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=b39f0e2cd4b753d9c1102f3d8e63ea6256f8c6f9;hpb=2ea1fb1e8751ac7272c421820000449525664f02;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index b39f0e2..0ec9ee0 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,14 +20,22 @@ */ 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; @@ -44,12 +52,18 @@ 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; @@ -67,17 +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
@@ -94,7 +108,7 @@ import groovy.util.GroovyScriptEngine; * @author $author$ * @version $Revision$ */ -public class Jalview implements ApplicationSingletonI +public class Jalview implements ApplicationSingletonI, JalviewJSApi { public static Jalview getInstance() @@ -127,6 +141,36 @@ public class Jalview implements ApplicationSingletonI 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; @@ -232,50 +276,12 @@ public class Jalview implements ApplicationSingletonI */ public static void main(String[] args) { - // setLogging(); // BH - for event debugging in JavaScript + // 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 */ @@ -283,7 +289,11 @@ public class Jalview implements ApplicationSingletonI { boolean isJS = Platform.isJS(); - if (!isJS) + if (isJS) + { + Platform.setAppClass(this); + } + else { System.setSecurityManager(null); } @@ -298,6 +308,16 @@ public class Jalview implements ApplicationSingletonI String usrPropsFile = aparser.getValue(ArgsParser.PROPS); Cache.loadProperties(usrPropsFile); + + 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(); @@ -329,13 +349,6 @@ public class Jalview implements ApplicationSingletonI 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! @@ -391,7 +404,13 @@ public class Jalview implements ApplicationSingletonI 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"); @@ -444,7 +463,21 @@ public class Jalview implements ApplicationSingletonI 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 = Desktop.getInstance(); desktop.setInBatchMode(true); // indicate we are starting up @@ -510,15 +543,50 @@ public class Jalview implements ApplicationSingletonI } } + 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 = (isJS ? null : aparser.getValue(ArgsParser.GROOVY, true)); String file = aparser.getValue(ArgsParser.OPEN, true); - String file2 = (isJavaAppletTag ? aparser.getAppletValue("file2", null) - : null); + // 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); @@ -530,11 +598,30 @@ public class Jalview implements ApplicationSingletonI System.out.println("No files to open!"); System.exit(1); } - boolean haveImport = checkStartVamas(aparser); + boolean haveImport = false;// checkStartVamas(aparser); // Finally, deal with the remaining input data. long progress = -1; + if (file == null && isJavaAppletTag) + { + // Maybe the sequences are added as parameters + StringBuffer data = new StringBuffer("PASTE"); + int i = 1; + while ((file = aparser.getAppletValue("sequence" + i, null)) != null) + { + data.append(file.toString() + "\n"); + i++; + } + if (data.length() > 5) + { + file = data.toString(); + } + } + + String data; + if (file != null) { + if (!headless) { desktop.setProgressBar( @@ -581,9 +668,32 @@ public class Jalview implements ApplicationSingletonI // TODO ? } - AlignFrame af = new FileLoader(!headless).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"); @@ -602,9 +712,8 @@ public class Jalview implements ApplicationSingletonI { // TODO ? } - AlignFrame af2 = new FileLoader(!headless).loadFileWaitTillLoaded( - file2, - protocol, format); + AlignFrame af2 = new FileLoader(!headless) + .LoadFileWaitTillLoaded(file2, protocol, format); if (af2 == null) { System.out.println("error"); @@ -615,6 +724,8 @@ public class Jalview implements ApplicationSingletonI af.getViewport().getAlignment(), af2.getViewport().getAlignment(), "", AlignViewport.SPLIT_FRAME); + System.out.println( + "CMD [-open2 " + file2 + "] executed successfully!"); } } @@ -622,7 +733,7 @@ public class Jalview implements ApplicationSingletonI // TODO: file2 How to implement file2 for the applet spit screen? - String data = aparser.getValue(ArgsParser.COLOUR, true); + data = aparser.getValue(ArgsParser.COLOUR, true); if (data != null) { data.replaceAll("%20", " "); @@ -666,6 +777,13 @@ public class Jalview implements ApplicationSingletonI 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)) { @@ -675,13 +793,30 @@ public class Jalview implements ApplicationSingletonI 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)) @@ -689,10 +824,16 @@ public class Jalview implements ApplicationSingletonI 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) { @@ -735,11 +876,11 @@ public class Jalview implements ApplicationSingletonI + "] executed successfully!"); groovyscript = null; } - checkOutputFile(aparser, af, format); - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); - } + } + createOutputFiles(aparser, af, format); + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); } } } @@ -792,8 +933,7 @@ public class Jalview implements ApplicationSingletonI } startUpAlframe = new FileLoader(!headless) - .loadFileWaitTillLoaded(file, protocol, - format); + .LoadFileWaitTillLoaded(file, protocol, format); // extract groovy arguments before anything else. } @@ -821,112 +961,39 @@ public class Jalview implements ApplicationSingletonI } desktop.setInBatchMode(false); } - } - - private boolean checkStartVamas(ArgsParser aparser) - { - String vamsasImport = aparser.getValue(ArgsParser.VDOC); - String vamsasSession = aparser.getValue(ArgsParser.VSESS); - if (vamsasImport == null && vamsasSession == null) - { - return false; - } - if (desktop == null || headless) - { - System.out.println( - "Headless vamsas sessions not yet supported. Sorry."); - System.exit(1); - } - boolean haveImport = (vamsasImport != null); - if (haveImport) - { - // if we have a file, start a new session and import it. - boolean inSession = false; - 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()); - } - } - 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(); - } - } - return haveImport; + return null; } - private void checkOutputFile(ArgsParser aparser, AlignFrame af, + /** + * 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) { - // PNG filename - // SVG filename - // HTML filename - // biojsmsa filename String outputFormat = aparser.nextValue(); String file = aparser.nextValue(); + // System.out.println("format " + outputFormat); + if (outputFormat.equalsIgnoreCase("png")) { af.createPNG(new File(file)); @@ -1210,6 +1277,12 @@ public class Jalview implements ApplicationSingletonI */ public void quit() { + if (jsFunctionExec != null) + { + jsFunctionExec.tidyUp(); + jsFunctionExec = null; + } + if (desktop != null) { desktop.quit(); @@ -1221,23 +1294,6 @@ public class Jalview implements ApplicationSingletonI } /** - * 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 @@ -1248,8 +1304,23 @@ public class Jalview implements ApplicationSingletonI 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) { @@ -1361,9 +1432,745 @@ public class Jalview implements ApplicationSingletonI "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); + } + }; - 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