ch.javasoft.metabolic.efm.config.Generator.java Source code

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Here is the source code for ch.javasoft.metabolic.efm.config.Generator.java

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/*
 * =============================================================================
 * 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 
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
 * 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.
 * =============================================================================
 */
package ch.javasoft.metabolic.efm.config;

import java.util.Arrays;

import org.dom4j.Attribute;

import ch.javasoft.metabolic.Reaction;
import ch.javasoft.util.StringUtil;
import ch.javasoft.xml.config.XmlConfigException;

/**
 * <tt>Generator</tt> specifies the type of generating set to be computed. 
 * Different generating sets define the flux cone, {@link #Gfm} is the minimal
 * set of generators. The sets differ in how reversible reactions are handled.  
 */
public enum Generator {
    /** 
     * Elementary Flux Modes
     * <p>
     * All reversible reactions are split into 2 irreversible reactions. 
     * <p>  
     * Two-cycles corresponding to split reversible reactions are excluded.
     */
    Efm,
    /** 
     * Extreme Pathways
     * <p>
     * Internal reversible reactions are split into 2 irreversible reactions. 
     * Reversible exchange reactions are kept unchanged.
     * <p>  
     * Two-cycles corresponding to split reversible reactions are excluded.
     */
    Ep,
    /** 
     * Generating Flux Modes
     * <p>
     * Reversible reactions are not split since they do not shape the flux cone.
     */
    Gfm;

    public static Generator parse(Attribute attribute) throws XmlConfigException {
        final String str = attribute.getValue();
        try {
            return valueOf(StringUtil.toTitleCase(str));
        } catch (IllegalArgumentException ex) {
            throw new XmlConfigException(
                    "invalid value for generator, expected " + Arrays.toString(values()) + ", but found: " + str,
                    attribute);
        }
    }

    /**
     * Returns true if reactions are split during computation, which is always
     * true for Efm, and true for Ep if it is not an exchange reaction. For 
     * Gfm, this method always returns false. 
     */
    public boolean splitReversibleReactions(boolean exchange) {
        return this == Efm || !exchange && this == Ep;
    }

    /**
     * Returns true if this reaction is to split, without considering no-split
     * reactions from the config. This is true for reversible reactions for 
     * Efm and true for reversible non-exchange reactions for Ep.
     */
    public boolean splitReaction(Reaction reac) {
        if (this == Gfm)
            return false;
        if (!reac.getConstraints().isReversible())
            return false;
        return this == Efm || this == Ep && !reac.isExternal();
    }
}