X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=763b10bb2bfaa86834c17d5b7431527d534dd6bf;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=50e3559272b0c3054c979567f18a092288608304;hpb=55356b1071b5352edd68ce25a5d3dc3c60dcdc2d;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 50e3559..763b10b 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,32 +20,44 @@ */ package jalview.bin; +import groovy.lang.Binding; +import groovy.util.GroovyScriptEngine; + +import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.PromptUserConfig; +import jalview.io.AppletFormatAdapter; +import jalview.io.BioJsHTMLOutput; +import jalview.io.FileLoader; +import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.NewickFile; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.UserColourScheme; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.jws2.Jws2Discoverer; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; +import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; -import java.lang.reflect.Constructor; import java.net.MalformedURLException; import java.net.URI; import java.net.URL; -import java.net.URLDecoder; import java.security.AllPermission; import java.security.CodeSource; import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; -import java.util.Hashtable; +import java.util.HashMap; import java.util.Map; import java.util.Vector; @@ -61,11 +73,21 @@ import javax.swing.UIManager; */ public class Jalview { + /* + * singleton instance of this class + */ + private static Jalview instance; + + private Desktop desktop; + + public static AlignFrame currentAlignFrame; + static { // grab all the rights we can the JVM Policy.setPolicy(new Policy() { + @Override public PermissionCollection getPermissions(CodeSource codesource) { Permissions perms = new Permissions(); @@ -73,6 +95,7 @@ public class Jalview return (perms); } + @Override public void refresh() { } @@ -80,6 +103,71 @@ public class Jalview } /** + * keep track of feature fetching tasks. + * + * @author JimP + * + */ + class FeatureFetcher + { + /* + * TODO: generalise to track all jalview events to orchestrate batch + * processing events. + */ + + private int queued = 0; + + private int running = 0; + + public FeatureFetcher() + { + + } + + public void addFetcher(final AlignFrame af, + final Vector dasSources) + { + final long id = System.currentTimeMillis(); + queued++; + final FeatureFetcher us = this; + new Thread(new Runnable() + { + + @Override + public void run() + { + synchronized (us) + { + queued--; + running++; + } + + af.setProgressBar(MessageManager + .getString("status.das_features_being_retrived"), id); + af.featureSettings_actionPerformed(null); + af.featureSettings.fetchDasFeatures(dasSources, true); + af.setProgressBar(null, id); + synchronized (us) + { + running--; + } + } + }).start(); + } + + public synchronized boolean allFinished() + { + return queued == 0 && running == 0; + } + + } + + public static Jalview getInstance() + { + return instance; + } + + /** * main class for Jalview application * * @param args @@ -87,17 +175,21 @@ public class Jalview */ public static void main(String[] args) { + instance = new Jalview(); + instance.doMain(args); + } + + /** + * @param args + */ + void doMain(String[] args) + { + System.setSecurityManager(null); System.out.println("Java version: " + System.getProperty("java.version")); System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); - if (new Platform().isAMac()) - { - System.setProperty("com.apple.mrj.application.apple.menu.about.name", - "Jalview"); - System.setProperty("apple.laf.useScreenMenuBar", "true"); - } ArgsParser aparser = new ArgsParser(args); boolean headless = false; @@ -113,7 +205,14 @@ public class Jalview System.setProperty("java.awt.headless", "true"); headless = true; } - Cache.loadProperties(aparser.getValue("props")); // must do this before + String usrPropsFile = aparser.getValue("props"); + Cache.loadProperties(usrPropsFile); // must do this before + if (usrPropsFile != null) + { + System.out.println("CMD [-props " + usrPropsFile + + "] executed successfully!"); + } + // anything else! final String jabawsUrl = aparser.getValue("jabaws"); @@ -122,6 +221,8 @@ public class Jalview try { Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + System.out.println("CMD [-jabaws " + jabawsUrl + + "] executed successfully!"); } catch (MalformedURLException e) { System.err.println("Invalid jabaws parameter: " + jabawsUrl @@ -156,7 +257,7 @@ public class Jalview try { Cache.initLogger(); - } catch (java.lang.NoClassDefFoundError error) + } catch (NoClassDefFoundError error) { error.printStackTrace(); System.out @@ -165,7 +266,7 @@ public class Jalview System.exit(0); } - Desktop desktop = null; + desktop = null; try { @@ -173,6 +274,30 @@ public class Jalview } catch (Exception ex) { } + if (Platform.isAMac()) + { + System.setProperty("com.apple.mrj.application.apple.menu.about.name", + "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); + try + { + UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel()); + } catch (Throwable e) + { + System.err.println("Failed to set QuaQua look and feel: " + + e.toString()); + } + } + + /* + * configure 'full' SO model if preferences say to, + * else use the default (SO Lite) + */ + if (Cache.getDefault("USE_FULL_SO", false)) + { + SequenceOntologyFactory.setInstance(new SequenceOntology()); + } if (!headless) { @@ -184,6 +309,11 @@ public class Jalview { startUsageStats(desktop); } + else + { + System.err.println("CMD [-nousagestats] executed successfully!"); + } + if (!aparser.contains("noquestionnaire")) { String url = aparser.getValue("questionnaire"); @@ -193,6 +323,8 @@ public class Jalview // questionnaire Cache.log.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); } else { @@ -207,16 +339,26 @@ public class Jalview Cache.log.debug("Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); - } } } - desktop.checkForNews(); + else + { + System.err.println("CMD [-noquestionnaire] executed successfully!"); + } + + if (!aparser.contains("nonews")) + { + desktop.checkForNews(); + } + + BioJsHTMLOutput.updateBioJS(); } String file = null, protocol = null, format = null, data = null; - jalview.io.FileLoader fileLoader = new jalview.io.FileLoader(); - Vector getFeatures = null; // vector of das source nicknames to fetch + FileLoader fileLoader = new FileLoader(!headless); + Vector getFeatures = null; // vector of das source nicknames to + // fetch // features from // loading is done. String groovyscript = null; // script to execute after all loading is @@ -230,8 +372,8 @@ public class Jalview System.out.println("No files to open!"); System.exit(1); } - String vamsasImport = aparser.getValue("vdoc"), vamsasSession = aparser - .getValue("vsess"); + String vamsasImport = aparser.getValue("vdoc"); + String vamsasSession = aparser.getValue("vsess"); if (vamsasImport != null || vamsasSession != null) { if (desktop == null || headless) @@ -246,13 +388,13 @@ public class Jalview { try { - String viprotocol = jalview.io.AppletFormatAdapter + String viprotocol = AppletFormatAdapter .checkProtocol(vamsasImport); if (viprotocol == jalview.io.FormatAdapter.FILE) { inSession = desktop.vamsasImport(new File(vamsasImport)); } - else if (viprotocol == jalview.io.FormatAdapter.URL) + else if (viprotocol == FormatAdapter.URL) { inSession = desktop.vamsasImport(new URL(vamsasImport)); } @@ -321,14 +463,15 @@ public class Jalview { if (!headless) { - desktop.setProgressBar(MessageManager.getString("status.processing_commandline_args"), + desktop.setProgressBar(MessageManager + .getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } - System.out.println("Opening file: " + file); + System.out.println("CMD [-open " + file + "] executed successfully!"); if (!file.startsWith("http://")) { - if (!(new java.io.File(file)).exists()) + if (!(new File(file)).exists()) { System.out.println("Can't find " + file); if (headless) @@ -338,9 +481,9 @@ public class Jalview } } - protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); + protocol = AppletFormatAdapter.checkProtocol(file); - format = new jalview.io.IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); @@ -350,24 +493,26 @@ public class Jalview } else { - + setCurrentAlignFrame(af); data = aparser.getValue("colour", true); if (data != null) { data.replaceAll("%20", " "); - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); + ColourSchemeI cs = ColourSchemeProperty.getColour(af + .getViewport().getAlignment(), data); if (cs == null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); + UserColourScheme ucs = new UserColourScheme("white"); ucs.parseAppletParameter(data); cs = ucs; } - - System.out.println("colour is " + data); + else + { + System.out.println("CMD [-color " + data + + "] executed successfully!"); + } af.changeColour(cs); } @@ -376,35 +521,54 @@ public class Jalview if (data != null) { af.parseFeaturesFile(data, - jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println("CMD groups[-" + data + + "] executed successfully!"); } data = aparser.getValue("features", true); if (data != null) { af.parseFeaturesFile(data, - jalview.io.AppletFormatAdapter.checkProtocol(data)); - System.out.println("Added " + data); + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println("CMD [-features " + data + + "] executed successfully!"); } data = aparser.getValue("annotations", true); if (data != null) { af.loadJalviewDataFile(data, null, null, null); - System.out.println("Added " + data); + // System.out.println("Added " + data); + System.out.println("CMD [-annotations " + data + + "] executed successfully!"); } // set or clear the sortbytree flag. if (aparser.contains("sortbytree")) { af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } } if (aparser.contains("no-annotation")) { af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + System.out.println("CMD no-annotation executed successfully!"); + } } if (aparser.contains("nosortbytree")) { af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } } data = aparser.getValue("tree", true); if (data != null) @@ -412,13 +576,14 @@ public class Jalview jalview.io.NewickFile fin = null; try { - fin = new jalview.io.NewickFile(data, - jalview.io.AppletFormatAdapter.checkProtocol(data)); + System.out.println("CMD [-tree " + data + + "] executed successfully!"); + fin = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); if (fin != null) { af.getViewport().setCurrentTree( af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); } } catch (IOException ex) { @@ -454,18 +619,10 @@ public class Jalview { // Execute the groovy script after we've done all the rendering stuff // and before any images or figures are generated. - if (jalview.bin.Cache.groovyJarsPresent()) - { - System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] - { desktop, af }); - } - else - { - System.err - .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " - + groovyscript); - } + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); groovyscript = null; } String imageName = "unnamed.png"; @@ -476,14 +633,14 @@ public class Jalview if (format.equalsIgnoreCase("png")) { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); + af.createPNG(new File(file)); + imageName = (new File(file)).getName(); System.out.println("Creating PNG image: " + file); continue; } else if (format.equalsIgnoreCase("svg")) { - File imageFile = new java.io.File(file); + File imageFile = new File(file); imageName = imageFile.getName(); af.createSVG(imageFile); System.out.println("Creating SVG image: " + file); @@ -491,22 +648,24 @@ public class Jalview } else if (format.equalsIgnoreCase("html")) { - File imageFile = new java.io.File(file); + File imageFile = new File(file); imageName = imageFile.getName(); - new HtmlSvgOutput(new java.io.File(file), af.alignPanel); + new HtmlSvgOutput(new File(file), af.alignPanel); System.out.println("Creating HTML image: " + file); continue; } else if (format.equalsIgnoreCase("imgMap")) { - af.createImageMap(new java.io.File(file), imageName); + af.createImageMap(new File(file), imageName); System.out.println("Creating image map: " + file); continue; } else if (format.equalsIgnoreCase("eps")) { - System.out.println("Creating EPS file: " + file); - af.createEPS(new java.io.File(file)); + File outputFile = new File(file); + System.out.println("Creating EPS file: " + + outputFile.getAbsolutePath()); + af.createEPS(outputFile); continue; } @@ -563,7 +722,7 @@ public class Jalview } else { - format = new jalview.io.IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, @@ -585,11 +744,10 @@ public class Jalview // Once all other stuff is done, execute any groovy scripts (in order) if (groovyscript != null) { - if (jalview.bin.Cache.groovyJarsPresent()) + if (Cache.groovyJarsPresent()) { System.out.println("Executing script " + groovyscript); - executeGroovyScript(groovyscript, new Object[] - { desktop, startUpAlframe }); + executeGroovyScript(groovyscript, startUpAlframe); } else { @@ -626,6 +784,7 @@ public class Jalview + "-pileup FILE\tCreate alignment file FILE in Pileup format\n" + "-pir FILE\tCreate alignment file FILE in PIR format.\n" + "-blc FILE\tCreate alignment file FILE in BLC format.\n" + + "-json FILE\tCreate alignment file FILE in JSON format.\n" + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n" + "-png FILE\tCreate PNG image FILE from alignment.\n" + "-svg FILE\tCreate SVG image FILE from alignment.\n" @@ -634,6 +793,7 @@ public class Jalview + "-eps FILE\tCreate EPS file FILE from alignment.\n" + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n" + "-noquestionnaire\tTurn off questionnaire check.\n" + + "-nonews\tTurn off check for Jalview news.\n" + "-nousagestats\tTurn off google analytics tracking for this session.