X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=e98ea638a5b8d0cc0844d8beca81dcd1612c6d79;hb=564c47bdd60cf84046269e45d2f85f39408e4441;hp=50e3559272b0c3054c979567f18a092288608304;hpb=55356b1071b5352edd68ce25a5d3dc3c60dcdc2d;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 50e3559..e98ea63 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. * @@ -20,64 +20,234 @@ */ package jalview.bin; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.io.HtmlSvgOutput; -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.URISyntaxException; 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.HashMap; import java.util.Hashtable; import java.util.Map; import java.util.Vector; +import javax.swing.LookAndFeel; import javax.swing.UIManager; +import com.threerings.getdown.util.LaunchUtil; + +import groovy.lang.Binding; +import groovy.util.GroovyScriptEngine; +import jalview.api.AlignCalcWorkerI; +import jalview.api.AlignViewportI; +import jalview.api.JalviewApp; +import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.ext.so.SequenceOntology; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.AlignmentPanel; +import jalview.gui.CalculationChooser; +import jalview.gui.Desktop; +import jalview.gui.Preferences; +import jalview.gui.PromptUserConfig; +import jalview.gui.StructureViewer; +import jalview.io.AppletFormatAdapter; +import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.FileLoader; +import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.NewickFile; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.javascript.JSFunctionExec; +import jalview.javascript.MouseOverStructureListener; +import jalview.renderer.seqfeatures.FeatureRenderer; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.structure.SelectionSource; +import jalview.structure.VamsasSource; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; +import netscape.javascript.JSObject; + /** * Main class for Jalview Application
*
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview + * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \ + * jalview.bin.Jalview + * + * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \ + * jalview.bin.Jalview jalview.bin.Jalview + * + * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not + * embellish '*' to e.g. '*.jar') * * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements JalviewJSApi { static { - // grab all the rights we can the JVM - Policy.setPolicy(new Policy() + Platform.getURLCommandArguments(); + } + + private boolean headless; + + // singleton instance of this class + + private static Jalview instance; + + private Desktop desktop; + + public static AlignFrame currentAlignFrame; + + public boolean isJavaAppletTag; + + public String appletResourcePath; + + JalviewAppLoader appLoader; + + protected JSFunctionExec jsFunctionExec; + + private boolean noCalculation, noMenuBar, noStatus; + + private boolean noAnnotation; + + public boolean getStartCalculations() + { + return !noCalculation; + } + + public boolean getAllowMenuBar() + { + return !noMenuBar; + } + + public boolean getShowStatus() + { + return !noStatus; + } + + public boolean getShowAnnotation() + { + return !noAnnotation; + } + + static + { + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - public PermissionCollection getPermissions(CodeSource codesource) + // grab all the rights we can for the JVM + Policy.setPolicy(new Policy() { - Permissions perms = new Permissions(); - perms.add(new AllPermission()); - return (perms); - } + @Override + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + @Override + public void refresh() + { + } + }); + } + } + + /** + * 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 refresh() + } + + 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.setProgressBar(null, id); + synchronized (us) + { + running--; + } + } + }).start(); + } + + public synchronized boolean allFinished() + { + return queued == 0 && running == 0; + } + + } + + public static Jalview getInstance() + { + return instance; } + + + private final static boolean doPlatformLogging = false; /** * main class for Jalview application @@ -87,49 +257,122 @@ public class Jalview */ public static void main(String[] args) { - System.out.println("Java version: " - + System.getProperty("java.version")); + if (doPlatformLogging) + { + Platform.startJavaLogging(); + } + + instance = new Jalview(); + instance.doMain(args); + } + + /** + * @param args + */ + void doMain(String[] args) + { + + boolean isJS = Platform.isJS(); + if (isJS) + { + Platform.setAppClass(this); + } + else + { + System.setSecurityManager(null); + } + + System.out + .println("Java version: " + System.getProperty("java.version")); + System.out.println("Java Home: " + System.getProperty("java.home")); System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); - if (new Platform().isAMac()) + String val = System.getProperty("sys.install4jVersion"); + if (val != null) + { + System.out.println("Install4j version: " + val); + } + val = System.getProperty("installer_template_version"); + if (val != null) + { + System.out.println("Install4j template version: " + val); + } + val = System.getProperty("launcher_version"); + if (val != null) { - System.setProperty("com.apple.mrj.application.apple.menu.about.name", - "Jalview"); - System.setProperty("apple.laf.useScreenMenuBar", "true"); + System.out.println("Launcher version: " + val); } + // report Jalview version + Cache.loadBuildProperties(true); + ArgsParser aparser = new ArgsParser(args); - boolean headless = false; + headless = false; + + String usrPropsFile = aparser.getValue("props"); + + Cache.loadProperties(usrPropsFile); // must do this before - if (aparser.contains("help") || aparser.contains("h")) + if (isJS) { - showUsage(); - System.exit(0); + isJavaAppletTag = aparser.isApplet(); + if (isJavaAppletTag) + { + Preferences.setAppletDefaults(); + Cache.loadProperties(usrPropsFile); // again, because we + // might be changing defaults here? + } + System.out.println( + " found: " + aparser.getValue("Info.j2sAppletID")); + appletResourcePath = aparser.getValue("Info.resourcePath"); } - if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) + else + /** + * Java only + * + * @j2sIgnore + */ { - System.setProperty("java.awt.headless", "true"); - headless = true; - } - Cache.loadProperties(aparser.getValue("props")); // must do this before - // anything else! - final String jabawsUrl = aparser.getValue("jabaws"); - if (jabawsUrl != null) - { - try + if (usrPropsFile != null) { - Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); - } catch (MalformedURLException e) + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); + } + if (aparser.contains("help") || aparser.contains("h")) { - System.err.println("Invalid jabaws parameter: " + jabawsUrl - + " ignored"); + showUsage(); + System.exit(0); + } + // ?>> + if (aparser.contains("nodisplay") || aparser.contains("nogui") + || aparser.contains("headless")) + { + System.setProperty("java.awt.headless", "true"); + headless = true; + } + // < 0) + { + final File appdir = new File(appdirString); + new Thread() + { + @Override + public void run() + { + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); } + + // completed one way or another + // extract groovy argument and execute if necessary + groovyscript = aparser.getValue("groovy", true); + } + + String file = aparser.getValue("open", true); + + if (file == null && desktop == null) + { + System.out.println("No files to open!"); + System.exit(1); + } + long progress = -1; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + FileFormatI format = null; // Finally, deal with the remaining input data. if (file != null) { 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 (!Platform.isJS()) + /** + * ignore in JavaScript -- can't just file existence - could load it? + * + * @j2sIgnore + */ { - if (!(new java.io.File(file)).exists()) + if (!file.startsWith("http://") && !file.startsWith("https://")) + // BH 2019 added https check for Java { - System.out.println("Can't find " + file); - if (headless) + if (!(new File(file)).exists()) { - System.exit(1); + System.out.println("Can't find " + file); + if (headless) + { + System.exit(1); + } } } } + String fileFormat = (isJavaAppletTag + ? aparser.getAppletValue("format", null) + : null); + protocol = AppletFormatAdapter.checkProtocol(file); + try + { + format = (isJavaAppletTag && fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } - protocol = jalview.io.AppletFormatAdapter.checkProtocol(file); - - format = new jalview.io.IdentifyFile().Identify(file, protocol); + if (aparser.contains(ArgsParser.NOMENUBAR)) + { + noMenuBar = true; + System.out.println("CMD [nomenu] executed successfully!"); + } - AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, - format); - if (af == null) + if (aparser.contains(ArgsParser.NOSTATUS)) { - System.out.println("error"); + noStatus = true; + System.out.println("CMD [nostatus] executed successfully!"); + } + + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) + { + noAnnotation = true; + System.out.println("CMD no-annotation executed successfully!"); + } + if (aparser.contains(ArgsParser.NOCALCULATION)) + { + noCalculation = true; + System.out.println("CMD [nocalculation] executed successfully!"); + } + + AlignFrame af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, + protocol, format); + if (af == null) + { + System.out.println("error"); } else { - data = aparser.getValue("colour", true); + // JalviewLite interface for JavaScript allows second file open + String file2 = aparser.getValue(ArgsParser.OPEN2, true); + if (file2 != null) + { + protocol = AppletFormatAdapter.checkProtocol(file2); + try + { + format = new IdentifyFile().identify(file2, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } + AlignFrame af2 = new FileLoader(!headless) + .LoadFileWaitTillLoaded(file2, protocol, format); + if (af2 == null) + { + System.out.println("error"); + } + else + { + AlignViewport.openLinkedAlignmentAs(af, + af.getViewport().getAlignment(), + af2.getViewport().getAlignment(), "", + AlignViewport.SPLIT_FRAME); + System.out.println( + "CMD [-open2 " + file2 + "] executed successfully!"); + } + } + setCurrentAlignFrame(af); + + String data = aparser.getValue(ArgsParser.COLOUR, true); if (data != null) { data.replaceAll("%20", " "); - jalview.schemes.ColourSchemeI cs = jalview.schemes.ColourSchemeProperty - .getColour(af.getViewport().getAlignment(), data); + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); - if (cs == null) + if (cs != null) { - jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( - "white"); - ucs.parseAppletParameter(data); - cs = ucs; + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } - - System.out.println("colour is " + data); af.changeColour(cs); } // Must maintain ability to use the groups flag - data = aparser.getValue("groups", true); + data = aparser.getValue(ArgsParser.GROUPS, 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 groups[-" + data + "] executed successfully!"); } - data = aparser.getValue("features", true); + data = aparser.getValue(ArgsParser.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); + data = aparser.getValue(ArgsParser.