text: /**
   * Filename    : TestLayoutWriting.cpp
   * Description : Unit tests for writing layout in the context of a complete model.
   * Organization: European Media Laboratories Research gGmbH
   * Created     : 2007-02-23
   *
   * Copyright 2007 European Media Laboratories Research gGmbH
   *
   * 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; either version 2.1 of the License, or
   * any later version.
   *
   * This library is distributed in the hope that it will be useful, but
   * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
   * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.  The software and
   * documentation provided hereunder is on an "as is" basis, and the
   * European Media Laboratories Research gGmbH have no obligations to
   * provide maintenance, support, updates, enhancements or modifications.
   * In no event shall the European Media Laboratories Research gGmbH be
   * liable to any party for direct, indirect, special, incidental or
   * consequential damages, including lost profits, arising out of the use of
   * this software and its documentation, even if the European Media
   * Laboratories Research gGmbH have been advised of the possibility of such
   * damage.  See the GNU Lesser General Public License for more details.
   *
   * You should have received a copy of the GNU Lesser General Public License
   * along with this library; if not, write to the Free Software Foundation,
   * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
   *
   * The original code contained here was initially developed by:
   *
   *     Ralph Gauges
   *     Bioinformatics Group
   *     European Media Laboratories Research gGmbH
   *     Schloss-Wolfsbrunnenweg 31c
   *     69118 Heidelberg
   *     Germany
   *
   *     http://www.eml-research.de/english/Research/BCB/
   *     mailto:ralph.gauges@eml-r.villa-bosch.de
   *
   * Contributor(s):
   */
  
  
  #include <iostream>
  
  #include <locale.h>
  
  #include <sbml/common/common.h>
  
  #include <sbml/packages/layout/extension/LayoutModelPlugin.h>
  #include <sbml/packages/layout/sbml/Layout.h>
  #include <sbml/packages/layout/sbml/GraphicalObject.h>
  #include <sbml/packages/layout/sbml/CompartmentGlyph.h>
  #include <sbml/packages/layout/sbml/SpeciesGlyph.h>
  #include <sbml/packages/layout/sbml/ReactionGlyph.h>
  #include <sbml/packages/layout/sbml/TextGlyph.h>
  #include <sbml/packages/layout/sbml/SpeciesReferenceGlyph.h>
  #include <sbml/packages/layout/sbml/LineSegment.h>
  #include <sbml/packages/layout/sbml/CubicBezier.h>
  #include <sbml/packages/layout/sbml/Curve.h>
  #include <sbml/packages/layout/sbml/Point.h>
  #include <sbml/packages/layout/sbml/Dimensions.h>
  #include <sbml/Reaction.h>
  #include <sbml/Species.h>
  #include <sbml/Compartment.h>
  #include <sbml/Model.h>
  #include <sbml/SBMLDocument.h>
  #include <sbml/SBMLWriter.h>
  
  #include <check.h>
  
  
  #include <sbml/xml/XMLInputStream.h>
  #include <sbml/xml/XMLNode.h>
  #include "utility.h"
  
  LIBSBML_CPP_NAMESPACE_USE
  
  BEGIN_C_DECLS
  
  static LayoutPkgNamespaces* LN;
  
    void
  LayoutWritingTest_setup (void)
  {
    LN = new LayoutPkgNamespaces(2,1);
  }
  
