X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=290f92062b30a3da5cecea1c40f6d5996a4f9495;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=c8e453d29e8797140989d06fff668498332470cf;hpb=1ceb01789338f289cee6e2ae938e971ecc2c0191;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index c8e453d..290f920 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,6 +20,8 @@ */ package jalview.bin; +import java.awt.GraphicsEnvironment; + import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -37,22 +39,27 @@ import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; import java.util.HashMap; +import java.util.Locale; 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; +import javax.swing.UIManager.LookAndFeelInfo; import com.threerings.getdown.util.LaunchUtil; import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; +import jalview.api.AlignCalcWorkerI; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; import jalview.gui.Desktop; +import jalview.gui.Preferences; import jalview.gui.PromptUserConfig; import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; @@ -60,6 +67,7 @@ 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; @@ -67,6 +75,8 @@ import jalview.io.NewickFile; import jalview.io.gff.SequenceOntologyFactory; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.util.ChannelProperties; +import jalview.util.HttpUtils; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.jws2.Jws2Discoverer; @@ -86,20 +96,67 @@ import jalview.ws.jws2.Jws2Discoverer; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements ApplicationSingletonI { - static + // 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() { - Platform.getURLCommandArguments(); + return (Jalview) ApplicationSingletonProvider + .getInstance(Jalview.class); } - // singleton instance of this class + private Jalview() + { + Platform.getURLCommandArguments(); + } - private static Jalview instance; private Desktop desktop; - public static AlignFrame currentAlignFrame; + public AlignFrame currentAlignFrame; + + public String appletResourcePath; + + public String j2sAppletID; + + 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; + } static { @@ -188,10 +245,7 @@ public class Jalview } - public static Jalview getInstance() - { - return instance; - } + private final static boolean doPlatformLogging = false; /** * main class for Jalview application @@ -201,50 +255,17 @@ public class Jalview */ public static void main(String[] args) { - // setLogging(); // BH - for event debugging in JavaScript - instance = new Jalview(); - instance.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 - * - */ + if (doPlatformLogging) { - System.out.println("not in js"); + Platform.startJavaLogging(); } - // 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"); - } + getInstance().doMain(args); } + + + /** * @param args @@ -252,7 +273,8 @@ public class Jalview void doMain(String[] args) { - if (!Platform.isJS()) + boolean isJS = Platform.isJS(); + if (!isJS) { System.setSecurityManager(null); } @@ -280,45 +302,63 @@ public class Jalview } // report Jalview version - Cache.loadBuildProperties(true); + Cache.getInstance().loadBuildProperties(true); ArgsParser aparser = new ArgsParser(args); boolean headless = false; String usrPropsFile = aparser.getValue("props"); Cache.loadProperties(usrPropsFile); // must do this before - if (usrPropsFile != null) + boolean allowServices = true; + + if (isJS) { - System.out.println( - "CMD [-props " + usrPropsFile + "] executed successfully!"); + j2sAppletID = Platform.getAppID(null); + Preferences.setAppletDefaults(); + Cache.loadProperties(usrPropsFile); // again, because we + // might be changing defaults here? + appletResourcePath = (String) aparser.getAppletValue("resourcepath", + null, true); } - if (!Platform.isJS()) + else /** * Java only * * @j2sIgnore */ { + if (usrPropsFile != null) + { + System.out.println( + "CMD [-props " + usrPropsFile + "] executed successfully!"); + } if (aparser.contains("help") || aparser.contains("h")) { showUsage(); System.exit(0); } + // BH note: Only -nodisplay is official; others are deprecated? if (aparser.contains("nodisplay") || aparser.contains("nogui") - || aparser.contains("headless")) + || aparser.contains("headless") + || GraphicsEnvironment.isHeadless()) { - System.setProperty("java.awt.headless", "true"); + if (!isJS) { + // BH Definitely not a good idea in JavaScript; + // probably should not be here for Java, either. + System.setProperty("java.awt.headless", "true"); + } headless = true; } // anything else! - final String jabawsUrl = aparser.getValue("jabaws"); - if (jabawsUrl != null) + final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS); + allowServices = !