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);
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>
178 * @throws InterruptedException
179 * @throws IOException
181 public static void main(String[] args)
183 instance = new Jalview();
184 instance.doMain(args);
189 * @throws InterruptedException
190 * @throws IOException
192 void doMain(String[] args)
194 System.setSecurityManager(null);
196 .println("Java version: " + System.getProperty("java.version"));
197 System.out.println(System.getProperty("os.arch") + " "
198 + System.getProperty("os.name") + " "
199 + System.getProperty("os.version"));
201 ArgsParser aparser = new ArgsParser(args);
202 boolean headless = false;
204 if (aparser.contains("help") || aparser.contains("h"))
209 if (aparser.contains("nodisplay") || aparser.contains("nogui")
210 || aparser.contains("headless"))
212 System.setProperty("java.awt.headless", "true");
215 String usrPropsFile = aparser.getValue("props");
216 Cache.loadProperties(usrPropsFile); // must do this before
217 if (usrPropsFile != null)
220 "CMD [-props " + usrPropsFile + "] executed successfully!");
225 final String jabawsUrl = aparser.getValue("jabaws");
226 if (jabawsUrl != null)
230 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
232 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
233 } catch (MalformedURLException e)
236 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
240 String defs = aparser.getValue("setprop");
243 int p = defs.indexOf('=');
246 System.err.println("Ignoring invalid setprop argument : " + defs);
250 System.out.println("Executing setprop argument: " + defs);
251 // DISABLED FOR SECURITY REASONS
252 // TODO: add a property to allow properties to be overriden by cli args
253 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
255 defs = aparser.getValue("setprop");
257 if (System.getProperty("java.awt.headless") != null
258 && System.getProperty("java.awt.headless").equals("true"))
262 System.setProperty("http.agent",
263 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
267 } catch (NoClassDefFoundError error)
269 error.printStackTrace();
270 System.out.println("\nEssential logging libraries not found."
271 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
279 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
280 } catch (Exception ex)
283 if (Platform.isAMac())
285 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
287 System.setProperty("apple.laf.useScreenMenuBar", "true");
290 UIManager.setLookAndFeel(
291 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel());
292 } catch (Throwable e)
295 "Failed to set QuaQua look and feel: " + e.toString());
300 * configure 'full' SO model if preferences say to,
301 * else use the default (SO Lite)
303 if (Cache.getDefault("USE_FULL_SO", false))
305 SequenceOntologyFactory.setInstance(new SequenceOntology());
310 desktop = new Desktop();
311 desktop.setInBatchMode(true); // indicate we are starting up
312 desktop.setVisible(true);
313 desktop.startServiceDiscovery();
314 if (!aparser.contains("nousagestats"))
316 startUsageStats(desktop);
320 System.err.println("CMD [-nousagestats] executed successfully!");
323 if (!aparser.contains("noquestionnaire"))
325 String url = aparser.getValue("questionnaire");
328 // Start the desktop questionnaire prompter with the specified
330 Cache.log.debug("Starting questionnaire url at " + url);
331 desktop.checkForQuestionnaire(url);
333 "CMD questionnaire[-" + url + "] executed successfully!");
337 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
339 // Start the desktop questionnaire prompter with the specified
342 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
344 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
346 "Starting questionnaire with default url: " + defurl);
347 desktop.checkForQuestionnaire(defurl);
353 System.err.println("CMD [-noquestionnaire] executed successfully!");
356 if (!aparser.contains("nonews"))
358 desktop.checkForNews();
361 BioJsHTMLOutput.updateBioJS();
364 String file = null, data = null;
365 FileFormatI format = null;
366 DataSourceType protocol = null;
367 FileLoader fileLoader = new FileLoader(!headless);
368 Vector<String> getFeatures = null; // vector of das source nicknames to
372 String groovyscript = null; // script to execute after all loading is
373 // completed one way or another
374 // extract groovy argument and execute if necessary
375 groovyscript = aparser.getValue("groovy", true);
376 file = aparser.getValue("open", true);
378 if (file == null && desktop == null)
380 System.out.println("No files to open!");
383 String vamsasImport = aparser.getValue("vdoc");
384 String vamsasSession = aparser.getValue("vsess");
385 if (vamsasImport != null || vamsasSession != null)
387 if (desktop == null || headless)
390 "Headless vamsas sessions not yet supported. Sorry.");
393 // if we have a file, start a new session and import it.
