xref: /dports/biology/libsbml/libsbml-5.19.0/src/sbml/Model.cpp

/**
 * @file    Model.cpp
 * @brief   Implementation of Model.
 * @author  Ben Bornstein
 *
 * <!--------------------------------------------------------------------------
 * This file is part of libSBML.  Please visit http://sbml.org for more
 * information about SBML, and the latest version of libSBML.
 *
 * Copyright (C) 2020 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. University of Heidelberg, Heidelberg, Germany
 *     3. University College London, London, UK
 *
 * Copyright (C) 2019 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2013-2018 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *     3. University of Heidelberg, Heidelberg, Germany
 *
 * Copyright (C) 2009-2013 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
 *
 * Copyright (C) 2006-2008 by the California Institute of Technology,
 *     Pasadena, CA, USA
 *
 * Copyright (C) 2002-2005 jointly by the following organizations:
 *     1. California Institute of Technology, Pasadena, CA, USA
 *     2. Japan Science and Technology Agency, Japan
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation.  A copy of the license agreement is provided
 * in the file named "LICENSE.txt" included with this software distribution
 * and also available online as http://sbml.org/software/libsbml/license.html
 * ---------------------------------------------------------------------- -->*/

#include <sbml/xml/XMLNode.h>
#include <sbml/xml/XMLAttributes.h>
#include <sbml/xml/XMLInputStream.h>
#include <sbml/xml/XMLOutputStream.h>

#include <sbml/annotation/RDFAnnotation.h>
#include <sbml/math/ASTNode.h>

#include <sbml/SBMLDocument.h>
#include <sbml/SBO.h>
#include <sbml/SBMLVisitor.h>
#include <sbml/SBMLError.h>
#include <sbml/KineticLaw.h>

#include <sbml/Model.h>

#include <sbml/ModifierSpeciesReference.h>
#include <sbml/SimpleSpeciesReference.h>

#include <sbml/AlgebraicRule.h>
#include <sbml/AssignmentRule.h>
#include <sbml/RateRule.h>

#include <sbml/util/IdentifierTransformer.h>
#include <sbml/util/ElementFilter.h>
#include <sbml/util/IdFilter.h>
#include <sbml/util/MetaIdFilter.h>

#include <sbml/extension/SBMLExtensionRegistry.h>
#include <sbml/extension/SBasePlugin.h>



/** @cond doxygenIgnored */
using namespace std;
/** @endcond */

LIBSBML_CPP_NAMESPACE_BEGIN
#ifdef __cplusplus

Model::Model (unsigned int level, unsigned int version) :
   SBase ( level, version )
 , mSubstanceUnits   ( "" )
 , mTimeUnits        ( "" )
 , mVolumeUnits      ( "" )
 , mAreaUnits        ( "" )
 , mLengthUnits      ( "" )
 , mExtentUnits      ( "" )
 , mConversionFactor ( "" )
 , mFunctionDefinitions (level,version)
 , mUnitDefinitions     (level,version)
 , mCompartmentTypes    (level,version)
 , mSpeciesTypes        (level,version)
 , mCompartments        (level,version)
 , mSpecies             (level,version)
 , mParameters          (level,version)
 , mInitialAssignments  (level,version)
 , mRules               (level,version)
 , mConstraints         (level,version)
 , mReactions           (level,version)
 , mEvents              (level,version)
 , mFormulaUnitsData ( NULL  )
 , mIdList (  )
 , mMetaidList ( )
 , mUnitsDataMap ()
{
  if (!hasValidLevelVersionNamespaceCombination())
    throw SBMLConstructorException();

  connectToChild();
}


Model::Model (SBMLNamespaces * sbmlns) :
   SBase             ( sbmlns )
 , mSubstanceUnits   ( "" )
 , mTimeUnits        ( "" )
 , mVolumeUnits      ( "" )
 , mAreaUnits        ( "" )
 , mLengthUnits      ( "" )
 , mExtentUnits      ( "" )
 , mConversionFactor ( "" )
 , mFunctionDefinitions (sbmlns)
 , mUnitDefinitions     (sbmlns)
 , mCompartmentTypes    (sbmlns)
 , mSpeciesTypes        (sbmlns)
 , mCompartments        (sbmlns)
 , mSpecies             (sbmlns)
 , mParameters          (sbmlns)
 , mInitialAssignments  (sbmlns)
 , mRules               (sbmlns)
 , mConstraints         (sbmlns)
 , mReactions           (sbmlns)
 , mEvents              (sbmlns)
 , mFormulaUnitsData ( NULL  )
 , mIdList (  )
 , mMetaidList ( )
 , mUnitsDataMap ()
{
  if (!hasValidLevelVersionNamespaceCombination())
  {
    throw SBMLConstructorException(getElementName(), sbmlns);
  }

  connectToChild();
  loadPlugins(sbmlns);

}


/*
 * Destroys this Model.
 */
Model::~Model ()
{
  if (mFormulaUnitsData != NULL)
  {
    unsigned int size = mFormulaUnitsData->getSize();
    while (size > 0)
    {
      delete static_cast<FormulaUnitsData*>( mFormulaUnitsData->remove(0) );
      size--;
    }
    delete mFormulaUnitsData;
  }
  mEvents.clear();
  mUnitsDataMap.clear();
}


/*
 * Copy constructor.
 */
Model::Model(const Model& orig)
  : SBase                (orig)
  , mSubstanceUnits      (orig.mSubstanceUnits)
  , mTimeUnits           (orig.mTimeUnits)
  , mVolumeUnits         (orig.mVolumeUnits)
  , mAreaUnits           (orig.mAreaUnits)
  , mLengthUnits         (orig.mLengthUnits)
  , mExtentUnits         (orig.mExtentUnits)
  , mConversionFactor    (orig.mConversionFactor)
  , mFunctionDefinitions (orig.mFunctionDefinitions)
  , mUnitDefinitions     (orig.mUnitDefinitions)
  , mCompartmentTypes    (orig.mCompartmentTypes)
  , mSpeciesTypes        (orig.mSpeciesTypes)
  , mCompartments        (orig.mCompartments)
  , mSpecies             (orig.mSpecies)
  , mParameters          (orig.mParameters)
  , mInitialAssignments  (orig.mInitialAssignments)
  , mRules               (orig.mRules)
  , mConstraints         (orig.mConstraints)
  , mReactions           (orig.mReactions)
  , mEvents              (orig.mEvents)
  , mFormulaUnitsData    (NULL)
  , mIdList              (orig.mIdList)
  , mMetaidList          (orig.mMetaidList)
  , mUnitsDataMap        ()
{

  if (orig.mFormulaUnitsData != NULL)
  {
    this->mFormulaUnitsData = new List();
    unsigned int i, iMax = orig.mFormulaUnitsData->getSize();
    for (i = 0; i < iMax; ++i)
    {
      FormulaUnitsData *newFud = static_cast<FormulaUnitsData*>
        (orig.mFormulaUnitsData->get(i))->clone();
      this->mFormulaUnitsData->add((void *)newFud);
      std::string id = newFud->getUnitReferenceId();
      int typecode = newFud->getComponentTypecode();

      KeyValue key(id, typecode);
      mUnitsDataMap.insert(make_pair(key, newFud));
    }
  }
  connectToChild();

}


/*
 * Assignment operator
 */
Model& Model::operator=(const Model& rhs)
{
  if(&rhs!=this)
  {
    this->SBase::operator = (rhs);
    mSubstanceUnits       = rhs.mSubstanceUnits ;
    mTimeUnits            = rhs.mTimeUnits ;
    mVolumeUnits          = rhs.mVolumeUnits ;
    mAreaUnits            = rhs.mAreaUnits ;
    mLengthUnits          = rhs.mLengthUnits ;
    mExtentUnits          = rhs.mExtentUnits ;
    mConversionFactor     = rhs.mConversionFactor ;
    mFunctionDefinitions  = rhs.mFunctionDefinitions;
    mUnitDefinitions      = rhs.mUnitDefinitions;
    mCompartmentTypes     = rhs.mCompartmentTypes;
    mSpeciesTypes         = rhs.mSpeciesTypes;
    mCompartments         = rhs.mCompartments;
    mSpecies              = rhs.mSpecies;
    mParameters           = rhs.mParameters;
    mInitialAssignments   = rhs.mInitialAssignments;
    mRules                = rhs.mRules;
    mConstraints          = rhs.mConstraints;
    mReactions            = rhs.mReactions;
    mEvents               = rhs.mEvents;


    if (this->mFormulaUnitsData  != NULL)
    {
      unsigned int size = this->mFormulaUnitsData->getSize();
      while (size--)
        delete static_cast<FormulaUnitsData*>(
                          this->mFormulaUnitsData->remove(0) );
      delete this->mFormulaUnitsData;
      mUnitsDataMap.clear();
    }

    if(rhs.mFormulaUnitsData != NULL)
    {
      this->mFormulaUnitsData  = new List();
      unsigned int i,iMax = rhs.mFormulaUnitsData->getSize();
      for(i = 0; i < iMax; ++i)
      {
        FormulaUnitsData *newFud = static_cast<FormulaUnitsData*>
          (rhs.mFormulaUnitsData->get(i))->clone();
        this->mFormulaUnitsData->add((void *)newFud);
        std::string id = newFud->getUnitReferenceId();
        int typecode = newFud->getComponentTypecode();

        KeyValue key(id, typecode);
        mUnitsDataMap.insert(make_pair(key, newFud));
      }
    }
    else
    {
      this->mFormulaUnitsData = NULL;
      mUnitsDataMap.clear();
    }
  }

  mIdList     = rhs.mIdList;
  mMetaidList = rhs.mMetaidList;

  connectToChild();

  return *this;
}


/** @cond doxygenLibsbmlInternal */
bool
Model::accept (SBMLVisitor& v) const
{
  v.visit(*this);

  mFunctionDefinitions.accept(v);
  mUnitDefinitions    .accept(v);
  mCompartmentTypes   .accept(v);
  mSpeciesTypes       .accept(v);
  mCompartments       .accept(v);
  mSpecies            .accept(v);
  mParameters         .accept(v);
  mInitialAssignments .accept(v);
  mRules              .accept(v);
  mConstraints        .accept(v);
  mReactions          .accept(v);
  mEvents             .accept(v);

  v.leave(*this);

  return true;
}
/** @endcond */


/*
 * @return a (deep) copy of this Model.
 */
Model*
Model::clone () const
{
  return new Model(*this);
}

SBase*
Model::getElementBySId(const std::string& id)
{
  if (id.empty()) return NULL;
  SBase* obj = mFunctionDefinitions.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mUnitDefinitions.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mCompartmentTypes.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mSpeciesTypes.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mCompartments.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mSpecies.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mParameters.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mReactions.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mInitialAssignments.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mRules.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mConstraints.getElementBySId(id);
  if (obj != NULL) return obj;
  obj = mEvents.getElementBySId(id);
  if (obj != NULL) return obj;

  return getElementFromPluginsBySId(id);
}


SBase*
Model::getElementByMetaId(const std::string& metaid)
{
  if (metaid.empty()) return NULL;
  if (mFunctionDefinitions.getMetaId()==metaid) return &mFunctionDefinitions;
  if (mUnitDefinitions.getMetaId()==metaid) return &mUnitDefinitions;
  if (mCompartmentTypes.getMetaId()==metaid) return &mCompartmentTypes;
  if (mSpeciesTypes.getMetaId()==metaid) return &mSpeciesTypes;
  if (mCompartments.getMetaId()==metaid) return &mCompartments;
  if (mSpecies.getMetaId()==metaid) return &mSpecies;
  if (mParameters.getMetaId()==metaid) return &mParameters;
  if (mInitialAssignments.getMetaId()==metaid) return &mInitialAssignments;
  if (mRules.getMetaId()==metaid) return &mRules;
  if (mConstraints.getMetaId()==metaid) return &mConstraints;
  if (mReactions.getMetaId()==metaid) return &mReactions;
  if (mEvents.getMetaId()==metaid) return &mEvents;

  SBase* obj = mFunctionDefinitions.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mUnitDefinitions.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mCompartmentTypes.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mSpeciesTypes.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mCompartments.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mSpecies.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mParameters.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mInitialAssignments.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mRules.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mConstraints.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mReactions.getElementByMetaId(metaid);
  if (obj != NULL) return obj;
  obj = mEvents.getElementByMetaId(metaid);
  if (obj != NULL) return obj;

  return getElementFromPluginsByMetaId(metaid);
}


List*
Model::getAllElements(ElementFilter *filter)
{
  List* ret = new List();
  List* sublist = NULL;

  ADD_FILTERED_LIST(ret, sublist, mFunctionDefinitions, filter);
  ADD_FILTERED_LIST(ret, sublist, mUnitDefinitions, filter);
  ADD_FILTERED_LIST(ret, sublist, mCompartmentTypes, filter);
  ADD_FILTERED_LIST(ret, sublist, mSpeciesTypes, filter);
  ADD_FILTERED_LIST(ret, sublist, mCompartments, filter);
  ADD_FILTERED_LIST(ret, sublist, mSpecies, filter);
  ADD_FILTERED_LIST(ret, sublist, mParameters, filter);
  ADD_FILTERED_LIST(ret, sublist, mInitialAssignments, filter);
  ADD_FILTERED_LIST(ret, sublist, mRules, filter);
  ADD_FILTERED_LIST(ret, sublist, mConstraints, filter);
  ADD_FILTERED_LIST(ret, sublist, mReactions, filter);
  ADD_FILTERED_LIST(ret, sublist, mEvents, filter);

  ADD_FILTERED_FROM_PLUGIN(ret, sublist, filter);

  return ret;
}


/** @cond doxygenLibsbmlInternal */
int
Model::renameAllIds(IdentifierTransformer* idTransformer, ElementFilter* filter)
{
  if (idTransformer == NULL)
  return LIBSBML_OPERATION_SUCCESS;

  //get all elements
  List* allElements = getAllElements(filter);