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!"); } + + // JavaScript feature + + if (aparser.contains(ArgsParser.SHOWOVERVIEW)) + { + af.overviewMenuItem_actionPerformed(null); + System.out.println("CMD [showoverview] executed successfully!"); + } + // set or clear the sortbytree flag. - if (aparser.contains("sortbytree")) + if (aparser.contains(ArgsParser.SORTBYTREE)) { af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } } - if (aparser.contains("no-annotation")) + + boolean doUpdateAnnotation = false; + /** + * we do this earlier in JalviewJS because of a complication with + * SHOWOVERVIEW + * + * For now, just fixing this in JalviewJS. + * + * + * @j2sIgnore + * + */ { - af.getViewport().setShowAnnotation(false); + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) + { + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + doUpdateAnnotation = true; + System.out + .println("CMD no-annotation executed successfully!"); + } + } } - if (aparser.contains("nosortbytree")) + + + if (aparser.contains(ArgsParser.NOSORTBYTREE)) { af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) + { + doUpdateAnnotation = true; + System.out + .println("CMD [-nosortbytree] executed successfully!"); + } + } + if (doUpdateAnnotation) + { // BH 2019.07.24 + af.setMenusForViewport(); + af.alignPanel.updateLayout(); } - data = aparser.getValue("tree", true); + + data = aparser.getValue(ArgsParser.TREE, true); if (data != null) { - jalview.io.NewickFile fin = null; try { - fin = new jalview.io.NewickFile(data, - jalview.io.AppletFormatAdapter.checkProtocol(data)); - if (fin != null) - { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - System.out.println("Added tree " + data); - } + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + NewickFile nf = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); } catch (IOException ex) { System.err.println("Couldn't add tree " + data); @@ -429,175 +857,107 @@ public class Jalview // TODO - load PDB structure(s) to alignment JAL-629 // (associate with identical sequence in alignment, or a specified // sequence) - - getFeatures = checkDasArguments(aparser); - if (af != null && getFeatures != null) + if (isJavaAppletTag) { - FeatureFetcher ff = startFeatureFetching(getFeatures); - if (ff != null) - { - while (!ff.allFinished() || af.operationInProgress()) - { - // wait around until fetching is finished. - try - { - Thread.sleep(100); - } catch (Exception e) - { - - } - } - } - getFeatures = null; // have retrieved features - forget them now. + loadAppletParams(aparser, af); } - if (groovyscript != null) + else if (!isJS) + /** + * Java only + * + * @j2sIgnore + */ { - // 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()) + if (groovyscript != null) { + // Execute the groovy script after we've done all the rendering + // stuff + // and before any images or figures are generated. 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); - } - groovyscript = null; - } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - format = aparser.nextValue(); - file = aparser.nextValue(); - - if (format.equalsIgnoreCase("png")) - { - af.createPNG(new java.io.File(file)); - imageName = (new java.io.File(file)).getName(); - System.out.println("Creating PNG image: " + file); - continue; - } - else if (format.equalsIgnoreCase("svg")) - { - File imageFile = new java.io.File(file); - imageName = imageFile.getName(); - af.createSVG(imageFile); - System.out.println("Creating SVG image: " + file); - continue; + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + groovyscript = null; } - else if (format.equalsIgnoreCase("html")) - { - File imageFile = new java.io.File(file); - imageName = imageFile.getName(); - new HtmlSvgOutput(new java.io.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); - 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)); - continue; - } - - if (af.saveAlignment(file, format)) - { - System.out.println("Written alignment in " + format - + " format to " + file); - } - else - { - System.out.println("Error writing file " + file + " in " - + format + " format!!"); - } - } - + createOutputFiles(aparser, af, format); while (aparser.getSize() > 0) { System.out.println("Unknown arg: " + aparser.nextValue()); } } } + + AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user // //////////////////// - if (!headless && file == null && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + if (!isJS && !headless && file == null + && Cache.getDefault("SHOW_STARTUP_FILE", true)) + /** + * Java only + * + * @j2sIgnore + */ { - file = jalview.bin.Cache.getDefault( - "STARTUP_FILE", - jalview.bin.Cache.getDefault("www.jalview.org", - "http://www.jalview.org") + file = Cache.getDefault("STARTUP_FILE", + Cache.getDefault("www.jalview.org", "http://www.jalview.org") + "/examples/exampleFile_2_7.jar"); - if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")) + if (file.equals( + "http://www.jalview.org/examples/exampleFile_2_3.jar")) { // hardwire upgrade of the startup file file.replace("_2_3.jar", "_2_7.jar"); // and remove the stale setting - jalview.bin.Cache.removeProperty("STARTUP_FILE"); + Cache.removeProperty("STARTUP_FILE"); } - protocol = "File"; + protocol = DataSourceType.FILE; if (file.indexOf("http:") > -1) { - protocol = "URL"; + protocol = DataSourceType.URL; } if (file.endsWith(".jar")) { - format = "Jalview"; + format = FileFormat.Jalview; } else { - format = new jalview.io.IdentifyFile().Identify(file, protocol); + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e) + { + // TODO what? + } } startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); - getFeatures = checkDasArguments(aparser); - // extract groovy arguments before anything else. - } - // If the user has specified features to be retrieved, - // or a groovy script to be executed, do them if they - // haven't been done already - // fetch features for the default alignment - if (getFeatures != null) - { - if (startUpAlframe != null) - { - startFeatureFetching(getFeatures); - } + } + + // extract groovy arguments before anything else. // 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 { - System.err - .