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."
84 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires."
85 + "-noquestionnaire\tTurn off questionnaire check."
86 + "-dasserver nickname=URL\tAdd and enable a das server with given nickname (alphanumeric or underscores only) for retrieval of features for all alignments."
87 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them."
88 + "-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)"
89 + "\n\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
93 Cache.loadProperties(aparser.getValue("props")); // must do this before
96 if (aparser.contains("nodisplay"))
98 System.setProperty("java.awt.headless", "true");
100 if (System.getProperty("java.awt.headless") != null
101 && System.getProperty("java.awt.headless").equals("true"))
109 } catch (java.lang.NoClassDefFoundError error)
111 error.printStackTrace();
113 .println("\nEssential logging libraries not found."
114 + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
118 Desktop desktop = null;
122 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()
123 // UIManager.getCrossPlatformLookAndFeelClassName()
124 // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
125 // "javax.swing.plaf.metal.MetalLookAndFeel"
126 // "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
127 // "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
130 } catch (Exception ex)
135 desktop = new Desktop();
136 desktop.setVisible(true);
137 desktop.discoverer.start();
138 if (!aparser.contains("noquestionnaire"))
140 String url = aparser.getValue("questionnaire");
143 // Start the desktop questionnaire prompter with the specified
145 Cache.log.debug("Starting questionnaire url at " + url);
146 desktop.checkForQuestionnaire(url);
150 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
152 // Start the desktop questionnaire prompter with the specified
155 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
157 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
158 Cache.log.debug("Starting questionnaire with default url: "
160 desktop.checkForQuestionnaire(defurl);
167 String file = null, protocol = null, format = null, data = null;
168 jalview.io.FileLoader fileLoader = new jalview.io.FileLoader();
169 Vector getFeatures = null; // vector of das source nicknames to fetch
172 String groovyscript = null; // script to execute after all loading is
173 // completed one way or another
174 // extract groovy argument and execute if necessary
175 groovyscript = aparser.getValue("groovy");
176 file = aparser.getValue("open");
178 if (file == null && desktop == null)
180 System.out.println("No files to open!");
186 System.out.println("Opening file: " + file);
188 if (!file.startsWith("http://"))
190 if (!(new java.io.File(file)).exists())
192 System.out.println("Can't find " + file);
200 protocol = checkProtocol(file);
202 format = new jalview.io.IdentifyFile().Identify(file, protocol);
204 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
209 System.out.println("error");
213 data = aparser.getValue("colour");
216 data.replaceAll("%20", " ");
218 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
219 .getColour(af.getViewport().getAlignment(), data);
223 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
225 ucs.parseAppletParameter(data);
229 System.out.println("colour is " + data);
233 // Must maintain ability to use the groups flag
234 data = aparser.getValue("groups");
237 af.parseFeaturesFile(data, checkProtocol(data));
238 System.out.println("Added " + data);
240 data = aparser.getValue("features");
243 af.parseFeaturesFile(data, checkProtocol(data));
244 System.out.println("Added " + data);
247 data = aparser.getValue("annotations");
250 af.loadJalviewDataFile(data);
251 System.out.println("Added " + data);
253 data = aparser.getValue("tree");
256 jalview.io.NewickFile fin = null;
259 fin = new jalview.io.NewickFile(data, checkProtocol(data));
262 af.getViewport().setCurrentTree(
263 af.ShowNewickTree(fin, data).getTree());
264 System.out.println("Added tree " + data);
266 } catch (IOException ex)
268 System.err.println("Couldn't add tree " + data);
269 ex.printStackTrace(System.err);
272 getFeatures = checkDasArguments(aparser);
273 if (af != null && getFeatures != null)
275 startFeatureFetching(getFeatures);
276 // need to block until fetching is complete.
277 while (af.operationInProgress())
279 // wait around until fetching is finished.
283 } catch (Exception e)
289 if (groovyscript != null)
291 // Execute the groovy script after we've done all the rendering stuff
292 // and before any images or figures are generated.
