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

Example 6 with Arguments

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

the class DistanceMatrixInsertionTest method main.

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.StringOption("BEAST_XML", "FILENAME", "Specify a BEAST XML file"), new Arguments.StringOption("update_choice", "UPDATECHOICE", "Specify a function by which to update the tree"), new Arguments.Option("help", "Print this information and stop") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        System.out.println();
        System.out.println(ae.getMessage());
        System.out.println();
        //printUsage(arguments);
        System.exit(1);
    }
    String inputFile = null;
    if (arguments.hasOption("BEAST_XML")) {
        inputFile = arguments.getStringOption("BEAST_XML");
    } else {
        throw new RuntimeException("No BEAST XML file specified.");
    }
    String choice = "";
    if (arguments.hasOption("update_choice")) {
        choice = arguments.getStringOption("update_choice");
    } else {
        throw new RuntimeException("Update mechanism needs to be specified.");
    }
    CheckPointUpdaterApp.UpdateChoice chosen = null;
    for (CheckPointUpdaterApp.UpdateChoice ch : CheckPointUpdaterApp.UpdateChoice.values()) {
        if (choice.equals(ch.getName())) {
            chosen = ch;
            break;
        }
    }
    if (chosen == null) {
        throw new RuntimeException("Incorrect update mechanism specified.");
    }
    //Create and set up the window.
    JFrame frame = new JFrame("Test distance matrix");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    DistanceMatrixInsertionTest test = new DistanceMatrixInsertionTest(inputFile, chosen);
    test.setOpaque(true);
    frame.setContentPane(test);
    //Display the window.
    frame.pack();
    frame.setVisible(true);
//System.exit(0);
}

Example 7 with Arguments

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

the class ContinuousTreeToKML method main.

public static void main(String[] args) {
    // altitutude of the root of the 3D trees
    double altitude = 0;
    // required to convert heights to calendar dates
    double mostRecentDate = 2010;
    String coordinateLabel = "loc";
    boolean makeTreeSlices = false;
    double[] sliceTimes = null;
    double treeSliceBranchWidth = 3;
    // shows complete branch for slice if time is more recent than the branch's midpoint
    boolean showBranchAtMidPoint = false;
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.StringOption(ANNOTATION, "location annotation label", "specifies the label used for location coordinates annotation [default=location]"), new Arguments.RealOption(ALTITUDE, "specifies the altitude of the root of the 3D tree [default=no 3D tree]"), new Arguments.RealOption(MRSD, "specifies the most recent sampling data in fractional years to rescale time [default=2010]"), new Arguments.StringOption(SLICES, "time", "specifies a slice time-list [default=none]"), new Arguments.StringOption(SLICEMIDPOINT, falseTrue, false, "shows complete branch for sliced tree if time is more recent than the branch's midpoint [default=false"), new Arguments.Option(HELP, "option to print this message") });
    try {
        arguments.parseArguments(args);
    } catch (Arguments.ArgumentException ae) {
        progressStream.println(ae);
        printUsage(arguments);
        System.exit(1);
    }
    if (args.length == 0 || arguments.hasOption(HELP)) {
        printUsage(arguments);
        System.exit(0);
    }
    if (arguments.hasOption(MRSD)) {
        mostRecentDate = arguments.getRealOption(MRSD);
    }
    if (arguments.hasOption(ALTITUDE)) {
        altitude = arguments.getRealOption(ALTITUDE);
    }
    String annotationLabel = arguments.getStringOption(ANNOTATION);
    if (annotationLabel != null) {
        coordinateLabel = annotationLabel;
    }
    String sliceString = arguments.getStringOption(SLICES);
    if (sliceString != null) {
        makeTreeSlices = true;
        try {
            sliceTimes = DiscreteTreeToKML.parseVariableLengthDoubleArray(sliceString);
        } catch (Arguments.ArgumentException ae) {
            System.err.println("error reading slice heights");
            ae.printStackTrace();
            return;
        }
        makeTreeSlices = true;
    }
    if (arguments.hasOption(SLICEBW)) {
        treeSliceBranchWidth = arguments.getRealOption(SLICEBW);
    }
    String midpointString = arguments.getStringOption(SLICEMIDPOINT);
    if (midpointString != null && midpointString.compareToIgnoreCase("true") == 0) {
        showBranchAtMidPoint = true;
    }
    final String[] args2 = arguments.getLeftoverArguments();
    String inputFileName = null;
    String outputFileName = null;
    switch(args2.length) {
        case 0:
            printUsage(arguments);
            System.exit(1);
        case 1:
            inputFileName = args2[0];
            outputFileName = inputFileName + ".kml";
            break;
        case 2:
            inputFileName = args2[0];
            outputFileName = args2[1];
            break;
        default:
            {
                System.err.println("Unknown option: " + args2[2]);
                System.err.println();
                printUsage(arguments);
                System.exit(1);
            }
    }
    RootedTree tree = null;
    try {
        TreeImporter importer = new NexusImporter(new FileReader(inputFileName));
        tree = (RootedTree) importer.importNextTree();
    } catch (ImportException e) {
        e.printStackTrace();
        return;
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    ContinuousKML exporter = new ContinuousKML(tree, inputFileName, altitude, mostRecentDate, coordinateLabel);
    try {
        BufferedWriter out1 = new BufferedWriter(new FileWriter(outputFileName));
        StringBuffer buffer = new StringBuffer();
        //we write the general tree stuff, but when making slices we do not include everything in the buffer compilation
        exporter.writeTreeToKML();
        if (makeTreeSlices) {
            for (int i = 0; i < sliceTimes.length; i++) {
                //                    System.out.println(sliceTimes[i]);
                exporter.writeTreeToKML(sliceTimes[i], treeSliceBranchWidth, showBranchAtMidPoint);
            }
        }
        exporter.compileBuffer(buffer, makeTreeSlices);
        out1.write(buffer.toString());
        out1.close();
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
}