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script " + System.err.println( + "Sorry. Groovy Support is not available, so ignoring the provided groovy script " + groovyscript); } } + // and finally, turn off batch mode indicator - if the desktop still exists if (desktop != null) { @@ -609,10 +969,113 @@ public class Jalview } } + /** + * Writes an output file for each format (if any) specified in the + * command-line arguments. Supported formats are currently + * + * A format parameter should be followed by a parameter specifying the output + * file name. {@code imgMap} parameters should follow those for the + * corresponding alignment image output. + * + * @param aparser + * @param af + * @param format + */ + private void createOutputFiles(ArgsParser aparser, AlignFrame af, + FileFormatI format) + { + String imageName = "unnamed.png"; + while (aparser.getSize() > 1) + { + String outputFormat = aparser.nextValue(); + String file = aparser.nextValue(); + + if (outputFormat.equalsIgnoreCase("png")) + { + af.createPNG(new File(file)); + imageName = (new File(file)).getName(); + System.out.println("Creating PNG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("svg")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + af.createSVG(imageFile); + System.out.println("Creating SVG image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("html")) + { + File imageFile = new File(file); + imageName = imageFile.getName(); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(file); + System.out.println("Creating HTML image: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("biojsmsa")) + { + if (file == null) + { + System.err.println("The output html file must not be null"); + return; + } + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(file); + System.out.println("Creating BioJS MSA Viwer HTML file: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("imgMap")) + { + af.createImageMap(new File(file), imageName); + System.out.println("Creating image map: " + file); + continue; + } + else if (outputFormat.equalsIgnoreCase("eps")) + { + File outputFile = new File(file); + System.out.println( + "Creating EPS file: " + outputFile.getAbsolutePath()); + af.createEPS(outputFile); + continue; + } + + af.saveAlignment(file, format); + if (af.isSaveAlignmentSuccessful()) + { + System.out.println( + "Written alignment in " + format + " format to " + file); + } + else + { + System.out.println("Error writing file " + file + " in " + format + + " format!!"); + } + + } + + } + private static void showUsage() { - System.out - .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" + System.out.println( + "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n" + "-nodisplay\tRun Jalview without User Interface.\n" + "-props FILE\tUse the given Jalview properties file instead of users default.\n" + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n" @@ -626,26 +1089,26 @@ 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" + "-html FILE\tCreate HTML file from alignment.\n" + + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n" + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n" + "-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" // + - // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)" + // "-setprop PROPERTY=VALUE\tSet the given Jalview property, + // after all other properties files have been read\n\t + // (quote the 'PROPERTY=VALUE' pair to ensure spaces are + // passed in correctly)" + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n" - + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n" - + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n" - + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\n" + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n" - // + - // "-vdoc vamsas-document\tImport vamsas document into new session or join existing session with same URN\n" - // + "-vses vamsas-session\tJoin session with given URN\n" + "-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" + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n"); } @@ -655,24 +1118,24 @@ 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, - "USAGESTATS", - "Jalview Usage Statistics", + PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop, + "USAGESTATS", "Jalview Usage Statistics", "Do you want to help make Jalview better by enabling " + "the collection of usage statistics with Google Analytics ?" + "\n\n(you can enable or disable usage tracking in the preferences)", new Runnable() { + @Override public void run() { - Cache.log - .debug("Initialising googletracker for usage stats."); + Cache.log.debug( + "Initialising googletracker for usage stats."); Cache.initGoogleTracker(); Cache.log.debug("Tracking enabled."); } }, new Runnable() { + @Override public void run() { Cache.log.debug("Not enabling Google Tracking."); @@ -690,14 +1153,8 @@ 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 */ @@ -712,10 +1169,10 @@ public class Jalview try { tfile = File.createTempFile("jalview", "groovy"); - PrintWriter outfile = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(tfile))); + PrintWriter outfile = new PrintWriter( + new OutputStreamWriter(new FileOutputStream(tfile))); BufferedReader br = new BufferedReader( - new java.io.InputStreamReader(System.in)); + new InputStreamReader(System.in)); String line = null; while ((line = br.readLine()) != null) { @@ -728,8 +1185,8 @@ public class Jalview } catch (Exception ex) { System.err.println("Failed to read from STDIN into tempfile " - + ((tfile == null) ? "(tempfile wasn't created)" : tfile - .toString())); + + ((tfile == null) ? "(tempfile wasn't created)" + : tfile.toString())); ex.printStackTrace(); return; } @@ -738,8 +1195,8 @@ public class Jalview sfile = tfile.toURI().toURL(); } catch (Exception x) { - System.err - .println("Unexpected Malformed URL Exception for temporary file created from STDIN: " + System.err.println( + "Unexpected Malformed URL Exception for temporary file created from STDIN: " + tfile.toURI()); x.printStackTrace(); return; @@ -779,76 +1236,23 @@ 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++) - { - 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++; - } + Map vbinding = new HashMap<>(); + vbinding.put("Jalview", this); + if (af != null) + { + vbinding.put("currentAlFrame", af); } - Class gbindingc = cl.loadClass("groovy.lang.Binding"); - Constructor gbcons; - Object gbinding; - try + Binding gbinding = new Binding(vbinding); + GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile }); + gse.run(sfile.toString(), gbinding); + if ("STDIN".equals(groovyscript)) { - gbcons = gbindingc.getConstructor(Map.class); - gbinding = gbcons.newInstance(vbinding); - } catch (NoSuchMethodException x) - { - // 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); - } - ; - 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; + // delete temp file that we made - + // only if it was successfully executed + tfile.delete(); + } } catch (Exception e) { System.err.println("Exception Whilst trying to execute file " + sfile @@ -856,266 +1260,850 @@ public class Jalview e.printStackTrace(System.err); } - if (success && groovyscript.equals("STDIN")) + } + + public static boolean isHeadlessMode() + { + String isheadless = System.getProperty("java.awt.headless"); + if (isheadless != null && isheadless.equalsIgnoreCase("true")) { - // delete temp file that we made - but only if it was successfully - // executed - tfile.delete(); + return true; } + return false; + } + + public AlignFrame[] getAlignFrames() + { + return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } + : Desktop.getAlignFrames(); + } /** - * Check commandline for any das server definitions or any fetchfrom switches + * Quit method delegates to Desktop.quit - unless running in headless mode + * when it just ends the JVM + */ + public void quit() + { + if (desktop != null) + { + desktop.quit(); + } + else + { + System.exit(0); + } + } + + public static AlignFrame getCurrentAlignFrame() + { + return Jalview.currentAlignFrame; + } + + public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + { + Jalview.currentAlignFrame = currentAlignFrame; + } + + /** + * Get the SwingJS applet ID and combine that with the frameType + * + * @param frameType + * "alignment", "desktop", etc., or null + * @return + */ + public static String getAppID(String frameType) + { + String id = Cache.getProperty("Info.j2sAppletID"); + if (id == null) + { + id = "jalview"; + } + return id + (frameType == null ? "" : "-" + frameType); + } + + /** + * Handle all JalviewLite applet parameters * - * @return vector of DAS source nicknames to retrieve from + * @param aparser + * @param af */ - private static Vector checkDasArguments(ArgsParser aparser) + private void loadAppletParams(ArgsParser aparser, AlignFrame af) { - Vector source = null; - String data; - String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE); - while ((data = aparser.getValue("dasserver", true)) != null) + JalviewApp app = new JalviewApp() { - String nickname = null; - String url = null; - boolean seq = false, feat = true; - int pos = data.indexOf('='); - // determine capabilities - if (pos > 0) + + // TODO BH 2019 + // + // These are methods that are in JalviewLite that various classes call + // but are not in JalviewLiteJsApi. Or, even if they are, other classes + // call + // them to JalviewLite directly. Some may not be necessary, but they have + // to + // be at least mentioned here, or the classes calling them should + // reference + // JalviewLite itself. + + private boolean alignPDBStructures; // From JalviewLite; not implemented + + private Hashtable> jsmessages; + + private Hashtable jshashes; + + @Override + public String getParameter(String name) { - nickname = data.substring(0, pos); + return aparser.getAppletValue(name, null); } - url = data.substring(pos + 1); - if (url != null - && (url.startsWith("http:") || url - .startsWith("sequence:http:"))) + + @Override + public boolean getDefaultParameter(String name, boolean def) { - if (nickname == null) - { - nickname = url; - } - if (locsources == null) - { - locsources = ""; - } - else - { - locsources += "\t"; - } - locsources = locsources + nickname + "|" + url; - System.err - .println("NOTE! dasserver parameter not yet really supported (got args of " - + nickname + "|" + url); - if (source == null) + String stn; + return ((stn = getParameter(name)) == null ? def + : "true".equalsIgnoreCase(stn)); + } + + /** + * Get the applet-like document base even though this is an application. + */ + @Override + public