2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.ext.so.SequenceOntology;
24 import jalview.gui.AlignFrame;
25 import jalview.gui.Desktop;
26 import jalview.gui.PromptUserConfig;
27 import jalview.io.AppletFormatAdapter;
28 import jalview.io.BioJsHTMLOutput;
29 import jalview.io.DataSourceType;
30 import jalview.io.FileFormat;
31 import jalview.io.FileFormatException;
32 import jalview.io.FileFormatI;
33 import jalview.io.FileLoader;
34 import jalview.io.HtmlSvgOutput;
35 import jalview.io.IdentifyFile;
36 import jalview.io.NewickFile;
37 import jalview.io.gff.SequenceOntologyFactory;
38 import jalview.schemes.ColourSchemeI;
39 import jalview.schemes.ColourSchemeProperty;
40 import jalview.util.MessageManager;
41 import jalview.util.Platform;
42 import jalview.ws.jws2.Jws2Discoverer;
44 import java.io.BufferedReader;
46 import java.io.FileOutputStream;
47 import java.io.IOException;
48 import java.io.InputStreamReader;
49 import java.io.OutputStreamWriter;
50 import java.io.PrintWriter;
51 import java.net.MalformedURLException;
53 import java.net.URISyntaxException;
55 import java.util.HashMap;
57 import java.util.Vector;
59 import javax.swing.LookAndFeel;
60 import javax.swing.UIManager;
62 import com.sun.xml.ws.policy.Policy;
64 import groovy.lang.Binding;
65 import groovy.util.GroovyScriptEngine;
68 * Main class for Jalview Application <br>
70 * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
73 * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
74 * jalview.bin.Jalview jalview.bin.Jalview
76 * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
77 * embellish '*' to e.g. '*.jar')
85 * singleton instance of this class
87 private static Jalview instance;
89 private Desktop desktop;
91 public static AlignFrame currentAlignFrame;
95 // grab all the rights we can the JVM
96 Policy.createEmptyPolicy();
98 Policy.setPolicy(new Policy()
101 public PermissionCollection getPermissions(CodeSource codesource)
103 Permissions perms = new Permissions();
104 perms.add(new AllPermission());
109 public void refresh()
117 * keep track of feature fetching tasks.
125 * TODO: generalise to track all jalview events to orchestrate batch
129 private int queued = 0;
131 private int running = 0;
133 public FeatureFetcher()
138 public void addFetcher(final AlignFrame af,
139 final Vector<String> dasSources)
141 final long id = System.currentTimeMillis();
143 final FeatureFetcher us = this;
144 new Thread(new Runnable()
156 af.setProgressBar(MessageManager
157 .getString("status.das_features_being_retrived"), id);
158 af.featureSettings_actionPerformed(null);
159 af.setProgressBar(null, id);
168 public synchronized boolean allFinished()
170 return queued == 0 && running == 0;
175 public static Jalview getInstance()
181 * main class for Jalview application
184 * open <em>filename</em>
186 public static void main(String[] args)
188 instance = new Jalview();
189 instance.doMain(args);
195 void doMain(String[] args)
197 System.setSecurityManager(null);
199 .println("Java version: " + System.getProperty("java.version"));
200 System.out.println(System.getProperty("os.arch") + " "
201 + System.getProperty("os.name") + " "
202 + System.getProperty("os.version"));
204 ArgsParser aparser = new ArgsParser(args);
205 boolean headless = false;
207 if (aparser.contains("help") || aparser.contains("h"))
212 if (aparser.contains("nodisplay") || aparser.contains("nogui")
213 || aparser.contains("headless"))
215 System.setProperty("java.awt.headless", "true");
218 String usrPropsFile = aparser.getValue("props");
219 Cache.loadProperties(usrPropsFile); // must do this before
220 if (usrPropsFile != null)
223 "CMD [-props " + usrPropsFile + "] executed successfully!");
228 final String jabawsUrl = aparser.getValue("jabaws");
229 if (jabawsUrl != null)
233 Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
235 "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
236 } catch (MalformedURLException e)
239 "Invalid jabaws parameter: " + jabawsUrl + " ignored");
243 String defs = aparser.getValue("setprop");
246 int p = defs.indexOf('=');
249 System.err.println("Ignoring invalid setprop argument : " + defs);
253 System.out.println("Executing setprop argument: " + defs);
254 // DISABLED FOR SECURITY REASONS
255 // TODO: add a property to allow properties to be overriden by cli args
256 // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
258 defs = aparser.getValue("setprop");
260 if (System.getProperty("java.awt.headless") != null
261 && System.getProperty("java.awt.headless").equals("true"))
265 System.setProperty("http.agent",
266 "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
270 } catch (NoClassDefFoundError error)
272 error.printStackTrace();
