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 jalview.ext.so.SequenceOntology;
24 import jalview.gui.AlignFrame;
25 import jalview.gui.Desktop;
26 import jalview.gui.PromptUserConfig;
27 import jalview.io.AppletFormatAdapter;
28 import jalview.io.BioJsHTMLOutput;
29 import jalview.io.DataSourceType;
30 import jalview.io.FileFormat;
31 import jalview.io.FileFormatException;
32 import jalview.io.FileFormatI;
33 import jalview.io.FileLoader;
34 import jalview.io.HtmlSvgOutput;
35 import jalview.io.IdentifyFile;
36 import jalview.io.NewickFile;
37 import jalview.io.gff.SequenceOntologyFactory;
38 import jalview.schemes.ColourSchemeI;
39 import jalview.schemes.ColourSchemeProperty;
40 import jalview.util.MessageManager;
41 import jalview.util.Platform;
42 import jalview.ws.jws2.Jws2Discoverer;
44 import java.io.BufferedReader;
46 import java.io.FileOutputStream;
47 import java.io.IOException;
48 import java.io.InputStreamReader;
49 import java.io.OutputStreamWriter;
50 import java.io.PrintWriter;
51 import java.net.MalformedURLException;
53 import java.net.URISyntaxException;
55 import java.security.AllPermission;
56 import java.security.CodeSource;
57 import java.security.PermissionCollection;
58 import java.security.Permissions;
59 import java.security.Policy;
60 import java.util.HashMap;
62 import java.util.Vector;
64 import javax.swing.LookAndFeel;
65 import javax.swing.UIManager;
67 import com.threerings.getdown.util.LaunchUtil;
69 import groovy.lang.Binding;
70 import groovy.util.GroovyScriptEngine;
73 * Main class for Jalview Application <br>
75 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
78 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
79 * jalview.bin.Jalview jalview.bin.Jalview
81 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
82 * embellish '*' to e.g. '*.jar')
90 * singleton instance of this class
92 private static Jalview instance;
94 private Desktop desktop;
96 public static AlignFrame currentAlignFrame;
100 // grab all the rights we can the JVM
101 Policy.setPolicy(new Policy()
104 public PermissionCollection getPermissions(CodeSource codesource)
106 Permissions perms = new Permissions();
107 perms.add(new AllPermission());
112 public void refresh()
119 * keep track of feature fetching tasks.
127 * TODO: generalise to track all jalview events to orchestrate batch
131 private int queued = 0;
133 private int running = 0;
135 public FeatureFetcher()
140 public void addFetcher(final AlignFrame af,
141 final Vector<String> dasSources)
143 final long id = System.currentTimeMillis();
145 final FeatureFetcher us = this;
146 new Thread(new Runnable()
158 af.setProgressBar(MessageManager
159 .getString("status.das_features_being_retrived"), id);
160 af.featureSettings_actionPerformed(null);
161 af.setProgressBar(null, id);
170 public synchronized boolean allFinished()
172 return queued == 0 && running == 0;
177 public static Jalview getInstance()
183 * main class for Jalview application
186 * open <em>filename</em>
188 public static void main(String[] args)
190 instance = new Jalview();
191 instance.doMain(args);
197 void doMain(String[] args)
199 System.setSecurityManager(null);
201 .println("Java version: " + System.getProperty("java.version"));
202 System.out.println(System.getProperty("os.arch") + " "
203 + System.getProperty("os.name") + " "
204 + System.getProperty("os.version"));
206 ArgsParser aparser = new ArgsParser(args);
207 boolean headless = false;
209 if (aparser.contains("help") || aparser.contains("h"))
214 if (aparser.contains("nodisplay") || aparser.contains("nogui")
215 || aparser.contains("headless"))
217 System.setProperty("java.awt.headless", "true");
220 String usrPropsFile = aparser.getValue("props");
221 Cache.loadProperties(usrPropsFile); // must do this before
222 if (usrPropsFile != null)
225 "CMD [-props " + usrPropsFile + "] executed successfully!");
230 final String jabawsUrl = aparser.getValue("jabaws");
231 if (jabawsUrl != null)
235 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
237 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
238 } catch (MalformedURLException e)
241 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
245 String defs = aparser.getValue("setprop");
248 int p = defs.indexOf('=');
251 System.err.println("Ignoring invalid setprop argument : " + defs);
255 System.out.println("Executing setprop argument: " + defs);
256 // DISABLED FOR SECURITY REASONS
257 // TODO: add a property to allow properties to be overriden by cli args
258 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
260 defs = aparser.getValue("setprop");
262 if (System.getProperty("java.awt.headless") != null
263 && System.getProperty("java.awt.headless").equals("true"))
267 System.setProperty("http.agent",
268 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
272 } catch (NoClassDefFoundError error)
274 error.printStackTrace();
