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

Example 16 with Date

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

the class TreeModelParser method setPrecisionBounds.

private void setPrecisionBounds(Parameter newParameter, Taxon taxon) {
    Date date = taxon.getDate();
    if (date != null) {
        double precision = date.getPrecision();
        if (precision > 0.0) {
            // taxon date not specified to exact value so add appropriate bounds
            double upper = Taxon.getHeightFromDate(date);
            double lower = Taxon.getHeightFromDate(date);
            if (date.isBackwards()) {
                upper += precision;
            } else {
                lower -= precision;
            }
            // set the bounds for the given precision
            newParameter.addBounds(new Parameter.DefaultBounds(upper, lower, 1));
            // set the initial value to be mid-point
            newParameter.setParameterValue(0, (upper + lower) / 2);
        }
    }
}

Example 17 with Date

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

the class SamplesPanel method timeScaleChanged.

public final void timeScaleChanged() {
    Units.Type units = Units.Type.YEARS;
    switch(unitsCombo.getSelectedIndex()) {
        case 0:
            units = Units.Type.YEARS;
            break;
        case 1:
            units = Units.Type.MONTHS;
            break;
        case 2:
            units = Units.Type.DAYS;
            break;
    }
    boolean backwards = directionCombo.getSelectedIndex() == 1;
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Date date = taxonList.getTaxon(i).getDate();
        double d = date.getTimeValue();
        Date newDate = createDate(d, units, backwards, 0.0);
        newDate.setPrecision(date.getPrecision());
        taxonList.getTaxon(i).setDate(newDate);
    }
    calculateHeights();
    dataTableModel.fireTableDataChanged();
    frame.timeScaleChanged();
}

Example 18 with Date

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

the class DataLikelihoodTester2 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;
}

Example 19 with Date

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

the class BigFastTreeModelParser method setUncertaintyBounds.

private void setUncertaintyBounds(Parameter newParameter, Taxon taxon) {
    Date date = taxon.getDate();
    if (date != null) {
        double uncertainty = date.getUncertainty();
        if (uncertainty > 0.0) {
            // taxon date not specified to exact value so add appropriate bounds
            double upper = Taxon.getHeightFromDate(date);
            double lower = Taxon.getHeightFromDate(date);
            if (date.isBackwards()) {
                upper += uncertainty;
            } else {
                lower -= uncertainty;
            }
            // set the bounds for the given precision
            newParameter.addBounds(new Parameter.DefaultBounds(upper, lower, 1));
            // set the initial value to be mid-point
            newParameter.setParameterValue(0, (upper + lower) / 2);
        }
    }
}

Example 20 with Date

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

the class TreeModelParser method setUncertaintyBounds.

private void setUncertaintyBounds(Parameter newParameter, Taxon taxon) {
    Date date = taxon.getDate();
    if (date != null) {
        double uncertainty = date.getUncertainty();
        if (uncertainty > 0.0) {
            // taxon date not specified to exact value so add appropriate bounds
            double upper = Taxon.getHeightFromDate(date);
            double lower = Taxon.getHeightFromDate(date);
            if (date.isBackwards()) {
                upper += uncertainty;
            } else {
                lower -= uncertainty;
            }
            // set the bounds for the given precision
            newParameter.addBounds(new Parameter.DefaultBounds(upper, lower, 1));
            // set the initial value to be mid-point
            newParameter.setParameterValue(0, (upper + lower) / 2);
        }
    }
}