2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 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 + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments.\n"
87 +"\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
88 +"\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n"
89 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
90 + "-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"
91 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
95 Cache.loadProperties(aparser.getValue("props")); // must do this before
98 if (aparser.contains("nodisplay"))
100 System.setProperty("java.awt.headless", "true");
102 if (System.getProperty("java.awt.headless") != null
103 && System.getProperty("java.awt.headless").equals("true"))
111 } catch (java.lang.NoClassDefFoundError error)
113 error.printStackTrace();
115 .println("\nEssential logging libraries not found."
116 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
120 Desktop desktop = null;
124 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
125 // UIManager.getCrossPlatformLookAndFeelClassName()
126 // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
127 // "javax.swing.plaf.metal.MetalLookAndFeel"
128 // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
129 // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
132 } catch (Exception ex)
137 desktop = new Desktop();
138 desktop.setVisible(true);
139 desktop.discoverer.start();
140 if (!aparser.contains("noquestionnaire"))
142 String url = aparser.getValue("questionnaire");
145 // Start the desktop questionnaire prompter with the specified
147 Cache.log.debug("Starting questionnaire url at " + url);
148 desktop.checkForQuestionnaire(url);
152 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
154 // Start the desktop questionnaire prompter with the specified
157 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
159 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
160 Cache.log.debug("Starting questionnaire with default url: "
162 desktop.checkForQuestionnaire(defurl);
169 String file = null, protocol = null, format = null, data = null;
170 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
171 Vector getFeatures = null; // vector of das source nicknames to fetch
174 String groovyscript = null; // script to execute after all loading is
175 // completed one way or another
176 // extract groovy argument and execute if necessary
177 groovyscript = aparser.getValue("groovy");
178 file = aparser.getValue("open");
180 if (file == null && desktop == null)
182 System.out.println("No files to open!");
188 System.out.println("Opening file: " + file);
190 if (!file.startsWith("http://"))
192 if (!(new java.io.File(file)).exists())
194 System.out.println("Can't find " + file);
202 protocol = checkProtocol(file);
204 format = new jalview.io.IdentifyFile().Identify(file, protocol);
206 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
211 System.out.println("error");
215 data = aparser.getValue("colour");
218 data.replaceAll("%20", " ");
220 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
221 .getColour(af.getViewport().getAlignment(), data);
225 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
227 ucs.parseAppletParameter(data);
231 System.out.println("colour is " + data);
235 // Must maintain ability to use the groups flag
236 data = aparser.getValue("groups");
239 af.parseFeaturesFile(data, checkProtocol(data));
240 System.out.println("Added " + data);
242 data = aparser.getValue("features");
245 af.parseFeaturesFile(data, checkProtocol(data));
246 System.out.println("Added " + data);
249 data = aparser.getValue("annotations");
252 af.loadJalviewDataFile(data);
253 System.out.println("Added " + data);
255 data = aparser.getValue("tree");
258 jalview.io.NewickFile fin = null;
261 fin = new jalview.io.NewickFile(data, checkProtocol(data));
264 af.getViewport().setCurrentTree(
265 af.ShowNewickTree(fin, data).getTree());
266 System.out.println("Added tree " + data);
268 } catch (IOException ex)
270 System.err.println("Couldn't add tree " + data);
271 ex.printStackTrace(System.err);
274 getFeatures = checkDasArguments(aparser);
275 if (af != null && getFeatures != null)
277 startFeatureFetching(getFeatures);
278 // need to block until fetching is complete.
279 while (af.operationInProgress())
281 // wait around until fetching is finished.
285 } catch (Exception e)
291 if (groovyscript != null)
293 // Execute the groovy script after we've done all the rendering stuff
294 // and before any images or figures are generated.