275 System.out.println("\nEssential logging libraries not found."
276 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
284 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
285 } catch (Exception ex)
287 System.err.println("Unexpected Look and Feel Exception");
288 ex.printStackTrace();
290 if (Platform.isAMac())
293 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
295 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
297 System.setProperty("apple.laf.useScreenMenuBar", "true");
298 if (lookAndFeel != null)
302 UIManager.setLookAndFeel(lookAndFeel);
303 } catch (Throwable e)
306 "Failed to set QuaQua look and feel: " + e.toString());
309 if (lookAndFeel == null
310 || !(lookAndFeel.getClass().isAssignableFrom(
311 UIManager.getLookAndFeel().getClass()))
312 || !UIManager.getLookAndFeel().getClass().toString()
313 .toLowerCase().contains("quaqua"))
318 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
319 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
320 } catch (Throwable e)
323 "Failed to reset look and feel: " + e.toString());
329 * configure 'full' SO model
331 if (Cache.getDefault("USE_FULL_SO", true))
333 SequenceOntologyFactory.setInstance(new SequenceOntology());
338 desktop = new Desktop();
339 desktop.setInBatchMode(true); // indicate we are starting up
343 JalviewTaskbar.setTaskbar(this);
344 } catch (Exception e)
346 System.out.println("Cannot set Taskbar");
347 // e.printStackTrace();
348 } catch (Throwable t)
350 System.out.println("Cannot set Taskbar");
351 // t.printStackTrace();
354 desktop.setVisible(true);
355 desktop.startServiceDiscovery();
356 if (!aparser.contains("nousagestats"))
358 startUsageStats(desktop);
362 System.err.println("CMD [-nousagestats] executed successfully!");
365 if (!aparser.contains("noquestionnaire"))
367 String url = aparser.getValue("questionnaire");
370 // Start the desktop questionnaire prompter with the specified
372 Cache.log.debug("Starting questionnaire url at " + url);
373 desktop.checkForQuestionnaire(url);
375 "CMD questionnaire[-" + url + "] executed successfully!");
379 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
381 // Start the desktop questionnaire prompter with the specified
384 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
386 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
388 "Starting questionnaire with default url: " + defurl);
389 desktop.checkForQuestionnaire(defurl);
395 System.err.println("CMD [-noquestionnaire] executed successfully!");
398 if (!aparser.contains("nonews"))
400 desktop.checkForNews();
403 BioJsHTMLOutput.updateBioJS();
406 // Move any new getdown-launcher-new.jar into place over old
407 // getdown-launcher.jar
408 String appdirString = System.getProperty("getdownappdir");
409 if (appdirString != null && appdirString.length() > 0)
411 final File appdir = new File(appdirString);
417 LaunchUtil.upgradeGetdown(
418 new File(appdir, "getdown-launcher-old.jar"),
419 new File(appdir, "getdown-launcher.jar"),
420 new File(appdir, "getdown-launcher-new.jar"));
425 String file = null, data = null;
426 FileFormatI format = null;
427 DataSourceType protocol = null;
428 FileLoader fileLoader = new FileLoader(!headless);
430 String groovyscript = null; // script to execute after all loading is
431 // completed one way or another
432 // extract groovy argument and execute if necessary
433 groovyscript = aparser.getValue("groovy", true);
434 file = aparser.getValue("open", true);
436 if (file == null && desktop == null)
438 System.out.println("No files to open!");
442 // Finally, deal with the remaining input data.
447 desktop.setProgressBar(
449 .getString("status.processing_commandline_args"),
450 progress = System.currentTimeMillis());
452 System.out.println("CMD [-open " + file + "] executed successfully!");
454 if (!file.startsWith("http://"))
456 if (!(new File(file)).exists())
458 System.out.println("Can't find " + file);
466 protocol = AppletFormatAdapter.checkProtocol(file);
470 format = new IdentifyFile().identify(file, protocol);
471 } catch (FileFormatException e1)
476 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
480 System.out.println("error");
484 setCurrentAlignFrame(af);
485 data = aparser.getValue("colour", true);
488 data.replaceAll("%20", " ");
490 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
491 af.getViewport(), af.getViewport().getAlignment(), data);
496 "CMD [-color " + data + "] executed successfully!");
501 // Must maintain ability to use the groups flag
502 data = aparser.getValue("groups", true);
505 af.parseFeaturesFile(data,
506 AppletFormatAdapter.checkProtocol(data));
507 // System.out.println("Added " + data);
509 "CMD groups[-" + data + "] executed successfully!");
511 data = aparser.getValue("features", true);
514 af.parseFeaturesFile(data,
515 AppletFormatAdapter.checkProtocol(data));
516 // System.out.println("Added " + data);
518 "CMD [-features " + data + "] executed successfully!");
521 data = aparser.getValue("annotations", true);
524 af.loadJalviewDataFile(data, null, null, null);
525 // System.out.println("Added " + data);
527 "CMD [-annotations " + data + "] executed successfully!");
529 // set or clear the sortbytree flag.