    void 
  LayoutWritingTest_teardown (void)
  {
    delete LN;
  }
  
  
  START_TEST (test_LayoutWriting)
  {
    std::string s = 
      "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
      "<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\">"
      "  <model id=\"TestModel\">"
      "          <annotation>"
      "  <listOfLayouts xmlns=\"http://projects.eml.org/bcb/sbml/level2\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">"
      "    <layout id=\"Layout_1\">"
      "      <dimensions width=\"2320\" height=\"1000\"/>"
      "      <listOfCompartmentGlyphs>"
      "        <compartmentGlyph id=\"CompartmentGlyph_1\" compartment=\"Hepatocyte\">"
      "          <boundingBox id=\"bb_compartment\">"
      "            <position x=\"10\" y=\"10\"/>"
      "            <dimensions width=\"2300\" height=\"980\"/>"
      "          </boundingBox>"
      "        </compartmentGlyph>"
      "        <compartmentGlyph id=\"Mito1_Glyph\" compartment=\"Mito_1\">"
      "          <boundingBox id=\"bb_mito1\">"
      "            <position x=\"100\" y=\"100\"/>"
      "            <dimensions width=\"300\" height=\"100\"/>"
      "          </boundingBox>"
      "        </compartmentGlyph>"
      "        <compartmentGlyph id=\"Mito2_Glyph\" compartment=\"Mito_2\">"
      "          <boundingBox id=\"bb_mito2\">"
      "            <position x=\"200\" y=\"650\"/>"
      "            <dimensions width=\"300\" height=\"100\"/>"
      "          </boundingBox>"
      "        </compartmentGlyph>"
      "        <compartmentGlyph id=\"Mito3_Glyph_2\" compartment=\"Mito_3\">"
      "          <boundingBox id=\"bb_mito3_2\">"
      "            <position x=\"1470\" y=\"30\"/>"
      "            <dimensions width=\"820\" height=\"536\"/>"
      "          </boundingBox>"
      "        </compartmentGlyph>"
      "      </listOfCompartmentGlyphs>"
      "      <listOfSpeciesGlyphs>"
      "        <speciesGlyph id=\"SpeciesGlyph_malate_cyt\" species=\"malate_cyt\">"
      "          <boundingBox id=\"bb_sg_malate_cyt\">"
      "            <position x=\"580\" y=\"280\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_oxaloacetate_cyt\" species=\"oxaloacetate_cyt\">"
      "          <boundingBox id=\"bb_sg_oxaloacetate_cyt\">"
      "            <position x=\"580\" y=\"480\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_aspartate_cyt\" species=\"aspartate_cyt\">"
      "          <boundingBox id=\"bb_sg_aspartate_cyt\">"
      "            <position x=\"580\" y=\"680\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_glutamate_cyt\" species=\"glutamate_cyt\">"
      "          <boundingBox id=\"bb_sg_glutamate_cyt\">"
      "            <position x=\"800\" y=\"610\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_aKetoglutarate_cyt\" species=\"aKetoglutarate_cyt\">"
      "          <boundingBox id=\"bb_sg_aKetoglutarate_cyt\">"
      "            <position x=\"860\" y=\"500\"/>"
      "            <dimensions width=\"280\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_nad_cyt\" species=\"nad_cyt\">"
      "          <boundingBox id=\"bb_sg_nad_cyt\">"
      "            <position x=\"520\" y=\"350\"/>"
      "            <dimensions width=\"100\" height=\"24\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_nadh_cyt\" species=\"nadh_cyt\">"
      "          <boundingBox id=\"bb_sg_nadh_cyt\">"
      "            <position x=\"520\" y=\"430\"/>"
      "            <dimensions width=\"100\" height=\"24\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_h_cyt\" species=\"h_cyt\">"
      "          <boundingBox id=\"bb_sg_h_cyt\">"
      "            <position x=\"430\" y=\"430\"/>"
      "            <dimensions width=\"40\" height=\"24\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_malate_mito3\" species=\"malate_mito3\">"
      "          <boundingBox id=\"bb_sg_malate_mito3\">"
      "            <position x=\"1850\" y=\"80\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_oxaloacetate_mito3\" species=\"oxaloacetate_mito3\">"
      "          <boundingBox id=\"bb_sg_oxaloacetate_mito3\">"
      "            <position x=\"1850\" y=\"280\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_aspartate_mito3\" species=\"aspartate_mito3\">"
      "          <boundingBox id=\"bb_sg_aspartate_mito3\">"
      "            <position x=\"1850\" y=\"480\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_glutamate_mito3\" species=\"glutamate_mito3\">"
      "          <boundingBox id=\"bb_sg_glutamate_mito3\">"
      "            <position x=\"1550\" y=\"430\"/>"
      "            <dimensions width=\"240\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_aKetoglutarate_mito3\" species=\"aKetoglutarate_mito3\">"
      "          <boundingBox id=\"bb_sg_aKetoglutarate_mito3\">"
      "            <position x=\"1530\" y=\"300\"/>"
      "            <dimensions width=\"280\" height=\"36\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_nad_mito3\" species=\"nad_mito3\">"
      "          <boundingBox id=\"bb_sg_nad_mito3\">"
      "            <position x=\"2050\" y=\"150\"/>"
      "            <dimensions width=\"100\" height=\"24\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_nadh_mito3\" species=\"nadh_mito3\">"
      "          <boundingBox id=\"bb_sg_nadh_mito3\">"
      "            <position x=\"2050\" y=\"230\"/>"
      "            <dimensions width=\"100\" height=\"24\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "        <speciesGlyph id=\"SpeciesGlyph_h_mito3\" species=\"h_mito3\">"
      "          <boundingBox id=\"bb_sg_h_mito3\">"
      "            <position x=\"2200\" y=\"230\"/>"
      "            <dimensions width=\"40\" height=\"24\"/>"
      "          </boundingBox>"
      "        </speciesGlyph>"
      "      </listOfSpeciesGlyphs>"
      "      <listOfReactionGlyphs>"
      "        <reactionGlyph id=\"rg_malatedh_cyt\" reaction=\"reaction_malatedh_cyt\">"
      "          <curve>"
      "            <listOfCurveSegments>"
      "              <curveSegment xsi:type=\"LineSegment\">"
      "                <start x=\"700\" y=\"381\"/>"
      "                <end x=\"700\" y=\"415\"/>"
      "              </curveSegment>"
      "            </listOfCurveSegments>"
      "          </curve>"
      "          <listOfSpeciesReferenceGlyphs>"
      "            <speciesReferenceGlyph id=\"srg_malate_cyt_1\" speciesReference=\"sr_malate_cyt\" speciesGlyph=\"SpeciesGlyph_malate_cyt\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"700\" y=\"381\"/>"
      "                    <end x=\"700\" y=\"316\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_nad_cyt\" speciesReference=\"sr_nad_cyt\" speciesGlyph=\"SpeciesGlyph_nad_cyt\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"700\" y=\"381\"/>"
      "                    <end x=\"620\" y=\"362\"/>"
      "                    <basePoint1 x=\"700\" y=\"362\"/>"
      "                    <basePoint2 x=\"700\" y=\"362\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_oxaloacetate_cyt_1\" speciesReference=\"sr_oxaloacetate_cyt_1\" speciesGlyph=\"SpeciesGlyph_oxaloacetate_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"700\" y=\"415\"/>"
      "                    <end x=\"700\" y=\"480\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_nadh_cyt\" speciesReference=\"sr_nadh_cyt\" speciesGlyph=\"SpeciesGlyph_nadh_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"700\" y=\"415\"/>"
      "                    <end x=\"620\" y=\"442\"/>"
      "                    <basePoint1 x=\"700\" y=\"442\"/>"
      "                    <basePoint2 x=\"700\" y=\"442\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_h_cyt\" speciesReference=\"sr_h_cyt\" speciesGlyph=\"SpeciesGlyph_h_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"700\" y=\"415\"/>"
      "                    <end x=\"470\" y=\"430\"/>"
      "                    <basePoint1 x=\"570\" y=\"415\"/>"
      "                    <basePoint2 x=\"570\" y=\"415\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "          </listOfSpeciesReferenceGlyphs>"
      "        </reactionGlyph>"
      "        <reactionGlyph id=\"rg_aspartateat_cyt\" reaction=\"reaction_aspartateat_cyt\">"
      "          <curve>"
      "            <listOfCurveSegments>"
      "              <curveSegment xsi:type=\"LineSegment\">"
      "                <start x=\"700\" y=\"581\"/>"
      "                <end x=\"700\" y=\"615\"/>"
      "              </curveSegment>"
      "            </listOfCurveSegments>"
      "          </curve>"
      "          <listOfSpeciesReferenceGlyphs>"
      "            <speciesReferenceGlyph id=\"srg_oxaloacetate_cyt_2\" speciesReference=\"sr_oxaloacetate_cyt_2\" speciesGlyph=\"SpeciesGlyph_oxaloacetate_cyt\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"700\" y=\"581\"/>"
      "                    <end x=\"700\" y=\"516\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_glutamate_cyt_1\" speciesReference=\"sr_glutamate_cyt_1\" speciesGlyph=\"SpeciesGlyph_glutamate_cyt\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"700\" y=\"581\"/>"
      "                    <end x=\"800\" y=\"628\"/>"
      "                    <basePoint1 x=\"750\" y=\"581\"/>"
      "                    <basePoint2 x=\"750\" y=\"628\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_aspartate_cyt_1\" speciesReference=\"sr_aspartate_cyt_1\" speciesGlyph=\"SpeciesGlyph_aspartate_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"700\" y=\"615\"/>"
      "                    <end x=\"700\" y=\"680\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_aKetoglutaratecyt_1\" speciesReference=\"sr_aKetoglutarate_cyt_1\" speciesGlyph=\"SpeciesGlyph_aKetoglutarate_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"700\" y=\"615\"/>"
      "                    <end x=\"860\" y=\"515\"/>"
      "                    <basePoint1 x=\"790\" y=\"615\"/>"
      "                    <basePoint2 x=\"790\" y=\"515\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "          </listOfSpeciesReferenceGlyphs>"
      "        </reactionGlyph>"
      "        <reactionGlyph id=\"rg_malatedh_mito3\" reaction=\"reaction_malatedh_mito3\">"
      "          <curve>"
      "            <listOfCurveSegments>"
      "              <curveSegment xsi:type=\"LineSegment\">"
      "                <start x=\"1970\" y=\"181\"/>"
      "                <end x=\"1970\" y=\"215\"/>"
      "              </curveSegment>"
      "            </listOfCurveSegments>"
      "          </curve>"
      "          <listOfSpeciesReferenceGlyphs>"
      "            <speciesReferenceGlyph id=\"srg_malate_mito3_1\" speciesReference=\"sr_malate_mito3\" speciesGlyph=\"SpeciesGlyph_malate_mito3\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1970\" y=\"181\"/>"
      "                    <end x=\"1970\" y=\"116\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_nad_mito3\" speciesReference=\"sr_nad_mito3\" speciesGlyph=\"SpeciesGlyph_nad_mito3\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1970\" y=\"181\"/>"
      "                    <end x=\"2050\" y=\"162\"/>"
      "                    <basePoint1 x=\"1970\" y=\"162\"/>"
      "                    <basePoint2 x=\"1970\" y=\"162\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_oxaloacetate_mito3_1\" speciesReference=\"sr_oxaloacetate_mito3_1\" speciesGlyph=\"SpeciesGlyph_oxaloacetate_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1970\" y=\"215\"/>"
      "                    <end x=\"1970\" y=\"280\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_nadh_mito3\" speciesReference=\"sr_nadh_mito3\" speciesGlyph=\"SpeciesGlyph_nadh_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1970\" y=\"215\"/>"
      "                    <end x=\"2050\" y=\"242\"/>"
      "                    <basePoint1 x=\"1970\" y=\"242\"/>"
      "                    <basePoint2 x=\"1970\" y=\"242\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_h_mito3\" speciesReference=\"sr_h_mito3\" speciesGlyph=\"SpeciesGlyph_h_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1970\" y=\"215\"/>"
      "                    <end x=\"2200\" y=\"230\"/>"
      "                    <basePoint1 x=\"2100\" y=\"215\"/>"
      "                    <basePoint2 x=\"2100\" y=\"215\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "          </listOfSpeciesReferenceGlyphs>"
      "        </reactionGlyph>"
      "        <reactionGlyph id=\"rg_aspartateat_mito3\" reaction=\"reaction_aspartateat_mito3\">"
      "          <curve>"
      "            <listOfCurveSegments>"
      "              <curveSegment xsi:type=\"LineSegment\">"
      "                <start x=\"1970\" y=\"381\"/>"
      "                <end x=\"1970\" y=\"415\"/>"
      "              </curveSegment>"
      "            </listOfCurveSegments>"
      "          </curve>"
      "          <listOfSpeciesReferenceGlyphs>"
      "            <speciesReferenceGlyph id=\"srg_oxaloacetate_mito3_2\" speciesReference=\"sr_oxaloacetate_mito3_2\" speciesGlyph=\"SpeciesGlyph_oxaloacetate_mito3\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1970\" y=\"381\"/>"
      "                    <end x=\"1970\" y=\"316\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_glutamate_mito3_1\" speciesReference=\"sr_glutamate_mito3_1\" speciesGlyph=\"SpeciesGlyph_glutamate_mito3\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1970\" y=\"381\"/>"
      "                    <end x=\"1790\" y=\"448\"/>"
      "                    <basePoint1 x=\"1880\" y=\"381\"/>"
      "                    <basePoint2 x=\"1880\" y=\"448\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_aspartate_mito3_1\" speciesReference=\"sr_aspartate_mito3_1\" speciesGlyph=\"SpeciesGlyph_aspartate_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1970\" y=\"415\"/>"
      "                    <end x=\"1970\" y=\"480\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_aKetoglutaratemito3_1\" speciesReference=\"sr_aKetoglutarate_mito3_1\" speciesGlyph=\"SpeciesGlyph_aKetoglutarate_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1970\" y=\"415\"/>"
      "                    <end x=\"1810\" y=\"315\"/>"
      "                    <basePoint1 x=\"1880\" y=\"415\"/>"
      "                    <basePoint2 x=\"1880\" y=\"315\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "          </listOfSpeciesReferenceGlyphs>"
      "        </reactionGlyph>"
      "        <reactionGlyph id=\"rg_aspartateCarrier\" reaction=\"aspartateCarrier\">"
      "          <curve>"
      "            <listOfCurveSegments>"
      "              <curveSegment xsi:type=\"LineSegment\">"
      "                <start x=\"1420\" y=\"530\"/>"
      "                <end x=\"1360\" y=\"550\"/>"
      "              </curveSegment>"
      "            </listOfCurveSegments>"
      "          </curve>"
      "          <listOfSpeciesReferenceGlyphs>"
      "            <speciesReferenceGlyph id=\"srg_aspartate_mito3_2\" speciesReference=\"sr_aspartate_mito3_2\" speciesGlyph=\"SpeciesGlyph_aspartate_mito3\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1420\" y=\"530\"/>"
      "                    <end x=\"1850\" y=\"498\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_aspartate_cyt_2\" speciesReference=\"sr_aspartate_cyt_2\" speciesGlyph=\"SpeciesGlyph_aspartate_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1360\" y=\"550\"/>"
      "                    <end x=\"820\" y=\"698\"/>"
      "                    <basePoint1 x=\"1390\" y=\"698\"/>"
      "                    <basePoint2 x=\"1390\" y=\"698\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_glutamate_cyt_2\" speciesReference=\"sr_glutamate_cyt_2\" speciesGlyph=\"SpeciesGlyph_glutamate_cyt\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1420\" y=\"530\"/>"
      "                    <end x=\"1050\" y=\"628\"/>"
      "                    <basePoint1 x=\"1390\" y=\"648\"/>"
      "                    <basePoint2 x=\"1390\" y=\"648\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_glutamate_mito3_2\" speciesReference=\"sr_glutamate_mito3_2\" speciesGlyph=\"SpeciesGlyph_glutamate_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1360\" y=\"550\"/>"
      "                    <end x=\"1550\" y=\"448\"/>"
      "                    <basePoint1 x=\"1390\" y=\"448\"/>"
      "                    <basePoint2 x=\"1390\" y=\"448\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "          </listOfSpeciesReferenceGlyphs>"
      "        </reactionGlyph>"
      "        <reactionGlyph id=\"rg_malateCarrier\" reaction=\"malateCarrier\">"
      "          <curve>"
      "            <listOfCurveSegments>"
      "              <curveSegment xsi:type=\"LineSegment\">"
      "                <start x=\"1420\" y=\"320\"/>"
      "                <end x=\"1360\" y=\"340\"/>"
      "              </curveSegment>"
      "            </listOfCurveSegments>"
      "          </curve>"
      "          <listOfSpeciesReferenceGlyphs>"
      "            <speciesReferenceGlyph id=\"srg_aKetoglutarate_mito3_2\" speciesReference=\"sr_aKetoglutarate_mito3_2\" speciesGlyph=\"SpeciesGlyph_aKetoglutarate_mito3\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1420\" y=\"320\"/>"
      "                    <end x=\"1530\" y=\"318\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_aKetoglutarate_cyt_2\" speciesReference=\"sr_aKetoglutarate_cyt_2\" speciesGlyph=\"SpeciesGlyph_aKetoglutarate_cyt\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"LineSegment\">"
      "                    <start x=\"1360\" y=\"340\"/>"
      "                    <end x=\"1140\" y=\"518\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_malate_cyt_2\" speciesReference=\"sr_malate_cyt_2\" speciesGlyph=\"SpeciesGlyph_malate_cyt\" role=\"substrate\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1420\" y=\"320\"/>"
      "                    <end x=\"820\" y=\"298\"/>"
      "                    <basePoint1 x=\"1390\" y=\"250\"/>"
      "                    <basePoint2 x=\"1390\" y=\"250\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "            <speciesReferenceGlyph id=\"srg_malate_mito3_2\" speciesReference=\"sr_malate_mito3_2\" speciesGlyph=\"SpeciesGlyph_malate_mito3\" role=\"product\">"
