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;
42 import java.util.logging.ConsoleHandler;
43 import java.util.logging.Level;
44 import java.util.logging.Logger;
46 import javax.swing.LookAndFeel;
47 import javax.swing.UIManager;
49 import com.threerings.getdown.util.LaunchUtil;
51 import groovy.lang.Binding;
52 import groovy.util.GroovyScriptEngine;
53 import jalview.ext.so.SequenceOntology;
54 import jalview.gui.AlignFrame;
55 import jalview.gui.Desktop;
56 import jalview.gui.PromptUserConfig;
57 import jalview.io.AppletFormatAdapter;
58 import jalview.io.BioJsHTMLOutput;
59 import jalview.io.DataSourceType;
60 import jalview.io.FileFormat;
61 import jalview.io.FileFormatException;
62 import jalview.io.FileFormatI;
63 import jalview.io.FileLoader;
64 import jalview.io.HtmlSvgOutput;
65 import jalview.io.IdentifyFile;
66 import jalview.io.NewickFile;
67 import jalview.io.gff.SequenceOntologyFactory;
68 import jalview.schemes.ColourSchemeI;
69 import jalview.schemes.ColourSchemeProperty;
70 import jalview.util.MessageManager;
71 import jalview.util.Platform;
72 import jalview.ws.jws2.Jws2Discoverer;
75 * Main class for Jalview Application <br>
77 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
80 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
81 * jalview.bin.Jalview jalview.bin.Jalview
83 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
84 * embellish '*' to e.g. '*.jar')
93 Platform.getURLCommandArguments();
96 // singleton instance of this class
98 private static Jalview instance;
100 private Desktop desktop;
102 public static AlignFrame currentAlignFrame;
106 if (!Platform.isJS())
113 // grab all the rights we can for the JVM
114 Policy.setPolicy(new Policy()
117 public PermissionCollection getPermissions(CodeSource codesource)
119 Permissions perms = new Permissions();
120 perms.add(new AllPermission());
125 public void refresh()
133 * keep track of feature fetching tasks.
141 * TODO: generalise to track all jalview events to orchestrate batch processing
145 private int queued = 0;
147 private int running = 0;
149 public FeatureFetcher()
154 public void addFetcher(final AlignFrame af,
155 final Vector<String> dasSources)
157 final long id = System.currentTimeMillis();
159 final FeatureFetcher us = this;
160 new Thread(new Runnable()
172 af.setProgressBar(MessageManager
173 .getString("status.das_features_being_retrived"), id);
174 af.featureSettings_actionPerformed(null);
175 af.setProgressBar(null, id);
184 public synchronized boolean allFinished()
186 return queued == 0 && running == 0;
191 public static Jalview getInstance()
197 * main class for Jalview application
200 * open <em>filename</em>
202 public static void main(String[] args)
204 // setLogging(); // BH - for event debugging in JavaScript
205 instance = new Jalview();
206 instance.doMain(args);
209 private static void logClass(String name)
211 // BH - for event debugging in JavaScript
212 ConsoleHandler consoleHandler = new ConsoleHandler();
213 consoleHandler.setLevel(Level.ALL);
214 Logger logger = Logger.getLogger(name);
215 logger.setLevel(Level.ALL);
216 logger.addHandler(consoleHandler);
219 @SuppressWarnings("unused")
220 private static void setLogging()
228 System.out.println("not in js");
231 // BH - for event debugging in JavaScript (Java mode only)
232 if (!Platform.isJS())
239 Logger.getLogger("").setLevel(Level.ALL);
240 logClass("java.awt.EventDispatchThread");
241 logClass("java.awt.EventQueue");
242 logClass("java.awt.Component");
243 logClass("java.awt.focus.Component");
244 logClass("java.awt.focus.DefaultKeyboardFocusManager");
252 void doMain(String[] args)
255 if (!Platform.isJS())
257 System.setSecurityManager(null);
261 .println("Java version: " + System.getProperty("java.version"));
262 System.out.println("Java Home: " + System.getProperty("java.home"));
263 System.out.println(System.getProperty("os.arch") + " "
264 + System.getProperty("os.name") + " "
265 + System.getProperty("os.version"));
266 String val = System.getProperty("sys.install4jVersion");
269 System.out.println("Install4j version: " + val);
271 val = System.getProperty("installer_template_version");
274 System.out.println("Install4j template version: " + val);
276 val = System.getProperty("launcher_version");
279 System.out.println("Launcher version: " + val);
282 // report Jalview version
283 Cache.loadBuildProperties(true);
285 ArgsParser aparser = new ArgsParser(args);
286 boolean headless = false;
288 String usrPropsFile = aparser.getValue("props");
289 Cache.loadProperties(usrPropsFile); // must do this before
290 if (usrPropsFile != null)
293 "CMD [-props " + usrPropsFile + "] executed successfully!");