530 if (aparser.contains("sortbytree"))
532 af.getViewport().setSortByTree(true);
533 if (af.getViewport().getSortByTree())
535 System.out.println("CMD [-sortbytree] executed successfully!");
538 if (aparser.contains("no-annotation"))
540 af.getViewport().setShowAnnotation(false);
541 if (!af.getViewport().isShowAnnotation())
543 System.out.println("CMD no-annotation executed successfully!");
546 if (aparser.contains("nosortbytree"))
548 af.getViewport().setSortByTree(false);
549 if (!af.getViewport().getSortByTree())
552 .println("CMD [-nosortbytree] executed successfully!");
555 data = aparser.getValue("tree", true);
561 "CMD [-tree " + data + "] executed successfully!");
562 NewickFile nf = new NewickFile(data,
563 AppletFormatAdapter.checkProtocol(data));
565 .setCurrentTree(af.showNewickTree(nf, data).getTree());
566 } catch (IOException ex)
568 System.err.println("Couldn't add tree " + data);
569 ex.printStackTrace(System.err);
572 // TODO - load PDB structure(s) to alignment JAL-629
573 // (associate with identical sequence in alignment, or a specified
575 if (groovyscript != null)
577 // Execute the groovy script after we've done all the rendering stuff
578 // and before any images or figures are generated.
579 System.out.println("Executing script " + groovyscript);
580 executeGroovyScript(groovyscript, af);
581 System.out.println("CMD groovy[" + groovyscript
582 + "] executed successfully!");
585 String imageName = "unnamed.png";
586 while (aparser.getSize() > 1)
588 String outputFormat = aparser.nextValue();
589 file = aparser.nextValue();
591 if (outputFormat.equalsIgnoreCase("png"))
593 af.createPNG(new File(file));
594 imageName = (new File(file)).getName();
595 System.out.println("Creating PNG image: " + file);
598 else if (outputFormat.equalsIgnoreCase("svg"))
600 File imageFile = new File(file);
601 imageName = imageFile.getName();
602 af.createSVG(imageFile);
603 System.out.println("Creating SVG image: " + file);
606 else if (outputFormat.equalsIgnoreCase("html"))
608 File imageFile = new File(file);
609 imageName = imageFile.getName();
610 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
611 htmlSVG.exportHTML(file);
613 System.out.println("Creating HTML image: " + file);
616 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
620 System.err.println("The output html file must not be null");
625 BioJsHTMLOutput.refreshVersionInfo(
626 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
627 } catch (URISyntaxException e)
631 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
632 bjs.exportHTML(file);
634 .println("Creating BioJS MSA Viwer HTML file: " + file);
637 else if (outputFormat.equalsIgnoreCase("imgMap"))
639 af.createImageMap(new File(file), imageName);
640 System.out.println("Creating image map: " + file);
643 else if (outputFormat.equalsIgnoreCase("eps"))
645 File outputFile = new File(file);
647 "Creating EPS file: " + outputFile.getAbsolutePath());
648 af.createEPS(outputFile);
652 if (af.saveAlignment(file, format))
654 System.out.println("Written alignment in " + format
655 + " format to " + file);
659 System.out.println("Error writing file " + file + " in "
660 + format + " format!!");
665 while (aparser.getSize() > 0)
667 System.out.println("Unknown arg: " + aparser.nextValue());
671 AlignFrame startUpAlframe = null;
672 // We'll only open the default file if the desktop is visible.
674 // ////////////////////
676 if (!headless && file == null
677 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
679 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
680 jalview.bin.Cache.getDefault("www.jalview.org",
681 "http://www.jalview.org")
682 + "/examples/exampleFile_2_7.jar");
684 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
686 // hardwire upgrade of the startup file
687 file.replace("_2_3.jar", "_2_7.jar");
688 // and remove the stale setting
689 jalview.bin.Cache.removeProperty("STARTUP_FILE");
692 protocol = DataSourceType.FILE;
694 if (file.indexOf("http:") > -1)
696 protocol = DataSourceType.URL;
699 if (file.endsWith(".jar"))
701 format = FileFormat.Jalview;
707 format = new IdentifyFile().identify(file, protocol);
708 } catch (FileFormatException e)
714 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
716 // extract groovy arguments before anything else.