URL getDocumentBase() + { + return Platform.getDocumentBase(); + } + + /** + * Get the applet-like code base even though this is an application. + */ + @Override + public URL getCodeBase() + { + return Platform.getCodeBase(); + } + + @Override + public AlignViewportI getViewport() + { + return af.getViewport(); + } + + /** + * features + * + */ + @Override + public boolean parseFeaturesFile(String filename, + DataSourceType protocol) + { + return af.parseFeaturesFile(filename, protocol); + } + + /** + * scorefile + * + */ + @Override + public boolean loadScoreFile(String sScoreFile) throws IOException + { + af.loadJalviewDataFile(sScoreFile, null, null, null); + return true; + } + + /** + * annotations, jpredfile, jnetfile + * + */ + @Override + public void updateForAnnotations() + { + af.updateForAnnotations(); + } + + @Override + public void loadTree(NewickFile fin, String treeFile) + throws IOException + { + // n/a -- already done by standard Jalview command line processing + } + + @Override + public void setAlignPdbStructures(boolean defaultParameter) + { + alignPDBStructures = true; + } + + @Override + public void newStructureView(PDBEntry pdb, SequenceI[] seqs, + String[] chains, DataSourceType protocol) + { + StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs); + } + + @Override + public void setFeatureGroupState(String[] groups, boolean state) + { + af.setFeatureGroupState(groups, state); + } + + @Override + public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, + String[][] chains, String[] protocols) + { + System.err.println( + "Jalview applet interface alignedStructureView not implemented"); + } + + @Override + public void newFeatureSettings() + { + System.err.println( + "Jalview applet interface newFeatureSettings not implemented"); + } + + private Vector jsExecQueue; + + @Override + public Vector getJsExecQueue(JSFunctionExec exec) + { + jsFunctionExec = exec; + return (jsExecQueue == null ? (jsExecQueue = new Vector<>()) + : jsExecQueue); + } + +// AppletContext deprecated +// +// @Override +// public AppletContext getAppletContext() +// { +// // TODO Auto-generated method stub +// return null; +// } +// + @Override + public boolean isJsfallbackEnabled() + { + // TODO Auto-generated method stub + return false; + } + + @Override + public JSObject getJSObject() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public StructureSelectionManagerProvider getStructureSelectionManagerProvider() + { + // TODO Q: what exactly is this? BH + return null; + } + + @Override + public void updateColoursFromMouseOver(Object source, + MouseOverStructureListener mouseOverStructureListener) + { + // TODO Auto-generated method stub + + } + + @Override + public Object[] getSelectionForListener(SequenceGroup seqsel, + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source, Object alignFrame) + { + return appLoader.getSelectionForListener(getCurrentAlignFrame(), + seqsel, colsel, hidden, source, alignFrame); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public Hashtable getJSHashes() + { + return (jshashes == null ? (jshashes = new Hashtable<>()) + : jshashes); + } + + @Override + public Hashtable> getJSMessages() + { + return (jsmessages == null ? (jsmessages = new Hashtable<>()) + : jsmessages); + } + + @Override + public Object getFrameForSource(VamsasSource source) + { + if (source != null) { - source = new Vector(); + AlignFrame af; + if (source instanceof jalview.gui.AlignViewport + && source == (af = getCurrentAlignFrame()).getViewport()) + { + // should be valid if it just generated an event! + return af; + } + // TODO: ensure that if '_af' is specified along with a handler + // function, then only events from that alignFrame are sent to that + // function } - source.addElement(nickname); + return null; + } + + @Override + public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp) + { + return new jalview.gui.FeatureRenderer((AlignmentPanel) vp); } - } // loop until no more server entries are found. - if (locsources != null && locsources.indexOf('|') > -1) + + }; + + appLoader = new JalviewAppLoader(true); + appLoader.load(app); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() + */ + @Override + public String getSelectedSequences() + { + return getSelectedSequencesFrom(getCurrentAlignFrame()); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) + */ + @Override + public String getSelectedSequences(String sep) + { + return getSelectedSequencesFrom(getCurrentAlignFrame(), sep); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame) + */ + @Override + public String getSelectedSequencesFrom(AlignFrame alf) + { + if (alf == null) { - Cache.log.debug("Setting local source list in properties file to:\n" - + locsources); - Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources); + alf = getCurrentAlignFrame(); } - while ((data = aparser.getValue("fetchfrom", true)) != null) + return getSelectedSequencesFrom(alf, null); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + @Override + public String getSelectedSequencesFrom(AlignFrame alf, String sep) + { + if (alf == null) { - System.out.println("adding source '" + data + "'"); - if (source == null) - { - source = new Vector(); - } - source.addElement(data); + alf = getCurrentAlignFrame(); } - return source; + return appLoader.getSelectedSequencesFrom(alf, sep); } /** - * start a feature fetcher for every alignment frame * - * @param dasSources + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) */ - private static FeatureFetcher startFeatureFetching(final Vector dasSources) + @Override + public