/**
 * Filename    : TestSBMLHandler.cpp
 * Description : Unit tests for SBMLHandler with respect the the layout extension.
 * Organization: European Media Laboratories Research gGmbH
 * Created     : 2005-10-11
 *
 * Copyright 2005 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 <common/common.h>
#include <common/extern.h>

#include "sbml/SBMLReader.h"
#include "sbml/SBMLDocument.h"
#include "sbml/Model.h"
#include "sbml/Reaction.h"
#include "sbml/Compartment.h"
#include "sbml/Species.h"
#include "sbml/SpeciesReference.h"

#include "sbml/layout/Layout.h"
#include "sbml/layout/Dimensions.h"
#include "sbml/layout/CompartmentGlyph.h"
#include "sbml/layout/SpeciesGlyph.h"
#include "sbml/layout/ReactionGlyph.h"
#include "sbml/layout/TextGlyph.h"
#include "sbml/layout/LineSegment.h"
#include "sbml/layout/CubicBezier.h"

#include <check.h>


BEGIN_C_DECLS

#define s "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\
<sbml xmlns=\"http://www.sbml.org/sbml/level2\" level=\"2\" version=\"1\">\
  <model id=\"TestModel with modifiers\">\
          <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=\"400\" height=\"230\">\
      </dimensions>\
      <listOfCompartmentGlyphs>\
        <compartmentGlyph id=\"CompartmentGlyph_1\" compartment=\"Yeast\">\
          <boundingBox id=\"bb1\">\
            <position x=\"5\" y=\"5\">\
            </position>\
            <dimensions width=\"390\" height=\"220\">\
            </dimensions>\
          </boundingBox>\
        </compartmentGlyph>\
      </listOfCompartmentGlyphs>\
      <listOfSpeciesGlyphs>\
        <speciesGlyph id=\"SpeciesGlyph_Glucose\" species=\"Glucose\">\
          <boundingBox id=\"bb2\">\
            <position x=\"105\" y=\"20\">\
            </position>\
            <dimensions width=\"130\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </speciesGlyph>\
        <speciesGlyph id=\"SpeciesGlyph_G6P\" species=\"Glucose-6-phosphate\">\
          <boundingBox id=\"bb5\">\
            <position x=\"50\" y=\"190\">\
            </position>\
            <dimensions width=\"270\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </speciesGlyph>\
        <speciesGlyph id=\"SpeciesGlyph_ATP\" species=\"ATP\">\
          <boundingBox id=\"bb3\">\
            <position x=\"270\" y=\"70\">\
            </position>\
            <dimensions width=\"80\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </speciesGlyph>\
        <speciesGlyph id=\"glyph_ADP\" species=\"ADP\">\
          <boundingBox id=\"bb4\">\
            <position x=\"270\" y=\"140\">\
            </position>\
            <dimensions width=\"80\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </speciesGlyph>\
        <speciesGlyph id=\"SpeciesGlyph_Pi\" species=\"Pi\">\
          <boundingBox id=\"bb6\">\
            <position x=\"50\" y=\"100\">\
            </position>\
            <dimensions width=\"60\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </speciesGlyph>\
      </listOfSpeciesGlyphs>\
      <listOfReactionGlyphs>\
        <reactionGlyph id=\"glyph_Hexokinase\" reaction=\"Hexokinase\">\
          <curve>\
            <listOfCurveSegments>\
              <curveSegment xsi:type=\"LineSegment\">\
                <start x=\"170\" y=\"100\">\
                </start>\
                <end x=\"170\" y=\"130\">\
                </end>\
              </curveSegment>\
            </listOfCurveSegments>\
          </curve>\
          <listOfSpeciesReferenceGlyphs>\
            <speciesReferenceGlyph id=\"SpeciesReferenceGlyph_Glucose\" speciesReference=\"SpeciesReference_Glucose\" speciesGlyph=\"SpeciesGlyph_Glucose\" role=\"substrate\">\
              <curve>\
                <listOfCurveSegments>\
                  <curveSegment xsi:type=\"LineSegment\">\
                    <start x=\"170\" y=\"100\">\
                    </start>\
