Examples with Date dr.evolution.util.Date used on opensource projects

Example 11 with Date

use of dr.evolution.util.Date in project beast-mcmc by beast-dev.

the class TreeUtils method getTipDates.

/**
 * Gets the tip dates from a tree.
 */
public static void getTipDates(Tree tree, Variate dates) {
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        Object date = taxon.getAttribute("date");
        if (date != null) {
            if (date instanceof Date) {
                dates.add(((Date) date).getTimeValue());
            } else {
                try {
                    dates.add(Double.parseDouble(date.toString()));
                } catch (NumberFormatException nfe) {
                    dates.add(0.0);
                }
            }
        } else {
            dates.add(0.0);
        }
    }
}

Example 12 with Date

use of dr.evolution.util.Date in project beast-mcmc by beast-dev.

the class TreeUtils method setHeightsFromDates.

/**
 * Sets the tip heights from the tip dates
 */
public static void setHeightsFromDates(MutableTree tree) {
    Date mostRecent = null;
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        Taxon taxon = tree.getNodeTaxon(tree.getExternalNode(i));
        Date date = (Date) taxon.getAttribute("date");
        if (date != null) {
            if ((mostRecent == null) || date.after(mostRecent)) {
                mostRecent = date;
            }
        }
    }
    TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
    for (int i = 0; i < tree.getExternalNodeCount(); i++) {
        NodeRef node = tree.getExternalNode(i);
        Taxon taxon = tree.getNodeTaxon(node);
        Date date = (Date) taxon.getAttribute("date");
        if (date != null) {
            double height = timeScale.convertTime(date.getTimeValue(), date);
            tree.setNodeHeight(node, height);
        } else {
            tree.setNodeHeight(node, 0.0);
        }
    }
    adjustInternalHeights(tree, tree.getRoot());
    if (mostRecent != null) {
        tree.setUnits(mostRecent.getUnits());
    }
}

Example 13 with Date

use of dr.evolution.util.Date in project beast-mcmc by beast-dev.

the class TemporalRooting method setHeightsFromDates.

private void setHeightsFromDates(FlexibleTree tree) {
    Date mostRecent = null;
    for (int i = 0; i < taxa.getTaxonCount(); i++) {
        Date date = taxa.getTaxon(i).getDate();
        if ((date != null) && (mostRecent == null || date.after(mostRecent))) {
            mostRecent = date;
        }
    }
    if (mostRecent != null) {
        TimeScale timeScale = new TimeScale(mostRecent.getUnits(), true, mostRecent.getAbsoluteTimeValue());
        double time0 = timeScale.convertTime(mostRecent.getTimeValue(), mostRecent);
        for (int i = 0; i < tree.getExternalNodeCount(); i++) {
            NodeRef tip = tree.getExternalNode(i);
            Date date = tree.getNodeTaxon(tip).getDate();
            if (date != null) {
                tree.setNodeHeight(tip, timeScale.convertTime(date.getTimeValue(), date) - time0);
            } else {
                tree.setNodeHeight(tip, 0.0);
            }
        }
    }
}

Example 14 with Date

use of dr.evolution.util.Date in project beast-mcmc by beast-dev.

the class PLCoalescentSimulator method main.

