2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
28 import java.net.URLDecoder;
29 import java.security.AllPermission;
30 import java.security.CodeSource;
31 import java.security.PermissionCollection;
32 import java.security.Permissions;
33 import java.security.Policy;
39 import jalview.io.AppletFormatAdapter;
42 * Main class for Jalview Application <br>
44 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
53 // grab all the rights we can the JVM
54 Policy.setPolicy(new Policy()
56 public PermissionCollection getPermissions(CodeSource codesource)
58 Permissions perms = new Permissions();
59 perms.add(new AllPermission());
70 * main class for Jalview application
73 * open <em>filename</em>
75 public static void main(String[] args)
77 System.out.println("Java version: "
78 + System.getProperty("java.version"));
79 System.out.println(System.getProperty("os.arch") + " "
80 + System.getProperty("os.name") + " "
81 + System.getProperty("os.version"));
83 ArgsParser aparser = new ArgsParser(args);
84 boolean headless = false;
86 if (aparser.contains("help") || aparser.contains("h"))
89 .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
90 + "-nodisplay\tRun Jalview without User Interface.\n"
91 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
92 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
93 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
94 + "-features FILE\tUse the given file to mark features on the alignment.\n"
95 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
96 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
97 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
98 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
99 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
100 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
101 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
102 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
103 + "-png FILE\tCreate PNG image FILE from alignment.\n"
104 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
105 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
106 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
107 + "-noquestionnaire\tTurn off questionnaire check.\n"
108 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
109 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
111 // "-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)"
112 + "-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"
113 + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
114 + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
115 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
117 // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
118 // + "-vses vamsas-session\tJoin session with given URN\n"
119 + "-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"
120 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
123 Cache.loadProperties(aparser.getValue("props")); // must do this before
125 String defs = aparser.getValue("setprop");
128 int p = defs.indexOf('=');
131 System.err.println("Ignoring invalid setprop argument : " + defs);
135 System.out.println("Executing setprop argument: " + defs);
136 // DISABLED FOR SECURITY REASONS
137 // TODO: add a property to allow properties to be overriden by cli args
138 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
140 defs = aparser.getValue("setprop");
142 if (aparser.contains("nodisplay"))
144 System.setProperty("java.awt.headless", "true");
146 if (System.getProperty("java.awt.headless") != null
147 && System.getProperty("java.awt.headless").equals("true"))
155 } catch (java.lang.NoClassDefFoundError error)
157 error.printStackTrace();
159 .println("\nEssential logging libraries not found."
160 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
164 Desktop desktop = null;
168 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
169 // UIManager.getCrossPlatformLookAndFeelClassName()
170 // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
171 // "javax.swing.plaf.metal.MetalLookAndFeel"
172 // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
173 // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
176 } catch (Exception ex)
181 desktop = new Desktop();
182 desktop.setVisible(true);
183 desktop.startServiceDiscovery();
184 if (!aparser.contains("nousagestats"))
186 startUsageStats(desktop);
188 if (!aparser.contains("noquestionnaire"))
190 String url = aparser.getValue("questionnaire");
193 // Start the desktop questionnaire prompter with the specified
195 Cache.log.debug("Starting questionnaire url at " + url);
196 desktop.checkForQuestionnaire(url);
200 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
202 // Start the desktop questionnaire prompter with the specified
205 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
207 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
208 Cache.log.debug("Starting questionnaire with default url: "
210 desktop.checkForQuestionnaire(defurl);
217 String file = null, protocol = null, format = null, data = null;
218 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
219 Vector getFeatures = null; // vector of das source nicknames to fetch
222 String groovyscript = null; // script to execute after all loading is
223 // completed one way or another
224 // extract groovy argument and execute if necessary
225 groovyscript = aparser.getValue("groovy", true);
226 file = aparser.getValue("open", true);
228 if (file == null && desktop == null)
230 System.out.println("No files to open!");
233 String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser
235 if (vamsasImport != null || vamsasSession != null)
237 if (desktop == null || headless)
240 .println("Headless vamsas sessions not yet supported. Sorry.");
243 // if we have a file, start a new session and import it.