                    <end x=\"170\" y=\"50\">\
                    </end>\
                  </curveSegment>\
                </listOfCurveSegments>\
              </curve>\
            </speciesReferenceGlyph>\
            <speciesReferenceGlyph id=\"SpeciesReferenceGlyph_ATP\" speciesReference=\"SpeciesReference_ATP\" speciesGlyph=\"SpeciesGlyph_ATP\" role=\"sidesubstrate\">\
              <curve>\
                <listOfCurveSegments>\
                  <curveSegment xsi:type=\"CubicBezier\">\
                    <start x=\"170\" y=\"100\">\
                    </start>\
                    <end x=\"260\" y=\"80\">\
                    </end>\
                    <basePoint1 x=\"170\" y=\"80\">\
                    </basePoint1>\
                    <basePoint2 x=\"170\" y=\"80\">\
                    </basePoint2>\
                  </curveSegment>\
                </listOfCurveSegments>\
              </curve>\
            </speciesReferenceGlyph>\
            <speciesReferenceGlyph id=\"SpeciesReferenceGlyph_G6P_1\" speciesReference=\"SpeciesReference_G6P\" speciesGlyph=\"SpeciesGlyph_G6P\" role=\"product\">\
              <curve>\
                <listOfCurveSegments>\
                  <curveSegment xsi:type=\"LineSegment\">\
                    <start x=\"170\" y=\"130\">\
                    </start>\
                    <end x=\"170\" y=\"180\">\
                    </end>\
                  </curveSegment>\
                </listOfCurveSegments>\
              </curve>\
            </speciesReferenceGlyph>\
            <speciesReferenceGlyph id=\"SpeciesReferenceGlyph_ADP\" speciesReference=\"SpeciesReference_ADP\" speciesGlyph=\"glyph_ADP\" role=\"sideproduct\">\
              <curve>\
                <listOfCurveSegments>\
                  <curveSegment xsi:type=\"CubicBezier\">\
                    <start x=\"170\" y=\"130\">\
                    </start>\
                    <end x=\"260\" y=\"150\">\
                    </end>\
                    <basePoint1 x=\"170\" y=\"150\">\
                    </basePoint1>\
                    <basePoint2 x=\"170\" y=\"150\">\
                    </basePoint2>\
                  </curveSegment>\
                </listOfCurveSegments>\
              </curve>\
            </speciesReferenceGlyph>\
            <speciesReferenceGlyph id=\"SpeciesReferenceGlyph_G6P_2\" speciesReference=\"ModifierSpeciesReference_G6P\" speciesGlyph=\"SpeciesGlyph_G6P\" role=\"inhibitor\">\
              <curve>\
                <listOfCurveSegments>\
                  <curveSegment xsi:type=\"CubicBezier\">\
                    <start x=\"45\" y=\"200\">\
                    </start>\
                    <end x=\"165\" y=\"120\">\
                    </end>\
                    <basePoint1 x=\"0\" y=\"200\">\
                    </basePoint1>\
                    <basePoint2 x=\"0\" y=\"120\">\
                    </basePoint2>\
                  </curveSegment>\
                </listOfCurveSegments>\
              </curve>\
            </speciesReferenceGlyph>\
            <speciesReferenceGlyph id=\"SpeciesReferenceGlyph_PI\" speciesReference=\"ModifierSpeciesReference_Pi\" speciesGlyph=\"SpeciesGlyph_Pi\" role=\"activator\">\
              <curve>\
                <listOfCurveSegments>\
                  <curveSegment xsi:type=\"CubicBezier\">\
                    <start x=\"115\" y=\"110\">\
                    </start>\
                    <end x=\"165\" y=\"110\">\
                    </end>\
                    <basePoint1 x=\"140\" y=\"110\">\
                    </basePoint1>\
                    <basePoint2 x=\"140\" y=\"110\">\
                    </basePoint2>\
                  </curveSegment>\
                </listOfCurveSegments>\
              </curve>\
            </speciesReferenceGlyph>\
          </listOfSpeciesReferenceGlyphs>\
        </reactionGlyph>\
