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

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Here is the source code for ch.javasoft.metabolic.efm.config.Normalize.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.Norm;
import ch.javasoft.xml.config.XmlConfigException;

/**
 * <tt>Normalize</tt> defines the normalization method to use when outputting
 * flux values. This class is used for configuration purposes, its constants
 * correspond to thos of {@link Norm}.
 */
public enum Normalize {
    /** Maximum absolute value is 1*/
    max(ch.javasoft.metabolic.Norm.max),
    /** Minimum absolute value is 1*/
    min(ch.javasoft.metabolic.Norm.min),
    /** Use norm 2, that is, the vector length is 1*/
    norm2(ch.javasoft.metabolic.Norm.norm2),
    /** 
     * Like norm 2, but all values are squared, possibly negative. To get the
     * original value, take the square root of the absolute value and keep the
     * sign, that is, <tt>v = sgn(v2) * sqrt(abs(v2))</tt>
     * <p>
     * This normalization method is useful if exact arithmetic is used, and no
     * square root is supported for fraction numbers. 
     */
    squared(ch.javasoft.metabolic.Norm.squared),
    /** Do not normalize at all*/
    none(ch.javasoft.metabolic.Norm.none);
    private Normalize(Norm norm) {
        this.norm = norm;
    }

    public final Norm norm;

    /**
     * Parse a norm string and return the appropriate constant, or throw
     * an exception if not recognized as such.
     */
    public static Normalize parse(Attribute attribute) throws XmlConfigException {
        final String str = attribute.getValue();
        try {
            return valueOf(str.toLowerCase());
        } catch (IllegalArgumentException ex) {
            throw new XmlConfigException(
                    "invalid value for norm, expected " + Arrays.toString(values()) + ", but found: " + str,
                    attribute);
        }
    }

    /**
     * Returns the Normalize instance corresponding to the given Norm value.
     */
    public static Normalize valueOf(Norm norm) {
        for (Normalize n : values()) {
            if (n.norm == norm)
                return n;
        }
        throw new RuntimeException("no such normalize constant: " + norm);
    }

    /**
     * Returns true if the normalization method does not cause truncation.
     */
    public boolean isExact() {
        return !Normalize.norm2.equals(this);
    }
}