2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 import java.io.BufferedReader;
22 import java.io.FileOutputStream;
23 import java.io.IOException;
24 import java.io.OutputStreamWriter;
25 import java.io.PrintWriter;
26 import java.lang.reflect.Constructor;
27 import java.net.MalformedURLException;
30 import java.net.URLDecoder;
31 import java.security.AllPermission;
32 import java.security.CodeSource;
33 import java.security.PermissionCollection;
34 import java.security.Permissions;
35 import java.security.Policy;
41 import jalview.util.Platform;
44 * Main class for Jalview Application <br>
46 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
55 // grab all the rights we can the JVM
56 Policy.setPolicy(new Policy()
58 public PermissionCollection getPermissions(CodeSource codesource)
60 Permissions perms = new Permissions();
61 perms.add(new AllPermission());
72 * main class for Jalview application
75 * open <em>filename</em>
77 public static void main(String[] args)
79 System.out.println("Java version: "
80 + System.getProperty("java.version"));
81 System.out.println(System.getProperty("os.arch") + " "
82 + System.getProperty("os.name") + " "
83 + System.getProperty("os.version"));
84 if (new Platform().isAMac())
86 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
88 System.setProperty("apple.laf.useScreenMenuBar", "true");
91 ArgsParser aparser = new ArgsParser(args);
92 boolean headless = false;
94 if (aparser.contains("help") || aparser.contains("h"))
97 .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
98 + "-nodisplay\tRun Jalview without User Interface.\n"
99 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
100 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
101 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
102 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
103 + "-features FILE\tUse the given file to mark features on the alignment.\n"
104 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
105 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
106 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
107 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
108 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
109 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
110 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
111 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
112 + "-png FILE\tCreate PNG image FILE from alignment.\n"
113 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
114 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
115 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
116 + "-noquestionnaire\tTurn off questionnaire check.\n"
117 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
118 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
120 // "-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)"
121 + "-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"
122 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
123 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
124 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
126 // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
127 // + "-vses vamsas-session\tJoin session with given URN\n"
128 + "-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"
129 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
132 Cache.loadProperties(aparser.getValue("props")); // must do this before
134 String defs = aparser.getValue("setprop");
137 int p = defs.indexOf('=');
140 System.err.println("Ignoring invalid setprop argument : " + defs);
144 System.out.println("Executing setprop argument: " + defs);
145 // DISABLED FOR SECURITY REASONS
146 // TODO: add a property to allow properties to be overriden by cli args
147 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
149 defs = aparser.getValue("setprop");
151 if (aparser.contains("nodisplay"))
153 System.setProperty("java.awt.headless", "true");
155 if (System.getProperty("java.awt.headless") != null
156 && System.getProperty("java.awt.headless").equals("true"))
160 System.setProperty("http.agent", "Jalview Desktop/"+Cache.getDefault("VERSION", "Unknown"));
164 } catch (java.lang.NoClassDefFoundError error)
166 error.printStackTrace();
168 .println("\nEssential logging libraries not found."
169 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
173 Desktop desktop = null;
177 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
178 } catch (Exception ex)
184 desktop = new Desktop();
185 desktop.setInBatchMode(true); // indicate we are starting up
186 desktop.setVisible(true);
187 desktop.startServiceDiscovery();
188 if (!aparser.contains("nousagestats"))
190 startUsageStats(desktop);
192 if (!aparser.contains("noquestionnaire"))
194 String url = aparser.getValue("questionnaire");
197 // Start the desktop questionnaire prompter with the specified
199 Cache.log.debug("Starting questionnaire url at " + url);
200 desktop.checkForQuestionnaire(url);
204 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
206 // Start the desktop questionnaire prompter with the specified
209 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
211 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
212 Cache.log.debug("Starting questionnaire with default url: "
214 desktop.checkForQuestionnaire(defurl);
219 desktop.checkForNews();
222 String file = null, protocol = null, format = null, data = null;
223 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
224 Vector getFeatures = null; // vector of das source nicknames to fetch
227 String groovyscript = null; // script to execute after all loading is
228 // completed one way or another
229 // extract groovy argument and execute if necessary
230 groovyscript = aparser.getValue("groovy", true);
231 file = aparser.getValue("open", true);
233 if (file == null && desktop == null)
235 System.out.println("No files to open!");
238 String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
240 if (vamsasImport != null || vamsasSession != null)
242 if (desktop == null || headless)
245 .println("Headless vamsas sessions not yet supported. Sorry.");
248 // if we have a file, start a new session and import it.
