Examples with Arguments dr.app.util.Arguments used on opensource projects

Example 1 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class BeautiApp method main.

// Main entry point
public static void main(String[] args) {
    // There is a major issue with languages that use the comma as a decimal separator.
    // To ensure compatibility between programs in the package, enforce the US locale.
    Locale.setDefault(Locale.US);
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.Option("advanced", "Enable advanced & developer features"), new Arguments.Option("version", "Print the version and credits and stop"), new Arguments.Option("help", "Print this information and stop") });
    int argumentCount = 0;
    try {
        argumentCount = arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        printTitle();
        System.out.println();
        System.out.println(ae.getMessage());
        System.out.println();
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption("help")) {
        printTitle();
        printUsage(arguments);
        System.exit(0);
    }
    if (arguments.hasOption("version")) {
        printTitle();
    }
    advanced = arguments.hasOption("advanced");
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 1) {
        System.err.println("Unknown option: " + args2[1]);
        System.err.println();
        printUsage(arguments);
        return;
    }
    //        if (args2.length > 1) {
    //
    //            if (args.length != 3) {
    //                printTitle();
    //                printUsage(arguments);
    //                System.exit(1);
    //            }
    //
    //            String inputFileName = args[0];
    //            String templateFileName = args[1];
    //            String outputFileName = args[2];
    //
    //            new CommandLineBeauti(inputFileName, templateFileName, outputFileName);
    //
    //        } else {
    String inputFileName = null;
    if (args2.length == 1) {
        inputFileName = args2[0];
    }
    if (OSType.isMac()) {
        System.setProperty("apple.awt.graphics.UseQuartz", "true");
        System.setProperty("apple.awt.antialiasing", "true");
        System.setProperty("apple.awt.rendering", "VALUE_RENDER_QUALITY");
        System.setProperty("apple.laf.useScreenMenuBar", "true");
        System.setProperty("apple.awt.draggableWindowBackground", "true");
        System.setProperty("apple.awt.showGrowBox", "true");
        try {
            // set the Quaqua Look and Feel in the UIManager
            javax.swing.SwingUtilities.invokeAndWait(new Runnable() {

                public void run() {
                    try {
                        try {
                            // We need to do this using dynamic class loading to avoid other platforms
                            // having to link to this class. If the Quaqua library is not on the classpath
                            // it simply won't be used.
                            Class<?> qm = Class.forName("ch.randelshofer.quaqua.QuaquaManager");
                            Method method = qm.getMethod("setExcludedUIs", Set.class);
                            Set<String> excludes = new HashSet<String>();
                            excludes.add("Button");
                            excludes.add("ToolBar");
                            method.invoke(null, excludes);
                        } catch (Throwable e) {
                        }
                        //set the Quaqua Look and Feel in the UIManager
                        UIManager.setLookAndFeel("ch.randelshofer.quaqua.QuaquaLookAndFeel");
                        lafLoaded = true;
                    } catch (Exception e) {
                    }
                }
            });
        } catch (Exception e) {
        }
        UIManager.put("SystemFont", new Font("Lucida Grande", Font.PLAIN, 13));
        UIManager.put("SmallSystemFont", new Font("Lucida Grande", Font.PLAIN, 11));
    }
    try {
        if (!lafLoaded) {
            try {
                // set the System Look and Feel in the UIManager
                javax.swing.SwingUtilities.invokeAndWait(new Runnable() {