394 boolean inSession = false;
395 if (vamsasImport != null)
399 DataSourceType viprotocol = AppletFormatAdapter
400 .checkProtocol(vamsasImport);
401 if (viprotocol == DataSourceType.FILE)
403 inSession = desktop.vamsasImport(new File(vamsasImport));
405 else if (viprotocol == DataSourceType.URL)
407 inSession = desktop.vamsasImport(new URL(vamsasImport));
410 } catch (Exception e)
412 System.err.println("Exeption when importing " + vamsasImport
413 + " as a vamsas document.");
418 System.err.println("Failed to import " + vamsasImport
419 + " as a vamsas document.");
423 System.out.println("Imported Successfully into new session "
424 + desktop.getVamsasApplication().getCurrentSession());
427 if (vamsasSession != null)
429 if (vamsasImport != null)
431 // close the newly imported session and import the Jalview specific
432 // remnants into the new session later on.
433 desktop.vamsasStop_actionPerformed(null);
435 // now join the new session
438 if (desktop.joinVamsasSession(vamsasSession))
441 "Successfully joined vamsas session " + vamsasSession);
445 System.err.println("WARNING: Failed to join vamsas session "
448 } catch (Exception e)
451 "ERROR: Failed to join vamsas session " + vamsasSession);
454 if (vamsasImport != null)
456 // the Jalview specific remnants can now be imported into the new
457 // session at the user's leisure.
459 "Skipping Push for import of data into existing vamsas session."); // TODO:
464 // desktop.getVamsasApplication().push_update();
469 // Finally, deal with the remaining input data.
474 desktop.setProgressBar(
476 .getString("status.processing_commandline_args"),
477 progress = System.currentTimeMillis());
479 System.out.println("CMD [-open " + file + "] executed successfully!");
481 if (!file.startsWith("http://"))
483 if (!(new File(file)).exists())
485 System.out.println("Can't find " + file);
493 protocol = AppletFormatAdapter.checkProtocol(file);
497 format = new IdentifyFile().identify(file, protocol);
498 } catch (FileFormatException e1)
503 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
507 System.out.println("error");
511 setCurrentAlignFrame(af);
512 data = aparser.getValue("colour", true);
515 data.replaceAll("%20", " ");
517 ColourSchemeI cs = ColourSchemeProperty
518 .getColourScheme(af.getViewport().getAlignment(), data);
523 "CMD [-color " + data + "] executed successfully!");
528 // Must maintain ability to use the groups flag
529 data = aparser.getValue("groups", true);
532 af.parseFeaturesFile(data,
533 AppletFormatAdapter.checkProtocol(data));
534 // System.out.println("Added " + data);
536 "CMD groups[-" + data + "] executed successfully!");
538 data = aparser.getValue("features", true);
541 af.parseFeaturesFile(data,
542 AppletFormatAdapter.checkProtocol(data));
543 // System.out.println("Added " + data);
545 "CMD [-features " + data + "] executed successfully!");
548 data = aparser.getValue("annotations", true);
551 af.loadJalviewDataFile(data, null, null, null);
552 // System.out.println("Added " + data);
554 "CMD [-annotations " + data + "] executed successfully!");
556 // set or clear the sortbytree flag.
557 if (aparser.contains("sortbytree"))
559 af.getViewport().setSortByTree(true);
560 if (af.getViewport().getSortByTree())
562 System.out.println("CMD [-sortbytree] executed successfully!");
565 if (aparser.contains("no-annotation"))
567 af.getViewport().setShowAnnotation(false);
568 if (!af.getViewport().isShowAnnotation())
570 System.out.println("CMD no-annotation executed successfully!");
573 if (aparser.contains("nosortbytree"))
575 af.getViewport().setSortByTree(false);
576 if (!af.getViewport().getSortByTree())
579 .println("CMD [-nosortbytree] executed successfully!");
582 data = aparser.getValue("tree", true);
588 "CMD [-tree " + data + "] executed successfully!");
589 NewickFile nf = new NewickFile(data,
590 AppletFormatAdapter.checkProtocol(data));
592 .setCurrentTree(af.showNewickTree(nf, data).getTree());
593 } catch (IOException ex)
595 System.err.println("Couldn't add tree " + data);
596 ex.printStackTrace(System.err);
599 // TODO - load PDB structure(s) to alignment JAL-629
600 // (associate with identical sequence in alignment, or a specified
603 getFeatures = checkDasArguments(aparser);
604 if (af != null && getFeatures != null)
606 FeatureFetcher ff = startFeatureFetching(getFeatures);
609 while (!ff.allFinished() || af.operationInProgress())
611 // wait around until fetching is finished.
615 } catch (Exception e)
621 getFeatures = null; // have retrieved features - forget them now.
623 if (groovyscript != null)
625 // Execute the groovy script after we've done all the rendering stuff
626 // and before any images or figures are generated.
