2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.gui.AlignFrame;
24 import jalview.gui.Desktop;
25 import jalview.util.MessageManager;
26 import jalview.util.Platform;
27 import jalview.ws.jws2.Jws2Discoverer;
29 import java.awt.event.ActionEvent;
30 import java.awt.event.ActionListener;
31 import java.io.BufferedReader;
33 import java.io.FileOutputStream;
34 import java.io.IOException;
35 import java.io.OutputStreamWriter;
36 import java.io.PrintWriter;
37 import java.lang.reflect.Constructor;
38 import java.net.MalformedURLException;
41 import java.net.URLDecoder;
42 import java.security.AllPermission;
43 import java.security.CodeSource;
44 import java.security.PermissionCollection;
45 import java.security.Permissions;
46 import java.security.Policy;
47 import java.util.Hashtable;
49 import java.util.Vector;
51 import javax.swing.UIManager;
54 * Main class for Jalview Application <br>
56 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
65 // grab all the rights we can the JVM
66 Policy.setPolicy(new Policy()
68 public PermissionCollection getPermissions(CodeSource codesource)
70 Permissions perms = new Permissions();
71 perms.add(new AllPermission());
82 * Put protein=true for get a protein example
84 private static boolean protein = false;
87 * main class for Jalview application
90 * open <em>filename</em>
92 public static void main(String[] args)
94 System.out.println("Java version: "
95 + System.getProperty("java.version"));
96 System.out.println(System.getProperty("os.arch") + " "
97 + System.getProperty("os.name") + " "
98 + System.getProperty("os.version"));
99 if (new Platform().isAMac())
101 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
103 System.setProperty("apple.laf.useScreenMenuBar", "true");
106 ArgsParser aparser = new ArgsParser(args);
107 boolean headless = false;
109 if (aparser.contains("help") || aparser.contains("h"))
114 if (aparser.contains("nodisplay") || aparser.contains("nogui")
115 || aparser.contains("headless"))
117 System.setProperty("java.awt.headless", "true");
120 Cache.loadProperties(aparser.getValue("props")); // must do this before
123 final String jabawsUrl = aparser.getValue("jabaws");
124 if (jabawsUrl != null)
128 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
129 } catch (MalformedURLException e)
131 System.err.println("Invalid jabaws parameter: " + jabawsUrl
136 String defs = aparser.getValue("setprop");
139 int p = defs.indexOf('=');
142 System.err.println("Ignoring invalid setprop argument : " + defs);
146 System.out.println("Executing setprop argument: " + defs);
147 // DISABLED FOR SECURITY REASONS
148 // TODO: add a property to allow properties to be overriden by cli args
149 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
151 defs = aparser.getValue("setprop");
153 if (System.getProperty("java.awt.headless") != null
154 && System.getProperty("java.awt.headless").equals("true"))
158 System.setProperty("http.agent",
159 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
163 } catch (java.lang.NoClassDefFoundError error)
165 error.printStackTrace();
167 .println("\nEssential logging libraries not found."
168 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
172 Desktop desktop = null;
176 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
177 } catch (Exception ex)
183 desktop = new Desktop();
184 desktop.setInBatchMode(true); // indicate we are starting up
185 desktop.setVisible(true);
186 desktop.startServiceDiscovery();
187 if (!aparser.contains("nousagestats"))
189 startUsageStats(desktop);
191 if (!aparser.contains("noquestionnaire"))
193 String url = aparser.getValue("questionnaire");
196 // Start the desktop questionnaire prompter with the specified
198 Cache.log.debug("Starting questionnaire url at " + url);
199 desktop.checkForQuestionnaire(url);
203 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
205 // Start the desktop questionnaire prompter with the specified
208 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
210 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
211 Cache.log.debug("Starting questionnaire with default url: "
213 desktop.checkForQuestionnaire(defurl);
218 desktop.checkForNews();
221 String file = null, protocol = null, format = null, data = null;
222 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
223 Vector getFeatures = null; // vector of das source nicknames to fetch
226 String groovyscript = null; // script to execute after all loading is
227 // completed one way or another
228 // extract groovy argument and execute if necessary
229 groovyscript = aparser.getValue("groovy", true);
230 file = aparser.getValue("open", true);
232 if (file == null && desktop == null)
234 System.out.println("No files to open!");
237 String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
239 if (vamsasImport != null || vamsasSession != null)
241 if (desktop == null || headless)
244 .println("Headless vamsas sessions not yet supported. Sorry.");
247 // if we have a file, start a new session and import it.