244 boolean inSession = false;
245 if (vamsasImport != null)
249 String viprotocol = Jalview.checkProtocol(vamsasImport);
250 if (viprotocol == jalview.io.FormatAdapter.FILE)
252 inSession = desktop.vamsasImport(new File(vamsasImport));
254 else if (viprotocol == jalview.io.FormatAdapter.URL)
256 inSession = desktop.vamsasImport(new URL(vamsasImport));
259 } catch (Exception e)
261 System.err.println("Exeption when importing " + vamsasImport
262 + " as a vamsas document.");
267 System.err.println("Failed to import " + vamsasImport
268 + " as a vamsas document.");
272 System.out.println("Imported Successfully into new session "
273 + desktop.getVamsasApplication().getCurrentSession());
276 if (vamsasSession != null)
278 if (vamsasImport != null)
280 // close the newly imported session and import the Jalview specific
281 // remnants into the new session later on.
282 desktop.vamsasStop_actionPerformed(null);
284 // now join the new session
287 if (desktop.joinVamsasSession(vamsasSession))
289 System.out.println("Successfully joined vamsas session "
294 System.err.println("WARNING: Failed to join vamsas session "
297 } catch (Exception e)
299 System.err.println("ERROR: Failed to join vamsas session "
303 if (vamsasImport != null)
305 // the Jalview specific remnants can now be imported into the new
306 // session at the user's leisure.
308 .info("Skipping Push for import of data into existing vamsas session."); // TODO:
313 // desktop.getVamsasApplication().push_update();
317 // Finally, deal with the remaining input data.
320 System.out.println("Opening file: " + file);
322 if (!file.startsWith("http://"))
324 if (!(new java.io.File(file)).exists())
326 System.out.println("Can't find " + file);
334 protocol = checkProtocol(file);
336 format = new jalview.io.IdentifyFile().Identify(file, protocol);
338 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
342 System.out.println("error");
346 data = aparser.getValue("colour", true);
349 data.replaceAll("%20", " ");
351 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
352 .getColour(af.getViewport().getAlignment(), data);
356 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
358 ucs.parseAppletParameter(data);
362 System.out.println("colour is " + data);
366 // Must maintain ability to use the groups flag
367 data = aparser.getValue("groups", true);
370 af.parseFeaturesFile(data, checkProtocol(data));
371 System.out.println("Added " + data);
373 data = aparser.getValue("features", true);
376 af.parseFeaturesFile(data, checkProtocol(data));
377 System.out.println("Added " + data);
380 data = aparser.getValue("annotations", true);
383 af.loadJalviewDataFile(data);
384 System.out.println("Added " + data);
386 // set or clear the sortbytree flag.
387 if (aparser.contains("sortbytree"))
389 af.getViewport().setSortByTree(true);
391 if (aparser.contains("nosortbytree"))
393 af.getViewport().setSortByTree(false);
395 data = aparser.getValue("tree", true);
398 jalview.io.NewickFile fin = null;
401 fin = new jalview.io.NewickFile(data, checkProtocol(data));
404 af.getViewport().setCurrentTree(
405 af.ShowNewickTree(fin, data).getTree());
406 System.out.println("Added tree " + data);
408 } catch (IOException ex)
410 System.err.println("Couldn't add tree " + data);
411 ex.printStackTrace(System.err);
414 // todo - load PDB structure to alignment
415 // (associate with identical sequence in alignment, or a specified
418 getFeatures = checkDasArguments(aparser);
419 if (af != null && getFeatures != null)
421 FeatureFetcher ff = startFeatureFetching(getFeatures);
423 while (!ff.allFinished() || af.operationInProgress())
425 // wait around until fetching is finished.
429 } catch (Exception e)
434 getFeatures = null; // have retrieved features - forget them now.
436 if (groovyscript != null)
438 // Execute the groovy script after we've done all the rendering stuff
439 // and before any images or figures are generated.
440 if (jalview.bin.Cache.groovyJarsPresent())
442 System.out.println("Executing script " + groovyscript);
443 executeGroovyScript(groovyscript, desktop);
448 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
453 String imageName = "unnamed.png";
454 while (aparser.getSize() > 1)
456 format = aparser.nextValue();
457 file = aparser.nextValue();
459 if (format.equalsIgnoreCase("png"))
461 af.createPNG(new java.io.File(file));
462 imageName = (new java.io.File(file)).getName();
463 System.out.println("Creating PNG image: " + file);
466 else if (format.equalsIgnoreCase("imgMap"))
468 af.createImageMap(new java.io.File(file), imageName);
469 System.out.println("Creating image map: " + file);
472 else if (format.equalsIgnoreCase("eps"))
474 System.out.println("Creating EPS file: " + file);
475 af.createEPS(new java.io.File(file));
479 if (af.saveAlignment(file, format))
481 System.out.println("Written alignment in " + format
482 + " format to " + file);
486 System.out.println("Error writing file " + file + " in " + format
492 while (aparser.getSize() > 0)
494 System.out.println("Unknown arg: " + aparser.nextValue());
497 AlignFrame startUpAlframe = null;
498 // We'll only open the default file if the desktop is visible.