  //Rename the SIds, UnitSIds, and MetaIDs
  renameIDs(allElements, idTransformer);

  delete allElements;

  return LIBSBML_OPERATION_SUCCESS;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::renameIDs(List* elements, IdentifierTransformer* idTransformer)
{
  if (elements == NULL || elements->getSize() == 0 || idTransformer == NULL)
    return;

  vector<pair<string, string> > renamedSIds;
  vector<pair<string, string> > renamedUnitSIds;
  vector<pair<string, string> > renamedMetaIds;
  vector<pair<string, string> >::iterator it;

  for (unsigned long el=0; el < elements->getSize(); ++el)
  {
    SBase* element = static_cast<SBase*>(elements->get((unsigned int)el));
    string id = element->getId();
    string metaid = element->getMetaId();
    element->transformIdentifiers(idTransformer);

    if (element->getTypeCode() == SBML_LOCAL_PARAMETER)
  {
      element->setId(id); //Change it back.  This would perhaps be better served by overriding 'prependStringToAllIdentifiers' but hey.
    }
    string newid = element->getId();
    string newmetaid = element->getMetaId();
    if (id != newid)
  {
      int type = element->getTypeCode();
      if (type==SBML_UNIT_DEFINITION)
    {
        renamedUnitSIds.push_back(make_pair(id, newid));
      }
      //else if (type==SBML_COMP_PORT)
    //{
      //  //Do nothing--these can only be referenced from outside the Model, so they need to be handled specially.
      //  // (In the default case, we throw them away).
      //}
      else
    {
        //This is a little dangerous, but hey!  What's a little danger between friends!
        //(What we are assuming is that any attribute you can get with 'getId' is of the type 'SId')
        renamedSIds.push_back(make_pair(id, newid));
      }
    }
    if (metaid != newmetaid)
  {
      renamedMetaIds.push_back(make_pair(metaid, newmetaid));
    }
  }

  for (unsigned long el = 0; el< elements->getSize(); ++el)
  {
    SBase* element = static_cast<SBase*>(elements->get((unsigned int)el));

    for (it = renamedSIds.begin(); it != renamedSIds.end(); ++it)
  {
      element->renameSIdRefs((*it).first, (*it).second);
    }

    for (it = renamedUnitSIds.begin(); it != renamedUnitSIds.end(); ++it)
  {
      element->renameUnitSIdRefs((*it).first, (*it).second);
    }

    for (it = renamedMetaIds.begin(); it != renamedMetaIds.end(); ++it)
  {
      element->renameMetaIdRefs((*it).first, (*it).second);
    }
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the id of this SBML object.
 */
const string&
Model::getId () const
{
  return mId;
}
/** @endcond */


/*
 * @return the name of this SBML object.
 */
const string&
Model::getName () const
{
  return (getLevel() == 1) ? mId : mName;
}


/*
 * Returns the value of the "substanceUnits" attribute of this Model.
 */
const std::string&
Model::getSubstanceUnits () const
{
  return mSubstanceUnits;
}


/*
 * Returns the value of the "timeUnits" attribute of this Model.
 */
const std::string&
Model::getTimeUnits () const
{
  return mTimeUnits;
}

/*
 * Returns the value of the "volumeUnits" attribute of this Model.
 */
const std::string&
Model::getVolumeUnits () const
{
  return mVolumeUnits;
}


/*
 * Returns the value of the "areaUnits" attribute of this Model.
 */
const std::string&
Model::getAreaUnits () const
{
  return mAreaUnits;
}


/*
 * Returns the value of the "lengthUnits" attribute of this Model.
 */
const std::string&
Model::getLengthUnits () const
{
  return mLengthUnits;
}


/*
 * Returns the value of the "extentUnits" attribute of this Model.
 */
const std::string&
Model::getExtentUnits () const
{
  return mExtentUnits;
}


/*
 * Returns the value of the "conversionFactor" attribute of this Model.
 */
const std::string&
Model::getConversionFactor () const
{
  return mConversionFactor;
}



/*
 * @return @c true if the id of this SBML object has been set, false
 * otherwise.
 */
bool
Model::isSetId () const
{
  return (mId.empty() == false);
}


/*
 * @return @c true if the name of this SBML object is set, false
 * otherwise.
 */
bool
Model::isSetName () const
{
  return (getLevel() == 1) ? (mId.empty() == false) :
                            (mName.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "substanceUnits" attribute is set.
 */
bool
Model::isSetSubstanceUnits () const
{
  return (mSubstanceUnits.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "timeUnits" attribute is set.
 */
bool
Model::isSetTimeUnits () const
{
  return (mTimeUnits.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "volumeUnits" attribute is set.
 */
bool
Model::isSetVolumeUnits () const
{
  return (mVolumeUnits.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "areaUnits" attribute is set.
 */
bool
Model::isSetAreaUnits () const
{
  return (mAreaUnits.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "lengthUnits" attribute is set.
 */
bool
Model::isSetLengthUnits () const
{
  return (mLengthUnits.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "extentUnits" attribute is set.
 */
bool
Model::isSetExtentUnits () const
{
  return (mExtentUnits.empty() == false);
}


/*
 * Predicate returning @c true if this
 * Model's "conversionFactor" attribute is set.
 */
bool
Model::isSetConversionFactor () const
{
  return (mConversionFactor.empty() == false);
}


/*
 * Sets the id of this SBML object to a copy of @p sid.
 */
int
Model::setId (const std::string& sid)
{
  /* since the setId function has been used as an
   * alias for setName we cant require it to only
   * be used on a L2 model
   */
/*  if (getLevel() == 1)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
*/
  if (!(SyntaxChecker::isValidInternalSId(sid)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mId = sid;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the name of this SBML object to a copy of name.
 */
int
Model::setName (const std::string& name)
{
  /* if this is setting an L2 name the type is string
   * whereas if it is setting an L1 name its type is SId
   */
  if (getLevel() == 1)
  {
    if (!(SyntaxChecker::isValidInternalSId(name)))
    {
      return LIBSBML_INVALID_ATTRIBUTE_VALUE;
    }
    else
    {
      mId = name;
      return LIBSBML_OPERATION_SUCCESS;
    }
  }
  else
  {
    mName = name;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setSubstanceUnits (const std::string& units)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mSubstanceUnits = units;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setTimeUnits (const std::string& units)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mTimeUnits = units;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setVolumeUnits (const std::string& units)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mVolumeUnits = units;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setAreaUnits (const std::string& units)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mAreaUnits = units;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setLengthUnits (const std::string& units)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mLengthUnits = units;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setExtentUnits (const std::string& units)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalUnitSId(units)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mExtentUnits = units;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Sets the substanceUnits of this SBML object.
 */
int
Model::setConversionFactor (const std::string& id)
{
  if (getLevel() < 3)
  {
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }
  else if (!(SyntaxChecker::isValidInternalSId(id)))
  {
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  else
  {
    mConversionFactor = id;
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Unsets the id of this SBML object.
 */
int
Model::unsetId ()
{
  mId.erase();

  if (mId.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the name of this SBML object.
 */
int
Model::unsetName ()
{
  if (getLevel() == 1)
  {
    mId.erase();
  }
  else
  {
    mName.erase();
  }

  if (getLevel() == 1 && mId.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else if (mName.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}



/*
 * Unsets the SubstanceUnits of this SBML object.
 */
int
Model::unsetSubstanceUnits ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mSubstanceUnits.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mSubstanceUnits.erase();

  if (mSubstanceUnits.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the TimeUnits of this SBML object.
 */
int
Model::unsetTimeUnits ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mTimeUnits.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mTimeUnits.erase();

  if (mTimeUnits.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the VolumeUnits of this SBML object.
 */
int
Model::unsetVolumeUnits ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mVolumeUnits.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mVolumeUnits.erase();

  if (mVolumeUnits.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the AreaUnits of this SBML object.
 */
int
Model::unsetAreaUnits ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mAreaUnits.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mAreaUnits.erase();

  if (mAreaUnits.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the LengthUnits of this SBML object.
 */
int
Model::unsetLengthUnits ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mLengthUnits.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mLengthUnits.erase();

  if (mLengthUnits.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the LengthUnits of this SBML object.
 */
int
Model::unsetExtentUnits ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mExtentUnits.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mExtentUnits.erase();

  if (mExtentUnits.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Unsets the ConversionFactor of this SBML object.
 */
int
Model::unsetConversionFactor ()
{
  /* only in L3 */
  if (getLevel() < 3)
  {
    mConversionFactor.erase();
    return LIBSBML_UNEXPECTED_ATTRIBUTE;
  }

  mConversionFactor.erase();

  if (mConversionFactor.empty())
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else
  {
    return LIBSBML_OPERATION_FAILED;
  }
}


/*
 * Adds a copy of the given FunctionDefinition to this Model.
 */
int
Model::addFunctionDefinition (const FunctionDefinition* fd)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(fd));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getFunctionDefinition(fd->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mFunctionDefinitions.append(fd);
  }
}


/*
 * Adds a copy of the given UnitDefinition to this Model.
 */
int
Model::addUnitDefinition (const UnitDefinition* ud)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(ud));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getUnitDefinition(ud->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mUnitDefinitions.append(ud);
  }
}


/*
 * Adds a copy of the given CompartmentType to this Model.
 */
int
Model::addCompartmentType (const CompartmentType* ct)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(ct));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getCompartmentType(ct->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mCompartmentTypes.append(ct);
  }
}


/*
 * Adds a copy of the given SpeciesType to this Model.
 */
int
Model::addSpeciesType (const SpeciesType* st)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(st));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getSpeciesType(st->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mSpeciesTypes.append(st);
  }
}


/*
 * Adds a copy of the given Compartment to this Model.
 */
int
Model::addCompartment (const Compartment* c)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(c));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getCompartment(c->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mCompartments.append(c);
  }
}


/*
 * Adds a copy of the given Species to this Model.
 */
int
Model::addSpecies (const Species* s)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(s));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getSpecies(s->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mSpecies.append(s);
  }
}


/*
 * Adds a copy of the given Parameter to this Model.
 */
int
Model::addParameter (const Parameter* p)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(p));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getParameter(p->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    /* hack so that this will accept a local parameter !! */
    if (p->getTypeCode() == SBML_LOCAL_PARAMETER)
    {
      Parameter p1(*p);
      return mParameters.append(&p1);
    }
    else
    {
      return mParameters.append(p);
    }
  }
}


/*
 * Adds a copy of the given InitialAssignment to this Model.
 */
int
Model::addInitialAssignment (const InitialAssignment* ia)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(ia));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getInitialAssignment(ia->getSymbol()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mInitialAssignments.append(ia);
  }
}


/*
 * Adds a copy of the given Rule to this Model.
 */
int
Model::addRule (const Rule* r)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(r));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (!r->isAlgebraic()
         && getRule(r->getVariable()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mRules.append(r);
  }
}


/*
 * Adds a copy of the given Constraint to this Model.
 */
int
Model::addConstraint (const Constraint* c)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(c));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else
  {
    return mConstraints.append(c);
  }
}


/*
 * Adds a copy of the given Reaction to this Model.
 */
int
Model::addReaction (const Reaction* r)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(r));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (getReaction(r->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mReactions.append(r);
  }
}


/*
 * Adds a copy of the given Event to this Model.
 */
int
Model::addEvent (const Event* e)
{
  int returnValue = checkCompatibility(static_cast<const SBase *>(e));
  if (returnValue != LIBSBML_OPERATION_SUCCESS)
  {
    return returnValue;
  }
  else if (e->isSetId() && getEvent(e->getId()) != NULL)
  {
    // an object with this id already exists
    return LIBSBML_DUPLICATE_OBJECT_ID;
  }
  else
  {
    return mEvents.append(e);
  }
}


/*
 * Creates a new FunctionDefinition inside this Model and returns it.
 */
FunctionDefinition*
Model::createFunctionDefinition ()
{
  FunctionDefinition* fd = NULL;

  try
  {
    fd = new FunctionDefinition(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (fd != NULL) mFunctionDefinitions.appendAndOwn(fd);

  return fd;
}


/*
 * Creates a new UnitDefinition inside this Model and returns it.
 */
UnitDefinition*
Model::createUnitDefinition ()
{
  UnitDefinition* ud = NULL;

  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (ud != NULL) mUnitDefinitions.appendAndOwn(ud);

  return ud;
}


/*
 * Creates a new Unit inside this Model and returns a pointer to it.  The
 * Unit is added to the last UnitDefinition created.
 *
 * If a UnitDefinitions does not exist for this model, a new Unit is not
 * created and @c NULL is returned.
 */
Unit*
Model::createUnit ()
{
  unsigned int size = getNumUnitDefinitions();
  return (size > 0) ? getUnitDefinition(size - 1)->createUnit() : NULL;
}


