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 groovy.lang.Binding;
24 import groovy.util.GroovyScriptEngine;
26 import jalview.ext.so.SequenceOntology;
27 import jalview.gui.AlignFrame;
28 import jalview.gui.Desktop;
29 import jalview.gui.PromptUserConfig;
30 import jalview.io.AppletFormatAdapter;
31 import jalview.io.BioJsHTMLOutput;
32 import jalview.io.FileLoader;
33 import jalview.io.FormatAdapter;
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.schemes.UserColourScheme;
41 import jalview.util.MessageManager;
42 import jalview.util.Platform;
43 import jalview.ws.jws2.Jws2Discoverer;
45 import java.io.BufferedReader;
47 import java.io.FileOutputStream;
48 import java.io.IOException;
49 import java.io.InputStreamReader;
50 import java.io.OutputStreamWriter;
51 import java.io.PrintWriter;
52 import java.net.MalformedURLException;
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.UIManager;
67 * Main class for Jalview Application <br>
69 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
77 * singleton instance of this class
79 private static Jalview instance;
81 private Desktop desktop;
83 public static AlignFrame currentAlignFrame;
87 // grab all the rights we can the JVM
88 Policy.setPolicy(new Policy()
91 public PermissionCollection getPermissions(CodeSource codesource)
93 Permissions perms = new Permissions();
94 perms.add(new AllPermission());
106 * keep track of feature fetching tasks.
114 * TODO: generalise to track all jalview events to orchestrate batch
118 private int queued = 0;
120 private int running = 0;
122 public FeatureFetcher()
127 public void addFetcher(final AlignFrame af,
128 final Vector<String> dasSources)
130 final long id = System.currentTimeMillis();
132 final FeatureFetcher us = this;
133 new Thread(new Runnable()
145 af.setProgressBar(MessageManager
146 .getString("status.das_features_being_retrived"), id);
147 af.featureSettings_actionPerformed(null);
148 af.featureSettings.fetchDasFeatures(dasSources, true);
149 af.setProgressBar(null, id);
158 public synchronized boolean allFinished()
160 return queued == 0 && running == 0;
165 public static Jalview getInstance()
171 * main class for Jalview application
174 * open <em>filename</em>
176 public static void main(String[] args)
178 instance = new Jalview();
179 instance.doMain(args);
185 void doMain(String[] args)
187 System.setSecurityManager(null);
188 System.out.println("Java version: "
189 + System.getProperty("java.version"));
190 System.out.println(System.getProperty("os.arch") + " "
191 + System.getProperty("os.name") + " "
192 + System.getProperty("os.version"));
194 ArgsParser aparser = new ArgsParser(args);
195 boolean headless = false;
197 if (aparser.contains("help") || aparser.contains("h"))
202 if (aparser.contains("nodisplay") || aparser.contains("nogui")
203 || aparser.contains("headless"))
205 System.setProperty("java.awt.headless", "true");
208 String usrPropsFile = aparser.getValue("props");
209 Cache.loadProperties(usrPropsFile); // must do this before
210 if (usrPropsFile != null)
212 System.out.println("CMD [-props " + usrPropsFile
213 + "] executed successfully!");
218 final String jabawsUrl = aparser.getValue("jabaws");
219 if (jabawsUrl != null)
223 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
224 System.out.println("CMD [-jabaws " + jabawsUrl
225 + "] executed successfully!");
226 } catch (MalformedURLException e)
228 System.err.println("Invalid jabaws parameter: " + jabawsUrl
233 String defs = aparser.getValue("setprop");
236 int p = defs.indexOf('=');
239 System.err.println("Ignoring invalid setprop argument : " + defs);
243 System.out.println("Executing setprop argument: " + defs);
244 // DISABLED FOR SECURITY REASONS
245 // TODO: add a property to allow properties to be overriden by cli args
246 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
248 defs = aparser.getValue("setprop");
250 if (System.getProperty("java.awt.headless") != null
251 && System.getProperty("java.awt.headless").equals("true"))
255 System.setProperty("http.agent",
256 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
260 } catch (NoClassDefFoundError error)
262 error.printStackTrace();
264 .println("\nEssential logging libraries not found."