      </listOfReactionGlyphs>\
      <listOfTextGlyphs>\
        <textGlyph id=\"TextGlyph_Glucose\" graphicalObject=\"SpeciesGlyph_Glucose\" originOfText=\"Glucose\">\
          <boundingBox id=\"bbA\">\
            <position x=\"115\" y=\"20\">\
            </position>\
            <dimensions width=\"110\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </textGlyph>\
        <textGlyph id=\"TextGlyph_G6P\" graphicalObject=\"SpeciesGlyph_G6P\" originOfText=\"Glucose-6-phosphate\">\
          <boundingBox id=\"bbD\">\
            <position x=\"60\" y=\"190\">\
            </position>\
            <dimensions width=\"250\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </textGlyph>\
        <textGlyph id=\"TextGlyph_ATP\" graphicalObject=\"SpeciesGlyph_ATP\" originOfText=\"ATP\">\
          <boundingBox id=\"bbB\">\
            <position x=\"280\" y=\"70\">\
            </position>\
            <dimensions width=\"60\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </textGlyph>\
        <textGlyph id=\"TextGlyph_ADP\" graphicalObject=\"glyph_ADP\" originOfText=\"ADP\">\
          <boundingBox id=\"bbC\">\
            <position x=\"280\" y=\"140\">\
            </position>\
            <dimensions width=\"60\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </textGlyph>\
        <textGlyph id=\"TextGlyph_PI\" graphicalObject=\"SpeciesGlyph_Pi\" originOfText=\"Pi\">\
          <boundingBox id=\"bbE\">\
            <position x=\"60\" y=\"100\">\
            </position>\
            <dimensions width=\"40\" height=\"20\">\
            </dimensions>\
          </boundingBox>\
        </textGlyph>\
      </listOfTextGlyphs>\
    </layout>\
  </listOfLayouts>\
 </annotation>\
    <listOfCompartments>\
      <compartment id=\"Yeast\"/>\
    </listOfCompartments>\
    <listOfSpecies>\
      <species id=\"Glucose\" compartment=\"Yeast\"/>\
      <species id=\"Glucose-6-phosphate\" compartment=\"Yeast\"/>\
      <species id=\"ATP\" compartment=\"Yeast\"/>\
      <species id=\"ADP\" compartment=\"Yeast\"/>\
      <species id=\"Pi\" compartment=\"Yeast\"/>\
    </listOfSpecies>\
    <listOfReactions>\
      <reaction id=\"Hexokinase\" reversible=\"false\">\
        <listOfReactants>\
          <speciesReference species=\"Glucose\">\
            <annotation>\
              <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"SpeciesReference_Glucose\"/>\
            </annotation>\
          </speciesReference>\
          <speciesReference species=\"ATP\">\
            <annotation>\
              <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"SpeciesReference_ATP\"/>\
            </annotation>\
          </speciesReference>\
        </listOfReactants>\
        <listOfProducts>\
          <speciesReference species=\"Glucose-6-phosphate\">\
            <annotation>\
              <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"SpeciesReference_G6P\"/>\
            </annotation>\
          </speciesReference>\
          <speciesReference species=\"ADP\">\
            <annotation>\
              <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"SpeciesReference_ADP\"/>\
            </annotation>\
          </speciesReference>\
        </listOfProducts>\
        <listOfModifiers>\
          <modifierSpeciesReference species=\"Glucose-6-phosphate\">\
            <annotation>\
              <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"ModifierSpeciesReference_G6P\"/>\
            </annotation>\
          </modifierSpeciesReference>\
          <modifierSpeciesReference species=\"Pi\">\
            <annotation>\
              <layoutId xmlns=\"http://projects.eml.org/bcb/sbml/level2\" id=\"ModifierSpeciesReference_Pi\"/>\
            </annotation>\
          </modifierSpeciesReference>\
        </listOfModifiers>\
      </reaction>\
    </listOfReactions>\
  </model>\
</sbml>\
"