                    public void run() {
                        try {
                            UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
                        } catch (Exception e) {
                            e.printStackTrace();
                        }
                    }
                });
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
        java.net.URL url = BeautiApp.class.getResource("images/beauti.png");
        Icon icon = null;
        if (url != null) {
            icon = new ImageIcon(url);
        }
        final String nameString = "BEAUti";
        final String versionString = version.getVersionString();
        String aboutString = "<html>" + "<div style=\"font-family:HelveticaNeue-Light, 'Helvetica Neue Light', Helvetica, Arial, 'Lucida Grande',sans-serif; font-weight: 100\">" + "<center>" + "<div style=\"font-size:13\"><p>Bayesian Evolutionary Analysis Utility<br>" + "Version " + versionString + ", " + version.getDateString() + "</p>" + "<p>by Alexei J. Drummond, Andrew Rambaut, Marc A. Suchard and Walter Xie</p></div>" + "<hr><div style=\"font-size:11;\">Part of the BEAST package:" + version.getHTMLCredits() + "</div></center></div></html>";
        String websiteURLString = "http://beast.bio.ed.ac.uk/BEAUti";
        String helpURLString = "http://beast.bio.ed.ac.uk/BEAUti";
        System.setProperty("BEAST & BEAUTi Version", version.getVersion());
        BeautiApp app = new BeautiApp(nameString, aboutString, icon, websiteURLString, helpURLString);
        app.setDocumentFrameFactory(new DocumentFrameFactory() {

            public DocumentFrame createDocumentFrame(Application app, MenuBarFactory menuBarFactory) {
                return new BeautiFrame(nameString);
            }
        });
        app.initialize();
        if (inputFileName != null) {
            app.doOpen(inputFileName);
        } else {
            app.doNew();
        }
    } catch (Exception e) {
        JOptionPane.showMessageDialog(new JFrame(), "Fatal exception: " + e, "Please report this to the authors", JOptionPane.ERROR_MESSAGE);
        e.printStackTrace();
    }
//        }
}

Example 2 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class BeastRemote method main.

public static void main(String[] oldArgs) throws java.io.IOException {
    // First populate args from MPI.WORLD
    // String[] args = null;
    MPI.Init(oldArgs);
    System.err.println(oldArgs[0]);
    System.err.println(oldArgs[1]);
    System.err.println(oldArgs[2]);
    int rank = MPI.COMM_WORLD.Rank();
    int argLength = oldArgs.length - 3;
    String[] args = new String[argLength];
    for (int i = 0; i < argLength; i++) {
        args[i] = oldArgs[i + 3];
        System.err.println(i + " : " + args[i]);
        if (args[i].contains(".xml")) {
            // append rank
            args[i] = args[i].replace(".xml", Integer.toString(rank) + ".xml");
            System.err.println("Attempting to load: " + args[i]);
        }
    }
    /*  for (String str : args)
                      System.err.println(str);*/
    //System.exit(1);
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.Option("verbose", "verbose XML parsing messages"), new Arguments.Option("warnings", "Show warning messages about BEAST XML file"), new Arguments.Option("window", "provide a console window"), new Arguments.Option("working", "change working directory to input file's directory"), new Arguments.LongOption("seed", "specify a random number generator seed"), new Arguments.Option("help", "option to print this message") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println();
        System.out.println(ae.getMessage());
        System.out.println();
        printTitle();
        printUsage(arguments);
        MPI.Finalize();
        System.exit(1);
    }
    if (arguments.hasOption("help")) {
        printTitle();
        printUsage(arguments);
        MPI.Finalize();
        System.exit(0);
    }
    boolean verbose = arguments.hasOption("verbose");
    // if dev, then auto turn on, otherwise default to turn off
    boolean parserWarning = arguments.hasOption("pwarning");
    //        boolean window = arguments.hasOption("window");
    boolean working = arguments.hasOption("working");
    long seed = MathUtils.getSeed();
    if (arguments.hasOption("seed")) {
        seed = arguments.getLongOption("seed");
        MathUtils.setSeed(seed);
    }
    //		if (System.getProperty("dr.app.beast.main.window", "false").toLowerCase().equals("true")) {
    //			window = true;
    //		}
    BeastConsoleApp consoleApp = null;
    /*		if (window) {
			System.setProperty("com.apple.macos.useScreenMenuBar", "true");
			System.setProperty("apple.laf.useScreenMenuBar", "true");
			System.setProperty("apple.awt.showGrowBox", "true");

			javax.swing.Icon icon = IconUtils.getIcon(BeastMain.class, "images/beast.png");