273 System.out.println("\nEssential logging libraries not found."
274 + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
282 UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
283 } catch (Exception ex)
285 System.err.println("Unexpected Look and Feel Exception");
286 ex.printStackTrace();
288 if (Platform.isAMac())
291 LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
293 System.setProperty("com.apple.mrj.application.apple.menu.about.name",
295 System.setProperty("apple.laf.useScreenMenuBar", "true");
296 if (lookAndFeel != null)
300 UIManager.setLookAndFeel(lookAndFeel);
301 } catch (Throwable e)
304 "Failed to set QuaQua look and feel: " + e.toString());
307 if (lookAndFeel == null || !(lookAndFeel.getClass()
308 .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
309 || !UIManager.getLookAndFeel().getClass().toString()
310 .toLowerCase().contains("quaqua"))
315 "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
316 UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
317 } catch (Throwable e)
320 "Failed to reset look and feel: " + e.toString());
326 * configure 'full' SO model if preferences say to,
327 * else use the default (SO Lite)
329 if (Cache.getDefault("USE_FULL_SO", false))
331 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)
345 } catch (Throwable t)
350 desktop.setVisible(true);
351 desktop.startServiceDiscovery();
352 if (!aparser.contains("nousagestats"))
354 startUsageStats(desktop);
358 System.err.println("CMD [-nousagestats] executed successfully!");
361 if (!aparser.contains("noquestionnaire"))
363 String url = aparser.getValue("questionnaire");
366 // Start the desktop questionnaire prompter with the specified
368 Cache.log.debug("Starting questionnaire url at " + url);
369 desktop.checkForQuestionnaire(url);
371 "CMD questionnaire[-" + url + "] executed successfully!");
375 if (Cache.getProperty("NOQUESTIONNAIRES") == null)
377 // Start the desktop questionnaire prompter with the specified
380 // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
382 String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
384 "Starting questionnaire with default url: " + defurl);
385 desktop.checkForQuestionnaire(defurl);
391 System.err.println("CMD [-noquestionnaire] executed successfully!");
394 if (!aparser.contains("nonews"))
396 desktop.checkForNews();
399 BioJsHTMLOutput.updateBioJS();
402 String file = null, data = null;
403 FileFormatI format = null;
404 DataSourceType protocol = null;
405 FileLoader fileLoader = new FileLoader(!headless);
407 String groovyscript = null; // script to execute after all loading is
408 // completed one way or another
409 // extract groovy argument and execute if necessary
410 groovyscript = aparser.getValue("groovy", true);
411 file = aparser.getValue("open", true);
413 if (file == null && desktop == null)
415 System.out.println("No files to open!");
418 String vamsasImport = aparser.getValue("vdoc");
419 String vamsasSession = aparser.getValue("vsess");
420 if (vamsasImport != null || vamsasSession != null)
422 if (desktop == null || headless)
425 "Headless vamsas sessions not yet supported. Sorry.");
428 // if we have a file, start a new session and import it.
429 boolean inSession = false;
430 if (vamsasImport != null)
434 DataSourceType viprotocol = AppletFormatAdapter
435 .checkProtocol(vamsasImport);
436 if (viprotocol == DataSourceType.FILE)
438 inSession = desktop.vamsasImport(new File(vamsasImport));
440 else if (viprotocol == DataSourceType.URL)
442 inSession = desktop.vamsasImport(new URL(vamsasImport));
445 } catch (Exception e)
447 System.err.println("Exeption when importing " + vamsasImport
448 + " as a vamsas document.");
453 System.err.println("Failed to import " + vamsasImport
454 + " as a vamsas document.");
458 System.out.println("Imported Successfully into new session "
459 + desktop.getVamsasApplication().getCurrentSession());
462 if (vamsasSession != null)
464 if (vamsasImport != null)
466 // close the newly imported session and import the Jalview specific
467 // remnants into the new session later on.