public static void main(String[] arg) throws IOException {
    // READ DEMOGRAPHIC FUNCTION
    String filename = arg[0];
    BufferedReader reader = new BufferedReader(new FileReader(filename));
    double popSizeScale = 1.0;
    double generationTime = 1.0;
    if (arg.length > 2) {
        popSizeScale = Double.parseDouble(arg[2]);
    }
    if (arg.length > 3) {
        generationTime = Double.parseDouble(arg[3]);
    }
    PrintWriter populationFuncLogger = null;
    if (arg.length > 5) {
        String logFileName = arg[5];
        if (logFileName.equals("-")) {
            populationFuncLogger = new PrintWriter(System.out);
        } else {
            populationFuncLogger = new PrintWriter(new FileWriter(logFileName));
        }
    }
    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();
    // READ SAMPLE TIMES
    String samplesFilename = arg[1];
    reader = new BufferedReader(new FileReader(samplesFilename));
    line = reader.readLine();
    Taxa taxa = new Taxa();
    int id = 0;
    while (line != null) {
        if (!line.startsWith("#")) {
            tokens = line.split("[\t ]+");
            if (tokens.length == 4) {
                double t0 = Double.parseDouble(tokens[0]);
                double t1 = Double.parseDouble(tokens[1]);
                double dt = Double.parseDouble(tokens[2]);
                int k = Integer.parseInt(tokens[3]);
                for (double time = t0; time <= t1; time += dt) {
                    double sampleTime = time / generationTime;
                    for (int i = 0; i < k; i++) {
                        Taxon taxon = new Taxon("t" + id);
                        taxon.setAttribute(dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
                        taxa.addTaxon(taxon);
                        id += 1;
                    }
                }
            } else {
                // sample times are in the same units as simulation
                double sampleTime = Double.parseDouble(tokens[0]) / generationTime;
                int count = Integer.parseInt(tokens[1]);
                for (int i = 0; i < count; i++) {
                    Taxon taxon = new Taxon(id + "");
                    taxon.setAttribute(dr.evolution.util.Date.DATE, new Date(sampleTime, Units.Type.GENERATIONS, true));
                    taxa.addTaxon(taxon);
                    id += 1;
                }
            }
        }
        line = reader.readLine();
    }
    double minTheta = Double.MAX_VALUE;
    double maxTheta = 0.0;
    PrintWriter out;
    if (arg.length > 4) {
        out = new PrintWriter(new FileWriter(arg[4]));
    } else {
        out = new PrintWriter(System.out);
    }
    int pp = 0;
    for (List<Double> popSize : popSizes) {
        double[] thetas = new double[popSize.size()];
        double[] intervals = new double[times.size() - 1];
        if (populationFuncLogger != null) {
            populationFuncLogger.println("# " + pp);
            ++pp;
        }
        // must reverse the direction of the model
        for (int j = intervals.length; j > 0; j--) {
            intervals[intervals.length - j] = times.get(j) - times.get(j - 1);
            final double theta = popSize.get(j) * popSizeScale;
            thetas[intervals.length - j] = theta;
            if (theta < minTheta) {
                minTheta = theta;
            }
            if (theta > maxTheta) {
                maxTheta = theta;
            }
            final double t = times.get(intervals.length) - times.get(j);
            if (populationFuncLogger != null) {
                populationFuncLogger.println(t + "\t" + theta);
            }
        }
        if (debug != null) {
            debug.println("min theta = " + minTheta);
            debug.println("max theta = " + maxTheta);
        }
        PiecewiseLinearPopulation demo = new PiecewiseLinearPopulation(intervals, thetas, Units.Type.GENERATIONS);
        CoalescentSimulator simulator = new CoalescentSimulator();
        Tree tree = simulator.simulateTree(taxa, demo);
        out.println(TreeUtils.newick(tree));
        if (debug != null) {
            debug.println(TreeUtils.newick(tree));
        }
    }
    if (populationFuncLogger != null) {
        populationFuncLogger.flush();
        populationFuncLogger.close();
    }
    out.flush();
    out.close();
}

Example 15 with Date

use of dr.evolution.util.Date in project beast-mcmc by beast-dev.

the class DataLikelihoodTester method createAlignment.

private static SimpleAlignment createAlignment(Object[][] taxa_sequence, DataType dataType) {
    SimpleAlignment alignment = new SimpleAlignment();
    alignment.setDataType(dataType);
    // alignment.setDataType(Nucleotides.INSTANCE);
    // 6, 17
    Taxon[] taxa = new Taxon[taxa_sequence[0].length];
    System.out.println("Taxon len = " + taxa_sequence[0].length);
    System.out.println("Alignment len = " + taxa_sequence[1].length);
    if (taxa_sequence.length > 2)
        System.out.println("Date len = " + taxa_sequence[2].length);
    for (int i = 0; i < taxa_sequence[0].length; i++) {
        taxa[i] = new Taxon(taxa_sequence[0][i].toString());
        if (taxa_sequence.length > 2) {
            Date date = new Date((Double) taxa_sequence[2][i], Units.Type.YEARS, (Boolean) taxa_sequence[3][0]);
            taxa[i].setDate(date);
        }
        // taxonList.addTaxon(taxon);
        Sequence sequence = new Sequence(taxa_sequence[1][i].toString());
        sequence.setTaxon(taxa[i]);
        sequence.setDataType(dataType);
        alignment.addSequence(sequence);
    }
    return alignment;
}