2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 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 features from
171 String groovyscript = null; // script to execute after all loading is completed one way or another
172 // extract groovy argument and execute if necessary
173 groovyscript = aparser.getValue("groovy");
174 file = aparser.getValue("open");
176 if (file == null && desktop == null)
178 System.out.println("No files to open!");
184 System.out.println("Opening file: " + file);
186 if (!file.startsWith("http://"))
188 if (!(new java.io.File(file)).exists())
190 System.out.println("Can't find " + file);
198 protocol = checkProtocol(file);
200 format = new jalview.io.IdentifyFile().Identify(file, protocol);
202 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
207 System.out.println("error");
211 data = aparser.getValue("colour");
214 data.replaceAll("%20", " ");
216 jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty
217 .getColour(af.getViewport().getAlignment(), data);
221 jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
223 ucs.parseAppletParameter(data);
227 System.out.println("colour is " + data);
231 // Must maintain ability to use the groups flag
232 data = aparser.getValue("groups");
235 af.parseFeaturesFile(data, checkProtocol(data));
236 System.out.println("Added " + data);
238 data = aparser.getValue("features");
241 af.parseFeaturesFile(data, checkProtocol(data));
242 System.out.println("Added " + data);
245 data = aparser.getValue("annotations");
248 af.loadJalviewDataFile(data);
249 System.out.println("Added " + data);
251 data = aparser.getValue("tree");
254 jalview.io.NewickFile fin = null;
257 fin = new jalview.io.NewickFile(data, checkProtocol(data));
260 af.getViewport().setCurrentTree(
261 af.ShowNewickTree(fin, data).getTree());
262 System.out.println("Added tree " + data);
264 } catch (IOException ex)
266 System.err.println("Couldn't add tree " + data);
267 ex.printStackTrace(System.err);
270 getFeatures = checkDasArguments(aparser);
271 if (af != null && getFeatures!=null)
273 startFeatureFetching(getFeatures);
274 // need to block until fetching is complete.
275 while (af.operationInProgress())
277 // wait around until fetching is finished.
280 } catch (Exception e)
286 if (groovyscript!=null)
288 // Execute the groovy script after we've done all the rendering stuff
289 // and before any images or figures are generated.
290 if (jalview.bin.Cache.groovyJarsPresent())
292 System.out.println("Executing script "+groovyscript);
293 executeGroovyScript(groovyscript, desktop);
295 System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
299 String imageName = "unnamed.png";
300 while (aparser.getSize() > 1)
302 format = aparser.nextValue();
303 file = aparser.nextValue();
305 if (format.equalsIgnoreCase("png"))
307 af.createPNG(new java.io.File(file));
308 imageName = (new java.io.File(file)).getName();
309 System.out.println("Creating PNG image: " + file);
312 else if (format.equalsIgnoreCase("imgMap"))
314 af.createImageMap(new java.io.File(file), imageName);
315 System.out.println("Creating image map: " + file);
318 else if (format.equalsIgnoreCase("eps"))
320 System.out.println("Creating EPS file: " + file);
321 af.createEPS(new java.io.File(file));
325 if (af.saveAlignment(file, format))
327 System.out.println("Written alignment in " + format
328 + " format to " + file);
332 System.out.println("Error writing file " + file + " in " + format
338 while (aparser.getSize() > 0)
340 System.out.println("Unknown arg: " + aparser.nextValue());
343 AlignFrame startUpAlframe = null;
344 // We'll only open the default file if the desktop is visible.
346 // ////////////////////
347 if (!headless && file == null
348 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
350 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
351 "http://www.jalview.org/examples/exampleFile_2_3.jar");
355 if (file.indexOf("http:") > -1)
360 if (file.endsWith(".jar"))
366 format = new jalview.io.IdentifyFile().Identify(file, protocol);
369 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
371 getFeatures = checkDasArguments(aparser);
372 // extract groovy arguments before anything else.
374 // Once all loading is done. Retrieve features.
375 if (getFeatures!=null)
377 if (startUpAlframe!=null)
379 startFeatureFetching(getFeatures);
382 if (groovyscript!=null)
384 if (jalview.bin.Cache.groovyJarsPresent())
386 System.out.println("Executing script "+groovyscript);
387 executeGroovyScript(groovyscript, desktop);
389 System.err.println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "+groovyscript);
393 // Once all other stuff is done, execute any groovy scripts (in order)
396 * Locate the given string as a file and pass it to the groovy interpreter.
397 * @param groovyscript the script to execute
398 * @param jalviewContext the Jalview Desktop object passed in to the groovy binding as the 'Jalview' object.
