/*
* LatentFactorHamiltonianMCParser.java
*
* Copyright (c) 2002-2017 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.inference.operators.hmc.deprecated;
import dr.evomodel.continuous.FullyConjugateMultivariateTraitLikelihood;
import dr.inference.operators.hmc.deprecated.LatentFactorHamiltonianMC;
import dr.inference.model.LatentFactorModel;
import dr.inference.operators.CoercionMode;
import dr.xml.*;
/**
* Created by max on 12/2/15.
*/
@Deprecated
public class LatentFactorHamiltonianMCParser extends AbstractXMLObjectParser {
public static final String LATENT_FACTOR_MODEL_HAMILTONIAN_MC="LatentFactorHamiltonianMC";
public static final String WEIGHT="weight";
public static final String N_STEPS="nSteps";
public static final String STEP_SIZE="stepSize";
public static final String MOMENTUM_SD="momentumSd";
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
LatentFactorModel lfm=(LatentFactorModel) xo.getChild(LatentFactorModel.class);
FullyConjugateMultivariateTraitLikelihood tree=(FullyConjugateMultivariateTraitLikelihood) xo.getChild(FullyConjugateMultivariateTraitLikelihood.class);
double weight=xo.getDoubleAttribute(WEIGHT);
CoercionMode mode=CoercionMode.parseMode(xo);
int nSteps=xo.getIntegerAttribute(N_STEPS);
double stepSize=xo.getDoubleAttribute(STEP_SIZE);
double momentumSd= xo.getDoubleAttribute(MOMENTUM_SD);
return new LatentFactorHamiltonianMC(lfm, tree, weight, mode, stepSize, nSteps, momentumSd);
}
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private static final XMLSyntaxRule[] rules = {
AttributeRule.newDoubleRule(WEIGHT),
AttributeRule.newDoubleRule(STEP_SIZE),
AttributeRule.newIntegerRule(N_STEPS),
AttributeRule.newDoubleRule(MOMENTUM_SD),
new ElementRule(LatentFactorModel.class),
new ElementRule(FullyConjugateMultivariateTraitLikelihood.class),
};
@Override
public String getParserDescription() {
return "Hamiltonian Monte Carlo For factors";
}
@Override
public Class getReturnType() {
return LatentFactorHamiltonianMC.class;
}
@Override
public String getParserName() {
return LATENT_FACTOR_MODEL_HAMILTONIAN_MC;
}
}