X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0ec9ee0e685c5e38f347014808b105283af6f945;hb=refs%2Fheads%2FJAL-3253-applet-SwingJS-omnibus;hp=cb2b469de9a1929909536d97f5ff9e09bf43fb59;hpb=4b0220906ff60a04786c3f3eb95fa306407f27c7;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index cb2b469..0ec9ee0 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,32 +20,50 @@ */ package jalview.bin; +import jalview.api.AlignCalcWorkerI; +import jalview.api.AlignFrameI; import jalview.api.AlignViewportI; import jalview.api.JalviewApp; +import jalview.api.StructureSelectionManagerProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +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 java.applet.AppletContext; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -63,17 +81,17 @@ 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.SwingUtilities; import javax.swing.UIManager; import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; +import netscape.javascript.JSObject; /** * Main class for Jalview Application
@@ -90,18 +108,17 @@ import groovy.util.GroovyScriptEngine; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements ApplicationSingletonI, JalviewJSApi { public static Jalview getInstance() { - Instance i = Instance.getInstance(); - return (i.jalview == null ? i.jalview = new Jalview() : i.jalview); + return (Jalview) ApplicationSingletonProvider + .getInstance(Jalview.class); } - public Jalview() + private Jalview() { - Instance.getInstance().jalview = this; } static @@ -124,6 +141,36 @@ public class Jalview public String appletResourcePath; + JalviewAppLoader appLoader; + + protected JSFunctionExec jsFunctionExec; + + private boolean noCalculation, noMenuBar, noStatus; + + private boolean noAnnotation; + + public static final String TERMINATOR_LINE = "Jalview argument parsing complete."; + + public boolean getStartCalculations() + { + return !noCalculation; + } + + public boolean getAllowMenuBar() + { + return !noMenuBar; + } + + public boolean getShowStatus() + { + return !noStatus; + } + + public boolean getShowAnnotation() + { + return !noAnnotation; + } + public static AlignFrame getCurrentAlignFrame() { return getInstance().currentAlignFrame; @@ -229,57 +276,24 @@ public class Jalview */ public static void main(String[] args) { - // setLogging(); // BH - for event debugging in JavaScript - new Jalview().doMain(args); + // Platform.startJavaLogging(); + getInstance().doMain(args); } - private static void logClass(String name) - { - // BH - for event debugging in JavaScript - ConsoleHandler consoleHandler = new ConsoleHandler(); - consoleHandler.setLevel(Level.ALL); - Logger logger = Logger.getLogger(name); - logger.setLevel(Level.ALL); - logger.addHandler(consoleHandler); - } @SuppressWarnings("unused") - private static void setLogging() - { - - /** - * @j2sIgnore - * - */ - { - System.out.println("not in js"); - } - - // BH - for event debugging in JavaScript (Java mode only) - if (!Platform.isJS()) - /** - * Java only - * - * @j2sIgnore - */ - { - Logger.getLogger("").setLevel(Level.ALL); - logClass("java.awt.EventDispatchThread"); - logClass("java.awt.EventQueue"); - logClass("java.awt.Component"); - logClass("java.awt.focus.Component"); - logClass("java.awt.focus.DefaultKeyboardFocusManager"); - } - - } - /** * @param args */ void doMain(String[] args) { - if (!Platform.isJS()) + boolean isJS = Platform.isJS(); + if (isJS) + { + Platform.setAppClass(this); + } + else { System.setSecurityManager(null); } @@ -294,7 +308,17 @@ public class Jalview String usrPropsFile = aparser.getValue(ArgsParser.PROPS); Cache.loadProperties(usrPropsFile); - if (Platform.isJS()) + + if (aparser.contains(ArgsParser.NODISPLAY) + || aparser.contains(ArgsParser.NOGUI) + || aparser.contains(ArgsParser.HEADLESS) + || "true".equals(System.getProperty("java.awt.headless"))) + { + headless = true; + setSynchronous(true); + } + + if (isJS) { isJavaAppletTag = aparser.isApplet(); if (isJavaAppletTag) @@ -325,13 +349,6 @@ public class Jalview showUsage(); System.exit(0); } - if (aparser.contains(ArgsParser.NODISPLAY) - || aparser.contains(ArgsParser.NOGUI) - || aparser.contains(ArgsParser.HEADLESS) - || "true".equals(System.getProperty("java.awt.headless"))) - { - headless = true; - } // anything else! @@ -363,7 +380,7 @@ public class Jalview else { System.out.println("Executing setprop argument: " + defs); - if (Platform.isJS()) + if (isJS) { Cache.setProperty(defs.substring(0, p), defs.substring(p + 1)); } @@ -387,7 +404,13 @@ public class Jalview try { - UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); + if (!isJS && Platform.isWin()) + { + UIManager.setLookAndFeel( + headless ? "javax.swing.plaf.metal.MetalLookAndFeel" + : UIManager.getSystemLookAndFeelClassName()); + // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); + } } catch (Exception ex) { System.err.println("Unexpected Look and Feel Exception"); @@ -435,18 +458,32 @@ public class Jalview * configure 'full' SO model if preferences say to, * else use the default (SO Lite) */ - if (Cache.getDefault("USE_FULL_SO", false)) + if (Cache.getDefault(Preferences.USE_FULL_SO, false)) { - SequenceOntologyFactory.setInstance(new SequenceOntology()); + SequenceOntologyFactory.setSequenceOntology(new SequenceOntology()); } - if (!headless) + if (headless) + { + // If this is not tested, then + + if (aparser.contains(ArgsParser.NOUSAGESTATS)) + { + System.err.println("CMD [-nousagestats] executed successfully!"); + } + if (aparser.contains(ArgsParser.NOQUESTIONNAIRE)) + { + System.err.println("CMD [-noquestionnaire] executed successfully!"); + } + + } + else { - desktop = new Desktop(); + desktop = Desktop.getInstance(); desktop.setInBatchMode(true); // indicate we are starting up desktop.setVisible(true); - if (!Platform.isJS()) + if (!isJS) /** * Java only * @@ -477,7 +514,7 @@ public class Jalview } else { - if (Cache.getProperty("NOQUESTIONNAIRES") == null) + if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null) { // Start the desktop questionnaire prompter with the specified // questionnaire @@ -506,111 +543,85 @@ public class Jalview } } - String data = null; - FileFormatI format = null; - DataSourceType protocol = null; - FileLoader fileLoader = new FileLoader(!headless); + parseArguments(aparser, true); + System.err.println(TERMINATOR_LINE); + } + + /** + * Allow an outside entity to initiate the second half of argument parsing + * (only). + * + * @param args + * @return null is good + */ + @Override + public Object parseArguments(String[] args) + { + + try + { + ArgsParser aparser = new ArgsParser(args); + return parseArguments(aparser, false); + } catch (Throwable t) + { + return t; + } + } + + /** + * + * @param aparser + * @param isStartup + * @return + */ + private Object parseArguments(ArgsParser aparser, boolean isStartup) + { + boolean isJS = Platform.isJS(); + Desktop desktop = (headless ? null : Desktop.getInstance()); // script to execute after all loading is // completed one way or another // extract groovy argument and execute if necessary - String groovyscript = aparser.getValue(ArgsParser.GROOVY, true); + String groovyscript = (isJS ? null + : aparser.getValue(ArgsParser.GROOVY, true)); String file = aparser.getValue(ArgsParser.OPEN, true); + // BH this here to allow split frame; not working as of 5/17/2019 + String file2 = aparser.getValue(ArgsParser.OPEN2, true); + String fileFormat = (isJavaAppletTag + ? aparser.getAppletValue("format", null) + : null); + FileFormatI format = null; + DataSourceType protocol = null; if (file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } - String vamsasImport = aparser.getValue(ArgsParser.VDOC); - String vamsasSession = aparser.getValue(ArgsParser.VSESS); - if (vamsasImport != null || vamsasSession != null) + boolean haveImport = false;// checkStartVamas(aparser); + // Finally, deal with the remaining input data. + long progress = -1; + if (file == null && isJavaAppletTag) { - 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) + // Maybe the sequences are added as parameters + StringBuffer data = new StringBuffer("PASTE"); + int i = 1; + while ((file = aparser.getAppletValue("sequence" + i, null)) != null) { - try - { - DataSourceType viprotocol = AppletFormatAdapter - .checkProtocol(vamsasImport); - if (viprotocol == DataSourceType.FILE) - { - inSession = desktop.vamsasImport(new File(vamsasImport)); - } - else if (viprotocol == DataSourceType.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()); - } + data.append(file.toString() + "\n"); + i++; } - if (vamsasSession != null) + if (data.length() > 5) { - 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(); - } + file = data.toString(); } } - long progress = -1; - // Finally, deal with the remaining input data. + + String data; + if (file != null) { + if (!headless) { desktop.setProgressBar( @@ -618,9 +629,8 @@ public class Jalview .getString("status.processing_commandline_args"), progress = System.currentTimeMillis()); } - System.out.println("CMD [-open " + file + "] executed successfully!"); - if (!Platform.isJS()) + if (!isJS) /** * ignore in JavaScript -- can't just check file existence - could load * it? @@ -646,21 +656,83 @@ public class Jalview try { - format = new IdentifyFile().identify(file, protocol); + format = (isJavaAppletTag && fileFormat != null + ? FileFormats.getInstance().forName(fileFormat) + : null); + if (format == null) + { + format = new IdentifyFile().identify(file, protocol); + } } catch (FileFormatException e1) { // TODO ? } - AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, - format); + if (aparser.contains(ArgsParser.NOMENUBAR)) + { + noMenuBar = true; + System.out.println("CMD [nomenu] executed successfully!"); + } + + if (aparser.contains(ArgsParser.NOSTATUS)) + { + 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 { + System.out + .println("CMD [-open " + file + "] executed successfully!"); + 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); + + // TODO: file2 How to implement file2 for the applet spit screen? + data = aparser.getValue(ArgsParser.COLOUR, true); if (data != null) { @@ -705,6 +777,13 @@ public class Jalview