295 if (jalview.bin.Cache.groovyJarsPresent())
297 System.out.println("Executing script " + groovyscript);
298 executeGroovyScript(groovyscript, desktop);
303 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
308 String imageName = "unnamed.png";
309 while (aparser.getSize() > 1)
311 format = aparser.nextValue();
312 file = aparser.nextValue();
314 if (format.equalsIgnoreCase("png"))
316 af.createPNG(new java.io.File(file));
317 imageName = (new java.io.File(file)).getName();
318 System.out.println("Creating PNG image: " + file);
321 else if (format.equalsIgnoreCase("imgMap"))
323 af.createImageMap(new java.io.File(file), imageName);
324 System.out.println("Creating image map: " + file);
327 else if (format.equalsIgnoreCase("eps"))
329 System.out.println("Creating EPS file: " + file);
330 af.createEPS(new java.io.File(file));
334 if (af.saveAlignment(file, format))
336 System.out.println("Written alignment in " + format
337 + " format to " + file);
341 System.out.println("Error writing file " + file + " in " + format
347 while (aparser.getSize() > 0)
349 System.out.println("Unknown arg: " + aparser.nextValue());
352 AlignFrame startUpAlframe = null;
353 // We'll only open the default file if the desktop is visible.
355 // ////////////////////
356 if (!headless && file == null
357 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
359 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
360 "http://www.jalview.org/examples/exampleFile_2_3.jar");
364 if (file.indexOf("http:") > -1)
369 if (file.endsWith(".jar"))
375 format = new jalview.io.IdentifyFile().Identify(file, protocol);
378 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
380 getFeatures = checkDasArguments(aparser);
381 // extract groovy arguments before anything else.
383 // Once all loading is done. Retrieve features.
384 if (getFeatures != null)
386 if (startUpAlframe != null)
388 startFeatureFetching(getFeatures);
391 if (groovyscript != null)
393 if (jalview.bin.Cache.groovyJarsPresent())
395 System.out.println("Executing script " + groovyscript);
396 executeGroovyScript(groovyscript, desktop);
401 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
406 // Once all other stuff is done, execute any groovy scripts (in order)
410 * Locate the given string as a file and pass it to the groovy interpreter.
412 * @param groovyscript
413 * the script to execute
414 * @param jalviewContext
415 * the Jalview Desktop object passed in to the groovy binding
416 * as the 'Jalview' object.
418 private static void executeGroovyScript(String groovyscript,
419 Object jalviewContext)
421 if (jalviewContext == null)
424 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
427 if (groovyscript.trim().equals("STDIN"))
429 // read from stdin into a tempfile and execute it
432 sfile = File.createTempFile("jalview", "groovy");
433 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
434 new FileOutputStream(sfile)));
435 BufferedReader br = new BufferedReader(
436 new java.io.InputStreamReader(System.in));
438 while ((line = br.readLine()) != null)
440 outfile.write(line + "\n");
446 } catch (Exception ex)
448 System.err.println("Failed to read from STDIN into tempfile "
449 + ((sfile == null) ? "(tempfile wasn't created)" : sfile
451 ex.printStackTrace();
457 sfile = new File(groovyscript);
461 System.err.println("File '" + groovyscript + "' does not exist.");
464 if (!sfile.canRead())
466 System.err.println("File '" + groovyscript + "' cannot be read.");
469 if (sfile.length() < 1)
471 System.err.println("File '" + groovyscript + "' is empty.");
474 boolean success = false;
478 * The following code performs the GroovyScriptEngine invocation using
479 * reflection, and is equivalent to this fragment from the embedding
480 * groovy documentation on the groovy site: <code> import
481 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
483 * String[] roots = new String[] { "/my/groovy/script/path" };
484 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
485 * new Binding(); binding.setVariable("input", "world");
486 * gse.run("hello.groovy", binding); </code>
488 ClassLoader cl = jalviewContext.getClass().getClassLoader();