265 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
273 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
274 } catch (Exception ex)
277 if (Platform.isAMac())
279 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
281 System.setProperty("apple.laf.useScreenMenuBar", "true");
284 UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
286 } catch (Throwable e)
288 System.err.println("Failed to set QuaQua look and feel: "
294 * configure 'full' SO model unless preferences say not to
296 if (!Cache.getDefault("USE_SO_LITE", false))
298 SequenceOntologyFactory.setInstance(new SequenceOntology());
303 desktop = new Desktop();
304 desktop.setInBatchMode(true); // indicate we are starting up
305 desktop.setVisible(true);
306 desktop.startServiceDiscovery();
307 if (!aparser.contains("nousagestats"))
309 startUsageStats(desktop);
313 System.err.println("CMD [-nousagestats] executed successfully!");
316 if (!aparser.contains("noquestionnaire"))
318 String url = aparser.getValue("questionnaire");
321 // Start the desktop questionnaire prompter with the specified
323 Cache.log.debug("Starting questionnaire url at " + url);
324 desktop.checkForQuestionnaire(url);
325 System.out.println("CMD questionnaire[-" + url
326 + "] executed successfully!");
330 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
332 // Start the desktop questionnaire prompter with the specified
335 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
337 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
338 Cache.log.debug("Starting questionnaire with default url: "
340 desktop.checkForQuestionnaire(defurl);
346 System.err.println("CMD [-noquestionnaire] executed successfully!");
349 if (!aparser.contains("nonews"))
351 desktop.checkForNews();
354 BioJsHTMLOutput.updateBioJS();
357 String file = null, protocol = null, format = null, data = null;
358 FileLoader fileLoader = new FileLoader(!headless);
359 Vector<String> getFeatures = null; // vector of das source nicknames to
363 String groovyscript = null; // script to execute after all loading is
364 // completed one way or another
365 // extract groovy argument and execute if necessary
366 groovyscript = aparser.getValue("groovy", true);
367 file = aparser.getValue("open", true);
369 if (file == null && desktop == null)
371 System.out.println("No files to open!");
374 String vamsasImport = aparser.getValue("vdoc");
375 String vamsasSession = aparser.getValue("vsess");
376 if (vamsasImport != null || vamsasSession != null)
378 if (desktop == null || headless)
381 .println("Headless vamsas sessions not yet supported. Sorry.");
384 // if we have a file, start a new session and import it.
385 boolean inSession = false;
386 if (vamsasImport != null)
390 String viprotocol = AppletFormatAdapter
391 .checkProtocol(vamsasImport);
392 if (viprotocol == jalview.io.FormatAdapter.FILE)
394 inSession = desktop.vamsasImport(new File(vamsasImport));
396 else if (viprotocol == FormatAdapter.URL)
398 inSession = desktop.vamsasImport(new URL(vamsasImport));
401 } catch (Exception e)
403 System.err.println("Exeption when importing " + vamsasImport
404 + " as a vamsas document.");
409 System.err.println("Failed to import " + vamsasImport
410 + " as a vamsas document.");
414 System.out.println("Imported Successfully into new session "
415 + desktop.getVamsasApplication().getCurrentSession());
418 if (vamsasSession != null)
420 if (vamsasImport != null)
422 // close the newly imported session and import the Jalview specific
423 // remnants into the new session later on.
424 desktop.vamsasStop_actionPerformed(null);
426 // now join the new session
429 if (desktop.joinVamsasSession(vamsasSession))
431 System.out.println("Successfully joined vamsas session "
436 System.err.println("WARNING: Failed to join vamsas session "
439 } catch (Exception e)
441 System.err.println("ERROR: Failed to join vamsas session "
445 if (vamsasImport != null)
447 // the Jalview specific remnants can now be imported into the new
448 // session at the user's leisure.
450 .info("Skipping Push for import of data into existing vamsas session."); // TODO:
455 // desktop.getVamsasApplication().push_update();
460 // Finally, deal with the remaining input data.
