Examples with Options ml.options.Options used on opensource projects

Example 1 with Options

use of ml.options.Options in project beast-mcmc by beast-dev.

the class VariableCoalescentSimulator method main.

public static void main(String[] arg) throws IOException {
    long startTime = System.currentTimeMillis();
    Options options = new Options(arg, 0, 7);
    options.getSet().addOption("g", Options.Separator.EQUALS, Options.Multiplicity.ZERO_OR_ONE);
    options.getSet().addOption("n", Options.Separator.EQUALS, Options.Multiplicity.ZERO_OR_ONE);
    options.getSet().addOption("p", Options.Separator.EQUALS, Options.Multiplicity.ZERO_OR_ONE);
    options.getSet().addOption("se", Options.Separator.EQUALS, Options.Multiplicity.ZERO_OR_ONE);
    options.getSet().addOption("ss", Options.Separator.EQUALS, Options.Multiplicity.ZERO_OR_ONE);
    options.getSet().addOption("reps", Options.Separator.EQUALS, Options.Multiplicity.ZERO_OR_ONE);
    options.getSet().addOption("f", Options.Multiplicity.ZERO_OR_ONE);
    if (!options.check()) {
        System.out.println(options.getCheckErrors());
        System.out.println();
        printUsage();
        System.exit(1);
    }
    double generationTime = 1.0;
    double popSizeScale = 1.0;
    int n = 50;
    double ss = -1;
    double se = -1;
    int reps = 1;
    boolean timeForward = options.getSet().isSet("f");
    if (options.getSet().isSet("g")) {
        String g = options.getSet().getOption("g").getResultValue(0);
        generationTime = Double.parseDouble(g);
        System.out.println("generation time = " + g);
    }
    if (options.getSet().isSet("n")) {
        String sampleSize = options.getSet().getOption("n").getResultValue(0);
        n = Integer.parseInt(sampleSize);
        System.out.println("sample size = " + n);
    }
    if (options.getSet().isSet("p")) {
        String p = options.getSet().getOption("p").getResultValue(0);
        popSizeScale = Double.parseDouble(p);
        System.out.println("population size scale factor = " + p);
    }
    if (options.getSet().isSet("ss")) {
        String sampleStart = options.getSet().getOption("ss").getResultValue(0);
        ss = Double.parseDouble(sampleStart);
        System.out.println("sample start time = " + ss);
    }
    if (options.getSet().isSet("se")) {
        String sampleEnd = options.getSet().getOption("se").getResultValue(0);
        se = Double.parseDouble(sampleEnd);
        System.out.println("sample end time = " + se);
    }
    if (options.getSet().isSet("reps")) {
        String replicates = options.getSet().getOption("reps").getResultValue(0);
        reps = Integer.parseInt(replicates);
        System.out.println("replicates = " + reps);
    }
    String filename = options.getSet().getData().get(0);
    String outfile = options.getSet().getData().get(1);
    // READ DEMOGRAPHIC FUNCTION
    BufferedReader reader = new BufferedReader(new FileReader(filename));
    List<Double> times = new ArrayList<Double>();
    String line = reader.readLine();
    String[] tokens = line.trim().split("[\t ]+");
    if (tokens.length < 2)
        throw new RuntimeException();
    ArrayList<ArrayList> popSizes = new ArrayList<ArrayList>();
    while (line != null) {
        double time = Double.parseDouble(tokens[0]) / generationTime;
        times.add(time);
        for (int i = 1; i < tokens.length; i++) {
            popSizes.add(new ArrayList<Double>());
            popSizes.get(i - 1).add(Double.parseDouble(tokens[i]));
        }
        line = reader.readLine();
        if (line != null) {
            tokens = line.trim().split("[\t ]+");
            if (tokens.length != popSizes.size() + 1)
                throw new RuntimeException();
        }
    }
    reader.close();
    // GENERATE SAMPLE
    double lastTime = times.get(times.size() - 1);
    if (ss == -1) {
        ss = timeForward ? lastTime : times.get(0);
    }
    if (se == -1) {
        se = timeForward ? lastTime : times.get(0);
    }
    double dt = (se - ss) / ((double) n - 1.0);
    double time = ss;
    Taxa taxa = new Taxa();
    for (int i = 0; i < n; i++) {
        double sampleTime;
        if (timeForward) {
            sampleTime = (lastTime - time) / generationTime;
        } else
            sampleTime = time / generationTime;
        Taxon taxon = new Taxon(i + "");
        taxon.setAttribute(dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
        taxa.addTaxon(taxon);
        time += dt;
    }
    double minTheta = Double.MAX_VALUE;
    double maxTheta = 0.0;
    PrintWriter out = new PrintWriter(new FileWriter(outfile));
    int popHistory = 0;
    PiecewiseLinearPopulation[] demography = new PiecewiseLinearPopulation[popSizes.size()];
    for (List<Double> popSize : popSizes) {
        double[] thetas = new double[popSize.size()];
        double[] intervals = new double[times.size() - 1];
        for (int i = intervals.length; i >= 0; i--) {
            int j = timeForward ? intervals.length - i : i - 1;
            int k = timeForward ? i : intervals.length - i + 1;
            if (i != 0)
                intervals[j] = times.get(k) - times.get(k - 1);
            double theta = popSize.get(k) * popSizeScale;
            thetas[j] = theta;
            if (theta < minTheta) {
                minTheta = theta;
            }
            if (theta > maxTheta) {
                maxTheta = theta;
            }
        // System.out.println(t + "\t" + theta);
        }
        System.out.println("N" + popHistory + "(t) range = [" + minTheta + ", " + maxTheta + "]");
        demography[popHistory] = new PiecewiseLinearPopulation(intervals, thetas, Units.Type.GENERATIONS);
        popHistory += 1;
    }
    CoalescentSimulator simulator = new CoalescentSimulator();
    for (int i = 0; i < reps; i++) {
        out.println("#rep " + i);
        for (int j = 0; j < demography.length; j++) {
            Tree tree = simulator.simulateTree(taxa, demography[j]);
            out.println(TreeUtils.newick(tree));
        // System.err.println(Tree.Utils.newick(tree));
        }
    }
    out.flush();
    out.close();
    long stopTime = System.currentTimeMillis();
    System.out.println("Took " + (stopTime - startTime) / 1000.0 + " seconds");
}