249 boolean inSession = false;
250 if (vamsasImport != null)
254 String viprotocol = jalview.io.AppletFormatAdapter
255 .checkProtocol(vamsasImport);
256 if (viprotocol == jalview.io.FormatAdapter.FILE)
258 inSession = desktop.vamsasImport(new File(vamsasImport));
260 else if (viprotocol == jalview.io.FormatAdapter.URL)
262 inSession = desktop.vamsasImport(new URL(vamsasImport));
265 } catch (Exception e)
267 System.err.println("Exeption when importing " + vamsasImport
268 + " as a vamsas document.");
273 System.err.println("Failed to import " + vamsasImport
274 + " as a vamsas document.");
278 System.out.println("Imported Successfully into new session "
279 + desktop.getVamsasApplication().getCurrentSession());
282 if (vamsasSession != null)
284 if (vamsasImport != null)
286 // close the newly imported session and import the Jalview specific
287 // remnants into the new session later on.
288 desktop.vamsasStop_actionPerformed(null);
290 // now join the new session
293 if (desktop.joinVamsasSession(vamsasSession))
295 System.out.println("Successfully joined vamsas session "
300 System.err.println("WARNING: Failed to join vamsas session "
303 } catch (Exception e)
305 System.err.println("ERROR: Failed to join vamsas session "
309 if (vamsasImport != null)
311 // the Jalview specific remnants can now be imported into the new
312 // session at the user's leisure.
314 .info("Skipping Push for import of data into existing vamsas session."); // TODO:
319 // desktop.getVamsasApplication().push_update();
324 // Finally, deal with the remaining input data.
329 desktop.setProgressBar("Processing commandline arguments...",
330 progress = System.currentTimeMillis());
332 System.out.println("Opening file: " + file);
334 if (!file.startsWith("http://"))
336 if (!(new java.io.File(file)).exists())
338 System.out.println("Can't find " + file);
346 protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
348 format = new jalview.io.IdentifyFile().Identify(file, protocol);
350 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
354 System.out.println("error");
359 data = aparser.getValue("colour", true);
362 data.replaceAll("%20", " ");
364 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
365 .getColour(af.getViewport().getAlignment(), data);
369 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
371 ucs.parseAppletParameter(data);
375 System.out.println("colour is " + data);
379 // Must maintain ability to use the groups flag
380 data = aparser.getValue("groups", true);
383 af.parseFeaturesFile(data,
384 jalview.io.AppletFormatAdapter.checkProtocol(data));
385 System.out.println("Added " + data);
387 data = aparser.getValue("features", true);
390 af.parseFeaturesFile(data,
391 jalview.io.AppletFormatAdapter.checkProtocol(data));
392 System.out.println("Added " + data);
395 data = aparser.getValue("annotations", true);
398 af.loadJalviewDataFile(data, null, null, null);
399 System.out.println("Added " + data);
401 // set or clear the sortbytree flag.
402 if (aparser.contains("sortbytree"))
404 af.getViewport().setSortByTree(true);
406 if (aparser.contains("nosortbytree"))
408 af.getViewport().setSortByTree(false);
410 data = aparser.getValue("tree", true);
413 jalview.io.NewickFile fin = null;
416 fin = new jalview.io.NewickFile(data,
417 jalview.io.AppletFormatAdapter.checkProtocol(data));
420 af.getViewport().setCurrentTree(
421 af.ShowNewickTree(fin, data).getTree());
422 System.out.println("Added tree " + data);
424 } catch (IOException ex)
426 System.err.println("Couldn't add tree " + data);
427 ex.printStackTrace(System.err);
430 // TODO - load PDB structure(s) to alignment JAL-629
431 // (associate with identical sequence in alignment, or a specified
434 getFeatures = checkDasArguments(aparser);
435 if (af != null && getFeatures != null)
437 FeatureFetcher ff = startFeatureFetching(getFeatures);
439 while (!ff.allFinished() || af.operationInProgress())
441 // wait around until fetching is finished.