      "              <curve>"
      "                <listOfCurveSegments>"
      "                  <curveSegment xsi:type=\"CubicBezier\">"
      "                    <start x=\"1360\" y=\"340\"/>"
      "                    <end x=\"1850\" y=\"98\"/>"
      "                    <basePoint1 x=\"1390\" y=\"150\"/>"
      "                    <basePoint2 x=\"1390\" y=\"150\"/>"
      "                  </curveSegment>"
      "                </listOfCurveSegments>"
      "              </curve>"
      "            </speciesReferenceGlyph>"
      "          </listOfSpeciesReferenceGlyphs>"
      "        </reactionGlyph>"
      "      </listOfReactionGlyphs>"
      "      <listOfTextGlyphs>"
      "        <textGlyph id=\"TextGlyph_Hepatocyte\" graphicalObject=\"CompartmentGlyph_1\" originOfText=\"Hepatocyte\">"
      "          <boundingBox id=\"bb_tg_compartment\">"
      "            <position x=\"50\" y=\"870\"/>"
      "            <dimensions width=\"300\" height=\"72\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_mito1\" graphicalObject=\"Mito1_Glyph\" originOfText=\"Mito_1\">"
      "          <boundingBox id=\"bb_tg_mito1\">"
      "            <position x=\"110\" y=\"110\"/>"
      "            <dimensions width=\"280\" height=\"72\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_mito2\" graphicalObject=\"Mito2_Glyph\" originOfText=\"Mito_2\">"
      "          <boundingBox id=\"bb_tg_mito2\">"
      "            <position x=\"210\" y=\"660\"/>"
      "            <dimensions width=\"280\" height=\"72\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_mito3_2\" graphicalObject=\"Mito3_Glyph_2\" originOfText=\"Mito_3\">"
      "          <boundingBox id=\"bb_tg_mito3_2\">"
      "            <position x=\"1475\" y=\"35\"/>"
      "            <dimensions width=\"200\" height=\"72\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_malate_cyt\" graphicalObject=\"SpeciesGlyph_malate_cyt\" originOfText=\"malate_cyt\">"
      "          <boundingBox id=\"bb_tg_malatate_cyt\">"
      "            <position x=\"590\" y=\"280\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_oxaloacetate_cyt\" graphicalObject=\"SpeciesGlyph_oxaloacetate_cyt\" originOfText=\"oxaloacetate_cyt\">"
      "          <boundingBox id=\"bb_tg_oxaloacetate_cyt\">"
      "            <position x=\"590\" y=\"480\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_aspartate_cyt\" graphicalObject=\"SpeciesGlyph_aspartate_cyt\" originOfText=\"aspartate_cyt\">"
      "          <boundingBox id=\"bb_tg_aspartate_cyt\">"
      "            <position x=\"590\" y=\"680\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_glutamate_cyt\" graphicalObject=\"SpeciesGlyph_glutamate_cyt\" originOfText=\"glutamate_cyt\">"
      "          <boundingBox id=\"bb_tg_glutamate_cyt\">"
      "            <position x=\"810\" y=\"610\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_aKetoglutarate_cyt\" graphicalObject=\"SpeciesGlyph_aKetoglutarate_cyt\" originOfText=\"aKetoglutarate_cyt\">"
      "          <boundingBox id=\"bb_tg_aKetoglutarate_cyt\">"
      "            <position x=\"870\" y=\"500\"/>"
      "            <dimensions width=\"260\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_nad_cyt\" graphicalObject=\"SpeciesGlyph_nad_cyt\" originOfText=\"nad_cyt\">"
      "          <boundingBox id=\"bb_tg_nad_cyt\">"
      "            <position x=\"525\" y=\"350\"/>"
      "            <dimensions width=\"80\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_nadh_cyt\" graphicalObject=\"SpeciesGlyph_nadh_cyt\" originOfText=\"nadh_cyt\">"
      "          <boundingBox id=\"bb_tg_nadh_cyt\">"
      "            <position x=\"525\" y=\"430\"/>"
      "            <dimensions width=\"80\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_h_cyt\" graphicalObject=\"SpeciesGlyph_h_cyt\" originOfText=\"h_cyt\">"
      "          <boundingBox id=\"bb_tg_h_cyt\">"
      "            <position x=\"435\" y=\"430\"/>"
      "            <dimensions width=\"30\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"tg_rg_malaltedh_cyt\" graphicalObject=\"rg_malatedh_cyt\" originOfText=\"reaction_malatedh_cyt\">"
      "          <boundingBox id=\"bb_tg_rg_malaltedh_cyt\">"
      "            <position x=\"700\" y=\"385\"/>"
      "            <dimensions width=\"210\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"tg_rg_aspartateat_cyt\" graphicalObject=\"rg_aspartateat_cyt\" originOfText=\"reaction_aspartateat_cyt\">"
      "          <boundingBox id=\"bb_tg_rg_aspartateat_cyt\">"
      "            <position x=\"440\" y=\"585\"/>"
      "            <dimensions width=\"260\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_malate_mito3\" graphicalObject=\"SpeciesGlyph_malate_mito3\" originOfText=\"malate_mito3\">"
      "          <boundingBox id=\"bb_tg_malatate_mito3\">"
      "            <position x=\"1860\" y=\"80\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_oxaloacetate_mito3\" graphicalObject=\"SpeciesGlyph_oxaloacetate_mito3\" originOfText=\"oxaloacetate_mito3\">"
      "          <boundingBox id=\"bb_tg_oxaloacetate_mito3\">"
      "            <position x=\"1860\" y=\"280\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_aspartate_mito3\" graphicalObject=\"SpeciesGlyph_aspartate_mito3\" originOfText=\"aspartate_mito3\">"
      "          <boundingBox id=\"bb_tg_aspartate_mito3\">"
      "            <position x=\"1860\" y=\"480\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_glutamate_mito3\" graphicalObject=\"SpeciesGlyph_glutamate_mito3\" originOfText=\"glutamate_mito3\">"
      "          <boundingBox id=\"bb_tg_glutamate_mito3\">"
      "            <position x=\"1560\" y=\"430\"/>"
      "            <dimensions width=\"220\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_aKetoglutarate_mito3\" graphicalObject=\"SpeciesGlyph_aKetoglutarate_mito3\" originOfText=\"aKetoglutarate_mito3\">"
      "          <boundingBox id=\"bb_tg_aKetoglutarate_mito3\">"
      "            <position x=\"1540\" y=\"300\"/>"
      "            <dimensions width=\"260\" height=\"36\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_nad_mito3\" graphicalObject=\"SpeciesGlyph_nad_mito3\" originOfText=\"nad_mito3\">"
      "          <boundingBox id=\"bb_tg_nad_mito3\">"
      "            <position x=\"2055\" y=\"150\"/>"
      "            <dimensions width=\"80\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_nadh_mito3\" graphicalObject=\"SpeciesGlyph_nadh_mito3\" originOfText=\"nadh_mito3\">"
      "          <boundingBox id=\"bb_tg_nadh_mito3\">"
      "            <position x=\"2055\" y=\"230\"/>"
      "            <dimensions width=\"80\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"TextGlyph_h_mito3\" graphicalObject=\"SpeciesGlyph_h_mito3\" originOfText=\"h_mito3\">"
      "          <boundingBox id=\"bb_tg_h_mito3\">"
      "            <position x=\"2205\" y=\"230\"/>"
      "            <dimensions width=\"30\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"tg_rg_malatedh_mito3\" graphicalObject=\"rg_malatedh_mito3\" originOfText=\"reaction_malatedh_mito3\">"
      "          <boundingBox id=\"bb_tg_rg_malatedh_mito3\">"
      "            <position x=\"1740\" y=\"185\"/>"
      "            <dimensions width=\"220\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"tg_rg_aspartateat_mito3\" graphicalObject=\"rg_aspartateat_mito3\" originOfText=\"reaction_aspartateat_mito3\">"
      "          <boundingBox id=\"bb_tg_rg_aspartateat_mito3\">"
      "            <position x=\"1970\" y=\"385\"/>"
      "            <dimensions width=\"260\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"tg_rg_aspartateCarrier\" graphicalObject=\"rg_aspartateCarrier\" originOfText=\"aspartateCarrier\">"
      "          <boundingBox id=\"bb_tg_rg_aspartateCarrier\">"
      "            <position x=\"1380\" y=\"500\"/>"
      "            <dimensions width=\"160\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "        <textGlyph id=\"tg_rg_malateCarrier\" graphicalObject=\"rg_malateCarrier\" originOfText=\"malateCarrier\">"
      "          <boundingBox id=\"bb_tg_rg_malateCarrier\">"
      "            <position x=\"1360\" y=\"330\"/>"
      "            <dimensions width=\"140\" height=\"24\"/>"
      "          </boundingBox>"
      "        </textGlyph>"
      "      </listOfTextGlyphs>"
      "    </layout>"
      "  </listOfLayouts>"
      "            </annotation>"
      "    <listOfCompartments>"
      "      <compartment id=\"Hepatocyte\" name=\"Hepatocyte\"/>"
      "      <compartment id=\"Mito_1\" name=\"Mito 1\" outside=\"Hepatocyte\"/>"
      "      <compartment id=\"Mito_2\" name=\"Mito 2\" outside=\"Hepatocyte\"/>"
      "      <compartment id=\"Mito_3\" name=\"Mito 3\" outside=\"Hepatocyte\"/>"
      "    </listOfCompartments>"
      "    <listOfSpecies>"
      "      <species id=\"malate_cyt\" name=\"Malate\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"malate_mito1\" name=\"Malate\" compartment=\"Mito_1\"/>"
      "      <species id=\"malate_mito2\" name=\"Malate\" compartment=\"Mito_2\"/>"
      "      <species id=\"malate_mito3\" name=\"Malate\" compartment=\"Mito_3\"/>"
      "      <species id=\"oxaloacetate_cyt\" name=\"Oxaloacetate\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"oxaloacetate_mito1\" name=\"Oxaloacetate\" compartment=\"Mito_1\"/>"
      "      <species id=\"oxaloacetate_mito2\" name=\"Oxaloacetate\" compartment=\"Mito_2\"/>"
      "      <species id=\"oxaloacetate_mito3\" name=\"Oxaloacetate\" compartment=\"Mito_3\"/>"
      "      <species id=\"aspartate_cyt\" name=\"Aspartate\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"aspartate_mito1\" name=\"Aspartate\" compartment=\"Mito_1\"/>"
      "      <species id=\"aspartate_mito2\" name=\"Aspartate\" compartment=\"Mito_2\"/>"
      "      <species id=\"aspartate_mito3\" name=\"Aspartate\" compartment=\"Mito_3\"/>"
      "      <species id=\"glutamate_cyt\" name=\"Glutamate\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"glutamate_mito1\" name=\"Glutamate\" compartment=\"Mito_1\"/>"
      "      <species id=\"glutamate_mito2\" name=\"Glutamate\" compartment=\"Mito_2\"/>"
      "      <species id=\"glutamate_mito3\" name=\"Glutamate\" compartment=\"Mito_3\"/>"
      "      <species id=\"aKetoglutarate_cyt\" name=\"alpha-Ketoglutarate\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"aKetoglutarate_mito1\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_1\"/>"
      "      <species id=\"aKetoglutarate_mito2\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_2\"/>"
      "      <species id=\"aKetoglutarate_mito3\" name=\"alpha-Ketoglutarate\" compartment=\"Mito_3\"/>"
      "      <species id=\"h_cyt\" name=\"H+\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"h_mito1\" name=\"H+\" compartment=\"Mito_1\"/>"
      "      <species id=\"h_mito2\" name=\"H+\" compartment=\"Mito_2\"/>"
      "      <species id=\"h_mito3\" name=\"H+\" compartment=\"Mito_3\"/>"
      "      <species id=\"nad_cyt\" name=\"NAD+\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"nad_mito1\" name=\"NAD+\" compartment=\"Mito_1\"/>"
      "      <species id=\"nad_mito2\" name=\"NAD+\" compartment=\"Mito_2\"/>"
      "      <species id=\"nad_mito3\" name=\"NAD+\" compartment=\"Mito_3\"/>"
      "      <species id=\"nadh_cyt\" name=\"NADH\" compartment=\"Hepatocyte\"/>"
      "      <species id=\"nadh_mito1\" name=\"NADH\" compartment=\"Mito_1\"/>"
      "      <species id=\"nadh_mito2\" name=\"NADH\" compartment=\"Mito_2\"/>"
      "      <species id=\"nadh_mito3\" name=\"NADH\" compartment=\"Mito_3\"/>"
      "    </listOfSpecies>"
      "    <listOfReactions>"
      "      <reaction id=\"reaction_malatedh_cyt\" name=\"malate dehydrogenase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"malate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_cyt\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"nad_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nad_cyt\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"nadh_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nadh_cyt\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"h_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_h_cyt\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"oxaloacetate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_cyt_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_aspartateat_cyt\" name=\"aspartate aminotransferase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"oxaloacetate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_cyt_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"glutamate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_cyt_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"aspartate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_cyt_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"aKetoglutarate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_cyt_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_malatedh_mito1\" name=\"malate dehydrogenase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"malate_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"nad_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nad_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"nadh_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nadh_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"h_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_h_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"oxaloacetate_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_mito1_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_aspartateat_mito1\" name=\"aspartate aminotransferase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"oxaloacetate_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_mito1_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"glutamate_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"aspartate_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"aKetoglutarate_mito1\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_mito1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_malatedh_mito2\" name=\"malate dehydrogenase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"malate_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"nad_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nad_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"nadh_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nadh_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"h_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_h_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"oxaloacetate_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_mito2_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_aspartateat_mito2\" name=\"aspartate aminotransferase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"oxaloacetate_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_mito2_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"glutamate_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"aspartate_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"aKetoglutarate_mito2\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_mito2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_malatedh_mito3\" name=\"malate dehydrogenase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"malate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_mito3\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"nad_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nad_mito3\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"nadh_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_nadh_mito3\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"h_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_h_mito3\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"oxaloacetate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_mito3_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"reaction_aspartateat_mito3\" name=\"aspartate aminotransferase\" reversible=\"false\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"oxaloacetate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_oxaloacetate_mito3_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"glutamate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_mito3_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"aspartate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_mito3_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"aKetoglutarate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_mito3_1\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"aspartateCarrier\" name=\"aspartate carrier\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"glutamate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_mito3_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"aspartate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_cyt_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"glutamate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_glutamate_cyt_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"aspartate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aspartate_mito3_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "      <reaction id=\"malateCarrier\" name=\"malate carrier\">"
      "        <listOfReactants>"
      "          <speciesReference species=\"aKetoglutarate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_mito3_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"malate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_cyt_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfReactants>"
      "        <listOfProducts>"
      "          <speciesReference species=\"aKetoglutarate_cyt\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_aKetoglutarate_cyt_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "          <speciesReference species=\"malate_mito3\">"
      "            <annotation>"
      "  <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"sr_malate_mito3_2\"/>"
      "</annotation>"
      "          </speciesReference>"
      "        </listOfProducts>"
      "      </reaction>"
      "    </listOfReactions>"
      "  </model>"
      "</sbml> "
      ;
  
