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", "metal" 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 = setMetalLookAndFeel();
400 System.err.println("Could not set requested laf=" + laf);
404 lafSet = setMacLookAndFeel();
407 System.err.println("Could not set requested laf=" + laf);
413 System.err.println("Requested laf=" + laf + " not implemented");
417 setSystemLookAndFeel();
418 if (Platform.isAMacAndNotJS())
425 * configure 'full' SO model if preferences say to, else use the default (full SO)
426 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
428 boolean soDefault = !Platform.isJS();
429 if (Cache.getDefault("USE_FULL_SO", soDefault))
431 SequenceOntologyFactory.setInstance(new SequenceOntology());
436 desktop = new Desktop();
437 desktop.setInBatchMode(true); // indicate we are starting up
441 JalviewTaskbar.setTaskbar(this);
442 } catch (Throwable t)
444 System.out.println("Error setting Taskbar: " + t.getMessage());
447 desktop.setVisible(true);
449 if (!Platform.isJS())
456 desktop.startServiceDiscovery();
457 if (!aparser.contains("nousagestats"))
459 startUsageStats(desktop);
463 System.err.println("CMD [-nousagestats] executed successfully!");
466 if (!aparser.contains("noquestionnaire"))
468 String url = aparser.getValue("questionnaire");
471 // Start the desktop questionnaire prompter with the specified
473 Cache.log.debug("Starting questionnaire url at " + url);
474 desktop.checkForQuestionnaire(url);
475 System.out.println("CMD questionnaire[-" + url
476 + "] executed successfully!");
480 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
482 // Start the desktop questionnaire prompter with the specified
485 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
487 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
489 "Starting questionnaire with default url: " + defurl);
490 desktop.checkForQuestionnaire(defurl);
497 .println("CMD [-noquestionnaire] executed successfully!");
500 if (!aparser.contains("nonews"))
502 desktop.checkForNews();
505 BioJsHTMLOutput.updateBioJS();
509 // Move any new getdown-launcher-new.jar into place over old
510 // getdown-launcher.jar
511 String appdirString = System.getProperty("getdownappdir");
512 if (appdirString != null && appdirString.length() > 0)
514 final File appdir = new File(appdirString);
520 LaunchUtil.upgradeGetdown(
521 new File(appdir, "getdown-launcher-old.jar"),
522 new File(appdir, "getdown-launcher.jar"),
523 new File(appdir, "getdown-launcher-new.jar"));
528 String file = null, data = null;
529 FileFormatI format = null;
530 DataSourceType protocol = null;
531 FileLoader fileLoader = new FileLoader(!headless);
533 String groovyscript = null; // script to execute after all loading is
534 // completed one way or another
535 // extract groovy argument and execute if necessary
536 groovyscript = aparser.getValue("groovy", true);
537 file = aparser.getValue("open", true);
539 if (file == null && desktop == null)
541 System.out.println("No files to open!");
545 // Finally, deal with the remaining input data.
550 desktop.setProgressBar(
552 .getString("status.processing_commandline_args"),
553 progress = System.currentTimeMillis());
555 System.out.println("CMD [-open " + file + "] executed successfully!");
557 if (!Platform.isJS())
559 * ignore in JavaScript -- can't just file existence - could load it?