445 } catch (Exception e)
450 getFeatures = null; // have retrieved features - forget them now.
452 if (groovyscript != null)
454 // Execute the groovy script after we've done all the rendering stuff
455 // and before any images or figures are generated.
456 if (jalview.bin.Cache.groovyJarsPresent())
458 System.out.println("Executing script " + groovyscript);
459 executeGroovyScript(groovyscript, new Object[]
465 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
470 String imageName = "unnamed.png";
471 while (aparser.getSize() > 1)
473 format = aparser.nextValue();
474 file = aparser.nextValue();
476 if (format.equalsIgnoreCase("png"))
478 af.createPNG(new java.io.File(file));
479 imageName = (new java.io.File(file)).getName();
480 System.out.println("Creating PNG image: " + file);
483 else if (format.equalsIgnoreCase("imgMap"))
485 af.createImageMap(new java.io.File(file), imageName);
486 System.out.println("Creating image map: " + file);
489 else if (format.equalsIgnoreCase("eps"))
491 System.out.println("Creating EPS file: " + file);
492 af.createEPS(new java.io.File(file));
496 if (af.saveAlignment(file, format))
498 System.out.println("Written alignment in " + format
499 + " format to " + file);
503 System.out.println("Error writing file " + file + " in "
504 + format + " format!!");
509 while (aparser.getSize() > 0)
511 System.out.println("Unknown arg: " + aparser.nextValue());
515 AlignFrame startUpAlframe = null;
516 // We'll only open the default file if the desktop is visible.
518 // ////////////////////
519 if (!headless && file == null && vamsasImport == null
520 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
522 file = jalview.bin.Cache.getDefault(
524 jalview.bin.Cache.getDefault("www.jalview.org",
525 "http://www.jalview.org")
526 + "/examples/exampleFile_2_7.jar");
527 if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar"))
529 // hardwire upgrade of the startup file
530 file.replace("_2_3.jar", "_2_7.jar");
531 // and remove the stale setting
532 jalview.bin.Cache.removeProperty("STARTUP_FILE");
537 if (file.indexOf("http:") > -1)
542 if (file.endsWith(".jar"))
548 format = new jalview.io.IdentifyFile().Identify(file, protocol);
551 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
553 getFeatures = checkDasArguments(aparser);
554 // extract groovy arguments before anything else.
556 // If the user has specified features to be retrieved,
557 // or a groovy script to be executed, do them if they
558 // haven't been done already
559 // fetch features for the default alignment
560 if (getFeatures != null)
562 if (startUpAlframe != null)
564 startFeatureFetching(getFeatures);
567 // Once all other stuff is done, execute any groovy scripts (in order)
568 if (groovyscript != null)
570 if (jalview.bin.Cache.groovyJarsPresent())
572 System.out.println("Executing script " + groovyscript);
573 executeGroovyScript(groovyscript, new Object[]
574 { desktop, startUpAlframe });
579 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
583 // and finally, turn off batch mode indicator - if the desktop still exists
588 desktop.setProgressBar(null, progress);
590 desktop.setInBatchMode(false);
594 private static void startUsageStats(final Desktop desktop)
597 * start a User Config prompt asking if we can log usage statistics.
599 jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
602 "Jalview Usage Statistics",
603 "Do you want to help make Jalview better by enabling "
604 + "the collection of usage statistics with Google Analytics ?"
605 + "\n\n(you can enable or disable usage tracking in the preferences)",
611 .info("Initialising googletracker for usage stats.");
612 Cache.initGoogleTracker();
613 Cache.log.debug("Tracking enabled.");
619 Cache.log.info("Not enabling Google Tracking.");
622 desktop.addDialogThread(prompter);
626 * Locate the given string as a file and pass it to the groovy interpreter.