/*
 * Creates a new CompartmentType inside this Model and returns it.
 */
CompartmentType*
Model::createCompartmentType ()
{
  CompartmentType* ct = NULL;

  try
  {
    ct = new CompartmentType(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (ct != NULL) mCompartmentTypes.appendAndOwn(ct);

  return ct;
}


/*
 * Creates a new SpeciesType inside this Model and returns it.
 */
SpeciesType*
Model::createSpeciesType ()
{
  SpeciesType* st = NULL;

  try
  {
    st = new SpeciesType(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (st != NULL) mSpeciesTypes.appendAndOwn(st);

  return st;
}


/*
 * Creates a new Compartment inside this Model and returns it.
 */
Compartment*
Model::createCompartment ()
{
  Compartment* c = NULL;

  try
  {
    c = new Compartment(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (c != NULL) mCompartments.appendAndOwn(c);

  return c;
}


/*
 * Creates a new Species inside this Model and returns it.
 */
Species*
Model::createSpecies ()
{
  Species* s = NULL;

  try
  {
    s = new Species(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (s != NULL) mSpecies.appendAndOwn(s);

  return s;
}


/*
 * Creates a new Parameter inside this Model and returns.
 */
Parameter*
Model::createParameter ()
{
  Parameter* p = NULL;

  try
  {
    p = new Parameter(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (p != NULL) mParameters.appendAndOwn(p);

  return p;
}


/*
 * Creates a new InitialAssignment inside this Model and returns it.
 */
InitialAssignment*
Model::createInitialAssignment ()
{
  InitialAssignment* ia = NULL;

  try
  {
    ia = new InitialAssignment(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (ia != NULL) mInitialAssignments.appendAndOwn(ia);

  return ia;
}


/*
 * Creates a new AlgebraicRule inside this Model and returns it.
 */
AlgebraicRule*
Model::createAlgebraicRule ()
{
  AlgebraicRule* ar = NULL;

  try
  {
    ar = new AlgebraicRule(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (ar != NULL) mRules.appendAndOwn(ar);

  return ar;
}


/*
 * Creates a new AssignmentRule inside this Model and returns it.
 */
AssignmentRule*
Model::createAssignmentRule ()
{
  AssignmentRule* ar = NULL;

  try
  {
    ar = new AssignmentRule(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (ar != NULL) mRules.appendAndOwn(ar);

  return ar;
}


/*
 * Creates a new RateRule inside this Model and returns it.
 */
RateRule*
Model::createRateRule ()
{
  RateRule* rr = NULL;

  try
  {
    rr = new RateRule(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (rr != NULL) mRules.appendAndOwn(rr);

  return rr;
}


/*
 * Creates a new Constraint inside this Model and returns it.
 */
Constraint*
Model::createConstraint ()
{
  Constraint* c = NULL;

  try
  {
    c = new Constraint(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (c != NULL) mConstraints.appendAndOwn(c);

  return c;
}


/*
 * Creates a new Reaction inside this Model and returns it.
 */
Reaction*
Model::createReaction ()
{
  Reaction* r = NULL;

  try
  {
    r = new Reaction(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (r != NULL) mReactions.appendAndOwn(r);

  return r;
}


/*
 * Creates a new Reactant (ie SpeciesReference) inside this Model and
 * returns a pointer to it.  The SpeciesReference is added to the reactants
 * of the last Reaction created.
 *
 * If a Reaction does not exist for this model, a new SpeciesReference is
 * not created and @c NULL is returned.
 */
SpeciesReference*
Model::createReactant ()
{
  unsigned int size = getNumReactions();
  return (size > 0) ? getReaction(size - 1)->createReactant() : NULL;
}


/*
 * Creates a new Product (ie SpeciesReference) inside this Model and
 * returns a pointer to it.  The SpeciesReference is added to the products
 * of the last Reaction created.
 *
 * If a Reaction does not exist for this model, a new SpeciesReference is
 * not created and @c NULL is returned.
 */
SpeciesReference*
Model::createProduct ()
{
  unsigned int size = getNumReactions();
  return (size > 0) ? getReaction(size - 1)->createProduct() : NULL;
}


/*
 * Creates a new Modifer (ie ModifierSpeciesReference) inside this Model
 * and returns a pointer to it.  The ModifierSpeciesReference is added to
 * the modifiers of the last Reaction created.
 *
 * If a Reaction does not exist for this model, a new
 * ModifierSpeciesReference is not created and @c NULL is returned.
 */
ModifierSpeciesReference*
Model::createModifier ()
{
  unsigned int size = getNumReactions();
  return (size > 0) ? getReaction(size - 1)->createModifier() : NULL;
}


/*
 * Creates a new KineticLaw inside this Model and returns a pointer to it.
 * The KineticLaw is associated with the last Reaction created.
 *
 * If a Reaction does not exist for this model, or a Reaction does exist,
 * but already has a KineticLaw, a new KineticLaw is not created and NULL
 * is returned.
 */
KineticLaw*
Model::createKineticLaw ()
{
  unsigned int size = getNumReactions();
  return (size > 0) ? getReaction(size - 1)->createKineticLaw() : NULL;
}


/*
 * Creates a new Parameter (of a KineticLaw) inside this Model and returns
 * a pointer to it.  The Parameter is associated with the KineticLaw of the
 * last Reaction created.
 *
 * If a Reaction does not exist for this model, or a KineticLaw for the
 * Reaction, a new Parameter is not created and @c NULL is returned.
 */
Parameter*
Model::createKineticLawParameter ()
{
  unsigned int size = getNumReactions();

  if (size > 0)
  {
    KineticLaw* kl = getReaction(size - 1)->getKineticLaw();
    if (kl != NULL) return kl->createParameter();
  }

  return NULL;
}


/*
 * Creates a new Parameter (of a KineticLaw) inside this Model and returns
 * a pointer to it.  The Parameter is associated with the KineticLaw of the
 * last Reaction created.
 *
 * If a Reaction does not exist for this model, or a KineticLaw for the
 * Reaction, a new Parameter is not created and @c NULL is returned.
 */
LocalParameter*
Model::createKineticLawLocalParameter ()
{
  unsigned int size = getNumReactions();

  if (size > 0)
  {
    KineticLaw* kl = getReaction(size - 1)->getKineticLaw();
    if (kl != NULL) return kl->createLocalParameter();
  }

  return NULL;
}


/*
 * Creates a new Event inside this Model and returns it.
 */
Event*
Model::createEvent ()
{
  Event* e = NULL;

  try
  {
    e = new Event(getSBMLNamespaces());
  }
  catch (...)
  {
    /* here we do not create a default object as the level/version must
     * match the parent object
     *
     * so do nothing
     */
    return NULL;
  }

  if (e != NULL) mEvents.appendAndOwn(e);

  return e;
}


/*
 * Creates a new EventAssignment inside this Model and returns a pointer to
 * it.  The EventAssignment is added to the the last Event created.
 *
 * If an Event does not exist for this model, a new EventAssignment is not
 * created and @c NULL is returned.
 */
EventAssignment*
Model::createEventAssignment ()
{
  unsigned int size = getNumEvents();
  return (size > 0) ? getEvent(size - 1)->createEventAssignment() : NULL;
}


/*
 * Creates a new Trigger inside this Model and returns a pointer to
 * it.  The Trigger is added to the the last Event created.
 *
 * If an Event does not exist for this model, a new Trigger is not
 * created and @c NULL is returned.
 */
Trigger*
Model::createTrigger ()
{
  unsigned int size = getNumEvents();
  return (size > 0) ? getEvent(size - 1)->createTrigger() : NULL;
}


/*
 * Creates a new Delay inside this Model and returns a pointer to
 * it.  The Delay is added to the the last Event created.
 *
 * If an Event does not exist for this model, a new Delay is not
 * created and @c NULL is returned.
 */
Delay*
Model::createDelay ()
{
  unsigned int size = getNumEvents();
  return (size > 0) ? getEvent(size - 1)->createDelay() : NULL;
}


/*
 * Sets the annotation of this SBML object to a copy of annotation.
 */
int
Model::setAnnotation (const XMLNode* annotation)
{
  int success = SBase::setAnnotation(annotation);

  if (success == 0)
  {
    //
    // delete existing mHistory
    //
    // existing mHistory (if any) needs to be deleted at any rate, otherwise
    // unsetAnnotation() ( setAnnotation(NULL) ) doesn't work as expected.
    // (These functions must clear all elements in an annotation.)
    //
    delete mHistory;
    mHistory = NULL;

    if(mAnnotation != NULL
       && RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
    {
      // parse mAnnotation (if any) and set mHistory
      mHistory = RDFAnnotationParser::parseRDFAnnotation(mAnnotation);
      mHistoryChanged = true;

    }
  }

  return success;
}


/*
 * Sets the annotation (by string) of this SBML object to a copy of annotation.
 */
int
Model::setAnnotation (const std::string& annotation)
{
  int success = LIBSBML_OPERATION_FAILED;
  if(annotation.empty())
  {
    unsetAnnotation();
    return LIBSBML_OPERATION_SUCCESS;
  }

  XMLNode* annt_xmln;
  if (getSBMLDocument())
  {
    XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
    annt_xmln = XMLNode::convertStringToXMLNode(annotation,xmlns);
  }
  else
  {
    annt_xmln = XMLNode::convertStringToXMLNode(annotation);
  }

  if(annt_xmln != NULL)
  {
    success = setAnnotation(annt_xmln);
    delete annt_xmln;
  }
  return success;
}


/*
 * Appends annotation to the existing annotations.
 * This allows other annotations to be preserved whilst
 * adding additional information.
 */
int
Model::appendAnnotation (const XMLNode* annotation)
{
  // take out any attempt to merge RDF

  return SBase::appendAnnotation(annotation);

//  int success = LIBSBML_OPERATION_FAILED;
//  if(annotation == NULL) return LIBSBML_OPERATION_SUCCESS;
//
//  XMLNode* new_annotation = NULL;
//  const string&  name = annotation->getName();
//
//  // check for annotation tags and add if necessary
//  if (name != "annotation")
//  {
//    XMLToken ann_t = XMLToken(XMLTriple("annotation", "", ""), XMLAttributes());
//    new_annotation = new XMLNode(ann_t);
//    new_annotation->addChild(*annotation);
//  }
//  else
//  {
//    new_annotation = annotation->clone();
//  }
//
//  // parse new_annotation and reset mHistory
//  if (RDFAnnotationParser::hasHistoryRDFAnnotation(new_annotation))
//  {
//    ModelHistory* new_mhistory = RDFAnnotationParser::parseRDFAnnotation(new_annotation);
//    if(new_mhistory != NULL)
//    {
//      delete mHistory;
//      mHistory = new_mhistory;
////      mHistoryChanged = true;
//    }
//  }
//
//  success = SBase::appendAnnotation(new_annotation);
//
//  delete new_annotation;
//
//  return success;
}


/*
 * Appends annotation (by string) to the existing annotations.
 * This allows other annotations to be preserved whilst
 * adding additional information.
 */
int
Model::appendAnnotation (const std::string& annotation)
{
  int success = LIBSBML_OPERATION_FAILED;
  XMLNode* annt_xmln;
  if (getSBMLDocument() != NULL)
  {
    XMLNamespaces* xmlns = getSBMLDocument()->getNamespaces();
    annt_xmln = XMLNode::convertStringToXMLNode(annotation,xmlns);
  }
  else
  {
    annt_xmln = XMLNode::convertStringToXMLNode(annotation);
  }

  if(annt_xmln != NULL)
  {
    success = appendAnnotation(annt_xmln);
    delete annt_xmln;
  }

  return success;
}


/** @cond doxygenLibsbmlInternal */
/*
 * Synchronizes the annotation of this SBML object.
 */
void
Model::syncAnnotation ()
{
  SBase::syncAnnotation();

  //if (mAnnotationChanged == false)
  //  return;

  //if (mHistoryChanged == false && mCVTermsChanged == false)
  //  return;
  //else
  //  reconstructRDFAnnotation();

  //bool hasRDF = false;
  //bool hasAdditionalRDF = false;
  //// determine status of existing annotation before doing anything
  //if (mAnnotation != NULL)
  //{
  //  hasRDF = RDFAnnotationParser::hasRDFAnnotation(mAnnotation);
  //  hasAdditionalRDF =
  //    RDFAnnotationParser::hasAdditionalRDFAnnotation(mAnnotation);
  //}

  //XMLNode * history = RDFAnnotationParser::parseModelHistory(this);

  //if(mAnnotation != NULL && hasRDF && mHistoryChanged == true)
  //{
  //  XMLNode* new_annotation = RDFAnnotationParser::deleteRDFAnnotation(mAnnotation);
  //  if(new_annotation == NULL)
  //  {
  //    XMLToken ann_token = XMLToken(XMLTriple("annotation", "", ""), XMLAttributes());
  //    new_annotation = new XMLNode(ann_token);
  //    new_annotation->addChild(*mAnnotation);
  //  }
  //  *mAnnotation = *new_annotation;
  //  delete new_annotation;
  //}

  //if (history != NULL)
  //{
  //  if (mHistoryChanged == true)
  //  {
  //    if (mAnnotation == NULL)
  //    {
  //      mAnnotation = history;
  //    }
  //    else
  //    {
  //      if (mAnnotation->isEnd())
  //      {
  //        mAnnotation->unsetEnd();
  //      }
  //      if (hasAdditionalRDF)
  //      {
  //        //need to insert the history into existing RDF
  //        unsigned int n = 0;
  //        while (n < mAnnotation->getNumChildren())
  //        {
  //          if (mAnnotation->getChild(n).getName() == "RDF")
  //          {
  //            mAnnotation->getChild(n).insertChild(0,
  //              history->getChild(0).getChild(0));
  //            break;
  //          }
  //          n++;
  //        }
  //      }
  //      else
  //      {
  //        mAnnotation->addChild(history->getChild(0));
  //      }
  //      delete history;
  //    }
  //  }
  //}
  //else
  //{
  //  // Annotations for CVTerm are added by the above RDFAnnotationParser::parseModelHistory(this)
  //  // if and only if mHistory is not NULL.
  //  // Thus, annotations for CVTerm (if any) needs to be added here if history (mHistory) is NULL.
  //  SBase::syncAnnotation();
  //}

}
/** @endcond */


/*
 * @return the list of FunctionDefinitions for this Model.
 */
const ListOfFunctionDefinitions*
Model::getListOfFunctionDefinitions () const
{
  return &mFunctionDefinitions;
}


/*
 * @return the list of FunctionDefinitions for this Model.
 */
ListOfFunctionDefinitions*
Model::getListOfFunctionDefinitions ()
{
  return &mFunctionDefinitions;
}


/*
 * @return the list of UnitDefinitions for this Model.
 */
const ListOfUnitDefinitions*
Model::getListOfUnitDefinitions () const
{
  return &mUnitDefinitions;
}


/*
 * @return the list of UnitDefinitions for this Model.
 */
ListOfUnitDefinitions*
Model::getListOfUnitDefinitions ()
{
  return &mUnitDefinitions;
}


/*
 * @return the list of CompartmentTypes for this Model.
 */
const ListOfCompartmentTypes*
Model::getListOfCompartmentTypes () const
{
  return &mCompartmentTypes;
}


/*
 * @return the list of CompartmentTypes for this Model.
 */
ListOfCompartmentTypes*
Model::getListOfCompartmentTypes ()
{
  return &mCompartmentTypes;
}


/*
 * @return the list of SpeciesTypes for this Model.
 */
const ListOfSpeciesTypes*
Model::getListOfSpeciesTypes () const
{
  return &mSpeciesTypes;
}


/*
 * @return the list of SpeciesTypes for this Model.
 */
ListOfSpeciesTypes*
Model::getListOfSpeciesTypes ()
{
  return &mSpeciesTypes;
}