static SBMLDocument *D;


void
SBMLHandlerTest_setup (void)
{
  D = NULL;
}

void 
SBMLHandlerTest_teardown (void)
{
  delete D;
}

START_TEST (test_SBMLHandler_Layout)
{
  SBMLReader reader=SBMLReader(); 

  D = reader.readSBMLFromString(s);
      	
  fail_unless(D!=NULL);

  Model* model=D->getModel();

  fail_unless(model!=NULL);

  // test compartments
  fail_unless(model->getNumCompartments()==1);

  Compartment* c=model->getCompartment(0);

  fail_unless(c!=NULL);

  fail_unless(c->isSetId());

  fail_unless(c->getId()=="Yeast");

  fail_unless(!c->isSetName());

  // test species
  fail_unless(model->getNumSpecies()==5);

  Species* species=model->getSpecies(0);

  fail_unless(species!=NULL);

  fail_unless(species->getCompartment()=="Yeast");

  fail_unless(species->isSetId());

  fail_unless(species->getId()=="Glucose");

  fail_unless(!species->isSetName());

  species=model->getSpecies(1);

  fail_unless(species!=NULL);

  fail_unless(species->getCompartment()=="Yeast");

  fail_unless(species->isSetId());

  fail_unless(species->getId()=="Glucose-6-phosphate");

  fail_unless(!species->isSetName());

  species=model->getSpecies(2);

  fail_unless(species!=NULL);

  fail_unless(species->getCompartment()=="Yeast");

  fail_unless(species->isSetId());

  fail_unless(species->getId()=="ATP");

  fail_unless(!species->isSetName());

  species=model->getSpecies(3);

  fail_unless(species!=NULL);

  fail_unless(species->getCompartment()=="Yeast");

  fail_unless(species->isSetId());

  fail_unless(species->getId()=="ADP");

  fail_unless(!species->isSetName());

  species=model->getSpecies(4);

  fail_unless(species!=NULL);

  fail_unless(species->getCompartment()=="Yeast");

  fail_unless(species->isSetId());

  fail_unless(species->getId()=="Pi");

  fail_unless(!species->isSetName());

  // test reactions
  fail_unless(model->getNumReactions()==1);

  Reaction* r=model->getReaction(0);

  fail_unless(r!=NULL);

  fail_unless(r->isSetId());

  fail_unless(r->getId()=="Hexokinase");

  fail_unless(!r->isSetName());

  fail_unless(r->getNumReactants()==2);

  SpeciesReference* sr=r->getReactant(0);

  fail_unless(sr!=NULL);

  fail_unless(sr->isSetSpecies());

  fail_unless(sr->getSpecies()=="Glucose");

  fail_unless(sr->isSetId());

  fail_unless(sr->getId()=="SpeciesReference_Glucose");

  sr=r->getReactant(1);

  fail_unless(sr!=NULL);

  fail_unless(sr->isSetSpecies());

  fail_unless(sr->getSpecies()=="ATP");

  fail_unless(sr->isSetId());

  fail_unless(sr->getId()=="SpeciesReference_ATP");
  
  fail_unless(r->getNumProducts()==2);

  sr=r->getProduct(0);

  fail_unless(sr!=NULL);

  fail_unless(sr->isSetSpecies());

  fail_unless(sr->getSpecies()=="Glucose-6-phosphate");

  fail_unless(sr->isSetId());

  fail_unless(sr->getId()=="SpeciesReference_G6P");

  sr=r->getProduct(1);

  fail_unless(sr!=NULL);

  fail_unless(sr->isSetSpecies());

  fail_unless(sr->getSpecies()=="ADP");

  fail_unless(sr->isSetId());

  fail_unless(sr->getId()=="SpeciesReference_ADP");
  
  
  fail_unless(r->getNumModifiers()==2);