465 desktop.setProgressBar(MessageManager
466 .getString("status.processing_commandline_args"),
467 progress = System.currentTimeMillis());
469 System.out.println("CMD [-open " + file + "] executed successfully!");
471 if (!file.startsWith("http://"))
473 if (!(new File(file)).exists())
475 System.out.println("Can't find " + file);
483 protocol = AppletFormatAdapter.checkProtocol(file);
485 format = new IdentifyFile().identify(file, protocol);
487 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
491 System.out.println("error");
495 setCurrentAlignFrame(af);
496 data = aparser.getValue("colour", true);
499 data.replaceAll("%20", " ");
501 ColourSchemeI cs = ColourSchemeProperty.getColour(af
502 .getViewport().getAlignment(), data);
506 UserColourScheme ucs = new UserColourScheme("white");
507 ucs.parseAppletParameter(data);
512 System.out.println("CMD [-color " + data
513 + "] executed successfully!");
518 // Must maintain ability to use the groups flag
519 data = aparser.getValue("groups", true);
522 af.parseFeaturesFile(data,
523 AppletFormatAdapter.checkProtocol(data));
524 // System.out.println("Added " + data);
525 System.out.println("CMD groups[-" + data
526 + "] executed successfully!");
528 data = aparser.getValue("features", true);
531 af.parseFeaturesFile(data,
532 AppletFormatAdapter.checkProtocol(data));
533 // System.out.println("Added " + data);
534 System.out.println("CMD [-features " + data
535 + "] executed successfully!");
538 data = aparser.getValue("annotations", true);
541 af.loadJalviewDataFile(data, null, null, null);
542 // System.out.println("Added " + data);
543 System.out.println("CMD [-annotations " + data
544 + "] executed successfully!");
546 // set or clear the sortbytree flag.
547 if (aparser.contains("sortbytree"))
549 af.getViewport().setSortByTree(true);
550 if (af.getViewport().getSortByTree())
552 System.out.println("CMD [-sortbytree] executed successfully!");
555 if (aparser.contains("no-annotation"))
557 af.getViewport().setShowAnnotation(false);
558 if (!af.getViewport().isShowAnnotation())
560 System.out.println("CMD no-annotation executed successfully!");
563 if (aparser.contains("nosortbytree"))
565 af.getViewport().setSortByTree(false);
566 if (!af.getViewport().getSortByTree())
569 .println("CMD [-nosortbytree] executed successfully!");
572 data = aparser.getValue("tree", true);
575 jalview.io.NewickFile fin = null;
578 System.out.println("CMD [-tree " + data
579 + "] executed successfully!");
580 fin = new NewickFile(data,
581 AppletFormatAdapter.checkProtocol(data));
584 af.getViewport().setCurrentTree(
585 af.ShowNewickTree(fin, data).getTree());
587 } catch (IOException ex)
589 System.err.println("Couldn't add tree " + data);
590 ex.printStackTrace(System.err);
593 // TODO - load PDB structure(s) to alignment JAL-629
594 // (associate with identical sequence in alignment, or a specified
597 getFeatures = checkDasArguments(aparser);
598 if (af != null && getFeatures != null)
600 FeatureFetcher ff = startFeatureFetching(getFeatures);
603 while (!ff.allFinished() || af.operationInProgress())
605 // wait around until fetching is finished.
609 } catch (Exception e)
615 getFeatures = null; // have retrieved features - forget them now.
617 if (groovyscript != null)
619 // Execute the groovy script after we've done all the rendering stuff
620 // and before any images or figures are generated.