293 if (jalview.bin.Cache.groovyJarsPresent())
295 System.out.println("Executing script " + groovyscript);
296 executeGroovyScript(groovyscript, desktop);
301 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
306 String imageName = "unnamed.png";
307 while (aparser.getSize() > 1)
309 format = aparser.nextValue();
310 file = aparser.nextValue();
312 if (format.equalsIgnoreCase("png"))
314 af.createPNG(new java.io.File(file));
315 imageName = (new java.io.File(file)).getName();
316 System.out.println("Creating PNG image: " + file);
319 else if (format.equalsIgnoreCase("imgMap"))
321 af.createImageMap(new java.io.File(file), imageName);
322 System.out.println("Creating image map: " + file);
325 else if (format.equalsIgnoreCase("eps"))
327 System.out.println("Creating EPS file: " + file);
328 af.createEPS(new java.io.File(file));
332 if (af.saveAlignment(file, format))
334 System.out.println("Written alignment in " + format
335 + " format to " + file);
339 System.out.println("Error writing file " + file + " in " + format
345 while (aparser.getSize() > 0)
347 System.out.println("Unknown arg: " + aparser.nextValue());
350 AlignFrame startUpAlframe = null;
351 // We'll only open the default file if the desktop is visible.
353 // ////////////////////
354 if (!headless && file == null
355 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
357 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
358 "http://www.jalview.org/examples/exampleFile_2_3.jar");
362 if (file.indexOf("http:") > -1)
367 if (file.endsWith(".jar"))
373 format = new jalview.io.IdentifyFile().Identify(file, protocol);
376 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
378 getFeatures = checkDasArguments(aparser);
379 // extract groovy arguments before anything else.
381 // Once all loading is done. Retrieve features.
382 if (getFeatures != null)
384 if (startUpAlframe != null)
386 startFeatureFetching(getFeatures);
389 if (groovyscript != null)
391 if (jalview.bin.Cache.groovyJarsPresent())
393 System.out.println("Executing script " + groovyscript);
394 executeGroovyScript(groovyscript, desktop);
399 .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
404 // Once all other stuff is done, execute any groovy scripts (in order)
408 * Locate the given string as a file and pass it to the groovy interpreter.
410 * @param groovyscript
411 * the script to execute
412 * @param jalviewContext
413 * the Jalview Desktop object passed in to the groovy binding
414 * as the 'Jalview' object.
416 private static void executeGroovyScript(String groovyscript,
417 Object jalviewContext)
419 if (jalviewContext == null)
422 .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
425 if (groovyscript.trim().equals("STDIN"))
427 // read from stdin into a tempfile and execute it
430 sfile = File.createTempFile("jalview", "groovy");
431 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
432 new FileOutputStream(sfile)));
433 BufferedReader br = new BufferedReader(
434 new java.io.InputStreamReader(System.in));
436 while ((line = br.readLine()) != null)
438 outfile.write(line + "\n");
444 } catch (Exception ex)
446 System.err.println("Failed to read from STDIN into tempfile "
447 + ((sfile == null) ? "(tempfile wasn't created)" : sfile
449 ex.printStackTrace();
455 sfile = new File(groovyscript);
459 System.err.println("File '" + groovyscript + "' does not exist.");
462 if (!sfile.canRead())
464 System.err.println("File '" + groovyscript + "' cannot be read.");
467 if (sfile.length() < 1)
469 System.err.println("File '" + groovyscript + "' is empty.");
472 boolean success = false;
476 * The following code performs the GroovyScriptEngine invocation using
477 * reflection, and is equivalent to this fragment from the embedding
478 * groovy documentation on the groovy site: <code> import
479 * groovy.lang.Binding; import groovy.util.GroovyScriptEngine;
481 * String[] roots = new String[] { "/my/groovy/script/path" };
482 * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding =
483 * new Binding(); binding.setVariable("input", "world");
484 * gse.run("hello.groovy", binding); </code>