    XMLInputStream *stream = new XMLInputStream (s.c_str(),false);
    XMLNode *node = new XMLNode(*stream);
  
    fail_unless(node != NULL);
  
    // create the document
    fail_unless(LN != NULL);
    SBMLDocument *document=new SBMLDocument(LN);
    fail_unless(document != NULL);
    // create the Model
  
    Model* model=document->createModel();
    model->setId("TestModel");
    document->setModel(model);
  
    // create the Compartment
  
    Compartment* compartment=model->createCompartment();
    compartment->setId("Hepatocyte");
    compartment->setName("Hepatocyte");
  
    Compartment* mito1=model->createCompartment();
    mito1->setId("Mito_1");
    mito1->setName("Mito 1");
    mito1->setOutside(compartment->getId());
  
    Compartment* mito2=model->createCompartment();
    mito2->setId("Mito_2");
    mito2->setName("Mito 2");
    mito2->setOutside(compartment->getId());
  
    Compartment* mito3=model->createCompartment();
    mito3->setId("Mito_3");
    mito3->setName("Mito 3");
    mito3->setOutside(compartment->getId());
  
  
    // create the Species
  
    // Malate
    Species* malate_cyt=model->createSpecies();
    malate_cyt->setId("malate_cyt");
    malate_cyt->setName("Malate");
    malate_cyt->setCompartment(compartment->getId());
  
    Species* malate_mito1=model->createSpecies();
    malate_mito1->setId("malate_mito1");
    malate_mito1->setCompartment(mito1->getId());
    malate_mito1->setName("Malate");
  
    Species* malate_mito2=model->createSpecies();
    malate_mito2->setId("malate_mito2");
    malate_mito2->setCompartment(mito2->getId());
    malate_mito2->setName("Malate");
  
    Species* malate_mito3=model->createSpecies();
    malate_mito3->setId("malate_mito3");
    malate_mito3->setCompartment(mito3->getId());
    malate_mito3->setName("Malate");
  
  
    // Oxaloacetate
    Species* oxaloacetate_cyt=model->createSpecies();
    oxaloacetate_cyt->setId("oxaloacetate_cyt");
    oxaloacetate_cyt->setName("Oxaloacetate");
    oxaloacetate_cyt->setCompartment(compartment->getId());
  
    Species* oxaloacetate_mito1=model->createSpecies();
    oxaloacetate_mito1->setId("oxaloacetate_mito1");
    oxaloacetate_mito1->setCompartment(mito1->getId());
    oxaloacetate_mito1->setName("Oxaloacetate");
  
    Species* oxaloacetate_mito2=model->createSpecies();
    oxaloacetate_mito2->setId("oxaloacetate_mito2");
    oxaloacetate_mito2->setCompartment(mito2->getId());
    oxaloacetate_mito2->setName("Oxaloacetate");
  
    Species* oxaloacetate_mito3=model->createSpecies();
    oxaloacetate_mito3->setId("oxaloacetate_mito3");
    oxaloacetate_mito3->setCompartment(mito3->getId());
    oxaloacetate_mito3->setName("Oxaloacetate");
  
  
    // Aspartate
    Species* aspartate_cyt=model->createSpecies();
    aspartate_cyt->setId("aspartate_cyt");
    aspartate_cyt->setName("Aspartate");
    aspartate_cyt->setCompartment(compartment->getId());
  
    Species* aspartate_mito1=model->createSpecies();
    aspartate_mito1->setId("aspartate_mito1");
    aspartate_mito1->setCompartment(mito1->getId());
    aspartate_mito1->setName("Aspartate");
  
    Species* aspartate_mito2=model->createSpecies();
    aspartate_mito2->setId("aspartate_mito2");
    aspartate_mito2->setCompartment(mito2->getId());
    aspartate_mito2->setName("Aspartate");
  
    Species* aspartate_mito3=model->createSpecies();
    aspartate_mito3->setId("aspartate_mito3");
    aspartate_mito3->setCompartment(mito3->getId());
    aspartate_mito3->setName("Aspartate");
  
  
    // Glutamate
    Species* glutamate_cyt=model->createSpecies();
    glutamate_cyt->setId("glutamate_cyt");
    glutamate_cyt->setName("Glutamate");
    glutamate_cyt->setCompartment(compartment->getId());
  
    Species* glutamate_mito1=model->createSpecies();
    glutamate_mito1->setId("glutamate_mito1");
    glutamate_mito1->setCompartment(mito1->getId());
    glutamate_mito1->setName("Glutamate");
  
    Species* glutamate_mito2=model->createSpecies();
    glutamate_mito2->setId("glutamate_mito2");
    glutamate_mito2->setCompartment(mito2->getId());
    glutamate_mito2->setName("Glutamate");
  
    Species* glutamate_mito3=model->createSpecies();
    glutamate_mito3->setId("glutamate_mito3");
    glutamate_mito3->setCompartment(mito3->getId());
    glutamate_mito3->setName("Glutamate");
  
  
    // alpha-Ketoglutarate
    Species* aKetoglutarate_cyt=model->createSpecies();
    aKetoglutarate_cyt->setId("aKetoglutarate_cyt");
    aKetoglutarate_cyt->setName("alpha-Ketoglutarate");
    aKetoglutarate_cyt->setCompartment(compartment->getId());
  
    Species* aKetoglutarate_mito1=model->createSpecies();
    aKetoglutarate_mito1->setId("aKetoglutarate_mito1");
    aKetoglutarate_mito1->setCompartment(mito1->getId());
    aKetoglutarate_mito1->setName("alpha-Ketoglutarate");
  
    Species* aKetoglutarate_mito2=model->createSpecies();
    aKetoglutarate_mito2->setId("aKetoglutarate_mito2");
    aKetoglutarate_mito2->setCompartment(mito2->getId());
    aKetoglutarate_mito2->setName("alpha-Ketoglutarate");
  
    Species* aKetoglutarate_mito3=model->createSpecies();
    aKetoglutarate_mito3->setId("aKetoglutarate_mito3");
    aKetoglutarate_mito3->setCompartment(mito3->getId());
    aKetoglutarate_mito3->setName("alpha-Ketoglutarate");
  
  
    // protons
    Species* h_cyt=model->createSpecies();
    h_cyt->setId("h_cyt");
    h_cyt->setName("H+");
    h_cyt->setCompartment(compartment->getId());
  
    Species* h_mito1=model->createSpecies();
    h_mito1->setId("h_mito1");
    h_mito1->setCompartment(mito1->getId());
    h_mito1->setName("H+");
  
    Species* h_mito2=model->createSpecies();
    h_mito2->setId("h_mito2");
    h_mito2->setCompartment(mito2->getId());
    h_mito2->setName("H+");
  
    Species* h_mito3=model->createSpecies();
    h_mito3->setId("h_mito3");
    h_mito3->setCompartment(mito3->getId());
    h_mito3->setName("H+");
  
  
    // NAD+
    Species* nad_cyt=model->createSpecies();
    nad_cyt->setId("nad_cyt");
    nad_cyt->setName("NAD+");
    nad_cyt->setCompartment(compartment->getId());
  
    Species* nad_mito1=model->createSpecies();
    nad_mito1->setId("nad_mito1");
    nad_mito1->setCompartment(mito1->getId());
    nad_mito1->setName("NAD+");
  
    Species* nad_mito2=model->createSpecies();
    nad_mito2->setId("nad_mito2");
    nad_mito2->setCompartment(mito2->getId());
    nad_mito2->setName("NAD+");
  
    Species* nad_mito3=model->createSpecies();
    nad_mito3->setId("nad_mito3");
    nad_mito3->setCompartment(mito3->getId());
    nad_mito3->setName("NAD+");
  
  
    // NADH
    Species* nadh_cyt=model->createSpecies();
    nadh_cyt->setId("nadh_cyt");
    nadh_cyt->setName("NADH");
    nadh_cyt->setCompartment(compartment->getId());
  
    Species* nadh_mito1=model->createSpecies();
    nadh_mito1->setId("nadh_mito1");
    nadh_mito1->setCompartment(mito1->getId());
    nadh_mito1->setName("NADH");
  
    Species* nadh_mito2=model->createSpecies();
    nadh_mito2->setId("nadh_mito2");
    nadh_mito2->setCompartment(mito2->getId());
    nadh_mito2->setName("NADH");
  
    Species* nadh_mito3=model->createSpecies();
    nadh_mito3->setId("nadh_mito3");
    nadh_mito3->setCompartment(mito3->getId());
    nadh_mito3->setName("NADH");
  
  
  
  
    // create the Reactions
  
    // Cytosol
  
    // Malate Dehydrogenase
    Reaction* malatedh_cyt=model->createReaction();
    malatedh_cyt->setId("reaction_malatedh_cyt");
    malatedh_cyt->setName("malate dehydrogenase");
    malatedh_cyt->setReversible(false);
  
    SpeciesReference* sr_malate_cyt=malatedh_cyt->createReactant();
    sr_malate_cyt->setSpecies(malate_cyt->getId());
    sr_malate_cyt->setId("sr_malate_cyt");
  
    SpeciesReference* sr_nad_cyt=malatedh_cyt->createReactant();
    sr_nad_cyt->setSpecies(nad_cyt->getId());
    sr_nad_cyt->setId("sr_nad_cyt");
  
    SpeciesReference* sr_nadh_cyt=malatedh_cyt->createProduct();
    sr_nadh_cyt->setSpecies(nadh_cyt->getId());
    sr_nadh_cyt->setId("sr_nadh_cyt");
  
    SpeciesReference* sr_h_cyt=malatedh_cyt->createProduct();
    sr_h_cyt->setSpecies(h_cyt->getId());
    sr_h_cyt->setId("sr_h_cyt");
  
    SpeciesReference* sr_oxaloacetate_cyt_1=malatedh_cyt->createProduct();
    sr_oxaloacetate_cyt_1->setSpecies(oxaloacetate_cyt->getId());
    sr_oxaloacetate_cyt_1->setId("sr_oxaloacetate_cyt_1");
  
    //Aspartate Aminotransferase
    Reaction* aspartateat_cyt=model->createReaction();
    aspartateat_cyt->setId("reaction_aspartateat_cyt");
    aspartateat_cyt->setName("aspartate aminotransferase");
    aspartateat_cyt->setReversible(false);
  
    SpeciesReference* sr_oxaloacetate_cyt_2=aspartateat_cyt->createReactant();
    sr_oxaloacetate_cyt_2->setSpecies(oxaloacetate_cyt->getId());
    sr_oxaloacetate_cyt_2->setId("sr_oxaloacetate_cyt_2");
  
    SpeciesReference* sr_glutamate_cyt_1=aspartateat_cyt->createReactant();
    sr_glutamate_cyt_1->setSpecies(glutamate_cyt->getId());
    sr_glutamate_cyt_1->setId("sr_glutamate_cyt_1");
  
    SpeciesReference* sr_aspartate_cyt_1=aspartateat_cyt->createProduct();
    sr_aspartate_cyt_1->setSpecies(aspartate_cyt->getId());
    sr_aspartate_cyt_1->setId("sr_aspartate_cyt_1");
  
    SpeciesReference* sr_aKetoglutarate_cyt_1=aspartateat_cyt->createProduct();
    sr_aKetoglutarate_cyt_1->setSpecies(aKetoglutarate_cyt->getId());
    sr_aKetoglutarate_cyt_1->setId("sr_aKetoglutarate_cyt_1");
  
