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.UIManager;
47 import javax.swing.UIManager.LookAndFeelInfo;
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 lafProp = System.getProperty("laf");
374 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
380 else if (lafSetting != null)
384 boolean lafSet = false;
387 case "crossplatform":
388 lafSet = setCrossPlatformLookAndFeel();
391 System.err.println("Could not set requested laf=" + laf);
395 lafSet = setSystemLookAndFeel();
398 System.err.println("Could not set requested laf=" + laf);
402 lafSet = setGtkLookAndFeel();
404 System.err.println("Could not set requested laf=" + laf);
408 lafSet = setMetalLookAndFeel();
410 System.err.println("Could not set requested laf=" + laf);
414 lafSet = setNimbusLookAndFeel();
416 System.err.println("Could not set requested laf=" + laf);
420 lafSet = setQuaquaLookAndFeel();
422 System.err.println("Could not set requested laf=" + laf);
426 lafSet = setVaquaLookAndFeel();
428 System.err.println("Could not set requested laf=" + laf);
432 lafSet = setMacLookAndFeel();
435 System.err.println("Could not set requested laf=" + laf);
441 System.err.println("Requested laf=" + laf + " not implemented");
445 setSystemLookAndFeel();
446 if (Platform.isLinux() && !Platform.isJS())
448 setMetalLookAndFeel();
450 if (Platform.isAMacAndNotJS())
457 * configure 'full' SO model if preferences say to, else use the default (full SO)
458 * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
460 boolean soDefault = !Platform.isJS();
461 if (Cache.getDefault("USE_FULL_SO", soDefault))
463 SequenceOntologyFactory.setInstance(new SequenceOntology());
468 desktop = new Desktop();
469 desktop.setInBatchMode(true); // indicate we are starting up
473 JalviewTaskbar.setTaskbar(this);
474 } catch (Throwable t)
476 System.out.println("Error setting Taskbar: " + t.getMessage());
479 desktop.setVisible(true);
481 if (!Platform.isJS())
488 desktop.startServiceDiscovery();
489 if (!aparser.contains("nousagestats"))
491 startUsageStats(desktop);
495 System.err.println("CMD [-nousagestats] executed successfully!");
498 if (!aparser.contains("noquestionnaire"))
500 String url = aparser.getValue("questionnaire");
503 // Start the desktop questionnaire prompter with the specified
505 Cache.log.debug("Starting questionnaire url at " + url);
506 desktop.checkForQuestionnaire(url);
507 System.out.println("CMD questionnaire[-" + url
508 + "] executed successfully!");
512 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
514 // Start the desktop questionnaire prompter with the specified
517 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
519 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
521 "Starting questionnaire with default url: " + defurl);
522 desktop.checkForQuestionnaire(defurl);
529 .println("CMD [-noquestionnaire] executed successfully!");
532 if (!aparser.contains("nonews"))
534 desktop.checkForNews();
537 BioJsHTMLOutput.updateBioJS();
541 // Move any new getdown-launcher-new.jar into place over old
542 // getdown-launcher.jar
543 String appdirString = System.getProperty("getdownappdir");
544 if (appdirString != null && appdirString.length() > 0)
546 final File appdir = new File(appdirString);
552 LaunchUtil.upgradeGetdown(
553 new File(appdir, "getdown-launcher-old.jar"),
554 new File(appdir, "getdown-launcher.jar"),
555 new File(appdir, "getdown-launcher-new.jar"));
560 String file = null, data = null;
561 FileFormatI format = null;
562 DataSourceType protocol = null;
563 FileLoader fileLoader = new FileLoader(!headless);
565 String groovyscript = null; // script to execute after all loading is
566 // completed one way or another
567 // extract groovy argument and execute if necessary
568 groovyscript = aparser.getValue("groovy", true);
569 file = aparser.getValue("open", true);
571 if (file == null && desktop == null)
573 System.out.println("No files to open!");
577 // Finally, deal with the remaining input data.
582 desktop.setProgressBar(
584 .getString("status.processing_commandline_args"),
585 progress = System.currentTimeMillis());
587 System.out.println("CMD [-open " + file + "] executed successfully!");
589 if (!Platform.isJS())
591 * ignore in JavaScript -- can't just file existence - could load it?
