X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=74babbbdc8d9ffe8a82f2ad44d852d2e9782641c;hb=8e98fa5a09e06ac59c965d030ed71b0158178a24;hp=d9de4692f1a0ca23eab66edb1d3fa50c584c77c0;hpb=1cec732f963ab102c9d8381203df8c8cba2a9ee4;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index d9de469..74babbb 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,7 +20,7 @@ */ package jalview.bin; -import jalview.api.AlignFrameI; +import jalview.api.AlignCalcWorkerI; import jalview.api.AlignViewportI; import jalview.api.JalviewApp; import jalview.api.StructureSelectionManagerProvider; @@ -83,9 +83,6 @@ 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; @@ -112,6 +109,22 @@ import netscape.javascript.JSObject; public class Jalview implements ApplicationSingletonI, JalviewJSApi { + // for testing those nasty messages you cannot ever find. + // static + // { + // System.setOut(new PrintStream(new ByteArrayOutputStream()) + // { + // @Override + // public void println(Object o) + // { + // if (o != null) + // { + // System.err.println(o); + // } + // } + // + // }); + // } public static Jalview getInstance() { return (Jalview) ApplicationSingletonProvider @@ -148,6 +161,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi private boolean noCalculation, noMenuBar, noStatus; + private boolean noAnnotation; + public boolean getStartCalculations() { return !noCalculation; @@ -163,6 +178,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi return !noStatus; } + public boolean getShowAnnotation() + { + return !noAnnotation; + } public static AlignFrame getCurrentAlignFrame() { @@ -267,53 +286,18 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi * @param args * open filename */ + @SuppressWarnings("unused") public static void main(String[] args) { - // setLogging(); // BH - for event debugging in JavaScript + if (false) + { + 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 */ @@ -321,7 +305,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi { boolean isJS = Platform.isJS(); - if (!isJS) + if (isJS) + { + Platform.setAppClass(this); + } + else { System.setSecurityManager(null); } @@ -336,6 +324,15 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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; + } + if (isJS) { isJavaAppletTag = aparser.isApplet(); @@ -367,13 +364,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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! @@ -429,7 +420,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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"); @@ -477,7 +474,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi * configure 'full' SO model if preferences say to, * else use the default (SO Lite) */ - if (Cache.getDefault(Preferences.USE_FULL_SO, false)) + // BH NOTE 2020.06.01 Jalview-JS/develop has this true for Java, false for + // JavaScript + if (Cache.getDefault(Preferences.USE_FULL_SO, !isJS)) { SequenceOntologyFactory.setSequenceOntology(new SequenceOntology()); } @@ -565,7 +564,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi try { ArgsParser aparser = new ArgsParser(args); - return parseArguments(aparser, false); + parseArguments(aparser, false); + return null; } catch (Throwable t) { return t; @@ -576,9 +576,9 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi * * @param aparser * @param isStartup - * @return + * @return null, indicating no error */ - private Object parseArguments(ArgsParser aparser, boolean isStartup) + private void parseArguments(ArgsParser aparser, boolean isStartup) { boolean isJS = Platform.isJS(); @@ -602,7 +602,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi System.out.println("No files to open!"); System.exit(1); } - boolean haveImport = checkStartVamas(aparser); // Finally, deal with the remaining input data. long progress = -1; if (file == null && isJavaAppletTag) @@ -672,14 +671,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // TODO ? } - if (aparser.contains(ArgsParser.SHOWOVERVIEW)) - { - jalview.bin.Cache.setPropertyNoSave(Preferences.SHOW_OVERVIEW, - "true"); - - System.out.println("CMD [showoverview] executed successfully!"); - } - if (aparser.contains(ArgsParser.NOMENUBAR)) { noMenuBar = true; @@ -692,6 +683,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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; @@ -734,11 +731,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi "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) { @@ -783,6 +777,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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)) { @@ -792,18 +793,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi System.out.println("CMD [-sortbytree] executed successfully!"); } } - + boolean doUpdateAnnotation = false; - - if (aparser.contains(ArgsParser.NOANNOTATION) - || aparser.contains(ArgsParser.NOANNOTATION2)) + /** + * 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)) { - doUpdateAnnotation = true; - 