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)
282 System.err.println("Unexpected Look and Feel Exception");
283 ex.printStackTrace();
285 if (Platform.isAMac())
287 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
289 System.setProperty("apple.laf.useScreenMenuBar", "true");
292 UIManager.setLookAndFeel(
293 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel());
294 } catch (Throwable e)
297 "Failed to set QuaQua look and feel: " + e.toString());
299 if (!ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel()
300 .equals(UIManager.getLookAndFeel()))
305 "Quaqua LaF not available. Using VAqua(4).");
306 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
307 } catch (Throwable e)
310 "Failed to reset look and feel: " + e.toString());
316 * configure 'full' SO model if preferences say to,
317 * else use the default (SO Lite)
319 if (Cache.getDefault("USE_FULL_SO", false))
321 SequenceOntologyFactory.setInstance(new SequenceOntology());
326 desktop = new Desktop();
327 desktop.setInBatchMode(true); // indicate we are starting up
328 desktop.setVisible(true);
329 desktop.startServiceDiscovery();
330 if (!aparser.contains("nousagestats"))
332 startUsageStats(desktop);
336 System.err.println("CMD [-nousagestats] executed successfully!");
339 if (!aparser.contains("noquestionnaire"))
341 String url = aparser.getValue("questionnaire");
344 // Start the desktop questionnaire prompter with the specified
346 Cache.log.debug("Starting questionnaire url at " + url);
347 desktop.checkForQuestionnaire(url);
349 "CMD questionnaire[-" + url + "] executed successfully!");
353 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
355 // Start the desktop questionnaire prompter with the specified
358 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
360 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
362 "Starting questionnaire with default url: " + defurl);
363 desktop.checkForQuestionnaire(defurl);
369 System.err.println("CMD [-noquestionnaire] executed successfully!");
372 if (!aparser.contains("nonews"))
374 desktop.checkForNews();
377 BioJsHTMLOutput.updateBioJS();
380 String file = null, data = null;
381 FileFormatI format = null;
382 DataSourceType protocol = null;
383 FileLoader fileLoader = new FileLoader(!headless);
384 Vector<String> getFeatures = null; // vector of das source nicknames to
388 String groovyscript = null; // script to execute after all loading is
389 // completed one way or another
390 // extract groovy argument and execute if necessary
391 groovyscript = aparser.getValue("groovy", true);
392 file = aparser.getValue("open", true);
394 if (file == null && desktop == null)
396 System.out.println("No files to open!");
399 String vamsasImport = aparser.getValue("vdoc");
400 String vamsasSession = aparser.getValue("vsess");
401 if (vamsasImport != null || vamsasSession != null)
403 if (desktop == null || headless)
406 "Headless vamsas sessions not yet supported. Sorry.");
409 // if we have a file, start a new session and import it.
410 boolean inSession = false;
411 if (vamsasImport != null)
415 DataSourceType viprotocol = AppletFormatAdapter
416 .checkProtocol(vamsasImport);
417 if (viprotocol == DataSourceType.FILE)
419 inSession = desktop.vamsasImport(new File(vamsasImport));
421 else if (viprotocol == DataSourceType.URL)
423 inSession = desktop.vamsasImport(new URL(vamsasImport));
426 } catch (Exception e)
428 System.err.println("Exeption when importing " + vamsasImport
429 + " as a vamsas document.");
434 System.err.println("Failed to import " + vamsasImport
435 + " as a vamsas document.");
439 System.out.println("Imported Successfully into new session "
440 + desktop.getVamsasApplication().getCurrentSession());
443 if (vamsasSession != null)
445 if (vamsasImport != null)
447 // close the newly imported session and import the Jalview specific
448 // remnants into the new session later on.
449 desktop.vamsasStop_actionPerformed(null);
451 // now join the new session
454 if (desktop.joinVamsasSession(vamsasSession))
457 "Successfully joined vamsas session " + vamsasSession);
461 System.err.println("WARNING: Failed to join vamsas session "
464 } catch (Exception e)
467 "ERROR: Failed to join vamsas session " + vamsasSession);
470 if (vamsasImport != null)
472 // the Jalview specific remnants can now be imported into the new
473 // session at the user's leisure.
475 "Skipping Push for import of data into existing vamsas session."); // TODO:
480 // desktop.getVamsasApplication().push_update();
485 // Finally, deal with the remaining input data.