  ModifierSpeciesReference* msr=r->getModifier(0);

  fail_unless(msr!=NULL);

  fail_unless(msr->isSetSpecies());

  fail_unless(msr->getSpecies()=="Glucose-6-phosphate");

  fail_unless(msr->isSetId());

  fail_unless(msr->getId()=="ModifierSpeciesReference_G6P");
  
  msr=r->getModifier(1);

  fail_unless(msr!=NULL);

  fail_unless(msr->isSetSpecies());

  fail_unless(msr->getSpecies()=="Pi");

  fail_unless(msr->isSetId());

  fail_unless(msr->getId()=="ModifierSpeciesReference_Pi");
 
  // test layout
  fail_unless(model->getListOfLayouts()->size()==1);

  Layout* l=model->getLayout(0);

  fail_unless(l!=NULL);

  fail_unless(l->isSetId());

  fail_unless(l->getId()=="Layout_1");
  
  Dimensions* dimensions=l->getDimensions();

  fail_unless(dimensions!=NULL);  
  
  fail_unless(dimensions->getWidth()==400.0);  
  
  fail_unless(dimensions->getHeight()==230.0);  
  
  fail_unless(dimensions->getDepth()==0.0);  

  // CompartmentGlyphs
  fail_unless(l->getNumCompartmentGlyphs()==1);

  CompartmentGlyph* cg=l->getCompartmentGlyph(0);

  fail_unless(cg!=NULL);

  fail_unless(cg->isSetId());

  fail_unless(cg->getId()=="CompartmentGlyph_1");

  fail_unless(cg->isSetCompartmentId());

  fail_unless(cg->getCompartmentId()=="Yeast");
 
  BoundingBox* bb=cg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bb1");

  Point* position=bb->getPosition();

  fail_unless(position->getXOffset()==5.0);
  
  fail_unless(position->getYOffset()==5.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==390.0);
  
  fail_unless(dimensions->getHeight()==220.0);
  
  fail_unless(dimensions->getDepth()==0.0);


  
  
  // SpeciesGlyphs
  fail_unless(l->getNumSpeciesGlyphs()==5);

  SpeciesGlyph* sg=l->getSpeciesGlyph(0);

  fail_unless(sg!=NULL);

  fail_unless(sg->isSetId());

  fail_unless(sg->getId()=="SpeciesGlyph_Glucose");

  fail_unless(sg->isSetSpeciesId());

  fail_unless(sg->getSpeciesId()=="Glucose");
      
  bb=sg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bb2");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==105.0);
  
  fail_unless(position->getYOffset()==20.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==130.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  sg=l->getSpeciesGlyph(1);

  fail_unless(sg!=NULL);

  fail_unless(sg->isSetId());

  fail_unless(sg->getId()=="SpeciesGlyph_G6P");

  fail_unless(sg->isSetSpeciesId());

  fail_unless(sg->getSpeciesId()=="Glucose-6-phosphate");
      
  bb=sg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bb5");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==50.0);
  
  fail_unless(position->getYOffset()==190.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==270.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  sg=l->getSpeciesGlyph(2);

  fail_unless(sg!=NULL);

  fail_unless(sg->isSetId());

  fail_unless(sg->getId()=="SpeciesGlyph_ATP");

  fail_unless(sg->isSetSpeciesId());

  fail_unless(sg->getSpeciesId()=="ATP");
      
  bb=sg->getBoundingBox();

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bb3");

  fail_unless(bb!=NULL);

  position=bb->getPosition();

  fail_unless(position->getXOffset()==270.0);
  
  fail_unless(position->getYOffset()==70.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==80.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  sg=l->getSpeciesGlyph(3);

  fail_unless(sg!=NULL);

  fail_unless(sg->isSetId());

  fail_unless(sg->getId()=="glyph_ADP");

  fail_unless(sg->isSetSpeciesId());

  fail_unless(sg->getSpeciesId()=="ADP");
      
  bb=sg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bb4");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==270.0);
  
  fail_unless(position->getYOffset()==140.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==80.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  sg=l->getSpeciesGlyph(4);

  fail_unless(sg!=NULL);

  fail_unless(sg->isSetId());

  fail_unless(sg->getId()=="SpeciesGlyph_Pi");

  fail_unless(sg->isSetSpeciesId());

  fail_unless(sg->getSpeciesId()=="Pi");
      
  bb=sg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bb6");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==50.0);
  
  fail_unless(position->getYOffset()==100.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==60.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  
  // ReactionGlyphs  
  fail_unless(l->getNumReactionGlyphs()==1);