596 if (!file.startsWith("http://") && !file.startsWith("https://"))
597 // BH 2019 added https check for Java
599 if (!(new File(file)).exists())
601 System.out.println("Can't find " + file);
610 protocol = AppletFormatAdapter.checkProtocol(file);
614 format = new IdentifyFile().identify(file, protocol);
615 } catch (FileFormatException e1)
620 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
624 System.out.println("error");
628 setCurrentAlignFrame(af);
629 data = aparser.getValue("colour", true);
632 data.replaceAll("%20", " ");
634 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
635 af.getViewport(), af.getViewport().getAlignment(), data);
640 "CMD [-color " + data + "] executed successfully!");
645 // Must maintain ability to use the groups flag
646 data = aparser.getValue("groups", true);
649 af.parseFeaturesFile(data,
650 AppletFormatAdapter.checkProtocol(data));
651 // System.out.println("Added " + data);
653 "CMD groups[-" + data + "] executed successfully!");
655 data = aparser.getValue("features", true);
658 af.parseFeaturesFile(data,
659 AppletFormatAdapter.checkProtocol(data));
660 // System.out.println("Added " + data);
662 "CMD [-features " + data + "] executed successfully!");
665 data = aparser.getValue("annotations", true);
668 af.loadJalviewDataFile(data, null, null, null);
669 // System.out.println("Added " + data);
671 "CMD [-annotations " + data + "] executed successfully!");
673 // set or clear the sortbytree flag.
674 if (aparser.contains("sortbytree"))
676 af.getViewport().setSortByTree(true);
677 if (af.getViewport().getSortByTree())
679 System.out.println("CMD [-sortbytree] executed successfully!");
682 if (aparser.contains("no-annotation"))
684 af.getViewport().setShowAnnotation(false);
685 if (!af.getViewport().isShowAnnotation())
687 System.out.println("CMD no-annotation executed successfully!");
690 if (aparser.contains("nosortbytree"))
692 af.getViewport().setSortByTree(false);
693 if (!af.getViewport().getSortByTree())
696 .println("CMD [-nosortbytree] executed successfully!");
699 data = aparser.getValue("tree", true);
705 "CMD [-tree " + data + "] executed successfully!");
706 NewickFile nf = new NewickFile(data,
707 AppletFormatAdapter.checkProtocol(data));
709 .setCurrentTree(af.showNewickTree(nf, data).getTree());
710 } catch (IOException ex)
712 System.err.println("Couldn't add tree " + data);
713 ex.printStackTrace(System.err);
716 // TODO - load PDB structure(s) to alignment JAL-629
717 // (associate with identical sequence in alignment, or a specified
719 if (groovyscript != null)
721 // Execute the groovy script after we've done all the rendering stuff
722 // and before any images or figures are generated.
723 System.out.println("Executing script " + groovyscript);
724 executeGroovyScript(groovyscript, af);
725 System.out.println("CMD groovy[" + groovyscript
726 + "] executed successfully!");
729 String imageName = "unnamed.png";
730 while (aparser.getSize() > 1)
732 String outputFormat = aparser.nextValue();
733 file = aparser.nextValue();
735 if (outputFormat.equalsIgnoreCase("png"))
737 af.createPNG(new File(file));
738 imageName = (new File(file)).getName();
739 System.out.println("Creating PNG image: " + file);
742 else if (outputFormat.equalsIgnoreCase("svg"))
744 File imageFile = new File(file);
745 imageName = imageFile.getName();
746 af.createSVG(imageFile);
747 System.out.println("Creating SVG image: " + file);
750 else if (outputFormat.equalsIgnoreCase("html"))
752 File imageFile = new File(file);
753 imageName = imageFile.getName();
754 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
755 htmlSVG.exportHTML(file);
757 System.out.println("Creating HTML image: " + file);
760 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
764 System.err.println("The output html file must not be null");
769 BioJsHTMLOutput.refreshVersionInfo(
770 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
771 } catch (URISyntaxException e)
775 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
776 bjs.exportHTML(file);
778 .println("Creating BioJS MSA Viwer HTML file: " + file);
781 else if (outputFormat.equalsIgnoreCase("imgMap"))
783 af.createImageMap(new File(file), imageName);
784 System.out.println("Creating image map: " + file);
787 else if (outputFormat.equalsIgnoreCase("eps"))
789 File outputFile = new File(file);
791 "Creating EPS file: " + outputFile.getAbsolutePath());
792 af.createEPS(outputFile);
796 af.saveAlignment(file, format);
797 if (af.isSaveAlignmentSuccessful())
799 System.out.println("Written alignment in " + format
800 + " format to " + file);
804 System.out.println("Error writing file " + file + " in "
805 + format + " format!!");
810 while (aparser.getSize() > 0)
812 System.out.println("Unknown arg: " + aparser.nextValue());
816 AlignFrame startUpAlframe = null;
817 // We'll only open the default file if the desktop is visible.