296 if (!Platform.isJS())
303 if (aparser.contains("help") || aparser.contains("h"))
308 if (aparser.contains("nodisplay") || aparser.contains("nogui")
309 || aparser.contains("headless"))
311 System.setProperty("java.awt.headless", "true");
316 final String jabawsUrl = aparser.getValue("jabaws");
317 if (jabawsUrl != null)
321 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
323 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
324 } catch (MalformedURLException e)
327 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
332 String defs = aparser.getValue("setprop");
335 int p = defs.indexOf('=');
338 System.err.println("Ignoring invalid setprop argument : " + defs);
342 System.out.println("Executing setprop argument: " + defs);
345 Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
348 defs = aparser.getValue("setprop");
350 if (System.getProperty("java.awt.headless") != null
351 && System.getProperty("java.awt.headless").equals("true"))
355 System.setProperty("http.agent",
356 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
360 } catch (NoClassDefFoundError error)
362 error.printStackTrace();
363 System.out.println("\nEssential logging libraries not found."
364 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
370 // property laf = "crossplatform", "system", "gtk" or "mac"
371 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
373 String laf = System.getProperty("laf", "none");
374 boolean lafSet = false;
377 case "crossplatform":
378 lafSet = setCrossPlatformLookAndFeel();
381 System.err.println("Could not set requested laf=" + laf);
385 lafSet = setSystemLookAndFeel();
388 System.err.println("Could not set requested laf=" + laf);
392 lafSet = setGtkLookAndFeel();
394 System.err.println("Could not set requested laf=" + laf);
398 lafSet = setMacLookAndFeel();
401 System.err.println("Could not set requested laf=" + laf);
407 System.err.println("Requested laf=" + laf + " not implemented");
411 setSystemLookAndFeel();
412 if (Platform.isAMacAndNotJS())
419 * configure 'full' SO model if preferences say to, else use the default (full SO)
420 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
422 boolean soDefault = !Platform.isJS();
423 if (Cache.getDefault("USE_FULL_SO", soDefault))
425 SequenceOntologyFactory.setInstance(new SequenceOntology());
430 desktop = new Desktop();
431 desktop.setInBatchMode(true); // indicate we are starting up
435 JalviewTaskbar.setTaskbar(this);
436 } catch (Throwable t)
438 System.out.println("Error setting Taskbar: " + t.getMessage());
441 desktop.setVisible(true);
443 if (!Platform.isJS())
450 desktop.startServiceDiscovery();
451 if (!aparser.contains("nousagestats"))
453 startUsageStats(desktop);
457 System.err.println("CMD [-nousagestats] executed successfully!");
460 if (!aparser.contains("noquestionnaire"))
462 String url = aparser.getValue("questionnaire");
465 // Start the desktop questionnaire prompter with the specified
467 Cache.log.debug("Starting questionnaire url at " + url);
468 desktop.checkForQuestionnaire(url);
469 System.out.println("CMD questionnaire[-" + url
470 + "] executed successfully!");
474 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
476 // Start the desktop questionnaire prompter with the specified
479 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
481 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
483 "Starting questionnaire with default url: " + defurl);
484 desktop.checkForQuestionnaire(defurl);
491 .println("CMD [-noquestionnaire] executed successfully!");
494 if (!aparser.contains("nonews"))
496 desktop.checkForNews();
499 BioJsHTMLOutput.updateBioJS();
503 // Move any new getdown-launcher-new.jar into place over old
504 // getdown-launcher.jar
505 String appdirString = System.getProperty("getdownappdir");
506 if (appdirString != null && appdirString.length() > 0)
508 final File appdir = new File(appdirString);
514 LaunchUtil.upgradeGetdown(
515 new File(appdir, "getdown-launcher-old.jar"),
516 new File(appdir, "getdown-launcher.jar"),
517 new File(appdir, "getdown-launcher-new.jar"));
522 String file = null, data = null;
523 FileFormatI format = null;
524 DataSourceType protocol = null;
525 FileLoader fileLoader = new FileLoader(!headless);
527 String groovyscript = null; // script to execute after all loading is
528 // completed one way or another
529 // extract groovy argument and execute if necessary
530 groovyscript = aparser.getValue("groovy", true);
531 file = aparser.getValue("open", true);
533 if (file == null && desktop == null)
535 System.out.println("No files to open!");
539 // Finally, deal with the remaining input data.
