2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import java.io.BufferedReader;
25 import java.io.FileOutputStream;
26 import java.io.IOException;
27 import java.io.InputStreamReader;
28 import java.io.OutputStreamWriter;
29 import java.io.PrintWriter;
30 import java.net.MalformedURLException;
32 import java.net.URISyntaxException;
34 import java.security.AllPermission;
35 import java.security.CodeSource;
36 import java.security.PermissionCollection;
37 import java.security.Permissions;
38 import java.security.Policy;
39 import java.util.HashMap;
41 import java.util.Vector;
43 import javax.swing.LookAndFeel;
44 import javax.swing.UIManager;
46 import com.threerings.getdown.util.LaunchUtil;
48 import groovy.lang.Binding;
49 import groovy.util.GroovyScriptEngine;
50 import jalview.ext.so.SequenceOntology;
51 import jalview.gui.AlignFrame;
52 import jalview.gui.Desktop;
53 import jalview.gui.PromptUserConfig;
54 import jalview.io.AppletFormatAdapter;
55 import jalview.io.BioJsHTMLOutput;
56 import jalview.io.DataSourceType;
57 import jalview.io.FileFormat;
58 import jalview.io.FileFormatException;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileLoader;
61 import jalview.io.HtmlSvgOutput;
62 import jalview.io.IdentifyFile;
63 import jalview.io.NewickFile;
64 import jalview.io.gff.SequenceOntologyFactory;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.ColourSchemeProperty;
67 import jalview.util.MessageManager;
68 import jalview.util.Platform;
69 import jalview.ws.jws2.Jws2Discoverer;
72 * Main class for Jalview Application <br>
74 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
77 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
78 * jalview.bin.Jalview jalview.bin.Jalview
80 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
81 * embellish '*' to e.g. '*.jar')
89 * singleton instance of this class
91 private static Jalview instance;
93 private Desktop desktop;
95 public static AlignFrame currentAlignFrame;
99 // grab all the rights we can the JVM
100 Policy.setPolicy(new Policy()
103 public PermissionCollection getPermissions(CodeSource codesource)
105 Permissions perms = new Permissions();
106 perms.add(new AllPermission());
111 public void refresh()
118 * keep track of feature fetching tasks.
126 * TODO: generalise to track all jalview events to orchestrate batch processing
130 private int queued = 0;
132 private int running = 0;
134 public FeatureFetcher()
139 public void addFetcher(final AlignFrame af,
140 final Vector<String> dasSources)
142 final long id = System.currentTimeMillis();
144 final FeatureFetcher us = this;
145 new Thread(new Runnable()
157 af.setProgressBar(MessageManager
158 .getString("status.das_features_being_retrived"), id);
159 af.featureSettings_actionPerformed(null);
160 af.setProgressBar(null, id);
169 public synchronized boolean allFinished()
171 return queued == 0 && running == 0;
176 public static Jalview getInstance()
182 * main class for Jalview application
185 * open <em>filename</em>
187 public static void main(String[] args)
189 instance = new Jalview();
190 instance.doMain(args);
196 void doMain(String[] args)
198 System.setSecurityManager(null);
200 .println("Java version: " + System.getProperty("java.version"));
201 System.out.println("Java Home: " + System.getProperty("java.home"));
202 System.out.println(System.getProperty("os.arch") + " "
203 + System.getProperty("os.name") + " "
204 + System.getProperty("os.version"));
205 String val = System.getProperty("sys.install4jVersion");
208 System.out.println("Install4j version: " + val);
210 val = System.getProperty("installer_template_version");
213 System.out.println("Install4j template version: " + val);
215 val = System.getProperty("launcher_version");
218 System.out.println("Launcher version: " + val);
221 // report Jalview version
222 Cache.loadBuildProperties(true);
224 ArgsParser aparser = new ArgsParser(args);
225 boolean headless = false;
227 if (aparser.contains("help") || aparser.contains("h"))
232 if (aparser.contains("nodisplay") || aparser.contains("nogui")
233 || aparser.contains("headless"))
235 System.setProperty("java.awt.headless", "true");
238 String usrPropsFile = aparser.getValue("props");
239 Cache.loadProperties(usrPropsFile); // must do this before
240 if (usrPropsFile != null)
243 "CMD [-props " + usrPropsFile + "] executed successfully!");
248 final String jabawsUrl = aparser.getValue("jabaws");
249 if (jabawsUrl != null)
253 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
255 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
256 } catch (MalformedURLException e)
259 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
263 String defs = aparser.getValue("setprop");
266 int p = defs.indexOf('=');
269 System.err.println("Ignoring invalid setprop argument : " + defs);
273 System.out.println("Executing setprop argument: " + defs);
274 // DISABLED FOR SECURITY REASONS
275 // TODO: add a property to allow properties to be overriden by cli args
276 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
278 defs = aparser.getValue("setprop");
280 if (System.getProperty("java.awt.headless") != null
281 && System.getProperty("java.awt.headless").equals("true"))
285 System.setProperty("http.agent",
286 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
290 } catch (NoClassDefFoundError error)
292 error.printStackTrace();