468 desktop.vamsasStop_actionPerformed(null);
470 // now join the new session
473 if (desktop.joinVamsasSession(vamsasSession))
476 "Successfully joined vamsas session " + vamsasSession);
480 System.err.println("WARNING: Failed to join vamsas session "
483 } catch (Exception e)
486 "ERROR: Failed to join vamsas session " + vamsasSession);
489 if (vamsasImport != null)
491 // the Jalview specific remnants can now be imported into the new
492 // session at the user's leisure.
494 "Skipping Push for import of data into existing vamsas session."); // TODO:
499 // desktop.getVamsasApplication().push_update();
504 // Finally, deal with the remaining input data.
509 desktop.setProgressBar(
511 .getString("status.processing_commandline_args"),
512 progress = System.currentTimeMillis());
514 System.out.println("CMD [-open " + file + "] executed successfully!");
516 if (!file.startsWith("http://"))
518 if (!(new File(file)).exists())
520 System.out.println("Can't find " + file);
528 protocol = AppletFormatAdapter.checkProtocol(file);
532 format = new IdentifyFile().identify(file, protocol);
533 } catch (FileFormatException e1)
538 AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
542 System.out.println("error");
546 setCurrentAlignFrame(af);
547 data = aparser.getValue("colour", true);
550 data.replaceAll("%20", " ");
552 ColourSchemeI cs = ColourSchemeProperty
553 .getColourScheme(af.getViewport(),
554 af.getViewport().getAlignment(), data);
559 "CMD [-color " + data + "] executed successfully!");
564 // Must maintain ability to use the groups flag
565 data = aparser.getValue("groups", true);
568 af.parseFeaturesFile(data,
569 AppletFormatAdapter.checkProtocol(data));
570 // System.out.println("Added " + data);
572 "CMD groups[-" + data + "] executed successfully!");
574 data = aparser.getValue("features", true);
577 af.parseFeaturesFile(data,
578 AppletFormatAdapter.checkProtocol(data));
579 // System.out.println("Added " + data);
581 "CMD [-features " + data + "] executed successfully!");
584 data = aparser.getValue("annotations", true);
587 af.loadJalviewDataFile(data, null, null, null);
588 // System.out.println("Added " + data);
590 "CMD [-annotations " + data + "] executed successfully!");
592 // set or clear the sortbytree flag.
593 if (aparser.contains("sortbytree"))
595 af.getViewport().setSortByTree(true);
596 if (af.getViewport().getSortByTree())
598 System.out.println("CMD [-sortbytree] executed successfully!");
601 if (aparser.contains("no-annotation"))
603 af.getViewport().setShowAnnotation(false);
604 if (!af.getViewport().isShowAnnotation())
606 System.out.println("CMD no-annotation executed successfully!");
609 if (aparser.contains("nosortbytree"))
611 af.getViewport().setSortByTree(false);
612 if (!af.getViewport().getSortByTree())
615 .println("CMD [-nosortbytree] executed successfully!");
618 data = aparser.getValue("tree", true);
624 "CMD [-tree " + data + "] executed successfully!");
625 NewickFile nf = new NewickFile(data,
626 AppletFormatAdapter.checkProtocol(data));
628 .setCurrentTree(af.showNewickTree(nf, data).getTree());
629 } catch (IOException ex)
631 System.err.println("Couldn't add tree " + data);
632 ex.printStackTrace(System.err);
635 // TODO - load PDB structure(s) to alignment JAL-629
636 // (associate with identical sequence in alignment, or a specified
638 if (groovyscript != null)
640 // Execute the groovy script after we've done all the rendering stuff
641 // and before any images or figures are generated.