Example 8 with Arguments

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

the class TreeDensityKML method main.

//Main method
public static void main(String[] args) throws IOException {
    String inputFileName = null;
    String outputFileName = 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.IntegerOption("skip", "skip over this many trees per sample [default = 1]"), 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");
    }
    int skipEvery = 1;
    if (arguments.hasOption("skip")) {
        skipEvery = arguments.getIntegerOption("skip");
    }
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 2) {
        System.err.println("Unknown option: " + args2[2]);
        System.err.println();
        printUsage(arguments);
        System.exit(1);
    }
    if (args2.length == 2) {
        inputFileName = args2[0];
        outputFileName = args2[1];
    } else {
        System.err.println("Missing input or output file name");
        printUsage(arguments);
        System.exit(1);
    }
    new TreeDensityKML(burnin, skipEvery, inputFileName, outputFileName);
    System.exit(0);
}

Example 9 with Arguments

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

the class RootToTip method main.

//Main method
public static void main(String[] args) throws IOException {
    String inputFileName = null;
    String outputFileName = null;
    printTitle();
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.IntegerOption("burnin", "the number of trees to be ignored as 'burn-in' [default = 0]"), new Arguments.StringOption("dateorder", "date_order", "order of date field in taxon name: first, last, 1, 2 etc. [default = last]"), //                        new Arguments.StringOption("outgroup", "{taxon list}", "one or more taxa that will be used to root the tree(s) [default = find root]"),
    new Arguments.Option("keeproot", "keep the existing root of the input trees [default = estimate root]"), new Arguments.Option("writetree", "Write the optimally rooted tree to the output file"), 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 = 0;
    if (arguments.hasOption("burnin")) {
        burnin = arguments.getIntegerOption("burnin");
    }
    String dateOrder = "LAST";
    if (arguments.hasOption("dateorder")) {
        dateOrder = arguments.getStringOption("dateorder").toUpperCase();
    }
    String outgroup = null;
    if (arguments.hasOption("outgroup")) {
        outgroup = arguments.getStringOption("dateorder").toUpperCase();
    }
    boolean keepRoot = arguments.hasOption("keeproot");
    boolean writeTree = arguments.hasOption("writetree");
    String[] args2 = arguments.getLeftoverArguments();
    if (args2.length > 2) {
        System.err.println("Unknown option: " + args2[2]);
        System.err.println();
        printUsage(arguments);
        System.exit(1);
    }
    if (args2.length == 0) {
        System.err.println("Missing input file name");
        printUsage(arguments);
        System.exit(1);
    }
    inputFileName = args2[0];
    if (args2.length == 2) {
        outputFileName = args2[1];
    }
    new RootToTip(burnin, dateOrder, keepRoot, outgroup, writeTree, inputFileName, outputFileName);
    System.exit(0);
}