  
    // Mito 1
  
    // Malate Dehydrogenase
    Reaction* malatedh_mito1=model->createReaction();
    malatedh_mito1->setId("reaction_malatedh_mito1");
    malatedh_mito1->setName("malate dehydrogenase");
    malatedh_mito1->setReversible(false);
  
    SpeciesReference* sr_malate_mito1=malatedh_mito1->createReactant();
    sr_malate_mito1->setSpecies(malate_mito1->getId());
    sr_malate_mito1->setId("sr_malate_mito1");
  
    SpeciesReference* sr_nad_mito1=malatedh_mito1->createReactant();
    sr_nad_mito1->setSpecies(nad_mito1->getId());
    sr_nad_mito1->setId("sr_nad_mito1");
  
    SpeciesReference* sr_nadh_mito1=malatedh_mito1->createProduct();
    sr_nadh_mito1->setSpecies(nadh_mito1->getId());
    sr_nadh_mito1->setId("sr_nadh_mito1");
  
    SpeciesReference* sr_h_mito1=malatedh_mito1->createProduct();
    sr_h_mito1->setSpecies(h_mito1->getId());
    sr_h_mito1->setId("sr_h_mito1");
  
    SpeciesReference* sr_oxaloacetate_mito1_1=malatedh_mito1->createProduct();
    sr_oxaloacetate_mito1_1->setSpecies(oxaloacetate_mito1->getId());
    sr_oxaloacetate_mito1_1->setId("sr_oxaloacetate_mito1_1");
  
    //Aspartate Aminotransferase
    Reaction* aspartateat_mito1=model->createReaction();
    aspartateat_mito1->setId("reaction_aspartateat_mito1");
    aspartateat_mito1->setName("aspartate aminotransferase");
    aspartateat_mito1->setReversible(false);
  
    SpeciesReference* sr_oxaloacetate_mito1_2=aspartateat_mito1->createReactant();
    sr_oxaloacetate_mito1_2->setSpecies(oxaloacetate_mito1->getId());
    sr_oxaloacetate_mito1_2->setId("sr_oxaloacetate_mito1_2");
  
    SpeciesReference* sr_glutamate_mito1=aspartateat_mito1->createReactant();
    sr_glutamate_mito1->setSpecies(glutamate_mito1->getId());
    sr_glutamate_mito1->setId("sr_glutamate_mito1");
  
    SpeciesReference* sr_aspartate_mito1=aspartateat_mito1->createProduct();
    sr_aspartate_mito1->setSpecies(aspartate_mito1->getId());
    sr_aspartate_mito1->setId("sr_aspartate_mito1");
  
    SpeciesReference* sr_aKetoglutarate_mito1=aspartateat_mito1->createProduct();
    sr_aKetoglutarate_mito1->setSpecies(aKetoglutarate_mito1->getId());
    sr_aKetoglutarate_mito1->setId("sr_aKetoglutarate_mito1");
  
  
    // Mito 2
  
    // Malate Dehydrogenase
    Reaction* malatedh_mito2=model->createReaction();
    malatedh_mito2->setId("reaction_malatedh_mito2");
    malatedh_mito2->setName("malate dehydrogenase");
    malatedh_mito2->setReversible(false);
  
    SpeciesReference* sr_malate_mito2=malatedh_mito2->createReactant();
    sr_malate_mito2->setSpecies(malate_mito2->getId());
    sr_malate_mito2->setId("sr_malate_mito2");
  
    SpeciesReference* sr_nad_mito2=malatedh_mito2->createReactant();
    sr_nad_mito2->setSpecies(nad_mito2->getId());
    sr_nad_mito2->setId("sr_nad_mito2");
  
    SpeciesReference* sr_nadh_mito2=malatedh_mito2->createProduct();
    sr_nadh_mito2->setSpecies(nadh_mito2->getId());
    sr_nadh_mito2->setId("sr_nadh_mito2");
  
    SpeciesReference* sr_h_mito2=malatedh_mito2->createProduct();
    sr_h_mito2->setSpecies(h_mito2->getId());
    sr_h_mito2->setId("sr_h_mito2");
  
    SpeciesReference* sr_oxaloacetate_mito2_1=malatedh_mito2->createProduct();
    sr_oxaloacetate_mito2_1->setSpecies(oxaloacetate_mito2->getId());
    sr_oxaloacetate_mito2_1->setId("sr_oxaloacetate_mito2_1");
  
    //Aspartate Aminotransferase
    Reaction* aspartateat_mito2=model->createReaction();
    aspartateat_mito2->setId("reaction_aspartateat_mito2");
    aspartateat_mito2->setName("aspartate aminotransferase");
    aspartateat_mito2->setReversible(false);
  
    SpeciesReference* sr_oxaloacetate_mito2_2=aspartateat_mito2->createReactant();
    sr_oxaloacetate_mito2_2->setSpecies(oxaloacetate_mito2->getId());
    sr_oxaloacetate_mito2_2->setId("sr_oxaloacetate_mito2_2");
  
    SpeciesReference* sr_glutamate_mito2=aspartateat_mito2->createReactant();
    sr_glutamate_mito2->setSpecies(glutamate_mito2->getId());
    sr_glutamate_mito2->setId("sr_glutamate_mito2");
  
    SpeciesReference* sr_aspartate_mito2=aspartateat_mito2->createProduct();
    sr_aspartate_mito2->setSpecies(aspartate_mito2->getId());
    sr_aspartate_mito2->setId("sr_aspartate_mito2");
  
    SpeciesReference* sr_aKetoglutarate_mito2=aspartateat_mito2->createProduct();
    sr_aKetoglutarate_mito2->setSpecies(aKetoglutarate_mito2->getId());
    sr_aKetoglutarate_mito2->setId("sr_aKetoglutarate_mito2");
  
  
    // Mito 3
  
    // Malate Dehydrogenase
    Reaction* malatedh_mito3=model->createReaction();
    malatedh_mito3->setId("reaction_malatedh_mito3");
    malatedh_mito3->setName("malate dehydrogenase");
    malatedh_mito3->setReversible(false);
  
    SpeciesReference* sr_malate_mito3=malatedh_mito3->createReactant();
    sr_malate_mito3->setSpecies(malate_mito3->getId());
    sr_malate_mito3->setId("sr_malate_mito3");
  
    SpeciesReference* sr_nad_mito3=malatedh_mito3->createReactant();
    sr_nad_mito3->setSpecies(nad_mito3->getId());
    sr_nad_mito3->setId("sr_nad_mito3");
  
    SpeciesReference* sr_nadh_mito3=malatedh_mito3->createProduct();
    sr_nadh_mito3->setSpecies(nadh_mito3->getId());
    sr_nadh_mito3->setId("sr_nadh_mito3");
  
    SpeciesReference* sr_h_mito3=malatedh_mito3->createProduct();
    sr_h_mito3->setSpecies(h_mito3->getId());
    sr_h_mito3->setId("sr_h_mito3");
  
    SpeciesReference* sr_oxaloacetate_mito3_1=malatedh_mito3->createProduct();
    sr_oxaloacetate_mito3_1->setSpecies(oxaloacetate_mito3->getId());
    sr_oxaloacetate_mito3_1->setId("sr_oxaloacetate_mito3_1");
  
    //Aspartate Aminotransferase
    Reaction* aspartateat_mito3=model->createReaction();
    aspartateat_mito3->setId("reaction_aspartateat_mito3");
    aspartateat_mito3->setName("aspartate aminotransferase");
    aspartateat_mito3->setReversible(false);
  
    SpeciesReference* sr_oxaloacetate_mito3_2=aspartateat_mito3->createReactant();
    sr_oxaloacetate_mito3_2->setSpecies(oxaloacetate_mito3->getId());
    sr_oxaloacetate_mito3_2->setId("sr_oxaloacetate_mito3_2");
  
  
    SpeciesReference* sr_glutamate_mito3_1=aspartateat_mito3->createReactant();
    sr_glutamate_mito3_1->setSpecies(glutamate_mito3->getId());
    sr_glutamate_mito3_1->setId("sr_glutamate_mito3_1");
  
  
    SpeciesReference* sr_aspartate_mito3_1=aspartateat_mito3->createProduct();
    sr_aspartate_mito3_1->setSpecies(aspartate_mito3->getId());
    sr_aspartate_mito3_1->setId("sr_aspartate_mito3_1");
  
  
    SpeciesReference* sr_aKetoglutarate_mito3_1=aspartateat_mito3->createProduct();
    sr_aKetoglutarate_mito3_1->setSpecies(aKetoglutarate_mito3->getId());
    sr_aKetoglutarate_mito3_1->setId("sr_aKetoglutarate_mito3_1");
  
  
    // aspartate carrier
  
    Reaction* aspartateCarrier=model->createReaction();
    aspartateCarrier->setId("aspartateCarrier");
    aspartateCarrier->setName("aspartate carrier");
    aspartateCarrier->setReversible(true);
  
    SpeciesReference* sr_glutamate_mito3_2=aspartateCarrier->createReactant();
    sr_glutamate_mito3_2->setSpecies(glutamate_mito3->getId());
    sr_glutamate_mito3_2->setId("sr_glutamate_mito3_2");
  
    SpeciesReference* sr_aspartate_cyt_2=aspartateCarrier->createReactant();
    sr_aspartate_cyt_2->setSpecies(aspartate_cyt->getId());
    sr_aspartate_cyt_2->setId("sr_aspartate_cyt_2");
  
    SpeciesReference* sr_glutamate_cyt_2=aspartateCarrier->createProduct();
    sr_glutamate_cyt_2->setSpecies(glutamate_cyt->getId());
    sr_glutamate_cyt_2->setId("sr_glutamate_cyt_2");
  
    SpeciesReference* sr_aspartate_mito3_2=aspartateCarrier->createProduct();
    sr_aspartate_mito3_2->setSpecies(aspartate_mito3->getId());
    sr_aspartate_mito3_2->setId("sr_aspartate_mito3_2");
  
    // malate carrier
  
    Reaction* malateCarrier=model->createReaction();
    malateCarrier->setId("malateCarrier");
    malateCarrier->setName("malate carrier");
    malateCarrier->setReversible(true);
  
    SpeciesReference* sr_aKetoglutarate_mito3_2=malateCarrier->createReactant();
    sr_aKetoglutarate_mito3_2->setSpecies(aKetoglutarate_mito3->getId());
    sr_aKetoglutarate_mito3_2->setId("sr_aKetoglutarate_mito3_2");
  
    SpeciesReference* sr_malate_cyt_2=malateCarrier->createReactant();
    sr_malate_cyt_2->setSpecies(malate_cyt->getId());
    sr_malate_cyt_2->setId("sr_malate_cyt_2");
  
    SpeciesReference* sr_aKetoglutarate_cyt_2=malateCarrier->createProduct();
    sr_aKetoglutarate_cyt_2->setSpecies(aKetoglutarate_cyt->getId());
    sr_aKetoglutarate_cyt_2->setId("sr_aKetoglutarate_cyt_2");
  
    SpeciesReference* sr_malate_mito3_2=malateCarrier->createProduct();
    sr_malate_mito3_2->setSpecies(malate_mito3->getId());
    sr_malate_mito3_2->setId("sr_malate_mito3_2");
  
  
    /////////// create the Layout
  
    LayoutModelPlugin* mplugin = static_cast<LayoutModelPlugin*>(model->getPlugin("layout"));  
    fail_unless(mplugin != NULL);
    Layout* layout=mplugin->createLayout();
  
    layout->setId("Layout_1");
    Dimensions dim(LN,2320.0,1000.0);
    layout->setDimensions(&dim);
  
  
    // create the CompartmentGlyph
  
    CompartmentGlyph* compartmentGlyph=layout->createCompartmentGlyph();
    compartmentGlyph->setId("CompartmentGlyph_1");
    compartmentGlyph->setCompartmentId(compartment->getId());
    BoundingBox bb=BoundingBox(LN,"bb_compartment",10,10,2300,980);
    compartmentGlyph->setBoundingBox(&bb);
  