486 ClassLoader cl = jalviewContext.getClass().getClassLoader();
487 Class gbindingc = cl.loadClass("groovy.lang.Binding");
488 Constructor gbcons = gbindingc.getConstructor(null);
489 Object gbinding = gbcons.newInstance(null);
490 java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable",
492 { String.class, Object.class });
493 setvar.invoke(gbinding, new Object[]
494 { "Jalview", jalviewContext });
495 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
496 Constructor gseccons = gsec.getConstructor(new Class[]
497 { URL[].class }); // String[].class });
498 Object gse = gseccons.newInstance(new Object[]
500 { sfile.toURL() } }); // .toString() } });
501 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]
502 { String.class, gbindingc });
503 run.invoke(gse, new Object[]
504 { sfile.getName(), gbinding });
506 } catch (Exception e)
508 System.err.println("Exception Whilst trying to execute file " + sfile
509 + " as a groovy script.");
510 e.printStackTrace(System.err);
513 if (success && groovyscript.equals("STDIN"))
515 // delete temp file that we made - but only if it was successfully
522 * Check commandline for any das server definitions or any fetchfrom switches
524 * @return vector of DAS source nicknames to retrieve from
526 private static Vector checkDasArguments(ArgsParser aparser)
528 Vector source = null;
530 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
531 while ((data = aparser.getValue("dasserver")) != null)
533 String nickname = null;
535 int pos = data.indexOf('=');
538 nickname = data.substring(0, pos);
540 url = data.substring(pos + 1);
541 if (url != null && url.startsWith("http:"))
543 if (nickname == null)
547 if (locsources == null)
555 locsources = locsources + nickname + "|" + url;
557 .println("NOTE! dasserver parameter not yet really supported (got args of "
558 + nickname + "|" + url);
561 source = new Vector();
563 source.addElement(nickname);
565 } // loop until no more server entries are found.
566 if (locsources != null && locsources.indexOf('|') > -1)
568 Cache.log.debug("Setting local source list in properties file to:\n"
570 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
572 while ((data = aparser.getValue("fetchfrom")) != null)
574 System.out.println("adding source '" + data + "'");
577 source = new Vector();
579 source.addElement(data);
585 * start a feature fetcher for every alignment frame
589 private static void startFeatureFetching(final Vector dasSources)
591 AlignFrame afs[] = Desktop.getAlignframes();
592 if (afs == null || afs.length == 0)
596 for (int i = 0; i < afs.length; i++)
598 final AlignFrame af = afs[i];
599 SwingUtilities.invokeLater(new Runnable()
604 af.featureSettings_actionPerformed(null);
605 af.featureSettings.fetchDasFeatures(dasSources);
611 private static String checkProtocol(String file)
613 String protocol = jalview.io.FormatAdapter.FILE;
615 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
617 protocol = jalview.io.FormatAdapter.URL;
624 * Notes: this argParser does not distinguish between parameter switches,
625 * parameter values and argument text. If an argument happens to be identical to
626 * a parameter, it will be taken as such (even though it didn't have a '-'
629 * @author Andrew Waterhouse and JBP documented.
636 public ArgsParser(String[] args)
638 vargs = new Vector();
639 for (int i = 0; i < args.length; i++)
641 String arg = args[i].trim();
642 if (arg.charAt(0) == '-')
644 arg = arg.substring(1);
646 vargs.addElement(arg);
651 * check for and remove first occurence of arg+parameter in arglist.
654 * @return return the argument following the given arg if arg was in list.
656 public String getValue(String arg)
658 int index = vargs.indexOf(arg);
662 ret = vargs.elementAt(index + 1).toString();
663 vargs.removeElementAt(index);
664 vargs.removeElementAt(index);
670 * check for and remove first occurence of arg in arglist.
673 * @return true if arg was present in argslist.
675 public boolean contains(String arg)
677 if (vargs.contains(arg))
679 vargs.removeElement(arg);
688 public String nextValue()
690 return vargs.remove(0).toString();