719 // Once all other stuff is done, execute any groovy scripts (in order)
720 if (groovyscript != null)
722 if (Cache.groovyJarsPresent())
724 System.out.println("Executing script " + groovyscript);
725 executeGroovyScript(groovyscript, startUpAlframe);
730 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
734 // and finally, turn off batch mode indicator - if the desktop still exists
739 desktop.setProgressBar(null, progress);
741 desktop.setInBatchMode(false);
745 private static void showUsage()
748 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
749 + "-nodisplay\tRun Jalview without User Interface.\n"
750 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
751 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
752 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
753 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
754 + "-features FILE\tUse the given file to mark features on the alignment.\n"
755 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
756 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
757 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
758 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
759 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
760 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
761 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
762 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
763 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
764 + "-png FILE\tCreate PNG image FILE from alignment.\n"
765 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
766 + "-html FILE\tCreate HTML file from alignment.\n"
767 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
768 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
769 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
770 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
771 + "-noquestionnaire\tTurn off questionnaire check.\n"
772 + "-nonews\tTurn off check for Jalview news.\n"
773 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
774 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
776 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
777 // after all other properties files have been read\n\t
778 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
779 // passed in correctly)"
780 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
781 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
782 + "-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"
783 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
786 private static void startUsageStats(final Desktop desktop)
789 * start a User Config prompt asking if we can log usage statistics.
791 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
792 "USAGESTATS", "Jalview Usage Statistics",
793 "Do you want to help make Jalview better by enabling "
794 + "the collection of usage statistics with Google Analytics ?"
795 + "\n\n(you can enable or disable usage tracking in the preferences)",
802 "Initialising googletracker for usage stats.");
803 Cache.initGoogleTracker();
804 Cache.log.debug("Tracking enabled.");
811 Cache.log.debug("Not enabling Google Tracking.");
814 desktop.addDialogThread(prompter);
818 * Locate the given string as a file and pass it to the groovy interpreter.
820 * @param groovyscript
821 * the script to execute
822 * @param jalviewContext
823 * the Jalview Desktop object passed in to the groovy
824 * binding as the 'Jalview' object.
826 private void executeGroovyScript(String groovyscript, AlignFrame af)
829 * for scripts contained in files
836 if (groovyscript.trim().equals("STDIN"))
838 // read from stdin into a tempfile and execute it
841 tfile = File.createTempFile("jalview", "groovy");
842 PrintWriter outfile = new PrintWriter(
843 new OutputStreamWriter(new FileOutputStream(tfile)));
844 BufferedReader br = new BufferedReader(
845 new InputStreamReader(System.in));
847 while ((line = br.readLine()) != null)
849 outfile.write(line + "\n");
855 } catch (Exception ex)
857 System.err.println("Failed to read from STDIN into tempfile "
858 + ((tfile == null) ? "(tempfile wasn't created)"
859 : tfile.toString()));
860 ex.printStackTrace();
865 sfile = tfile.toURI().toURL();
866 } catch (Exception x)
869 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
879 sfile = new URI(groovyscript).toURL();
880 } catch (Exception x)
882 tfile = new File(groovyscript);
885 System.err.println("File '" + groovyscript + "' does not exist.");
888 if (!tfile.canRead())
890 System.err.println("File '" + groovyscript + "' cannot be read.");
893 if (tfile.length() < 1)
895 System.err.println("File '" + groovyscript + "' is empty.");
900 sfile = tfile.getAbsoluteFile().toURI().toURL();
901 } catch (Exception ex)
903 System.err.println("Failed to create a file URL for "
904 + tfile.getAbsoluteFile());
911 Map<String, java.lang.Object> vbinding = new HashMap<>();
912 vbinding.put("Jalview", this);
915 vbinding.put("currentAlFrame", af);
917 Binding gbinding = new Binding(vbinding);
918 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
919 gse.run(sfile.toString(), gbinding);
920 if ("STDIN".equals(groovyscript))
922 // delete temp file that we made -
923 // only if it was successfully executed
926 } catch (Exception e)
928 System.err.println("Exception Whilst trying to execute file " + sfile
929 + " as a groovy script.");
930 e.printStackTrace(System.err);
935 public static boolean isHeadlessMode()
937 String isheadless = System.getProperty("java.awt.headless");
938 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
945 public AlignFrame[] getAlignFrames()
947 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
948 : Desktop.getAlignFrames();
953 * Quit method delegates to Desktop.quit - unless running in headless mode when
954 * it just ends the JVM
968 public static AlignFrame getCurrentAlignFrame()
970 return Jalview.currentAlignFrame;
973 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
975 Jalview.currentAlignFrame = currentAlignFrame;