GMRFSkyrideBlockUpdateOperatorParser.java

/*
 * GMRFSkyrideBlockUpdateOperatorParser.java
 *
 * Copyright (c) 2002-2015 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.evomodelxml.coalescent.operators;

import dr.evomodel.coalescent.GMRFMultilocusSkyrideLikelihood;
import dr.evomodel.coalescent.GMRFSkyrideLikelihood;
import dr.evomodel.coalescent.operators.GMRFMultilocusSkyrideBlockUpdateOperator;
import dr.evomodel.coalescent.operators.GMRFSkyrideBlockUpdateOperator;
import dr.inference.operators.CoercableMCMCOperator;
import dr.inference.operators.CoercionMode;
import dr.inference.operators.MCMCOperator;
import dr.math.MathUtils;
import dr.xml.*;

import java.io.IOException;
import java.util.logging.*;

/**
 *
 */
public class GMRFSkyrideBlockUpdateOperatorParser extends AbstractXMLObjectParser {

    public static final String BLOCK_UPDATE_OPERATOR = "gmrfBlockUpdateOperator";
    public static final String GRID_BLOCK_UPDATE_OPERATOR = "gmrfGridBlockUpdateOperator";
    public static final String SCALE_FACTOR = "scaleFactor";
    public static final String MAX_ITERATIONS = "maxIterations";
    public static final String STOP_VALUE = "stopValue";
    public static final String KEEP_LOG_RECORD = "keepLogRecord";
    public static final String OLD_SKYRIDE = "oldSkyride";

    public String getParserName() {
        return BLOCK_UPDATE_OPERATOR;
    }

    public String[] getParserNames() {
        return new String[]{
                getParserName(),
                GRID_BLOCK_UPDATE_OPERATOR,
        };
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {

        boolean logRecord = xo.getAttribute(KEEP_LOG_RECORD, false);

        Handler gmrfHandler;
        Logger gmrfLogger = Logger.getLogger("dr.evomodel.coalescent.operators.GMRFSkyrideBlockUpdateOperator");
        gmrfLogger.setUseParentHandlers(false);

        if (logRecord) {
            gmrfLogger.setLevel(Level.FINE);

            try {
                gmrfHandler = new FileHandler("GMRFBlockUpdate.log." + MathUtils.getSeed());
            } catch (IOException e) {
                throw new RuntimeException(e.getMessage());
            }
            gmrfHandler.setLevel(Level.FINE);

            gmrfHandler.setFormatter(new XMLFormatter() {
                public String format(LogRecord record) {
                    return "<record>\n \t<message>\n\t" + record.getMessage()
                            + "\n\t</message>\n<record>\n";
                }
            });

            gmrfLogger.addHandler(gmrfHandler);
        }

        CoercionMode mode = CoercionMode.parseMode(xo);
        if (mode == CoercionMode.DEFAULT) mode = CoercionMode.COERCION_ON;

        double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
        double scaleFactor = xo.getDoubleAttribute(SCALE_FACTOR);
        if (scaleFactor == 1.0) {
            mode = CoercionMode.COERCION_OFF;
        }

//            if (scaleFactor <= 0.0) {
//                throw new XMLParseException("scaleFactor must be greater than 0.0");
        if (scaleFactor < 1.0) {
            throw new XMLParseException("scaleFactor must be greater than or equal to 1.0");
        }

        int maxIterations = xo.getAttribute(MAX_ITERATIONS, 200);

        double stopValue = xo.getAttribute(STOP_VALUE, 0.01);


        if (xo.getAttribute(OLD_SKYRIDE, true)
                && !(xo.getName().compareTo(GRID_BLOCK_UPDATE_OPERATOR) == 0)
                ) {
            GMRFSkyrideLikelihood gmrfLikelihood = (GMRFSkyrideLikelihood) xo.getChild(GMRFSkyrideLikelihood.class);
            return new GMRFSkyrideBlockUpdateOperator(gmrfLikelihood, weight, mode, scaleFactor,
                    maxIterations, stopValue);
        } else {
            GMRFMultilocusSkyrideLikelihood gmrfMultilocusLikelihood = (GMRFMultilocusSkyrideLikelihood) xo.getChild(GMRFMultilocusSkyrideLikelihood.class);
            return new GMRFMultilocusSkyrideBlockUpdateOperator(gmrfMultilocusLikelihood, weight, mode, scaleFactor,
                    maxIterations, stopValue);
        }

    }

    //************************************************************************
    // AbstractXMLObjectParser implementation
    //************************************************************************

    public String getParserDescription() {
        return "This element returns a GMRF block-update operator for the joint distribution of the population sizes and precision parameter.";
    }

    public Class getReturnType() {
        return MCMCOperator.class;
    }

    public XMLSyntaxRule[] getSyntaxRules() {
        return rules;
    }

    private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
            AttributeRule.newDoubleRule(SCALE_FACTOR),
            AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
            AttributeRule.newBooleanRule(CoercableMCMCOperator.AUTO_OPTIMIZE, true),
            AttributeRule.newDoubleRule(STOP_VALUE, true),
            AttributeRule.newIntegerRule(MAX_ITERATIONS, true),
            AttributeRule.newBooleanRule(OLD_SKYRIDE, true),
            new ElementRule(GMRFSkyrideLikelihood.class)
    };

}