642 System.out.println("Executing script " + groovyscript);
643 executeGroovyScript(groovyscript, af);
644 System.out.println("CMD groovy[" + groovyscript
645 + "] executed successfully!");
648 String imageName = "unnamed.png";
649 while (aparser.getSize() > 1)
651 String outputFormat = aparser.nextValue();
652 file = aparser.nextValue();
654 if (outputFormat.equalsIgnoreCase("png"))
656 af.createPNG(new File(file));
657 imageName = (new File(file)).getName();
658 System.out.println("Creating PNG image: " + file);
661 else if (outputFormat.equalsIgnoreCase("svg"))
663 File imageFile = new File(file);
664 imageName = imageFile.getName();
665 af.createSVG(imageFile);
666 System.out.println("Creating SVG image: " + file);
669 else if (outputFormat.equalsIgnoreCase("html"))
671 File imageFile = new File(file);
672 imageName = imageFile.getName();
673 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
674 htmlSVG.exportHTML(file);
676 System.out.println("Creating HTML image: " + file);
679 else if (outputFormat.equalsIgnoreCase("biojsmsa"))
683 System.err.println("The output html file must not be null");
688 BioJsHTMLOutput.refreshVersionInfo(
689 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
690 } catch (URISyntaxException e)
694 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
695 bjs.exportHTML(file);
697 .println("Creating BioJS MSA Viwer HTML file: " + file);
700 else if (outputFormat.equalsIgnoreCase("imgMap"))
702 af.createImageMap(new File(file), imageName);
703 System.out.println("Creating image map: " + file);
706 else if (outputFormat.equalsIgnoreCase("eps"))
708 File outputFile = new File(file);
710 "Creating EPS file: " + outputFile.getAbsolutePath());
711 af.createEPS(outputFile);
715 if (af.saveAlignment(file, format))
717 System.out.println("Written alignment in " + format
718 + " format to " + file);
722 System.out.println("Error writing file " + file + " in "
723 + format + " format!!");
728 while (aparser.getSize() > 0)
730 System.out.println("Unknown arg: " + aparser.nextValue());
734 AlignFrame startUpAlframe = null;
735 // We'll only open the default file if the desktop is visible.
737 // ////////////////////
739 if (!headless && file == null && vamsasImport == null
740 && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
742 file = jalview.bin.Cache.getDefault("STARTUP_FILE",
743 jalview.bin.Cache.getDefault("www.jalview.org",
744 "http://www.jalview.org")
745 + "/examples/exampleFile_2_7.jar");
747 "http://www.jalview.org/examples/exampleFile_2_3.jar"))
749 // hardwire upgrade of the startup file
750 file.replace("_2_3.jar", "_2_7.jar");
751 // and remove the stale setting
752 jalview.bin.Cache.removeProperty("STARTUP_FILE");
755 protocol = DataSourceType.FILE;
757 if (file.indexOf("http:") > -1)
759 protocol = DataSourceType.URL;
762 if (file.endsWith(".jar"))
764 format = FileFormat.Jalview;
770 format = new IdentifyFile().identify(file, protocol);
771 } catch (FileFormatException e)
777 startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
779 // extract groovy arguments before anything else.
782 // Once all other stuff is done, execute any groovy scripts (in order)
783 if (groovyscript != null)
785 if (Cache.groovyJarsPresent())
787 System.out.println("Executing script " + groovyscript);
788 executeGroovyScript(groovyscript, startUpAlframe);
793 "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
797 // and finally, turn off batch mode indicator - if the desktop still exists
802 desktop.setProgressBar(null, progress);
804 desktop.setInBatchMode(false);
808 private static void showUsage()
811 "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
812 + "-nodisplay\tRun Jalview without User Interface.\n"
813 + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
814 + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
815 + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
816 + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
817 + "-features FILE\tUse the given file to mark features on the alignment.\n"
818 + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
819 + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
820 + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
821 + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
822 + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
823 + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
824 + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
825 + "-json FILE\tCreate alignment file FILE in JSON format.\n"
826 + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
827 + "-png FILE\tCreate PNG image FILE from alignment.\n"
828 + "-svg FILE\tCreate SVG image FILE from alignment.\n"
829 + "-html FILE\tCreate HTML file from alignment.\n"
830 + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
831 + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
832 + "-eps FILE\tCreate EPS file FILE from alignment.\n"
833 + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
834 + "-noquestionnaire\tTurn off questionnaire check.\n"
835 + "-nonews\tTurn off check for Jalview news.\n"
836 + "-nousagestats\tTurn off google analytics tracking for this session.\n"
837 + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
839 // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
840 // after all other properties files have been read\n\t
841 // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
842 // passed in correctly)"
843 + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
844 + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
846 // "-vdoc vamsas-document\tImport vamsas document into new
847 // session or join existing session with same URN\n"
848 // + "-vses vamsas-session\tJoin session with given URN\n"
849 + "-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"
850 + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
853 private static void startUsageStats(final Desktop desktop)
856 * start a User Config prompt asking if we can log usage statistics.