/*
 * @return the list of Compartments for this Model.
 */
const ListOfCompartments*
Model::getListOfCompartments () const
{
  return &mCompartments;
}


/*
 * @return the list of Compartments for this Model.
 */
ListOfCompartments*
Model::getListOfCompartments ()
{
  return &mCompartments;
}


/*
 * @return the list of Species for this Model.
 */
const ListOfSpecies*
Model::getListOfSpecies () const
{
  return &mSpecies;
}


/*
 * @return the list of Species for this Model.
 */
ListOfSpecies*
Model::getListOfSpecies ()
{
  return &mSpecies;
}


/*
 * @return the list of Parameters for this Model.
 */
const ListOfParameters*
Model::getListOfParameters () const
{
  return &mParameters;
}


/*
 * @return the list of Parameters for this Model.
 */
ListOfParameters*
Model::getListOfParameters ()
{
  return &mParameters;
}


/*
 * @return the list of InitialAssignments for this Model.
 */
const ListOfInitialAssignments*
Model::getListOfInitialAssignments () const
{
  return &mInitialAssignments;
}


/*
 * @return the list of InitialAssignment for this Model.
 */
ListOfInitialAssignments*
Model::getListOfInitialAssignments ()
{
  return &mInitialAssignments;
}


/*
 * @return the list of Rules for this Model.
 */
const ListOfRules*
Model::getListOfRules () const
{
  return &mRules;
}


/*
 * @return the list of Rules for this Model.
 */
ListOfRules*
Model::getListOfRules ()
{
  return &mRules;
}


/*
 * @return the list of Constraints for this Model.
 */
const ListOfConstraints*
Model::getListOfConstraints () const
{
  return &mConstraints;
}


/*
 * @return the list of Constraints for this Model.
 */
ListOfConstraints*
Model::getListOfConstraints ()
{
  return &mConstraints;
}


/*
 * @return the list of Reactions for this Model.
 */
const ListOfReactions*
Model::getListOfReactions () const
{
  return &mReactions;
}


/*
 * @return the list of Reactions for this Model.
 */
ListOfReactions*
Model::getListOfReactions ()
{
  return &mReactions;
}


/*
 * @return the list of Events for this Model.
 */
const ListOfEvents*
Model::getListOfEvents () const
{
  return &mEvents;
}


/*
 * @return the list of Events for this Model.
 */
ListOfEvents*
Model::getListOfEvents ()
{
  return &mEvents;
}


/*
 * @return the nth FunctionDefinition of this Model.
 */
const FunctionDefinition*
Model::getFunctionDefinition (unsigned int n) const
{
  return static_cast<const FunctionDefinition*>( mFunctionDefinitions.get(n) );
}


/*
 * @return the nth FunctionDefinition of this Model.
 */
FunctionDefinition*
Model::getFunctionDefinition (unsigned int n)
{
  return static_cast<FunctionDefinition*>( mFunctionDefinitions.get(n) );
}


/*
 * @return the FunctionDefinition in this Model with the given @p id or @c NULL
 * if no such FunctionDefinition exists.
 */
const FunctionDefinition*
Model::getFunctionDefinition (const std::string& sid) const
{
  return static_cast<const FunctionDefinition*>(mFunctionDefinitions.get(sid));
}


/*
 * @return the FunctionDefinition in this Model with the given @p id or @c NULL
 * if no such FunctionDefinition exists.
 */
FunctionDefinition*
Model::getFunctionDefinition (const std::string& sid)
{
  return static_cast<FunctionDefinition*>( mFunctionDefinitions.get(sid) );
}


/*
 * @return the nth UnitDefinition of this Model.
 */
const UnitDefinition*
Model::getUnitDefinition (unsigned int n) const
{
  return static_cast<const UnitDefinition*>( mUnitDefinitions.get(n) );
}


/*
 * @return the nth UnitDefinition of this Model.
 */
UnitDefinition*
Model::getUnitDefinition (unsigned int n)
{
  return static_cast<UnitDefinition*>( mUnitDefinitions.get(n) );
}


/*
 * @return the UnitDefinition in this Model with the given @p id or @c NULL if no
 * such UnitDefinition exists.
 */
const UnitDefinition*
Model::getUnitDefinition (const std::string& sid) const
{
  return static_cast<const UnitDefinition*>( mUnitDefinitions.get(sid) );
}


/*
 * @return the UnitDefinition in this Model with the given @p id or @c NULL if no
 * such UnitDefinition exists.
 */
UnitDefinition*
Model::getUnitDefinition (const std::string& sid)
{
  return static_cast<UnitDefinition*>( mUnitDefinitions.get(sid) );
}


/*
 * @return the nth CompartmentType of this Model.
 */
const CompartmentType*
Model::getCompartmentType (unsigned int n) const
{
  return static_cast<const CompartmentType*>( mCompartmentTypes.get(n) );
}


/*
 * @return the nth CompartmentType of this Model.
 */
CompartmentType*
Model::getCompartmentType (unsigned int n)
{
  return static_cast<CompartmentType*>( mCompartmentTypes.get(n) );
}


/*
 * @return the CompartmentType in this Model with the given @p id or @c NULL if
 * no such CompartmentType exists.
 */
const CompartmentType*
Model::getCompartmentType (const std::string& sid) const
{
  return static_cast<const CompartmentType*>( mCompartmentTypes.get(sid) );
}


/*
 * @return the CompartmentType in this Model with the given @p id or @c NULL if
 * no such CompartmentType exists.
 */
CompartmentType*
Model::getCompartmentType (const std::string& sid)
{
  return static_cast<CompartmentType*>( mCompartmentTypes.get(sid) );
}


/*
 * @return the nth SpeciesType of this Model.
 */
const SpeciesType*
Model::getSpeciesType (unsigned int n) const
{
  return static_cast<const SpeciesType*>( mSpeciesTypes.get(n) );
}


/*
 * @return the nth SpeciesType of this Model.
 */
SpeciesType*
Model::getSpeciesType (unsigned int n)
{
  return static_cast<SpeciesType*>( mSpeciesTypes.get(n) );
}


/*
 * @return the SpeciesType in this Model with the given @p id or @c NULL if
 * no such SpeciesType exists.
 */
const SpeciesType*
Model::getSpeciesType (const std::string& sid) const
{
  return static_cast<const SpeciesType*>( mSpeciesTypes.get(sid) );
}


/*
 * @return the SpeciesType in this Model with the given @p id or @c NULL if
 * no such SpeciesType exists.
 */
SpeciesType*
Model::getSpeciesType (const std::string& sid)
{
  return static_cast<SpeciesType*>( mSpeciesTypes.get(sid) );
}


/*
 * @return the nth Compartment of this Model.
 */
const Compartment*
Model::getCompartment (unsigned int n) const
{
  return static_cast<const Compartment*>( mCompartments.get(n) );
}


/*
 * @return the nth Compartment of this Model.
 */
Compartment*
Model::getCompartment (unsigned int n)
{
  return static_cast<Compartment*>( mCompartments.get(n) );
}


/*
 * @return the Compartment in this Model with the given @p id or @c NULL if no
 * such Compartment exists.
 */
const Compartment*
Model::getCompartment (const std::string& sid) const
{
  return static_cast<const Compartment*>( mCompartments.get(sid) );
}


/*
 * @return the Compartment in this Model with the given @p id or @c NULL if no
 * such Compartment exists.
 */
Compartment*
Model::getCompartment (const std::string& sid)
{
  return static_cast<Compartment*>( mCompartments.get(sid) );
}


/*
 * @return the nth Species of this Model.
 */
const Species*
Model::getSpecies (unsigned int n) const
{
  return static_cast<const Species*>( mSpecies.get(n) );
}


/*
 * @return the nth Species of this Model.
 */
Species*
Model::getSpecies (unsigned int n)
{
  return static_cast<Species*>( mSpecies.get(n) );
}


/*
 * @return the Species in this Model with the given @p id or @c NULL if no such
 * Species exists.
 */
const Species*
Model::getSpecies (const std::string& sid) const
{
  return static_cast<const Species*>( mSpecies.get(sid) );
}


/*
 * @return the Species in this Model with the given @p id or @c NULL if no such
 * Species exists.
 */
Species*
Model::getSpecies (const std::string& sid)
{
  return static_cast<Species*>( mSpecies.get(sid) );
}


/*
 * @return the nth Parameter of this Model.
 */
const Parameter*
Model::getParameter (unsigned int n) const
{
  return static_cast<const Parameter*>( mParameters.get(n) );
}


/*
 * @return the nth Parameter of this Model.
 */
Parameter*
Model::getParameter (unsigned int n)
{
  return static_cast<Parameter*>( mParameters.get(n) );
}


/*
 * @return the Parameter in this Model with the given @p id or @c NULL if no such
 * Parameter exists.
 */
const Parameter*
Model::getParameter (const std::string& sid) const
{
  return static_cast<const Parameter*>( mParameters.get(sid) );
}


/*
 * @return the Parameter in this Model with the given @p id or @c NULL if no such
 * Parameter exists.
 */
Parameter*
Model::getParameter (const std::string& sid)
{
  return static_cast<Parameter*>( mParameters.get(sid) );
}


/*
 * @return the nth InitialAssignment of this Model.
 */
const InitialAssignment*
Model::getInitialAssignment (unsigned int n) const
{
  return static_cast<const InitialAssignment*>( mInitialAssignments.get(n) );
}


/*
 * @return the nth InitialAssignment of this Model.
 */
InitialAssignment*
Model::getInitialAssignment (unsigned int n)
{
  return static_cast<InitialAssignment*>( mInitialAssignments.get(n) );
}


/*
 * @return the InitialAssignment in this Model with the given symbol or
 * @c NULL if no such InitialAssignment exists.
 */
const InitialAssignment*
Model::getInitialAssignment (const std::string& symbol) const
{
  return static_cast<const InitialAssignment*>
  (
    mInitialAssignments.get(symbol)
  );
}

/*
 * @return the InitialAssignment in this Model with the given symbol or
 * @c NULL if no such InitialAssignment exists.
 */
const InitialAssignment*
Model::getInitialAssignmentBySymbol(const std::string& symbol) const
{
  return getInitialAssignment(symbol);
}


/*
 * @return the InitialAssignment in this Model with the given symbol or
 * @c NULL if no such InitialAssignment exists.
 */
InitialAssignment*
Model::getInitialAssignment (const std::string& symbol)
{
  return static_cast<InitialAssignment*>( mInitialAssignments.get(symbol) );
}


/*
 * @return the InitialAssignment in this Model with the given symbol or
 * @c NULL if no such InitialAssignment exists.
 */
InitialAssignment*
Model::getInitialAssignmentBySymbol(const std::string& symbol)
{
  return getInitialAssignment(symbol);
}


/*
 * @return the nth Rule of this Model.
 */
const Rule*
Model::getRule (unsigned int n) const
{
  return static_cast<const Rule*>( mRules.get(n) );
}


/*
 * @return the nth Rule of this Model.
 */
Rule*
Model::getRule (unsigned int n)
{
  return static_cast<Rule*>( mRules.get(n) );
}


/*
 * @return the Rule in this Model with the given variable or @c NULL if no
 * such Rule exists.
 */
const Rule*
Model::getRule (const std::string& variable) const
{
  return static_cast<const Rule*>( mRules.get(variable) );
}


/*
 * @return the Rule in this Model with the given symbol or @c NULL if no
 * such Rule exists.
 */
Rule*
Model::getRule (const std::string& variable)
{
  return static_cast<Rule*>( mRules.get(variable) );
}


/*
 * @return the Rule in this Model with the given variable or @c NULL if no
 * such Rule exists.
 */
const Rule*
Model::getRuleByVariable(const std::string& variable) const
{
  return getRule(variable);
}


/*
 * @return the Rule in this Model with the given symbol or @c NULL if no
 * such Rule exists.
 */
Rule*
Model::getRuleByVariable(const std::string& variable)
{
  return getRule(variable);
}



/*
 * @return the Rule in this Model with the given variable or @c NULL if no
 * such Rule exists.
 */
const AssignmentRule*
Model::getAssignmentRule (const std::string& variable) const
{
  const Rule * rule = static_cast<const Rule*>( mRules.get(variable) );

  if (rule != NULL && rule->getTypeCode() == SBML_ASSIGNMENT_RULE)
  {
    return static_cast<const AssignmentRule*>(rule);
  }
  else
  {
    return NULL;
  }
}


/*
 * @return the Rule in this Model with the given symbol or @c NULL if no
 * such Rule exists.
 */
AssignmentRule*
Model::getAssignmentRule (const std::string& variable)
{
  Rule * rule = static_cast<Rule*>( mRules.get(variable) );

  if (rule != NULL && rule->getTypeCode() == SBML_ASSIGNMENT_RULE)
  {
    return static_cast<AssignmentRule*>(rule);
  }
  else
  {
    return NULL;
  }
}



/*
 * @return the Rule in this Model with the given variable or @c NULL if no
 * such Rule exists.
 */
const RateRule*
Model::getRateRule (const std::string& variable) const
{
  const Rule * rule = static_cast<const Rule*>( mRules.get(variable) );

  if (rule != NULL && rule->getTypeCode() == SBML_RATE_RULE)
  {
    return static_cast<const RateRule*>(rule);
  }
  else
  {
    return NULL;
  }
}


/*
 * @return the Rule in this Model with the given symbol or @c NULL if no
 * such Rule exists.
 */
RateRule*
Model::getRateRule (const std::string& variable)
{
  Rule * rule = static_cast<Rule*>( mRules.get(variable) );

  if (rule != NULL && rule->getTypeCode() == SBML_RATE_RULE)
  {
    return static_cast<RateRule*>(rule);
  }
  else
  {
    return NULL;
  }
}


/*
 * @return the Rule in this Model with the given variable or @c NULL if no
 * such Rule exists.
 */
const AssignmentRule*
Model::getAssignmentRuleByVariable(const std::string& variable) const
{
  return getAssignmentRule(variable);
}


/*
 * @return the Rule in this Model with the given symbol or @c NULL if no
 * such Rule exists.
 */
AssignmentRule*
Model::getAssignmentRuleByVariable(const std::string& variable)
{
  return getAssignmentRule(variable);
}