248 boolean inSession = false;
249 if (vamsasImport != null)
253 String viprotocol = jalview.io.AppletFormatAdapter
254 .checkProtocol(vamsasImport);
255 if (viprotocol == jalview.io.FormatAdapter.FILE)
257 inSession = desktop.vamsasImport(new File(vamsasImport));
259 else if (viprotocol == jalview.io.FormatAdapter.URL)
261 inSession = desktop.vamsasImport(new URL(vamsasImport));
264 } catch (Exception e)
266 System.err.println("Exeption when importing " + vamsasImport
267 + " as a vamsas document.");
272 System.err.println("Failed to import " + vamsasImport
273 + " as a vamsas document.");
277 System.out.println("Imported Successfully into new session "
278 + desktop.getVamsasApplication().getCurrentSession());
281 if (vamsasSession != null)
283 if (vamsasImport != null)
285 // close the newly imported session and import the Jalview specific
286 // remnants into the new session later on.
287 desktop.vamsasStop_actionPerformed(null);
289 // now join the new session
292 if (desktop.joinVamsasSession(vamsasSession))
294 System.out.println("Successfully joined vamsas session "
299 System.err.println("WARNING: Failed to join vamsas session "
302 } catch (Exception e)
304 System.err.println("ERROR: Failed to join vamsas session "
308 if (vamsasImport != null)
310 // the Jalview specific remnants can now be imported into the new
311 // session at the user's leisure.
313 .info("Skipping Push for import of data into existing vamsas session."); // TODO:
318 // desktop.getVamsasApplication().push_update();
323 // Finally, deal with the remaining input data.
328 desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"),
329 progress = System.currentTimeMillis());
331 System.out.println("Opening file: " + file);
333 if (!file.startsWith("http://"))
335 if (!(new java.io.File(file)).exists())
337 System.out.println("Can't find " + file);
345 protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
347 format = new jalview.io.IdentifyFile().Identify(file, protocol);
349 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
353 System.out.println("error");
358 data = aparser.getValue("colour", true);
361 data.replaceAll("%20", " ");
363 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
364 .getColour(af.getViewport().getAlignment(), data);
368 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
370 ucs.parseAppletParameter(data);
374 System.out.println("colour is " + data);
378 // Must maintain ability to use the groups flag
379 data = aparser.getValue("groups", true);
382 af.parseFeaturesFile(data,
383 jalview.io.AppletFormatAdapter.checkProtocol(data));
384 System.out.println("Added " + data);
386 data = aparser.getValue("features", true);
389 af.parseFeaturesFile(data,
390 jalview.io.AppletFormatAdapter.checkProtocol(data));
391 System.out.println("Added " + data);
394 data = aparser.getValue("annotations", true);
397 af.loadJalviewDataFile(data, null, null, null);
398 System.out.println("Added " + data);
400 // set or clear the sortbytree flag.
401 if (aparser.contains("sortbytree"))
403 af.getViewport().setSortByTree(true);
405 if (aparser.contains("nosortbytree"))
407 af.getViewport().setSortByTree(false);
409 data = aparser.getValue("tree", true);
412 jalview.io.NewickFile fin = null;
415 fin = new jalview.io.NewickFile(data,
416 jalview.io.AppletFormatAdapter.checkProtocol(data));
419 af.getViewport().setCurrentTree(
420 af.ShowNewickTree(fin, data).getTree());
421 System.out.println("Added tree " + data);
423 } catch (IOException ex)
425 System.err.println("Couldn't add tree " + data);
426 ex.printStackTrace(System.err);
429 // TODO - load PDB structure(s) to alignment JAL-629
430 // (associate with identical sequence in alignment, or a specified
433 getFeatures = checkDasArguments(aparser);
434 if (af != null && getFeatures != null)
436 FeatureFetcher ff = startFeatureFetching(getFeatures);
439 while (!ff.allFinished() || af.operationInProgress())
441 // wait around until fetching is finished.
445 } catch (Exception e)
451 getFeatures = null; // have retrieved features - forget them now.