			String nameString = "BEAST " + version.getVersionString();
			String aboutString = "<html><center><p>Bayesian Evolutionary Analysis Sampling Trees<br>" +
					"Version " + version.getVersionString() + ", 2002-2006</p>" +
					"<p>by<br>" +
					"Alexei J. Drummond and Andrew Rambaut</p>" +
					"<p>Department of Computer Science, University of Auckland<br>" +
					"<a href=\"mailto:alexei@cs.auckland.ac.nz\">alexei@cs.auckland.ac.nz</a></p>" +
					"<p>Institute of Evolutionary Biology, University of Edinburgh<br>" +
					"<a href=\"mailto:a.rambaut@ed.ac.uk\">a.rambaut@ed.ac.uk</a></p>" +
					"<p><a href=\"http://evolve.zoo.ox.ac.uk/beast/\">http://evolve.zoo.ox.ac.uk/beast/</a></p>" +
					"<p>Source code distributed under the GNU LGPL:<br>" +
					"<a href=\"http://github.com/beast-dev/beast-mcmc/\">http://github.com/beast-dev/beast-mcmc/</a></p>" +
					"<p>Additional programming by:<br>" +
					"Roald Forsberg, Gerton Lunter, Sidney Markowitz, Oliver Pybus</p>" +
					"<p>Thanks to Korbinian Strimmer for use of his code</p>" +
					"</center></html>";

			consoleApp = new BeastConsoleApp(nameString, aboutString, icon);
		}*/
    // Remote can never be interactive
    String inputFileName;
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 1) {
        System.err.println("Unknown option: " + args2[1]);
        System.err.println();
        printTitle();
        printUsage(arguments);
        MPI.Finalize();
        System.exit(1);
    }
    File inputFile = null;
    if (args2.length > 0) {
        inputFileName = args2[0];
        inputFile = new File(inputFileName);
    }
    if (inputFile != null && working) {
        System.setProperty("user.dir", inputFile.getParent());
    }
    printTitle();
    System.out.println();
    System.out.println("Random number seed: " + seed);
    System.out.println();
    new BeastRemote(inputFile, consoleApp, verbose, parserWarning);
    //System.err.println("Did I get here");
    if (rank == 0)
        terminateSlaves();
    MPI.Finalize();
}

Example 3 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class AntigenicPlotter method main.

//Main method
public static void main(String[] args) throws IOException {
    String inputFileName = null;
    String outputFileName = null;
    String treeFileName = null;
    printTitle();
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.IntegerOption("burnin", "the number of states to be considered as 'burn-in' [default = 0]"), new Arguments.Option("discrete", "generated under the discrete antigenic model [default = continuous]"), new Arguments.Option("tab", "generate tab delimited file [default = KML]"), new Arguments.Option("help", "option to print this message") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption("help")) {
        printUsage(arguments);
        System.exit(0);
    }
    int burnin = -1;
    if (arguments.hasOption("burnin")) {
        burnin = arguments.getIntegerOption("burnin");
    }
    boolean tabFormat = arguments.hasOption("tab");
    boolean discreteModel = arguments.hasOption("discrete");
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 3) {
        System.err.println("Unknown option: " + args2[3]);
        System.err.println();
        printUsage(arguments);
        System.exit(1);
    }
    if (args2.length == 2) {
        inputFileName = args2[0];
        outputFileName = args2[1];
    } else if (args2.length == 3) {
        inputFileName = args2[0];
        treeFileName = args2[1];
        outputFileName = args2[2];
    } else {
        System.err.println("Missing input or output file name");
        printUsage(arguments);
        System.exit(1);
    }
    new AntigenicPlotter(burnin, tabFormat, discreteModel, inputFileName, treeFileName, outputFileName);
    System.exit(0);
}

Example 4 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class BeastParserDoc method main.

