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.UIManager;
66 import groovy.lang.Binding;
67 import groovy.util.GroovyScriptEngine;
70 * Main class for Jalview Application <br>
72 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
80 * singleton instance of this class
82 private static Jalview instance;
84 private Desktop desktop;
86 public static AlignFrame currentAlignFrame;
90 // grab all the rights we can the JVM
91 Policy.setPolicy(new Policy()
94 public PermissionCollection getPermissions(CodeSource codesource)
96 Permissions perms = new Permissions();
97 perms.add(new AllPermission());
102 public void refresh()
109 * keep track of feature fetching tasks.
117 * TODO: generalise to track all jalview events to orchestrate batch
121 private int queued = 0;
123 private int running = 0;
125 public FeatureFetcher()
130 public void addFetcher(final AlignFrame af,
131 final Vector<String> dasSources)
133 final long id = System.currentTimeMillis();
135 final FeatureFetcher us = this;
136 new Thread(new Runnable()
148 af.setProgressBar(MessageManager
149 .getString("status.das_features_being_retrived"), id);
150 af.featureSettings_actionPerformed(null);
151 af.featureSettings.fetchDasFeatures(dasSources, true);
152 af.setProgressBar(null, id);
158 }, "FeatureFetcherThread").start();
161 public synchronized boolean allFinished()
163 return queued == 0 && running == 0;
168 public static Jalview getInstance()
174 * main class for Jalview application
177 * open <em>filename</em>
179 public static void main(String[] args)
181 instance = new Jalview();
182 instance.doMain(args);
188 void doMain(String[] args)
190 System.setSecurityManager(null);
192 .println("Java version: " + System.getProperty("java.version"));
193 System.out.println(System.getProperty("os.arch") + " "
194 + System.getProperty("os.name") + " "
195 + System.getProperty("os.version"));
197 ArgsParser aparser = new ArgsParser(args);
198 boolean headless = false;
200 if (aparser.contains("help") || aparser.contains("h"))
205 if (aparser.contains("nodisplay") || aparser.contains("nogui")
206 || aparser.contains("headless"))
208 System.setProperty("java.awt.headless", "true");
211 String usrPropsFile = aparser.getValue("props");
212 Cache.loadProperties(usrPropsFile); // must do this before
213 if (usrPropsFile != null)
216 "CMD [-props " + usrPropsFile + "] executed successfully!");
221 final String jabawsUrl = aparser.getValue("jabaws");
222 if (jabawsUrl != null)
226 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
228 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
229 } catch (MalformedURLException e)
232 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
236 String defs = aparser.getValue("setprop");
239 int p = defs.indexOf('=');
242 System.err.println("Ignoring invalid setprop argument : " + defs);
246 System.out.println("Executing setprop argument: " + defs);
247 // DISABLED FOR SECURITY REASONS
248 // TODO: add a property to allow properties to be overriden by cli args
249 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
251 defs = aparser.getValue("setprop");
253 if (System.getProperty("java.awt.headless") != null
254 && System.getProperty("java.awt.headless").equals("true"))
258 System.setProperty("http.agent",
259 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
263 } catch (NoClassDefFoundError error)
265 error.printStackTrace();