/*
 * @return the Rule in this Model with the given variable or @c NULL if no
 * such Rule exists.
 */
const RateRule*
Model::getRateRuleByVariable(const std::string& variable) const
{
  return getRateRule(variable);
}


/*
 * @return the Rule in this Model with the given symbol or @c NULL if no
 * such Rule exists.
 */
RateRule*
Model::getRateRuleByVariable(const std::string& variable)
{
  return getRateRule(variable);
}


/*
 * @return the nth Constraint of this Model.
 */
const Constraint*
Model::getConstraint (unsigned int n) const
{
  return static_cast<const Constraint*>( mConstraints.get(n) );
}


/*
 * @return the nth Constraint of this Model.
 */
Constraint*
Model::getConstraint (unsigned int n)
{
  return static_cast<Constraint*>( mConstraints.get(n) );
}


/*
 * @return the nth Reaction of this Model.
 */
const Reaction*
Model::getReaction (unsigned int n) const
{
  return static_cast<const Reaction*>( mReactions.get(n) );
}


/*
 * @return the nth Reaction of this Model.
 */
Reaction*
Model::getReaction (unsigned int n)
{
  return static_cast<Reaction*>( mReactions.get(n) );
}


/*
 * @return the Reaction in this Model with the given @p id or @c NULL if no such
 * Reaction exists.
 */
const Reaction*
Model::getReaction (const std::string& sid) const
{
  return static_cast<const Reaction*>( mReactions.get(sid) );
}


/*
 * @return the Reaction in this Model with the given @p id or @c NULL if no such
 * Reaction exists.
 */
Reaction*
Model::getReaction (const std::string& sid)
{
  return static_cast<Reaction*>( mReactions.get(sid) );
}


/**
 * Get a SpeciesReference object based on its identifier.
 */
SpeciesReference*
Model::getSpeciesReference (const std::string& sid)
{
  SpeciesReference* sr = NULL;
  for (unsigned int i = 0; i < getNumReactions(); i++)
  {
    sr = getReaction(i)->getReactant(sid);
    if (sr != NULL) break;

    sr = getReaction(i)->getProduct(sid);
    if (sr != NULL) break;
  }

  return sr;
}

const SpeciesReference*
Model::getSpeciesReference (const std::string& sid) const
{
  const SpeciesReference* sr = NULL;
  for (unsigned int i = 0; i < getNumReactions(); i++)
  {
    sr = getReaction(i)->getReactant(sid);
    if (sr != NULL) break;

    sr = getReaction(i)->getProduct(sid);
    if (sr != NULL) break;
  }

  return sr;
}


const ModifierSpeciesReference*
Model::getModifierSpeciesReference (const std::string& sid) const
{
  const ModifierSpeciesReference* sr = NULL;
  for (unsigned int i = 0; i < getNumReactions(); i++)
  {
    sr = getReaction(i)->getModifier(sid);
    if (sr != NULL) break;
  }

  return sr;
}


ModifierSpeciesReference*
Model::getModifierSpeciesReference (const std::string& sid)
{
  ModifierSpeciesReference* sr = NULL;
  for (unsigned int i = 0; i < getNumReactions(); i++)
  {
    sr = getReaction(i)->getModifier(sid);
    if (sr != NULL) break;
  }

  return sr;
}


/*
 * @return the nth Event of this Model.
 */
const Event*
Model::getEvent (unsigned int n) const
{
  return static_cast<const Event*>( mEvents.get(n) );
}


/*
 * @return the nth Event of this Model.
 */
Event*
Model::getEvent (unsigned int n)
{
  return static_cast<Event*>( mEvents.get(n) );
}


/*
 * @return the Event in this Model with the given @p id or @c NULL if no such
 * Event exists.
 */
const Event*
Model::getEvent (const std::string& sid) const
{
  return static_cast<const Event*>( mEvents.get(sid) );
}


/*
 * @return the Event in this Model with the given @p id or @c NULL if no such
 * Event exists.
 */
Event*
Model::getEvent (const std::string& sid)
{
  return static_cast<Event*>( mEvents.get(sid) );
}


/*
 * @return the number of FunctionDefinitions in this Model.
 */
unsigned int
Model::getNumFunctionDefinitions () const
{
  return mFunctionDefinitions.size();
}


/*
 * @return the number of UnitDefinitions in this Model.
 */
unsigned int
Model::getNumUnitDefinitions () const
{
  return mUnitDefinitions.size();
}


/*
 * @return the number of CompartmentTypes in this Model.
 */
unsigned int
Model::getNumCompartmentTypes () const
{
  return mCompartmentTypes.size();
}


/*
 * @return the number of SpeciesTypes in this Model.
 */
unsigned int
Model::getNumSpeciesTypes () const
{
  return mSpeciesTypes.size();
}


/*
 * @return the number of Compartments in this Model.
 */
unsigned int
Model::getNumCompartments () const
{
  return mCompartments.size();
}


/*
 * @return the number of Species in this Model.
 */
unsigned int
Model::getNumSpecies () const
{
  return mSpecies.size();
}


/*
 * @return the number of Species in this Model with boundaryCondition set
 * to true.
 */
unsigned int
Model::getNumSpeciesWithBoundaryCondition () const
{
  unsigned int count = 0;

  for(unsigned int i = 0; i < mSpecies.size(); i++)
  {
    if (getSpecies(i)->getBoundaryCondition())
      count++;
  }
  return count;
}


/*
 * @return the number of Parameters in this Model.  Parameters defined in
 * KineticLaws are not included.
 */
unsigned int
Model::getNumParameters () const
{
  return mParameters.size();
}


/*
 * @return the number of InitialAssignments in this Model.
 */
unsigned int
Model::getNumInitialAssignments () const
{
  return mInitialAssignments.size();
}


/*
 * @return the number of Rules in this Model.
 */
unsigned int
Model::getNumRules () const
{
  return mRules.size();
}


/*
 * @return the number of Constraints in this Model.
 */
unsigned int
Model::getNumConstraints () const
{
  return mConstraints.size();
}


/*
 * @return the number of Reactions in this Model.
 */
unsigned int
Model::getNumReactions () const
{
  return mReactions.size();
}


/*
 * @return the number of Events in this Model.
 */
unsigned int
Model::getNumEvents () const
{
  return mEvents.size();
}

int Model::removeFromParentAndDelete()
{
  SBase* parent = getParentSBMLObject();
  if (parent==NULL) return LIBSBML_OPERATION_FAILED;
  SBMLDocument* parentDoc= static_cast<SBMLDocument*>(parent);
  if (parentDoc== NULL) return LIBSBML_OPERATION_FAILED;
  return parentDoc->setModel(NULL);
}


/** @cond doxygenLibsbmlInternal */
/*
 * @return @c true if the given ASTNode is a boolean.  Often times, this
 * question can be answered with the ASTNode's own isBoolean() method,
 * but if the AST is an expression that calls a function defined in the
 * Model's ListOf FunctionDefinitions, the model is needed for lookup
 * context.
 */
LIBSBML_EXTERN
bool
Model::isBoolean (const ASTNode* node) const
{
  if (node == NULL)
  {
    return false;
  }

  else if ( node->isBoolean() )
  {
    return true;
  }

  else if (node->getType() == AST_FUNCTION)
  {
    const FunctionDefinition* fd = getFunctionDefinition( node->getName() );

    if (fd != NULL && fd->isSetMath())
    {
      return isBoolean( fd->getBody() );
    }
    else
    {
      return false;
    }
  }

  else if (node->getType() == AST_FUNCTION_PIECEWISE)
  {
    for (unsigned int c = 0; c < node->getNumChildren(); c += 2)
    {
      if ( !isBoolean( node->getChild(c) ) ) return false;
    }

    return true;
  }

  return false;
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
/*
 * Sets the parent SBMLDocument of this SBML object.
 */
void
Model::setSBMLDocument (SBMLDocument* d)
{
  SBase::setSBMLDocument(d);

  mFunctionDefinitions.setSBMLDocument(d);
  mUnitDefinitions    .setSBMLDocument(d);
  mCompartmentTypes   .setSBMLDocument(d);
  mSpeciesTypes       .setSBMLDocument(d);
  mCompartments       .setSBMLDocument(d);
  mSpecies            .setSBMLDocument(d);
  mParameters         .setSBMLDocument(d);
  mInitialAssignments .setSBMLDocument(d);
  mRules              .setSBMLDocument(d);
  mConstraints        .setSBMLDocument(d);
  mReactions          .setSBMLDocument(d);
  mEvents             .setSBMLDocument(d);

}

/*
 * Sets this SBML object to child SBML objects (if any).
 * (Creates a child-parent relationship by the parent)
  */
void
Model::connectToChild()
{
      SBase::connectToChild();
    mFunctionDefinitions.connectToParent(this);
    mUnitDefinitions    .connectToParent(this);
    mCompartmentTypes   .connectToParent(this);
    mSpeciesTypes       .connectToParent(this);
    mCompartments       .connectToParent(this);
    mSpecies            .connectToParent(this);
    mParameters         .connectToParent(this);
    mInitialAssignments .connectToParent(this);
    mRules              .connectToParent(this);
    mConstraints        .connectToParent(this);
    mReactions          .connectToParent(this);
    mEvents             .connectToParent(this);
}


/**
 * Enables/Disables the given package with this element and child
 * elements (if any).
 * (This is an internal implementation for enablePackage function)
 */
void
Model::enablePackageInternal(const std::string& pkgURI,
                             const std::string& pkgPrefix, bool flag)
{
  SBase::enablePackageInternal(pkgURI,pkgPrefix,flag);

  mFunctionDefinitions.enablePackageInternal(pkgURI,pkgPrefix,flag);
  mUnitDefinitions    .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mCompartmentTypes   .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mSpeciesTypes       .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mCompartments       .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mSpecies            .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mParameters         .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mInitialAssignments .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mRules              .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mConstraints        .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mReactions          .enablePackageInternal(pkgURI,pkgPrefix,flag);
  mEvents             .enablePackageInternal(pkgURI,pkgPrefix,flag);
}


void
Model::updateSBMLNamespace(const std::string& pkg, unsigned int level,
  unsigned int version)
{
  SBase::updateSBMLNamespace(pkg, level, version);

  mFunctionDefinitions.updateSBMLNamespace(pkg, level, version);
  mUnitDefinitions.updateSBMLNamespace(pkg, level, version);
  mCompartmentTypes.updateSBMLNamespace(pkg, level, version);
  mSpeciesTypes.updateSBMLNamespace(pkg, level, version);
  mCompartments.updateSBMLNamespace(pkg, level, version);
  mSpecies.updateSBMLNamespace(pkg, level, version);
  mParameters.updateSBMLNamespace(pkg, level, version);
  mInitialAssignments.updateSBMLNamespace(pkg, level, version);
  mRules.updateSBMLNamespace(pkg, level, version);
  mConstraints.updateSBMLNamespace(pkg, level, version);
  mReactions.updateSBMLNamespace(pkg, level, version);
  mEvents.updateSBMLNamespace(pkg, level, version);

}
/** @endcond */


/*
 * @return the typecode (int) of this SBML object or SBML_UNKNOWN
 * (default).
 *
 * @see getElementName()
 */
int
Model::getTypeCode () const
{
  return SBML_MODEL;
}


/*
 * @return the name of this element ie "model".

 */
const string&
Model::getElementName () const
{
  static const string name = "model";
  return name;
}


bool
Model::hasRequiredElements() const
{
  bool allPresent = true;

  /* required attributes for model: compart(L1); species (L1V1)
   * reaction (L1V1)
   */

  if (getLevel() == 1)
  {
    if (getNumCompartments() == 0)
      allPresent = false;

    if (getVersion() == 1)
    {
      if (getNumSpecies() == 0)
        allPresent = false;
      if (getNumReactions() == 0)
        allPresent = false;
    }
  }
  return allPresent;
}


/**
 * Removes the nth FunctionDefinition object from this Model object and
 * returns a pointer to it.
 */
FunctionDefinition*
Model::removeFunctionDefinition (unsigned int n)
{
  return mFunctionDefinitions.remove(n);
}


/**
 * Removes the FunctionDefinition object with the given identifier from this Model
 * object and returns a pointer to it.
 */
FunctionDefinition*
Model::removeFunctionDefinition (const std::string& sid)
{
  return mFunctionDefinitions.remove(sid);
}


/**
 * Removes the nth UnitDefinition object from this Model object and
 * returns a pointer to it.
 */
UnitDefinition*
Model::removeUnitDefinition (unsigned int n)
{
  return mUnitDefinitions.remove(n);
}


/**
 * Removes the UnitDefinition object with the given identifier from this Model
 * object and returns a pointer to it.
 */
UnitDefinition*
Model::removeUnitDefinition (const std::string& sid)
{
  return mUnitDefinitions.remove(sid);
}


/**
 * Removes the nth CompartmentType object from this Model object and
 * returns a pointer to it.
 */
CompartmentType*
Model::removeCompartmentType (unsigned int n)
{
  return mCompartmentTypes.remove(n);
}


/**
 * Removes the CompartmentType object with the given identifier from this Model
 * object and returns a pointer to it.
 */
CompartmentType*
Model::removeCompartmentType (const std::string& sid)
{
  return mCompartmentTypes.remove(sid);
}


/**
 * Removes the nth SpeciesType object from this Model object and
 * returns a pointer to it.
 */
SpeciesType*
Model::removeSpeciesType (unsigned int n)
{
  return mSpeciesTypes.remove(n);
}


/**
 * Removes the SpeciesType object with the given identifier from this Model
 * object and returns a pointer to it.
 */
SpeciesType*
Model::removeSpeciesType (const std::string& sid)
{
  return mSpeciesTypes.remove(sid);
}


/**
 * Removes the nth Compartment object from this Model object and
 * returns a pointer to it.
 */
Compartment*
Model::removeCompartment (unsigned int n)
{
  return mCompartments.remove(n);
}


/**
 * Removes the Compartment object with the given identifier from this Model
 * object and returns a pointer to it.
 */
Compartment*
Model::removeCompartment (const std::string& sid)
{
  return mCompartments.remove(sid);
}