500 // ////////////////////
501 if (!headless && file == null && vamsasImport == null
502 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
504 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
505 "http://www.jalview.org/examples/exampleFile_2_3.jar");
509 if (file.indexOf("http:") > -1)
514 if (file.endsWith(".jar"))
520 format = new jalview.io.IdentifyFile().Identify(file, protocol);
523 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
525 getFeatures = checkDasArguments(aparser);
526 // extract groovy arguments before anything else.
528 // If the user has specified features to be retrieved,
529 // or a groovy script to be executed, do them if they
530 // haven't been done already
531 // fetch features for the default alignment
532 if (getFeatures != null)
534 if (startUpAlframe != null)
536 startFeatureFetching(getFeatures);
539 // execute a groovy script.
540 if (groovyscript != null)
542 if (jalview.bin.Cache.groovyJarsPresent())
544 System.out.println("Executing script " + groovyscript);
545 executeGroovyScript(groovyscript, desktop);
550 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
555 // Once all other stuff is done, execute any groovy scripts (in order)
558 private static void startUsageStats(final Desktop desktop)
561 * start a User Config prompt asking if we can log usage statistics.
563 jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(
566 "Jalview Usage Statistics",
567 "Do you want to help make Jalview better by enabling "
568 + "the collection of usage statistics with Google Analytics ?"
569 + "\n\n(you can enable or disable usage tracking in the preferences)",
575 .info("Initialising googletracker for usage stats.");
576 Cache.initGoogleTracker();
577 Cache.log.debug("Tracking enabled.");
583 Cache.log.info("Not enabling Google Tracking.");
586 SwingUtilities.invokeLater(prompter);
590 * Locate the given string as a file and pass it to the groovy interpreter.
592 * @param groovyscript
593 * the script to execute
594 * @param jalviewContext
595 * the Jalview Desktop object passed in to the groovy binding as the
598 private static void executeGroovyScript(String groovyscript,
599 Object jalviewContext)
601 if (jalviewContext == null)
604 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
607 if (groovyscript.trim().equals("STDIN"))
609 // read from stdin into a tempfile and execute it
612 sfile = File.createTempFile("jalview", "groovy");
613 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
614 new FileOutputStream(sfile)));
615 BufferedReader br = new BufferedReader(
616 new java.io.InputStreamReader(System.in));
618 while ((line = br.readLine()) != null)
620 outfile.write(line + "\n");
626 } catch (Exception ex)
628 System.err.println("Failed to read from STDIN into tempfile "
629 + ((sfile == null) ? "(tempfile wasn't created)" : sfile
631 ex.printStackTrace();
637 sfile = new File(groovyscript);
641 System.err.println("File '" + groovyscript + "' does not exist.");
644 if (!sfile.canRead())
646 System.err.println("File '" + groovyscript + "' cannot be read.");
649 if (sfile.length() < 1)
651 System.err.println("File '" + groovyscript + "' is empty.");
654 boolean success = false;
658 * The following code performs the GroovyScriptEngine invocation using
659 * reflection, and is equivalent to this fragment from the embedding
660 * groovy documentation on the groovy site: <code> import
661 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
663 * String[] roots = new String[] { "/my/groovy/script/path" };
664 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding
665 * = new Binding(); binding.setVariable("input", "world");
666 * gse.run("hello.groovy", binding); </code>
668 ClassLoader cl = jalviewContext.getClass().getClassLoader();
669 Class gbindingc = cl.loadClass("groovy.lang.Binding");
670 Constructor gbcons = gbindingc.getConstructor(null);
671 Object gbinding = gbcons.newInstance(null);
672 java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
674 { String.class, Object.class });
675 setvar.invoke(gbinding, new Object[]
676 { "Jalview", jalviewContext });
677 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
678 Constructor gseccons = gsec.getConstructor(new Class[]
679 { URL[].class }); // String[].class });
680 Object gse = gseccons.newInstance(new Object[]
682 { sfile.toURL() } }); // .toString() } });
