/*
* GaussianProcessSkytrackBlockUpdateOperatorParser.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.GaussianProcessSkytrackLikelihood;
import dr.evomodel.coalescent.operators.GaussianProcessSkytrackBlockUpdateOperator;
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 GaussianProcessSkytrackBlockUpdateOperatorParser extends AbstractXMLObjectParser {
public static final String BLOCK_UPDATE_OPERATOR = "gpBlockUpdateOperator";
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 Object parseXMLObject(XMLObject xo) throws XMLParseException {
boolean logRecord = xo.getAttribute(KEEP_LOG_RECORD, false);
Handler gmrfHandler;
Logger gmrfLogger = Logger.getLogger("dr.evomodel.coalescent.operators.GaussianProcessSkytrackBlockUpdateOperator");
gmrfLogger.setUseParentHandlers(false);
if (logRecord) {
gmrfLogger.setLevel(Level.FINE);
try {
gmrfHandler = new FileHandler("GPBlockUpdate.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 <= 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)) {
GaussianProcessSkytrackLikelihood gpLikelihood = (GaussianProcessSkytrackLikelihood) xo.getChild(GaussianProcessSkytrackLikelihood.class);
return new GaussianProcessSkytrackBlockUpdateOperator(gpLikelihood, weight, mode, scaleFactor,
maxIterations, stopValue);
}else{
GaussianProcessSkytrackLikelihood gpLikelihood = (GaussianProcessSkytrackLikelihood) xo.getChild(GaussianProcessSkytrackLikelihood.class);
return new GaussianProcessSkytrackBlockUpdateOperator(gpLikelihood, weight, mode, scaleFactor,
maxIterations, stopValue);
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a GP block-update operator for the joint distribution of the population sizes and precision parameter.";
}
public Class getReturnType() {
return GaussianProcessSkytrackBlockUpdateOperator.class;
// 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(GaussianProcessSkytrackLikelihood.class)
};
}