2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
21 import java.io.BufferedReader;
23 import java.io.FileOutputStream;
24 import java.io.IOException;
25 import java.io.OutputStreamWriter;
26 import java.io.PrintWriter;
27 import java.lang.reflect.Constructor;
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
52 // grab all the rights we can the JVM
53 Policy.setPolicy( new Policy() {
54 public PermissionCollection
55 getPermissions(CodeSource codesource) {
56 Permissions perms = new Permissions();
57 perms.add(new AllPermission());
60 public void refresh(){
65 * main class for Jalview application
68 * open <em>filename</em>
70 public static void main(String[] args)
72 System.out.println("Java version: "
73 + System.getProperty("java.version"));
74 System.out.println(System.getProperty("os.arch") + " "
75 + System.getProperty("os.name") + " "
76 + System.getProperty("os.version"));
78 ArgsParser aparser = new ArgsParser(args);
79 boolean headless = false;
81 if (aparser.contains("help") || aparser.contains("h"))
84 .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
85 + "-nodisplay\tRun Jalview without User Interface.\n"
86 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
87 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
88 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
89 + "-features FILE\tUse the given file to mark features on the alignment.\n"
90 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
91 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
92 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
93 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
94 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
95 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
96 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
97 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
98 + "-png FILE\tCreate PNG image FILE from alignment.\n"
99 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
100 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
101 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
102 + "-noquestionnaire\tTurn off questionnaire check.\n"
103 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
104 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
105 // + "-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)"
106 + "-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"
107 +"\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
108 +"\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
109 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
110 // + "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n"
111 // + "-vses vamsas-session\tJoin session with given URN\n"
112 + "-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"
113 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
116 Cache.loadProperties(aparser.getValue("props")); // must do this before
118 String defs = aparser.getValue("setprop");
121 int p = defs.indexOf('=');
124 System.err.println("Ignoring invalid setprop argument : "+defs);
126 System.out.println("Executing setprop argument: "+defs);
127 // DISABLED FOR SECURITY REASONS
128 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
130 defs = aparser.getValue("setprop");
132 if (aparser.contains("nodisplay"))
134 System.setProperty("java.awt.headless", "true");
136 if (System.getProperty("java.awt.headless") != null
137 && System.getProperty("java.awt.headless").equals("true"))
145 } catch (java.lang.NoClassDefFoundError error)
147 error.printStackTrace();
149 .println("\nEssential logging libraries not found."
150 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
154 Desktop desktop = null;
158 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
159 // UIManager.getCrossPlatformLookAndFeelClassName()
160 // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
161 // "javax.swing.plaf.metal.MetalLookAndFeel"
162 // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
163 // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
167 } catch (Exception ex)
172 desktop = new Desktop();
173 desktop.setVisible(true);
174 desktop.discoverer.start();
175 if (!aparser.contains("nousagestats") && Cache.getDefault("USAGESTATS", true)) {
176 Cache.log.info("Initialising googletracker for usage stats.");
177 Cache.initGoogleTracker();
178 Cache.log.debug("Tracking enabled.");
180 Cache.log.info("Not enabling Google Tracking.");
182 if (!aparser.contains("noquestionnaire"))
184 String url = aparser.getValue("questionnaire");
187 // Start the desktop questionnaire prompter with the specified
189 Cache.log.debug("Starting questionnaire url at " + url);
190 desktop.checkForQuestionnaire(url);
194 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
196 // Start the desktop questionnaire prompter with the specified
199 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
201 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
202 Cache.log.debug("Starting questionnaire with default url: "
204 desktop.checkForQuestionnaire(defurl);
211 String file = null, protocol = null, format = null, data = null;
212 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
213 Vector getFeatures = null; // vector of das source nicknames to fetch
216 String groovyscript = null; // script to execute after all loading is
217 // completed one way or another
218 // extract groovy argument and execute if necessary
219 groovyscript = aparser.getValue("groovy");
220 file = aparser.getValue("open");
222 if (file == null && desktop == null)
224 System.out.println("No files to open!");
227 String vamsasImport=aparser.getValue("vdoc"),vamsasSession=aparser.getValue("vsess");
228 if (vamsasImport!=null || vamsasSession!=null)
230 if (desktop==null || headless)
232 System.out.println("Headless vamsas sessions not yet supported. Sorry.");
235 // if we have a file, start a new session and import it.