void highlight(String sequenceId, String position, + String alignedPosition) { - FeatureFetcher ff = new FeatureFetcher(); - AlignFrame afs[] = Desktop.getAlignframes(); - if (afs == null || afs.length == 0) + highlightIn(null, sequenceId, position, alignedPosition); + } + + @Override + public void highlightIn(AlignFrame alf, String sequenceId, + String position, String alignedPosition) + { + if (alf == null) { - return null; + alf = getCurrentAlignFrame(); } - for (int i = 0; i < afs.length; i++) + appLoader.highlightIn(alf, sequenceId, position, alignedPosition); + } + + @Override + public void select(String sequenceIds, String columns) + { + selectIn(getCurrentAlignFrame(), sequenceIds, columns, null); + } + + @Override + public void select(String sequenceIds, String columns, String sep) + { + selectIn(null, sequenceIds, columns, sep); + } + + @Override + public void selectIn(AlignFrame alf, String sequenceIds, String columns) + { + selectIn(alf, sequenceIds, columns, null); + } + + @Override + public void selectIn(AlignFrame alf, String sequenceIds, String columns, + String sep) + { + if (alf == null) { - ff.addFetcher(afs[i], dasSources); + alf = getCurrentAlignFrame(); } - return ff; + appLoader.selectIn(alf, sequenceIds, columns, sep); } -} -/** - * 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. - * - */ + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); + } -class rnabuttonlistener implements ActionListener -{ - public void actionPerformed(ActionEvent arg0) + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); + } + + @Override + public String getAlignmentOrder() { - System.out.println("Good idea ! "); + return getAlignmentFrom(getCurrentAlignFrame(), null); + } + @Override + public String getAlignmentOrderFrom(AlignFrame alf) + { + return getAlignmentFrom(alf, null); } -} -class pbuttonlistener implements ActionListener -{ - public void actionPerformed(ActionEvent arg0) + @Override + public String getAlignmentOrderFrom(AlignFrame alf, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAlignmentOrderFrom(alf, sep); + } + @Override + public String orderBy(String order, String undoName) + { + return orderBy(order, undoName, null); } -} -class ArgsParser -{ - Vector vargs = null; + @Override + public String orderBy(String order, String undoName, String sep) + { + return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep); + } - public ArgsParser(String[] args) + @Override + public String orderAlignmentBy(AlignFrame alf, String order, + String undoName, String sep) { - vargs = new Vector(); - for (int i = 0; i < args.length; i++) + if (alf == null) { - String arg = args[i].trim(); - if (arg.charAt(0) == '-') - { - arg = arg.substring(1); - } - vargs.addElement(arg); + alf = getCurrentAlignFrame(); } + return appLoader.orderAlignmentBy(alf, order, undoName, sep); } - /** - * 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) + @Override + public String getAlignment(String format) + { + return getAlignmentFrom(null, format, null); + } + + @Override + public String getAlignmentFrom(AlignFrame alf, String format) + { + return getAlignmentFrom(alf, format, null); + } + + @Override + public String getAlignment(String format, String suffix) + { + return getAlignmentFrom(getCurrentAlignFrame(), format, suffix); + } + + @Override + public String getAlignmentFrom(AlignFrame alf, String format, + String suffix) + { + return appLoader.getAlignmentFrom(alf, format, suffix); + } + + @Override + public void loadAnnotation(String annotation) { - return getValue(arg, false); + loadAnnotationFrom(getCurrentAlignFrame(), annotation); } - public String getValue(String arg, boolean utf8decode) + @Override + public void loadAnnotationFrom(AlignFrame alf, String annotation) { - int index = vargs.indexOf(arg); - String dc = null, ret = null; - if (index != -1) + if (alf == null) { - 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 - } - } + alf = getCurrentAlignFrame(); + } + appLoader.loadAnnotationFrom(alf, annotation); + } + + @Override + public void loadFeatures(String features, boolean autoenabledisplay) + { + loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay); + } + + @Override + public boolean loadFeaturesFrom(AlignFrame alf, String features, + boolean autoenabledisplay) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay); + } + + @Override + public String getFeatures(String format) + { + return getFeaturesFrom(null, format); + } + + @Override + public String getFeaturesFrom(AlignFrame alf, String format) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); } - return ret; + return appLoader.getFeaturesFrom(alf, format); + } + + @Override + public String getAnnotation() + { + return getAnnotationFrom(null); + } + + @Override + public String getAnnotationFrom(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAnnotationFrom(alf); + } + + // @Override + // public AlignFrame newView() + // { + // return newViewFrom(null, null); + // } + // + // @Override + // public AlignFrame newView(String name) + // { + // return newViewFrom(null, name); + // } + // + // @Override + // public AlignFrame newViewFrom(AlignFrame alf) + // { + // return newViewFrom(alf, null); + // } + // + // @Override + // public AlignFrame newViewFrom(AlignFrame alf, String name) + // { + // if (alf == null) + // { + // alf = getCurrentAlignFrame(); + // } + // return appLoader.newViewFrom(alf, name); + // } + + @Override + public AlignFrame loadAlignment(String text, String title) + { + return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT, title); + } + + @Override + public