("none".equals(jabawsUrl)); + if (allowServices && jabawsUrl != null) { try { - Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl); + Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl); System.out.println( "CMD [-jabaws " + jabawsUrl + "] executed successfully!"); } catch (MalformedURLException e) @@ -329,7 +369,7 @@ public class Jalview } } - String defs = aparser.getValue("setprop"); + String defs = aparser.getValue(ArgsParser.SETPROP); while (defs != null) { int p = defs.indexOf('='); @@ -340,7 +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)); } @@ -367,57 +407,13 @@ public class Jalview desktop = null; - try - { - UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); - } catch (Exception ex) - { - System.err.println("Unexpected Look and Feel Exception"); - ex.printStackTrace(); - } - if (Platform.isAMacAndNotJS()) - { - - LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager - .getLookAndFeel(); - System.setProperty("com.apple.mrj.application.apple.menu.about.name", - "Jalview"); - System.setProperty("apple.laf.useScreenMenuBar", "true"); - if (lookAndFeel != null) - { - try - { - UIManager.setLookAndFeel(lookAndFeel); - } catch (Throwable e) - { - System.err.println( - "Failed to set QuaQua look and feel: " + e.toString()); - } - } - if (lookAndFeel == null - || !(lookAndFeel.getClass().isAssignableFrom( - UIManager.getLookAndFeel().getClass())) - || !UIManager.getLookAndFeel().getClass().toString() - .toLowerCase().contains("quaqua")) - { - try - { - System.err.println( - "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976"); - UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel"); - } catch (Throwable e) - { - System.err.println( - "Failed to reset look and feel: " + e.toString()); - } - } - } + setLookAndFeel(); /* * configure 'full' SO model if preferences say to, else use the default (full SO) * - as JS currently doesn't have OBO parsing, it must use 'Lite' version */ - boolean soDefault = !Platform.isJS(); + boolean soDefault = !isJS; if (Cache.getDefault("USE_FULL_SO", soDefault)) { SequenceOntologyFactory.setInstance(new SequenceOntology()); @@ -425,27 +421,45 @@ public class Jalview if (!headless) { - desktop = new Desktop(); + Desktop.nosplash = aparser.contains("nosplash"); + desktop = Desktop.getInstance(); desktop.setInBatchMode(true); // indicate we are starting up try { JalviewTaskbar.setTaskbar(this); + } catch (Exception e) + { + Cache.log.info("Cannot set Taskbar"); + Cache.log.error(e.getMessage()); + // e.printStackTrace(); } catch (Throwable t) { - System.out.println("Error setting Taskbar: " + t.getMessage()); + Cache.log.info("Cannot set Taskbar"); + Cache.log.error(t.getMessage()); + // t.printStackTrace(); } + // set Proxy settings before all the internet calls + Cache.setProxyPropertiesFromPreferences(); desktop.setVisible(true); - if (!Platform.isJS()) + if (isJS) + { + Cache.setProperty("SHOW_JWS2_SERVICES", "false"); + } + if (allowServices && !aparser.contains("nowebservicediscovery")) + { + desktop.startServiceDiscovery(); + } + + if (!isJS) /** * Java only * * @j2sIgnore */ { - desktop.startServiceDiscovery(); if (!aparser.contains("nousagestats")) { startUsageStats(desktop); @@ -476,7 +490,7 @@ public class Jalview // String defurl = // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // // - String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl"; + String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl"; Cache.log.debug( "Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); @@ -497,45 +511,127 @@ public class Jalview BioJsHTMLOutput.updateBioJS(); } } + parseArguments(aparser, true); + } - // Move any new getdown-launcher-new.jar into place over old - // getdown-launcher.jar - String appdirString = System.getProperty("getdownappdir"); - if (appdirString != null && appdirString.length() > 0) + /** + * Parse all command-line String[] arguments as well as all JavaScript-derived + * parameters from Info. + * + * We