293 System.out.println("\nEssential logging libraries not found."
294 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
302 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
303 } catch (Exception ex)
305 System.err.println("Unexpected Look and Feel Exception");
306 ex.printStackTrace();
308 if (Platform.isAMac())
311 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
313 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
315 System.setProperty("apple.laf.useScreenMenuBar", "true");
316 if (lookAndFeel != null)
320 UIManager.setLookAndFeel(lookAndFeel);
321 } catch (Throwable e)
324 "Failed to set QuaQua look and feel: " + e.toString());
327 if (lookAndFeel == null
328 || !(lookAndFeel.getClass().isAssignableFrom(
329 UIManager.getLookAndFeel().getClass()))
330 || !UIManager.getLookAndFeel().getClass().toString()
331 .toLowerCase().contains("quaqua"))
336 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
337 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
338 } catch (Throwable e)
341 "Failed to reset look and feel: " + e.toString());
347 * configure 'full' SO model if preferences say to, else use the default (SO
350 if (Cache.getDefault("USE_FULL_SO", true))
352 SequenceOntologyFactory.setInstance(new SequenceOntology());
358 desktop = new Desktop();
359 desktop.setInBatchMode(true); // indicate we are starting up
363 JalviewTaskbar.setTaskbar(this);
364 } catch (Exception e)
366 System.out.println("Cannot set Taskbar");
367 // e.printStackTrace();
368 } catch (Throwable t)
370 System.out.println("Cannot set Taskbar");
371 // t.printStackTrace();
374 desktop.setVisible(true);
375 desktop.startServiceDiscovery();
376 if (!aparser.contains("nousagestats"))
378 startUsageStats(desktop);
382 System.err.println("CMD [-nousagestats] executed successfully!");
385 if (!aparser.contains("noquestionnaire"))
387 String url = aparser.getValue("questionnaire");
390 // Start the desktop questionnaire prompter with the specified
392 Cache.log.debug("Starting questionnaire url at " + url);
393 desktop.checkForQuestionnaire(url);
395 "CMD questionnaire[-" + url + "] executed successfully!");
399 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
401 // Start the desktop questionnaire prompter with the specified
404 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
406 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
408 "Starting questionnaire with default url: " + defurl);
409 desktop.checkForQuestionnaire(defurl);
415 System.err.println("CMD [-noquestionnaire] executed successfully!");
418 if (!aparser.contains("nonews"))
420 desktop.checkForNews();
423 BioJsHTMLOutput.updateBioJS();
426 // Move any new getdown-launcher-new.jar into place over old
427 // getdown-launcher.jar
428 String appdirString = System.getProperty("getdownappdir");
429 if (appdirString != null && appdirString.length() > 0)
431 final File appdir = new File(appdirString);
437 LaunchUtil.upgradeGetdown(
438 new File(appdir, "getdown-launcher-old.jar"),
439 new File(appdir, "getdown-launcher.jar"),
440 new File(appdir, "getdown-launcher-new.jar"));
445 String file = null, data = null;
446 FileFormatI format = null;
447 DataSourceType protocol = null;
448 FileLoader fileLoader = new FileLoader(!headless);
450 String groovyscript = null; // script to execute after all loading is
451 // completed one way or another
452 // extract groovy argument and execute if necessary
453 groovyscript = aparser.getValue("groovy", true);
454 file = aparser.getValue("open", true);
456 if (file == null && desktop == null)
458 System.out.println("No files to open!");
462 // Finally, deal with the remaining input data.
467 desktop.setProgressBar(
469 .getString("status.processing_commandline_args"),
470 progress = System.currentTimeMillis());
472 System.out.println("CMD [-open " + file + "] executed successfully!");
474 if (!file.startsWith("http://"))
476 if (!(new File(file)).exists())
478 System.out.println("Can't find " + file);
486 protocol = AppletFormatAdapter.checkProtocol(file);
490 format = new IdentifyFile().identify(file, protocol);
491 } catch (FileFormatException e1)
496 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
500 System.out.println("error");
504 setCurrentAlignFrame(af);
505 data = aparser.getValue("colour", true);
508 data.replaceAll("%20", " ");
510 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
511 af.getViewport(), af.getViewport().getAlignment(), data);
516 "CMD [-color " + data + "] executed successfully!");
521 // Must maintain ability to use the groups flag
522 data = aparser.getValue("groups", true);
525 af.parseFeaturesFile(data,
526 AppletFormatAdapter.checkProtocol(data));
527 // System.out.println("Added " + data);
529 "CMD groups[-" + data + "] executed successfully!");
531 data = aparser.getValue("features", true);
534 af.parseFeaturesFile(data,
535 AppletFormatAdapter.checkProtocol(data));
536 // System.out.println("Added " + data);
538 "CMD [-features " + data + "] executed successfully!");
541 data = aparser.getValue("annotations", true);
544 af.loadJalviewDataFile(data, null, null, null);
545 // System.out.println("Added " + data);
547 "CMD [-annotations " + data + "] executed successfully!");
549 // set or clear the sortbytree flag.