System.out.println( "CMD [-annotations " + data + "] executed successfully!"); } + + 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(ArgsParser.SORTBYTREE)) { @@ -714,13 +793,30 @@ public class Jalview System.out.println("CMD [-sortbytree] executed successfully!"); } } - if (aparser.contains(ArgsParser.NOANNOTATION) - || aparser.contains(ArgsParser.NOANNOTATION2)) + + 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 (!af.getViewport().isShowAnnotation()) + if (aparser.contains(ArgsParser.NOANNOTATION) + || aparser.contains(ArgsParser.NOANNOTATION2)) { - System.out.println("CMD no-annotation executed successfully!"); + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + doUpdateAnnotation = true; + System.out + .println("CMD no-annotation executed successfully!"); + } } } if (aparser.contains(ArgsParser.NOSORTBYTREE)) @@ -728,10 +824,16 @@ public class Jalview 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(ArgsParser.TREE, true); if (data != null) { @@ -752,114 +854,34 @@ public class Jalview // TODO - load PDB structure(s) to alignment JAL-629 // (associate with identical sequence in alignment, or a specified // sequence) - 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, af); - System.out.println("CMD groovy[" + groovyscript - + "] executed successfully!"); - groovyscript = null; - } - if (isJavaAppletTag) { loadAppletParams(aparser, af); } - else + else if (!isJS) + /** + * Java only + * + * @j2sIgnore + */ { - - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - // PNG filename - // SVG filename - // HTML filename - // biojsmsa filename - String outputFormat = aparser.nextValue(); - 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!!"); - } - - } - - while (aparser.getSize() > 0) + if (groovyscript != null) { - System.out.println("Unknown arg: " + aparser.nextValue()); + // 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, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); + groovyscript = null; } } + createOutputFiles(aparser, af, format); + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); + } } } AlignFrame startUpAlframe = null; @@ -867,8 +889,7 @@ public class Jalview // And the user // //////////////////// - if (!Platform.isJS() && !headless && file == null - && vamsasImport == null + if (!isJS && !headless && file == null && !haveImport && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) /** * Java only @@ -911,8 +932,8 @@ public class Jalview } } - startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol, - format); + startUpAlframe = new FileLoader(!headless) + .LoadFileWaitTillLoaded(file, protocol, format); // extract groovy arguments before anything else. } @@ -940,6 +961,112 @@ public class Jalview } desktop.setInBatchMode(false); } + + return null; + } + + /** + * 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(); + // System.out.println("format " + outputFormat); + + 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() @@ -1150,6 +1277,12 @@ public class Jalview */ public void quit() { + if (jsFunctionExec != null) + { + jsFunctionExec.tidyUp(); + jsFunctionExec = null; + } + if (desktop != null) { desktop.quit(); @@ -1161,28 +1294,32 @@ public class Jalview } /** - * Get the SwingJS applet ID and combine that with the frameType + * Handle all JalviewLite applet parameters * - * @param frameType - * "alignment", "desktop", etc., or null - * @return + * @param aparser + * @param af */ - public static String getAppID(String frameType) - { - String id = Cache.getProperty("Info.j2sAppletID"); - if (id == null) - { - id = "jalview"; - } - return id + (frameType == null ? "" : "-" + frameType); - } - private void loadAppletParams(ArgsParser aparser, AlignFrame af) { - Jalview me = this; 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) @@ -1198,12 +1335,18 @@ public class Jalview : "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() { @@ -1213,79 +1356,821 @@ public class Jalview @Override public AlignViewportI getViewport() { - return Jalview.getCurrentAlignFrame().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 { - Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null, - null, null); + af.loadJalviewDataFile(sScoreFile, null, null, null); return true; } + /** + * annotations, jpredfile, jnetfile + * + */ @Override - public boolean parseFeaturesFile(String filename, - DataSourceType protocol) + public void updateForAnnotations() { - return af.parseFeaturesFile(filename, protocol); + af.updateForAnnotations(); } @Override public void loadTree(NewickFile fin, String treeFile) throws IOException { - // n/a -- already done + // n/a -- already done by standard Jalview command line processing } @Override public void setAlignPdbStructures(boolean defaultParameter) { - // TODO Auto-generated method stub - + alignPDBStructures = true; } @Override public void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol) { - // TODO Auto-generated method stub + 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) { - // TODO Auto-generated method stub + 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 