    TextGlyph* tg=layout->createTextGlyph();
    tg->setId("TextGlyph_Hepatocyte");
    tg->setOriginOfTextId(compartment->getId());
    bb=BoundingBox(LN,"bb_tg_compartment",50,870,300,72);
    tg->setBoundingBox(&bb);
    tg->setGraphicalObjectId(compartmentGlyph->getId());
  
    CompartmentGlyph* mito1Glyph=layout->createCompartmentGlyph();
    mito1Glyph->setId("Mito1_Glyph");
    mito1Glyph->setCompartmentId(mito1->getId());
    bb=BoundingBox(LN,"bb_mito1",100,100,300,100);
    mito1Glyph->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_mito1");
    tg->setOriginOfTextId(mito1->getId());
    bb=BoundingBox(LN,"bb_tg_mito1",110,110,280,72);
    tg->setBoundingBox(&bb);
    tg->setGraphicalObjectId(mito1Glyph->getId());
  
  
    CompartmentGlyph* mito2Glyph=layout->createCompartmentGlyph();
    mito2Glyph->setId("Mito2_Glyph");
    mito2Glyph->setCompartmentId(mito2->getId());
    bb=BoundingBox(LN,"bb_mito2",200,650,300,100);
    mito2Glyph->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_mito2");
    tg->setOriginOfTextId(mito2->getId());
    bb=BoundingBox(LN,"bb_tg_mito2",210,660,280,72);
    tg->setBoundingBox(&bb);
    tg->setGraphicalObjectId(mito2Glyph->getId());
  
    CompartmentGlyph* mito3Glyph_2=layout->createCompartmentGlyph();
    mito3Glyph_2->setId("Mito3_Glyph_2");
    mito3Glyph_2->setCompartmentId(mito3->getId());
    bb=BoundingBox(LN,"bb_mito3_2",1470,30,820,536);
    mito3Glyph_2->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_mito3_2");
    tg->setOriginOfTextId(mito3->getId());
    bb=BoundingBox(LN,"bb_tg_mito3_2",1475,35,200,72);
    tg->setBoundingBox(&bb);
    tg->setGraphicalObjectId(mito3Glyph_2->getId());
  
  
  
  
    // create the SpeciesGlyphs
  
    // Cytosol
  
    // Malate cyt
    SpeciesGlyph* speciesGlyph_malate_cyt=layout->createSpeciesGlyph();
    speciesGlyph_malate_cyt->setId("SpeciesGlyph_malate_cyt");
    speciesGlyph_malate_cyt->setSpeciesId(malate_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_malate_cyt",580,280,240,36);
    speciesGlyph_malate_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_malate_cyt");
    bb=BoundingBox(LN,"bb_tg_malatate_cyt",590,280,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(malate_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_malate_cyt->getId());
  
    // Oxaloacetate cyt
    SpeciesGlyph* speciesGlyph_oxaloacetate_cyt=layout->createSpeciesGlyph();
    speciesGlyph_oxaloacetate_cyt->setId("SpeciesGlyph_oxaloacetate_cyt");
    speciesGlyph_oxaloacetate_cyt->setSpeciesId(oxaloacetate_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_oxaloacetate_cyt",580,480,240,36);
    speciesGlyph_oxaloacetate_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_oxaloacetate_cyt");
    bb=BoundingBox(LN,"bb_tg_oxaloacetate_cyt",590,480,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(oxaloacetate_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_oxaloacetate_cyt->getId());
  
    // Aspartate cyt
    SpeciesGlyph* speciesGlyph_aspartate_cyt=layout->createSpeciesGlyph();
    speciesGlyph_aspartate_cyt->setId("SpeciesGlyph_aspartate_cyt");
    speciesGlyph_aspartate_cyt->setSpeciesId(aspartate_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_aspartate_cyt",580,680,240,36);
    speciesGlyph_aspartate_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_aspartate_cyt");
    bb=BoundingBox(LN,"bb_tg_aspartate_cyt",590,680,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aspartate_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_aspartate_cyt->getId());
  
    // Glutamate cyt
    SpeciesGlyph* speciesGlyph_glutamate_cyt=layout->createSpeciesGlyph();
    speciesGlyph_glutamate_cyt->setId("SpeciesGlyph_glutamate_cyt");
    speciesGlyph_glutamate_cyt->setSpeciesId(glutamate_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_glutamate_cyt",800,610,240,36);
    speciesGlyph_glutamate_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_glutamate_cyt");
    bb=BoundingBox(LN,"bb_tg_glutamate_cyt",810,610,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(glutamate_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_glutamate_cyt->getId());
  
    // alpha-Ketoglutarate cyt
    SpeciesGlyph* speciesGlyph_aKetoglutarate_cyt=layout->createSpeciesGlyph();
    speciesGlyph_aKetoglutarate_cyt->setId("SpeciesGlyph_aKetoglutarate_cyt");
    speciesGlyph_aKetoglutarate_cyt->setSpeciesId(aKetoglutarate_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_aKetoglutarate_cyt",860,500,280,36);
    speciesGlyph_aKetoglutarate_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_aKetoglutarate_cyt");
    bb=BoundingBox(LN,"bb_tg_aKetoglutarate_cyt",870,500,260,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aKetoglutarate_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_aKetoglutarate_cyt->getId());
  
    // NAD+ cyt
    SpeciesGlyph* speciesGlyph_nad_cyt=layout->createSpeciesGlyph();
    speciesGlyph_nad_cyt->setId("SpeciesGlyph_nad_cyt");
    speciesGlyph_nad_cyt->setSpeciesId(nad_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_nad_cyt",520,350,100,24);
    speciesGlyph_nad_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_nad_cyt");
    bb=BoundingBox(LN,"bb_tg_nad_cyt",525,350,80,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(nad_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_nad_cyt->getId());
  
    // NADH cyt
    SpeciesGlyph* speciesGlyph_nadh_cyt=layout->createSpeciesGlyph();
    speciesGlyph_nadh_cyt->setId("SpeciesGlyph_nadh_cyt");
    speciesGlyph_nadh_cyt->setSpeciesId(nadh_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_nadh_cyt",520,430,100,24);
    speciesGlyph_nadh_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_nadh_cyt");
    bb=BoundingBox(LN,"bb_tg_nadh_cyt",525,430,80,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(nadh_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_nadh_cyt->getId());
  
    // H+ cyt
    SpeciesGlyph* speciesGlyph_h_cyt=layout->createSpeciesGlyph();
    speciesGlyph_h_cyt->setId("SpeciesGlyph_h_cyt");
    speciesGlyph_h_cyt->setSpeciesId(h_cyt->getId());
    bb=BoundingBox(LN,"bb_sg_h_cyt",430,430,40,24);
    speciesGlyph_h_cyt->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_h_cyt");
    bb=BoundingBox(LN,"bb_tg_h_cyt",435,430,30,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(h_cyt->getId());
    tg->setGraphicalObjectId(speciesGlyph_h_cyt->getId());
  
  
    // create the ReactionGlyphs
  
    ReactionGlyph* rg_malatedh_cyt=layout->createReactionGlyph();
    rg_malatedh_cyt->setId("rg_malatedh_cyt");
    rg_malatedh_cyt->setReactionId(malatedh_cyt->getId());
  
    Curve* curve=rg_malatedh_cyt->getCurve();
    LineSegment* ls=curve->createLineSegment();
    Point p(LN,700,381);
    ls->setStart(&p);
    p=Point(LN,700,415);
    ls->setEnd(&p);
  
    tg=layout->createTextGlyph();
    tg->setId("tg_rg_malaltedh_cyt");
    bb=BoundingBox(LN,"bb_tg_rg_malaltedh_cyt",700,385,210,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(malatedh_cyt->getId());
    tg->setGraphicalObjectId(rg_malatedh_cyt->getId());
  
  
    ReactionGlyph* rg_aspartateat_cyt=layout->createReactionGlyph();
    rg_aspartateat_cyt->setId("rg_aspartateat_cyt");
    rg_aspartateat_cyt->setReactionId(aspartateat_cyt->getId());
  
    curve=rg_aspartateat_cyt->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,700,581);
    ls->setStart(&p);
    p=Point(LN,700,615);
    ls->setEnd(&p);
  
    tg=layout->createTextGlyph();
    tg->setId("tg_rg_aspartateat_cyt");
    bb=BoundingBox(LN,"bb_tg_rg_aspartateat_cyt",440,585,260,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aspartateat_cyt->getId());
    tg->setGraphicalObjectId(rg_aspartateat_cyt->getId());
  
  
  
    // add the SpeciesReferenceGlyphs
  
    SpeciesReferenceGlyph* srg_malate_cyt_1=rg_malatedh_cyt->createSpeciesReferenceGlyph();
    srg_malate_cyt_1->setId("srg_malate_cyt_1");
    srg_malate_cyt_1->setSpeciesGlyphId(speciesGlyph_malate_cyt->getId());
    srg_malate_cyt_1->setSpeciesReferenceId(sr_malate_cyt->getId());
    srg_malate_cyt_1->setRole(SPECIES_ROLE_SUBSTRATE);
  
    ls=srg_malate_cyt_1->createLineSegment();
    p=Point(LN,700,381);
    ls->setStart(&p);
    p=Point(LN,700,316);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_nad_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
    srg_nad_cyt->setId("srg_nad_cyt");
    srg_nad_cyt->setSpeciesGlyphId(speciesGlyph_nad_cyt->getId());
    srg_nad_cyt->setSpeciesReferenceId(sr_nad_cyt->getId());
    srg_nad_cyt->setRole(SPECIES_ROLE_SUBSTRATE);
  
    CubicBezier* cb=srg_nad_cyt->createCubicBezier();
    p=Point(LN,700,381);
    cb->setStart(&p);
    p=Point(LN,700,362);
    cb->setBasePoint1(&p);
    p=Point(LN,700,362);
    cb->setBasePoint2(&p);
    p=Point(LN,620,362);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_oxaloacetate_cyt_1=rg_malatedh_cyt->createSpeciesReferenceGlyph();
    srg_oxaloacetate_cyt_1->setId("srg_oxaloacetate_cyt_1");
    srg_oxaloacetate_cyt_1->setSpeciesGlyphId(speciesGlyph_oxaloacetate_cyt->getId());
    srg_oxaloacetate_cyt_1->setSpeciesReferenceId(sr_oxaloacetate_cyt_1->getId());
    srg_oxaloacetate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_oxaloacetate_cyt_1->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,700,415);
    ls->setStart(&p);
    p=Point(LN,700,480);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_nadh_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
    srg_nadh_cyt->setId("srg_nadh_cyt");
    srg_nadh_cyt->setSpeciesGlyphId(speciesGlyph_nadh_cyt->getId());
    srg_nadh_cyt->setSpeciesReferenceId(sr_nadh_cyt->getId());
    srg_nadh_cyt->setRole(SPECIES_ROLE_PRODUCT);
  
    cb=srg_nadh_cyt->createCubicBezier();
    p=Point(LN,700,415);
    cb->setStart(&p);
    p=Point(LN,700,442);
    cb->setBasePoint1(&p);
    p=Point(LN,700,442);
    cb->setBasePoint2(&p);
    p=Point(LN,620,442);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_h_cyt=rg_malatedh_cyt->createSpeciesReferenceGlyph();
    srg_h_cyt->setId("srg_h_cyt");
    srg_h_cyt->setSpeciesGlyphId(speciesGlyph_h_cyt->getId());
    srg_h_cyt->setSpeciesReferenceId(sr_h_cyt->getId());
    srg_h_cyt->setRole(SPECIES_ROLE_PRODUCT);
  