683 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
684 { String.class, gbindingc });
685 run.invoke(gse, new Object[]
686 { sfile.getName(), gbinding });
688 } catch (Exception e)
690 System.err.println("Exception Whilst trying to execute file " + sfile
691 + " as a groovy script.");
692 e.printStackTrace(System.err);
695 if (success && groovyscript.equals("STDIN"))
697 // delete temp file that we made - but only if it was successfully
704 * Check commandline for any das server definitions or any fetchfrom switches
706 * @return vector of DAS source nicknames to retrieve from
708 private static Vector checkDasArguments(ArgsParser aparser)
710 Vector source = null;
712 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
713 while ((data = aparser.getValue("dasserver", true)) != null)
715 String nickname = null;
717 boolean seq = false, feat = true;
718 int pos = data.indexOf('=');
719 // determine capabilities
722 nickname = data.substring(0, pos);
724 url = data.substring(pos + 1);
726 && (url.startsWith("http:") || url
727 .startsWith("sequence:http:")))
729 if (nickname == null)
733 if (locsources == null)
741 locsources = locsources + nickname + "|" + url;
743 .println("NOTE! dasserver parameter not yet really supported (got args of "
744 + nickname + "|" + url);
747 source = new Vector();
749 source.addElement(nickname);
751 } // loop until no more server entries are found.
752 if (locsources != null && locsources.indexOf('|') > -1)
754 Cache.log.debug("Setting local source list in properties file to:\n"
756 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
758 while ((data = aparser.getValue("fetchfrom", true)) != null)
760 System.out.println("adding source '" + data + "'");
763 source = new Vector();
765 source.addElement(data);
771 * start a feature fetcher for every alignment frame
775 private static FeatureFetcher startFeatureFetching(final Vector dasSources)
777 FeatureFetcher ff = new FeatureFetcher();
778 AlignFrame afs[] = Desktop.getAlignframes();
779 if (afs == null || afs.length == 0)
783 for (int i = 0; i < afs.length; i++)
785 ff.addFetcher(afs[i], dasSources);
790 private static String checkProtocol(String file)
792 String protocol = jalview.io.FormatAdapter.FILE;
794 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
796 protocol = jalview.io.FormatAdapter.URL;
803 * Notes: this argParser does not distinguish between parameter switches,
804 * parameter values and argument text. If an argument happens to be identical to
805 * a parameter, it will be taken as such (even though it didn't have a '-'
808 * @author Andrew Waterhouse and JBP documented.
815 public ArgsParser(String[] args)
817 vargs = new Vector();
818 for (int i = 0; i < args.length; i++)
820 String arg = args[i].trim();
821 if (arg.charAt(0) == '-')
823 arg = arg.substring(1);
825 vargs.addElement(arg);
830 * check for and remove first occurence of arg+parameter in arglist.
833 * @return return the argument following the given arg if arg was in list.
835 public String getValue(String arg)
837 return getValue(arg, false);
840 public String getValue(String arg, boolean utf8decode)
842 int index = vargs.indexOf(arg);
843 String dc = null, ret = null;
846 ret = vargs.elementAt(index + 1).toString();
847 vargs.removeElementAt(index);
848 vargs.removeElementAt(index);
849 if (utf8decode && ret != null)
853 dc = URLDecoder.decode(ret, "UTF-8");
855 } catch (Exception e)
857 // TODO: log failure to decode
865 * check for and remove first occurence of arg in arglist.
868 * @return true if arg was present in argslist.
870 public boolean contains(String arg)
872 if (vargs.contains(arg))
874 vargs.removeElement(arg);
883 public String nextValue()
885 return vargs.remove(0).toString();
896 * keep track of feature fetching tasks.
904 * TODO: generalise to track all jalview events to orchestrate batch
908 private int queued = 0;
910 private int running = 0;
912 public FeatureFetcher()
917 public void addFetcher(final AlignFrame af, final Vector dasSources)
919 final long id = System.currentTimeMillis();
921 final FeatureFetcher us = this;
922 new Thread(new Runnable()
933 af.setProgressBar("DAS features being retrieved...", id);
934 af.featureSettings_actionPerformed(null);
935 af.featureSettings.fetchDasFeatures(dasSources, true);
936 af.setProgressBar(null, id);
945 public synchronized boolean allFinished()
947 return queued == 0 && running == 0;