void updateForLoader() + 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 void setFeatureGroupState(String[] groups, boolean state) + 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 newFeatureSettings() + 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); + } + }; - new JalviewAppLoader(true).load(app); + 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(AlignFrameI 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(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf, String sequenceIds, String columns) + { + selectIn(alf, sequenceIds, columns, null); + } + + @Override + public void selectIn(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf) + { + return getAlignmentFrom(alf, null); + } + + @Override + public String getAlignmentOrderFrom(AlignFrameI 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(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf, String format, + String suffix) + { + return appLoader.getAlignmentFrom(alf, format, suffix); + } + + @Override + public void loadAnnotation(String annotation) + { + loadAnnotationFrom(getCurrentAlignFrame(), annotation); + } + + @Override + public void loadAnnotationFrom(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf, String format) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeaturesFrom(alf, format, true, false); + } + + @Override + public String getAnnotation() + { + return getAnnotationFrom(null); + } + + @Override + public String getAnnotationFrom(AlignFrameI alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAnnotationFrom(alf); + } + + @Override + public AlignFrameI newView() + { + return newViewFrom(null, null); + } + + @Override + public AlignFrameI newView(String name) + { + return newViewFrom(null, name); + } + + @Override + public AlignFrameI newViewFrom(AlignFrameI alf) + { + return newViewFrom(alf, null); + } + + @Override + public AlignFrameI newViewFrom(AlignFrameI alf, String name) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.newViewFrom(alf, name); + } + + @Override + public AlignFrameI loadAlignment(String text, String title) + { + return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT, title); + } + + @Override + public boolean addPdbFile(AlignFrameI alFrame, String sequenceId, + String pdbEntryString, String pdbFile) + { + if (alFrame == null) + { + alFrame = getCurrentAlignFrame(); + } + return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, + pdbFile); + } + + @Override + public void scrollViewToIn(AlignFrameI alf, String topRow, + String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToIn(alf, topRow, leftHandColumn); + } + + @Override + public void scrollViewToRowIn(AlignFrameI alf, String topRow) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToRowIn(alf, topRow); + } + + @Override + public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToColumnIn(alf, leftHandColumn); + } + + @Override + public String getFeatureGroups() + { + return getFeatureGroupsOn(null); + } + + @Override + public String getFeatureGroupsOn(AlignFrameI alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOn(alf); + } + + @Override + public String getFeatureGroupsOfState(boolean visible) + { + return getFeatureGroupsOfStateOn(null, visible); + } + + @Override + public String getFeatureGroupsOfStateOn(AlignFrameI 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(AlignFrameI 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(AlignFrameI 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(AlignFrameI af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(AlignFrameI 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(AlignFrameI 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); + } + + /** + * flag to allow selected Runnable and Thread processes to run synchronously + * + * JAL-3563 + * + */ + private static boolean isSynchronous = false; + + /** + * Set Jalview to run selected processes synchronously in test and headless + * environments. + * + * JAL-3563 + * + * @param b + * @author Bob Hanson + */ + public static void setSynchronous(boolean b) + { + isSynchronous = b; + } + + /** + * Allows optional synchronous running of a Runnable that would otherwise use + * SwingUtilities.invokeLater. + * + * JAL-3563 + * + * @param t + * @author Bob Hanson + */ + public static boolean isSynchronous() + { + return isSynchronous; + } + + /** + * Allows optional synchronous running of a Runnable that would otherwise use + * SwingUtilities.invokeLater. + * + * JAL-3563 + * + * @param t + * @author Bob Hanson + */ + public static void execRunnable(Runnable r) + { + if (isSynchronous()) + { + r.run(); + } + else + { + SwingUtilities.invokeLater(r); + } + } + + /** + * Allows optional synchronous running of a thread that would otherwise be run + * using start(). + * + * JAL-3563 + * + * @param t + * @author Bob Hanson + */ + public static void execThread(Thread t) + { + if (isSynchronous()) + { + t.run(); + } + else + { + t.start(); + } + } + + /** + * 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); } -} +} \ No newline at end of file