/*
 * =============================================================================
 * Simplified BSD License, see http://www.opensource.org/licenses/
 * -----------------------------------------------------------------------------
 * Copyright (c) 2008-2009, Marco Terzer, Zurich, Switzerland
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without 
 * modification, are permitted provided that the following conditions are met:
 * 
 *     * Redistributions of source code must retain the above copyright notice, 
 *       this list of conditions and the following disclaimer.
 *     * Redistributions in binary form must reproduce the above copyright 
 *       notice, this list of conditions and the following disclaimer in the 
 *       documentation and/or other materials provided with the distribution.
 *     * Neither the name of the Swiss Federal Institute of Technology Zurich 
 *       nor the names of its contributors may be used to endorse or promote 
 *       products derived from this software without specific prior written 
 *       permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
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 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
 * POSSIBILITY OF SUCH DAMAGE.
 * =============================================================================
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package ch.javasoft.polco.metabolic;

import java.util.logging.Level;

import org.dom4j.DocumentException;
import org.dom4j.Element;

import ch.javasoft.factory.ConfigException;
import ch.javasoft.metabolic.efm.ElementaryFluxModes;
import ch.javasoft.metabolic.efm.config.Config;
import ch.javasoft.polco.config.Phase;
import ch.javasoft.polco.config.PolcoConfig;
import ch.javasoft.polco.config.XmlElement;
import ch.javasoft.util.numeric.Zero;
import ch.javasoft.xml.config.ConstConfigParser;
import ch.javasoft.xml.config.XmlConfig;
import ch.javasoft.xml.config.XmlConfigException;
import ch.javasoft.xml.config.XmlUtil;
import ch.javasoft.xml.factory.XmlConfiguredFactory;

/**
 * The <code>EfmExtremeRayEnumeratorFactory</code> returns a new 
 * {@link EfmExtremeRayEnumerator} instance. The xml configuration is used to 
 * initialize the {@link ElementaryFluxModes} implementation.
 */
public class EfmExtremeRayEnumeratorFactory implements XmlConfiguredFactory<EfmExtremeRayEnumerator> {
	public EfmExtremeRayEnumerator create(Element config) throws ConfigException {
		final Zero zero; 
		final boolean allowMatrixRowScaling;
		try {
			final XmlConfig xmlConfig = XmlConfig.getXmlConfig(config.getDocument());
			PolcoConfig.tracePolcoConfig(LogPkg.LOGGER, Level.INFO, xmlConfig);
			ElementaryFluxModes.setImpl(
				Config.getEfmImpl(xmlConfig, Config.getConfigEfmImpl(xmlConfig))
			);
			final Element elConfig	= PolcoConfig.getPolcoConfig(xmlConfig);
			final Element elConvert	= XmlUtil.getRequiredSingleChildElement(elConfig, XmlElement.convert);
			final Element elMatrix	= XmlUtil.getRequiredSingleChildElement(elConvert, XmlElement.matrix_scaling);
			allowMatrixRowScaling = ConstConfigParser.parseBooleanConstant(elMatrix);
			zero = PolcoConfig.getZero(xmlConfig, Phase.Core);
		} 
		catch (DocumentException e) {
			throw new ConfigException(e, XmlUtil.getElementPath(config, true));
		} 
		catch (XmlConfigException e) {
			throw new ConfigException(e, XmlUtil.getElementPath(config, true));
		}
		return new EfmExtremeRayEnumerator(zero, allowMatrixRowScaling);
	}
}