544 desktop.setProgressBar(
546 .getString("status.processing_commandline_args"),
547 progress = System.currentTimeMillis());
549 System.out.println("CMD [-open " + file + "] executed successfully!");
551 if (!Platform.isJS())
553 * ignore in JavaScript -- can't just file existence - could load it?
558 if (!file.startsWith("http://") && !file.startsWith("https://"))
559 // BH 2019 added https check for Java
561 if (!(new File(file)).exists())
563 System.out.println("Can't find " + file);
572 protocol = AppletFormatAdapter.checkProtocol(file);
576 format = new IdentifyFile().identify(file, protocol);
577 } catch (FileFormatException e1)
582 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
586 System.out.println("error");
590 setCurrentAlignFrame(af);
591 data = aparser.getValue("colour", true);
594 data.replaceAll("%20", " ");
596 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
597 af.getViewport(), af.getViewport().getAlignment(), data);
602 "CMD [-color " + data + "] executed successfully!");
607 // Must maintain ability to use the groups flag
608 data = aparser.getValue("groups", true);
611 af.parseFeaturesFile(data,
612 AppletFormatAdapter.checkProtocol(data));
613 // System.out.println("Added " + data);
615 "CMD groups[-" + data + "] executed successfully!");
617 data = aparser.getValue("features", true);
620 af.parseFeaturesFile(data,
621 AppletFormatAdapter.checkProtocol(data));
622 // System.out.println("Added " + data);
624 "CMD [-features " + data + "] executed successfully!");
627 data = aparser.getValue("annotations", true);
630 af.loadJalviewDataFile(data, null, null, null);
631 // System.out.println("Added " + data);
633 "CMD [-annotations " + data + "] executed successfully!");
635 // set or clear the sortbytree flag.
636 if (aparser.contains("sortbytree"))
638 af.getViewport().setSortByTree(true);
639 if (af.getViewport().getSortByTree())
641 System.out.println("CMD [-sortbytree] executed successfully!");
644 if (aparser.contains("no-annotation"))
646 af.getViewport().setShowAnnotation(false);
647 if (!af.getViewport().isShowAnnotation())
649 System.out.println("CMD no-annotation executed successfully!");
652 if (aparser.contains("nosortbytree"))
654 af.getViewport().setSortByTree(false);
655 if (!af.getViewport().getSortByTree())
658 .println("CMD [-nosortbytree] executed successfully!");
661 data = aparser.getValue("tree", true);
667 "CMD [-tree " + data + "] executed successfully!");
668 NewickFile nf = new NewickFile(data,
669 AppletFormatAdapter.checkProtocol(data));
671 .setCurrentTree(af.showNewickTree(nf, data).getTree());
672 } catch (IOException ex)
674 System.err.println("Couldn't add tree " + data);
675 ex.printStackTrace(System.err);
678 // TODO - load PDB structure(s) to alignment JAL-629
679 // (associate with identical sequence in alignment, or a specified
681 if (groovyscript != null)
683 // Execute the groovy script after we've done all the rendering stuff
684 // and before any images or figures are generated.