    cb=srg_h_cyt->createCubicBezier();
    p=Point(LN,700,415); 
    cb->setStart(&p);
    p=Point(LN,570,415);
    cb->setBasePoint1(&p);
    p=Point(LN,570,415);
    cb->setBasePoint2(&p);
    p=Point(LN,470,430);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_oxaloacetate_cyt_2=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
    srg_oxaloacetate_cyt_2->setId("srg_oxaloacetate_cyt_2");
    srg_oxaloacetate_cyt_2->setSpeciesGlyphId(speciesGlyph_oxaloacetate_cyt->getId());
    srg_oxaloacetate_cyt_2->setSpeciesReferenceId(sr_oxaloacetate_cyt_2->getId());
    srg_oxaloacetate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_oxaloacetate_cyt_2->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,700,581);
    ls->setStart(&p);
    p=Point(LN,700,516);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_glutamate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
    srg_glutamate_cyt_1->setId("srg_glutamate_cyt_1");
    srg_glutamate_cyt_1->setSpeciesGlyphId(speciesGlyph_glutamate_cyt->getId());
    srg_glutamate_cyt_1->setSpeciesReferenceId(sr_glutamate_cyt_1->getId());
    srg_glutamate_cyt_1->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_glutamate_cyt_1->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,700,581);
    cb->setStart(&p);
    p=Point(LN,750,581);
    cb->setBasePoint1(&p);
    p=Point(LN,750,628);
    cb->setBasePoint2(&p);
    p=Point(LN,800,628);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_aspartate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
    srg_aspartate_cyt_1->setId("srg_aspartate_cyt_1");
    srg_aspartate_cyt_1->setSpeciesGlyphId(speciesGlyph_aspartate_cyt->getId());
    srg_aspartate_cyt_1->setSpeciesReferenceId(sr_aspartate_cyt_1->getId());
    srg_aspartate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_aspartate_cyt_1->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,700,615);
    ls->setStart(&p);
    p=Point(LN,700,680);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_aKetoglutarate_cyt_1=rg_aspartateat_cyt->createSpeciesReferenceGlyph();
    srg_aKetoglutarate_cyt_1->setId("srg_aKetoglutaratecyt_1");
    srg_aKetoglutarate_cyt_1->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_cyt->getId());
    srg_aKetoglutarate_cyt_1->setSpeciesReferenceId(sr_aKetoglutarate_cyt_1->getId());
    srg_aKetoglutarate_cyt_1->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_aKetoglutarate_cyt_1->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,700,615);
    cb->setStart(&p);
    p=Point(LN,790,615);
    cb->setBasePoint1(&p);
    p=Point(LN,790,515);
    cb->setBasePoint2(&p);
    p=Point(LN,860,515);
    cb->setEnd(&p);
  
  
    // Malate mito3
    SpeciesGlyph* speciesGlyph_malate_mito3=layout->createSpeciesGlyph();
    speciesGlyph_malate_mito3->setId("SpeciesGlyph_malate_mito3");
    speciesGlyph_malate_mito3->setSpeciesId(malate_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_malate_mito3",1850,80,240,36);
    speciesGlyph_malate_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_malate_mito3");
    bb=BoundingBox(LN,"bb_tg_malatate_mito3",1860,80,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(malate_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_malate_mito3->getId());
  
    // Oxaloacetate mito3
    SpeciesGlyph* speciesGlyph_oxaloacetate_mito3=layout->createSpeciesGlyph();
    speciesGlyph_oxaloacetate_mito3->setId("SpeciesGlyph_oxaloacetate_mito3");
    speciesGlyph_oxaloacetate_mito3->setSpeciesId(oxaloacetate_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_oxaloacetate_mito3",1850,280,240,36);
    speciesGlyph_oxaloacetate_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_oxaloacetate_mito3");
    bb=BoundingBox(LN,"bb_tg_oxaloacetate_mito3",1860,280,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(oxaloacetate_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_oxaloacetate_mito3->getId());
  
    // Aspartate mito3
    SpeciesGlyph* speciesGlyph_aspartate_mito3=layout->createSpeciesGlyph();
    speciesGlyph_aspartate_mito3->setId("SpeciesGlyph_aspartate_mito3");
    speciesGlyph_aspartate_mito3->setSpeciesId(aspartate_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_aspartate_mito3",1850,480,240,36);
    speciesGlyph_aspartate_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_aspartate_mito3");
    bb=BoundingBox(LN,"bb_tg_aspartate_mito3",1860,480,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aspartate_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_aspartate_mito3->getId());
  
    // Glutamate mito3
    SpeciesGlyph* speciesGlyph_glutamate_mito3=layout->createSpeciesGlyph();
    speciesGlyph_glutamate_mito3->setId("SpeciesGlyph_glutamate_mito3");
    speciesGlyph_glutamate_mito3->setSpeciesId(glutamate_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_glutamate_mito3",1550,430,240,36);
    speciesGlyph_glutamate_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_glutamate_mito3");
    bb=BoundingBox(LN,"bb_tg_glutamate_mito3",1560,430,220,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(glutamate_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_glutamate_mito3->getId());
  
    // alpha-Ketoglutarate mito3
    SpeciesGlyph* speciesGlyph_aKetoglutarate_mito3=layout->createSpeciesGlyph();
    speciesGlyph_aKetoglutarate_mito3->setId("SpeciesGlyph_aKetoglutarate_mito3");
    speciesGlyph_aKetoglutarate_mito3->setSpeciesId(aKetoglutarate_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_aKetoglutarate_mito3",1530,300,280,36);
    speciesGlyph_aKetoglutarate_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_aKetoglutarate_mito3");
    bb=BoundingBox(LN,"bb_tg_aKetoglutarate_mito3",1540,300,260,36);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aKetoglutarate_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_aKetoglutarate_mito3->getId());
  
    // NAD+ mito3
    SpeciesGlyph* speciesGlyph_nad_mito3=layout->createSpeciesGlyph();
    speciesGlyph_nad_mito3->setId("SpeciesGlyph_nad_mito3");
    speciesGlyph_nad_mito3->setSpeciesId(nad_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_nad_mito3",2050,150,100,24);
    speciesGlyph_nad_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_nad_mito3");
    bb=BoundingBox(LN,"bb_tg_nad_mito3",2055,150,80,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(nad_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_nad_mito3->getId());
  
    // NADH mito3
    SpeciesGlyph* speciesGlyph_nadh_mito3=layout->createSpeciesGlyph();
    speciesGlyph_nadh_mito3->setId("SpeciesGlyph_nadh_mito3");
    speciesGlyph_nadh_mito3->setSpeciesId(nadh_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_nadh_mito3",2050,230,100,24);
    speciesGlyph_nadh_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_nadh_mito3");
    bb=BoundingBox(LN,"bb_tg_nadh_mito3",2055,230,80,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(nadh_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_nadh_mito3->getId());
  
    // H+ mito3
    SpeciesGlyph* speciesGlyph_h_mito3=layout->createSpeciesGlyph();
    speciesGlyph_h_mito3->setId("SpeciesGlyph_h_mito3");
    speciesGlyph_h_mito3->setSpeciesId(h_mito3->getId());
    bb=BoundingBox(LN,"bb_sg_h_mito3",2200,230,40,24);
    speciesGlyph_h_mito3->setBoundingBox(&bb);
  
    tg=layout->createTextGlyph();
    tg->setId("TextGlyph_h_mito3");
    bb=BoundingBox(LN,"bb_tg_h_mito3",2205,230,30,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(h_mito3->getId());
    tg->setGraphicalObjectId(speciesGlyph_h_mito3->getId());
  
  
    // create the ReactionGlyphs
  
    ReactionGlyph* rg_malatedh_mito3=layout->createReactionGlyph();
    rg_malatedh_mito3->setId("rg_malatedh_mito3");
    rg_malatedh_mito3->setReactionId(malatedh_mito3->getId());
  
    curve=rg_malatedh_mito3->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1970,181);
    ls->setStart(&p);
    p=Point(LN,1970,215);
    ls->setEnd(&p);
  
    tg=layout->createTextGlyph();
    tg->setId("tg_rg_malatedh_mito3");
    bb=BoundingBox(LN,"bb_tg_rg_malatedh_mito3",1740,185,220,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(malatedh_mito3->getId());
    tg->setGraphicalObjectId(rg_malatedh_mito3->getId());
  
    ReactionGlyph* rg_aspartateat_mito3=layout->createReactionGlyph();
    rg_aspartateat_mito3->setId("rg_aspartateat_mito3");
    rg_aspartateat_mito3->setReactionId(aspartateat_mito3->getId());
  
    curve=rg_aspartateat_mito3->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1970,381);
    ls->setStart(&p);
    p=Point(LN,1970,415);
    ls->setEnd(&p);
  
    tg=layout->createTextGlyph();
    tg->setId("tg_rg_aspartateat_mito3");
    bb=BoundingBox(LN,"bb_tg_rg_aspartateat_mito3",1970,385,260,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aspartateat_mito3->getId());
    tg->setGraphicalObjectId(rg_aspartateat_mito3->getId());
  
  
    // add the SpeciesReferenceGlyphs
  
    SpeciesReferenceGlyph* srg_malate_mito3_1=rg_malatedh_mito3->createSpeciesReferenceGlyph();
    srg_malate_mito3_1->setId("srg_malate_mito3_1");
    srg_malate_mito3_1->setSpeciesGlyphId(speciesGlyph_malate_mito3->getId());
    srg_malate_mito3_1->setSpeciesReferenceId(sr_malate_mito3->getId());
    srg_malate_mito3_1->setRole(SPECIES_ROLE_SUBSTRATE);
  
    ls=srg_malate_mito3_1->createLineSegment();
    p=Point(LN,1970,181);
    ls->setStart(&p);
    p=Point(LN,1970,116);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_nad_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
    srg_nad_mito3->setId("srg_nad_mito3");
    srg_nad_mito3->setSpeciesGlyphId(speciesGlyph_nad_mito3->getId());
    srg_nad_mito3->setSpeciesReferenceId(sr_nad_mito3->getId());
    srg_nad_mito3->setRole(SPECIES_ROLE_SUBSTRATE);
  
    cb=srg_nad_mito3->createCubicBezier();
    p=Point(LN,1970,181);
    cb->setStart(&p);
    p=Point(LN,1970,162);
    cb->setBasePoint1(&p);
    p=Point(LN,1970,162);
    cb->setBasePoint2(&p);
    p=Point(LN,2050,162);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_oxaloacetate_mito3_1=rg_malatedh_mito3->createSpeciesReferenceGlyph();
    srg_oxaloacetate_mito3_1->setId("srg_oxaloacetate_mito3_1");
    srg_oxaloacetate_mito3_1->setSpeciesGlyphId(speciesGlyph_oxaloacetate_mito3->getId());
    srg_oxaloacetate_mito3_1->setSpeciesReferenceId(sr_oxaloacetate_mito3_1->getId());
    srg_oxaloacetate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_oxaloacetate_mito3_1->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1970,215);
    ls->setStart(&p);
    p=Point(LN,1970,280);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_nadh_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
    srg_nadh_mito3->setId("srg_nadh_mito3");
    srg_nadh_mito3->setSpeciesGlyphId(speciesGlyph_nadh_mito3->getId());
    srg_nadh_mito3->setSpeciesReferenceId(sr_nadh_mito3->getId());
    srg_nadh_mito3->setRole(SPECIES_ROLE_PRODUCT);
  
    cb=srg_nadh_mito3->createCubicBezier();
    p=Point(LN,1970,215);
    cb->setStart(&p);
    p=Point(LN,1970,242);
    cb->setBasePoint1(&p);
    p=Point(LN,1970,242);
    cb->setBasePoint2(&p);
    p=Point(LN,2050,242);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_h_mito3=rg_malatedh_mito3->createSpeciesReferenceGlyph();
    srg_h_mito3->setId("srg_h_mito3");
    srg_h_mito3->setSpeciesGlyphId(speciesGlyph_h_mito3->getId());
    srg_h_mito3->setSpeciesReferenceId(sr_h_mito3->getId());
    srg_h_mito3->setRole(SPECIES_ROLE_PRODUCT);
  
    cb=srg_h_mito3->createCubicBezier();
    p=Point(LN,1970,215);
    cb->setStart(&p);
    p=Point(LN,2100,215);
    cb->setBasePoint1(&p);
    p=Point(LN,2100,215);
    cb->setBasePoint2(&p);
    p=Point(LN,2200,230);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_oxaloacetate_mito3_2=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
    srg_oxaloacetate_mito3_2->setId("srg_oxaloacetate_mito3_2");
    srg_oxaloacetate_mito3_2->setSpeciesGlyphId(speciesGlyph_oxaloacetate_mito3->getId());
    srg_oxaloacetate_mito3_2->setSpeciesReferenceId(sr_oxaloacetate_mito3_2->getId());
    srg_oxaloacetate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_oxaloacetate_mito3_2->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1970,381);
    ls->setStart(&p);
    p=Point(LN,1970,316);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_glutamate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
    srg_glutamate_mito3_1->setId("srg_glutamate_mito3_1");
    srg_glutamate_mito3_1->setSpeciesGlyphId(speciesGlyph_glutamate_mito3->getId());
    srg_glutamate_mito3_1->setSpeciesReferenceId(sr_glutamate_mito3_1->getId());
    srg_glutamate_mito3_1->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_glutamate_mito3_1->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1970,381);
    cb->setStart(&p);
    p=Point(LN,1880,381);
    cb->setBasePoint1(&p);
    p=Point(LN,1880,448);
    cb->setBasePoint2(&p);
    p=Point(LN,1790,448);
    cb->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_aspartate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
    srg_aspartate_mito3_1->setId("srg_aspartate_mito3_1");
    srg_aspartate_mito3_1->setSpeciesGlyphId(speciesGlyph_aspartate_mito3->getId());
    srg_aspartate_mito3_1->setSpeciesReferenceId(sr_aspartate_mito3_1->getId());
    srg_aspartate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_aspartate_mito3_1->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1970,415);
    ls->setStart(&p);
    p=Point(LN,1970,480);
    ls->setEnd(&p);
  
