xmlmanager.java

java实现的遗传算法

/*
 * This file is part of JGAP.
 *
 * JGAP offers a dual license model containing the LGPL as well as the MPL.
 *
 * For licencing information please see the file license.txt included with JGAP
 * or have a look at the top of class org.jgap.Chromosome which representatively
 * includes the JGAP license policy applicable for any file delivered with JGAP.
 */
package org.jgap.xml;

import java.io.*;
import java.util.*;
import javax.xml.parsers.*;
import javax.xml.transform.*;
import javax.xml.transform.dom.*;
import javax.xml.transform.stream.*;

import org.jgap.*;
import org.w3c.dom.*;

/**
 * The XMLManager performs marshalling of genetic entity instances
 * (such as Chromosomes and Genotypes) to XML representations of those
 * entities, as well as unmarshalling. All of the methods in this class are
 * static, so no construction is required (or allowed).
 *
 * @author Neil Rotstan
 * @author Klaus Meffert
 * @since 1.0
 */
public class XMLManager {

  /** String containing the CVS revision. Read out via reflection!*/
  private final static String CVS_REVISION = "$Revision: 1.12 $";

  /**
   * Constant representing the name of the genotype XML element tag.
   */
  private static final String GENOTYPE_TAG = "genotype";

  /**
   * Constant representing the name of the chromosome XML element tag.
   */
  private static final String CHROMOSOME_TAG = "chromosome";

  /**
   * Constant representing the name of the gene XML element tag.
   */
  private static final String GENES_TAG = "genes";

  /**
   * Constant representing the name of the gene XML element tag.
   */
  private static final String GENE_TAG = "gene";

  private static final String ALLELE_TAG = "allele";

  /**
   * Constant representing the name of the size XML attribute that is
   * added to genotype and chromosome elements to describe their size.
   */
  private static final String SIZE_ATTRIBUTE = "size";

  /**
   * Constant representing the fully-qualified name of the concrete
   * Gene class that was marshalled.
   */
  private static final String CLASS_ATTRIBUTE = "class";

  /**
   * Shared DocumentBuilder, which is used to create new DOM Document
   * instances.
   */
  private static final DocumentBuilder m_documentCreator;

  /**
   * Shared lock object used for synchronization purposes.
   */
  private static final Object m_lock = new Object();

  /**
   * @author Neil Rotstan
   * @since 1.0
   */
  static {
    try {
      m_documentCreator =
          DocumentBuilderFactory.newInstance().newDocumentBuilder();
    }
    catch (ParserConfigurationException parserError) {
      throw new RuntimeException(
          "XMLManager: Unable to setup DocumentBuilder: " +
          parserError.getMessage());
    }
  }

  /**
   * Private constructor. All methods in this class are static, so no
   * construction is allowed.
   */
  private XMLManager() {
  }

  /**
   * Marshall a Chromosome instance to an XML Document representation,
   * including its contained Gene instances.
   *
   * @param a_subject The chromosome to represent as an XML document.
   * @return a Document object representing the given Chromosome.
   *
   * @author Neil Rotstan
   * @since 1.0
   * @deprecated use XMLDocumentBuilder instead
   */
  public static Document representChromosomeAsDocument(Chromosome a_subject) {
    // DocumentBuilders do not have to be thread safe, so we have to
    // protect creation of the Document with a synchronized block.
    // -------------------------------------------------------------
    Document chromosomeDocument;
    synchronized (m_lock) {
      chromosomeDocument = m_documentCreator.newDocument();
    }
    Element chromosomeElement =
        representChromosomeAsElement(a_subject, chromosomeDocument);
    chromosomeDocument.appendChild(chromosomeElement);
    return chromosomeDocument;
  }

  /**
   * Marshall a Genotype to an XML Document representation, including its
   * population of Chromosome instances.
   *
   * @param a_subject The genotype to represent as an XML document.
   * @return a Document object representing the given Genotype.
   *
   * @author Neil Rotstan
   * @since 1.0
   * @deprecated use XMLDocumentBuilder instead
   */
  public static Document representGenotypeAsDocument(Genotype a_subject) {
    // DocumentBuilders do not have to be thread safe, so we have to
    // protect creation of the Document with a synchronized block.
    // -------------------------------------------------------------
    Document genotypeDocument;
    synchronized (m_lock) {
      genotypeDocument = m_documentCreator.newDocument();
    }
    Element genotypeElement =
        representGenotypeAsElement(a_subject, genotypeDocument);
    genotypeDocument.appendChild(genotypeElement);
    return genotypeDocument;
  }

  /**
   * Marshall an array of Genes to an XML Element representation.
   *
   * @param a_geneValues The genes to represent as an XML element.
   * @param a_xmlDocument A Document instance that will be used to create
   *                      the Element instance. Note that the element will
   *                      NOT be added to the document by this method.
   * @return an Element object representing the given genes.
   *
   * @author Neil Rotstan
   * @author Klaus Meffert
   * @since 1.0
   * @deprecated use XMLDocumentBuilder instead
   */
  public static Element representGenesAsElement(Gene[] a_geneValues,
                                                Document a_xmlDocument) {
    // Create the parent genes element.
    // --------------------------------
    Element genesElement = a_xmlDocument.createElement(GENES_TAG);
    // Now add gene sub-elements for each gene in the given array.
    // ---------------------------------------------------------------
    Element geneElement;
    for (int i = 0; i < a_geneValues.length; i++) {
      // Create the allele element for this gene.
      // ----------------------------------------
      geneElement = a_xmlDocument.createElement(GENE_TAG);
      // Add the class attribute and set its value to the class
      // name of the concrete class representing the current Gene.
      // ---------------------------------------------------------
      geneElement.setAttribute(CLASS_ATTRIBUTE,
                               a_geneValues[i].getClass().getName());
      // Create a text node to contain the string representation of
      // the gene's value (allele).
      // ----------------------------------------------------------
      Element alleleRepresentation = representAlleleAsElement(a_geneValues[i],
          a_xmlDocument);
      // And now add the text node to the gene element, and then
      // add the gene element to the genes element.
      // ---------------------------------------------------------
      geneElement.appendChild(alleleRepresentation);
      genesElement.appendChild(geneElement);
    }
    return genesElement;
  }

