 + "-html FILE\tCreate HTML file from alignment.\n"
817 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
818 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
819 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
820 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
821 + "-noquestionnaire\tTurn off questionnaire check.\n"
822 + "-nonews\tTurn off check for Jalview news.\n"
823 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
824 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
826 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
827 // after all other properties files have been read\n\t
828 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
829 // passed in correctly)"
830 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
831 + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
832 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
833 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
834 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
836 // "-vdoc vamsas-document\tImport vamsas document into new
837 // session or join existing session with same URN\n"
838 // + "-vses vamsas-session\tJoin session with given URN\n"
839 + "-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"
840 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
843 private static void startUsageStats(final Desktop desktop)
846 * start a User Config prompt asking if we can log usage statistics.
848 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
849 "USAGESTATS", "Jalview Usage Statistics",
850 "Do you want to help make Jalview better by enabling "
851 + "the collection of usage statistics with Google Analytics ?"
852 + "\n\n(you can enable or disable usage tracking in the preferences)",
859 "Initialising googletracker for usage stats.");
860 Cache.initGoogleTracker();
861 Cache.log.debug("Tracking enabled.");
868 Cache.log.debug("Not enabling Google Tracking.");
871 desktop.addDialogThread(prompter);
875 * Locate the given string as a file and pass it to the groovy interpreter.
877 * @param groovyscript
878 * the script to execute
879 * @param jalviewContext
880 * the Jalview Desktop object passed in to the groovy binding as the
883 private void executeGroovyScript(String groovyscript, AlignFrame af)
886 * for scripts contained in files
893 if (groovyscript.trim().equals("STDIN"))
895 // read from stdin into a tempfile and execute it
898 tfile = File.createTempFile("jalview", "groovy");
899 PrintWriter outfile = new PrintWriter(
900 new OutputStreamWriter(new FileOutputStream(tfile)));
901 BufferedReader br = new BufferedReader(
902 new InputStreamReader(System.in));
904 while ((line = br.readLine()) != null)
906 outfile.write(line + "\n");
912 } catch (Exception ex)
914 System.err.println("Failed to read from STDIN into tempfile "
915 + ((tfile == null) ? "(tempfile wasn't created)"
916 : tfile.toString()));
917 ex.printStackTrace();
922 sfile = tfile.toURI().toURL();
923 } catch (Exception x)
926 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
936 sfile = new URI(groovyscript).toURL();
937 } catch (Exception x)
939 tfile = new File(groovyscript);
942 System.err.println("File '" + groovyscript + "' does not exist.");
945 if (!tfile.canRead())
947 System.err.println("File '" + groovyscript + "' cannot be read.");
950 if (tfile.length() < 1)
952 System.err.println("File '" + groovyscript + "' is empty.");
957 sfile = tfile.getAbsoluteFile().toURI().toURL();
958 } catch (Exception ex)
960 System.err.println("Failed to create a file URL for "
961 + tfile.getAbsoluteFile());
968 Map<String, Object> vbinding = new HashMap<>();
969 vbinding.put("Jalview", this);
972 vbinding.put("currentAlFrame", af);
974 Binding gbinding = new Binding(vbinding);
975 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
976 gse.run(sfile.toString(), gbinding);
977 if ("STDIN".equals(groovyscript))
979 // delete temp file that we made -
980 // only if it was successfully executed
983 } catch (Exception e)
985 System.err.println("Exception Whilst trying to execute file " + sfile
986 + " as a groovy script.");
987 e.printStackTrace(System.err);
992 public static boolean isHeadlessMode()
994 String isheadless = System.getProperty("java.awt.headless");
995 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1002 public AlignFrame[] getAlignFrames()
1004 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1005 : Desktop.getAlignFrames();
1010 * Quit method delegates to Desktop.quit - unless running in headless mode
1011 * when it just ends the JVM
1015 if (desktop != null)
1025 public static AlignFrame getCurrentAlignFrame()
1027 return Jalview.currentAlignFrame;
1030 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1032 Jalview.currentAlignFrame = currentAlignFrame;