621 System.out.println("Executing script " + groovyscript);
622 executeGroovyScript(groovyscript, af);
623 System.out.println("CMD groovy[" + groovyscript
624 + "] executed successfully!");
627 String imageName = "unnamed.png";
628 while (aparser.getSize() > 1)
630 format = aparser.nextValue();
631 file = aparser.nextValue();
633 if (format.equalsIgnoreCase("png"))
635 af.createPNG(new File(file));
636 imageName = (new File(file)).getName();
637 System.out.println("Creating PNG image: " + file);
640 else if (format.equalsIgnoreCase("svg"))
642 File imageFile = new File(file);
643 imageName = imageFile.getName();
644 af.createSVG(imageFile);
645 System.out.println("Creating SVG image: " + file);
648 else if (format.equalsIgnoreCase("html"))
650 File imageFile = new File(file);
651 imageName = imageFile.getName();
652 new HtmlSvgOutput(new File(file), af.alignPanel);
653 System.out.println("Creating HTML image: " + file);
656 else if (format.equalsIgnoreCase("imgMap"))
658 af.createImageMap(new File(file), imageName);
659 System.out.println("Creating image map: " + file);
662 else if (format.equalsIgnoreCase("eps"))
664 File outputFile = new File(file);
665 System.out.println("Creating EPS file: "
666 + outputFile.getAbsolutePath());
667 af.createEPS(outputFile);
671 if (af.saveAlignment(file, format))
673 System.out.println("Written alignment in " + format
674 + " format to " + file);
678 System.out.println("Error writing file " + file + " in "
679 + format + " format!!");
684 while (aparser.getSize() > 0)
686 System.out.println("Unknown arg: " + aparser.nextValue());
690 AlignFrame startUpAlframe = null;
691 // We'll only open the default file if the desktop is visible.
693 // ////////////////////
695 if (!headless && file == null && vamsasImport == null
696 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
698 file = jalview.bin.Cache.getDefault(
700 jalview.bin.Cache.getDefault("www.jalview.org",
701 "http://www.jalview.org")
702 + "/examples/exampleFile_2_7.jar");
703 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
705 // hardwire upgrade of the startup file
706 file.replace("_2_3.jar", "_2_7.jar");
707 // and remove the stale setting
708 jalview.bin.Cache.removeProperty("STARTUP_FILE");
713 if (file.indexOf("http:") > -1)
718 if (file.endsWith(".jar"))
724 format = new IdentifyFile().identify(file, protocol);
727 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
729 getFeatures = checkDasArguments(aparser);
730 // extract groovy arguments before anything else.
732 // If the user has specified features to be retrieved,
733 // or a groovy script to be executed, do them if they
734 // haven't been done already
735 // fetch features for the default alignment
736 if (getFeatures != null)
738 if (startUpAlframe != null)
740 startFeatureFetching(getFeatures);
743 // Once all other stuff is done, execute any groovy scripts (in order)
744 if (groovyscript != null)
746 if (Cache.groovyJarsPresent())
748 System.out.println("Executing script " + groovyscript);
749 executeGroovyScript(groovyscript, startUpAlframe);
754 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
758 // and finally, turn off batch mode indicator - if the desktop still exists
763 desktop.setProgressBar(null, progress);
765 desktop.setInBatchMode(false);
769 private static void showUsage()
772 .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
773 + "-nodisplay\tRun Jalview without User Interface.\n"
774 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
775 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
776 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
777 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
778 + "-features FILE\tUse the given file to mark features on the alignment.\n"
779 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
780 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
781 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
782 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
783 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
784 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
785 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
786 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
787 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
788 + "-png FILE\tCreate PNG image FILE from alignment.\n"
789 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
790 + "-html FILE\tCreate HTML file from alignment.\n"
791 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
792 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
793 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
794 + "-noquestionnaire\tTurn off questionnaire check.\n"
795 + "-nonews\tTurn off check for Jalview news.\n"
796 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
797 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
799 // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
800 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
801 + "-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"
802 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
803 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
804 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
806 // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
807 // + "-vses vamsas-session\tJoin session with given URN\n"
808 + "-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"
809 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
812 private static void startUsageStats(final Desktop desktop)
815 * start a User Config prompt asking if we can log usage statistics.
817 PromptUserConfig prompter = new PromptUserConfig(
820 "Jalview Usage Statistics",
821 "Do you want to help make Jalview better by enabling "
822 + "the collection of usage statistics with Google Analytics ?"
823 + "\n\n(you can enable or disable usage tracking in the preferences)",
830 .debug("Initialising googletracker for usage stats.");
831 Cache.initGoogleTracker();
832 Cache.log.debug("Tracking enabled.");
839 Cache.log.debug("Not enabling Google Tracking.");
842 desktop.addDialogThread(prompter);
846 * Locate the given string as a file and pass it to the groovy interpreter.