  /**
   *
   * @param gene Gene
   * @param a_xmlDocument Document
   * @return Element
   *
   * @author Klaus Meffert
   * @since 2.0
   */
  private static Element representAlleleAsElement(Gene gene,
                                                  Document a_xmlDocument) {
    Element alleleElement = a_xmlDocument.createElement(ALLELE_TAG);
    alleleElement.setAttribute("class", gene.getClass().getName());
    alleleElement.setAttribute("value", gene.getPersistentRepresentation());
    return alleleElement;
  }

  /**
   * Marshall a Chromosome instance to an XML Element representation,
   * including its contained Genes as sub-elements. This may be useful in
   * scenarios where representation as an entire Document is undesirable,
   * such as when the representation of this Chromosome is to be combined
   * with other elements in a single Document.
   *
   * @param a_subject The chromosome to represent as an XML element.
   * @param a_xmlDocument A Document instance that will be used to create
   *                      the Element instance. Note that the element will
   *                      NOT be added to the document by this method.
   * @return an Element object representing the given Chromosome.
   *
   * @author Neil Rotstan
   * @since 1.0
   * @deprecated use XMLDocumentBuilder instead
   */
  public static Element representChromosomeAsElement(Chromosome a_subject,
      Document a_xmlDocument) {
    // Start by creating an element for the chromosome and its size
    // attribute, which represents the number of genes in the chromosome.
    // ------------------------------------------------------------------
    Element chromosomeElement =
        a_xmlDocument.createElement(CHROMOSOME_TAG);
    chromosomeElement.setAttribute(SIZE_ATTRIBUTE,
                                   Integer.toString(a_subject.size()));
    // Next create the genes element with its nested gene elements,
    // which will contain string representations of the alleles.
    // --------------------------------------------------------------
    Element genesElement = representGenesAsElement(a_subject.getGenes(),
        a_xmlDocument);
    // Add the new genes element to the chromosome element and then
    // return the chromosome element.
    // -------------------------------------------------------------
    chromosomeElement.appendChild(genesElement);
    return chromosomeElement;
  }

  /**
   * Marshall a Genotype instance into an XML Element representation,
   * including its population of Chromosome instances as sub-elements.
   * This may be useful in scenarios where representation as an
   * entire Document is undesirable, such as when the representation
   * of this Genotype is to be combined with other elements in a
   * single Document.
   *
   * @param a_subject The genotype to represent as an XML element.
   * @param a_xmlDocument A Document instance that will be used to create
   *                      the Element instance. Note that the element will
   *                      NOT be added to the document by this method.
   * @return an Element object representing the given Genotype.
   *
   * @author Neil Rotstan
   * @since 1.0
   * @deprecated use XMLDocumentBuilder instead
   */
  public static Element representGenotypeAsElement(Genotype a_subject,
      Document a_xmlDocument) {
    Population population = a_subject.getPopulation();
    // Start by creating the genotype element and its size attribute,
    // which represents the number of chromosomes present in the
    // genotype.
    // --------------------------------------------------------------
    Element genotypeTag = a_xmlDocument.createElement(GENOTYPE_TAG);
    genotypeTag.setAttribute(SIZE_ATTRIBUTE,
                             Integer.toString(population.size()));
    // Next, add nested elements for each of the chromosomes in the
    // genotype.
    // ------------------------------------------------------------
    for (int i = 0; i < population.size(); i++) {
      Element chromosomeElement =
          representChromosomeAsElement(population.getChromosome(i), a_xmlDocument);
      genotypeTag.appendChild(chromosomeElement);
    }
    return genotypeTag;
  }

  /**
   * Unmarshall a Chromosome instance from a given XML Element
   * representation.
   *
   * @param a_activeConfiguration current Configuration object
   * @param a_xmlElement The XML Element representation of the Chromosome.
   *
   * @return A new Chromosome instance setup with the data from the XML
   *         Element representation.
   *
   * @throws ImproperXMLException if the given Element is improperly
   *         structured or missing data.
   * @throws UnsupportedRepresentationException if the actively configured
   *         Gene implementation does not support the string representation
   *         of the alleles used in the given XML document.
   * @throws GeneCreationException if there is a problem creating or
   *                                 populating an Gene instance.
   *
   * @author Neil Rotstan
   * @since 1.0
   */
  public static Gene[] getGenesFromElement(
      Configuration a_activeConfiguration, Element a_xmlElement)
      throws ImproperXMLException, UnsupportedRepresentationException,
      GeneCreationException {
    // Do some sanity checking. Make sure the XML Element isn't null and
    // that it in fact represents a set of genes.
    // -----------------------------------------------------------------
    if (a_xmlElement == null ||
        ! (a_xmlElement.getTagName().equals(GENES_TAG))) {
      throw new ImproperXMLException(
          "Unable to build Chromosome instance from XML Element: " +
          "given Element is not a 'genes' element.");
    }
    List genes = new ArrayList();
    // Extract the nested gene elements.
    // ---------------------------------------------------------