266 System.out.println("\nEssential logging libraries not found."
267 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
275 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
276 } catch (Exception ex)
279 if (Platform.isAMac())
281 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
283 System.setProperty("apple.laf.useScreenMenuBar", "true");
286 UIManager.setLookAndFeel(
287 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel());
288 } catch (Throwable e)
291 "Failed to set QuaQua look and feel: " + e.toString());
296 * configure 'full' SO model if preferences say to,
297 * else use the default (SO Lite)
299 if (Cache.getDefault("USE_FULL_SO", false))
301 SequenceOntologyFactory.setInstance(new SequenceOntology());
306 desktop = new Desktop();
307 desktop.setInBatchMode(true); // indicate we are starting up
308 desktop.setVisible(true);
309 desktop.startServiceDiscovery();
310 if (!aparser.contains("nousagestats"))
312 startUsageStats(desktop);
316 System.err.println("CMD [-nousagestats] executed successfully!");
319 if (!aparser.contains("noquestionnaire"))
321 String url = aparser.getValue("questionnaire");
324 // Start the desktop questionnaire prompter with the specified
326 Cache.log.debug("Starting questionnaire url at " + url);
327 desktop.checkForQuestionnaire(url);
329 "CMD questionnaire[-" + url + "] executed successfully!");
333 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
335 // Start the desktop questionnaire prompter with the specified
338 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
340 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
342 "Starting questionnaire with default url: " + defurl);
343 desktop.checkForQuestionnaire(defurl);
349 System.err.println("CMD [-noquestionnaire] executed successfully!");
352 if (!aparser.contains("nonews"))
354 desktop.checkForNews();
357 BioJsHTMLOutput.updateBioJS();
360 String file = null, data = null;
361 FileFormatI format = null;
362 DataSourceType protocol = null;
363 FileLoader fileLoader = new FileLoader(!headless);
364 Vector<String> getFeatures = null; // vector of das source nicknames to
368 String groovyscript = null; // script to execute after all loading is
369 // completed one way or another
370 // extract groovy argument and execute if necessary
371 groovyscript = aparser.getValue("groovy", true);
372 file = aparser.getValue("open", true);
374 if (file == null && desktop == null)
376 System.out.println("No files to open!");
379 String vamsasImport = aparser.getValue("vdoc");
380 String vamsasSession = aparser.getValue("vsess");
381 if (vamsasImport != null || vamsasSession != null)
383 if (desktop == null || headless)
386 "Headless vamsas sessions not yet supported. Sorry.");
389 // if we have a file, start a new session and import it.
390 boolean inSession = false;
391 if (vamsasImport != null)
395 DataSourceType viprotocol = AppletFormatAdapter
396 .checkProtocol(vamsasImport);
397 if (viprotocol == DataSourceType.FILE)
399 inSession = desktop.vamsasImport(new File(vamsasImport));
401 else if (viprotocol == DataSourceType.URL)
403 inSession = desktop.vamsasImport(new URL(vamsasImport));
406 } catch (Exception e)
408 System.err.println("Exeption when importing " + vamsasImport
409 + " as a vamsas document.");
414 System.err.println("Failed to import " + vamsasImport
415 + " as a vamsas document.");
419 System.out.println("Imported Successfully into new session "
420 + desktop.getVamsasApplication().getCurrentSession());
423 if (vamsasSession != null)
425 if (vamsasImport != null)
427 // close the newly imported session and import the Jalview specific
428 // remnants into the new session later on.
429 desktop.vamsasStop_actionPerformed(null);
431 // now join the new session
434 if (desktop.joinVamsasSession(vamsasSession))
437 "Successfully joined vamsas session " + vamsasSession);
441 System.err.println("WARNING: Failed to join vamsas session "
444 } catch (Exception e)
447 "ERROR: Failed to join vamsas session " + vamsasSession);
450 if (vamsasImport != null)
452 // the Jalview specific remnants can now be imported into the new
453 // session at the user's leisure.
455 "Skipping Push for import of data into existing vamsas session."); // TODO:
460 // desktop.getVamsasApplication().push_update();
465 // Finally, deal with the remaining input data.
470 desktop.setProgressBar(
472 .getString("status.processing_commandline_args"),
473 progress = System.currentTimeMillis());
475 System.out.println("CMD [-open " + file + "] executed successfully!");
477 if (!file.startsWith("http://"))
479 if (!(new File(file)).exists())
481 System.out.println("Can't find " + file);
489 protocol = AppletFormatAdapter.checkProtocol(file);
493 format = new IdentifyFile().identify(file, protocol);
494 } catch (FileFormatException e1)
499 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
503 System.out.println("error");
507 setCurrentAlignFrame(af);
508 data = aparser.getValue("colour", true);
511 data.replaceAll("%20", " ");
513 ColourSchemeI cs = ColourSchemeProperty
514 .getColourScheme(af.getViewport().getAlignment(), data);
519 "CMD [-color " + data + "] executed successfully!");
524 // Must maintain ability to use the groups flag
525 data = aparser.getValue("groups", true);
528 af.parseFeaturesFile(data,
529 AppletFormatAdapter.checkProtocol(data));
530 // System.out.println("Added " + data);
532 "CMD groups[-" + data + "] executed successfully!");
534 data = aparser.getValue("features", true);
537 af.parseFeaturesFile(data,
538 AppletFormatAdapter.checkProtocol(data));
539 // System.out.println("Added " + data);
541 "CMD [-features " + data + "] executed successfully!");
544 data = aparser.getValue("annotations", true);
547 af.loadJalviewDataFile(data, null, null, null);
548 // System.out.println("Added " + data);
550 "CMD [-annotations " + data + "] executed successfully!");
552 // set or clear the sortbytree flag.