236 boolean inSession = false;
237 if (vamsasImport!=null)
240 String viprotocol = Jalview.checkProtocol(vamsasImport);
241 if (viprotocol == jalview.io.FormatAdapter.FILE) {
242 inSession = desktop.vamsasImport(new File(vamsasImport));
243 } else if (viprotocol == jalview.io.FormatAdapter.URL) {
244 inSession = desktop.vamsasImport(new URL(vamsasImport));
247 } catch (Exception e)
249 System.err.println("Exeption when importing "+vamsasImport+" as a vamsas document.");
253 System.err.println("Failed to import "+vamsasImport+" as a vamsas document.");
255 System.out.println("Imported Successfully into new session "+desktop.getVamsasApplication().getCurrentSession());
258 if (vamsasSession!=null) {
259 if (vamsasImport!=null) {
260 // close the newly imported session and import the Jalview specific remnants into the new session later on.
261 desktop.vamsasStop_actionPerformed(null);
263 // now join the new session
265 if (desktop.joinVamsasSession(vamsasSession)) {
266 System.out.println("Successfully joined vamsas session "+vamsasSession);
268 System.err.println("WARNING: Failed to join vamsas session "+vamsasSession);
270 } catch (Exception e)
272 System.err.println("ERROR: Failed to join vamsas session "+vamsasSession);
275 if (vamsasImport!=null) {
276 // the Jalview specific remnants can now be imported into the new session at the user's leisure.
277 Cache.log.info("Skipping Push for import of data into existing vamsas session."); // TODO: enable this when debugged
278 // desktop.getVamsasApplication().push_update();
282 // Finally, deal with the remaining input data.
285 System.out.println("Opening file: " + file);
287 if (!file.startsWith("http://"))
289 if (!(new java.io.File(file)).exists())
291 System.out.println("Can't find " + file);
299 protocol = checkProtocol(file);
301 format = new jalview.io.IdentifyFile().Identify(file, protocol);
303 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
307 System.out.println("error");
311 data = aparser.getValue("colour");
314 data.replaceAll("%20", " ");
316 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
317 .getColour(af.getViewport().getAlignment(), data);
321 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
323 ucs.parseAppletParameter(data);
327 System.out.println("colour is " + data);
331 // Must maintain ability to use the groups flag
332 data = aparser.getValue("groups");
335 af.parseFeaturesFile(data, checkProtocol(data));
336 System.out.println("Added " + data);
338 data = aparser.getValue("features");
341 af.parseFeaturesFile(data, checkProtocol(data));
342 System.out.println("Added " + data);
345 data = aparser.getValue("annotations");
348 af.loadJalviewDataFile(data);
349 System.out.println("Added " + data);
351 // set or clear the sortbytree flag.
352 if (aparser.contains("sortbytree"))
354 af.getViewport().setSortByTree(true);
356 if (aparser.contains("nosortbytree"))
358 af.getViewport().setSortByTree(false);
360 data = aparser.getValue("tree");
363 jalview.io.NewickFile fin = null;
366 fin = new jalview.io.NewickFile(data, checkProtocol(data));
369 af.getViewport().setCurrentTree(
370 af.ShowNewickTree(fin, data).getTree());
371 System.out.println("Added tree " + data);
373 } catch (IOException ex)
375 System.err.println("Couldn't add tree " + data);
376 ex.printStackTrace(System.err);
379 getFeatures = checkDasArguments(aparser);
380 if (af != null && getFeatures != null)
382 startFeatureFetching(getFeatures);
383 // need to block until fetching is complete.
384 while (af.operationInProgress())
386 // wait around until fetching is finished.