848 * @param groovyscript
849 * the script to execute
850 * @param jalviewContext
851 * the Jalview Desktop object passed in to the groovy binding as the
854 private void executeGroovyScript(String groovyscript, AlignFrame af)
857 * for scripts contained in files
864 if (groovyscript.trim().equals("STDIN"))
866 // read from stdin into a tempfile and execute it
869 tfile = File.createTempFile("jalview", "groovy");
870 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
871 new FileOutputStream(tfile)));
872 BufferedReader br = new BufferedReader(new InputStreamReader(
875 while ((line = br.readLine()) != null)
877 outfile.write(line + "\n");
883 } catch (Exception ex)
885 System.err.println("Failed to read from STDIN into tempfile "
886 + ((tfile == null) ? "(tempfile wasn't created)" : tfile
888 ex.printStackTrace();
893 sfile = tfile.toURI().toURL();
894 } catch (Exception x)
897 .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
907 sfile = new URI(groovyscript).toURL();
908 } catch (Exception x)
910 tfile = new File(groovyscript);
913 System.err.println("File '" + groovyscript + "' does not exist.");
916 if (!tfile.canRead())
918 System.err.println("File '" + groovyscript + "' cannot be read.");
921 if (tfile.length() < 1)
923 System.err.println("File '" + groovyscript + "' is empty.");
928 sfile = tfile.getAbsoluteFile().toURI().toURL();
929 } catch (Exception ex)
931 System.err.println("Failed to create a file URL for "
932 + tfile.getAbsoluteFile());
939 Map<String, Object> vbinding = new HashMap<String, Object>();
940 vbinding.put("Jalview", this);
943 vbinding.put("currentAlFrame", af);
945 Binding gbinding = new Binding(vbinding);
946 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
947 gse.run(sfile.toString(), gbinding);
948 if ("STDIN".equals(groovyscript))
950 // delete temp file that we made -
951 // only if it was successfully executed
954 } catch (Exception e)
956 System.err.println("Exception Whilst trying to execute file " + sfile
957 + " as a groovy script.");
958 e.printStackTrace(System.err);
964 * Check commandline for any das server definitions or any fetchfrom switches
966 * @return vector of DAS source nicknames to retrieve from
968 private static Vector<String> checkDasArguments(ArgsParser aparser)
970 Vector<String> source = null;
972 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
973 while ((data = aparser.getValue("dasserver", true)) != null)
975 String nickname = null;
977 int pos = data.indexOf('=');
978 // determine capabilities
981 nickname = data.substring(0, pos);
983 url = data.substring(pos + 1);
985 && (url.startsWith("http:") || url
986 .startsWith("sequence:http:")))
988 if (nickname == null)
992 if (locsources == null)
1000 locsources = locsources + nickname + "|" + url;
1002 .println("NOTE! dasserver parameter not yet really supported (got args of "
1003 + nickname + "|" + url);
1006 source = new Vector<String>();
1008 source.addElement(nickname);
1010 System.out.println("CMD [-dasserver " + data
1011 + "] executed successfully!");
1012 } // loop until no more server entries are found.
1013 if (locsources != null && locsources.indexOf('|') > -1)
1015 Cache.log.debug("Setting local source list in properties file to:\n"
1017 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
1019 while ((data = aparser.getValue("fetchfrom", true)) != null)
1021 System.out.println("adding source '" + data + "'");
1024 source = new Vector<String>();
1026 source.addElement(data);
1032 * start a feature fetcher for every alignment frame
1036 private FeatureFetcher startFeatureFetching(
1037 final Vector<String> dasSources)
1039 FeatureFetcher ff = new FeatureFetcher();
1040 AlignFrame afs[] = Desktop.getAlignFrames();
1041 if (afs == null || afs.length == 0)
1045 for (int i = 0; i < afs.length; i++)
1047 ff.addFetcher(afs[i], dasSources);
1052 public static boolean isHeadlessMode()
1054 String isheadless = System.getProperty("java.awt.headless");
1055 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1062 public AlignFrame[] getAlignFrames()
1064 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1065 : Desktop.getAlignFrames();
1070 * Quit method delegates to Desktop.quit - unless running in headless mode
1071 * when it just ends the JVM
1075 if (desktop != null)
1085 public static AlignFrame getCurrentAlignFrame()
1087 return Jalview.currentAlignFrame;
1090 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1092 Jalview.currentAlignFrame = currentAlignFrame;