553 if (aparser.contains("sortbytree"))
555 af.getViewport().setSortByTree(true);
556 if (af.getViewport().getSortByTree())
558 System.out.println("CMD [-sortbytree] executed successfully!");
561 if (aparser.contains("no-annotation"))
563 af.getViewport().setShowAnnotation(false);
564 if (!af.getViewport().isShowAnnotation())
566 System.out.println("CMD no-annotation executed successfully!");
569 if (aparser.contains("nosortbytree"))
571 af.getViewport().setSortByTree(false);
572 if (!af.getViewport().getSortByTree())
575 .println("CMD [-nosortbytree] executed successfully!");
578 data = aparser.getValue("tree", true);
584 "CMD [-tree " + data + "] executed successfully!");
585 NewickFile nf = new NewickFile(data,
586 AppletFormatAdapter.checkProtocol(data));
588 .setCurrentTree(af.showNewickTree(nf, data).getTree());
589 } catch (IOException ex)
591 System.err.println("Couldn't add tree " + data);
592 ex.printStackTrace(System.err);
595 // TODO - load PDB structure(s) to alignment JAL-629
596 // (associate with identical sequence in alignment, or a specified
599 getFeatures = checkDasArguments(aparser);
600 if (af != null && getFeatures != null)
602 FeatureFetcher ff = startFeatureFetching(getFeatures);
605 while (!ff.allFinished() || af.operationInProgress())
607 // wait around until fetching is finished.
611 } catch (Exception e)
617 getFeatures = null; // have retrieved features - forget them now.
619 if (groovyscript != null)
621 // Execute the groovy script after we've done all the rendering stuff
622 // and before any images or figures are generated.
623 System.out.println("Executing script " + groovyscript);
624 executeGroovyScript(groovyscript, af);
625 System.out.println("CMD groovy[" + groovyscript
626 + "] executed successfully!");
629 String imageName = "unnamed.png";
630 while (aparser.getSize() > 1)
632 String outputFormat = aparser.nextValue();
633 file = aparser.nextValue();
635 if (outputFormat.equalsIgnoreCase("png"))
637 af.createPNG(new File(file));
638 imageName = (new File(file)).getName();
639 System.out.println("Creating PNG image: " + file);
642 else if (outputFormat.equalsIgnoreCase("svg"))
644 File imageFile = new File(file);
645 imageName = imageFile.getName();
646 af.createSVG(imageFile);
647 System.out.println("Creating SVG image: " + file);
650 else if (outputFormat.equalsIgnoreCase("html"))
652 File imageFile = new File(file);
653 imageName = imageFile.getName();
654 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
655 htmlSVG.exportHTML(file);
657 System.out.println("Creating HTML image: " + file);
660 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
664 System.err.println("The output html file must not be null");
669 BioJsHTMLOutput.refreshVersionInfo(
670 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
671 } catch (URISyntaxException e)
675 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
676 bjs.exportHTML(file);
678 .println("Creating BioJS MSA Viwer HTML file: " + file);
681 else if (outputFormat.equalsIgnoreCase("imgMap"))
683 af.createImageMap(new File(file), imageName);
684 System.out.println("Creating image map: " + file);
687 else if (outputFormat.equalsIgnoreCase("eps"))
689 File outputFile = new File(file);
691 "Creating EPS file: " + outputFile.getAbsolutePath());
692 af.createEPS(outputFile);
696 if (af.saveAlignment(file, format))
698 System.out.println("Written alignment in " + format
699 + " format to " + file);
703 System.out.println("Error writing file " + file + " in "
704 + format + " format!!");
709 while (aparser.getSize() > 0)
711 System.out.println("Unknown arg: " + aparser.nextValue());
715 AlignFrame startUpAlframe = null;
716 // We'll only open the default file if the desktop is visible.