685 System.out.println("Executing script " + groovyscript);
686 executeGroovyScript(groovyscript, af);
687 System.out.println("CMD groovy[" + groovyscript
688 + "] executed successfully!");
691 String imageName = "unnamed.png";
692 while (aparser.getSize() > 1)
694 String outputFormat = aparser.nextValue();
695 file = aparser.nextValue();
697 if (outputFormat.equalsIgnoreCase("png"))
699 af.createPNG(new File(file));
700 imageName = (new File(file)).getName();
701 System.out.println("Creating PNG image: " + file);
704 else if (outputFormat.equalsIgnoreCase("svg"))
706 File imageFile = new File(file);
707 imageName = imageFile.getName();
708 af.createSVG(imageFile);
709 System.out.println("Creating SVG image: " + file);
712 else if (outputFormat.equalsIgnoreCase("html"))
714 File imageFile = new File(file);
715 imageName = imageFile.getName();
716 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
717 htmlSVG.exportHTML(file);
719 System.out.println("Creating HTML image: " + file);
722 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
726 System.err.println("The output html file must not be null");
731 BioJsHTMLOutput.refreshVersionInfo(
732 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
733 } catch (URISyntaxException e)
737 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
738 bjs.exportHTML(file);
740 .println("Creating BioJS MSA Viwer HTML file: " + file);
743 else if (outputFormat.equalsIgnoreCase("imgMap"))
745 af.createImageMap(new File(file), imageName);
746 System.out.println("Creating image map: " + file);
749 else if (outputFormat.equalsIgnoreCase("eps"))
751 File outputFile = new File(file);
753 "Creating EPS file: " + outputFile.getAbsolutePath());
754 af.createEPS(outputFile);
758 af.saveAlignment(file, format);
759 if (af.isSaveAlignmentSuccessful())
761 System.out.println("Written alignment in " + format
762 + " format to " + file);
766 System.out.println("Error writing file " + file + " in "
767 + format + " format!!");
772 while (aparser.getSize() > 0)
774 System.out.println("Unknown arg: " + aparser.nextValue());
778 AlignFrame startUpAlframe = null;
779 // We'll only open the default file if the desktop is visible.
781 // ////////////////////
783 if (!Platform.isJS() && !headless && file == null
784 && Cache.getDefault("SHOW_STARTUP_FILE", true))
791 file = Cache.getDefault("STARTUP_FILE",
792 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
793 + "/examples/exampleFile_2_7.jar");
795 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
797 // hardwire upgrade of the startup file
798 file.replace("_2_3.jar", "_2_7.jar");
799 // and remove the stale setting
800 Cache.removeProperty("STARTUP_FILE");
803 protocol = DataSourceType.FILE;
805 if (file.indexOf("http:") > -1)
807 protocol = DataSourceType.URL;
810 if (file.endsWith(".jar"))
812 format = FileFormat.Jalview;
818 format = new IdentifyFile().identify(file, protocol);
819 } catch (FileFormatException e)
825 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
827 // extract groovy arguments before anything else.
830 // Once all other stuff is done, execute any groovy scripts (in order)
831 if (groovyscript != null)
833 if (Cache.groovyJarsPresent())
835 System.out.println("Executing script " + groovyscript);
836 executeGroovyScript(groovyscript, startUpAlframe);
841 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
845 // and finally, turn off batch mode indicator - if the desktop still exists
850 desktop.setProgressBar(null, progress);
852 desktop.setInBatchMode(false);
856 private static boolean setCrossPlatformLookAndFeel()
861 UIManager.setLookAndFeel(
862 UIManager.getCrossPlatformLookAndFeelClassName());
864 } catch (Exception ex)
866 System.err.println("Unexpected Look and Feel Exception");
867 ex.printStackTrace();
872 private static boolean setSystemLookAndFeel()
877 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
879 } catch (Exception ex)
881 System.err.println("Unexpected Look and Feel Exception");
882 ex.printStackTrace();
887 private static boolean setGtkLookAndFeel()
890 String laf = "com.sun.java.swing.plaf.gtk.GTKLookAndFeel";
893 UIManager.setLookAndFeel(laf);
895 } catch (Exception ex)
897 System.err.println("Unexpected Look and Feel Exception");
898 ex.printStackTrace();
903 private static boolean setMacLookAndFeel()
906 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
908 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
910 System.setProperty("apple.laf.useScreenMenuBar", "true");
911 if (lookAndFeel != null)
915 UIManager.setLookAndFeel(lookAndFeel);
917 } catch (Throwable e)
920 "Failed to set QuaQua look and feel: " + e.toString());
923 if (lookAndFeel == null
924 || !(lookAndFeel.getClass().isAssignableFrom(
925 UIManager.getLookAndFeel().getClass()))
926 || !UIManager.getLookAndFeel().getClass().toString()
927 .toLowerCase().contains("quaqua"))
932 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
933 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
935 } catch (Throwable e)
938 .println("Failed to reset look and feel: " + e.toString());
944 private static void showUsage()
947 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
948 + "-nodisplay\tRun Jalview without User Interface.\n"
949 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
950 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
951 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
952 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
953 + "-features FILE\tUse the given file to mark features on the alignment.\n"
954 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
955 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
956 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
957 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
958 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
959 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
960 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
961 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
962 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
963 + "-png FILE\tCreate PNG image FILE from alignment.\n"
964 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
965 + "-html FILE\tCreate HTML file from alignment.\n"
966 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
967 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
968 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
969 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
970 + "-noquestionnaire\tTurn off questionnaire check.\n"
971 + "-nonews\tTurn off check for Jalview news.\n"
972 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
973 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
975 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
976 // after all other properties files have been read\n\t
977 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
978 // passed in correctly)"
979 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
980 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
981 + "-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"
982 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
985 private static void startUsageStats(final Desktop desktop)
988 * start a User Config prompt asking if we can log usage statistics.