390 } catch (Exception e)
396 if (groovyscript != null)
398 // Execute the groovy script after we've done all the rendering stuff
399 // and before any images or figures are generated.
400 if (jalview.bin.Cache.groovyJarsPresent())
402 System.out.println("Executing script " + groovyscript);
403 executeGroovyScript(groovyscript, desktop);
408 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
413 String imageName = "unnamed.png";
414 while (aparser.getSize() > 1)
416 format = aparser.nextValue();
417 file = aparser.nextValue();
419 if (format.equalsIgnoreCase("png"))
421 af.createPNG(new java.io.File(file));
422 imageName = (new java.io.File(file)).getName();
423 System.out.println("Creating PNG image: " + file);
426 else if (format.equalsIgnoreCase("imgMap"))
428 af.createImageMap(new java.io.File(file), imageName);
429 System.out.println("Creating image map: " + file);
432 else if (format.equalsIgnoreCase("eps"))
434 System.out.println("Creating EPS file: " + file);
435 af.createEPS(new java.io.File(file));
439 if (af.saveAlignment(file, format))
441 System.out.println("Written alignment in " + format
442 + " format to " + file);
446 System.out.println("Error writing file " + file + " in " + format
452 while (aparser.getSize() > 0)
454 System.out.println("Unknown arg: " + aparser.nextValue());
457 AlignFrame startUpAlframe = null;
458 // We'll only open the default file if the desktop is visible.
460 // ////////////////////
461 if (!headless && file == null && vamsasImport==null
462 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
464 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
465 "http://www.jalview.org/examples/exampleFile_2_3.jar");
469 if (file.indexOf("http:") > -1)
474 if (file.endsWith(".jar"))
480 format = new jalview.io.IdentifyFile().Identify(file, protocol);
483 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
485 getFeatures = checkDasArguments(aparser);
486 // extract groovy arguments before anything else.
488 // Once all loading is done. Retrieve features.
489 if (getFeatures != null)
491 if (startUpAlframe != null)
493 startFeatureFetching(getFeatures);
496 if (groovyscript != null)
498 if (jalview.bin.Cache.groovyJarsPresent())
500 System.out.println("Executing script " + groovyscript);
501 executeGroovyScript(groovyscript, desktop);
506 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
511 // Once all other stuff is done, execute any groovy scripts (in order)
515 * Locate the given string as a file and pass it to the groovy interpreter.
517 * @param groovyscript
518 * the script to execute
519 * @param jalviewContext
520 * the Jalview Desktop object passed in to the groovy binding
521 * as the 'Jalview' object.
523 private static void executeGroovyScript(String groovyscript,
524 Object jalviewContext)
526 if (jalviewContext == null)
529 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
532 if (groovyscript.trim().equals("STDIN"))
534 // read from stdin into a tempfile and execute it
537 sfile = File.createTempFile("jalview", "groovy");
538 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
539 new FileOutputStream(sfile)));
540 BufferedReader br = new BufferedReader(
541 new java.io.InputStreamReader(System.in));
543 while ((line = br.readLine()) != null)
545 outfile.write(line + "\n");
551 } catch (Exception ex)
553 System.err.println("Failed to read from STDIN into tempfile "
554 + ((sfile == null) ? "(tempfile wasn't created)" : sfile
556 ex.printStackTrace();
562 sfile = new File(groovyscript);
566 System.err.println("File '" + groovyscript + "' does not exist.");
569 if (!sfile.canRead())
571 System.err.println("File '" + groovyscript + "' cannot be read.");
574 if (sfile.length() < 1)
576 System.err.println("File '" + groovyscript + "' is empty.");
579 boolean success = false;
583 * The following code performs the GroovyScriptEngine invocation using
584 * reflection, and is equivalent to this fragment from the embedding
585 * groovy documentation on the groovy site: <code> import
586 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
588 * String[] roots = new String[] { "/my/groovy/script/path" };
589 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
590 * new Binding(); binding.setVariable("input", "world");