627 System.out.println("Executing script " + groovyscript);
628 executeGroovyScript(groovyscript, af);
629 System.out.println("CMD groovy[" + groovyscript
630 + "] executed successfully!");
633 String imageName = "unnamed.png";
634 while (aparser.getSize() > 1)
636 String outputFormat = aparser.nextValue();
637 file = aparser.nextValue();
639 if (outputFormat.equalsIgnoreCase("png"))
641 af.createPNG(new File(file));
642 imageName = (new File(file)).getName();
643 System.out.println("Creating PNG image: " + file);
646 else if (outputFormat.equalsIgnoreCase("svg"))
648 File imageFile = new File(file);
649 imageName = imageFile.getName();
650 af.createSVG(imageFile);
651 System.out.println("Creating SVG image: " + file);
654 else if (outputFormat.equalsIgnoreCase("html"))
656 File imageFile = new File(file);
657 imageName = imageFile.getName();
658 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
659 htmlSVG.exportHTML(file);
661 System.out.println("Creating HTML image: " + file);
664 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
668 System.err.println("The output html file must not be null");
673 BioJsHTMLOutput.refreshVersionInfo(
674 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
675 } catch (URISyntaxException e)
679 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
680 bjs.exportHTML(file);
682 .println("Creating BioJS MSA Viwer HTML file: " + file);
685 else if (outputFormat.equalsIgnoreCase("imgMap"))
687 af.createImageMap(new File(file), imageName);
688 System.out.println("Creating image map: " + file);
691 else if (outputFormat.equalsIgnoreCase("eps"))
693 File outputFile = new File(file);
695 "Creating EPS file: " + outputFile.getAbsolutePath());
696 af.createEPS(outputFile);
700 if (af.saveAlignment(file, format))
702 System.out.println("Written alignment in " + format
703 + " format to " + file);
707 System.out.println("Error writing file " + file + " in "
708 + format + " format!!");
713 while (aparser.getSize() > 0)
715 System.out.println("Unknown arg: " + aparser.nextValue());
719 AlignFrame startUpAlframe = null;
720 // We'll only open the default file if the desktop is visible.
722 // ////////////////////
724 if (!headless && file == null && vamsasImport == null
725 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
727 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
728 jalview.bin.Cache.getDefault("www.jalview.org",
729 "http://www.jalview.org")
730 + "/examples/exampleFile_2_7.jar");
732 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
734 // hardwire upgrade of the startup file
735 file.replace("_2_3.jar", "_2_7.jar");
736 // and remove the stale setting
737 jalview.bin.Cache.removeProperty("STARTUP_FILE");
740 protocol = DataSourceType.FILE;
742 if (file.indexOf("http:") > -1)
744 protocol = DataSourceType.URL;
747 if (file.endsWith(".jar"))
749 format = FileFormat.Jalview;
755 format = new IdentifyFile().identify(file, protocol);
756 } catch (FileFormatException e)
762 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
764 getFeatures = checkDasArguments(aparser);
765 // extract groovy arguments before anything else.
767 // If the user has specified features to be retrieved,
768 // or a groovy script to be executed, do them if they
769 // haven't been done already
770 // fetch features for the default alignment
771 if (getFeatures != null)
773 if (startUpAlframe != null)
775 startFeatureFetching(getFeatures);
778 // Once all other stuff is done, execute any groovy scripts (in order)
779 if (groovyscript != null)
781 if (Cache.groovyJarsPresent())
783 System.out.println("Executing script " + groovyscript);
784 executeGroovyScript(groovyscript, startUpAlframe);
789 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
793 // and finally, turn off batch mode indicator - if the desktop still exists
798 desktop.setProgressBar(null, progress);
800 desktop.setInBatchMode(false);
804 private static void showUsage()
807 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
808 + "-nodisplay\tRun Jalview without User Interface.\n"
809 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
810 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
811 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
812 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
813 + "-features FILE\tUse the given file to mark features on the alignment.\n"
814 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
815 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
816 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
817 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
818 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
819 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
820 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
821 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
822 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
823 + "-png FILE\tCreate PNG image FILE from alignment.\n"
824 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
825 + "-html FILE\tCreate HTML file from alignment.\n"
826 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
827 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
828 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
829 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
830 + "-noquestionnaire\tTurn off questionnaire check.\n"
831 + "-nonews\tTurn off check for Jalview news.\n"
832 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
833 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
835 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
836 // after all other properties files have been read\n\t
837 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
838 // passed in correctly)"
839 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
840 + "-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"
841 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
842 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
843 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
845 // "-vdoc vamsas-document\tImport vamsas document into new
846 // session or join existing session with same URN\n"
847 // + "-vses vamsas-session\tJoin session with given URN\n"
848 + "-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"
849 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
852 private static void startUsageStats(final Desktop desktop)
855 * start a User Config prompt asking if we can log usage statistics.
857 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
858 "USAGESTATS", "Jalview Usage Statistics",
859 "Do you want to help make Jalview better by enabling "
860 + "the collection of usage statistics with Google Analytics ?"