819 // ////////////////////
821 if (!Platform.isJS() && !headless && file == null
822 && Cache.getDefault("SHOW_STARTUP_FILE", true))
829 file = Cache.getDefault("STARTUP_FILE",
830 Cache.getDefault("www.jalview.org", "http://www.jalview.org")
831 + "/examples/exampleFile_2_7.jar");
833 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
835 // hardwire upgrade of the startup file
836 file.replace("_2_3.jar", "_2_7.jar");
837 // and remove the stale setting
838 Cache.removeProperty("STARTUP_FILE");
841 protocol = DataSourceType.FILE;
843 if (file.indexOf("http:") > -1)
845 protocol = DataSourceType.URL;
848 if (file.endsWith(".jar"))
850 format = FileFormat.Jalview;
856 format = new IdentifyFile().identify(file, protocol);
857 } catch (FileFormatException e)
863 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
865 // extract groovy arguments before anything else.
868 // Once all other stuff is done, execute any groovy scripts (in order)
869 if (groovyscript != null)
871 if (Cache.groovyJarsPresent())
873 System.out.println("Executing script " + groovyscript);
874 executeGroovyScript(groovyscript, startUpAlframe);
879 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
883 // and finally, turn off batch mode indicator - if the desktop still exists
888 desktop.setProgressBar(null, progress);
890 desktop.setInBatchMode(false);
894 private static boolean setCrossPlatformLookAndFeel()
896 return setGenericLookAndFeel(false);
899 private static boolean setSystemLookAndFeel()
901 return setGenericLookAndFeel(true);
904 private static boolean setGenericLookAndFeel(boolean system)
909 UIManager.setLookAndFeel(
910 system ? UIManager.getSystemLookAndFeelClassName()
911 : UIManager.getCrossPlatformLookAndFeelClassName());
913 } catch (Exception ex)
915 System.err.println("Unexpected Look and Feel Exception");
916 ex.printStackTrace();
921 private static boolean setSpecificLookAndFeel(String name,
922 String className, boolean nameStartsWith)
927 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
929 if (info.getName() != null && nameStartsWith
930 ? info.getName().toLowerCase()
931 .startsWith(name.toLowerCase())
932 : info.getName().toLowerCase().equals(name.toLowerCase()))
934 className = info.getClassName();
938 UIManager.setLookAndFeel(className);
940 } catch (Exception ex)
942 System.err.println("Unexpected Look and Feel Exception");
943 ex.printStackTrace();
948 private static boolean setGtkLookAndFeel()
950 return setSpecificLookAndFeel("gtk",
951 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
954 private static boolean setMetalLookAndFeel()
956 return setSpecificLookAndFeel("metal",
957 "javax.swing.plaf.metal.MetalLookAndFeel", false);
960 private static boolean setNimbusLookAndFeel()
962 return setSpecificLookAndFeel("nimbus",
963 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
966 private static boolean setQuaquaLookAndFeel()
968 return setSpecificLookAndFeel("quaqua",
969 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
974 private static boolean setVaquaLookAndFeel()
976 return setSpecificLookAndFeel("vaqua",
977 "org.violetlib.aqua.AquaLookAndFeel", false);
980 private static boolean setMacLookAndFeel()
983 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
985 System.setProperty("apple.laf.useScreenMenuBar", "true");
986 set = setQuaquaLookAndFeel();
987 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
988 .toLowerCase().contains("quaqua"))
990 set = setVaquaLookAndFeel();
995 private static void showUsage()
998 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
999 + "-nodisplay\tRun Jalview without User Interface.\n"
1000 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
1001 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
1002 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
1003 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
1004 + "-features FILE\tUse the given file to mark features on the alignment.\n"
1005 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
1006 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
1007 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
1008 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
1009 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
1010 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
1011 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
1012 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
1013 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
1014 + "-png FILE\tCreate PNG image FILE from alignment.\n"
1015 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
1016 + "-html FILE\tCreate HTML file from alignment.\n"
1017 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
1018 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
1019 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
1020 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
1021 + "-noquestionnaire\tTurn off questionnaire check.\n"
1022 + "-nonews\tTurn off check for Jalview news.\n"
1023 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
1024 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
1026 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
1027 // after all other properties files have been read\n\t
1028 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
1029 // passed in correctly)"
1030 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
1031 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
1032 + "-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"
1033 + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
1034 + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
1035 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
1038 private static void startUsageStats(final Desktop desktop)
1041 * start a User Config prompt asking if we can log usage statistics.
