Examples with TKF91Likelihood dr.oldevomodel.indel.TKF91Likelihood used on opensource projects

Example 1 with TKF91Likelihood

use of dr.oldevomodel.indel.TKF91Likelihood in project beast-mcmc by beast-dev.

the class IstvanOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TKF91Likelihood likelihood = (TKF91Likelihood) xo.getChild(TKF91Likelihood.class);
    double weight = xo.getDoubleAttribute("weight");
    double iP = xo.getDoubleAttribute("iP");
    double exponent = xo.getDoubleAttribute("exponent");
    double gapPenalty = xo.getDoubleAttribute("gapPenalty");
    return new IstvanOperator(iP, exponent, gapPenalty, weight, likelihood);
}

Example 2 with TKF91Likelihood

use of dr.oldevomodel.indel.TKF91Likelihood in project beast-mcmc by beast-dev.

the class TKF91LikelihoodParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    GammaSiteModel siteModel = (GammaSiteModel) xo.getChild(GammaSiteModel.class);
    TKF91Model tkfModel = (TKF91Model) xo.getChild(TKF91Model.class);
    return new TKF91Likelihood(tree, alignment, siteModel, tkfModel);
}