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

Example 1 with Units

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

the class ScaledPiecewiseModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(EPOCH_SIZES);
    Parameter epochSizes = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(TREE_MODEL);
    TreeModel treeModel = (TreeModel) cxo.getChild(TreeModel.class);
    boolean isLinear = xo.getBooleanAttribute("linear");
    return new ScaledPiecewiseModel(epochSizes, treeModel, isLinear, units);
}

Example 2 with Units

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

the class TwoEpochDemographicModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(EPOCH_1);
    DemographicModel demo1 = (DemographicModel) cxo.getChild(DemographicModel.class);
    cxo = xo.getChild(EPOCH_2);
    DemographicModel demo2 = (DemographicModel) cxo.getChild(DemographicModel.class);
    cxo = xo.getChild(TRANSITION_TIME);
    Parameter timeParameter = (Parameter) cxo.getChild(Parameter.class);
    return new TwoEpochDemographicModel(demo1, demo2, timeParameter, units);
}

Example 3 with Units

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

the class PeakAndDeclineModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(PEAK_VALUE);
    Parameter peakValueParam = (Parameter) cxo.getChild(Parameter.class);
    Parameter rParam;
    cxo = xo.getChild(SHAPE);
    rParam = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(PEAK_TIME);
    Parameter peakTimeParam = (Parameter) cxo.getChild(Parameter.class);
    return new PeakAndDeclineModel(peakValueParam, rParam, peakTimeParam, units);
}

Example 4 with Units

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

the class PiecewisePopulationModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject obj = xo.getChild(EPOCH_WIDTHS);
    double[] epochWidths = obj.getDoubleArrayAttribute(WIDTHS);
    if (xo.hasChildNamed(EPOCH_SIZES)) {
        Parameter epochSizes = (Parameter) xo.getElementFirstChild(EPOCH_SIZES);
        boolean isLinear = false;
        if (xo.hasAttribute(LINEAR)) {
            isLinear = xo.getBooleanAttribute(LINEAR);
        }
        return new PiecewisePopulationModel(PIECEWISE_POPULATION, epochSizes, epochWidths, isLinear, units);
    } else {
        Parameter populationSize = (Parameter) xo.getElementFirstChild(POPULATION_SIZE);
        Parameter growthRates = (Parameter) xo.getElementFirstChild(GROWTH_RATES);
        return new PiecewisePopulationModel(PIECEWISE_POPULATION, populationSize, growthRates, epochWidths, units);
    }
}

Example 5 with Units

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

the class PowerLawGrowthModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    XMLObject cxo = xo.getChild(N0);
    Parameter N0Param = (Parameter) cxo.getChild(Parameter.class);
    Parameter rParam;
    cxo = xo.getChild(POWER);
    rParam = (Parameter) cxo.getChild(Parameter.class);
    return new PowerLawGrowthModel(N0Param, rParam, units);
}