2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
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;
34 import jalview.io.AppletFormatAdapter;
37 * Main class for Jalview Application <br>
39 * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
48 * main class for Jalview application
51 * open <em>filename</em>
53 public static void main(String[] args)
55 System.out.println("Java version: "
56 + System.getProperty("java.version"));
57 System.out.println(System.getProperty("os.arch") + " "
58 + System.getProperty("os.name") + " "
59 + System.getProperty("os.version"));
61 ArgsParser aparser = new ArgsParser(args);
62 boolean headless = false;
64 if (aparser.contains("help") || aparser.contains("h"))
67 .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
68 + "-nodisplay\tRun Jalview without User Interface.\n"
69 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
70 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
71 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
72 + "-features FILE\tUse the given file to mark features on the alignment.\n"
73 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
74 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
75 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
76 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
77 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
78 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
79 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
80 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
81 + "-png FILE\tCreate PNG image FILE from alignment.\n"
82 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
83 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
84 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
85 + "-noquestionnaire\tTurn off questionnaire check.\n"
86 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
87 + "-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"
88 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
89 + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed\n\t\t(if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
90 + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
94 Cache.loadProperties(aparser.getValue("props")); // must do this before
97 if (aparser.contains("nodisplay"))
99 System.setProperty("java.awt.headless", "true");
101 if (System.getProperty("java.awt.headless") != null
102 && System.getProperty("java.awt.headless").equals("true"))
110 } catch (java.lang.NoClassDefFoundError error)
112 error.printStackTrace();
114 .println("\nEssential logging libraries not found."
115 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
119 Desktop desktop = null;
123 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
124 // UIManager.getCrossPlatformLookAndFeelClassName()
125 // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
126 // "javax.swing.plaf.metal.MetalLookAndFeel"
127 // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
128 // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
131 } catch (Exception ex)
136 desktop = new Desktop();
137 desktop.setVisible(true);
138 desktop.discoverer.start();
139 if (!aparser.contains("nousagestats")) {
140 startUsageStats(desktop);
142 if (!aparser.contains("noquestionnaire"))
144 String url = aparser.getValue("questionnaire");
147 // Start the desktop questionnaire prompter with the specified
149 Cache.log.debug("Starting questionnaire url at " + url);
150 desktop.checkForQuestionnaire(url);
154 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
156 // Start the desktop questionnaire prompter with the specified
159 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
161 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
162 Cache.log.debug("Starting questionnaire with default url: "
164 desktop.checkForQuestionnaire(defurl);
171 String file = null, protocol = null, format = null, data = null;
172 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
173 Vector getFeatures = null; // vector of das source nicknames to fetch
176 String groovyscript = null; // script to execute after all loading is
177 // completed one way or another
178 // extract groovy argument and execute if necessary
179 groovyscript = aparser.getValue("groovy");
180 file = aparser.getValue("open");
182 if (file == null && desktop == null)
184 System.out.println("No files to open!");
190 System.out.println("Opening file: " + file);
192 if (!file.startsWith("http://"))
194 if (!(new java.io.File(file)).exists())
196 System.out.println("Can't find " + file);
204 protocol = checkProtocol(file);
206 format = new jalview.io.IdentifyFile().Identify(file, protocol);
208 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
213 System.out.println("error");
217 data = aparser.getValue("colour");
220 data.replaceAll("%20", " ");
222 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
223 .getColour(af.getViewport().getAlignment(), data);
227 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
229 ucs.parseAppletParameter(data);
233 System.out.println("colour is " + data);
237 // Must maintain ability to use the groups flag
238 data = aparser.getValue("groups");
241 af.parseFeaturesFile(data, checkProtocol(data));
242 System.out.println("Added " + data);
244 data = aparser.getValue("features");
247 af.parseFeaturesFile(data, checkProtocol(data));
248 System.out.println("Added " + data);
251 data = aparser.getValue("annotations");
254 af.loadJalviewDataFile(data);
255 System.out.println("Added " + data);
257 data = aparser.getValue("tree");
260 jalview.io.NewickFile fin = null;
263 fin = new jalview.io.NewickFile(data, checkProtocol(data));
266 af.getViewport().setCurrentTree(
267 af.ShowNewickTree(fin, data).getTree());
268 System.out.println("Added tree " + data);
270 } catch (IOException ex)
272 System.err.println("Couldn't add tree " + data);
273 ex.printStackTrace(System.err);
276 getFeatures = checkDasArguments(aparser);
277 if (af != null && getFeatures != null)
279 startFeatureFetching(getFeatures);
280 // need to block until fetching is complete.
