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=bb2038e889e71e34af4d4edb7275eaba5b1f17bf;hpb=26ee59562604fa9164e895e3ca07e11398a6c8a0;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index bb2038e..0ec9ee0 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; @@ -83,11 +84,9 @@ 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; @@ -146,6 +145,32 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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; @@ -251,71 +276,12 @@ 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 +289,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi { boolean isJS = Platform.isJS(); - if (!isJS) + if (isJS) + { + Platform.setAppClass(this); + } + else { System.setSecurityManager(null); } @@ -338,6 +308,16 @@ 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; + setSynchronous(true); + } + if (isJS) { isJavaAppletTag = aparser.isApplet(); @@ -369,13 +349,6 @@ 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 +404,13 @@ 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"); @@ -484,7 +463,21 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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 @@ -551,8 +544,36 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } 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(); @@ -569,7 +590,6 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi String fileFormat = (isJavaAppletTag ? aparser.getAppletValue("format", null) : null); - FileFormatI format = null; DataSourceType protocol = null; @@ -578,7 +598,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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) @@ -597,8 +617,11 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } } + String data; + if (file != null) { + if (!headless) { desktop.setProgressBar( @@ -645,7 +668,31 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // TODO ? } - AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file, + 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) { @@ -666,7 +713,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi // TODO ? } AlignFrame af2 = new FileLoader(!headless) - .loadFileWaitTillLoaded(file2, protocol, format); + .LoadFileWaitTillLoaded(file2, protocol, format); if (af2 == null) { System.out.println("error"); @@ -686,7 +733,7 @@ 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", " "); @@ -730,6 +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)) { @@ -739,18 +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)) @@ -810,11 +876,11 @@ 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()); - } + } + createOutputFiles(aparser, af, format); + while (aparser.getSize() > 0) + { + System.out.println("Unknown arg: " + aparser.nextValue()); } } } @@ -867,7 +933,7 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi } startUpAlframe = new FileLoader(!headless) - .loadFileWaitTillLoaded(file, protocol, format); + .LoadFileWaitTillLoaded(file, protocol, format); // extract groovy arguments before anything else. } @@ -899,111 +965,35 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi 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 + *