X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=98dc0399a5d420471d75fc4d7ae311cc3e75e554;hb=b93f8af382bb2fbdb0c974558bcef57750d1bdd6;hp=bcb4e7b50fcb9b017fa5a17f4cc75d94f08d917d;hpb=e60cacff9260c47c12cf34a7e191678cfc97d265;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index bcb4e7b..98dc039 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,28 +20,46 @@ */ package jalview.bin; -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.AlignmentPanel; +import jalview.gui.CalculationChooser; import jalview.gui.Desktop; 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.FileLoader; -import jalview.io.FormatAdapter; 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.schemes.UserColourScheme; +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; +import java.applet.AppletContext; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -59,48 +77,110 @@ 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 java.util.logging.ConsoleHandler; +import java.util.logging.Level; +import java.util.logging.Logger; +import javax.swing.LookAndFeel; import javax.swing.UIManager; +import com.threerings.getdown.util.LaunchUtil; + +import groovy.lang.Binding; +import groovy.util.GroovyScriptEngine; + /** * 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 { - /* - * singleton instance of this class - */ + static + { + Platform.getURLCommandArguments(); + } + + // 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 { - // grab all the rights we can the JVM - Policy.setPolicy(new Policy() + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - @Override - public PermissionCollection getPermissions(CodeSource codesource) - { - Permissions perms = new Permissions(); - perms.add(new AllPermission()); - return (perms); - } - - @Override - public void refresh() - { - } - }); + // grab all the rights we can for the JVM + Policy.setPolicy(new Policy() + { + @Override + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + @Override + public void refresh() + { + } + }); + } } /** @@ -112,8 +192,8 @@ public class Jalview class FeatureFetcher { /* - * TODO: generalise to track all jalview events to orchestrate batch - * processing events. + * TODO: generalise to track all jalview events to orchestrate batch processing + * events. */ private int queued = 0; @@ -146,7 +226,6 @@ public class Jalview 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) { @@ -172,65 +251,100 @@ public class Jalview * main class for Jalview application * * @param args - * open filename + * open filename */ public static void main(String[] args) { + if (false) + { + Platform.startJavaLogging(); + } + instance = new Jalview(); instance.doMain(args); - } +} /** * @param args */ void doMain(String[] args) { - System.setSecurityManager(null); - System.out.println("Java version: " - + System.getProperty("java.version")); + + if (!Platform.isJS()) + { + 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")); + 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.out.println("Launcher version: " + val); + } + + // report Jalview version + Cache.loadBuildProperties(true); ArgsParser aparser = new ArgsParser(args); boolean headless = false; - if (aparser.contains("help") || aparser.contains("h")) - { - showUsage(); - System.exit(0); - } - if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) - { - System.setProperty("java.awt.headless", "true"); - headless = true; - } String usrPropsFile = aparser.getValue("props"); Cache.loadProperties(usrPropsFile); // must do this before if (usrPropsFile != null) { - System.out.println("CMD [-props " + usrPropsFile - + "] executed successfully!"); + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); } - // anything else! - - final String jabawsUrl = aparser.getValue("jabaws"); - if (jabawsUrl != null) + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - try + if (aparser.contains("help") || aparser.contains("h")) { - Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); - System.out.println("CMD [-jabaws " + jabawsUrl - + "] executed successfully!"); - } catch (MalformedURLException e) + showUsage(); + System.exit(0); + } + if (aparser.contains("nodisplay") || aparser.contains("nogui") + || aparser.contains("headless")) { - System.err.println("Invalid jabaws parameter: " + jabawsUrl - + " ignored"); + System.setProperty("java.awt.headless", "true"); + headless = true; + } + // anything else! + + final String jabawsUrl = aparser.getValue("jabaws"); + if (jabawsUrl != null) + { + try + { + Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + System.out.println( + "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); + } catch (MalformedURLException e) + { + System.err.println( + "Invalid jabaws parameter: " + jabawsUrl + " ignored"); + } } - } + } String defs = aparser.getValue("setprop"); while (defs != null) { @@ -242,9 +356,10 @@ public class Jalview else { System.out.println("Executing setprop argument: " + defs); - // DISABLED FOR SECURITY REASONS - // TODO: add a property to allow properties to be overriden by cli args - // Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + if (Platform.isJS()) + { + Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + } } defs = aparser.getValue("setprop"); } @@ -261,9 +376,8 @@ public class Jalview } catch (NoClassDefFoundError error) { error.printStackTrace(); - System.out - .println("\nEssential logging libraries not found." - + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview"); + System.out.println("\nEssential logging libraries not found." + + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"); System.exit(0); } @@ -274,28 +388,53 @@ public class Jalview UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception ex) { + System.err.println("Unexpected Look and Feel Exception"); + ex.printStackTrace(); } - if (Platform.isAMac()) + if (Platform.isAMacAndNotJS()) { + + LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel(); System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Jalview"); System.setProperty("apple.laf.useScreenMenuBar", "true"); - try + if (lookAndFeel != null) { - UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager - .getLookAndFeel()); - } catch (Throwable e) + try + { + UIManager.setLookAndFeel(lookAndFeel); + } catch (Throwable e) + { + System.err.println( + "Failed to set QuaQua look and feel: " + e.toString()); + } + } + if (lookAndFeel == null + || !(lookAndFeel.getClass().isAssignableFrom( + UIManager.getLookAndFeel().getClass())) + || !UIManager.getLookAndFeel().getClass().toString() + .toLowerCase().contains("quaqua")) { - System.err.println("Failed to set QuaQua look and feel: " - + e.toString()); + try + { + System.err.println( + "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976"); + UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel"); + } catch (Throwable e) + { + System.err.println( + "Failed to reset look and feel: " + e.toString()); + } } } /* - * configure 'full' SO model if preferences say to, - * else use the default (SO Lite) + * configure 'full' SO model if preferences say to, else use the default (full SO) + * - as JS currently doesn't have OBO parsing, it must use 'Lite' version */ - if (Cache.getDefault("USE_FULL_SO", false)) + boolean soDefault = !Platform.isJS(); + if (Cache.getDefault("USE_FULL_SO", soDefault)) { SequenceOntologyFactory.setInstance(new SequenceOntology()); } @@ -304,64 +443,101 @@ public class Jalview { desktop = new Desktop(); desktop.setInBatchMode(true); // indicate we are starting up - desktop.setVisible(true); - desktop.startServiceDiscovery(); - if (!aparser.contains("nousagestats")) + + try { - startUsageStats(desktop); - } - else + JalviewTaskbar.setTaskbar(this); + } catch (Throwable t) { - System.err.println("CMD [-nousagestats] executed successfully!"); + System.out.println("Error setting Taskbar: " + t.getMessage()); } - if (!aparser.contains("noquestionnaire")) + desktop.setVisible(true); + + if (!Platform.isJS()) + /** + * Java only + * + * @j2sIgnore + */ { - String url = aparser.getValue("questionnaire"); - if (url != null) + desktop.startServiceDiscovery(); + if (!aparser.contains("nousagestats")) { - // Start the desktop questionnaire prompter with the specified - // questionnaire - Cache.log.debug("Starting questionnaire url at " + url); - desktop.checkForQuestionnaire(url); - System.out.println("CMD questionnaire[-" + url - + "] executed successfully!"); + startUsageStats(desktop); } else { - if (Cache.getProperty("NOQUESTIONNAIRES") == null) + System.err.println("CMD [-nousagestats] executed successfully!"); + } + + if (!aparser.contains("noquestionnaire")) + { + String url = aparser.getValue("questionnaire"); + if (url != null) { // Start the desktop questionnaire prompter with the specified // questionnaire - // String defurl = - // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; - // // - String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; - Cache.log.debug("Starting questionnaire with default url: " - + defurl); - desktop.checkForQuestionnaire(defurl); + Cache.log.debug("Starting questionnaire url at " + url); + desktop.checkForQuestionnaire(url); + System.out.println("CMD questionnaire[-" + url + + "] executed successfully!"); + } + else + { + if (Cache.getProperty("NOQUESTIONNAIRES") == null) + { + // Start the desktop questionnaire prompter with the specified + // questionnaire + // String defurl = + // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; + // // + String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; + Cache.log.debug( + "Starting questionnaire with default url: " + defurl); + desktop.checkForQuestionnaire(defurl); + } } } - } - else - { - System.err.println("CMD [-noquestionnaire] executed successfully!"); - } + else + { + System.err + .println("CMD [-noquestionnaire] executed successfully!"); + } - if (!aparser.contains("nonews")) - { - desktop.checkForNews(); + if (!aparser.contains("nonews")) + { + desktop.checkForNews(); + } + + BioJsHTMLOutput.updateBioJS(); } + } - BioJsHTMLOutput.updateBioJS(); + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 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(); } - String file = null, protocol = null, format = null, data = null; + String file = null, data = null; + FileFormatI format = null; + DataSourceType protocol = null; 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 // completed one way or another // extract