Examples with CTMCScalePrior dr.evomodel.tree.CTMCScalePrior used on opensource projects

Example 1 with CTMCScalePrior

use of dr.evomodel.tree.CTMCScalePrior in project beast-mcmc by beast-dev.

the class CTMCScalePriorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    Parameter ctmcScale = (Parameter) xo.getElementFirstChild(SCALEPARAMETER);
    boolean reciprocal = xo.getAttribute(RECIPROCAL, false);
    boolean trial = xo.getAttribute(TRIAL, false);
    SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
    Logger.getLogger("dr.evolution").info("Creating CTMC Scale Reference Prior model.");
    return new CTMCScalePrior(MODEL_NAME, ctmcScale, treeModel, reciprocal, substitutionModel, trial);
}