858 PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
859 "USAGESTATS", "Jalview Usage Statistics",
860 "Do you want to help make Jalview better by enabling "
861 + "the collection of usage statistics with Google Analytics ?"
862 + "\n\n(you can enable or disable usage tracking in the preferences)",
869 "Initialising googletracker for usage stats.");
870 Cache.initGoogleTracker();
871 Cache.log.debug("Tracking enabled.");
878 Cache.log.debug("Not enabling Google Tracking.");
881 desktop.addDialogThread(prompter);
885 * Locate the given string as a file and pass it to the groovy interpreter.
887 * @param groovyscript
888 * the script to execute
889 * @param jalviewContext
890 * the Jalview Desktop object passed in to the groovy binding as the
893 private void executeGroovyScript(String groovyscript, AlignFrame af)
896 * for scripts contained in files
903 if (groovyscript.trim().equals("STDIN"))
905 // read from stdin into a tempfile and execute it
908 tfile = File.createTempFile("jalview", "groovy");
909 PrintWriter outfile = new PrintWriter(
910 new OutputStreamWriter(new FileOutputStream(tfile)));
911 BufferedReader br = new BufferedReader(
912 new InputStreamReader(System.in));
914 while ((line = br.readLine()) != null)
916 outfile.write(line + "\n");
922 } catch (Exception ex)
924 System.err.println("Failed to read from STDIN into tempfile "
925 + ((tfile == null) ? "(tempfile wasn't created)"
926 : tfile.toString()));
927 ex.printStackTrace();
932 sfile = tfile.toURI().toURL();
933 } catch (Exception x)
936 "Unexpected Malformed URL Exception for temporary file created from STDIN: "
946 sfile = new URI(groovyscript).toURL();
947 } catch (Exception x)
949 tfile = new File(groovyscript);
952 System.err.println("File '" + groovyscript + "' does not exist.");
955 if (!tfile.canRead())
957 System.err.println("File '" + groovyscript + "' cannot be read.");
960 if (tfile.length() < 1)
962 System.err.println("File '" + groovyscript + "' is empty.");
967 sfile = tfile.getAbsoluteFile().toURI().toURL();
968 } catch (Exception ex)
970 System.err.println("Failed to create a file URL for "
971 + tfile.getAbsoluteFile());
978 Map<String, java.lang.Object> vbinding = new HashMap<>();
979 vbinding.put("Jalview", this);
982 vbinding.put("currentAlFrame", af);
984 Binding gbinding = new Binding(vbinding);
985 GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile });
986 gse.run(sfile.toString(), gbinding);
987 if ("STDIN".equals(groovyscript))
989 // delete temp file that we made -
990 // only if it was successfully executed
993 } catch (Exception e)
995 System.err.println("Exception Whilst trying to execute file " + sfile
996 + " as a groovy script.");
997 e.printStackTrace(System.err);
1002 public static boolean isHeadlessMode()
1004 String isheadless = System.getProperty("java.awt.headless");
1005 if (isheadless != null && isheadless.equalsIgnoreCase("true"))
1012 public AlignFrame[] getAlignFrames()
1014 return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
1015 : Desktop.getAlignFrames();
1020 * Quit method delegates to Desktop.quit - unless running in headless mode
1021 * when it just ends the JVM
1025 if (desktop != null)
1035 public static AlignFrame getCurrentAlignFrame()
1037 return Jalview.currentAlignFrame;
1040 public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
1042 Jalview.currentAlignFrame = currentAlignFrame;