453 if (groovyscript != null)
455 // Execute the groovy script after we've done all the rendering stuff
456 // and before any images or figures are generated.
457 if (jalview.bin.Cache.groovyJarsPresent())
459 System.out.println("Executing script " + groovyscript);
460 executeGroovyScript(groovyscript, new Object[]
466 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
471 String imageName = "unnamed.png";
472 while (aparser.getSize() > 1)
474 format = aparser.nextValue();
475 file = aparser.nextValue();
477 if (format.equalsIgnoreCase("png"))
479 af.createPNG(new java.io.File(file));
480 imageName = (new java.io.File(file)).getName();
481 System.out.println("Creating PNG image: " + file);
484 else if (format.equalsIgnoreCase("svg"))
486 File imageFile = new java.io.File(file);
487 imageName = imageFile.getName();
488 af.createSVG(imageFile);
489 System.out.println("Creating SVG image: " + file);
492 else if (format.equalsIgnoreCase("imgMap"))
494 af.createImageMap(new java.io.File(file), imageName);
495 System.out.println("Creating image map: " + file);
498 else if (format.equalsIgnoreCase("eps"))
500 System.out.println("Creating EPS file: " + file);
501 af.createEPS(new java.io.File(file));
505 if (af.saveAlignment(file, format))
507 System.out.println("Written alignment in " + format
508 + " format to " + file);
512 System.out.println("Error writing file " + file + " in "
513 + format + " format!!");
518 while (aparser.getSize() > 0)
520 System.out.println("Unknown arg: " + aparser.nextValue());
524 AlignFrame startUpAlframe = null;
525 // We'll only open the default file if the desktop is visible.
527 // ////////////////////
529 if (!headless && file == null && vamsasImport == null
530 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)
533 file = jalview.bin.Cache.getDefault(
535 jalview.bin.Cache.getDefault("www.jalview.org",
536 "http://www.jalview.org")
537 + "/examples/exampleFile_2_7.jar");
538 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
540 // hardwire upgrade of the startup file
541 file.replace("_2_3.jar", "_2_7.jar");
542 // and remove the stale setting
543 jalview.bin.Cache.removeProperty("STARTUP_FILE");
548 if (file.indexOf("http:") > -1)
553 if (file.endsWith(".jar"))
559 format = new jalview.io.IdentifyFile().Identify(file, protocol);
562 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
564 getFeatures = checkDasArguments(aparser);
565 // extract groovy arguments before anything else.
567 // If the user has specified features to be retrieved,
568 // or a groovy script to be executed, do them if they
569 // haven't been done already
570 // fetch features for the default alignment
571 if (getFeatures != null)
573 if (startUpAlframe != null)
575 startFeatureFetching(getFeatures);
578 // Once all other stuff is done, execute any groovy scripts (in order)
579 if (groovyscript != null)
581 if (jalview.bin.Cache.groovyJarsPresent())
583 System.out.println("Executing script " + groovyscript);
584 executeGroovyScript(groovyscript, new Object[]
585 { desktop, startUpAlframe });
590 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
594 // and finally, turn off batch mode indicator - if the desktop still exists
599 desktop.setProgressBar(null, progress);
601 desktop.setInBatchMode(false);
605 private static void showUsage()
608 .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
609 + "-nodisplay\tRun Jalview without User Interface.\n"
610 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
611 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
612 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
613 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
614 + "-features FILE\tUse the given file to mark features on the alignment.\n"
615 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
616 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
617 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
618 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
619 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
620 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
621 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
622 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
623 + "-png FILE\tCreate PNG image FILE from alignment.\n"
624 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
625 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
626 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
627 + "-noquestionnaire\tTurn off questionnaire check.\n"
628 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
629 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
631 // "-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)"
632 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
633 + "-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"
634 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
635 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
636 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
638 // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
639 // + "-vses vamsas-session\tJoin session with given URN\n"
640 + "-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"
641 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
644 private static void startUsageStats(final Desktop desktop)
647 * start a User Config prompt asking if we can log usage statistics.
649 jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
652 "Jalview Usage Statistics",
653 "Do you want to help make Jalview better by enabling "
654 + "the collection of usage statistics with Google Analytics ?"