groovy argument and execute if necessary @@ -373,118 +549,49 @@ public class Jalview System.out.println("No files to open!"); System.exit(1); } - String vamsasImport = aparser.getValue("vdoc"); - String vamsasSession = aparser.getValue("vsess"); - if (vamsasImport != null || vamsasSession != null) - { - if (desktop == null || headless) - { - System.out - .println("Headless vamsas sessions not yet supported. Sorry."); - System.exit(1); - } - // if we have a file, start a new session and import it. - boolean inSession = false; - if (vamsasImport != null) - { - try - { - String viprotocol = AppletFormatAdapter - .checkProtocol(vamsasImport); - if (viprotocol == jalview.io.FormatAdapter.FILE) - { - inSession = desktop.vamsasImport(new File(vamsasImport)); - } - else if (viprotocol == FormatAdapter.URL) - { - inSession = desktop.vamsasImport(new URL(vamsasImport)); - } - - } catch (Exception e) - { - System.err.println("Exeption when importing " + vamsasImport - + " as a vamsas document."); - e.printStackTrace(); - } - if (!inSession) - { - System.err.println("Failed to import " + vamsasImport - + " as a vamsas document."); - } - else - { - System.out.println("Imported Successfully into new session " - + desktop.getVamsasApplication().getCurrentSession()); - } - } - if (vamsasSession != null) - { - if (vamsasImport != null) - { - // close the newly imported session and import the Jalview specific - // remnants into the new session later on. - desktop.vamsasStop_actionPerformed(null); - } - // now join the new session - try - { - if (desktop.joinVamsasSession(vamsasSession)) - { - System.out.println("Successfully joined vamsas session " - + vamsasSession); - } - else - { - System.err.println("WARNING: Failed to join vamsas session " - + vamsasSession); - } - } catch (Exception e) - { - System.err.println("ERROR: Failed to join vamsas session " - + vamsasSession); - e.printStackTrace(); - } - if (vamsasImport != null) - { - // the Jalview specific remnants can now be imported into the new - // session at the user's leisure. - Cache.log - .info("Skipping Push for import of data into existing vamsas session."); // TODO: - // enable - // this - // when - // debugged - // desktop.getVamsasApplication().push_update(); - } - } - } long progress = -1; // 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("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 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); + } } } } - protocol = AppletFormatAdapter.checkProtocol(file); + protocol = AppletFormatAdapter.checkProtocol(file); - format = new IdentifyFile().identify(file, protocol); + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e1) + { + // TODO ? + } AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); @@ -500,19 +607,13 @@ public class Jalview { data.replaceAll("%20", " "); - ColourSchemeI cs = ColourSchemeProperty.getColour(af - .getViewport().getAlignment(), data); + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); - if (cs == null) - { - UserColourScheme ucs = new UserColourScheme("white"); - ucs.parseAppletParameter(data); - cs = ucs; - } - else + if (cs != null) { - System.out.println("CMD [-color " + data - + "] executed successfully!"); + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } af.changeColour(cs); } @@ -524,8 +625,8 @@ public class Jalview af.parseFeaturesFile(data, AppletFormatAdapter.checkProtocol(data)); // System.out.println("Added " + data); - System.out.println("CMD groups[-" + data - + "] executed successfully!"); + System.out.println( + "CMD groups[-" + data + "] executed successfully!"); } data = aparser.getValue("features", true); if (data != null) @@ -533,8 +634,8 @@ public class Jalview af.parseFeaturesFile(data, AppletFormatAdapter.checkProtocol(data)); // System.out.println("Added " + data); - System.out.println("CMD [-features " + data - + "] executed successfully!"); + System.out.println( + "CMD [-features " + data + "] executed successfully!"); } data = aparser.getValue("annotations", true); @@ -542,8 +643,8 @@ public class Jalview { af.loadJalviewDataFile(data, null, null, null); // System.out.println("Added " + data); - System.out.println("CMD [-annotations " + data - + "] executed successfully!"); + System.out.println( + "CMD [-annotations " + data + "] executed successfully!"); } // set or clear the sortbytree flag. if (aparser.contains("sortbytree")) @@ -574,18 +675,14 @@ public class Jalview data = aparser.getValue("tree", true); if (data != null) { - jalview.io.NewickFile fin = null; try { - System.out.println("CMD [-tree " + data - + "] executed successfully!"); - fin = new NewickFile(data, + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + NewickFile nf = new NewickFile(data, AppletFormatAdapter.checkProtocol(data)); - if (fin != null) - { - af.getViewport().setCurrentTree( - af.ShowNewickTree(fin, data).getTree()); - } + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); } catch (IOException ex) { System.err.println("Couldn't add tree " + data); @@ -595,27 +692,6 @@ 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) - { - 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. - } if (groovyscript != null) { // Execute the groovy