/**
 * Removes the nth Species object from this Model object and
 * returns a pointer to it.
 */
Species*
Model::removeSpecies (unsigned int n)
{
  return mSpecies.remove(n);
}


/**
 * Removes the Species object with the given identifier from this Model
 * object and returns a pointer to it.
 */
Species*
Model::removeSpecies (const std::string& sid)
{
  return mSpecies.remove(sid);
}


/**
 * Removes the nth Parameter object from this Model object and
 * returns a pointer to it.
 */
Parameter*
Model::removeParameter (unsigned int n)
{
  return mParameters.remove(n);
}


/**
 * Removes the Parameter object with the given identifier from this Model
 * object and returns a pointer to it.
 */
Parameter*
Model::removeParameter (const std::string& sid)
{
  return mParameters.remove(sid);
}


/**
 * Removes the nth InitialAssignment object from this Model object and
 * returns a pointer to it.
 */
InitialAssignment*
Model::removeInitialAssignment (unsigned int n)
{
  return mInitialAssignments.remove(n);
}


/**
 * Removes the InitialAssignment object with the given identifier from this Model
 * object and returns a pointer to it.
 */
InitialAssignment*
Model::removeInitialAssignment (const std::string& sid)
{
  return mInitialAssignments.remove(sid);
}


/**
 * Removes the nth Rule object from this Model object and
 * returns a pointer to it.
 */
Rule*
Model::removeRule (unsigned int n)
{
  return mRules.remove(n);
}


/**
 * Removes the Rule object with the given identifier from this Model
 * object and returns a pointer to it.
 */
Rule*
Model::removeRule (const std::string& sid)
{
  return mRules.remove(sid);
}

/**
 * Removes the Rule object with the given variable from this Model
 * object and returns a pointer to it.
 */
Rule*
Model::removeRuleByVariable (const std::string& variable)
{
  return mRules.remove(variable);
}


/**
 * Removes the nth Constraint object from this Model object and
 * returns a pointer to it.
 */
Constraint*
Model::removeConstraint (unsigned int n)
{
  return mConstraints.remove(n);
}


/**
 * Removes the nth Reaction object from this Model object and
 * returns a pointer to it.
 */
Reaction*
Model::removeReaction (unsigned int n)
{
  return mReactions.remove(n);
}


/**
 * Removes the Reaction object with the given identifier from this Model
 * object and returns a pointer to it.
 */
Reaction*
Model::removeReaction (const std::string& sid)
{
  return mReactions.remove(sid);
}


/**
 * Removes the nth Event object from this Model object and
 * returns a pointer to it.
 */
Event*
Model::removeEvent (unsigned int n)
{
  return mEvents.remove(n);
}


/**
 * Removes the Event object with the given identifier from this Model
 * object and returns a pointer to it.
 */
Event*
Model::removeEvent (const std::string& sid)
{
  return mEvents.remove(sid);
}






/** @cond doxygenLibsbmlInternal */

/*
 * Returns the value of the "attributeName" attribute of this Model.
 */
int
Model::getAttribute(const std::string& attributeName, bool& value) const
{
  int return_value = SBase::getAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the value of the "attributeName" attribute of this Model.
 */
int
Model::getAttribute(const std::string& attributeName, int& value) const
{
  int return_value = SBase::getAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the value of the "attributeName" attribute of this Model.
 */
int
Model::getAttribute(const std::string& attributeName, double& value) const
{
  int return_value = SBase::getAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the value of the "attributeName" attribute of this Model.
 */
int
Model::getAttribute(const std::string& attributeName,
                    unsigned int& value) const
{
  int return_value = SBase::getAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the value of the "attributeName" attribute of this Model.
 */
int
Model::getAttribute(const std::string& attributeName,
                    std::string& value) const
{
  int return_value = SBase::getAttribute(attributeName, value);

  if (return_value == LIBSBML_OPERATION_SUCCESS)
  {
    return return_value;
  }

  if (attributeName == "substanceUnits")
  {
    value = getSubstanceUnits();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }
  else if (attributeName == "timeUnits")
  {
    value = getTimeUnits();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }
  else if (attributeName == "volumeUnits")
  {
    value = getVolumeUnits();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }
  else if (attributeName == "lengthUnits")
  {
    value = getLengthUnits();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }
  else if (attributeName == "areaUnits")
  {
    value = getAreaUnits();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }
  else if (attributeName == "extentUnits")
  {
    value = getExtentUnits();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }
  else if (attributeName == "conversionFactor")
  {
    value = getConversionFactor();
    return_value = LIBSBML_OPERATION_SUCCESS;
  }

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the value of the "attributeName" attribute of this Model.
 */
//int
//Model::getAttribute(const std::string& attributeName, const char* value) const
//{
//  int return_value = SBase::getAttribute(attributeName, value);
//
//  if (return_value == LIBSBML_OPERATION_SUCCESS)
//  {
//    return return_value;
//  }
//
//  if (attributeName == "substanceUnits")
//  {
//    value = getSubstanceUnits().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//  else if (attributeName == "timeUnits")
//  {
//    value = getTimeUnits().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//  else if (attributeName == "volumeUnits")
//  {
//    value = getVolumeUnits().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//  else if (attributeName == "lengthUnits")
//  {
//    value = getLengthUnits().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//  else if (attributeName == "areaUnits")
//  {
//    value = getAreaUnits().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//  else if (attributeName == "extentUnits")
//  {
//    value = getExtentUnits().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//  else if (attributeName == "conversionFactor")
//  {
//    value = getConversionFactor().c_str();
//    return_value = LIBSBML_OPERATION_SUCCESS;
//  }
//
//  return return_value;
//}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Predicate returning @c true if this Model's attribute "attributeName" is
 * set.
 */
bool
Model::isSetAttribute(const std::string& attributeName) const
{
  bool value = SBase::isSetAttribute(attributeName);

  if (attributeName == "substanceUnits")
  {
    value = isSetSubstanceUnits();
  }
  else if (attributeName == "timeUnits")
  {
    value = isSetTimeUnits();
  }
  else if (attributeName == "volumeUnits")
  {
    value = isSetVolumeUnits();
  }
  else if (attributeName == "lengthUnits")
  {
    value = isSetLengthUnits();
  }
  else if (attributeName == "areaUnits")
  {
    value = isSetAreaUnits();
  }
  else if (attributeName == "extentUnits")
  {
    value = isSetExtentUnits();
  }
  else if (attributeName == "conversionFactor")
  {
    value = isSetConversionFactor();
  }

  return value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Sets the value of the "attributeName" attribute of this Model.
 */
int
Model::setAttribute(const std::string& attributeName, bool value)
{
  int return_value = SBase::setAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Sets the value of the "attributeName" attribute of this Model.
 */
int
Model::setAttribute(const std::string& attributeName, int value)
{
  int return_value = SBase::setAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Sets the value of the "attributeName" attribute of this Model.
 */
int
Model::setAttribute(const std::string& attributeName, double value)
{
  int return_value = SBase::setAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Sets the value of the "attributeName" attribute of this Model.
 */
int
Model::setAttribute(const std::string& attributeName, unsigned int value)
{
  int return_value = SBase::setAttribute(attributeName, value);

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Sets the value of the "attributeName" attribute of this Model.
 */
int
Model::setAttribute(const std::string& attributeName,
                    const std::string& value)
{
  int return_value = SBase::setAttribute(attributeName, value);

  if (attributeName == "substanceUnits")
  {
    return_value = setSubstanceUnits(value);
  }
  else if (attributeName == "timeUnits")
  {
    return_value = setTimeUnits(value);
  }
  else if (attributeName == "volumeUnits")
  {
    return_value = setVolumeUnits(value);
  }
  else if (attributeName == "lengthUnits")
  {
    return_value = setLengthUnits(value);
  }
  else if (attributeName == "areaUnits")
  {
    return_value = setAreaUnits(value);
  }
  else if (attributeName == "extentUnits")
  {
    return_value = setExtentUnits(value);
  }
  else if (attributeName == "conversionFactor")
  {
    return_value = setConversionFactor(value);
  }

  return return_value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Sets the value of the "attributeName" attribute of this Model.
 */
//int
//Model::setAttribute(const std::string& attributeName, const char* value)
//{
//  int return_value = SBase::setAttribute(attributeName, value);
//
//  if (attributeName == "substanceUnits")
//  {
//    return_value = setSubstanceUnits(value);
//  }
//  else if (attributeName == "timeUnits")
//  {
//    return_value = setTimeUnits(value);
//  }
//  else if (attributeName == "volumeUnits")
//  {
//    return_value = setVolumeUnits(value);
//  }
//  else if (attributeName == "lengthUnits")
//  {
//    return_value = setLengthUnits(value);
//  }
//  else if (attributeName == "areaUnits")
//  {
//    return_value = setAreaUnits(value);
//  }
//  else if (attributeName == "extentUnits")
//  {
//    return_value = setExtentUnits(value);
//  }
//  else if (attributeName == "conversionFactor")
//  {
//    return_value = setConversionFactor(value);
//  }
//
//  return return_value;
//}
//
/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Unsets the value of the "attributeName" attribute of this Model.
 */
int
Model::unsetAttribute(const std::string& attributeName)
{
  int value = SBase::unsetAttribute(attributeName);

  if (attributeName == "substanceUnits")
  {
    value = unsetSubstanceUnits();
  }
  else if (attributeName == "timeUnits")
  {
    value = unsetTimeUnits();
  }
  else if (attributeName == "volumeUnits")
  {
    value = unsetVolumeUnits();
  }
  else if (attributeName == "lengthUnits")
  {
    value = unsetLengthUnits();
  }
  else if (attributeName == "areaUnits")
  {
    value = unsetAreaUnits();
  }
  else if (attributeName == "extentUnits")
  {
    value = unsetExtentUnits();
  }
  else if (attributeName == "conversionFactor")
  {
    value = unsetConversionFactor();
  }

  return value;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Creates and returns an new "elementName" object in this Model.
 */
SBase*
Model::createChildObject(const std::string& elementName)
{
  SBase* obj = NULL;

  if (elementName == "functionDefinition")
  {
    return createFunctionDefinition();
  }
  else if (elementName == "unitDefinition")
  {
    return createUnitDefinition();
  }
  else if (elementName == "compartment")
  {
    return createCompartment();
  }
  else if (elementName == "species")
  {
    return createSpecies();
  }
  else if (elementName == "parameter")
  {
    return createParameter();
  }
  else if (elementName == "initialAssignment")
  {
    return createInitialAssignment();
  }
  else if (elementName == "constraint")
  {
    return createConstraint();
  }
  else if (elementName == "reaction")
  {
    return createReaction();
  }
  else if (elementName == "event")
  {
    return createEvent();
  }
  else if (elementName == "assignmentRule")
  {
    return createAssignmentRule();
  }
  else if (elementName == "parameterAssignmentRule")
  {
    AssignmentRule *ar = createAssignmentRule();
    ar->setL1TypeCode(SBML_PARAMETER_RULE);
    return ar;
  }
  else if (elementName == "speciesAssignmentRule")
  {
    AssignmentRule *ar = createAssignmentRule();
    ar->setL1TypeCode(SBML_SPECIES_CONCENTRATION_RULE);
    return ar;
  }
  else if (elementName == "compartmentAssignmentRule")
  {
    AssignmentRule *ar = createAssignmentRule();
    ar->setL1TypeCode(SBML_COMPARTMENT_VOLUME_RULE);
    return ar;
  }
  else if (elementName == "parameterRateRule")
  {
    RateRule *ar = createRateRule();
    ar->setL1TypeCode(SBML_PARAMETER_RULE);
    return ar;
  }
  else if (elementName == "speciesRateRule")
  {
    RateRule *ar = createRateRule();
    ar->setL1TypeCode(SBML_SPECIES_CONCENTRATION_RULE);
    return ar;
  }
  else if (elementName == "compartmentRateRule")
  {
    RateRule *ar = createRateRule();
    ar->setL1TypeCode(SBML_COMPARTMENT_VOLUME_RULE);
    return ar;
  }
  else if (elementName == "rateRule")
  {
    return createRateRule();
  }
  else if (elementName == "algebraicRule")
  {
    return createAlgebraicRule();
  }
  else if (elementName == "compartmentType")
  {
    return createCompartmentType();
  }
  else if (elementName == "speciesType")
  {
    return createSpeciesType();
  }

  return obj;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Adds an new "elementName" object in this Model.
 */
int
Model::addChildObject(const std::string& elementName, const SBase* element)
{
  if (elementName == "functionDefinition" && element->getTypeCode() == SBML_FUNCTION_DEFINITION)
  {
    return addFunctionDefinition((const FunctionDefinition*)(element));
  }
  else if (elementName == "unitDefinition"  && element->getTypeCode() == SBML_UNIT_DEFINITION)
  {
    return addUnitDefinition((const UnitDefinition*)(element));
  }
  else if (elementName == "compartment"  && element->getTypeCode() == SBML_COMPARTMENT)
  {
    return addCompartment((const Compartment*)(element));
  }
  else if (elementName == "species"  && element->getTypeCode() == SBML_SPECIES)
  {
    return addSpecies((const Species*)(element));
  }
  else if (elementName == "parameter"  && element->getTypeCode() == SBML_PARAMETER)
  {
    return addParameter((const Parameter*)(element));
  }
  else if (elementName == "initialAssignment"  && element->getTypeCode() == SBML_INITIAL_ASSIGNMENT)
  {
    return addInitialAssignment((const InitialAssignment*)(element));
  }
  else if (elementName == "constraint"  && element->getTypeCode() == SBML_CONSTRAINT)
  {
    return addConstraint((const Constraint*)(element));
  }
  else if (elementName == "reaction"  && element->getTypeCode() == SBML_REACTION)
  {
    return addReaction((const Reaction*)(element));
  }
  else if (elementName == "event"  && element->getTypeCode() == SBML_EVENT)
  {
    return addEvent((const Event*)(element));
  }
  else if (elementName == "assignmentRule"  && element->getTypeCode() == SBML_ASSIGNMENT_RULE)
  {
    return addRule((const Rule*)(element));
  }
  else if (elementName == "rateRule"  && element->getTypeCode() == SBML_RATE_RULE)
  {
    return addRule((const Rule*)(element));
  }
  else if (elementName == "algebraicRule"  && element->getTypeCode() == SBML_ALGEBRAIC_RULE)
  {
    return addRule((const Rule*)(element));
  }
  else if (elementName == "compartmentType"  && element->getTypeCode() == SBML_COMPARTMENT_TYPE)
  {
    return addCompartmentType((const CompartmentType*)(element));
  }
  else if (elementName == "speciesType"  && element->getTypeCode() == SBML_SPECIES_TYPE)
  {
    return addSpeciesType((const SpeciesType*)(element));
  }