655 + "\n\n(you can enable or disable usage tracking in the preferences)",
661 .info("Initialising googletracker for usage stats.");
662 Cache.initGoogleTracker();
663 Cache.log.debug("Tracking enabled.");
669 Cache.log.info("Not enabling Google Tracking.");
672 desktop.addDialogThread(prompter);
676 * Locate the given string as a file and pass it to the groovy interpreter.
678 * @param groovyscript
679 * the script to execute
680 * @param jalviewContext
681 * the Jalview Desktop object passed in to the groovy binding as the
684 private static void executeGroovyScript(String groovyscript,
685 Object[] jalviewContext)
687 if (jalviewContext == null)
690 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
693 * for scripts contained in files
700 if (groovyscript.trim().equals("STDIN"))
702 // read from stdin into a tempfile and execute it
705 tfile = File.createTempFile("jalview", "groovy");
706 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
707 new FileOutputStream(tfile)));
708 BufferedReader br = new BufferedReader(
709 new java.io.InputStreamReader(System.in));
711 while ((line = br.readLine()) != null)
713 outfile.write(line + "\n");
719 } catch (Exception ex)
721 System.err.println("Failed to read from STDIN into tempfile "
722 + ((tfile == null) ? "(tempfile wasn't created)" : tfile
724 ex.printStackTrace();
729 sfile = tfile.toURI().toURL();
730 } catch (Exception x)
733 .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
743 sfile = new URI(groovyscript).toURL();
744 } catch (Exception x)
746 tfile = new File(groovyscript);
749 System.err.println("File '" + groovyscript + "' does not exist.");
752 if (!tfile.canRead())
754 System.err.println("File '" + groovyscript + "' cannot be read.");
757 if (tfile.length() < 1)
759 System.err.println("File '" + groovyscript + "' is empty.");
764 sfile = tfile.getAbsoluteFile().toURI().toURL();
765 } catch (Exception ex)
767 System.err.println("Failed to create a file URL for "
768 + tfile.getAbsoluteFile());
773 boolean success = false;
777 * The following code performs the GroovyScriptEngine invocation using
778 * reflection, and is equivalent to this fragment from the embedding
779 * groovy documentation on the groovy site: <code> import
780 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
782 * String[] roots = new String[] { "/my/groovy/script/path" };
783 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
784 * = new Binding(); binding.setVariable("input", "world");
785 * gse.run("hello.groovy", binding); </code>
789 int blen = ((jalviewContext[0] == null) ? 0 : 1)
790 + ((jalviewContext[1] == null) ? 0 : 1);
791 String cnames[] = new String[]
792 { "Jalview", "currentAlFrame" };
793 bspec = new Class[blen * 2];
794 binding = new Object[blen * 2];
796 ClassLoader cl = null;
797 Map vbinding = new Hashtable();
798 for (int jc = 0; jc < jalviewContext.length; jc++)
800 if (jalviewContext[jc] != null)
804 cl = jalviewContext[jc].getClass().getClassLoader();
806 bspec[blen * 2] = String.class;
807 bspec[blen * 2 + 1] = Object.class;
808 binding[blen * 2] = cnames[jc];
809 binding[blen * 2 + 1] = jalviewContext[jc];
810 vbinding.put(cnames[jc], jalviewContext[jc]);
814 Class gbindingc = cl.loadClass("groovy.lang.Binding");
819 gbcons = gbindingc.getConstructor(Map.class);
820 gbinding = gbcons.newInstance(vbinding);
821 } catch (NoSuchMethodException x)
823 // old style binding config - using series of string/object values to
825 gbcons = gbindingc.getConstructor(null);
826 gbinding = gbcons.newInstance(null);
827 java.lang.reflect.Method setvar = gbindingc.getMethod(
828 "setVariable", bspec);
829 setvar.invoke(gbinding, binding);
832 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
833 Constructor gseccons = gsec.getConstructor(new Class[]
834 { URL[].class }); // String[].class });
835 Object gse = gseccons.newInstance(new Object[]
837 { sfile } }); // .toString() } });
838 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
839 { String.class, gbindingc });
840 run.invoke(gse, new Object[]
841 { sfile.toString(), gbinding });
843 } catch (Exception e)
845 System.err.println("Exception Whilst trying to execute file " + sfile
846 + " as a groovy script.");
847 e.printStackTrace(System.err);
850 if (success && groovyscript.equals("STDIN"))
852 // delete temp file that we made - but only if it was successfully
859 * Check commandline for any das server definitions or any fetchfrom switches
861 * @return vector of DAS source nicknames to retrieve from
863 private static Vector checkDasArguments(ArgsParser aparser)
865 Vector source = null;
867 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
868 while ((data = aparser.getValue("dasserver", true)) != null)
870 String nickname = null;
872 boolean seq = false, feat = true;
873 int pos = data.indexOf('=');
874 // determine capabilities
877 nickname = data.substring(0, pos);
879 url = data.substring(pos + 1);
881 && (url.startsWith("http:") || url
882 .startsWith("sequence:http:")))
884 if (nickname == null)
888 if (locsources == null)
896 locsources = locsources + nickname + "|" + url;
898 .println("NOTE! dasserver parameter not yet really supported (got args of "
899 + nickname + "|" + url);
902 source = new Vector();
904 source.addElement(nickname);
906 } // loop until no more server entries are found.