script after we've done all the rendering stuff @@ -629,17 +705,17 @@ public class Jalview String imageName = "unnamed.png"; while (aparser.getSize() > 1) { - format = aparser.nextValue(); + String outputFormat = aparser.nextValue(); file = aparser.nextValue(); - if (format.equalsIgnoreCase("png")) + if (outputFormat.equalsIgnoreCase("png")) { af.createPNG(new File(file)); imageName = (new File(file)).getName(); System.out.println("Creating PNG image: " + file); continue; } - else if (format.equalsIgnoreCase("svg")) + else if (outputFormat.equalsIgnoreCase("svg")) { File imageFile = new File(file); imageName = imageFile.getName(); @@ -647,7 +723,7 @@ public class Jalview System.out.println("Creating SVG image: " + file); continue; } - else if (format.equalsIgnoreCase("html")) + else if (outputFormat.equalsIgnoreCase("html")) { File imageFile = new File(file); imageName = imageFile.getName(); @@ -657,7 +733,7 @@ public class Jalview System.out.println("Creating HTML image: " + file); continue; } - else if (format.equalsIgnoreCase("biojsmsa")) + else if (outputFormat.equalsIgnoreCase("biojsmsa")) { if (file == null) { @@ -666,34 +742,35 @@ public class Jalview } try { - BioJsHTMLOutput - .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + 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); + System.out + .println("Creating BioJS MSA Viwer HTML file: " + file); continue; } - else if (format.equalsIgnoreCase("imgMap")) + else if (outputFormat.equalsIgnoreCase("imgMap")) { af.createImageMap(new File(file), imageName); System.out.println("Creating image map: " + file); continue; } - else if (format.equalsIgnoreCase("eps")) + else if (outputFormat.equalsIgnoreCase("eps")) { File outputFile = new File(file); - System.out.println("Creating EPS file: " - + outputFile.getAbsolutePath()); + System.out.println( + "Creating EPS file: " + outputFile.getAbsolutePath()); af.createEPS(outputFile); continue; } - if (af.saveAlignment(file, format)) + af.saveAlignment(file, format); + if (af.isSaveAlignmentSuccessful()) { System.out.println("Written alignment in " + format + " format to " + file); @@ -717,54 +794,54 @@ public class Jalview // And the user // //////////////////// - if (!headless && file == null && vamsasImport == null - && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) + if (!Platform.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", + 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 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); - } - } + // Once all other stuff is done, execute any groovy scripts (in order) if (groovyscript != null) { @@ -775,8 +852,8 @@ public class Jalview } 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); } } @@ -793,8 +870,8 @@ public class Jalview 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" @@ -822,15 +899,12 @@ public class Jalview + "-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"); } @@ -840,10 +914,8 @@ public class Jalview /** * start a User Config prompt asking if we can log usage statistics. */ - PromptUserConfig prompter = new 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)", @@ -852,8 +924,8 @@ public class Jalview @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."); } @@ -872,10 +944,10 @@ public class Jalview * Locate the given string as a file and pass it to the groovy interpreter. * * @param groovyscript - * the script to execute + * the script to execute * @param jalviewContext - * the Jalview Desktop object passed in to the groovy binding as the - * 'Jalview' object. + * the Jalview Desktop object passed in to the groovy + * binding as the 'Jalview' object. */ private void executeGroovyScript(String groovyscript, AlignFrame af) { @@ -893,10 +965,10 @@ public class Jalview try { tfile = File.createTempFile("jalview", "groovy"); - PrintWriter outfile = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(tfile))); - BufferedReader br = new BufferedReader(new InputStreamReader( - System.in)); + PrintWriter outfile = new PrintWriter( + new OutputStreamWriter(new FileOutputStream(tfile))); + BufferedReader br = new BufferedReader( + new InputStreamReader(System.in)); String line = null; while ((line = br.readLine()) != null) { @@ -909,8 +981,8 @@ 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; } @@ -919,8 +991,8 @@ 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; @@ -962,7 +1034,7 @@ public class Jalview } try { - Map vbinding = new HashMap(); + Map vbinding = new HashMap<>(); vbinding.put("Jalview", this); if (af != null) { @@ -986,95 +1058,6 @@ public class Jalview } } - /** - * Check commandline for any das server definitions or any fetchfrom switches - * - * @return vector of DAS source nicknames to retrieve from - */ - private static Vector checkDasArguments(ArgsParser aparser) - { - 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; - int pos = data.indexOf('='); - // determine capabilities - if (pos > 0) - { - nickname = data.substring(0, pos); - } - url = data.substring(pos + 1); - if (url != null - && (url.startsWith("http:") || url - .startsWith("sequence:http:"))) - { - 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) - { - 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) - { - Cache.log.debug("Setting