628 * @param groovyscript
629 * the script to execute
630 * @param jalviewContext
631 * the Jalview Desktop object passed in to the groovy binding as the
634 private static void executeGroovyScript(String groovyscript,
635 Object[] jalviewContext)
637 if (jalviewContext == null)
640 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
643 * for scripts contained in files
650 if (groovyscript.trim().equals("STDIN"))
652 // read from stdin into a tempfile and execute it
655 tfile = File.createTempFile("jalview", "groovy");
656 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
657 new FileOutputStream(tfile)));
658 BufferedReader br = new BufferedReader(
659 new java.io.InputStreamReader(System.in));
661 while ((line = br.readLine()) != null)
663 outfile.write(line + "\n");
669 } catch (Exception ex)
671 System.err.println("Failed to read from STDIN into tempfile "
672 + ((tfile == null) ? "(tempfile wasn't created)" : tfile
674 ex.printStackTrace();
679 sfile = tfile.toURI().toURL();
680 } catch (Exception x)
683 .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
693 sfile = new URI(groovyscript).toURL();
694 } catch (Exception x)
696 tfile = new File(groovyscript);
699 System.err.println("File '" + groovyscript + "' does not exist.");
702 if (!tfile.canRead())
704 System.err.println("File '" + groovyscript + "' cannot be read.");
707 if (tfile.length() < 1)
709 System.err.println("File '" + groovyscript + "' is empty.");
714 sfile = tfile.getAbsoluteFile().toURI().toURL();
715 } catch (Exception ex)
717 System.err.println("Failed to create a file URL for "
718 + tfile.getAbsoluteFile());
723 boolean success = false;
727 * The following code performs the GroovyScriptEngine invocation using
728 * reflection, and is equivalent to this fragment from the embedding
729 * groovy documentation on the groovy site: <code> import
730 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
732 * String[] roots = new String[] { "/my/groovy/script/path" };
733 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
734 * = new Binding(); binding.setVariable("input", "world");
735 * gse.run("hello.groovy", binding); </code>
739 int blen = ((jalviewContext[0] == null) ? 0 : 1)
740 + ((jalviewContext[1] == null) ? 0 : 1);
741 String cnames[] = new String[]
742 { "Jalview", "currentAlFrame" };
743 bspec = new Class[blen * 2];
744 binding = new Object[blen * 2];
746 ClassLoader cl = null;
747 Map vbinding = new Hashtable();
748 for (int jc = 0; jc < jalviewContext.length; jc++)
750 if (jalviewContext[jc] != null)
754 cl = jalviewContext[jc].getClass().getClassLoader();
756 bspec[blen * 2] = String.class;
757 bspec[blen * 2 + 1] = Object.class;
758 binding[blen * 2] = cnames[jc];
759 binding[blen * 2 + 1] = jalviewContext[jc];
760 vbinding.put(cnames[jc], jalviewContext[jc]);
764 Class gbindingc = cl.loadClass("groovy.lang.Binding");
769 gbcons = gbindingc.getConstructor(Map.class);
770 gbinding = gbcons.newInstance(vbinding);
771 } catch (NoSuchMethodException x)
773 // old style binding config - using series of string/object values to
775 gbcons = gbindingc.getConstructor(null);
776 gbinding = gbcons.newInstance(null);
777 java.lang.reflect.Method setvar = gbindingc.getMethod(
778 "setVariable", bspec);
779 setvar.invoke(gbinding, binding);
782 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
783 Constructor gseccons = gsec.getConstructor(new Class[]
784 { URL[].class }); // String[].class });
785 Object gse = gseccons.newInstance(new Object[]
787 { sfile } }); // .toString() } });
788 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
789 { String.class, gbindingc });
790 run.invoke(gse, new Object[]
791 { sfile.toString(), gbinding });
793 } catch (Exception e)
795 System.err.println("Exception Whilst trying to execute file " + sfile
796 + " as a groovy script.");
797 e.printStackTrace(System.err);
800 if (success && groovyscript.equals("STDIN"))
802 // delete temp file that we made - but only if it was successfully
809 * Check commandline for any das server definitions or any fetchfrom switches
811 * @return vector of DAS source nicknames to retrieve from
813 private static Vector checkDasArguments(ArgsParser aparser)
815 Vector source = null;
817 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
818 while ((data = aparser.getValue("dasserver", true)) != null)
820 String nickname = null;
822 boolean seq = false, feat = true;
823 int pos = data.indexOf('=');
824 // determine capabilities
827 nickname = data.substring(0, pos);
829 url = data.substring(pos + 1);
831 && (url.startsWith("http:") || url
832 .startsWith("sequence:http:")))
834 if (nickname == null)
838 if (locsources == null)
846 locsources = locsources + nickname + "|" + url;
848 .println("NOTE! dasserver parameter not yet really supported (got args of "
849 + nickname + "|" + url);
852 source = new Vector();
854 source.addElement(nickname);
856 } // loop until no more server entries are found.