  ReactionGlyph* rg=l->getReactionGlyph(0);

  fail_unless(rg!=NULL);

  fail_unless(rg->isSetId());

  fail_unless(rg->getId()=="glyph_Hexokinase");

  fail_unless(rg->isSetReactionId());

  fail_unless(rg->getReactionId()=="Hexokinase");

  fail_unless(rg->isSetCurve());

  Curve* curve=rg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  LineSegment* ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_LINESEGMENT);

  Point* p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==100.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==130.0);
  
  fail_unless(p->getZOffset()==0.0);

  fail_unless(rg->getNumSpeciesReferenceGlyphs()==6);

  SpeciesReferenceGlyph* srg=rg->getSpeciesReferenceGlyph(0);

  fail_unless(srg!=NULL);

  fail_unless(srg->isSetId());

  fail_unless(srg->getId()=="SpeciesReferenceGlyph_Glucose");

  fail_unless(srg->isSetSpeciesReferenceId());

  fail_unless(srg->getSpeciesReferenceId()=="SpeciesReference_Glucose");

  fail_unless(srg->isSetSpeciesGlyphId());

  fail_unless(srg->getSpeciesGlyphId()=="SpeciesGlyph_Glucose");

  fail_unless(srg->getRole()==SPECIES_ROLE_SUBSTRATE);

  fail_unless(srg->isSetCurve());

  curve=srg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_LINESEGMENT);

  p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==100.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==50.0);
  
  fail_unless(p->getZOffset()==0.0);

  srg=rg->getSpeciesReferenceGlyph(1);

  fail_unless(srg!=NULL);

  fail_unless(srg->isSetId());

  fail_unless(srg->getId()=="SpeciesReferenceGlyph_ATP");

  fail_unless(srg->isSetSpeciesReferenceId());

  fail_unless(srg->getSpeciesReferenceId()=="SpeciesReference_ATP");

  fail_unless(srg->isSetSpeciesGlyphId());

  fail_unless(srg->getSpeciesGlyphId()=="SpeciesGlyph_ATP");

  fail_unless(srg->getRole()==SPECIES_ROLE_SIDESUBSTRATE);

  fail_unless(srg->isSetCurve());

  curve=srg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_CUBICBEZIER);

  p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==100.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==260.0);
  
  fail_unless(p->getYOffset()==80.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint1();
  
  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==80.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint2();

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==80.0);
  
  fail_unless(p->getZOffset()==0.0);

  srg=rg->getSpeciesReferenceGlyph(2);

  fail_unless(srg!=NULL);

  fail_unless(srg->isSetId());

  fail_unless(srg->getId()=="SpeciesReferenceGlyph_G6P_1");

  fail_unless(srg->isSetSpeciesReferenceId());

  fail_unless(srg->getSpeciesReferenceId()=="SpeciesReference_G6P");

  fail_unless(srg->isSetSpeciesGlyphId());

  fail_unless(srg->getSpeciesGlyphId()=="SpeciesGlyph_G6P");

  fail_unless(srg->getRole()==SPECIES_ROLE_PRODUCT);

  fail_unless(srg->isSetCurve());

  curve=srg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_LINESEGMENT);

  p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==130.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==180.0);
  
  fail_unless(p->getZOffset()==0.0);

  srg=rg->getSpeciesReferenceGlyph(3);

  fail_unless(srg!=NULL);

  fail_unless(srg->isSetId());

  fail_unless(srg->getId()=="SpeciesReferenceGlyph_ADP");