  return LIBSBML_OPERATION_FAILED;
}

/** @endcond */


/** @cond doxygenLibsbmlInternal */

/*
 * Adds an new "elementName" object in this Model.
 */
SBase*
Model::removeChildObject(const std::string& elementName, const std::string& id)
{
  if (elementName == "functionDefinition")
  {
    return removeFunctionDefinition(id);
  }
  else if (elementName == "unitDefinition")
  {
    return removeUnitDefinition(id);
  }
  else if (elementName == "compartment")
  {
    return removeCompartment(id);
  }
  else if (elementName == "species")
  {
    return removeSpecies(id);
  }
  else if (elementName == "parameter")
  {
    return removeParameter(id);
  }
  else if (elementName == "initialAssignment")
  {
    return removeInitialAssignment(id);
  }
  else if (elementName == "constraint")
  {
 //   return removeConstraint(id);
  }
  else if (elementName == "reaction")
  {
    return removeReaction(id);
  }
  else if (elementName == "event")
  {
    return removeEvent(id);
  }
  else if (elementName == "assignmentRule")
  {
    return removeRule(id);
  }
  else if (elementName == "rateRule")
  {
    return removeRule(id);
  }
  else if (elementName == "algebraicRule")
  {
    return removeRule(id);
  }
  else if (elementName == "compartmentType")
  {
    return removeCompartmentType(id);
  }
  else if (elementName == "speciesType")
  {
    return removeSpeciesType(id);
  }

  return NULL;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the number of "elementName" in this Model.
 */
unsigned int
Model::getNumObjects(const std::string& elementName)
{
  unsigned int n = 0;

  if (elementName == "functionDefinition")
  {
    return getNumFunctionDefinitions();
  }
  else if (elementName == "unitDefinition")
  {
    return getNumUnitDefinitions();
  }
  else if (elementName == "compartment")
  {
    return getNumCompartments();
  }
  else if (elementName == "species")
  {
    return getNumSpecies();
  }
  else if (elementName == "parameter")
  {
    return getNumParameters();
  }
  else if (elementName == "initialAssignment")
  {
    return getNumInitialAssignments();
  }
  else if (elementName == "constraint")
  {
    return getNumConstraints();
  }
  else if (elementName == "reaction")
  {
    return getNumReactions();
  }
  else if (elementName == "event")
  {
    return getNumEvents();
  }
  else if (elementName == "rule")
  {
    return getNumRules();
  }
  else if (elementName == "assignmentRule")
  {
    return getNumRules();
  }
  else if (elementName == "parameterAssignmentRule")
  {
    return getNumRules();
  }
  else if (elementName == "speciesAssignmentRule")
  {
    return getNumRules();
  }
  else if (elementName == "compartmentAssignmentRule")
  {
    return getNumRules();
  }
  else if (elementName == "parameterRateRule")
  {
    return getNumRules();
  }
  else if (elementName == "speciesRateRule")
  {
    return getNumRules();
  }
  else if (elementName == "compartmentRateRule")
  {
    return getNumRules();
  }
  else if (elementName == "rateRule")
  {
    return getNumRules();
  }
  else if (elementName == "algebraicRule")
  {
    return getNumRules();
  }
  else if (elementName == "compartmentType")
  {
    return getNumCompartmentTypes();
  }
  else if (elementName == "speciesType")
  {
    return getNumSpeciesTypes();
  }

  return n;
}

/** @endcond */



/** @cond doxygenLibsbmlInternal */

/*
 * Returns the nth object of "objectName" in this Model.
 */
SBase*
Model::getObject(const std::string& elementName, unsigned int index)
{
  SBase* obj = NULL;

  if (elementName == "functionDefinition")
  {
    return getFunctionDefinition(index);
  }
  else if (elementName == "unitDefinition")
  {
    return getUnitDefinition(index);
  }
  else if (elementName == "compartment")
  {
    return getCompartment(index);
  }
  else if (elementName == "species")
  {
    return getSpecies(index);
  }
  else if (elementName == "parameter")
  {
    return getParameter(index);
  }
  else if (elementName == "initialAssignment")
  {
    return getInitialAssignment(index);
  }
  else if (elementName == "constraint")
  {
    return getConstraint(index);
  }
  else if (elementName == "reaction")
  {
    return getReaction(index);
  }
  else if (elementName == "event")
  {
    return getEvent(index);
  }
  else if (elementName == "rule")
  {
    return getRule(index);
  }
  else if (elementName == "assignmentRule")
  {
    return getRule(index);
  }
  else if (elementName == "parameterAssignmentRule")
  {
    return getRule(index);
  }
  else if (elementName == "speciesAssignmentRule")
  {
    return getRule(index);
  }
  else if (elementName == "compartmentAssignmentRule")
  {
    return getRule(index);
  }
  else if (elementName == "parameterRateRule")
  {
    return getRule(index);
  }
  else if (elementName == "speciesRateRule")
  {
    return getRule(index);
  }
  else if (elementName == "compartmentRateRule")
  {
    return getRule(index);
  }
  else if (elementName == "rateRule")
 {
    return getRule(index);
  }
  else if (elementName == "algebraicRule")
  {
    return getRule(index);
  }
  else if (elementName == "compartmentType")
  {
    return getCompartmentType(index);
  }
  else if (elementName == "speciesType")
  {
    return getSpeciesType(index);
  }

  return obj;
}

/** @endcond */



int
Model::appendFrom(const Model* model)
{
  int ret = LIBSBML_OPERATION_SUCCESS;
  ret = mFunctionDefinitions.appendFrom(&model->mFunctionDefinitions);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mUnitDefinitions    .appendFrom(&model->mUnitDefinitions);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mCompartmentTypes   .appendFrom(&model->mCompartmentTypes);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mSpeciesTypes       .appendFrom(&model->mSpeciesTypes);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mCompartments       .appendFrom(&model->mCompartments);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mSpecies            .appendFrom(&model->mSpecies);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mParameters         .appendFrom(&model->mParameters);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mInitialAssignments .appendFrom(&model->mInitialAssignments);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mRules              .appendFrom(&model->mRules);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mConstraints        .appendFrom(&model->mConstraints);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mReactions          .appendFrom(&model->mReactions);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  ret = mEvents             .appendFrom(&model->mEvents);
  if (ret != LIBSBML_OPERATION_SUCCESS) return ret;

  for (size_t i=0; i < mPlugins.size(); i++) {
    ret = mPlugins[i]->appendFrom(model);
    if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  }
  return ret;
}

void
Model::renameSIdRefs(const std::string& oldid, const std::string& newid)
{
  SBase::renameSIdRefs(oldid, newid);
  if (isSetConversionFactor()) {
    if (getConversionFactor()==oldid) {
      setConversionFactor(newid);
    }
  }
}

void
Model::renameUnitSIdRefs(const std::string& oldid, const std::string& newid)
{
  SBase::renameUnitSIdRefs(oldid, newid);
  if (mSubstanceUnits == oldid) mSubstanceUnits = newid;
  if (mTimeUnits == oldid)      mTimeUnits = newid;
  if (mVolumeUnits == oldid)    mVolumeUnits = newid;
  if (mAreaUnits == oldid)      mAreaUnits = newid;
  if (mLengthUnits == oldid)    mLengthUnits = newid;
  if (mExtentUnits == oldid)    mExtentUnits = newid;
}

/** @cond doxygenLibsbmlInternal */
/*
 * Subclasses should override this method to read (and store) XHTML,
 * MathML, etc. directly from the XMLInputStream.
 *
 * @return @c true if the subclass read from the stream, false otherwise.
 */
bool
Model::readOtherXML (XMLInputStream& stream)
{
  bool          read = false;
  const string& name = stream.peek().getName();

  // This has to do additional work for reading annotations, so the code
  // here is copied and expanded from SBase::readNotes().

  if (name == "annotation")
  {
//    XMLNode* new_annotation = NULL;
    /* if annotation already exists then it is an error
     */
    if (mAnnotation != NULL)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant, getLevel(), getVersion(),
          "Only one <annotation> element is permitted inside a "
          "particular containing element.");
      }
      else
      {
        logError(MultipleAnnotations, getLevel(), getVersion(),
          "The SBML <model> element has multiple <annotation> children.");
      }
    }

    delete mAnnotation;
    mAnnotation = new XMLNode(stream);
    checkAnnotation();
    if (mCVTerms != NULL)
    {
      unsigned int size = mCVTerms->getSize();
      while (size--) delete static_cast<CVTerm*>( mCVTerms->remove(0) );
      delete mCVTerms;
    }
    mCVTerms = new List();
    delete mHistory;
    if (RDFAnnotationParser::hasHistoryRDFAnnotation(mAnnotation))
    {
      mHistory = RDFAnnotationParser::parseRDFAnnotation(mAnnotation,
                                            getMetaId().c_str(), &(stream));

      if (mHistory != NULL && mHistory->hasRequiredAttributes() == false)
      {
        logError(RDFNotCompleteModelHistory, getLevel(), getVersion(),
          "An invalid ModelHistory element has been stored.");
      }
      setModelHistory(mHistory);
    }
    else
      mHistory = NULL;
    if (RDFAnnotationParser::hasCVTermRDFAnnotation(mAnnotation))
      RDFAnnotationParser::parseRDFAnnotation(mAnnotation, mCVTerms,
                                                getMetaId().c_str(), &(stream));
//    new_annotation = RDFAnnotationParser::deleteRDFAnnotation(mAnnotation);
//    delete mAnnotation;
//    mAnnotation = new_annotation;

    // need to call set annotation
    for (size_t i=0; i < mPlugins.size(); i++)
    {
      mPlugins[i]->parseAnnotation(this, mAnnotation);
    }

    read = true;
  }

  /* ------------------------------
   *
   *   (EXTENSION)
   *
   * ------------------------------ */
  if ( SBase::readOtherXML(stream) )
    read = true;

  return read;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the SBML object corresponding to next XMLToken in the
 * XMLInputStream or @c NULL if the token was not recognized.
 */
SBase*
Model::createObject (XMLInputStream& stream)
{
  const string& name   = stream.peek().getName();
  SBase*        object = NULL;
  unsigned int level = getLevel();
  unsigned int version = getVersion();

  /* dont create objects for wrong levels/versions */
  if (name == "listOfFunctionDefinitions")
  {
    if (level == 1)
    {
      return NULL;
    }

    if (mFunctionDefinitions.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mFunctionDefinitions.setExplicitlyListed();
    object = &mFunctionDefinitions;
  }

  else if ( name == "listOfUnitDefinitions"    )
  {
    if (mUnitDefinitions.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mUnitDefinitions.setExplicitlyListed();
    object = &mUnitDefinitions;
  }

  else if ( name == "listOfCompartmentTypes"   )
  {
    if (level == 1
      || (level == 2 && version == 1)
      || level == 3)
    {
      return NULL;
    }
    if (mCompartmentTypes.size() != 0)
    {
      logError(NotSchemaConformant);
    }
    mCompartmentTypes.setExplicitlyListed();
    object = &mCompartmentTypes;
  }

  else if ( name == "listOfSpeciesTypes"       )
  {
    if (level == 1
      || (level == 2 && version == 1)
      || level == 3)
    {
      return NULL;
    }
    if (mSpeciesTypes.size() != 0)
    {
      logError(NotSchemaConformant);
    }
    mSpeciesTypes.setExplicitlyListed();
    object = &mSpeciesTypes;
  }

  else if ( name == "listOfCompartments"       )
  {
    if (mCompartments.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mCompartments.setExplicitlyListed();
    object = &mCompartments;
  }

  else if ( name == "listOfSpecies"            )
  {
    if (mSpecies.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mSpecies.setExplicitlyListed();
    object = &mSpecies;
  }

  else if ( name == "listOfParameters"         )
  {
    if (mParameters.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mParameters.setExplicitlyListed();
    object = &mParameters;
  }

  else if ( name == "listOfInitialAssignments" )
  {
    if (level == 1  || (level == 2 && version == 1))
    {
      return NULL;
    }
    if (mInitialAssignments.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mInitialAssignments.setExplicitlyListed();
    object = &mInitialAssignments;
  }

  else if ( name == "listOfRules"              )
  {
    if (mRules.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mRules.setExplicitlyListed();
    object = &mRules;
  }

  else if ( name == "listOfConstraints"        )
  {
    if (level == 1  || (level == 2 && version == 1))
    {
      return NULL;
    }
    if (mConstraints.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mConstraints.setExplicitlyListed();
    object = &mConstraints;
  }

  else if ( name == "listOfReactions"          )
  {
    if (mReactions.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mReactions.setExplicitlyListed();
    object = &mReactions;
  }

  else if ( name == "listOfEvents"             )
  {
    if (level == 1)
    {
      return NULL;
    }
    if (mEvents.size() != 0)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant);
      }
      else
      {
        logError(OneOfEachListOf);
      }
    }
    mEvents.setExplicitlyListed();
    object = &mEvents;
  }

  else if ( level == 1 && version == 1 )
  {
    if (name == "listOfSpecie")
    {
      if (mSpecies.size() != 0)
      {
        logError(NotSchemaConformant);
      }
      object = &mSpecies;
    }
  }

  return object;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/**
 * Subclasses should override this method to get the list of
 * expected attributes.
 * This function is invoked from corresponding readAttributes()
 * function.
 */
void
Model::addExpectedAttributes(ExpectedAttributes& attributes)
{
  SBase::addExpectedAttributes(attributes);