857 if (locsources != null && locsources.indexOf('|') > -1)
859 Cache.log.debug("Setting local source list in properties file to:\n"
861 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
863 while ((data = aparser.getValue("fetchfrom", true)) != null)
865 System.out.println("adding source '" + data + "'");
868 source = new Vector();
870 source.addElement(data);
876 * start a feature fetcher for every alignment frame
880 private static FeatureFetcher startFeatureFetching(final Vector dasSources)
882 FeatureFetcher ff = new FeatureFetcher();
883 AlignFrame afs[] = Desktop.getAlignframes();
884 if (afs == null || afs.length == 0)
888 for (int i = 0; i < afs.length; i++)
890 ff.addFetcher(afs[i], dasSources);
897 * Notes: this argParser does not distinguish between parameter switches,
898 * parameter values and argument text. If an argument happens to be identical to
899 * a parameter, it will be taken as such (even though it didn't have a '-'
902 * @author Andrew Waterhouse and JBP documented.
909 public ArgsParser(String[] args)
911 vargs = new Vector();
912 for (int i = 0; i < args.length; i++)
914 String arg = args[i].trim();
915 if (arg.charAt(0) == '-')
917 arg = arg.substring(1);
919 vargs.addElement(arg);
924 * check for and remove first occurence of arg+parameter in arglist.
927 * @return return the argument following the given arg if arg was in list.
929 public String getValue(String arg)
931 return getValue(arg, false);
934 public String getValue(String arg, boolean utf8decode)
936 int index = vargs.indexOf(arg);
937 String dc = null, ret = null;
940 ret = vargs.elementAt(index + 1).toString();
941 vargs.removeElementAt(index);
942 vargs.removeElementAt(index);
943 if (utf8decode && ret != null)
947 dc = URLDecoder.decode(ret, "UTF-8");
949 } catch (Exception e)
951 // TODO: log failure to decode
959 * check for and remove first occurence of arg in arglist.
962 * @return true if arg was present in argslist.
964 public boolean contains(String arg)
966 if (vargs.contains(arg))
968 vargs.removeElement(arg);
977 public String nextValue()
979 return vargs.remove(0).toString();
990 * keep track of feature fetching tasks.
998 * TODO: generalise to track all jalview events to orchestrate batch
1002 private int queued = 0;
1004 private int running = 0;
1006 public FeatureFetcher()
1011 public void addFetcher(final AlignFrame af, final Vector dasSources)
1013 final long id = System.currentTimeMillis();
1015 final FeatureFetcher us = this;
1016 new Thread(new Runnable()
1027 af.setProgressBar("DAS features being retrieved...", id);
1028 af.featureSettings_actionPerformed(null);
1029 af.featureSettings.fetchDasFeatures(dasSources, true);
1030 af.setProgressBar(null, id);
1039 public synchronized boolean allFinished()
1041 return queued == 0 && running == 0;