990 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
991 "USAGESTATS", "Jalview Usage Statistics",
992 "Do you want to help make Jalview better by enabling "
993 + "the collection of usage statistics with Google Analytics ?"
994 + "\n\n(you can enable or disable usage tracking in the preferences)",
1001 "Initialising googletracker for usage stats.");
1002 Cache.initGoogleTracker();
1003 Cache.log.debug("Tracking enabled.");
1010 Cache.log.debug("Not enabling Google Tracking.");
1013 desktop.addDialogThread(prompter);
1017 * Locate the given string as a file and pass it to the groovy interpreter.
1019 * @param groovyscript
1020 * the script to execute
1021 * @param jalviewContext
1022 * the Jalview Desktop object passed in to the groovy binding as the
1025 private void executeGroovyScript(String groovyscript, AlignFrame af)
1028 * for scripts contained in files
1035 if (groovyscript.trim().equals("STDIN"))
1037 // read from stdin into a tempfile and execute it
1040 tfile = File.createTempFile("jalview", "groovy");
1041 PrintWriter outfile = new PrintWriter(
1042 new OutputStreamWriter(new FileOutputStream(tfile)));
1043 BufferedReader br = new BufferedReader(
1044 new InputStreamReader(System.in));
1046 while ((line = br.readLine()) != null)
1048 outfile.write(line + "\n");
1054 } catch (Exception ex)
1056 System.err.println("Failed to read from STDIN into tempfile "
1057 + ((tfile == null) ? "(tempfile wasn't created)"
1058 : tfile.toString()));
1059 ex.printStackTrace();
1064 sfile = tfile.toURI().toURL();
1065 } catch (Exception x)
1068 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1070 x.printStackTrace();
1078 sfile = new URI(groovyscript).toURL();
1079 } catch (Exception x)
1081 tfile = new File(groovyscript);
1082 if (!tfile.exists())
1084 System.err.println("File '" + groovyscript + "' does not exist.");
1087 if (!tfile.canRead())
1089 System.err.println("File '" + groovyscript + "' cannot be read.");
1092 if (tfile.length() < 1)
1094 System.err.println("File '" + groovyscript + "' is empty.");
1099 sfile = tfile.getAbsoluteFile().toURI().toURL();
1100 } catch (Exception ex)
1102 System.err.println("Failed to create a file URL for "
1103 + tfile.getAbsoluteFile());
1110 Map<String, java.lang.Object> vbinding = new HashMap<>();
1111 vbinding.put("Jalview", this);
1114 vbinding.put("currentAlFrame", af);
1116 Binding gbinding = new Binding(vbinding);
1117 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1118 gse.run(sfile.toString(), gbinding);
1119 if ("STDIN".equals(groovyscript))
1121 // delete temp file that we made -
1122 // only if it was successfully executed
1125 } catch (Exception e)
1127 System.err.println("Exception Whilst trying to execute file " + sfile
1128 + " as a groovy script.");
1129 e.printStackTrace(System.err);
1134 public static boolean isHeadlessMode()
1136 String isheadless = System.getProperty("java.awt.headless");
1137 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1144 public AlignFrame[] getAlignFrames()
1146 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1147 : Desktop.getAlignFrames();
1152 * Quit method delegates to Desktop.quit - unless running in headless mode
1153 * when it just ends the JVM
1157 if (desktop != null)
1167 public static AlignFrame getCurrentAlignFrame()
1169 return Jalview.currentAlignFrame;
1172 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1174 Jalview.currentAlignFrame = currentAlignFrame;