Examples with NewickImporter jebl.evolution.io.NewickImporter used on opensource projects

Example 1 with NewickImporter

use of jebl.evolution.io.NewickImporter in project beast-mcmc by beast-dev.

the class LineageCountThroughTime method getLTT.

public static Variate[] getLTT(String treeFile, double minTime, double maxTime, int binCount, // number of trees to skip
int skip) throws IOException, ImportException {
    double delta = (maxTime - minTime) / (binCount - 1);
    BufferedReader reader = new BufferedReader(new FileReader(treeFile));
    String line = reader.readLine();
    TreeImporter importer;
    if (line.toUpperCase().startsWith("#NEXUS")) {
        importer = new NexusImporter(reader);
    } else {
        importer = new NewickImporter(reader, false);
    }
    int state = 0;
    while (importer.hasTree() && state < skip) {
        importer.importNextTree();
        state += 1;
    }
    // the age of the end of this group
    List<double[]> branchingTimes = new ArrayList<double[]>();
    state = 0;
    while (importer.hasTree()) {
        RootedTree tree = (RootedTree) importer.importNextTree();
        double[] bt = new double[tree.getInternalNodes().size()];
        int i = 0;
        for (Node node : tree.getInternalNodes()) {
            bt[i] = tree.getHeight(node);
            i++;
        }
        Arrays.sort(bt);
        branchingTimes.add(bt);
        state += 1;
    }
    Variate[] bins = new Variate[binCount];
    double height = 0;
    double n = branchingTimes.get(0).length;
    for (int k = 0; k < binCount; k++) {
        bins[k] = new Variate.D();
        if (height >= 0.0 && height <= maxTime) {
            for (state = 0; state < branchingTimes.size(); state++) {
                int index = 0;
                while (index < branchingTimes.get(state).length && branchingTimes.get(state)[index] < height) {
                    index += 1;
                }
                double lineageCount = 1;
                if (index < branchingTimes.get(state).length) {
                    lineageCount = n - index + 1;
                }
                bins[k].add(lineageCount);
            }
        }
        height += delta;
    }
    Variate xData = new Variate.D();
    Variate yDataMean = new Variate.D();
    Variate yDataMedian = new Variate.D();
    Variate yDataUpper = new Variate.D();
    Variate yDataLower = new Variate.D();
    double t = minTime;
    for (Variate bin : bins) {
        xData.add(t);
        if (bin.getCount() > 0) {
            yDataMean.add(bin.getMean());
            yDataMedian.add(bin.getQuantile(0.5));
            yDataLower.add(bin.getQuantile(0.025));
            yDataUpper.add(bin.getQuantile(0.975));
        } else {
            yDataMean.add(Double.NaN);
            yDataMedian.add(Double.NaN);
            yDataLower.add(Double.NaN);
            yDataUpper.add(Double.NaN);
        }
        t += delta;
    }
    return new Variate[] { xData, yDataMean };
}