564 if (!file.startsWith("http://") && !file.startsWith("https://"))
565 // BH 2019 added https check for Java
567 if (!(new File(file)).exists())
569 System.out.println("Can't find " + file);
578 protocol = AppletFormatAdapter.checkProtocol(file);
582 format = new IdentifyFile().identify(file, protocol);
583 } catch (FileFormatException e1)
588 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
592 System.out.println("error");
596 setCurrentAlignFrame(af);
597 data = aparser.getValue("colour", true);
600 data.replaceAll("%20", " ");
602 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
603 af.getViewport(), af.getViewport().getAlignment(), data);
608 "CMD [-color " + data + "] executed successfully!");
613 // Must maintain ability to use the groups flag
614 data = aparser.getValue("groups", true);
617 af.parseFeaturesFile(data,
618 AppletFormatAdapter.checkProtocol(data));
619 // System.out.println("Added " + data);
621 "CMD groups[-" + data + "] executed successfully!");
623 data = aparser.getValue("features", true);
626 af.parseFeaturesFile(data,
627 AppletFormatAdapter.checkProtocol(data));
628 // System.out.println("Added " + data);
630 "CMD [-features " + data + "] executed successfully!");
633 data = aparser.getValue("annotations", true);
636 af.loadJalviewDataFile(data, null, null, null);
637 // System.out.println("Added " + data);
639 "CMD [-annotations " + data + "] executed successfully!");
641 // set or clear the sortbytree flag.
642 if (aparser.contains("sortbytree"))
644 af.getViewport().setSortByTree(true);
645 if (af.getViewport().getSortByTree())
647 System.out.println("CMD [-sortbytree] executed successfully!");
650 if (aparser.contains("no-annotation"))
652 af.getViewport().setShowAnnotation(false);
653 if (!af.getViewport().isShowAnnotation())
655 System.out.println("CMD no-annotation executed successfully!");
658 if (aparser.contains("nosortbytree"))
660 af.getViewport().setSortByTree(false);
661 if (!af.getViewport().getSortByTree())
664 .println("CMD [-nosortbytree] executed successfully!");
667 data = aparser.getValue("tree", true);
673 "CMD [-tree " + data + "] executed successfully!");
674 NewickFile nf = new NewickFile(data,
675 AppletFormatAdapter.checkProtocol(data));
677 .setCurrentTree(af.showNewickTree(nf, data).getTree());
678 } catch (IOException ex)
680 System.err.println("Couldn't add tree " + data);
681 ex.printStackTrace(System.err);
684 // TODO - load PDB structure(s) to alignment JAL-629
685 // (associate with identical sequence in alignment, or a specified
687 if (groovyscript != null)
689 // Execute the groovy script after we've done all the rendering stuff
690 // and before any images or figures are generated.
691 System.out.println("Executing script " + groovyscript);
692 executeGroovyScript(groovyscript, af);
693 System.out.println("CMD groovy[" + groovyscript
694 + "] executed successfully!");
697 String imageName = "unnamed.png";
698 while (aparser.getSize() > 1)
700 String outputFormat = aparser.nextValue();
701 file = aparser.nextValue();
703 if (outputFormat.equalsIgnoreCase("png"))
705 af.createPNG(new File(file));
706 imageName = (new File(file)).getName();
707 System.out.println("Creating PNG image: " + file);
710 else if (outputFormat.equalsIgnoreCase("svg"))
712 File imageFile = new File(file);
713 imageName = imageFile.getName();
714 af.createSVG(imageFile);
715 System.out.println("Creating SVG image: " + file);
718 else if (outputFormat.equalsIgnoreCase("html"))
720 File imageFile = new File(file);
721 imageName = imageFile.getName();
722 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
723 htmlSVG.exportHTML(file);
725 System.out.println("Creating HTML image: " + file);
728 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
732 System.err.println("The output html file must not be null");
737 BioJsHTMLOutput.refreshVersionInfo(
738 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
739 } catch (URISyntaxException e)
743 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
744 bjs.exportHTML(file);
746 .println("Creating BioJS MSA Viwer HTML file: " + file);
749 else if (outputFormat.equalsIgnoreCase("imgMap"))
751 af.createImageMap(new File(file), imageName);
752 System.out.println("Creating image map: " + file);
755 else if (outputFormat.equalsIgnoreCase("eps"))
757 File outputFile = new File(file);
759 "Creating EPS file: " + outputFile.getAbsolutePath());
760 af.createEPS(outputFile);
764 af.saveAlignment(file, format);
765 if (af.isSaveAlignmentSuccessful())
767 System.out.println("Written alignment in " + format
768 + " format to " + file);
772 System.out.println("Error writing file " + file + " in "
773 + format + " format!!");
778 while (aparser.getSize() > 0)
780 System.out.println("Unknown arg: " + aparser.nextValue());
784 AlignFrame startUpAlframe = null;
785 // We'll only open the default file if the desktop is visible.