591 * gse.run("hello.groovy", binding); </code>
593 ClassLoader cl = jalviewContext.getClass().getClassLoader();
594 Class gbindingc = cl.loadClass("groovy.lang.Binding");
595 Constructor gbcons = gbindingc.getConstructor(null);
596 Object gbinding = gbcons.newInstance(null);
597 java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
599 { String.class, Object.class });
600 setvar.invoke(gbinding, new Object[]
601 { "Jalview", jalviewContext });
602 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
603 Constructor gseccons = gsec.getConstructor(new Class[]
604 { URL[].class }); // String[].class });
605 Object gse = gseccons.newInstance(new Object[]
607 { sfile.toURL() } }); // .toString() } });
608 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
609 { String.class, gbindingc });
610 run.invoke(gse, new Object[]
611 { sfile.getName(), gbinding });
613 } catch (Exception e)
615 System.err.println("Exception Whilst trying to execute file " + sfile
616 + " as a groovy script.");
617 e.printStackTrace(System.err);
620 if (success && groovyscript.equals("STDIN"))
622 // delete temp file that we made - but only if it was successfully
629 * Check commandline for any das server definitions or any fetchfrom switches
631 * @return vector of DAS source nicknames to retrieve from
633 private static Vector checkDasArguments(ArgsParser aparser)
635 Vector source = null;
637 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
638 while ((data = aparser.getValue("dasserver")) != null)
640 String nickname = null;
642 boolean seq=false,feat=true;
643 int pos = data.indexOf('=');
644 // determine capabilities
647 nickname = data.substring(0, pos);
649 url = data.substring(pos + 1);
650 if (url != null && (url.startsWith("http:") || url.startsWith("sequence:http:")))
652 if (nickname == null)
656 if (locsources == null)
664 locsources = locsources + nickname + "|" + url;
666 .println("NOTE! dasserver parameter not yet really supported (got args of "
667 + nickname + "|" + url);
670 source = new Vector();
672 source.addElement(nickname);
674 } // loop until no more server entries are found.
675 if (locsources != null && locsources.indexOf('|') > -1)
677 Cache.log.debug("Setting local source list in properties file to:\n"
679 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
681 while ((data = aparser.getValue("fetchfrom")) != null)
683 System.out.println("adding source '" + data + "'");
686 source = new Vector();
688 source.addElement(data);
694 * start a feature fetcher for every alignment frame
698 private static void startFeatureFetching(final Vector dasSources)
700 AlignFrame afs[] = Desktop.getAlignframes();
701 if (afs == null || afs.length == 0)
705 for (int i = 0; i < afs.length; i++)
707 final AlignFrame af = afs[i];
708 SwingUtilities.invokeLater(new Runnable()
713 af.featureSettings_actionPerformed(null);
714 af.featureSettings.fetchDasFeatures(dasSources);
720 private static String checkProtocol(String file)
722 String protocol = jalview.io.FormatAdapter.FILE;
724 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
726 protocol = jalview.io.FormatAdapter.URL;
733 * Notes: this argParser does not distinguish between parameter switches,
734 * parameter values and argument text. If an argument happens to be identical to
735 * a parameter, it will be taken as such (even though it didn't have a '-'
738 * @author Andrew Waterhouse and JBP documented.
745 public ArgsParser(String[] args)
747 vargs = new Vector();
748 for (int i = 0; i < args.length; i++)
750 String arg = args[i].trim();
751 if (arg.charAt(0) == '-')
753 arg = arg.substring(1);
755 vargs.addElement(arg);
760 * check for and remove first occurence of arg+parameter in arglist.
763 * @return return the argument following the given arg if arg was in list.
765 public String getValue(String arg)
767 int index = vargs.indexOf(arg);
771 ret = vargs.elementAt(index + 1).toString();
772 vargs.removeElementAt(index);
773 vargs.removeElementAt(index);
779 * check for and remove first occurence of arg in arglist.
782 * @return true if arg was present in argslist.
784 public boolean contains(String arg)
786 if (vargs.contains(arg))
788 vargs.removeElement(arg);
797 public String nextValue()
799 return vargs.remove(0).toString();