boolean addPdbFile(AlignFrame alFrame, String sequenceId, + String pdbEntryString, String pdbFile) + { + if (alFrame == null) + { + alFrame = getCurrentAlignFrame(); + } + return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, + pdbFile); + } + + @Override + public void scrollViewToIn(AlignFrame alf, String topRow, + String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToIn(alf, topRow, leftHandColumn); + } + + @Override + public void scrollViewToRowIn(AlignFrame alf, String topRow) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToRowIn(alf, topRow); + } + + @Override + public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToColumnIn(alf, leftHandColumn); + } + + @Override + public String getFeatureGroups() + { + return getFeatureGroupsOn(null); + } + + @Override + public String getFeatureGroupsOn(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOn(alf); + } + + @Override + public String getFeatureGroupsOfState(boolean visible) + { + return getFeatureGroupsOfStateOn(null, visible); + } + + @Override + public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOfStateOn(alf, visible); + } + + @Override + public void setFeatureGroupState(String groups, boolean state) + { // JalviewLite API + setFeatureGroupStateOn(null, groups, state); + } + + @Override + public void setFeatureGroupStateOn(AlignFrame alf, String groups, + boolean state) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.setFeatureGroupStateOn(alf, groups, state); + } + + @Override + public String getSeparator() + { + return appLoader.getSeparator(); + } + + @Override + public void setSeparator(String separator) + { + appLoader.setSeparator(separator); + } + + @Override + public String getJsMessage(String messageclass, String viewId) + { + // see http://www.jalview.org/examples/jalviewLiteJs.html + return null; + } + + /** + * Open a new Tree panel on the desktop statically. Params are standard (not + * set by Groovy). No dialog is opened. + * + * @param af + * @param treeType + * @param modelName + * @return null, or the string "label.you_need_at_least_n_sequences" if number + * of sequences selected is inappropriate + */ + @Override + public Object openTreePanel(AlignFrame af, String treeType, + String modelName) + { // JalviewJS api + if (af == null) + { + af = getCurrentAlignFrame(); + } + return CalculationChooser.openTreePanel(af, treeType, modelName, null); } /** - * check for and remove first occurence of arg in arglist. + * public static method for JalviewJS API to open a PCAPanel without + * necessarily using a dialog. * - * @param arg - * @return true if arg was present in argslist. + * @param af + * @param modelName + * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences" + * if number of sequences selected is inappropriate */ - public boolean contains(String arg) + @Override + public Object openPcaPanel(AlignFrame af, String modelName) { - if (vargs.contains(arg)) + if (af == null) { - vargs.removeElement(arg); - return true; + af = getCurrentAlignFrame(); } - else + return CalculationChooser.openPcaPanel(af, modelName, null); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + boolean suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, boolean suffix) + { + if (alf == null) { - return false; + alf = getCurrentAlignFrame(); } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, + "" + suffix); } - public String nextValue() + @Override + public String arrayToSeparatorList(String[] array) { - return vargs.remove(0).toString(); + return appLoader.arrayToSeparatorList(array); } - public int getSize() + @Override + public String[] separatorListToArray(String list) { - return vargs.size(); + return appLoader.separatorListToArray(list); } -} + //// probably not needed in JalviewJS -- From when Jmol and Jalview did not + //// have a direct connection? -/** - * keep track of feature fetching tasks. - * - * @author JimP - * - */ -class FeatureFetcher -{ - /* - * TODO: generalise to track all jalview events to orchestrate batch - * processing events. - */ + @Override + public void setMouseoverListener(String listener) + { + // TODO Auto-generated method stub - private int queued = 0; + } + + @Override + public void setMouseoverListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub - private int running = 0; + } - public FeatureFetcher() + @Override + public void setSelectionListener(String listener) { + // TODO Auto-generated method stub } - public void addFetcher(final AlignFrame af, final Vector dasSources) + @Override + public void setSelectionListener(AlignFrame af, String listener) { - final long id = System.currentTimeMillis(); - queued++; - final FeatureFetcher us = this; - new Thread(new Runnable() - { + // TODO Auto-generated method stub - public void run() - { - synchronized (us) - { - queued--; - running++; - } + } + + @Override + public void setStructureListener(String listener, String modelSet) + { + // TODO Auto-generated method stub + + } + + @Override + public void removeJavascriptListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub - 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() + @Override + public void mouseOverStructure(String pdbResNum, String chain, + String pdbfile) { - return queued == 0 && running == 0; + // TODO Auto-generated method stub + } -}; + @Override + public void showOverview() + { + currentAlignFrame.overviewMenuItem_actionPerformed(null); + } + + public void notifyWorker(AlignCalcWorkerI worker, String status) + { + // System.out.println("Jalview worker " + worker.getClass().getSimpleName() + // + " " + status); + } + +}