ARGTraceAnalysisParser.java

/*
 * ARGTraceAnalysisParser.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.evomodel.arg;

import dr.evomodel.tree.TreeTraceAnalysis;
import dr.xml.*;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.Reader;

/**
 * @author Marc A. Suchard
 */

public class ARGTraceAnalysisParser extends AbstractXMLObjectParser {

	public final static String ARG_TRACE_ANALYSIS = "argTraceAnalysis";
	public final static String BURN_IN = "burnIn";
	public static final String FILE_NAME = "fileName";

	public String getParserName() {
		return ARG_TRACE_ANALYSIS;
	}

	public Object parseXMLObject(XMLObject xo) throws XMLParseException {

		try {
			Reader reader;

			String fileName = xo.getStringAttribute(FILE_NAME);
			try {
				File file = new File(fileName);
				String name = file.getName();
				String parent = file.getParent();

				if (!file.isAbsolute()) {
					parent = System.getProperty("user.dir");
				}

//					System.out.println("Writing log file to "+parent+System.getProperty("path.separator")+name);
				reader = new FileReader(new File(parent, name));
			} catch (FileNotFoundException fnfe) {
				throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
			}

			int burnin = -1;
			if (xo.hasAttribute(BURN_IN)) {
				// leaving the burnin attribute off will result in 10% being used
				burnin = xo.getIntegerAttribute(BURN_IN);
			}

			ARGTraceAnalysis analysis = ARGTraceAnalysis.analyzeLogFile(new Reader[]{reader}, burnin, true);

			analysis.report();

			System.out.println();
			System.out.flush();

			return analysis;
		} catch (java.io.IOException ioe) {
			throw new XMLParseException(ioe.getMessage());
		}
	}

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

	public String getParserDescription() {
		return "Analyses and reports on a trace consisting of trees.";
	}

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

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

	private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
			new StringAttributeRule(FILE_NAME, "name of a tree log file", "trees.log"),
			AttributeRule.newIntegerRule(BURN_IN, true)
	};
}