  fail_unless(srg->isSetSpeciesReferenceId());

  fail_unless(srg->getSpeciesReferenceId()=="SpeciesReference_ADP");

  fail_unless(srg->isSetSpeciesGlyphId());

  fail_unless(srg->getSpeciesGlyphId()=="glyph_ADP");

  fail_unless(srg->getRole()==SPECIES_ROLE_SIDEPRODUCT);

  fail_unless(srg->isSetCurve());

  curve=srg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_CUBICBEZIER);

  p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==130.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==260.0);
  
  fail_unless(p->getYOffset()==150.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint1();
  
  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==150.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint2();

  fail_unless(p->getXOffset()==170.0);
  
  fail_unless(p->getYOffset()==150.0);
  
  fail_unless(p->getZOffset()==0.0);

  srg=rg->getSpeciesReferenceGlyph(4);

  fail_unless(srg!=NULL);

  fail_unless(srg->isSetId());

  fail_unless(srg->getId()=="SpeciesReferenceGlyph_G6P_2");

  fail_unless(srg->isSetSpeciesReferenceId());

  fail_unless(srg->getSpeciesReferenceId()=="ModifierSpeciesReference_G6P");

  fail_unless(srg->isSetSpeciesGlyphId());

  fail_unless(srg->getSpeciesGlyphId()=="SpeciesGlyph_G6P");

  fail_unless(srg->getRole()==SPECIES_ROLE_INHIBITOR);

  fail_unless(srg->isSetCurve());

  curve=srg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_CUBICBEZIER);

  p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==45.0);
  
  fail_unless(p->getYOffset()==200.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==165.0);
  
  fail_unless(p->getYOffset()==120.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint1();
  
  fail_unless(p->getXOffset()==0.0);
  
  fail_unless(p->getYOffset()==200.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint2();

  fail_unless(p->getXOffset()==0.0);
  
  fail_unless(p->getYOffset()==120.0);
  
  fail_unless(p->getZOffset()==0.0);

  srg=rg->getSpeciesReferenceGlyph(5);

  fail_unless(srg!=NULL);

  fail_unless(srg->isSetId());

  fail_unless(srg->getId()=="SpeciesReferenceGlyph_PI");

  fail_unless(srg->isSetSpeciesReferenceId());

  fail_unless(srg->getSpeciesReferenceId()=="ModifierSpeciesReference_Pi");

  fail_unless(srg->isSetSpeciesGlyphId());

  fail_unless(srg->getSpeciesGlyphId()=="SpeciesGlyph_Pi");

  fail_unless(srg->getRole()==SPECIES_ROLE_ACTIVATOR);

  fail_unless(srg->isSetCurve());

  curve=srg->getCurve();

  fail_unless(curve!=NULL);

  fail_unless(curve->getNumCurveSegments()==1);

  ls=curve->getCurveSegment(0);

  fail_unless(ls!=NULL);

  fail_unless(ls->getTypeCode()==SBML_LAYOUT_CUBICBEZIER);

  p=ls->getStart();

  fail_unless(p!=NULL);

  fail_unless(p->getXOffset()==115.0);
  
  fail_unless(p->getYOffset()==110.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=ls->getEnd();
  
  fail_unless(p->getXOffset()==165.0);
  
  fail_unless(p->getYOffset()==110.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint1();
  
  fail_unless(p->getXOffset()==140.0);
  
  fail_unless(p->getYOffset()==110.0);
  
  fail_unless(p->getZOffset()==0.0);

  p=dynamic_cast<CubicBezier*>(ls)->getBasePoint2();

  fail_unless(p->getXOffset()==140.0);
  
  fail_unless(p->getYOffset()==110.0);
  
  fail_unless(p->getZOffset()==0.0);

  // TextGlyphs  
  fail_unless(l->getNumTextGlyphs()==5);

