/*
* TraceAnalysisParser.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.inferencexml.trace;
import dr.inference.trace.*;
import dr.util.Attribute;
import dr.util.NumberFormatter;
import dr.xml.*;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.List;
/**
* @author Alexei Drummond
* @version $Id: TraceAnalysisParser.java,v 1.18 2005/05/24 20:26:00 rambaut Exp $
*/
public class TraceAnalysisParser extends AbstractXMLObjectParser {
public static final String TRACE_ANALYSIS = "traceAnalysis";
public static final String FILE_NAME = "fileName";
public static final String BURN_IN = "burnIn";
public static final String STD_ERROR = "stdError";
public static final String EXPECTATION = "expectation";
public static final String COMPUTE_MSE = "computeMSE";
public String getParserName() {
return TRACE_ANALYSIS;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String fileName = xo.getStringAttribute(FILE_NAME);
boolean withStdError = xo.getAttribute(STD_ERROR, false);
boolean computeMSE = xo.getAttribute(COMPUTE_MSE, false);
try {
File file = new File(fileName);
String name = file.getName();
String parent = file.getParent();
if (!file.isAbsolute()) {
parent = System.getProperty("user.dir");
}
file = new File(parent + File.separator, name);
if (file.exists()) {
fileName = file.getName();
// leaving the burnin attribute off will result in 10% being used
int burnin = xo.getAttribute(BURN_IN, -1);
TraceList traces = TraceAnalysis.report(fileName, burnin, null, withStdError);
for (int x = 0; x < xo.getChildCount(); x++) {
XMLObject child = (XMLObject) xo.getChild(x);
String statName = child.getStringAttribute(Attribute.NAME);
double expectation = child.getDoubleAttribute(Attribute.VALUE);
NumberFormatter formatter = new NumberFormatter(6);
formatter.setPadding(true);
formatter.setFieldWidth(14);
for (int i = 0; i < traces.getTraceCount(); i++) {
TraceDistribution distribution = traces.getDistributionStatistics(i);
TraceCorrelation corr = traces.getCorrelationStatistics(i);
if (traces.getTraceName(i).equals(statName)) {
double estimate = distribution.getMean();
double error = corr.getStdErrorOfMean();
System.out.print("E[" + statName + "] = " + formatter.format(expectation));
if (computeMSE) {
List values = traces.getValues(i);
double[] dv = new double[values.size()];
for (int j = 0; j < dv.length; j++) {
dv[j] = ((Number) values.get(j)).doubleValue();
}
double MSE = distribution.getMeanSquaredError(dv, expectation);
System.out.println(" MSE = " + formatter.format(MSE));
} else {
System.out.println("");
if (expectation > (estimate - (2 * error)) && expectation < (estimate + (2 * error))) {
System.out.println("OK: " + formatter.format(estimate) + " +- " + formatter.format(error) + "\n");
} else {
System.out.print("WARNING: " + formatter.format(estimate) + " +- " + formatter.format(error) + "\n");
}
}
}
}
}
System.out.println();
System.out.flush();
return traces;
} else {
throw new XMLParseException("Log file, " + parent + File.separator + name + " does not exist.");
}
} catch (FileNotFoundException fnfe) {
throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
} catch (java.io.IOException ioe) {
throw new XMLParseException(ioe.getMessage());
} catch (TraceException e) {
throw new XMLParseException(e.toString());
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "Performs a trace analysis. Estimates the mean of the various statistics in the given log file.";
}
public Class getReturnType() {
return TraceAnalysis[].class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new StringAttributeRule(FILE_NAME, "The name of a BEAST log file (can not include trees, which should be logged separately"),
AttributeRule.newIntegerRule(BURN_IN, true),
new ElementRule(EXPECTATION, new XMLSyntaxRule[]{AttributeRule.newStringRule("name"), AttributeRule.newStringRule("value")}, 0, Integer.MAX_VALUE),
AttributeRule.newBooleanRule(STD_ERROR, true),
AttributeRule.newBooleanRule(COMPUTE_MSE, true),
};
}