907 if (locsources != null && locsources.indexOf('|') > -1)
909 Cache.log.debug("Setting local source list in properties file to:\n"
911 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
913 while ((data = aparser.getValue("fetchfrom", true)) != null)
915 System.out.println("adding source '" + data + "'");
918 source = new Vector();
920 source.addElement(data);
926 * start a feature fetcher for every alignment frame
930 private static FeatureFetcher startFeatureFetching(final Vector dasSources)
932 FeatureFetcher ff = new FeatureFetcher();
933 AlignFrame afs[] = Desktop.getAlignframes();
934 if (afs == null || afs.length == 0)
938 for (int i = 0; i < afs.length; i++)
940 ff.addFetcher(afs[i], dasSources);
947 * Notes: this argParser does not distinguish between parameter switches,
948 * parameter values and argument text. If an argument happens to be identical to
949 * a parameter, it will be taken as such (even though it didn't have a '-'
952 * @author Andrew Waterhouse and JBP documented.
956 class rnabuttonlistener implements ActionListener
958 public void actionPerformed(ActionEvent arg0)
960 System.out.println("Good idea ! ");
965 class pbuttonlistener implements ActionListener
967 public void actionPerformed(ActionEvent arg0)
977 public ArgsParser(String[] args)
979 vargs = new Vector();
980 for (int i = 0; i < args.length; i++)
982 String arg = args[i].trim();
983 if (arg.charAt(0) == '-')
985 arg = arg.substring(1);
987 vargs.addElement(arg);
992 * check for and remove first occurence of arg+parameter in arglist.
995 * @return return the argument following the given arg if arg was in list.
997 public String getValue(String arg)
999 return getValue(arg, false);
1002 public String getValue(String arg, boolean utf8decode)
1004 int index = vargs.indexOf(arg);
1005 String dc = null, ret = null;
1008 ret = vargs.elementAt(index + 1).toString();
1009 vargs.removeElementAt(index);
1010 vargs.removeElementAt(index);
1011 if (utf8decode && ret != null)
1015 dc = URLDecoder.decode(ret, "UTF-8");
1017 } catch (Exception e)
1019 // TODO: log failure to decode
1027 * check for and remove first occurence of arg in arglist.
1030 * @return true if arg was present in argslist.
1032 public boolean contains(String arg)
1034 if (vargs.contains(arg))
1036 vargs.removeElement(arg);
1045 public String nextValue()
1047 return vargs.remove(0).toString();
1050 public int getSize()
1052 return vargs.size();
1058 * keep track of feature fetching tasks.
1063 class FeatureFetcher
1066 * TODO: generalise to track all jalview events to orchestrate batch
1067 * processing events.
1070 private int queued = 0;
1072 private int running = 0;
1074 public FeatureFetcher()
1079 public void addFetcher(final AlignFrame af, final Vector dasSources)
1081 final long id = System.currentTimeMillis();
1083 final FeatureFetcher us = this;
1084 new Thread(new Runnable()
1095 af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id);
1096 af.featureSettings_actionPerformed(null);
1097 af.featureSettings.fetchDasFeatures(dasSources, true);
1098 af.setProgressBar(null, id);
1107 public synchronized boolean allFinished()
1109 return queued == 0 && running == 0;