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)) @@ -863,20 +876,21 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi + "] 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()); } } } + AlignFrame startUpAlframe = null; // We'll only open the default file if the desktop is visible. // And the user // //////////////////// - if (!isJS && !headless && file == null && !haveImport + if (!isJS && !headless && file == null && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)) /** * Java only @@ -949,114 +963,37 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi desktop.setInBatchMode(false); } - return null; } - 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; - } - - 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)); @@ -1078,7 +1015,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi imageName = imageFile.getName(); HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); htmlSVG.exportHTML(file); - System.out.println("Creating HTML image: " + file); continue; } @@ -1644,8 +1580,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi * .AlignFrame) */ @Override - public String getSelectedSequencesFrom(AlignFrameI alf) + public String getSelectedSequencesFrom(AlignFrame alf) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return getSelectedSequencesFrom(alf, null); } @@ -1655,8 +1595,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi * .AlignFrame, java.lang.String) */ @Override - public String getSelectedSequencesFrom(AlignFrameI alf, String sep) + public String getSelectedSequencesFrom(AlignFrame alf, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getSelectedSequencesFrom(alf, sep); } @@ -1669,14 +1613,18 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public void highlight(String sequenceId, String position, String alignedPosition) { - highlightIn(getCurrentAlignFrame(), sequenceId, position, + highlightIn(null, sequenceId, position, alignedPosition); } @Override - public void highlightIn(AlignFrameI alf, String sequenceId, + public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.highlightIn(alf, sequenceId, position, alignedPosition); } @@ -1689,19 +1637,23 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public void select(String sequenceIds, String columns, String sep) { - selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep); + selectIn(null, sequenceIds, columns, sep); } @Override - public void selectIn(AlignFrameI alf, String sequenceIds, String columns) + public void selectIn(AlignFrame alf, String sequenceIds, String columns) { selectIn(alf, sequenceIds, columns, null); } @Override - public void selectIn(AlignFrameI alf, String sequenceIds, String columns, + public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.selectIn(alf, sequenceIds, columns, sep); } @@ -1709,14 +1661,18 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, String suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @Override - public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); } @@ -1727,14 +1683,18 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentOrderFrom(AlignFrameI alf) + public String getAlignmentOrderFrom(AlignFrame alf) { return getAlignmentFrom(alf, null); } @Override - public String getAlignmentOrderFrom(AlignFrameI alf, String sep) + public String getAlignmentOrderFrom(AlignFrame alf, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getAlignmentOrderFrom(alf, sep); } @@ -1751,9 +1711,13 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String orderAlignmentBy(AlignFrameI alf, String order, + public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.orderAlignmentBy(alf, order, undoName, sep); } @@ -1764,7 +1728,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentFrom(AlignFrameI alf, String format) + public String getAlignmentFrom(AlignFrame alf, String format) { return getAlignmentFrom(alf, format, null); } @@ -1776,7 +1740,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentFrom(AlignFrameI alf, String format, + public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { return appLoader.getAlignmentFrom(alf, format, suffix); @@ -1789,8 +1753,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void loadAnnotationFrom(AlignFrameI alf, String annotation) + public void loadAnnotationFrom(AlignFrame alf, String annotation) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.loadAnnotationFrom(alf, annotation); } @@ -1801,129 +1769,173 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public boolean loadFeaturesFrom(AlignFrameI alf, String features, + 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(getCurrentAlignFrame(), format); + return getFeaturesFrom(null, format); } @Override - public String getFeaturesFrom(AlignFrameI alf, String format) + public String getFeaturesFrom(AlignFrame alf, String format) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getFeaturesFrom(alf, format); } @Override public String getAnnotation() { - return getAnnotationFrom(getCurrentAlignFrame()); + return