Examples with TwoPhaseOperator dr.inference.operators.TwoPhaseOperator used on opensource projects

Example 1 with TwoPhaseOperator

use of dr.inference.operators.TwoPhaseOperator in project beast-mcmc by beast-dev.

the class TwoPhaseOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    if (DEBUG) {
        System.err.println("\nParsing TwoPhaseOperator");
    }
    final CoercionMode mode = CoercionMode.parseMode(xo);
    final double weight = xo.getDoubleAttribute(WEIGHT);
    final int initial = xo.getIntegerAttribute(INITIAL);
    final int burnin = xo.getIntegerAttribute(BURNIN);
    if (DEBUG) {
        System.err.println("child count: " + xo.getChildCount());
        System.err.println(xo.getChild(PHASE_ONE));
        System.err.println(xo.getChild(PHASE_ONE).getChildCount());
        System.err.println(xo.getChild(PHASE_TWO));
        System.err.println(xo.getChild(PHASE_TWO).getChildCount());
    }
    List<AbstractCoercableOperator> phaseOneOperators = new ArrayList<AbstractCoercableOperator>();
    int phaseOneCount = xo.getChild(PHASE_ONE).getChildCount();
    for (int i = 0; i < phaseOneCount; i++) {
        phaseOneOperators.add((AbstractCoercableOperator) xo.getChild(PHASE_ONE).getChild(i));
    }
    if (DEBUG) {
        System.err.println("arrayList one size: " + phaseOneOperators.size());
        for (int i = 0; i < phaseOneOperators.size(); i++) {
            System.err.println("  " + phaseOneOperators.get(i));
        }
    }
    /*List<AbstractCoercableOperator> phaseTwoOperators = new ArrayList<AbstractCoercableOperator>();
        int phaseTwoCount = xo.getChild(PHASE_TWO).getChildCount();
        for (int i = 0; i < phaseTwoCount; i++) {
            phaseTwoOperators.add((AbstractCoercableOperator)xo.getChild(PHASE_TWO).getChild(i));
        }*/
    List<AdaptableVarianceMultivariateNormalOperator> phaseTwoOperators = new ArrayList<AdaptableVarianceMultivariateNormalOperator>();
    int phaseTwoCount = xo.getChild(PHASE_TWO).getChildCount();
    for (int i = 0; i < phaseTwoCount; i++) {
        phaseTwoOperators.add((AdaptableVarianceMultivariateNormalOperator) xo.getChild(PHASE_TWO).getChild(i));
    }
    if (DEBUG) {
        System.err.println("arrayList two size: " + phaseTwoOperators.size());
        for (int i = 0; i < phaseTwoOperators.size(); i++) {
            System.err.println("  " + phaseTwoOperators.get(i));
        }
    }
    //keep track of the parameters of phase one here, as apparently we can't get to them afterwards
    //let's just get them from phase two, as there I can implement whatever I want
    List<Parameter> parameters = new ArrayList<Parameter>();
    for (int i = 0; i < phaseTwoCount; i++) {
        parameters.add(phaseTwoOperators.get(i).getParameter());
    }
    if (DEBUG) {
        System.err.println("parameter list size: " + parameters.size());
        for (int i = 0; i < parameters.size(); i++) {
            System.err.println("  " + parameters.get(i));
        }
    }
    return new TwoPhaseOperator(phaseOneOperators, phaseTwoOperators, parameters, initial, burnin, weight, mode);
}