861 + "\n\n(you can enable or disable usage tracking in the preferences)",
868 "Initialising googletracker for usage stats.");
869 Cache.initGoogleTracker();
870 Cache.log.debug("Tracking enabled.");
877 Cache.log.debug("Not enabling Google Tracking.");
880 desktop.addDialogThread(prompter);
884 * Locate the given string as a file and pass it to the groovy interpreter.
886 * @param groovyscript
887 * the script to execute
888 * @param jalviewContext
889 * the Jalview Desktop object passed in to the groovy binding as the
892 private void executeGroovyScript(String groovyscript, AlignFrame af)
895 * for scripts contained in files
902 if (groovyscript.trim().equals("STDIN"))
904 // read from stdin into a tempfile and execute it
907 tfile = File.createTempFile("jalview", "groovy");
908 PrintWriter outfile = new PrintWriter(
909 new OutputStreamWriter(new FileOutputStream(tfile)));
910 BufferedReader br = new BufferedReader(
911 new InputStreamReader(System.in));
913 while ((line = br.readLine()) != null)
915 outfile.write(line + "\n");
921 } catch (Exception ex)
923 System.err.println("Failed to read from STDIN into tempfile "
924 + ((tfile == null) ? "(tempfile wasn't created)"
925 : tfile.toString()));
926 ex.printStackTrace();
931 sfile = tfile.toURI().toURL();
932 } catch (Exception x)
935 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
945 sfile = new URI(groovyscript).toURL();
946 } catch (Exception x)
948 tfile = new File(groovyscript);
951 System.err.println("File '" + groovyscript + "' does not exist.");
954 if (!tfile.canRead())
956 System.err.println("File '" + groovyscript + "' cannot be read.");
959 if (tfile.length() < 1)
961 System.err.println("File '" + groovyscript + "' is empty.");
966 sfile = tfile.getAbsoluteFile().toURI().toURL();
967 } catch (Exception ex)
969 System.err.println("Failed to create a file URL for "
970 + tfile.getAbsoluteFile());
977 Map<String, Object> vbinding = new HashMap<>();
978 vbinding.put("Jalview", this);
981 vbinding.put("currentAlFrame", af);
983 Binding gbinding = new Binding(vbinding);
984 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
985 gse.run(sfile.toString(), gbinding);
986 if ("STDIN".equals(groovyscript))
988 // delete temp file that we made -
989 // only if it was successfully executed
992 } catch (Exception e)
994 System.err.println("Exception Whilst trying to execute file " + sfile
995 + " as a groovy script.");
996 e.printStackTrace(System.err);
1002 * Check commandline for any das server definitions or any fetchfrom switches
1004 * @return vector of DAS source nicknames to retrieve from
1006 private static Vector<String> checkDasArguments(ArgsParser aparser)
1008 Vector<String> source = null;
1010 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
1011 while ((data = aparser.getValue("dasserver", true)) != null)
1013 String nickname = null;
1015 int pos = data.indexOf('=');
1016 // determine capabilities
1019 nickname = data.substring(0, pos);
1021 url = data.substring(pos + 1);
1022 if (url != null && (url.startsWith("http:")
1023 || url.startsWith("sequence:http:")))
1025 if (nickname == null)
1029 if (locsources == null)
1037 locsources = locsources + nickname + "|" + url;
1039 "NOTE! dasserver parameter not yet really supported (got args of "
1040 + nickname + "|" + url);
1043 source = new Vector<>();
1045 source.addElement(nickname);
1048 "CMD [-dasserver " + data + "] executed successfully!");
1049 } // loop until no more server entries are found.
1050 if (locsources != null && locsources.indexOf('|') > -1)
1052 Cache.log.debug("Setting local source list in properties file to:\n"
1054 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
1056 while ((data = aparser.getValue("fetchfrom", true)) != null)
1058 System.out.println("adding source '" + data + "'");
1061 source = new Vector<>();
1063 source.addElement(data);
1069 * start a feature fetcher for every alignment frame
1073 private FeatureFetcher startFeatureFetching(
1074 final Vector<String> dasSources)
1076 FeatureFetcher ff = new FeatureFetcher();
1077 AlignFrame afs[] = Desktop.getAlignFrames();
1078 if (afs == null || afs.length == 0)
1082 for (int i = 0; i < afs.length; i++)
1084 ff.addFetcher(afs[i], dasSources);
1089 public static boolean isHeadlessMode()
1091 String isheadless = System.getProperty("java.awt.headless");
1092 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1099 public AlignFrame[] getAlignFrames()
1101 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1102 : Desktop.getAlignFrames();
1107 * Quit method delegates to Desktop.quit - unless running in headless mode
1108 * when it just ends the JVM
1112 if (desktop != null)
1122 public static AlignFrame getCurrentAlignFrame()
1124 return Jalview.currentAlignFrame;
1127 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1129 Jalview.currentAlignFrame = currentAlignFrame;