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.FileFormats;
34 import jalview.io.FileLoader;
35 import jalview.io.HtmlSvgOutput;
36 import jalview.io.IdentifyFile;
37 import jalview.io.NewickFile;
38 import jalview.io.gff.SequenceOntologyFactory;
39 import jalview.schemes.ColourSchemeI;
40 import jalview.schemes.ColourSchemeProperty;
41 import jalview.util.MessageManager;
42 import jalview.util.Platform;
43 import jalview.ws.jws2.Jws2Discoverer;
45 import java.io.BufferedReader;
47 import java.io.FileOutputStream;
48 import java.io.IOException;
49 import java.io.InputStreamReader;
50 import java.io.OutputStreamWriter;
51 import java.io.PrintWriter;
52 import java.net.MalformedURLException;
54 import java.net.URISyntaxException;
56 import java.security.AllPermission;
57 import java.security.CodeSource;
58 import java.security.PermissionCollection;
59 import java.security.Permissions;
60 import java.security.Policy;
61 import java.util.HashMap;
63 import java.util.Vector;
65 import javax.swing.UIManager;
66 import javax.swing.UIManager.LookAndFeelInfo;
68 import com.threerings.getdown.util.LaunchUtil;
70 import groovy.lang.Binding;
71 import groovy.util.GroovyScriptEngine;
72 import jalview.ext.so.SequenceOntology;
73 import jalview.gui.AlignFrame;
74 import jalview.gui.Desktop;
75 import jalview.gui.PromptUserConfig;
76 import jalview.io.AppletFormatAdapter;
77 import jalview.io.BioJsHTMLOutput;
78 import jalview.io.DataSourceType;
79 import jalview.io.FileFormat;
80 import jalview.io.FileFormatException;
81 import jalview.io.FileFormatI;
82 import jalview.io.FileLoader;
83 import jalview.io.HtmlSvgOutput;
84 import jalview.io.IdentifyFile;
85 import jalview.io.NewickFile;
86 import jalview.io.gff.SequenceOntologyFactory;
87 import jalview.schemes.ColourSchemeI;
88 import jalview.schemes.ColourSchemeProperty;
89 import jalview.util.MessageManager;
90 import jalview.util.Platform;
91 import jalview.ws.jws2.Jws2Discoverer;
94 * Main class for Jalview Application <br>
96 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
99 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
100 * jalview.bin.Jalview jalview.bin.Jalview
102 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
103 * embellish '*' to e.g. '*.jar')
106 * @version $Revision$
111 * singleton instance of this class
113 private static Jalview instance;
115 private Desktop desktop;
117 public static AlignFrame currentAlignFrame;
121 // grab all the rights we can the JVM
122 Policy.setPolicy(new Policy()
125 public PermissionCollection getPermissions(CodeSource codesource)
127 Permissions perms = new Permissions();
128 perms.add(new AllPermission());
133 public void refresh()
140 * keep track of feature fetching tasks.