//Main method
public static void main(String[] args) throws java.io.IOException, XMLParseException {
    printTitle();
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.Option("help", "option to print this message") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println(ae);
        printUsage(arguments);
        return;
    }
    if (arguments.hasOption("help")) {
        printUsage(arguments);
        return;
    }
    String outputDirectory = null;
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 1) {
        System.err.println("Unknown option: " + args2[1]);
        System.err.println();
        printUsage(arguments);
        return;
    }
    if (args2.length > 0) {
        outputDirectory = args2[0];
    }
    if (outputDirectory == null) {
        // No input file name was given so throw up a dialog box...
        outputDirectory = System.getProperty("user.dir") + System.getProperty("file.separator") + "release" + System.getProperty("file.separator") + "common" + System.getProperty("file.separator") + "doc" + System.getProperty("file.separator");
    }
    System.out.println("Output directory : " + outputDirectory);
    // BeastParserDoc(BeastParser parser, String directory, boolean wikiFormat)
    new BeastParserDoc(new BeastParser(new String[] {}, null, false, false, false), outputDirectory, true);
    System.exit(0);
}

Example 5 with Arguments

use of dr.app.util.Arguments in project beast-mcmc by beast-dev.

the class Branch2dRateToGrid method main.

public static void main(String[] args) throws IOException {
    String inputFileName = null;
    String outputFileName = null;
    String traitName = "location";
    boolean trait2DNoise = true;
    boolean rate2DNoise = false;
    Normalization normalize = Normalization.LENGTH;
    int burnin = -1;
    int skipEvery = 1;
    double latMax = 90;
    double latMin = -90;
    double longMax = 180;
    double longMin = -180;
    int gridXcells = 360;
    int gridYcells = 180;
    String rateString = "rate";
    double maxPathLength = Double.MAX_VALUE;
    double posteriorCutoff = 0;
    //slicing
    double[] sliceHeights = null;
    double mrsd = 0;
    boolean getStdevs = true;
    String discreteTraitName = null;
    String[] discreteTraitStates = null;
    String historyAnnotation = "history";
    printTitle();
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.IntegerOption(BURNIN, "the number of states to be considered as 'burn-in' [default = 0]"), new Arguments.IntegerOption(SKIP, "skip every i'th tree [default = 0]"), new Arguments.StringOption(TRAIT, "trait_name", "specifies an attribute to use to summarize the 2D trait info [default = location]"), new Arguments.StringOption(RATE_ATTRIBUTE, "rate_attribute", "specifies the trait rate attribute string [default=rate]"), new Arguments.Option(HELP, "option to print this message"), new Arguments.StringOption(TRAIT_NOISE, falseTrue, false, "add true noise to 2D traits [default = true])"), new Arguments.StringOption(RATE_NOISE, falseTrue, false, "add true noise to rates [default = true])"), new Arguments.StringOption(NORMALIZATION, enumNamesToStringArray(Normalization.values()), false, "tree normalization [default = length"), new Arguments.RealOption(LATMAX, "specifies the maximum latitude for the grid [default=90]"), new Arguments.RealOption(LATMIN, "specifies the minimum latitude for the grid [default=-90]"), new Arguments.RealOption(LONGMAX, "specifies the maximum longitude for the grid [default=180]"), new Arguments.RealOption(LONGMIN, "specifies the minimum longitude for the grid [default=-180]"), new Arguments.IntegerOption(GRIDXCELLS, "the number of cells along the x-axis (longitude) of the grid [default = 360]"), new Arguments.IntegerOption(GRIDYCELLS, "the number of cells along the y-axis (latitude) of the grid [default = 180]"), new Arguments.RealOption(MAXPATHLENGTH, "specifies the maximum (time) length a branch can go in one direction before adding Brownian noise to it [default=MAX_VALUE (no noise)]"), new Arguments.StringOption(SLICE_TIMES, "slice_times", "specifies a slice time-list [default=none]"), new Arguments.StringOption(SLICE_HEIGHTS, "slice_heights", "specifies a slice height-list [default=none]"), new Arguments.StringOption(SLICE_FILE_HEIGHTS, "heights_file", "specifies a file with a slice heights-list, is overwritten by