550 if (aparser.contains("sortbytree"))
552 af.getViewport().setSortByTree(true);
553 if (af.getViewport().getSortByTree())
555 System.out.println("CMD [-sortbytree] executed successfully!");
558 if (aparser.contains("no-annotation"))
560 af.getViewport().setShowAnnotation(false);
561 if (!af.getViewport().isShowAnnotation())
563 System.out.println("CMD no-annotation executed successfully!");
566 if (aparser.contains("nosortbytree"))
568 af.getViewport().setSortByTree(false);
569 if (!af.getViewport().getSortByTree())
572 .println("CMD [-nosortbytree] executed successfully!");
575 data = aparser.getValue("tree", true);
581 "CMD [-tree " + data + "] executed successfully!");
582 NewickFile nf = new NewickFile(data,
583 AppletFormatAdapter.checkProtocol(data));
585 .setCurrentTree(af.showNewickTree(nf, data).getTree());
586 } catch (IOException ex)
588 System.err.println("Couldn't add tree " + data);
589 ex.printStackTrace(System.err);
592 // TODO - load PDB structure(s) to alignment JAL-629
593 // (associate with identical sequence in alignment, or a specified
595 if (groovyscript != null)
597 // Execute the groovy script after we've done all the rendering stuff
598 // and before any images or figures are generated.
599 System.out.println("Executing script " + groovyscript);
600 executeGroovyScript(groovyscript, af);
601 System.out.println("CMD groovy[" + groovyscript
602 + "] executed successfully!");
605 String imageName = "unnamed.png";
606 while (aparser.getSize() > 1)
608 String outputFormat = aparser.nextValue();
609 file = aparser.nextValue();
611 if (outputFormat.equalsIgnoreCase("png"))
613 af.createPNG(new File(file));
614 imageName = (new File(file)).getName();
615 System.out.println("Creating PNG image: " + file);
618 else if (outputFormat.equalsIgnoreCase("svg"))
620 File imageFile = new File(file);
621 imageName = imageFile.getName();
622 af.createSVG(imageFile);
623 System.out.println("Creating SVG image: " + file);
626 else if (outputFormat.equalsIgnoreCase("html"))
628 File imageFile = new File(file);
629 imageName = imageFile.getName();
630 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
631 htmlSVG.exportHTML(file);
633 System.out.println("Creating HTML image: " + file);
636 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
640 System.err.println("The output html file must not be null");
645 BioJsHTMLOutput.refreshVersionInfo(
646 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
647 } catch (URISyntaxException e)
651 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
652 bjs.exportHTML(file);
654 .println("Creating BioJS MSA Viwer HTML file: " + file);
657 else if (outputFormat.equalsIgnoreCase("imgMap"))
659 af.createImageMap(new File(file), imageName);
660 System.out.println("Creating image map: " + file);
663 else if (outputFormat.equalsIgnoreCase("eps"))
665 File outputFile = new File(file);
667 "Creating EPS file: " + outputFile.getAbsolutePath());
668 af.createEPS(outputFile);
672 if (af.saveAlignment(file, format))
674 System.out.println("Written alignment in " + format
675 + " format to " + file);
679 System.out.println("Error writing file " + file + " in "
680 + format + " format!!");
685 while (aparser.getSize() > 0)
687 System.out.println("Unknown arg: " + aparser.nextValue());
691 AlignFrame startUpAlframe = null;
692 // We'll only open the default file if the desktop is visible.
694 // ////////////////////
696 if (!headless && file == null
697 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
699 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
700 jalview.bin.Cache.getDefault("www.jalview.org",
701 "http://www.jalview.org")
702 + "/examples/exampleFile_2_7.jar");
704 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
706 // hardwire upgrade of the startup file
707 file.replace("_2_3.jar", "_2_7.jar");
708 // and remove the stale setting
709 jalview.bin.Cache.removeProperty("STARTUP_FILE");
712 protocol = DataSourceType.FILE;
714 if (file.indexOf("http:") > -1)
716 protocol = DataSourceType.URL;
719 if (file.endsWith(".jar"))
721 format = FileFormat.Jalview;
727 format = new IdentifyFile().identify(file, protocol);
728 } catch (FileFormatException e)
734 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
736 // extract groovy arguments before anything else.