787 // ////////////////////
789 if (!Platform.isJS() && !headless && file == null
790 && Cache.getDefault("SHOW_STARTUP_FILE", true))
797 file = Cache.getDefault("STARTUP_FILE",
798 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
799 + "/examples/exampleFile_2_7.jar");
801 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
803 // hardwire upgrade of the startup file
804 file.replace("_2_3.jar", "_2_7.jar");
805 // and remove the stale setting
806 Cache.removeProperty("STARTUP_FILE");
809 protocol = DataSourceType.FILE;
811 if (file.indexOf("http:") > -1)
813 protocol = DataSourceType.URL;
816 if (file.endsWith(".jar"))
818 format = FileFormat.Jalview;
824 format = new IdentifyFile().identify(file, protocol);
825 } catch (FileFormatException e)
831 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
833 // extract groovy arguments before anything else.
836 // Once all other stuff is done, execute any groovy scripts (in order)
837 if (groovyscript != null)
839 if (Cache.groovyJarsPresent())
841 System.out.println("Executing script " + groovyscript);
842 executeGroovyScript(groovyscript, startUpAlframe);
847 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
851 // and finally, turn off batch mode indicator - if the desktop still exists
856 desktop.setProgressBar(null, progress);
858 desktop.setInBatchMode(false);
862 private static boolean setCrossPlatformLookAndFeel()
867 UIManager.setLookAndFeel(
868 UIManager.getCrossPlatformLookAndFeelClassName());
870 } catch (Exception ex)
872 System.err.println("Unexpected Look and Feel Exception");
873 ex.printStackTrace();
878 private static boolean setSystemLookAndFeel()
883 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
885 } catch (Exception ex)
887 System.err.println("Unexpected Look and Feel Exception");
888 ex.printStackTrace();
893 private static boolean setGtkLookAndFeel()
896 String laf = "com.sun.java.swing.plaf.gtk.GTKLookAndFeel";
899 UIManager.setLookAndFeel(laf);
901 } catch (Exception ex)
903 System.err.println("Unexpected Look and Feel Exception");
904 ex.printStackTrace();
909 private static boolean setMetalLookAndFeel()
912 String laf = "javax.swing.plaf.metal.MetalLookAndFeel";
915 UIManager.setLookAndFeel(laf);
917 } catch (Exception ex)
919 System.err.println("Unexpected Look and Feel Exception");
920 ex.printStackTrace();
925 private static boolean setMacLookAndFeel()
928 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
930 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
932 System.setProperty("apple.laf.useScreenMenuBar", "true");
933 if (lookAndFeel != null)
937 UIManager.setLookAndFeel(lookAndFeel);
939 } catch (Throwable e)
942 "Failed to set QuaQua look and feel: " + e.toString());
945 if (lookAndFeel == null
946 || !(lookAndFeel.getClass().isAssignableFrom(
947 UIManager.getLookAndFeel().getClass()))
948 || !UIManager.getLookAndFeel().getClass().toString()
949 .toLowerCase().contains("quaqua"))
954 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
955 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
957 } catch (Throwable e)
960 .println("Failed to reset look and feel: " + e.toString());
966 private static void showUsage()
969 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
970 + "-nodisplay\tRun Jalview without User Interface.\n"
971 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
972 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
973 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
974 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
975 + "-features FILE\tUse the given file to mark features on the alignment.\n"
976 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
977 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
978 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
979 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
980 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
981 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
982 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
983 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
984 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
985 + "-png FILE\tCreate PNG image FILE from alignment.\n"
986 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
987 + "-html FILE\tCreate HTML file from alignment.\n"
988 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
989 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
990 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
991 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
992 + "-noquestionnaire\tTurn off questionnaire check.\n"
993 + "-nonews\tTurn off check for Jalview news.\n"
994 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
995 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
997 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
998 // after all other properties files have been read\n\t
999 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1000 // passed in correctly)"
1001 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1002 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1003 + "-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"
1004 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
1007 private static void startUsageStats(final Desktop desktop)
1010 * start a User Config prompt asking if we can log usage statistics.
