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• LayoutParser.java

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org.sbml.jsbml.xml.parsers.LayoutParser Maven / Gradle / Ivy

/*
 * ----------------------------------------------------------------------------
 * This file is part of JSBML. Please visit 
 * for the latest version of JSBML and more information about SBML.
 *
 * Copyright (C) 2009-2017 jointly by the following organizations:
 * 1. The University of Tuebingen, Germany
 * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
 * 3. The California Institute of Technology, Pasadena, CA, USA
 * 4. The University of California, San Diego, La Jolla, CA, USA
 * 5. The Babraham Institute, Cambridge, UK
 * 
 * This library 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. A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as .
 * ----------------------------------------------------------------------------
 */
package org.sbml.jsbml.xml.parsers;

import static org.sbml.jsbml.ext.layout.LayoutConstants.listOfLayouts;

import java.text.MessageFormat;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;

import javax.swing.tree.TreeNode;

import org.apache.log4j.Logger;
import org.mangosdk.spi.ProviderFor;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.JSBML;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBase;
import org.sbml.jsbml.ext.ASTNodePlugin;
import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.CompartmentGlyph;
import org.sbml.jsbml.ext.layout.CubicBezier;
import org.sbml.jsbml.ext.layout.Curve;
import org.sbml.jsbml.ext.layout.CurveSegment;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutConstants;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.layout.LineSegment;
import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.TextGlyph;
import org.sbml.jsbml.util.filters.Filter;
import org.sbml.jsbml.xml.stax.SBMLObjectForXML;

/**
 * Parses the SBML level 2 layout extension package elements and
 * attributes. The namespaceURI URI of this parser is
 * "http://projects.eml.org/bcb/sbml/level2". This parser is
 * able to read and write elements of the layout package (implements
 * ReadingParser and WritingParser).
 * 
 * @author Nicolas Rodriguez
 * @author Sebastian Frölich
 * @author Andreas Dräger
 * @since 1.0
 * 
 */
@ProviderFor(ReadingParser.class)
public class LayoutParser implements ReadingParser, WritingParser, PackageParser {

  /**
   * A {@link Logger} for this class.
   */
  private static final transient Logger logger = Logger.getLogger(LayoutParser.class);

  /**
   * 
   */
  enum LayoutList {
    /**
     * 
     */
    listOfLayouts,
    /**
     * 
     */
    listOfSpeciesGlyphs,
    /**
     * 
     */
    listOfReactionGlyphs,
    /**
     * 
     */
    listOfTextGlyphs,
    /**
     * 
     */
    listOfCompartmentGlyphs,
    /**
     * 
     */
    none,
    /**
     * 
     */
    listOfCurveSegments,
    /**
     * 
     */
    listOfSpeciesReferenceGlyphs;
  }

  /**
   * The namespace URI of this parser.
   */
  private static final String namespaceURI = LayoutConstants.namespaceURI_L2;

  /**
   * 
   * @return the namespaceURI of this parser.
   */
  public static String getNamespaceURI() {
    return namespaceURI;
  }

  /**
   * The layoutList enum which represents the name of the list this parser is
   * currently reading.
   * 
   */
  private LayoutList groupList = LayoutList.none;

  /**
   * Log4j logger
   */
  private Logger log4jLogger = Logger.getLogger(LayoutParser.class);

  /**
   * This map contains all the relationships XML element name <=> matching
   * java class.
   */
  private HashMap> sbmlLayoutElements;

  /**
   * 
   */
  public LayoutParser() {
    super();
    sbmlLayoutElements = new HashMap>();
    JSBML.loadClasses(
      "org/sbml/jsbml/resources/cfg/SBMLLayoutElements.xml",
      sbmlLayoutElements);
  }

  /* (non-Javadoc)
   * @see org.sbml.jsbml.xml.parsers.WritingParser#getListOfSBMLElementsToWrite(java.lang.Object)
   */
  @Override
  @SuppressWarnings("unchecked")
  public List