X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=f59c37f16cae5d38c3848d231c4e168a08e9f57c;hb=edd94b99dba923b1d6da64e4cea1608dc640fae7;hp=047356bf088457a818a3dcf09806da7db8a7eeeb;hpb=f820a6e0b7ec599b0e040109c3361cdb3e6d9aa0;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 047356b..f59c37f 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,6 +20,7 @@ */ package jalview.bin; +import jalview.api.AlignCalcWorkerI; import jalview.api.AlignFrameI; import jalview.api.AlignViewportI; import jalview.api.JalviewApp; @@ -83,9 +84,6 @@ 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; @@ -146,6 +144,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi protected JSFunctionExec jsFunctionExec; + private boolean noCalculation, noMenuBar, noStatus; + + private boolean noAnnotation; + + public boolean getStartCalculations() + { + return !noCalculation; + } + + public boolean getAllowMenuBar() + { + return !noMenuBar; + } + + public boolean getShowStatus() + { + return !noStatus; + } + + public boolean getShowAnnotation() + { + return !noAnnotation; + } + public static AlignFrame getCurrentAlignFrame() { return getInstance().currentAlignFrame; @@ -251,71 +273,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi */ public static void main(String[] args) { - // setLogging(); // BH - for event debugging in JavaScript + // Platform.startJavaLogging(); getInstance().doMain(args); } - /** - * 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; - } - } - - 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 */ @@ -323,7 +286,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi { boolean isJS = Platform.isJS(); - if (!isJS) + if (isJS) + { + Platform.setAppClass(this); + } + else { System.setSecurityManager(null); } @@ -338,6 +305,15 @@ 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(); @@ -369,13 +345,7 @@ 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! @@ -431,7 +401,13 @@ 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"); @@ -553,8 +529,34 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi parseArguments(aparser, true); } - private Object parseArguments(ArgsParser aparser, - boolean isStartup) + /** + * 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(); @@ -570,7 +572,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi String fileFormat = (isJavaAppletTag ? aparser.getAppletValue("format", null) : null); - FileFormatI format = null; DataSourceType protocol = null; @@ -598,8 +599,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } } + String data; + if (file != null) { + if (!headless) { desktop.setProgressBar( @@ -646,6 +650,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // TODO ? } + 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) @@ -687,7 +715,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // 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", " "); @@ -731,6 +759,13 @@ 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)) { @@ -740,13 +775,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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)) @@ -754,10 +806,16 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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) { @@ -800,11 +858,11 @@ 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()); - } + } + checkOutputFile(aparser, af, format); + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); } } } @@ -994,6 +1052,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // biojsmsa filename String outputFormat = aparser.nextValue(); String file = aparser.nextValue(); + System.out.println("format " + outputFormat); + if (outputFormat.equalsIgnoreCase("png")) { af.createPNG(new File(file)); @@ -1321,6 +1381,17 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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; @@ -1472,7 +1543,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public StructureSelectionManagerProvider getStructureSelectionManagerProvider() { - // TODO Auto-generated method stub + // TODO Q: what exactly is this? BH return null; } @@ -1489,8 +1560,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame) { - // TODO Auto-generated method stub - return null; + return appLoader.getSelectionForListener(getCurrentAlignFrame(), + seqsel, colsel, hidden, source, alignFrame); } @Override @@ -1502,16 +1573,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public Hashtable getJSHashes() { - return (jshashes == null - ? (jshashes = new Hashtable<>()) + return (jshashes == null ? (jshashes = new Hashtable<>()) : jshashes); } @Override public Hashtable> getJSMessages() { - return (jsmessages == null - ? (jsmessages = new Hashtable<>()) + return (jsmessages == null ? (jsmessages = new Hashtable<>()) : jsmessages); } @@ -1602,11 +1671,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void highlightIn(AlignFrameI alf, - String sequenceId, String position, String alignedPosition) + public void highlightIn(AlignFrameI alf, String sequenceId, + String position, String alignedPosition) { - appLoader.highlightIn(alf, sequenceId, position, - alignedPosition); + appLoader.highlightIn(alf, sequenceId, position, alignedPosition); } @Override @@ -1622,15 +1690,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public void selectIn(AlignFrameI alf, String sequenceIds, - String columns) + 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) + public void selectIn(AlignFrameI alf, String sequenceIds, String columns, + String sep) { appLoader.selectIn(alf, sequenceIds, columns, sep); } @@ -1644,8 +1711,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getSelectedSequencesAsAlignmentFrom( - AlignFrameI alf, String format, String