281 while (af.operationInProgress())
283 // wait around until fetching is finished.
287 } catch (Exception e)
293 if (groovyscript != null)
295 // Execute the groovy script after we've done all the rendering stuff
296 // and before any images or figures are generated.
297 if (jalview.bin.Cache.groovyJarsPresent())
299 System.out.println("Executing script " + groovyscript);
300 executeGroovyScript(groovyscript, desktop);
305 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
310 String imageName = "unnamed.png";
311 while (aparser.getSize() > 1)
313 format = aparser.nextValue();
314 file = aparser.nextValue();
316 if (format.equalsIgnoreCase("png"))
318 af.createPNG(new java.io.File(file));
319 imageName = (new java.io.File(file)).getName();
320 System.out.println("Creating PNG image: " + file);
323 else if (format.equalsIgnoreCase("imgMap"))
325 af.createImageMap(new java.io.File(file), imageName);
326 System.out.println("Creating image map: " + file);
329 else if (format.equalsIgnoreCase("eps"))
331 System.out.println("Creating EPS file: " + file);
332 af.createEPS(new java.io.File(file));
336 if (af.saveAlignment(file, format))
338 System.out.println("Written alignment in " + format
339 + " format to " + file);
343 System.out.println("Error writing file " + file + " in " + format
349 while (aparser.getSize() > 0)
351 System.out.println("Unknown arg: " + aparser.nextValue());
354 AlignFrame startUpAlframe = null;
355 // We'll only open the default file if the desktop is visible.
357 // ////////////////////
358 if (!headless && file == null
359 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
361 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
362 "http://www.jalview.org/examples/exampleFile_2_3.jar");
366 if (file.indexOf("http:") > -1)
371 if (file.endsWith(".jar"))
377 format = new jalview.io.IdentifyFile().Identify(file, protocol);
380 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
382 getFeatures = checkDasArguments(aparser);
383 // extract groovy arguments before anything else.
385 // Once all loading is done. Retrieve features.
386 if (getFeatures != null)
388 if (startUpAlframe != null)
390 startFeatureFetching(getFeatures);
393 if (groovyscript != null)
395 if (jalview.bin.Cache.groovyJarsPresent())
397 System.out.println("Executing script " + groovyscript);
398 executeGroovyScript(groovyscript, desktop);
403 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
408 // Once all other stuff is done, execute any groovy scripts (in order)
411 private static void startUsageStats(final Desktop desktop)
414 * start a User Config prompt asking if we can log usage statistics.
416 jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig(desktop.desktop,"USAGESTATS", "Jalview Usage Statistics",
417 "Do you want to help make Jalview better by enabling "
418 +"the collection of usage statistics with Google Analytics ?"
419 +"\n\n(if you press cancel, you will be asked again next time)",
423 Cache.log.info("Initialising googletracker for usage stats.");
424 Cache.initGoogleTracker();
425 Cache.log.debug("Tracking enabled.");
430 Cache.log.info("Not enabling Google Tracking.");
433 SwingUtilities.invokeLater(prompter);
437 * Locate the given string as a file and pass it to the groovy interpreter.
439 * @param groovyscript
440 * the script to execute
441 * @param jalviewContext
442 * the Jalview Desktop object passed in to the groovy binding
443 * as the 'Jalview' object.