718 // ////////////////////
720 if (!headless && file == null && vamsasImport == null
721 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
723 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
724 jalview.bin.Cache.getDefault("www.jalview.org",
725 "http://www.jalview.org")
726 + "/examples/exampleFile_2_7.jar");
728 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
730 // hardwire upgrade of the startup file
731 file.replace("_2_3.jar", "_2_7.jar");
732 // and remove the stale setting
733 jalview.bin.Cache.removeProperty("STARTUP_FILE");
736 protocol = DataSourceType.FILE;
738 if (file.indexOf("http:") > -1)
740 protocol = DataSourceType.URL;
743 if (file.endsWith(".jar"))
745 format = FileFormat.Jalview;
751 format = new IdentifyFile().identify(file, protocol);
752 } catch (FileFormatException e)
758 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
760 getFeatures = checkDasArguments(aparser);
761 // extract groovy arguments before anything else.
763 // If the user has specified features to be retrieved,
764 // or a groovy script to be executed, do them if they
765 // haven't been done already
766 // fetch features for the default alignment
767 if (getFeatures != null)
769 if (startUpAlframe != null)
771 startFeatureFetching(getFeatures);
774 // Once all other stuff is done, execute any groovy scripts (in order)
775 if (groovyscript != null)
777 if (Cache.groovyJarsPresent())
779 System.out.println("Executing script " + groovyscript);
780 executeGroovyScript(groovyscript, startUpAlframe);
785 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
789 // and finally, turn off batch mode indicator - if the desktop still exists
794 desktop.setProgressBar(null, progress);
796 desktop.setInBatchMode(false);
800 private static void showUsage()
803 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
804 + "-nodisplay\tRun Jalview without User Interface.\n"
805 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
806 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
807 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
808 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
809 + "-features FILE\tUse the given file to mark features on the alignment.\n"
810 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
811 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
812 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
813 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
814 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
815 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
816 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
817 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
818 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
819 + "-png FILE\tCreate PNG image FILE from alignment.\n"
820 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
821 + "-html FILE\tCreate HTML file from alignment.\n"
822 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
823 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
824 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
825 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
826 + "-noquestionnaire\tTurn off questionnaire check.\n"
827 + "-nonews\tTurn off check for Jalview news.\n"
828 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
829 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
831 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
832 // after all other properties files have been read\n\t
833 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
834 // passed in correctly)"
835 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
836 + "-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"
837 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
838 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
839 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
841 // "-vdoc vamsas-document\tImport vamsas document into new
842 // session or join existing session with same URN\n"
843 // + "-vses vamsas-session\tJoin session with given URN\n"
844 + "-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"
845 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
848 private static void startUsageStats(final Desktop desktop)
851 * start a User Config prompt asking if we can log usage statistics.
853 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
854 "USAGESTATS", "Jalview Usage Statistics",
855 "Do you want to help make Jalview better by enabling "
856 + "the collection of usage statistics with Google Analytics ?"
857 + "\n\n(you can enable or disable usage tracking in the preferences)",
864 "Initialising googletracker for usage stats.");
865 Cache.initGoogleTracker();
866 Cache.log.debug("Tracking enabled.");
873 Cache.log.debug("Not enabling Google Tracking.");
876 desktop.addDialogThread(prompter);
880 * Locate the given string as a file and pass it to the groovy interpreter.
