Examples with SubtreeLeapOperator dr.evomodel.operators.SubtreeLeapOperator used on opensource projects

Example 1 with SubtreeLeapOperator

use of dr.evomodel.operators.SubtreeLeapOperator in project beast-mcmc by beast-dev.

the class SubtreeLeapOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    CoercionMode mode = CoercionMode.parseMode(xo);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final double size = xo.getAttribute("size", 1.0);
    final double prob = xo.getAttribute("accP", 0.234);
    if (Double.isInfinite(size) || size <= 0.0) {
        throw new XMLParseException("size attribute must be positive and not infinite. was " + size);
    }
    if (prob <= 0.0 || prob >= 1.0) {
        throw new XMLParseException("Target acceptance probability has to lie in (0, 1). Currently: " + prob);
    }
    SubtreeLeapOperator operator = new SubtreeLeapOperator(treeModel, weight, size, prob, mode);
    return operator;
}