490 desktop.setProgressBar(
492 .getString("status.processing_commandline_args"),
493 progress = System.currentTimeMillis());
495 System.out.println("CMD [-open " + file + "] executed successfully!");
497 if (!file.startsWith("http://"))
499 if (!(new File(file)).exists())
501 System.out.println("Can't find " + file);
509 protocol = AppletFormatAdapter.checkProtocol(file);
513 format = new IdentifyFile().identify(file, protocol);
514 } catch (FileFormatException e1)
519 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
523 System.out.println("error");
527 setCurrentAlignFrame(af);
528 data = aparser.getValue("colour", true);
531 data.replaceAll("%20", " ");
533 ColourSchemeI cs = ColourSchemeProperty
534 .getColourScheme(af.getViewport().getAlignment(), data);
539 "CMD [-color " + data + "] executed successfully!");
544 // Must maintain ability to use the groups flag
545 data = aparser.getValue("groups", true);
548 af.parseFeaturesFile(data,
549 AppletFormatAdapter.checkProtocol(data));
550 // System.out.println("Added " + data);
552 "CMD groups[-" + data + "] executed successfully!");
554 data = aparser.getValue("features", true);
557 af.parseFeaturesFile(data,
558 AppletFormatAdapter.checkProtocol(data));
559 // System.out.println("Added " + data);
561 "CMD [-features " + data + "] executed successfully!");
564 data = aparser.getValue("annotations", true);
567 af.loadJalviewDataFile(data, null, null, null);
568 // System.out.println("Added " + data);
570 "CMD [-annotations " + data + "] executed successfully!");
572 // set or clear the sortbytree flag.
573 if (aparser.contains("sortbytree"))
575 af.getViewport().setSortByTree(true);
576 if (af.getViewport().getSortByTree())
578 System.out.println("CMD [-sortbytree] executed successfully!");
581 if (aparser.contains("no-annotation"))
583 af.getViewport().setShowAnnotation(false);
584 if (!af.getViewport().isShowAnnotation())
586 System.out.println("CMD no-annotation executed successfully!");
589 if (aparser.contains("nosortbytree"))
591 af.getViewport().setSortByTree(false);
592 if (!af.getViewport().getSortByTree())
595 .println("CMD [-nosortbytree] executed successfully!");
598 data = aparser.getValue("tree", true);
604 "CMD [-tree " + data + "] executed successfully!");
605 NewickFile nf = new NewickFile(data,
606 AppletFormatAdapter.checkProtocol(data));
608 .setCurrentTree(af.showNewickTree(nf, data).getTree());
609 } catch (IOException ex)
611 System.err.println("Couldn't add tree " + data);
612 ex.printStackTrace(System.err);
615 // TODO - load PDB structure(s) to alignment JAL-629
616 // (associate with identical sequence in alignment, or a specified
619 getFeatures = checkDasArguments(aparser);
620 if (af != null && getFeatures != null)
622 FeatureFetcher ff = startFeatureFetching(getFeatures);
625 while (!ff.allFinished() || af.operationInProgress())
627 // wait around until fetching is finished.
631 } catch (Exception e)
637 getFeatures = null; // have retrieved features - forget them now.
639 if (groovyscript != null)
641 // Execute the groovy script after we've done all the rendering stuff
642 // and before any images or figures are generated.
643 System.out.println("Executing script " + groovyscript);
644 executeGroovyScript(groovyscript, af);
645 System.out.println("CMD groovy[" + groovyscript
646 + "] executed successfully!");
649 String imageName = "unnamed.png";
650 while (aparser.getSize() > 1)
652 String outputFormat = aparser.nextValue();
653 file = aparser.nextValue();
655 if (outputFormat.equalsIgnoreCase("png"))
657 af.createPNG(new File(file));
658 imageName = (new File(file)).getName();
659 System.out.println("Creating PNG image: " + file);
662 else if (outputFormat.equalsIgnoreCase("svg"))
664 File imageFile = new File(file);
665 imageName = imageFile.getName();
666 af.createSVG(imageFile);
667 System.out.println("Creating SVG image: " + file);
670 else if (outputFormat.equalsIgnoreCase("html"))
672 File imageFile = new File(file);
673 imageName = imageFile.getName();
674 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
675 htmlSVG.exportHTML(file);
677 System.out.println("Creating HTML image: " + file);
680 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
684 System.err.println("The output html file must not be null");
689 BioJsHTMLOutput.refreshVersionInfo(
690 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
691 } catch (URISyntaxException e)
695 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
696 bjs.exportHTML(file);
698 .println("Creating BioJS MSA Viwer HTML file: " + file);
701 else if (outputFormat.equalsIgnoreCase("imgMap"))
703 af.createImageMap(new File(file), imageName);
704 System.out.println("Creating image map: " + file);
707 else if (outputFormat.equalsIgnoreCase("eps"))
709 File outputFile = new File(file);
711 "Creating EPS file: " + outputFile.getAbsolutePath());
712 af.createEPS(outputFile);
716 if (af.saveAlignment(file, format))
718 System.out.println("Written alignment in " + format
719 + " format to " + file);
723 System.out.println("Error writing file " + file + " in "
724 + format + " format!!");
729 while (aparser.getSize() > 0)
731 System.out.println("Unknown arg: " + aparser.nextValue());
735 AlignFrame startUpAlframe = null;
736 // We'll only open the default file if the desktop is visible.