Example 10 with Arguments

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

the class TransmissionTreeToVirusTree method main.

public static void main(String[] args) {
    ModelType model = ModelType.CONSTANT;
    double startNe = 1;
    double growthRate = 0;
    double t50 = 0;
    Arguments arguments = new Arguments(new Arguments.Option[] { new Arguments.StringOption(DEMOGRAPHIC_MODEL, demographics, false, "The type of within-host" + " demographic function to use, default = constant"), new Arguments.RealOption(STARTING_POPULATION_SIZE, "The effective population size at time zero" + " (used in all models), default = 1"), new Arguments.RealOption(GROWTH_RATE, "The effective population size growth rate (used in" + " exponential and logistic models), default = 0"), new Arguments.RealOption(T50, "The time point, relative to the time of infection in backwards " + "time, at which the population is equal to half its final asymptotic value, in the " + "logistic model default = 0") });
    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);
    }
    if (arguments.hasOption(DEMOGRAPHIC_MODEL)) {
        String modelString = arguments.getStringOption(DEMOGRAPHIC_MODEL);
        if (modelString.toLowerCase().startsWith("c")) {
            model = ModelType.CONSTANT;
        } else if (modelString.toLowerCase().startsWith("e")) {
            model = ModelType.EXPONENTIAL;
        } else if (modelString.toLowerCase().startsWith("l")) {
            model = ModelType.LOGISTIC;
        } else {
            progressStream.print("Unrecognised demographic model type");
            System.exit(1);
        }
    }
    if (arguments.hasOption(STARTING_POPULATION_SIZE)) {
        startNe = arguments.getRealOption(STARTING_POPULATION_SIZE);
    }
    if (arguments.hasOption(GROWTH_RATE) && model != ModelType.CONSTANT) {
        growthRate = arguments.getRealOption(GROWTH_RATE);
    }
    if (arguments.hasOption(T50) && model == ModelType.LOGISTIC) {
        t50 = arguments.getRealOption(T50);
    }
    DemographicFunction demoFunction = null;
    switch(model) {
        case CONSTANT:
            {
                demoFunction = new ConstantPopulation(Units.Type.YEARS);
                ((ConstantPopulation) demoFunction).setN0(startNe);
            }
        case EXPONENTIAL:
            {
                demoFunction = new ExponentialGrowth(Units.Type.YEARS);
                ((ExponentialGrowth) demoFunction).setN0(startNe);
                ((ExponentialGrowth) demoFunction).setGrowthRate(growthRate);
            }
        case LOGISTIC:
            {
                demoFunction = new LogisticGrowthN0(Units.Type.YEARS);
                ((LogisticGrowthN0) demoFunction).setN0(startNe);
                ((LogisticGrowthN0) demoFunction).setGrowthRate(growthRate);
                ((LogisticGrowthN0) demoFunction).setT50(t50);
            }
    }
    final String[] args2 = arguments.getLeftoverArguments();
    if (args2.length != 3) {
        printUsage(arguments);
        System.exit(1);
    }
    String infectionsFileName = args2[0];
    String samplesFileName = args2[1];
    String outputFileRoot = args2[2];
    TransmissionTreeToVirusTree instance = new TransmissionTreeToVirusTree(samplesFileName, infectionsFileName, demoFunction, outputFileRoot);
    try {
        instance.run();
    } catch (IOException e) {
        e.printStackTrace();
    }
}