148 * TODO: generalise to track all jalview events to orchestrate batch processing
152 private int queued = 0;
154 private int running = 0;
156 public FeatureFetcher()
161 public void addFetcher(final AlignFrame af,
162 final Vector<String> dasSources)
164 final long id = System.currentTimeMillis();
166 final FeatureFetcher us = this;
167 new Thread(new Runnable()
179 af.setProgressBar(MessageManager
180 .getString("status.das_features_being_retrived"), id);
181 af.featureSettings_actionPerformed(null);
182 af.setProgressBar(null, id);
191 public synchronized boolean allFinished()
193 return queued == 0 && running == 0;
198 public static Jalview getInstance()
204 * main class for Jalview application
207 * open <em>filename</em>
209 public static void main(String[] args)
211 instance = new Jalview();
212 instance.doMain(args);
218 void doMain(String[] args)
220 System.setSecurityManager(null);
222 .println("Java version: " + System.getProperty("java.version"));
223 System.out.println("Java Home: " + System.getProperty("java.home"));
224 System.out.println(System.getProperty("os.arch") + " "
225 + System.getProperty("os.name") + " "
226 + System.getProperty("os.version"));
227 String val = System.getProperty("sys.install4jVersion");
230 System.out.println("Install4j version: " + val);
232 val = System.getProperty("installer_template_version");
235 System.out.println("Install4j template version: " + val);
237 val = System.getProperty("launcher_version");
240 System.out.println("Launcher version: " + val);
243 // report Jalview version
244 Cache.loadBuildProperties(true);
246 ArgsParser aparser = new ArgsParser(args);
247 boolean headless = false;
249 if (aparser.contains("help") || aparser.contains("h"))
254 if (aparser.contains("nodisplay") || aparser.contains("nogui")
255 || aparser.contains("headless"))
257 System.setProperty("java.awt.headless", "true");
260 String usrPropsFile = aparser.getValue("props");
261 Cache.loadProperties(usrPropsFile); // must do this before
262 if (usrPropsFile != null)
265 "CMD [-props " + usrPropsFile + "] executed successfully!");
270 final String jabawsUrl = aparser.getValue("jabaws");
271 if (jabawsUrl != null)
275 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
277 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
278 } catch (MalformedURLException e)
281 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
285 String defs = aparser.getValue("setprop");
288 int p = defs.indexOf('=');
291 System.err.println("Ignoring invalid setprop argument : " + defs);
295 System.out.println("Executing setprop argument: " + defs);
296 // DISABLED FOR SECURITY REASONS
297 // TODO: add a property to allow properties to be overriden by cli args
298 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
300 defs = aparser.getValue("setprop");
302 if (System.getProperty("java.awt.headless") != null
303 && System.getProperty("java.awt.headless").equals("true"))
307 System.setProperty("http.agent",
308 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
312 } catch (NoClassDefFoundError error)
314 error.printStackTrace();
315 System.out.println("\nEssential logging libraries not found."
316 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
325 * configure 'full' SO model if preferences say to, else use the default (SO
328 if (Cache.getDefault("USE_FULL_SO", true))
330 SequenceOntologyFactory.setInstance(new SequenceOntology());
336 desktop = new Desktop();
337 desktop.setInBatchMode(true); // indicate we are starting up
341 JalviewTaskbar.setTaskbar(this);
342 } catch (Exception e)
344 Cache.log.info("Cannot set Taskbar");
345 Cache.log.error(e.getMessage());
346 // e.printStackTrace();
347 } catch (Throwable t)
349 Cache.log.info("Cannot set Taskbar");
350 Cache.log.error(t.getMessage());
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);
651 FileFormatI outFormat=null;
653 outFormat = FileFormats.getInstance().forName(outputFormat);
654 } catch (Exception formatP) {
655 System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
657 if (outFormat != null)
659 if (!outFormat.isWritable())
662 "This version of Jalview does not support alignment export as "
667 if (af.saveAlignment(file, outFormat))
669 System.out.println("Written alignment in " + format
670 + " format to " + file);
674 System.out.println("Error writing file " + file + " in "
675 + format + " format!!");
681 while (aparser.getSize() > 0)
683 System.out.println("Unknown arg: " + aparser.nextValue());
687 AlignFrame startUpAlframe = null;
688 // We'll only open the default file if the desktop is visible.
690 // ////////////////////
692 if (!headless && file == null
693 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
695 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
696 jalview.bin.Cache.getDefault("www.jalview.org",
697 "http://www.jalview.org")
698 + "/examples/exampleFile_2_7.jar");
700 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
702 // hardwire upgrade of the startup file
703 file.replace("_2_3.jar", "_2_7.jar");
704 // and remove the stale setting
705 jalview.bin.Cache.removeProperty("STARTUP_FILE");
708 protocol = DataSourceType.FILE;
710 if (file.indexOf("http:") > -1)
712 protocol = DataSourceType.URL;
715 if (file.endsWith(".jar"))
717 format = FileFormat.Jalview;
723 format = new IdentifyFile().identify(file, protocol);
724 } catch (FileFormatException e)
730 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
732 // extract groovy arguments before anything else.