local source list in properties file to:\n" - + locsources); - Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources); - } - while ((data = aparser.getValue("fetchfrom", true)) != null) - { - System.out.println("adding source '" + data + "'"); - if (source == null) - { - source = new Vector(); - } - source.addElement(data); - } - return source; - } - - /** - * start a feature fetcher for every alignment frame - * - * @param dasSources - */ - private FeatureFetcher startFeatureFetching( - final Vector dasSources) - { - FeatureFetcher ff = new FeatureFetcher(); - AlignFrame afs[] = Desktop.getAlignFrames(); - if (afs == null || afs.length == 0) - { - return null; - } - for (int i = 0; i < afs.length; i++) - { - ff.addFetcher(afs[i], dasSources); - } - return ff; - } - public static boolean isHeadlessMode() { String isheadless = System.getProperty("java.awt.headless"); @@ -1093,8 +1076,8 @@ public class Jalview } /** - * Quit method delegates to Desktop.quit - unless running in headless mode - * when it just ends the JVM + * Quit method delegates to Desktop.quit - unless running in headless mode when + * it just ends the JVM */ public void quit() { @@ -1117,4 +1100,817 @@ public class Jalview { 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 + * + * @param aparser + * @param af + */ + private void loadAppletParams(ArgsParser aparser, AlignFrame af) + { + JalviewApp app = new JalviewApp() + { + + // 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) + { + return aparser.getAppletValue(name, null); + } + + @Override + public boolean getDefaultParameter(String name, boolean def) + { + 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); + } + + @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) + { + 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 + } + return null; + } + + @Override + public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp) + { + return new jalview.gui.FeatureRenderer((AlignmentPanel) vp); + } + + }; + + 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) + { + alf = getCurrentAlignFrame(); + } + 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) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesFrom(alf, sep); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + @Override + public void highlight(String sequenceId, String position, + String alignedPosition) + { + highlightIn(null, sequenceId, position, + alignedPosition); + } + + @Override + public void highlightIn(AlignFrame alf, String sequenceId, + String position, String alignedPosition) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + 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) + { + alf = getCurrentAlignFrame(); + } + appLoader.selectIn(alf, sequenceIds, columns, sep); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, + format, suffix); + } + + @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() + { + return getAlignmentFrom(getCurrentAlignFrame(), null); + } + + @Override + public String getAlignmentOrderFrom(AlignFrame alf) + { + return getAlignmentFrom(alf, null); + } + + @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); + } + + @Override + public String orderBy(String order, String undoName, String sep) + { + return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep); + } + + @Override + public String orderAlignmentBy(AlignFrame alf, String order, + String undoName, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.orderAlignmentBy(alf, order, undoName, sep); + } + + @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) + { + loadAnnotationFrom(getCurrentAlignFrame(), annotation); + } + + @Override + public void loadAnnotationFrom(AlignFrame alf, String annotation) + { + if (alf == null) + { + 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 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); + } + + /** + * public static method for JalviewJS API to open a PCAPanel without + * necessarily using a dialog. + * + * @param af + * @param modelName + * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences" + * if number of sequences selected is inappropriate + */ + @Override + public Object openPcaPanel(AlignFrame af, String modelName) + { + if (af == null) + { + af = getCurrentAlignFrame(); + } + 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) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, + "" + suffix); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public String[] separatorListToArray(String list) + { + return appLoader.separatorListToArray(list); + } + + //// probably not needed in JalviewJS -- From when Jmol and Jalview did not + //// have a direct connection? + + @Override + public void setMouseoverListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setMouseoverListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @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 + + } + + @Override + public void mouseOverStructure(String pdbResNum, String chain, + String pdbfile) + { + // 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); + } + + @Override + public Object parseArguments(String[] args) + { + // TODO Auto-generated method stub + return null; + } + + + + }