445 private static void executeGroovyScript(String groovyscript,
446 Object jalviewContext)
448 if (jalviewContext == null)
451 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
454 if (groovyscript.trim().equals("STDIN"))
456 // read from stdin into a tempfile and execute it
459 sfile = File.createTempFile("jalview", "groovy");
460 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
461 new FileOutputStream(sfile)));
462 BufferedReader br = new BufferedReader(
463 new java.io.InputStreamReader(System.in));
465 while ((line = br.readLine()) != null)
467 outfile.write(line + "\n");
473 } catch (Exception ex)
475 System.err.println("Failed to read from STDIN into tempfile "
476 + ((sfile == null) ? "(tempfile wasn't created)" : sfile
478 ex.printStackTrace();
484 sfile = new File(groovyscript);
488 System.err.println("File '" + groovyscript + "' does not exist.");
491 if (!sfile.canRead())
493 System.err.println("File '" + groovyscript + "' cannot be read.");
496 if (sfile.length() < 1)
498 System.err.println("File '" + groovyscript + "' is empty.");
501 boolean success = false;
505 * The following code performs the GroovyScriptEngine invocation using
506 * reflection, and is equivalent to this fragment from the embedding
507 * groovy documentation on the groovy site: <code> import
508 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
510 * String[] roots = new String[] { "/my/groovy/script/path" };
511 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
512 * new Binding(); binding.setVariable("input", "world");
513 * gse.run("hello.groovy", binding); </code>
515 ClassLoader cl = jalviewContext.getClass().getClassLoader();
516 Class gbindingc = cl.loadClass("groovy.lang.Binding");
517 Constructor gbcons = gbindingc.getConstructor(null);
518 Object gbinding = gbcons.newInstance(null);
519 java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
521 { String.class, Object.class });
522 setvar.invoke(gbinding, new Object[]
523 { "Jalview", jalviewContext });
524 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
525 Constructor gseccons = gsec.getConstructor(new Class[]
526 { URL[].class }); // String[].class });
527 Object gse = gseccons.newInstance(new Object[]
529 { sfile.toURL() } }); // .toString() } });
530 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
531 { String.class, gbindingc });
532 run.invoke(gse, new Object[]
533 { sfile.getName(), gbinding });
535 } catch (Exception e)
537 System.err.println("Exception Whilst trying to execute file " + sfile
538 + " as a groovy script.");
539 e.printStackTrace(System.err);
542 if (success && groovyscript.equals("STDIN"))
544 // delete temp file that we made - but only if it was successfully
551 * Check commandline for any das server definitions or any fetchfrom switches
553 * @return vector of DAS source nicknames to retrieve from
555 private static Vector checkDasArguments(ArgsParser aparser)
557 Vector source = null;
559 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
560 while ((data = aparser.getValue("dasserver")) != null)
562 String nickname = null;
564 int pos = data.indexOf('=');
567 nickname = data.substring(0, pos);
569 url = data.substring(pos + 1);
570 if (url != null && url.startsWith("http:"))
572 if (nickname == null)
576 if (locsources == null)
584 locsources = locsources + nickname + "|" + url;
586 .println("NOTE! dasserver parameter not yet really supported (got args of "
587 + nickname + "|" + url);
590 source = new Vector();
592 source.addElement(nickname);
594 } // loop until no more server entries are found.
595 if (locsources != null && locsources.indexOf('|') > -1)
597 Cache.log.debug("Setting local source list in properties file to:\n"
599 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
601 while ((data = aparser.getValue("fetchfrom")) != null)
603 System.out.println("adding source '" + data + "'");
606 source = new Vector();
608 source.addElement(data);
614 * start a feature fetcher for every alignment frame
618 private static void startFeatureFetching(final Vector dasSources)
620 AlignFrame afs[] = Desktop.getAlignframes();
621 if (afs == null || afs.length == 0)
625 for (int i = 0; i < afs.length; i++)
627 final AlignFrame af = afs[i];
628 SwingUtilities.invokeLater(new Runnable()
633 af.featureSettings_actionPerformed(null);
634 af.featureSettings.fetchDasFeatures(dasSources);
640 private static String checkProtocol(String file)
642 String protocol = jalview.io.FormatAdapter.FILE;
644 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
646 protocol = jalview.io.FormatAdapter.URL;
653 * Notes: this argParser does not distinguish between parameter switches,
654 * parameter values and argument text. If an argument happens to be identical to
655 * a parameter, it will be taken as such (even though it didn't have a '-'
658 * @author Andrew Waterhouse and JBP documented.
665 public ArgsParser(String[] args)
667 vargs = new Vector();
668 for (int i = 0; i < args.length; i++)
670 String arg = args[i].trim();
671 if (arg.charAt(0) == '-')
673 arg = arg.substring(1);
675 vargs.addElement(arg);
680 * check for and remove first occurence of arg+parameter in arglist.
683 * @return return the argument following the given arg if arg was in list.
685 public String getValue(String arg)
687 int index = vargs.indexOf(arg);
691 ret = vargs.elementAt(index + 1).toString();
692 vargs.removeElementAt(index);
693 vargs.removeElementAt(index);
699 * check for and remove first occurence of arg in arglist.
702 * @return true if arg was present in argslist.
704 public boolean contains(String arg)
706 if (vargs.contains(arg))
708 vargs.removeElement(arg);
717 public String nextValue()
719 return vargs.remove(0).toString();