  TextGlyph* tg=l->getTextGlyph(0);

  fail_unless(tg!=NULL);

  fail_unless(tg->isSetId());

  fail_unless(tg->getId()=="TextGlyph_Glucose");

  fail_unless(tg->isSetGraphicalObjectId());

  fail_unless(tg->getGraphicalObjectId()=="SpeciesGlyph_Glucose");

  fail_unless(tg->isSetOriginOfTextId());

  fail_unless(tg->getOriginOfTextId()=="Glucose");
  
  bb=tg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bbA");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==115.0);
  
  fail_unless(position->getYOffset()==20.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==110.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  tg=l->getTextGlyph(1);

  fail_unless(tg!=NULL);

  fail_unless(tg->isSetId());

  fail_unless(tg->getId()=="TextGlyph_G6P");

  fail_unless(tg->isSetGraphicalObjectId());

  fail_unless(tg->getGraphicalObjectId()=="SpeciesGlyph_G6P");

  fail_unless(tg->isSetOriginOfTextId());

  fail_unless(tg->getOriginOfTextId()=="Glucose-6-phosphate");
  
  bb=tg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bbD");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==60.0);
  
  fail_unless(position->getYOffset()==190.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==250.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  tg=l->getTextGlyph(2);

  fail_unless(tg!=NULL);

  fail_unless(tg->isSetId());

  fail_unless(tg->getId()=="TextGlyph_ATP");

  fail_unless(tg->isSetGraphicalObjectId());

  fail_unless(tg->getGraphicalObjectId()=="SpeciesGlyph_ATP");

  fail_unless(tg->isSetOriginOfTextId());

  fail_unless(tg->getOriginOfTextId()=="ATP");
  
  bb=tg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bbB");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==280.0);
  
  fail_unless(position->getYOffset()==70.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==60.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  tg=l->getTextGlyph(3);

  fail_unless(tg!=NULL);

  fail_unless(tg->isSetId());

  fail_unless(tg->getId()=="TextGlyph_ADP");

  fail_unless(tg->isSetGraphicalObjectId());

  fail_unless(tg->getGraphicalObjectId()=="glyph_ADP");

  fail_unless(tg->isSetOriginOfTextId());

  fail_unless(tg->getOriginOfTextId()=="ADP");
  
  bb=tg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bbC");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==280.0);
  
  fail_unless(position->getYOffset()==140.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==60.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  tg=l->getTextGlyph(4);

  fail_unless(tg!=NULL);

  fail_unless(tg->isSetId());

  fail_unless(tg->getId()=="TextGlyph_PI");

  fail_unless(tg->isSetGraphicalObjectId());

  fail_unless(tg->getGraphicalObjectId()=="SpeciesGlyph_Pi");

  fail_unless(tg->isSetOriginOfTextId());

  fail_unless(tg->getOriginOfTextId()=="Pi");
  
  bb=tg->getBoundingBox();

  fail_unless(bb!=NULL);

  fail_unless(bb->isSetId());

  fail_unless(bb->getId()=="bbE");

  position=bb->getPosition();

  fail_unless(position->getXOffset()==60.0);
  
  fail_unless(position->getYOffset()==100.0);
  
  fail_unless(position->getZOffset()==0.0);
  
  fail_unless(bb!=NULL);

  dimensions=bb->getDimensions();

  fail_unless(dimensions!=NULL);

  fail_unless(dimensions->getWidth()==40.0);
  
  fail_unless(dimensions->getHeight()==20.0);
  
  fail_unless(dimensions->getDepth()==0.0);

  // GraphicalObjects
  fail_unless(l->getNumAdditionalGraphicalObjects()==0);
  
}
END_TEST



Suite *
create_suite_SBMLHandler (void)
{
  Suite *suite = suite_create("SBMLHandler");
  TCase *tcase = tcase_create("SBMLHandler");

  tcase_add_checked_fixture( tcase,
                             SBMLHandlerTest_setup,
                             SBMLHandlerTest_teardown );


  tcase_add_test( tcase, test_SBMLHandler_Layout                            );
 
  suite_add_tcase(suite, tcase);

  return suite;
}




END_C_DECLS