1012 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1013 "USAGESTATS", "Jalview Usage Statistics",
1014 "Do you want to help make Jalview better by enabling "
1015 + "the collection of usage statistics with Google Analytics ?"
1016 + "\n\n(you can enable or disable usage tracking in the preferences)",
1023 "Initialising googletracker for usage stats.");
1024 Cache.initGoogleTracker();
1025 Cache.log.debug("Tracking enabled.");
1032 Cache.log.debug("Not enabling Google Tracking.");
1035 desktop.addDialogThread(prompter);
1039 * Locate the given string as a file and pass it to the groovy interpreter.
1041 * @param groovyscript
1042 * the script to execute
1043 * @param jalviewContext
1044 * the Jalview Desktop object passed in to the groovy binding as the
1047 private void executeGroovyScript(String groovyscript, AlignFrame af)
1050 * for scripts contained in files
1057 if (groovyscript.trim().equals("STDIN"))
1059 // read from stdin into a tempfile and execute it
1062 tfile = File.createTempFile("jalview", "groovy");
1063 PrintWriter outfile = new PrintWriter(
1064 new OutputStreamWriter(new FileOutputStream(tfile)));
1065 BufferedReader br = new BufferedReader(
1066 new InputStreamReader(System.in));
1068 while ((line = br.readLine()) != null)
1070 outfile.write(line + "\n");
1076 } catch (Exception ex)
1078 System.err.println("Failed to read from STDIN into tempfile "
1079 + ((tfile == null) ? "(tempfile wasn't created)"
1080 : tfile.toString()));
1081 ex.printStackTrace();
1086 sfile = tfile.toURI().toURL();
1087 } catch (Exception x)
1090 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1092 x.printStackTrace();
1100 sfile = new URI(groovyscript).toURL();
1101 } catch (Exception x)
1103 tfile = new File(groovyscript);
1104 if (!tfile.exists())
1106 System.err.println("File '" + groovyscript + "' does not exist.");
1109 if (!tfile.canRead())
1111 System.err.println("File '" + groovyscript + "' cannot be read.");
1114 if (tfile.length() < 1)
1116 System.err.println("File '" + groovyscript + "' is empty.");
1121 sfile = tfile.getAbsoluteFile().toURI().toURL();
1122 } catch (Exception ex)
1124 System.err.println("Failed to create a file URL for "
1125 + tfile.getAbsoluteFile());
1132 Map<String, java.lang.Object> vbinding = new HashMap<>();
1133 vbinding.put("Jalview", this);
1136 vbinding.put("currentAlFrame", af);
1138 Binding gbinding = new Binding(vbinding);
1139 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1140 gse.run(sfile.toString(), gbinding);
1141 if ("STDIN".equals(groovyscript))
1143 // delete temp file that we made -
1144 // only if it was successfully executed
1147 } catch (Exception e)
1149 System.err.println("Exception Whilst trying to execute file " + sfile
1150 + " as a groovy script.");
1151 e.printStackTrace(System.err);
1156 public static boolean isHeadlessMode()
1158 String isheadless = System.getProperty("java.awt.headless");
1159 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1166 public AlignFrame[] getAlignFrames()
1168 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1169 : Desktop.getAlignFrames();
1174 * Quit method delegates to Desktop.quit - unless running in headless mode
1175 * when it just ends the JVM
1179 if (desktop != null)
1189 public static AlignFrame getCurrentAlignFrame()
1191 return Jalview.currentAlignFrame;
1194 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1196 Jalview.currentAlignFrame = currentAlignFrame;