739 // Once all other stuff is done, execute any groovy scripts (in order)
740 if (groovyscript != null)
742 if (Cache.groovyJarsPresent())
744 System.out.println("Executing script " + groovyscript);
745 executeGroovyScript(groovyscript, startUpAlframe);
750 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
754 // and finally, turn off batch mode indicator - if the desktop still exists
759 desktop.setProgressBar(null, progress);
761 desktop.setInBatchMode(false);
765 private static void showUsage()
768 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
769 + "-nodisplay\tRun Jalview without User Interface.\n"
770 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
771 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
772 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
773 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
774 + "-features FILE\tUse the given file to mark features on the alignment.\n"
775 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
776 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
777 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
778 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
779 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
780 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
781 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
782 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
783 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
784 + "-png FILE\tCreate PNG image FILE from alignment.\n"
785 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
786 + "-html FILE\tCreate HTML file from alignment.\n"
787 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
788 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
789 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
790 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
791 + "-noquestionnaire\tTurn off questionnaire check.\n"
792 + "-nonews\tTurn off check for Jalview news.\n"
793 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
794 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
796 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
797 // after all other properties files have been read\n\t
798 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
799 // passed in correctly)"
800 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
801 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
802 + "-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"
803 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
806 private static void startUsageStats(final Desktop desktop)
809 * start a User Config prompt asking if we can log usage statistics.
811 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
812 "USAGESTATS", "Jalview Usage Statistics",
813 "Do you want to help make Jalview better by enabling "
814 + "the collection of usage statistics with Google Analytics ?"
815 + "\n\n(you can enable or disable usage tracking in the preferences)",
822 "Initialising googletracker for usage stats.");
823 Cache.initGoogleTracker();
824 Cache.log.debug("Tracking enabled.");
831 Cache.log.debug("Not enabling Google Tracking.");
834 desktop.addDialogThread(prompter);
838 * Locate the given string as a file and pass it to the groovy interpreter.
840 * @param groovyscript
841 * the script to execute
842 * @param jalviewContext
843 * the Jalview Desktop object passed in to the groovy binding as the
846 private void executeGroovyScript(String groovyscript, AlignFrame af)
849 * for scripts contained in files
856 if (groovyscript.trim().equals("STDIN"))
858 // read from stdin into a tempfile and execute it
861 tfile = File.createTempFile("jalview", "groovy");
862 PrintWriter outfile = new PrintWriter(
863 new OutputStreamWriter(new FileOutputStream(tfile)));
864 BufferedReader br = new BufferedReader(
865 new InputStreamReader(System.in));
867 while ((line = br.readLine()) != null)
869 outfile.write(line + "\n");
875 } catch (Exception ex)
877 System.err.println("Failed to read from STDIN into tempfile "
878 + ((tfile == null) ? "(tempfile wasn't created)"
879 : tfile.toString()));
880 ex.printStackTrace();
885 sfile = tfile.toURI().toURL();
886 } catch (Exception x)
889 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
899 sfile = new URI(groovyscript).toURL();
900 } catch (Exception x)
902 tfile = new File(groovyscript);
905 System.err.println("File '" + groovyscript + "' does not exist.");
908 if (!tfile.canRead())
910 System.err.println("File '" + groovyscript + "' cannot be read.");
913 if (tfile.length() < 1)
915 System.err.println("File '" + groovyscript + "' is empty.");
920 sfile = tfile.getAbsoluteFile().toURI().toURL();
921 } catch (Exception ex)
923 System.err.println("Failed to create a file URL for "
924 + tfile.getAbsoluteFile());
931 Map<String, java.lang.Object> vbinding = new HashMap<>();
932 vbinding.put("Jalview", this);
935 vbinding.put("currentAlFrame", af);
937 Binding gbinding = new Binding(vbinding);
938 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
939 gse.run(sfile.toString(), gbinding);
940 if ("STDIN".equals(groovyscript))
942 // delete temp file that we made -
943 // only if it was successfully executed
946 } catch (Exception e)
948 System.err.println("Exception Whilst trying to execute file " + sfile
949 + " as a groovy script.");
950 e.printStackTrace(System.err);
955 public static boolean isHeadlessMode()
957 String isheadless = System.getProperty("java.awt.headless");
958 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
965 public AlignFrame[] getAlignFrames()
967 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
968 : Desktop.getAlignFrames();
973 * Quit method delegates to Desktop.quit - unless running in headless mode
974 * when it just ends the JVM
988 public static AlignFrame getCurrentAlignFrame()
990 return Jalview.currentAlignFrame;
993 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
995 Jalview.currentAlignFrame = currentAlignFrame;