400 private static void executeGroovyScript(String groovyscript, Object jalviewContext)
402 if (jalviewContext==null)
404 System.err.println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled.");
407 if (groovyscript.trim().equals("STDIN"))
409 // read from stdin into a tempfile and execute it
411 sfile = File.createTempFile("jalview", "groovy");
412 PrintWriter outfile = new PrintWriter(new OutputStreamWriter(new FileOutputStream(sfile)));
413 BufferedReader br = new BufferedReader(new java.io.InputStreamReader(System.in));
415 while ((line=br.readLine())!=null)
417 outfile.write(line+"\n");
423 } catch (Exception ex)
425 System.err.println("Failed to read from STDIN into tempfile "+((sfile==null) ? "(tempfile wasn't created)" : sfile.toString()));
426 ex.printStackTrace();
430 sfile = new File(groovyscript);
434 System.err.println("File '"+groovyscript+"' does not exist.");
437 if (!sfile.canRead())
439 System.err.println("File '"+groovyscript+"' cannot be read.");
442 if (sfile.length()<1)
444 System.err.println("File '"+groovyscript+"' is empty.");
447 boolean success = false;
449 /* The following code performs the GroovyScriptEngine invocation using reflection,
450 * and is equivalent to this fragment from the embedding groovy documentation on
453 import groovy.lang.Binding;
454 import groovy.util.GroovyScriptEngine;
456 String[] roots = new String[] { "/my/groovy/script/path" };
457 GroovyScriptEngine gse = new GroovyScriptEngine(roots);
458 Binding binding = new Binding();
459 binding.setVariable("input", "world");
460 gse.run("hello.groovy", binding);
463 ClassLoader cl = jalviewContext.getClass().getClassLoader();
464 Class gbindingc = cl.loadClass("groovy.lang.Binding");
465 Constructor gbcons = gbindingc.getConstructor(null);
466 Object gbinding = gbcons.newInstance(null);
467 java.lang.reflect.Method setvar = gbindingc.getMethod("setVariable", new Class[] { String.class, Object.class} );
468 setvar.invoke(gbinding, new Object[] { "Jalview", jalviewContext});
469 Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine");
470 Constructor gseccons = gsec.getConstructor(new Class[] { URL[].class } ); // String[].class });
471 Object gse = gseccons.newInstance(new Object[] { new URL[] { sfile.toURL() } }); // .toString() } });
472 java.lang.reflect.Method run = gsec.getMethod("run", new Class[]{ String.class, gbindingc });
473 run.invoke(gse, new Object[] { sfile.getName(), gbinding });
475 } catch (Exception e)
477 System.err.println("Exception Whilst trying to execute file "+sfile+" as a groovy script.");
478 e.printStackTrace(System.err);
481 if (success && groovyscript.equals("STDIN"))
483 // delete temp file that we made - but only if it was successfully executed
488 * Check commandline for any das server definitions or any fetchfrom switches
489 * @return vector of DAS source nicknames to retrieve from
491 private static Vector checkDasArguments(ArgsParser aparser)
495 String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
496 while ((data = aparser.getValue("dasserver"))!=null)
498 String nickname = null;
500 int pos = data.indexOf('=');
503 nickname = data.substring(0, pos);
505 url = data.substring(pos + 1);
506 if (url != null && url.startsWith("http:"))
508 if (nickname == null)
512 if (locsources==null)
518 locsources=locsources+nickname+"|"+url;
520 .println("NOTE! dasserver parameter not yet really supported (got args of "
521 + nickname + "|" + url);
524 source = new Vector();
526 source.addElement(nickname);
528 } // loop until no more server entries are found.
529 if (locsources!=null && locsources.indexOf('|')>-1)
531 Cache.log.debug("Setting local source list in properties file to:\n"+locsources);
532 Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
534 while ((data = aparser.getValue("fetchfrom"))!=null)
536 System.out.println("adding source '"+data+"'");
539 source = new Vector();
541 source.addElement(data);
546 * start a feature fetcher for every alignment frame
549 private static void startFeatureFetching(final Vector dasSources)
551 AlignFrame afs[] = Desktop.getAlignframes();
552 if (afs==null || afs.length==0)
556 for (int i = 0; i<afs.length; i++)
558 final AlignFrame af = afs[i];
559 SwingUtilities.invokeLater(new Runnable() {
563 af.featureSettings_actionPerformed(null);
564 af.featureSettings.fetchDasFeatures(dasSources);
570 private static String checkProtocol(String file)
572 String protocol = jalview.io.FormatAdapter.FILE;
574 if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
576 protocol = jalview.io.FormatAdapter.URL;
583 * Notes: this argParser does not distinguish between parameter switches,
584 * parameter values and argument text. If an argument happens to be identical
585 * to a parameter, it will be taken as such (even though it didn't have a '-' prefixing it).
587 * @author Andrew Waterhouse and JBP documented.
594 public ArgsParser(String[] args)
596 vargs = new Vector();
597 for (int i = 0; i < args.length; i++)
599 String arg = args[i].trim();
600 if (arg.charAt(0) == '-')
602 arg = arg.substring(1);
604 vargs.addElement(arg);
608 * check for and remove first occurence of arg+parameter in arglist.
610 * @return return the argument following the given arg if arg was in list.
612 public String getValue(String arg)
614 int index = vargs.indexOf(arg);
618 ret = vargs.elementAt(index + 1).toString();
619 vargs.removeElementAt(index);
620 vargs.removeElementAt(index);
625 * check for and remove first occurence of arg in arglist.
627 * @return true if arg was present in argslist.
629 public boolean contains(String arg)
631 if (vargs.contains(arg))
633 vargs.removeElement(arg);
642 public String nextValue()
644 return vargs.remove(0).toString();