489 Class gbindingc = cl.loadClass("groovy.lang.Binding");
490 Constructor gbcons = gbindingc.getConstructor(null);
491 Object gbinding = gbcons.newInstance(null);
492 java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
494 { String.class, Object.class });
495 setvar.invoke(gbinding, new Object[]
496 { "Jalview", jalviewContext });
497 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
498 Constructor gseccons = gsec.getConstructor(new Class[]
499 { URL[].class }); // String[].class });
500 Object gse = gseccons.newInstance(new Object[]
502 { sfile.toURL() } }); // .toString() } });
503 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
504 { String.class, gbindingc });
505 run.invoke(gse, new Object[]
506 { sfile.getName(), gbinding });
508 } catch (Exception e)
510 System.err.println("Exception Whilst trying to execute file " + sfile
511 + " as a groovy script.");
512 e.printStackTrace(System.err);
515 if (success && groovyscript.equals("STDIN"))
517 // delete temp file that we made - but only if it was successfully
524 * Check commandline for any das server definitions or any fetchfrom switches
526 * @return vector of DAS source nicknames to retrieve from
528 private static Vector checkDasArguments(ArgsParser aparser)
530 Vector source = null;
532 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
533 while ((data = aparser.getValue("dasserver")) != null)
535 String nickname = null;
537 boolean seq=false,feat=true;
538 int pos = data.indexOf('=');
539 // determine capabilities
542 nickname = data.substring(0, pos);
544 url = data.substring(pos + 1);
545 if (url != null && (url.startsWith("http:") || url.startsWith("sequence:http:")))
547 if (nickname == null)
551 if (locsources == null)
559 locsources = locsources + nickname + "|" + url;
561 .println("NOTE! dasserver parameter not yet really supported (got args of "
562 + nickname + "|" + url);
565 source = new Vector();
567 source.addElement(nickname);
569 } // loop until no more server entries are found.
570 if (locsources != null && locsources.indexOf('|') > -1)
572 Cache.log.debug("Setting local source list in properties file to:\n"
574 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
576 while ((data = aparser.getValue("fetchfrom")) != null)
578 System.out.println("adding source '" + data + "'");
581 source = new Vector();
583 source.addElement(data);
589 * start a feature fetcher for every alignment frame
593 private static void startFeatureFetching(final Vector dasSources)
595 AlignFrame afs[] = Desktop.getAlignframes();
596 if (afs == null || afs.length == 0)
600 for (int i = 0; i < afs.length; i++)
602 final AlignFrame af = afs[i];
603 SwingUtilities.invokeLater(new Runnable()
608 af.featureSettings_actionPerformed(null);
609 af.featureSettings.fetchDasFeatures(dasSources);
615 private static String checkProtocol(String file)
617 String protocol = jalview.io.FormatAdapter.FILE;
619 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
621 protocol = jalview.io.FormatAdapter.URL;
628 * Notes: this argParser does not distinguish between parameter switches,
629 * parameter values and argument text. If an argument happens to be identical to
630 * a parameter, it will be taken as such (even though it didn't have a '-'
633 * @author Andrew Waterhouse and JBP documented.
640 public ArgsParser(String[] args)
642 vargs = new Vector();
643 for (int i = 0; i < args.length; i++)
645 String arg = args[i].trim();
646 if (arg.charAt(0) == '-')
648 arg = arg.substring(1);
650 vargs.addElement(arg);
655 * check for and remove first occurence of arg+parameter in arglist.
658 * @return return the argument following the given arg if arg was in list.
660 public String getValue(String arg)
662 int index = vargs.indexOf(arg);
666 ret = vargs.elementAt(index + 1).toString();
667 vargs.removeElementAt(index);
668 vargs.removeElementAt(index);
674 * check for and remove first occurence of arg in arglist.
677 * @return true if arg was present in argslist.
679 public boolean contains(String arg)
681 if (vargs.contains(arg))
683 vargs.removeElement(arg);
692 public String nextValue()
694 return vargs.remove(0).toString();