1043 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1044 "USAGESTATS", "Jalview Usage Statistics",
1045 "Do you want to help make Jalview better by enabling "
1046 + "the collection of usage statistics with Google Analytics ?"
1047 + "\n\n(you can enable or disable usage tracking in the preferences)",
1054 "Initialising googletracker for usage stats.");
1055 Cache.initGoogleTracker();
1056 Cache.log.debug("Tracking enabled.");
1063 Cache.log.debug("Not enabling Google Tracking.");
1066 desktop.addDialogThread(prompter);
1070 * Locate the given string as a file and pass it to the groovy interpreter.
1072 * @param groovyscript
1073 * the script to execute
1074 * @param jalviewContext
1075 * the Jalview Desktop object passed in to the groovy binding as the
1078 private void executeGroovyScript(String groovyscript, AlignFrame af)
1081 * for scripts contained in files
1088 if (groovyscript.trim().equals("STDIN"))
1090 // read from stdin into a tempfile and execute it
1093 tfile = File.createTempFile("jalview", "groovy");
1094 PrintWriter outfile = new PrintWriter(
1095 new OutputStreamWriter(new FileOutputStream(tfile)));
1096 BufferedReader br = new BufferedReader(
1097 new InputStreamReader(System.in));
1099 while ((line = br.readLine()) != null)
1101 outfile.write(line + "\n");
1107 } catch (Exception ex)
1109 System.err.println("Failed to read from STDIN into tempfile "
1110 + ((tfile == null) ? "(tempfile wasn't created)"
1111 : tfile.toString()));
1112 ex.printStackTrace();
1117 sfile = tfile.toURI().toURL();
1118 } catch (Exception x)
1121 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1123 x.printStackTrace();
1131 sfile = new URI(groovyscript).toURL();
1132 } catch (Exception x)
1134 tfile = new File(groovyscript);
1135 if (!tfile.exists())
1137 System.err.println("File '" + groovyscript + "' does not exist.");
1140 if (!tfile.canRead())
1142 System.err.println("File '" + groovyscript + "' cannot be read.");
1145 if (tfile.length() < 1)
1147 System.err.println("File '" + groovyscript + "' is empty.");
1152 sfile = tfile.getAbsoluteFile().toURI().toURL();
1153 } catch (Exception ex)
1155 System.err.println("Failed to create a file URL for "
1156 + tfile.getAbsoluteFile());
1163 Map<String, java.lang.Object> vbinding = new HashMap<>();
1164 vbinding.put("Jalview", this);
1167 vbinding.put("currentAlFrame", af);
1169 Binding gbinding = new Binding(vbinding);
1170 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1171 gse.run(sfile.toString(), gbinding);
1172 if ("STDIN".equals(groovyscript))
1174 // delete temp file that we made -
1175 // only if it was successfully executed
1178 } catch (Exception e)
1180 System.err.println("Exception Whilst trying to execute file " + sfile
1181 + " as a groovy script.");
1182 e.printStackTrace(System.err);
1187 public static boolean isHeadlessMode()
1189 String isheadless = System.getProperty("java.awt.headless");
1190 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1197 public AlignFrame[] getAlignFrames()
1199 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1200 : Desktop.getAlignFrames();
1205 * Quit method delegates to Desktop.quit - unless running in headless mode
1206 * when it just ends the JVM
1210 if (desktop != null)
1220 public static AlignFrame getCurrentAlignFrame()
1222 return Jalview.currentAlignFrame;
1225 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1227 Jalview.currentAlignFrame = currentAlignFrame;