allow for this method to be run from JavaScript. Basically allowing + * simple scripting. + * + * @param aparser + * @param isStartup + */ + public void parseArguments(ArgsParser aparser, boolean isStartup) + { + + String groovyscript = null; // script to execute after all loading is + boolean isJS = Platform.isJS(); + if (!isJS) + /** @j2sIgnore */ { - final File appdir = new File(appdirString); - new Thread() + // Move any new getdown-launcher-new.jar into place over old + // getdown-launcher.jar + String appdirString = System.getProperty("getdownappdir"); + if (appdirString != null && appdirString.length() > 0) { - @Override - public void run() + final File appdir = new File(appdirString); + new Thread() { - LaunchUtil.upgradeGetdown( - new File(appdir, "getdown-launcher-old.jar"), - new File(appdir, "getdown-launcher.jar"), - new File(appdir, "getdown-launcher-new.jar")); - } - }.start(); - } + @Override + public void run() + { + LaunchUtil.upgradeGetdown( + new File(appdir, "getdown-launcher-old.jar"), + new File(appdir, "getdown-launcher.jar"), + new File(appdir, "getdown-launcher-new.jar")); + } + }.start(); + } - String file = null, data = null; - FileFormatI format = null; - DataSourceType protocol = null; - FileLoader fileLoader = new FileLoader(!headless); + // completed one way or another + // extract groovy argument and execute if necessary + groovyscript = aparser.getValue("groovy", true); + } - String groovyscript = null; // script to execute after all loading is - // completed one way or another - // extract groovy argument and execute if necessary - groovyscript = aparser.getValue("groovy", true); - file = aparser.getValue("open", true); + String file = aparser.getValue("open", true); - if (file == null && desktop == null) + if (!isJS && file == null && desktop == null) { System.out.println("No files to open!"); System.exit(1); } + setDisplayParameters(aparser); + + // time to open a file. long progress = -1; + DataSourceType protocol = null; + FileLoader fileLoader = new FileLoader(!headless); + FileFormatI format = null; // Finally, deal with the remaining input data. - if (file != null) + AlignFrame af = null; + + JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null); + + if (file == null) + { + if (isJS) + { + // JalviewJS allows sequence1 sequence2 .... + + } + else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true)) + /** + * Java only + * + * @j2sIgnore + */ + { + + // We'll only open the default file if the desktop is visible. + // And the user + // //////////////////// + + file = Cache.getDefault("STARTUP_FILE", + Cache.getDefault("www.jalview.org", + "http://www.jalview.org") + + "/examples/exampleFile_2_7.jar"); + if (file.equals( + "http://www.jalview.org/examples/exampleFile_2_3.jar")) + { + // hardwire upgrade of the startup file + file.replace("_2_3.jar", "_2_7.jar"); + // and remove the stale setting + Cache.removeProperty("STARTUP_FILE"); + } + + protocol = DataSourceType.FILE; + + if (file.indexOf("http:") > -1) + { + protocol = DataSourceType.URL; + } + + if (file.endsWith(".jar")) + { + format = FileFormat.Jalview; + } + else + { + try + { + format = new IdentifyFile().identify(file, protocol); + } catch (FileFormatException e) + { + // TODO what? + } + } + af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format); + } + } + else { if (!headless) { @@ -553,8 +649,7 @@ public class Jalview * @j2sIgnore */ { - if (!file.startsWith("http://") && !file.startsWith("https://")) - // BH 2019 added https check for Java + if (!HttpUtils.startsWithHttpOrHttps(file)) { if (!(new File(file)).exists()) { @@ -567,290 +662,619 @@ public class Jalview } } + // JS Only argument to provide a format parameter to specify what format to use + String fileFormat = (isJS + ? (String) aparser.getAppletValue("format", null, true) + : null); protocol = AppletFormatAdapter.checkProtocol(file); try { - format = new IdentifyFile().identify(file, protocol); + format = (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, + af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol, format); if (af == null) { - System.out.println("error"); + System.out.println("jalview error - AlignFrame was not created"); } else { - setCurrentAlignFrame(af); - data = aparser.getValue("colour", true); - if (data != null) + + // JalviewLite interface for