738 // ////////////////////
740 if (!headless && file == null && vamsasImport == null
741 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
743 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
744 jalview.bin.Cache.getDefault("www.jalview.org",
745 "http://www.jalview.org")
746 + "/examples/exampleFile_2_7.jar");
748 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
750 // hardwire upgrade of the startup file
751 file.replace("_2_3.jar", "_2_7.jar");
752 // and remove the stale setting
753 jalview.bin.Cache.removeProperty("STARTUP_FILE");
756 protocol = DataSourceType.FILE;
758 if (file.indexOf("http:") > -1)
760 protocol = DataSourceType.URL;
763 if (file.endsWith(".jar"))
765 format = FileFormat.Jalview;
771 format = new IdentifyFile().identify(file, protocol);
772 } catch (FileFormatException e)
778 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
780 getFeatures = checkDasArguments(aparser);
781 // extract groovy arguments before anything else.
783 // If the user has specified features to be retrieved,
784 // or a groovy script to be executed, do them if they
785 // haven't been done already
786 // fetch features for the default alignment
787 if (getFeatures != null)
789 if (startUpAlframe != null)
791 startFeatureFetching(getFeatures);
794 // Once all other stuff is done, execute any groovy scripts (in order)
795 if (groovyscript != null)
797 if (Cache.groovyJarsPresent())
799 System.out.println("Executing script " + groovyscript);
800 executeGroovyScript(groovyscript, startUpAlframe);
805 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
809 // and finally, turn off batch mode indicator - if the desktop still exists
814 desktop.setProgressBar(null, progress);
816 desktop.setInBatchMode(false);
820 private static void showUsage()
823 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
824 + "-nodisplay\tRun Jalview without User Interface.\n"
825 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
826 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
827 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
828 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
829 + "-features FILE\tUse the given file to mark features on the alignment.\n"
830 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
831 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
832 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
833 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
834 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
835 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
836 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
837 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
838 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
839 + "-png FILE\tCreate PNG image FILE from alignment.\n"
840 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
841 + "-html FILE\tCreate HTML file from alignment.\n"
842 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
843 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
844 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
845 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
846 + "-noquestionnaire\tTurn off questionnaire check.\n"
847 + "-nonews\tTurn off check for Jalview news.\n"
848 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
849 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
851 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
852 // after all other properties files have been read\n\t
853 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
854 // passed in correctly)"
855 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
856 + "-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"
857 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
858 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
859 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
861 // "-vdoc vamsas-document\tImport vamsas document into new
862 // session or join existing session with same URN\n"
863 // + "-vses vamsas-session\tJoin session with given URN\n"
864 + "-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"
865 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
868 private static void startUsageStats(final Desktop desktop)
871 * start a User Config prompt asking if we can log usage statistics.
873 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
874 "USAGESTATS", "Jalview Usage Statistics",
875 "Do you want to help make Jalview better by enabling "
876 + "the collection of usage statistics with Google Analytics ?"
877 + "\n\n(you can enable or disable usage tracking in the preferences)",
884 "Initialising googletracker for usage stats.");
885 Cache.initGoogleTracker();
886 Cache.log.debug("Tracking enabled.");
893 Cache.log.debug("Not enabling Google Tracking.");
896 desktop.addDialogThread(prompter);
900 * Locate the given string as a file and pass it to the groovy interpreter.