command-line specification of slice heights [default=none]"), new Arguments.StringOption(SLICE_FILE_TIMES, "Times_file", "specifies a file with a slice Times-list, is overwritten by command-line specification of slice times [default=none]"), new Arguments.StringOption(STDEVS, falseTrue, true, "get standard deviations for the rates [default = true])"), new Arguments.RealOption(CUTOFF, "specifies the posterior cut-off for summarize grid values [default=-0]"), new Arguments.StringOption(DISCRETE_TRAIT_NAME, "discrete_traitName", "specifies the name for a discrete trait that is annotated to the tree nodes and by which states the grid needs to be summarized [default=none]"), new Arguments.StringOption(DISCRETE_TRAIT_STATES, "discrete_traitStates", "specifies the state of a discrete trait by which the grid needs to be summarized [default=none]"), new Arguments.StringOption(HISTORY_ANNOTATION, "history_annotation", "specifies the name for the history annotation for the discrete trait [default=history]") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        progressStream.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (arguments.hasOption(HELP)) {
        printUsage(arguments);
        System.exit(0);
    }
    try {
        if (arguments.hasOption(LATMAX)) {
            latMax = arguments.getRealOption(LATMAX);
        }
        if (arguments.hasOption(LATMIN)) {
            latMin = arguments.getRealOption(LATMIN);
        }
        if (arguments.hasOption(LONGMAX)) {
            longMax = arguments.getRealOption(LONGMAX);
        }
        if (arguments.hasOption(LONGMIN)) {
            longMin = arguments.getRealOption(LONGMIN);
        }
        if (arguments.hasOption(MAXPATHLENGTH)) {
            maxPathLength = arguments.getRealOption(MAXPATHLENGTH);
        }
        if (arguments.hasOption(GRIDXCELLS)) {
            gridXcells = arguments.getIntegerOption(GRIDXCELLS);
        }
        if (arguments.hasOption(GRIDYCELLS)) {
            gridYcells = arguments.getIntegerOption(GRIDYCELLS);
        }
        String traitRateString = arguments.getStringOption(RATE_ATTRIBUTE);
        if (traitRateString != null) {
            rateString = traitRateString;
        }
        if (arguments.hasOption(BURNIN)) {
            burnin = arguments.getIntegerOption(BURNIN);
            System.err.println("Ignoring a burnin of " + burnin + " trees.");
        }
        if (arguments.hasOption(SKIP)) {
            skipEvery = arguments.getIntegerOption(SKIP);
            System.err.println("Skipping every " + skipEvery + " trees.");
        }
        if (skipEvery < 1) {
            System.err.println("Skipping every " + skipEvery + " is not possible, no trees will be skipped");
            skipEvery = 1;
        }
        String traitString = arguments.getStringOption(TRAIT);
        if (traitString != null) {
            traitName = traitString;
        }
        String trait2DnoiseString = arguments.getStringOption(TRAIT_NOISE);
        if (trait2DnoiseString != null && trait2DnoiseString.compareToIgnoreCase("false") == 0)
            trait2DNoise = false;
        String rate2DNoiseString = arguments.getStringOption(TRAIT_NOISE);
        if (rate2DNoiseString != null && rate2DNoiseString.compareToIgnoreCase("true") == 0)
            rate2DNoise = true;
        String normalizeString = arguments.getStringOption(NORMALIZATION);
        if (normalizeString != null) {
            try {
                normalize = Normalization.valueOf(normalizeString.toUpperCase());
            } catch (IllegalArgumentException iae) {
                System.err.println("Unrecognized normalization mode: " + normalizeString);
            }
        }
        String sliceTimeString = arguments.getStringOption(SLICE_TIMES);
        if (sliceTimeString != null) {
            double[] sliceTimes = parseVariableLengthDoubleArray(sliceTimeString);
            sliceHeights = new double[sliceTimes.length];
            for (int i = 0; i < sliceTimes.length; i++) {
                if (mrsd == 0) {
                    sliceHeights[i] = sliceTimes[i];
                } else {
                    sliceHeights[i] = mrsd - sliceTimes[i];
                }
            }
        }
        String stdevString = arguments.getStringOption(STDEVS);
        if (stdevString != null && stdevString.compareToIgnoreCase("false") == 0)