getAnnotationFrom(null); } @Override - public String getAnnotationFrom(AlignFrameI alf) + public String getAnnotationFrom(AlignFrame alf) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getAnnotationFrom(alf); } - @Override - public AlignFrameI newView() - { - return newViewFrom(getCurrentAlignFrame(), null); - } - - @Override - public AlignFrameI newView(String name) - { - return newViewFrom(getCurrentAlignFrame(), name); - } - - @Override - public AlignFrameI newViewFrom(AlignFrameI alf) - { - return newViewFrom(alf, null); - } + // @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 AlignFrameI newViewFrom(AlignFrameI alf, String name) - { - return appLoader.newViewFrom(alf, name); - } - - @Override - public AlignFrameI loadAlignment(String text, String title) + public AlignFrame loadAlignment(String text, String title) { return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT, title); } @Override - public boolean addPdbFile(AlignFrameI alFrame, String sequenceId, + 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(AlignFrameI alf, String topRow, + public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.scrollViewToIn(alf, topRow, leftHandColumn); } @Override - public void scrollViewToRowIn(AlignFrameI alf, String topRow) + public void scrollViewToRowIn(AlignFrame alf, String topRow) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.scrollViewToRowIn(alf, topRow); } @Override - public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn) + public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } appLoader.scrollViewToColumnIn(alf, leftHandColumn); } @Override public String getFeatureGroups() { - return getFeatureGroupsOn(getCurrentAlignFrame()); + return getFeatureGroupsOn(null); } @Override - public String getFeatureGroupsOn(AlignFrameI alf) + public String getFeatureGroupsOn(AlignFrame alf) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getFeatureGroupsOn(alf); } @Override public String getFeatureGroupsOfState(boolean visible) { - return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible); + return getFeatureGroupsOfStateOn(null, visible); } @Override - public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible) + public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getFeatureGroupsOfStateOn(alf, visible); } @Override - public void setFeatureGroupStateOn(AlignFrameI alf, String groups, - boolean state) - { - setFeatureGroupStateOn(alf, groups, state); + public void setFeatureGroupState(String groups, boolean state) + { // JalviewLite API + setFeatureGroupStateOn(null, groups, state); } @Override - public void setFeatureGroupState(String groups, boolean state) + public void setFeatureGroupStateOn(AlignFrame alf, String groups, + boolean state) { - appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state); + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.setFeatureGroupStateOn(alf, groups, state); } @Override @@ -1958,7 +1970,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public Object openTreePanel(AlignFrame af, String treeType, String modelName) - { + { // JalviewJS api + if (af == null) + { + af = getCurrentAlignFrame(); + } return CalculationChooser.openTreePanel(af, treeType, modelName, null); } @@ -1974,6 +1990,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public Object openPcaPanel(AlignFrame af, String modelName) { + if (af == null) + { + af = getCurrentAlignFrame(); + } return CalculationChooser.openPcaPanel(af, modelName, null); } @@ -1981,14 +2001,18 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi public String getSelectedSequencesAsAlignment(String format, boolean suffix) { - return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + return getSelectedSequencesAsAlignmentFrom(null, format, suffix); } @Override - public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix) { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, "" + suffix); } @@ -2016,7 +2040,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void setMouseoverListener(AlignFrameI af, String listener) + public void setMouseoverListener(AlignFrame af, String listener) { // TODO Auto-generated method stub @@ -2030,7 +2054,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void setSelectionListener(AlignFrameI af, String listener) + public void setSelectionListener(AlignFrame af, String listener) { // TODO Auto-generated method stub @@ -2044,7 +2068,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void removeJavascriptListener(AlignFrameI af, String listener) + public void removeJavascriptListener(AlignFrame af, String listener) { // TODO Auto-generated method stub @@ -2058,5 +2082,17 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } + @Override + public void showOverview() + { + currentAlignFrame.overviewMenuItem_actionPerformed(null); + } + + public void notifyWorker(AlignCalcWorkerI worker, String status) + { + // System.out.println("Jalview worker " + worker.getClass().getSimpleName() + // + " " + status); + } } +