902 * @param groovyscript
903 * the script to execute
904 * @param jalviewContext
905 * the Jalview Desktop object passed in to the groovy binding as the
908 private void executeGroovyScript(String groovyscript, AlignFrame af)
911 * for scripts contained in files
918 if (groovyscript.trim().equals("STDIN"))
920 // read from stdin into a tempfile and execute it
923 tfile = File.createTempFile("jalview", "groovy");
924 PrintWriter outfile = new PrintWriter(
925 new OutputStreamWriter(new FileOutputStream(tfile)));
926 BufferedReader br = new BufferedReader(
927 new InputStreamReader(System.in));
929 while ((line = br.readLine()) != null)
931 outfile.write(line + "\n");
937 } catch (Exception ex)
939 System.err.println("Failed to read from STDIN into tempfile "
940 + ((tfile == null) ? "(tempfile wasn't created)"
941 : tfile.toString()));
942 ex.printStackTrace();
947 sfile = tfile.toURI().toURL();
948 } catch (Exception x)
951 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
961 sfile = new URI(groovyscript).toURL();
962 } catch (Exception x)
964 tfile = new File(groovyscript);
967 System.err.println("File '" + groovyscript + "' does not exist.");
970 if (!tfile.canRead())
972 System.err.println("File '" + groovyscript + "' cannot be read.");
975 if (tfile.length() < 1)
977 System.err.println("File '" + groovyscript + "' is empty.");
982 sfile = tfile.getAbsoluteFile().toURI().toURL();
983 } catch (Exception ex)
985 System.err.println("Failed to create a file URL for "
986 + tfile.getAbsoluteFile());
993 Map<String, Object> vbinding = new HashMap<>();
994 vbinding.put("Jalview", this);
997 vbinding.put("currentAlFrame", af);
999 Binding gbinding = new Binding(vbinding);
1000 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1001 gse.run(sfile.toString(), gbinding);
1002 if ("STDIN".equals(groovyscript))
1004 // delete temp file that we made -
1005 // only if it was successfully executed
1008 } catch (Exception e)
1010 System.err.println("Exception Whilst trying to execute file " + sfile
1011 + " as a groovy script.");
1012 e.printStackTrace(System.err);
1018 * Check commandline for any das server definitions or any fetchfrom switches
1020 * @return vector of DAS source nicknames to retrieve from
1022 private static Vector<String> checkDasArguments(ArgsParser aparser)
1024 Vector<String> source = null;
1026 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
1027 while ((data = aparser.getValue("dasserver", true)) != null)
1029 String nickname = null;
1031 int pos = data.indexOf('=');
1032 // determine capabilities
1035 nickname = data.substring(0, pos);
1037 url = data.substring(pos + 1);
1038 if (url != null && (url.startsWith("http:")
1039 || url.startsWith("sequence:http:")))
1041 if (nickname == null)
1045 if (locsources == null)
1053 locsources = locsources + nickname + "|" + url;
1055 "NOTE! dasserver parameter not yet really supported (got args of "
1056 + nickname + "|" + url);
1059 source = new Vector<>();
1061 source.addElement(nickname);
1064 "CMD [-dasserver " + data + "] executed successfully!");
1065 } // loop until no more server entries are found.
1066 if (locsources != null && locsources.indexOf('|') > -1)
1068 Cache.log.debug("Setting local source list in properties file to:\n"
1070 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
1072 while ((data = aparser.getValue("fetchfrom", true)) != null)
1074 System.out.println("adding source '" + data + "'");
1077 source = new Vector<>();
1079 source.addElement(data);
1085 * start a feature fetcher for every alignment frame
1089 private FeatureFetcher startFeatureFetching(
1090 final Vector<String> dasSources)
1092 FeatureFetcher ff = new FeatureFetcher();
1093 AlignFrame afs[] = Desktop.getAlignFrames();
1094 if (afs == null || afs.length == 0)
1098 for (int i = 0; i < afs.length; i++)
1100 ff.addFetcher(afs[i], dasSources);
1105 public static boolean isHeadlessMode()
1107 String isheadless = System.getProperty("java.awt.headless");
1108 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1115 public AlignFrame[] getAlignFrames()
1117 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1118 : Desktop.getAlignFrames();
1123 * Quit method delegates to Desktop.quit - unless running in headless mode
1124 * when it just ends the JVM
1128 if (desktop != null)
1138 public static AlignFrame getCurrentAlignFrame()
1140 return Jalview.currentAlignFrame;
1143 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1145 Jalview.currentAlignFrame = currentAlignFrame;