735 // Once all other stuff is done, execute any groovy scripts (in order)
736 if (groovyscript != null)
738 if (Cache.groovyJarsPresent())
740 System.out.println("Executing script " + groovyscript);
741 executeGroovyScript(groovyscript, startUpAlframe);
746 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
750 // and finally, turn off batch mode indicator - if the desktop still exists
755 desktop.setProgressBar(null, progress);
757 desktop.setInBatchMode(false);
761 private static void setLookAndFeel()
763 // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
765 // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
767 String lafProp = System.getProperty("laf");
768 String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
774 else if (lafSetting != null)
778 boolean lafSet = false;
781 case "crossplatform":
782 lafSet = setCrossPlatformLookAndFeel();
785 Cache.log.error("Could not set requested laf=" + laf);
789 lafSet = setSystemLookAndFeel();
792 Cache.log.error("Could not set requested laf=" + laf);
796 lafSet = setGtkLookAndFeel();
799 Cache.log.error("Could not set requested laf=" + laf);
803 lafSet = setMetalLookAndFeel();
806 Cache.log.error("Could not set requested laf=" + laf);
810 lafSet = setNimbusLookAndFeel();
813 Cache.log.error("Could not set requested laf=" + laf);
817 lafSet = setQuaquaLookAndFeel();
820 Cache.log.error("Could not set requested laf=" + laf);
824 lafSet = setVaquaLookAndFeel();
827 Cache.log.error("Could not set requested laf=" + laf);
831 lafSet = setMacLookAndFeel();
834 Cache.log.error("Could not set requested laf=" + laf);
840 Cache.log.error("Requested laf=" + laf + " not implemented");
844 setSystemLookAndFeel();
845 if (Platform.isLinux())
847 setMetalLookAndFeel();
849 if (Platform.isAMac())
856 private static boolean setCrossPlatformLookAndFeel()
858 return setGenericLookAndFeel(false);
861 private static boolean setSystemLookAndFeel()
863 return setGenericLookAndFeel(true);
866 private static boolean setGenericLookAndFeel(boolean system)
871 UIManager.setLookAndFeel(
872 system ? UIManager.getSystemLookAndFeelClassName()
873 : UIManager.getCrossPlatformLookAndFeelClassName());
875 } catch (Exception ex)
877 Cache.log.error("Unexpected Look and Feel Exception");
878 Cache.log.error(ex.getMessage());
879 Cache.log.debug(Cache.getStackTraceString(ex));
884 private static boolean setSpecificLookAndFeel(String name,
885 String className, boolean nameStartsWith)
890 for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
892 if (info.getName() != null && nameStartsWith
893 ? info.getName().toLowerCase()
894 .startsWith(name.toLowerCase())
895 : info.getName().toLowerCase().equals(name.toLowerCase()))
897 className = info.getClassName();
901 UIManager.setLookAndFeel(className);
903 } catch (Exception ex)
905 Cache.log.error("Unexpected Look and Feel Exception");
906 Cache.log.error(ex.getMessage());
907 Cache.log.debug(Cache.getStackTraceString(ex));
912 private static boolean setGtkLookAndFeel()
914 return setSpecificLookAndFeel("gtk",
915 "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
918 private static boolean setMetalLookAndFeel()
920 return setSpecificLookAndFeel("metal",
921 "javax.swing.plaf.metal.MetalLookAndFeel", false);
924 private static boolean setNimbusLookAndFeel()
926 return setSpecificLookAndFeel("nimbus",
927 "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
930 private static boolean setQuaquaLookAndFeel()
932 return setSpecificLookAndFeel("quaqua",
933 ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
938 private static boolean setVaquaLookAndFeel()
940 return setSpecificLookAndFeel("vaqua",
941 "org.violetlib.aqua.AquaLookAndFeel", false);
944 private static boolean setMacLookAndFeel()
947 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
949 System.setProperty("apple.laf.useScreenMenuBar", "true");
950 set = setQuaquaLookAndFeel();
951 if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
952 .toLowerCase().contains("quaqua"))
954 set = setVaquaLookAndFeel();
959 private static void showUsage()
962 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
963 + "-nodisplay\tRun Jalview without User Interface.\n"
964 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
965 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
966 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
967 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
968 + "-features FILE\tUse the given file to mark features on the alignment.\n"
969 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
970 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
971 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
972 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
973 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
974 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
975 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
976 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
977 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
978 + "-png FILE\tCreate PNG image FILE from alignment.\n"
979 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
980 + "-html FILE\tCreate HTML file from alignment.\n"
981 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
982 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
983 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
984 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
985 + "-noquestionnaire\tTurn off questionnaire check.\n"
986 + "-nonews\tTurn off check for Jalview news.\n"
987 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
988 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
990 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
991 // after all other properties files have been read\n\t
992 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
993 // passed in correctly)"
994 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
995 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
996 + "-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"
997 + "-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"
998 + "-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"
999 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
1002 private static void startUsageStats(final Desktop desktop)
1005 * start a User Config prompt asking if we can log usage statistics.