    SpeciesReferenceGlyph* srg_aKetoglutarate_mito3_1=rg_aspartateat_mito3->createSpeciesReferenceGlyph();
    srg_aKetoglutarate_mito3_1->setId("srg_aKetoglutaratemito3_1");
    srg_aKetoglutarate_mito3_1->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_mito3->getId());
    srg_aKetoglutarate_mito3_1->setSpeciesReferenceId(sr_aKetoglutarate_mito3_1->getId());
    srg_aKetoglutarate_mito3_1->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_aKetoglutarate_mito3_1->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1970,415);
    cb->setStart(&p);
    p=Point(LN,1880,415);
    cb->setBasePoint1(&p);
    p=Point(LN,1880,315);
    cb->setBasePoint2(&p);
    p=Point(LN,1810,315);
    cb->setEnd(&p);
  
    // add the transport reaction glyphs
  
    ReactionGlyph* rg_aspartateCarrier=layout->createReactionGlyph();
    rg_aspartateCarrier->setId("rg_aspartateCarrier");
    rg_aspartateCarrier->setReactionId(aspartateCarrier->getId());
  
    curve=rg_aspartateCarrier->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1420,530);
    ls->setStart(&p);
    p=Point(LN,1360,550);
    ls->setEnd(&p);
  
    tg=layout->createTextGlyph();
    tg->setId("tg_rg_aspartateCarrier");
    bb=BoundingBox(LN,"bb_tg_rg_aspartateCarrier",1380,500,160,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(aspartateCarrier->getId());
    tg->setGraphicalObjectId(rg_aspartateCarrier->getId());
  
  
    ReactionGlyph* rg_malateCarrier=layout->createReactionGlyph();
    rg_malateCarrier->setId("rg_malateCarrier");
    rg_malateCarrier->setReactionId(malateCarrier->getId());
  
    curve=rg_malateCarrier->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1420,320);
    ls->setStart(&p);
    p=Point(LN,1360,340);
    ls->setEnd(&p);
  
    tg=layout->createTextGlyph();
    tg->setId("tg_rg_malateCarrier");
    bb=BoundingBox(LN,"bb_tg_rg_malateCarrier",1360,330,140,24);
    tg->setBoundingBox(&bb);
    tg->setOriginOfTextId(malateCarrier->getId());
    tg->setGraphicalObjectId(rg_malateCarrier->getId());
  
  
  
    // add the SpeciesReferenceGlyphs for the transporters
  
    SpeciesReferenceGlyph* srg_aKetoglutarate_mito3_2=rg_malateCarrier->createSpeciesReferenceGlyph();
    srg_aKetoglutarate_mito3_2->setId("srg_aKetoglutarate_mito3_2");
    srg_aKetoglutarate_mito3_2->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_mito3->getId());
    srg_aKetoglutarate_mito3_2->setSpeciesReferenceId(sr_aKetoglutarate_mito3_2->getId());
    srg_aKetoglutarate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_aKetoglutarate_mito3_2->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1420,320);
    ls->setStart(&p);
    p=Point(LN,1530,318);
    ls->setEnd(&p);
  
  
    SpeciesReferenceGlyph* srg_aKetoglutarate_cyt_2=rg_malateCarrier->createSpeciesReferenceGlyph();
    srg_aKetoglutarate_cyt_2->setId("srg_aKetoglutarate_cyt_2");
    srg_aKetoglutarate_cyt_2->setSpeciesGlyphId(speciesGlyph_aKetoglutarate_cyt->getId());
    srg_aKetoglutarate_cyt_2->setSpeciesReferenceId(sr_aKetoglutarate_cyt_2->getId());
    srg_aKetoglutarate_cyt_2->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_aKetoglutarate_cyt_2->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1360,340);
    ls->setStart(&p);
    p=Point(LN,1140,518);
    ls->setEnd(&p);
  
  
    SpeciesReferenceGlyph* srg_malate_cyt_2=rg_malateCarrier->createSpeciesReferenceGlyph();
    srg_malate_cyt_2->setId("srg_malate_cyt_2");
    srg_malate_cyt_2->setSpeciesGlyphId(speciesGlyph_malate_cyt->getId());
    srg_malate_cyt_2->setSpeciesReferenceId(sr_malate_cyt_2->getId());
    srg_malate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_malate_cyt_2->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1420,320);
    cb->setStart(&p);
    p=Point(LN,1390,250);
    cb->setBasePoint1(&p);
    p=Point(LN,1390,250);
    cb->setBasePoint2(&p);
    p=Point(LN,820,298);
    cb->setEnd(&p);
  
  
    SpeciesReferenceGlyph* srg_malate_mito3_2=rg_malateCarrier->createSpeciesReferenceGlyph();
    srg_malate_mito3_2->setId("srg_malate_mito3_2");
    srg_malate_mito3_2->setSpeciesGlyphId(speciesGlyph_malate_mito3->getId());
    srg_malate_mito3_2->setSpeciesReferenceId(sr_malate_mito3_2->getId());
    srg_malate_mito3_2->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_malate_mito3_2->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1360,340);
    cb->setStart(&p);
    p=Point(LN,1390,150);
    cb->setBasePoint1(&p);
    p=Point(LN,1390,150);
    cb->setBasePoint2(&p);
    p=Point(LN,1850,98);
    cb->setEnd(&p);
  
  
  
  
  
  
    SpeciesReferenceGlyph* srg_aspartate_mito3_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
    srg_aspartate_mito3_2->setId("srg_aspartate_mito3_2");
    srg_aspartate_mito3_2->setSpeciesGlyphId(speciesGlyph_aspartate_mito3->getId());
    srg_aspartate_mito3_2->setSpeciesReferenceId(sr_aspartate_mito3_2->getId());
    srg_aspartate_mito3_2->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_aspartate_mito3_2->getCurve();
    ls=curve->createLineSegment();
    p=Point(LN,1420,530);
    ls->setStart(&p);
    p=Point(LN,1850,498);
    ls->setEnd(&p);
  
  
    SpeciesReferenceGlyph* srg_aspartate_cyt_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
    srg_aspartate_cyt_2->setId("srg_aspartate_cyt_2");
    srg_aspartate_cyt_2->setSpeciesGlyphId(speciesGlyph_aspartate_cyt->getId());
    srg_aspartate_cyt_2->setSpeciesReferenceId(sr_aspartate_cyt_2->getId());
    srg_aspartate_cyt_2->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_aspartate_cyt_2->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1360,550);
    cb->setStart(&p);
    p=Point(LN,1390,698);
    cb->setBasePoint1(&p);
    p=Point(LN,1390,698);
    cb->setBasePoint2(&p);
    p=Point(LN,820,698);
    cb->setEnd(&p);
  
  
    SpeciesReferenceGlyph* srg_glutamate_cyt_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
    srg_glutamate_cyt_2->setId("srg_glutamate_cyt_2");
    srg_glutamate_cyt_2->setSpeciesGlyphId(speciesGlyph_glutamate_cyt->getId());
    srg_glutamate_cyt_2->setSpeciesReferenceId(sr_glutamate_cyt_2->getId());
    srg_glutamate_cyt_2->setRole(SPECIES_ROLE_SUBSTRATE);
  
    curve=srg_glutamate_cyt_2->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1420,530);
    cb->setStart(&p);
    p=Point(LN,1390,648);
    cb->setBasePoint1(&p);
    p=Point(LN,1390,648);
    cb->setBasePoint2(&p);
    p=Point(LN,1050,628);
    cb->setEnd(&p);
  
  
    SpeciesReferenceGlyph* srg_glutamate_mito3_2=rg_aspartateCarrier->createSpeciesReferenceGlyph();
    srg_glutamate_mito3_2->setId("srg_glutamate_mito3_2");
    srg_glutamate_mito3_2->setSpeciesGlyphId(speciesGlyph_glutamate_mito3->getId());
    srg_glutamate_mito3_2->setSpeciesReferenceId(sr_glutamate_mito3_2->getId());
    srg_glutamate_mito3_2->setRole(SPECIES_ROLE_PRODUCT);
  
    curve=srg_glutamate_mito3_2->getCurve();
    cb=curve->createCubicBezier();
    p=Point(LN,1360,550);
    cb->setStart(&p);
    p=Point(LN,1390,448);
    cb->setBasePoint1(&p);
    p=Point(LN,1390,448);
    cb->setBasePoint2(&p);
    p=Point(LN,1550,448);
    cb->setEnd(&p);
  
    fail_unless(LN != NULL);
      
    SBMLWriter writer;    
    //bool result=writer.write(document,"example6.xml");
    //std::cout << "result of writing: " << result << std::endl; 
    char* writtenContent=writer.writeToString(document);
    //std::cout << writtenContent << std::endl;
  
    XMLInputStream *stream2 = new XMLInputStream(writtenContent,false);
    XMLNode *node2 = new XMLNode(*stream2);
    fail_unless(node->getName()=="sbml");
    fail_unless(node->getChild("model").getName()=="model");
    fail_unless(node->getChild("model").getChild("annotation").getName()=="annotation");
    fail_unless(node->getChild("model").getChild("annotation").getChild("listOfLayouts").getName()=="listOfLayouts");
    XMLNode& listOfLayouts1 = node->getChild("model").getChild("annotation").getChild("listOfLayouts");  
    fail_unless(listOfLayouts1.getName()=="listOfLayouts");
    
    fail_unless(node2->getName()=="sbml");
    fail_unless(node2->getChild("model").getName()=="model");
    fail_unless(node2->getChild("model").getChild("annotation").getName()=="annotation");
    XMLNode& listOfLayouts2= node2->getChild("model").getChild("annotation").getChild("listOfLayouts");
    fail_unless(listOfLayouts2.getName()=="listOfLayouts");
  
    // until the sbml element gets a namespace, we only compare the listOfLayouts element and all its children.
    fail_unless(listOfLayouts1.equals(listOfLayouts2));
    
    free(writtenContent);
    delete document;
    delete node;
    delete node2;
    delete stream2;
    delete stream;
  }
  END_TEST
  
    Suite *
  create_suite_LayoutWriting (void)
  {
    Suite *suite = suite_create("LayoutWriting");
    TCase *tcase = tcase_create("LayoutWriting");
  
    tcase_add_checked_fixture( tcase,
        LayoutWritingTest_setup,
        LayoutWritingTest_teardown );
  
  
    tcase_add_test( tcase, test_LayoutWriting                            );
    suite_add_tcase(suite, tcase);
  
    return suite;
  }
  
  
  
  END_C_DECLS
  