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

Example 11 with Units

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

the class EmpiricalPiecewiseModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(INTERVAL_WIDTHS);
    double[] intervalWidths = cxo.getDoubleArrayAttribute("values");
    cxo = xo.getChild(POPULATION_SIZES);
    Parameter popSizes = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(TAU);
    Parameter scaleParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(THRESHOLD);
    Parameter bParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(LAG);
    Parameter offsetParam = (Parameter) cxo.getChild(Parameter.class);
    return new EmpiricalPiecewiseModel(intervalWidths, popSizes, scaleParam, bParam, offsetParam, units);
}

Example 12 with Units

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

the class ExponentialConstantModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(POPULATION_SIZE);
    Parameter N0Param = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(GROWTH_RATE);
    Parameter logGrowthParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(TRANSITION_TIME);
    Parameter timeParam = (Parameter) cxo.getChild(Parameter.class);
    return new ExponentialConstantModel(N0Param, logGrowthParam, timeParam, units);
}

Example 13 with Units

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

the class ExponentialExponentialModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(POPULATION_SIZE);
    Parameter N0Param = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(GROWTH_RATE);
    Parameter growthParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(ANCESTRAL_GROWTH_RATE);
    Parameter ancestralGrowthParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(TRANSITION_TIME);
    Parameter timeParam = (Parameter) cxo.getChild(Parameter.class);
    return new ExponentialExponentialModel(N0Param, growthParam, ancestralGrowthParam, timeParam, units);
}

Example 14 with Units

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

the class LinearGrowthModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(SLOPE);
    Parameter slopeParam = (Parameter) cxo.getChild(Parameter.class);
    return new LinearGrowthModel(slopeParam, units);
}

Example 15 with Units

use of dr.evolution.util.Units 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.setUncertainty(date.getUncertainty());
        taxonList.getTaxon(i).setDate(newDate);
    }
    calculateHeights();
    dataTableModel.fireTableDataChanged();
    frame.timeScaleChanged();
}