1007 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
1008 "USAGESTATS", "Jalview Usage Statistics",
1009 "Do you want to help make Jalview better by enabling "
1010 + "the collection of usage statistics with Google Analytics ?"
1011 + "\n\n(you can enable or disable usage tracking in the preferences)",
1018 "Initialising googletracker for usage stats.");
1019 Cache.initGoogleTracker();
1020 Cache.log.debug("Tracking enabled.");
1027 Cache.log.debug("Not enabling Google Tracking.");
1030 desktop.addDialogThread(prompter);
1034 * Locate the given string as a file and pass it to the groovy interpreter.
1036 * @param groovyscript
1037 * the script to execute
1038 * @param jalviewContext
1039 * the Jalview Desktop object passed in to the groovy binding as the
1042 private void executeGroovyScript(String groovyscript, AlignFrame af)
1045 * for scripts contained in files
1052 if (groovyscript.trim().equals("STDIN"))
1054 // read from stdin into a tempfile and execute it
1057 tfile = File.createTempFile("jalview", "groovy");
1058 PrintWriter outfile = new PrintWriter(
1059 new OutputStreamWriter(new FileOutputStream(tfile)));
1060 BufferedReader br = new BufferedReader(
1061 new InputStreamReader(System.in));
1063 while ((line = br.readLine()) != null)
1065 outfile.write(line + "\n");
1071 } catch (Exception ex)
1073 System.err.println("Failed to read from STDIN into tempfile "
1074 + ((tfile == null) ? "(tempfile wasn't created)"
1075 : tfile.toString()));
1076 ex.printStackTrace();
1081 sfile = tfile.toURI().toURL();
1082 } catch (Exception x)
1085 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
1087 x.printStackTrace();
1095 sfile = new URI(groovyscript).toURL();
1096 } catch (Exception x)
1098 tfile = new File(groovyscript);
1099 if (!tfile.exists())
1101 System.err.println("File '" + groovyscript + "' does not exist.");
1104 if (!tfile.canRead())
1106 System.err.println("File '" + groovyscript + "' cannot be read.");
1109 if (tfile.length() < 1)
1111 System.err.println("File '" + groovyscript + "' is empty.");
1116 sfile = tfile.getAbsoluteFile().toURI().toURL();
1117 } catch (Exception ex)
1119 System.err.println("Failed to create a file URL for "
1120 + tfile.getAbsoluteFile());
1127 Map<String, java.lang.Object> vbinding = new HashMap<>();
1128 vbinding.put("Jalview", this);
1131 vbinding.put("currentAlFrame", af);
1133 Binding gbinding = new Binding(vbinding);
1134 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
1135 gse.run(sfile.toString(), gbinding);
1136 if ("STDIN".equals(groovyscript))
1138 // delete temp file that we made -
1139 // only if it was successfully executed
1142 } catch (Exception e)
1144 System.err.println("Exception Whilst trying to execute file " + sfile
1145 + " as a groovy script.");
1146 e.printStackTrace(System.err);
1151 public static boolean isHeadlessMode()
1153 String isheadless = System.getProperty("java.awt.headless");
1154 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1161 public AlignFrame[] getAlignFrames()
1163 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1164 : Desktop.getAlignFrames();
1169 * Quit method delegates to Desktop.quit - unless running in headless mode
1170 * when it just ends the JVM
1174 if (desktop != null)
1184 public static AlignFrame getCurrentAlignFrame()
1186 return Jalview.currentAlignFrame;
1189 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1191 Jalview.currentAlignFrame = currentAlignFrame;