sep) + public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + String format, String sep) { return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); } @@ -1663,8 +1730,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentOrderFrom(AlignFrameI alf, - String sep) + public String getAlignmentOrderFrom(AlignFrameI alf, String sep) { return appLoader.getAlignmentOrderFrom(alf, sep); } @@ -1682,8 +1748,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String orderAlignmentBy(AlignFrameI alf, - String order, String undoName, String sep) + public String orderAlignmentBy(AlignFrameI alf, String order, + String undoName, String sep) { return appLoader.orderAlignmentBy(alf, order, undoName, sep); } @@ -1695,8 +1761,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentFrom(AlignFrameI alf, - String format) + public String getAlignmentFrom(AlignFrameI alf, String format) { return getAlignmentFrom(alf, format, null); } @@ -1708,8 +1773,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getAlignmentFrom(AlignFrameI alf, - String format, String suffix) + public String getAlignmentFrom(AlignFrameI alf, String format, + String suffix) { return appLoader.getAlignmentFrom(alf, format, suffix); } @@ -1717,176 +1782,106 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi @Override public void loadAnnotation(String annotation) { - // TODO Auto-generated method stub - + loadAnnotationFrom(getCurrentAlignFrame(), annotation); } @Override - public void loadAnnotationFrom(AlignFrameI alf, - String annotation) + public void loadAnnotationFrom(AlignFrameI alf, String annotation) { - // TODO Auto-generated method stub - + appLoader.loadAnnotationFrom(alf, annotation); } @Override public void loadFeatures(String features, boolean autoenabledisplay) { - // TODO Auto-generated method stub - + loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay); } @Override - public boolean loadFeaturesFrom(AlignFrameI alf, - String features, boolean autoenabledisplay) + public boolean loadFeaturesFrom(AlignFrameI alf, String features, + boolean autoenabledisplay) { - // TODO Auto-generated method stub - return false; + return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay); } @Override public String getFeatures(String format) { - // TODO Auto-generated method stub - return null; + return getFeaturesFrom(getCurrentAlignFrame(), format); } @Override - public String getFeaturesFrom(AlignFrameI alf, - String format) + public String getFeaturesFrom(AlignFrameI alf, String format) { - // TODO Auto-generated method stub - return null; + return appLoader.getFeaturesFrom(alf, format); } @Override public String getAnnotation() { - // TODO Auto-generated method stub - return null; + return getAnnotationFrom(getCurrentAlignFrame()); } @Override public String getAnnotationFrom(AlignFrameI alf) { - // TODO Auto-generated method stub - return null; + return appLoader.getAnnotationFrom(alf); } @Override public AlignFrameI newView() { - // TODO Auto-generated method stub - return null; + return newViewFrom(getCurrentAlignFrame(), null); } @Override public AlignFrameI newView(String name) { - // TODO Auto-generated method stub - return null; + return newViewFrom(getCurrentAlignFrame(), name); } @Override public AlignFrameI newViewFrom(AlignFrameI alf) { - // TODO Auto-generated method stub - return null; + return newViewFrom(alf, null); } @Override public AlignFrameI newViewFrom(AlignFrameI alf, String name) { - // TODO Auto-generated method stub - return null; + return appLoader.newViewFrom(alf, name); } @Override - public AlignFrameI loadAlignment(String text, - String title) + public AlignFrameI loadAlignment(String text, String title) { return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT, title); } @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 boolean addPdbFile(AlignFrameI alFrame, - String sequenceId, String pdbEntryString, String pdbFile) + public boolean addPdbFile(AlignFrameI alFrame, String sequenceId, + String pdbEntryString, String pdbFile) { return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, pdbFile); } @Override - public void scrollViewToIn(AlignFrameI alf, - String topRow, String leftHandColumn) + public void scrollViewToIn(AlignFrameI alf, String topRow, + String leftHandColumn) { appLoader.scrollViewToIn(alf, topRow, leftHandColumn); } @Override - public void scrollViewToRowIn(AlignFrameI alf, - String topRow) + public void scrollViewToRowIn(AlignFrameI alf, String topRow) { appLoader.scrollViewToRowIn(alf, topRow); } @Override - public void scrollViewToColumnIn(AlignFrameI alf, - String leftHandColumn) + public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn) { appLoader.scrollViewToColumnIn(alf, leftHandColumn); } @@ -1910,15 +1905,14 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } @Override - public String getFeatureGroupsOfStateOn(AlignFrameI alf, - boolean visible) + public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible) { return appLoader.getFeatureGroupsOfStateOn(alf, visible); } @Override - public void setFeatureGroupStateOn(AlignFrameI alf, - String groups, boolean state) + public void setFeatureGroupStateOn(AlignFrameI alf, String groups, + boolean state) { setFeatureGroupStateOn(alf, groups, state); } @@ -1980,4 +1974,98 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi return CalculationChooser.openPcaPanel(af, modelName, null); } + @Override + public String getSelectedSequencesAsAlignment(String format, + boolean suffix) + { + return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(), + format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf, + String format, boolean suffix) + { + 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); + } + } +