            getStdevs = false;
        if (arguments.hasOption(CUTOFF)) {
            posteriorCutoff = arguments.getRealOption(CUTOFF);
        }
        String discreteTraitNameString = arguments.getStringOption(DISCRETE_TRAIT_NAME);
        if (discreteTraitNameString != null) {
            discreteTraitName = discreteTraitNameString;
            if (!arguments.hasOption(DISCRETE_TRAIT_STATES)) {
                System.err.print("a discrete trait name is specified (" + discreteTraitName + "), but no associated states of that trait are specified");
                System.exit(-1);
            }
        }
        String discreteTraitStatesString = arguments.getStringOption(DISCRETE_TRAIT_STATES);
        if (discreteTraitStatesString != null) {
            discreteTraitStates = parseVariableLengthStringArray(discreteTraitStatesString);
            if (discreteTraitName == null) {
                System.err.print("states for a discrete trait are specified, but no associated trait name for trait annotation is specified");
                System.exit(-1);
            }
        }
        String historyString = arguments.getStringOption(HISTORY_ANNOTATION);
        if (historyString != null) {
            historyAnnotation = historyString;
        }
        //slicing
        String sliceHeightString = arguments.getStringOption(SLICE_HEIGHTS);
        if (sliceHeightString != null) {
            if (sliceTimeString != null) {
                progressStream.println("Either sliceTimes, sliceHeights, timesFile or sliceCount" + "nt.");
                System.exit(-1);
            }
            sliceHeights = parseVariableLengthDoubleArray(sliceHeightString);
        }
        if (arguments.hasOption(SLICE_COUNT)) {
            int sliceCount = arguments.getIntegerOption(SLICE_COUNT);
            double startTime;
            if (arguments.hasOption(START_TIME)) {
                startTime = arguments.getRealOption(START_TIME);
            } else {
                progressStream.println("slice count specified, but no associated start time?");
                System.exit(-1);
                startTime = 0;
            }
            double delta;
            if (mrsd != 0) {
                if (sliceCount == 1) {
                    delta = (mrsd - startTime);
                } else {
                    delta = (mrsd - startTime) / (sliceCount - 1);
                }
            } else {
                if (sliceCount == 1) {
                    delta = startTime;
                } else {
                    delta = startTime / (sliceCount - 1);
                }
            }
            sliceHeights = new double[sliceCount];
            //                double height = mrsd - startTime;
            //                for (int i = 0; i < sliceCount; i++) {
            //                   sliceHeights[i] = height;
            //                   height -= delta;
            //                }
            double height = 0;
            for (int i = 0; i < sliceCount; i++) {
                sliceHeights[i] = height;
                height += delta;
            }
        }
        if ((sliceTimeString == null) && (sliceHeightString == null) && (!arguments.hasOption(SLICE_COUNT))) {
            sliceHeights = new double[] { 0 };
        }
    } catch (Arguments.ArgumentException e) {
        progressStream.println(e);
        printUsage(arguments);
        System.exit(-1);
    }
    final String[] args2 = arguments.getLeftoverArguments();
    switch(args2.length) {
        case 0:
            printUsage(arguments);
            System.exit(1);
        case 2:
            outputFileName = args2[1];
        // fall to
        case 1:
            inputFileName = args2[0];
            break;
        default:
            {
                System.err.println("Unknown option: " + args2[2]);
                System.err.println();
                printUsage(arguments);
                System.exit(1);
            }
    }
    Branch2dRateToGrid grid = new Branch2dRateToGrid(inputFileName, burnin, skipEvery, traitName, trait2DNoise, rate2DNoise, rateString, maxPathLength, normalize, latMin, latMax, longMin, longMax, gridXcells, gridYcells, sliceHeights, getStdevs, posteriorCutoff, discreteTraitName, discreteTraitStates, historyAnnotation);
    grid.output(outputFileName);
    System.exit(0);
}