\n" + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n" // + @@ -655,8 +815,8 @@ public class Jalview /** * start a User Config prompt asking if we can log usage statistics. */ - jalview.gui.PromptUserConfig prompter = new jalview.gui.PromptUserConfig( - desktop.desktop, + PromptUserConfig prompter = new PromptUserConfig( + Desktop.desktop, "USAGESTATS", "Jalview Usage Statistics", "Do you want to help make Jalview better by enabling " @@ -664,6 +824,7 @@ public class Jalview + "\n\n(you can enable or disable usage tracking in the preferences)", new Runnable() { + @Override public void run() { Cache.log @@ -673,6 +834,7 @@ public class Jalview } }, new Runnable() { + @Override public void run() { Cache.log.debug("Not enabling Google Tracking."); @@ -690,14 +852,8 @@ public class Jalview * the Jalview Desktop object passed in to the groovy binding as the * 'Jalview' object. */ - private static void executeGroovyScript(String groovyscript, - Object[] jalviewContext) + private void executeGroovyScript(String groovyscript, AlignFrame af) { - if (jalviewContext == null) - { - System.err - .println("Sorry. Groovy support is currently only available when running with the Jalview GUI enabled."); - } /** * for scripts contained in files */ @@ -714,8 +870,8 @@ public class Jalview tfile = File.createTempFile("jalview", "groovy"); PrintWriter outfile = new PrintWriter(new OutputStreamWriter( new FileOutputStream(tfile))); - BufferedReader br = new BufferedReader( - new java.io.InputStreamReader(System.in)); + BufferedReader br = new BufferedReader(new InputStreamReader( + System.in)); String line = null; while ((line = br.readLine()) != null) { @@ -779,76 +935,23 @@ public class Jalview } } } - boolean success = false; try { - /* - * The following code performs the GroovyScriptEngine invocation using - * reflection, and is equivalent to this fragment from the embedding - * groovy documentation on the groovy site: import - * groovy.lang.Binding; import groovy.util.GroovyScriptEngine; - * - * String[] roots = new String[] { "/my/groovy/script/path" }; - * GroovyScriptEngine gse = new GroovyScriptEngine(roots); Binding binding - * = new Binding(); binding.setVariable("input", "world"); - * gse.run("hello.groovy", binding); - */ - Class[] bspec; - Object[] binding; - int blen = ((jalviewContext[0] == null) ? 0 : 1) - + ((jalviewContext[1] == null) ? 0 : 1); - String cnames[] = new String[] - { "Jalview", "currentAlFrame" }; - bspec = new Class[blen * 2]; - binding = new Object[blen * 2]; - blen = 0; - ClassLoader cl = null; - Map vbinding = new Hashtable(); - for (int jc = 0; jc < jalviewContext.length; jc++) + Map vbinding = new HashMap(); + vbinding.put("Jalview", this); + if (af != null) { - if (jalviewContext[jc] != null) - { - if (cl == null) - { - cl = jalviewContext[jc].getClass().getClassLoader(); - } - bspec[blen * 2] = String.class; - bspec[blen * 2 + 1] = Object.class; - binding[blen * 2] = cnames[jc]; - binding[blen * 2 + 1] = jalviewContext[jc]; - vbinding.put(cnames[jc], jalviewContext[jc]); - blen++; - } + vbinding.put("currentAlFrame", af); } - Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons; - Object gbinding; - try - { - gbcons = gbindingc.getConstructor(Map.class); - gbinding = gbcons.newInstance(vbinding); - } catch (NoSuchMethodException x) + Binding gbinding = new Binding(vbinding); + GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile }); + gse.run(sfile.toString(), gbinding); + if ("STDIN".equals(groovyscript)) { - // old style binding config - using series of string/object values to - // setVariable. - gbcons = gbindingc.getConstructor(null); - gbinding = gbcons.newInstance(null); - java.lang.reflect.Method setvar = gbindingc.getMethod( - "setVariable", bspec); - setvar.invoke(gbinding, binding); + // delete temp file that we made - + // only if it was successfully executed + tfile.delete(); } - ; - Class gsec = cl.loadClass("groovy.util.GroovyScriptEngine"); - Constructor gseccons = gsec.getConstructor(new Class[] - { URL[].class }); // String[].class }); - Object gse = gseccons.newInstance(new Object[] - { new URL[] - { sfile } }); // .toString() } }); - java.lang.reflect.Method run = gsec.getMethod("run", new Class[] - { String.class, gbindingc }); - run.invoke(gse, new Object[] - { sfile.toString(), gbinding }); - success = true; } catch (Exception e) { System.err.println("Exception Whilst trying to execute file " + sfile @@ -856,12 +959,6 @@ public class Jalview e.printStackTrace(System.err); } - if (success && groovyscript.equals("STDIN")) - { - // delete temp file that we made - but only if it was successfully - // executed - tfile.delete(); - } } /** @@ -869,16 +966,15 @@ public class Jalview * * @return vector of DAS source nicknames to retrieve from */ - private static Vector checkDasArguments(ArgsParser aparser) + private static Vector checkDasArguments(ArgsParser aparser) { - Vector source = null; + Vector source = null; String data; String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); while ((data = aparser.getValue("dasserver", true)) != null) { String nickname = null; String url = null; - boolean seq = false, feat = true; int pos = data.indexOf('='); // determine capabilities if (pos > 0) @@ -908,10 +1004,12 @@ public class Jalview + nickname + "|" + url); if (source == null) { - source = new Vector(); + source = new Vector(); } source.addElement(nickname); } + System.out.println("CMD [-dasserver " + data + + "] executed successfully!"); } // loop until no more server entries are found. if (locsources != null && locsources.indexOf('|') > -1) { @@ -924,7 +1022,7 @@ public class Jalview System.out.println("adding source '" + data + "'"); if (source == null) { - source = new Vector(); + source = new Vector(); } source.addElement(data); } @@ -936,10 +1034,11 @@ public class Jalview * * @param dasSources */ - private static FeatureFetcher startFeatureFetching(final Vector dasSources) + private FeatureFetcher startFeatureFetching( + final Vector dasSources) { FeatureFetcher ff = new FeatureFetcher(); - AlignFrame afs[] = Desktop.getAlignframes(); + AlignFrame afs[] = Desktop.getAlignFrames(); if (afs == null || afs.length == 0) { return null; @@ -950,172 +1049,47 @@ public class Jalview } return ff; } -} - -/** - * Notes: this argParser does not distinguish between parameter switches, - * parameter values and argument text. If an argument happens to be identical to - * a parameter, it will be taken as such (even though it didn't have a '-' - * prefixing it). - * - * @author Andrew Waterhouse and JBP documented. - * - */ - -class rnabuttonlistener implements ActionListener -{ - public void actionPerformed(ActionEvent arg0) - { - System.out.println("Good idea ! "); - - } -} - -class pbuttonlistener implements ActionListener -{ - public void actionPerformed(ActionEvent arg0) - { - - } -} - -class ArgsParser -{ - Vector vargs = null; - public ArgsParser(String[] args) + public static boolean isHeadlessMode() { - vargs = new Vector(); - for (int i = 0; i < args.length; i++) + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) { - String arg = args[i].trim(); - if (arg.charAt(0) == '-') - { - arg = arg.substring(1); - } - vargs.addElement(arg); + return true; } + return false; } - /** - * check for and remove first occurence of arg+parameter in arglist. - * - * @param arg - * @return return the argument following the given arg if arg was in list. - */ - public String getValue(String arg) + public AlignFrame[] getAlignFrames() { - return getValue(arg, false); - } + return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } + : Desktop.getAlignFrames(); - public String getValue(String arg, boolean utf8decode) - { - int index = vargs.indexOf(arg); - String dc = null, ret = null; - if (index != -1) - { - ret = vargs.elementAt(index + 1).toString(); - vargs.removeElementAt(index); - vargs.removeElementAt(index); - if (utf8decode && ret != null) - { - try - { - dc = URLDecoder.decode(ret, "UTF-8"); - ret = dc; - } catch (Exception e) - { - // TODO: log failure to decode - } - } - } - return ret; } /** - * check for and remove first occurence of arg in arglist. - * - * @param arg - * @return true if arg was present in argslist. + * Quit method delegates to Desktop.quit - unless running in headless mode + * when it just ends the JVM */ - public boolean contains(String arg) + public void quit() { - if (vargs.contains(arg)) + if (desktop != null) { - vargs.removeElement(arg); - return true; + desktop.quit(); } else { - return false; + System.exit(0); } } - public String nextValue() + public static AlignFrame getCurrentAlignFrame() { - return vargs.remove(0).toString(); + return Jalview.currentAlignFrame; } - public int getSize() + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) { - return vargs.size(); + Jalview.currentAlignFrame = currentAlignFrame; } - } - -/** - * keep track of feature fetching tasks. - * - * @author JimP - * - */ -class FeatureFetcher -{ - /* - * TODO: generalise to track all jalview events to orchestrate batch - * processing events. - */ - - private int queued = 0; - - private int running = 0; - - public FeatureFetcher() - { - - } - - public void addFetcher(final AlignFrame af, final Vector dasSources) - { - final long id = System.currentTimeMillis(); - queued++; - final FeatureFetcher us = this; - new Thread(new Runnable() - { - - public void run() - { - synchronized (us) - { - queued--; - running++; - } - - af.setProgressBar(MessageManager.getString("status.das_features_being_retrived"), id); - af.featureSettings_actionPerformed(null); - af.featureSettings.fetchDasFeatures(dasSources, true); - af.setProgressBar(null, id); - synchronized (us) - { - running--; - } - } - }).start(); - } - - public synchronized boolean allFinished() - { - return queued == 0 && running == 0; - } - -};