882 * @param groovyscript
883 * the script to execute
884 * @param jalviewContext
885 * the Jalview Desktop object passed in to the groovy binding as the
888 private void executeGroovyScript(String groovyscript, AlignFrame af)
891 * for scripts contained in files
898 if (groovyscript.trim().equals("STDIN"))
900 // read from stdin into a tempfile and execute it
903 tfile = File.createTempFile("jalview", "groovy");
904 PrintWriter outfile = new PrintWriter(
905 new OutputStreamWriter(new FileOutputStream(tfile)));
906 BufferedReader br = new BufferedReader(
907 new InputStreamReader(System.in));
909 while ((line = br.readLine()) != null)
911 outfile.write(line + "\n");
917 } catch (Exception ex)
919 System.err.println("Failed to read from STDIN into tempfile "
920 + ((tfile == null) ? "(tempfile wasn't created)"
921 : tfile.toString()));
922 ex.printStackTrace();
927 sfile = tfile.toURI().toURL();
928 } catch (Exception x)
931 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
941 sfile = new URI(groovyscript).toURL();
942 } catch (Exception x)
944 tfile = new File(groovyscript);
947 System.err.println("File '" + groovyscript + "' does not exist.");
950 if (!tfile.canRead())
952 System.err.println("File '" + groovyscript + "' cannot be read.");
955 if (tfile.length() < 1)
957 System.err.println("File '" + groovyscript + "' is empty.");
962 sfile = tfile.getAbsoluteFile().toURI().toURL();
963 } catch (Exception ex)
965 System.err.println("Failed to create a file URL for "
966 + tfile.getAbsoluteFile());
973 Map<String, Object> vbinding = new HashMap<>();
974 vbinding.put("Jalview", this);
977 vbinding.put("currentAlFrame", af);
979 Binding gbinding = new Binding(vbinding);
980 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
981 gse.run(sfile.toString(), gbinding);
982 if ("STDIN".equals(groovyscript))
984 // delete temp file that we made -
985 // only if it was successfully executed
988 } catch (Exception e)
990 System.err.println("Exception Whilst trying to execute file " + sfile
991 + " as a groovy script.");
992 e.printStackTrace(System.err);
998 * Check commandline for any das server definitions or any fetchfrom switches
1000 * @return vector of DAS source nicknames to retrieve from
1002 private static Vector<String> checkDasArguments(ArgsParser aparser)
1004 Vector<String> source = null;
1006 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
1007 while ((data = aparser.getValue("dasserver", true)) != null)
1009 String nickname = null;
1011 int pos = data.indexOf('=');
1012 // determine capabilities
1015 nickname = data.substring(0, pos);
1017 url = data.substring(pos + 1);
1018 if (url != null && (url.startsWith("http:")
1019 || url.startsWith("sequence:http:")))
1021 if (nickname == null)
1025 if (locsources == null)
1033 locsources = locsources + nickname + "|" + url;
1035 "NOTE! dasserver parameter not yet really supported (got args of "
1036 + nickname + "|" + url);
1039 source = new Vector<>();
1041 source.addElement(nickname);
1044 "CMD [-dasserver " + data + "] executed successfully!");
1045 } // loop until no more server entries are found.
1046 if (locsources != null && locsources.indexOf('|') > -1)
1048 Cache.log.debug("Setting local source list in properties file to:\n"
1050 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
1052 while ((data = aparser.getValue("fetchfrom", true)) != null)
1054 System.out.println("adding source '" + data + "'");
1057 source = new Vector<>();
1059 source.addElement(data);
1065 * start a feature fetcher for every alignment frame
1069 private FeatureFetcher startFeatureFetching(
1070 final Vector<String> dasSources)
1072 FeatureFetcher ff = new FeatureFetcher();
1073 AlignFrame afs[] = Desktop.getAlignFrames();
1074 if (afs == null || afs.length == 0)
1078 for (int i = 0; i < afs.length; i++)
1080 ff.addFetcher(afs[i], dasSources);
1085 public static boolean isHeadlessMode()
1087 String isheadless = System.getProperty("java.awt.headless");
1088 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1095 public AlignFrame[] getAlignFrames()
1097 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1098 : Desktop.getAlignFrames();
1103 * Quit method delegates to Desktop.quit - unless running in headless mode
1104 * when it just ends the JVM
1108 if (desktop != null)
1118 public static AlignFrame getCurrentAlignFrame()
1120 return Jalview.currentAlignFrame;
1123 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1125 Jalview.currentAlignFrame = currentAlignFrame;