JavaScript allows second file open + String file2 = aparser.getValue(ArgsParser.OPEN2, true); + if (file2 != null) { - data.replaceAll("%20", " "); - - ColourSchemeI cs = ColourSchemeProperty.getColourScheme( - af.getViewport(), af.getViewport().getAlignment(), data); - - if (cs != null) + protocol = AppletFormatAdapter.checkProtocol(file2); + try { - System.out.println( - "CMD [-color " + data + "] executed successfully!"); + format = new IdentifyFile().identify(file2, protocol); + } catch (FileFormatException e1) + { + // TODO ? } - af.changeColour(cs); - } - - // Must maintain ability to use the groups flag - data = aparser.getValue("groups", true); - if (data != null) - { - af.parseFeaturesFile(data, - AppletFormatAdapter.checkProtocol(data)); - // System.out.println("Added " + data); - System.out.println( - "CMD groups[-" + data + "] executed successfully!"); - } - data = aparser.getValue("features", true); - if (data != null) - { - af.parseFeaturesFile(data, - AppletFormatAdapter.checkProtocol(data)); - // System.out.println("Added " + data); - System.out.println( - "CMD [-features " + data + "] executed successfully!"); - } - - data = aparser.getValue("annotations", true); - if (data != null) - { - af.loadJalviewDataFile(data, null, null, null); - // System.out.println("Added " + data); - System.out.println( - "CMD [-annotations " + data + "] executed successfully!"); - } - // set or clear the sortbytree flag. - if (aparser.contains("sortbytree")) - { - af.getViewport().setSortByTree(true); - if (af.getViewport().getSortByTree()) + AlignFrame af2 = new FileLoader(!headless) + .LoadFileWaitTillLoaded(file2, protocol, format); + if (af2 == null) { - System.out.println("CMD [-sortbytree] executed successfully!"); + System.out.println("error"); } - } - if (aparser.contains("no-annotation")) - { - af.getViewport().setShowAnnotation(false); - if (!af.getViewport().isShowAnnotation()) + else { - System.out.println("CMD no-annotation executed successfully!"); + AlignViewport.openLinkedAlignmentAs(af, + af.getViewport().getAlignment(), + af2.getViewport().getAlignment(), "", + AlignViewport.SPLIT_FRAME); + System.out.println( + "CMD [-open2 " + file2 + "] executed successfully!"); } } - if (aparser.contains("nosortbytree")) + // af is loaded - so set it as current frame + setCurrentAlignFrame(af); + + setFrameDependentProperties(aparser, af); + + if (isJS) { - af.getViewport().setSortByTree(false); - if (!af.getViewport().getSortByTree()) - { - System.out - .println("CMD [-nosortbytree] executed successfully!"); - } + jsApp.initFromParams(af); } - data = aparser.getValue("tree", true); - if (data != null) + else + /** + * Java only + * + * @j2sIgnore + */ { - try - { - System.out.println( - "CMD [-tree " + data + "] executed successfully!"); - NewickFile nf = new NewickFile(data, - AppletFormatAdapter.checkProtocol(data)); - af.getViewport() - .setCurrentTree(af.showNewickTree(nf, data).getTree()); - } catch (IOException ex) + if (groovyscript != null) { - System.err.println("Couldn't add tree " + data); - ex.printStackTrace(System.err); + // 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; } } - // 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 (!isJS || !isStartup) { + createOutputFiles(aparser, format); } - String imageName = "unnamed.png"; - while (aparser.getSize() > 1) - { - String outputFormat = aparser.nextValue(); - file = aparser.nextValue(); + } + if (headless) + { + af.getViewport().getCalcManager().shutdown(); + } + } + // extract groovy arguments before anything else. + // Once all other stuff is done, execute any groovy scripts (in order) + if (!isJS && groovyscript != null) + { + if (Cache.groovyJarsPresent()) + { + // TODO: DECIDE IF THIS SECOND PASS AT GROOVY EXECUTION IS STILL REQUIRED !! + System.out.println("Executing script " + groovyscript); + executeGroovyScript(groovyscript, af); + System.out.println("CMD groovy[" + groovyscript + + "] executed successfully!"); - 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); + } + else + { + System.err.println( + "Sorry. Groovy Support is not available, so ignoring the provided groovy script " + + groovyscript); + } + } - 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; - } + // and finally, turn off batch mode indicator - if the desktop still exists + if (desktop != null) + { + if (progress != -1) + { + desktop.setProgressBar(null, progress); + } + desktop.setInBatchMode(false); + } + + if (jsApp != null) { + jsApp.callInitCallback(); + } + } + + /** + * Set general display parameters irrespective of file loading or headlessness. + * + * @param aparser + */ + private void setDisplayParameters(ArgsParser aparser) + { + if (aparser.contains(ArgsParser.NOMENUBAR)) + { + noMenuBar = true; + System.out.println("CMD [nomenu] executed successfully!"); + } - 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!!"); - } + 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!"); + } + } - while (aparser.getSize() > 0) - { - System.out.println("Unknown arg: " + aparser.nextValue()); - } + + private void setFrameDependentProperties(ArgsParser aparser, + AlignFrame af) + { + String data = aparser.getValue(ArgsParser.COLOUR, true); + if (data != null) + { + data.replaceAll("%20", " "); + + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), data); + + if (cs != null) + { + System.out.println( + "CMD [-color " + data + "] executed successfully!"); } + af.changeColour(cs); } - AlignFrame startUpAlframe = null; - // We'll only open the default file if the desktop is visible. - // And the user - // //////////////////// - if (!Platform.isJS() && !headless && file == null - && Cache.getDefault("SHOW_STARTUP_FILE", true)) + // Must maintain ability to use the groups flag + data = aparser.getValue(ArgsParser.GROUPS, true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD groups[-" + data + "] executed successfully!"); + } + data = aparser.getValue(ArgsParser.FEATURES, true); + if (data != null) + { + af.parseFeaturesFile(data, + AppletFormatAdapter.checkProtocol(data)); + // System.out.println("Added " + data); + System.out.println( + "CMD [-features " + data + "] executed successfully!"); + } + data = aparser.getValue(ArgsParser.ANNOTATIONS, true); + if (data != null) + { + af.loadJalviewDataFile(data, null, null, null); + // System.out.println("Added " + data); + System.out.println( + "CMD [-annotations " + data + "] executed successfully!"); + } + + // JavaScript feature + + 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)) + { + af.getViewport().setSortByTree(true); + if (af.getViewport().getSortByTree()) + { + System.out.println("CMD [-sortbytree] executed successfully!"); + } + } + + boolean doUpdateAnnotation = false; /** - * Java only + * we do this earlier in JalviewJS because of a complication with + * SHOWOVERVIEW + * + * For now, just fixing this in JalviewJS. + * * * @j2sIgnore + * */ { - file = Cache.getDefault("STARTUP_FILE", - Cache.getDefault("www.jalview.org", "http://www.jalview.org") - + "/examples/exampleFile_2_7.jar"); - if (file.equals( - "http://www.jalview.org/examples/exampleFile_2_3.jar")) + if (noAnnotation) { - // hardwire upgrade of the startup file - file.replace("_2_3.jar", "_2_7.jar"); - // and remove the stale setting - Cache.removeProperty("STARTUP_FILE"); + af.getViewport().setShowAnnotation(false); + if (!af.getViewport().isShowAnnotation()) + { + doUpdateAnnotation = true; + } } + } - protocol = DataSourceType.FILE; - - if (file.indexOf("http:") > -1) + if (aparser.contains(ArgsParser.NOSORTBYTREE)) + { + af.getViewport().setSortByTree(false); + if (!af.getViewport().getSortByTree()) { - protocol = DataSourceType.URL; + doUpdateAnnotation = true; + System.out + .println("CMD [-nosortbytree] executed successfully!"); } + } + if (doUpdateAnnotation) + { // BH 2019.07.24 + af.setMenusForViewport(); + af.alignPanel.updateLayout(); + } - if (file.endsWith(".jar")) + data = aparser.getValue(ArgsParser.TREE, true); + if (data != null) + { + try + { + NewickFile nf = new NewickFile(data, + AppletFormatAdapter.checkProtocol(data)); + af.getViewport() + .setCurrentTree(af.showNewickTree(nf, data).getTree()); + System.out.println( + "CMD [-tree " + data + "] executed successfully!"); + } catch (IOException ex) { - format = FileFormat.Jalview; + System.err.println("Couldn't add tree " + data); + ex.printStackTrace(System.err); } - else + } + // TODO - load PDB structure(s) to alignment JAL-629 + // (associate with identical sequence in alignment, or a specified + // sequence) + + } + + /** + * Writes an output file for each format (if any) specified in the + * command-line arguments. Supported formats are currently + *