  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  switch (level)
  {
  case 1:
    attributes.add("name");
    break;
  case 2:
    attributes.add("name");
    attributes.add("id");
    if (version == 2)
    {
      attributes.add("sboTerm");
    }
    break;
  case 3:
  default:
    attributes.add("name");
    attributes.add("id");
    attributes.add("substanceUnits");
    attributes.add("timeUnits");
    attributes.add("volumeUnits");
    attributes.add("areaUnits");
    attributes.add("lengthUnits");
    attributes.add("extentUnits");
    attributes.add("conversionFactor");
    break;
  }
}

/*
 * Subclasses should override this method to read values from the given
 * XMLAttributes set into their specific fields.  Be sure to call your
 * parent's implementation of this method as well.
 */
void
Model::readAttributes (const XMLAttributes& attributes,
                       const ExpectedAttributes& expectedAttributes)
{
  const unsigned int level   = getLevel  ();

  SBase::readAttributes(attributes, expectedAttributes);

  switch (level)
  {
  case 1:
    readL1Attributes(attributes);
    break;
  case 2:
    readL2Attributes(attributes);
    break;
  case 3:
  default:
    readL3Attributes(attributes);
    break;
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * Subclasses should override this method to read values from the given
 * XMLAttributes set into their specific fields.  Be sure to call your
 * parent's implementation of this method as well.
 */
void
Model::readL1Attributes (const XMLAttributes& attributes)
{
  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  //
  // name: SName  { use="optional" }  (L1v1, L1v2)
  //   id: SId    { use="optional" }  (L2v1 -> )
  //
  bool assigned = attributes.readInto("name", mId, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mId.size() == 0)
  {
    logEmptyString("name", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalSId(mId))
    logError(InvalidIdSyntax, level, version, "The id '" + mId + "' does not conform to the syntax.");

}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * Subclasses should override this method to read values from the given
 * XMLAttributes set into their specific fields.  Be sure to call your
 * parent's implementation of this method as well.
 */
void
Model::readL2Attributes (const XMLAttributes& attributes)
{
  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  //
  //   id: SId    { use="optional" }  (L2v1 -> )
  //
  bool assigned = attributes.readInto("id", mId, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mId.size() == 0)
  {
    logEmptyString("id", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalSId(mId))
    logError(InvalidIdSyntax, level, version, "The id '" + mId + "' does not conform to the syntax.");

  //
  // name: string  { use="optional" }  (L2v1 ->)
  //
  attributes.readInto("name", mName, getErrorLog(), false, getLine(), getColumn());

  //
  // sboTerm: SBOTerm { use="optional" }  (L2v2 ->)
  //
  if (version == 2)
    mSBOTerm = SBO::readTerm(attributes, this->getErrorLog(), level, version,
        getLine(), getColumn());

}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * Subclasses should override this method to read values from the given
 * XMLAttributes set into their specific fields.  Be sure to call your
 * parent's implementation of this method as well.
 */
void
Model::readL3Attributes (const XMLAttributes& attributes)
{
  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  bool assigned;
  //
  //   id: SId    { use="optional" }  (L2v1 -> )
  //
  // for l3v2 sbase will read this as generically optional
  // we want to log errors relating to the specific object
  if (version == 1)
  {
    assigned = attributes.readInto("id", mId, getErrorLog(), false,
      getLine(), getColumn());
    if (assigned && mId.size() == 0)
    {
      logEmptyString("id", level, version, "<model>");
    }
    if (!SyntaxChecker::isValidInternalSId(mId))
    {
      logError(InvalidIdSyntax, level, version, "The id '" + mId +
      "' does not conform to the syntax.");
    }

    //
    // name: string  { use="optional" }  (L2v1 ->)
    //
    attributes.readInto("name", mName, getErrorLog(), false,
                                       getLine(), getColumn());
  }


  //
  // substanceUnits: string  { use="optional" }  (L3v1 ->)
  //
  assigned = attributes.readInto("substanceUnits", mSubstanceUnits, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mSubstanceUnits.size() == 0)
  {
    logEmptyString("substanceUnits", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalUnitSId(mSubstanceUnits))
  {
    logError(InvalidUnitIdSyntax, getLevel(), getVersion(), "The substanceUnits attribute '" + mSubstanceUnits + "' does not conform to the syntax.");
  }

  //
  // timeUnits: string  { use="optional" }  (L3v1 ->)
  //
  assigned = attributes.readInto("timeUnits", mTimeUnits, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mTimeUnits.size() == 0)
  {
    logEmptyString("timeUnits", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalUnitSId(mTimeUnits))
  {
    logError(InvalidUnitIdSyntax, getLevel(), getVersion(), "The timeUnits attribute '" + mTimeUnits + "' does not conform to the syntax.");
  }

  //
  // volumeUnits: string  { use="optional" }  (L3v1 ->)
  //
  assigned = attributes.readInto("volumeUnits", mVolumeUnits, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mVolumeUnits.size() == 0)
  {
    logEmptyString("volumeUnits", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalUnitSId(mVolumeUnits))
  {
    logError(InvalidUnitIdSyntax, getLevel(), getVersion(), "The volumeUnits attribute '" + mVolumeUnits + "' does not conform to the syntax.");
  }

  //
  // areaUnits: string  { use="optional" }  (L3v1 ->)
  //
  assigned = attributes.readInto("areaUnits", mAreaUnits, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mAreaUnits.size() == 0)
  {
    logEmptyString("areaUnits", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalUnitSId(mAreaUnits))
  {
    logError(InvalidUnitIdSyntax, getLevel(), getVersion(), "The areaUnits attribute '" + mAreaUnits + "' does not conform to the syntax.");
  }

  //
  // lengthUnits: string  { use="optional" }  (L3v1 ->)
  //
  assigned = attributes.readInto("lengthUnits", mLengthUnits, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mLengthUnits.size() == 0)
  {
    logEmptyString("lengthUnits", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalUnitSId(mLengthUnits))
  {
    logError(InvalidUnitIdSyntax, getLevel(), getVersion(), "The lengthUnits attribute '" + mLengthUnits + "' does not conform to the syntax.");
  }

  //
  // extentUnits: string  { use="optional" }  (L3v1 ->)
  //
  assigned = attributes.readInto("extentUnits", mExtentUnits, getErrorLog(), false, getLine(), getColumn());
  if (assigned && mExtentUnits.size() == 0)
  {
    logEmptyString("extentUnits", level, version, "<model>");
  }
  if (!SyntaxChecker::isValidInternalUnitSId(mExtentUnits))
  {
    logError(InvalidUnitIdSyntax, getLevel(), getVersion(), "The extentUnits attribute '" + mExtentUnits + "' does not conform to the syntax.");
  }

  //
  // conversionFactor: string  { use="optional" }  (L3v1 ->)
  //
  attributes.readInto("conversionFactor", mConversionFactor, getErrorLog(), false, getLine(), getColumn());
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * Subclasses should override this method to write their XML attributes
 * to the XMLOutputStream.  Be sure to call your parent's implementation
 * of this method as well.
 */
void
Model::writeAttributes (XMLOutputStream& stream) const
{
  SBase::writeAttributes(stream);

  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  //
  // sboTerm: SBOTerm { use="optional" }  (L2v2->)
  //
  // sboTerm for L2V3 or later is written in SBase::writeAttributes()
  //
  if ( (level == 2) && (version == 2) )
  {
    SBO::writeTerm(stream, mSBOTerm);
  }

  // for L3V2 and above SBase will write this out
  if (level < 3 || (level == 3 && version == 1))
  {
  //
  // name: SName   { use="required" }  (L1v1, L1v2)
  //   id: SId     { use="required" }  (L2v1->)
  //
  const string id = (level == 1) ? "name" : "id";
  stream.writeAttribute(id, mId);
  }
  if (level > 1)
  {
    // for L3V2 and above SBase will write this out
    if (level < 3 || (level == 3 && version == 1))
    {
      //
      // name: string  { use="optional" }  (L2v1->)
      //
      stream.writeAttribute("name", mName);
    }
  }

  if (level > 2)
  {
    //
    // substanceUnits: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("substanceUnits", mSubstanceUnits);

    //
    // timeUnits: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("timeUnits", mTimeUnits);

    //
    // volumeUnits: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("volumeUnits", mVolumeUnits);

    //
    // areaUnits: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("areaUnits", mAreaUnits);

    //
    // lengthUnits: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("lengthUnits", mLengthUnits);

    //
    // extentUnits: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("extentUnits", mExtentUnits);

    //
    // conversionFactor: string  { use="optional" }  (L3v1 ->)
    //
    stream.writeAttribute("conversionFactor", mConversionFactor);

  }

  //
  // (EXTENSION)
  //
  SBase::writeExtensionAttributes(stream);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * Subclasses should override this method to write out their contained
 * SBML objects as XML elements.  Be sure to call your parent's
 * implementation of this method as well.
 */
void
Model::writeElements (XMLOutputStream& stream) const
{
  if (mNotes != NULL)
  {
    mNotes->writeToStream(stream);
  }
  Model * m = const_cast <Model *> (this);
  m->syncAnnotation();
  if ( mAnnotation ) stream << *mAnnotation;

  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  // for l3v2 there may not be any elements in the listOf but
  // if there is other information i.e. attributes/notes/annotations
  // we write out the empty wrapper with this information
  if (level == 3 && version > 1)
  {
    if (mFunctionDefinitions.hasOptionalElements() == true ||
        mFunctionDefinitions.hasOptionalAttributes() == true ||
        mFunctionDefinitions.isExplicitlyListed())
    {
      mFunctionDefinitions.write(stream);
    }

    if (mUnitDefinitions.hasOptionalElements() == true ||
        mUnitDefinitions.hasOptionalAttributes() == true ||
        mUnitDefinitions.isExplicitlyListed())
    {
      mUnitDefinitions.write(stream);
    }

    if (mCompartments.hasOptionalElements() == true ||
        mCompartments.hasOptionalAttributes() == true ||
        mCompartments.isExplicitlyListed())
    {
      mCompartments.write(stream);
    }

    if (mSpecies.hasOptionalElements() == true ||
        mSpecies.hasOptionalAttributes() == true ||
        mSpecies.isExplicitlyListed())
    {
      mSpecies.write(stream);
    }

    if (mParameters.hasOptionalElements() == true ||
        mParameters.hasOptionalAttributes() == true ||
        mParameters.isExplicitlyListed())
    {
      mParameters.write(stream);
    }

    if (mInitialAssignments.hasOptionalElements() == true ||
        mInitialAssignments.hasOptionalAttributes() == true ||
        mInitialAssignments.isExplicitlyListed())
    {
      mInitialAssignments.write(stream);
    }

    if (mRules.hasOptionalElements() == true ||
        mRules.hasOptionalAttributes() == true ||
        mRules.isExplicitlyListed())
    {
      mRules.write(stream);
    }

    if (mConstraints.hasOptionalElements() == true ||
        mConstraints.hasOptionalAttributes() == true ||
        mConstraints.isExplicitlyListed())
    {
      mConstraints.write(stream);
    }

    if (mReactions.hasOptionalElements() == true ||
        mReactions.hasOptionalAttributes() == true ||
        mReactions.isExplicitlyListed())
    {
      mReactions.write(stream);
    }

    if (mEvents.hasOptionalElements() == true ||
        mEvents.hasOptionalAttributes() == true ||
        mEvents.isExplicitlyListed())
    {
      mEvents.write(stream);
    }
  }
  else
  {
      // code as before
    if (level > 1 && getNumFunctionDefinitions() > 0 )
    {
      mFunctionDefinitions.write(stream);
    }

    if ( getNumUnitDefinitions() > 0 ) mUnitDefinitions.write(stream);

    if (level == 2 && version > 1)
    {
      if ( getNumCompartmentTypes() > 0 ) mCompartmentTypes.write(stream);
      if ( getNumSpeciesTypes    () > 0 ) mSpeciesTypes    .write(stream);
    }

    if ( getNumCompartments() > 0 ) mCompartments.write(stream);
    if ( getNumSpecies     () > 0 ) mSpecies     .write(stream);
    if ( getNumParameters  () > 0 ) mParameters  .write(stream);

    if (level > 2 || (level == 2 && version > 1))
    {
      if ( getNumInitialAssignments() > 0 ) mInitialAssignments.write(stream);
    }

    if ( getNumRules() > 0 ) mRules.write(stream);

    if (level > 2 || (level == 2 && version > 1))
    {
      if ( getNumConstraints() > 0 ) mConstraints.write(stream);
    }

    if ( getNumReactions() > 0 ) mReactions.write(stream);

    if (level > 1 && getNumEvents () > 0 )
    {
      mEvents.write(stream);
    }
  }

  //
  // (EXTENSION)
  //
  SBase::writeExtensionElements(stream);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the ordinal position of the element with respect to its siblings
 * or -1 (default) to indicate the position is not significant.
 */
int
Model::getElementPosition () const
{
  return 2;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void Model::populatePerTimeUnitDefinition(FormulaUnitsData *fud)
{
  FormulaUnitsData *tempFUD = getFormulaUnitsData("time", SBML_MODEL);

  // if time is undeclared so we do not set the perTime unit
  if (tempFUD->getContainsUndeclaredUnits() == false)
  {
    UnitDefinition * temp = tempFUD->getUnitDefinition();
    UnitDefinition *existingUD = fud->getUnitDefinition()->clone();

    for (unsigned int n = 0; n < temp->getNumUnits(); n++)
    {
      Unit * u = temp->getUnit(n)->clone();
      u->setExponent(u->getExponent() * -1);
      existingUD->addUnit(u);
      delete u;
    }

    UnitDefinition::simplify(existingUD);

    fud->setPerTimeUnitDefinition(existingUD);
  }
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void Model::createSpeciesReferenceUnitsData(SpeciesReference* sr,
                                  UnitFormulaFormatter* unitFormatter)
{
  FormulaUnitsData * fud;

  if (sr->isSetStoichiometryMath())
  {
    fud = createFormulaUnitsData(sr->getSpecies(), SBML_STOICHIOMETRY_MATH);
    //fud->setUnitReferenceId(sr->getSpecies());
    sr->getStoichiometryMath()->setInternalId(sr->getSpecies());
    //fud->setComponentTypecode(SBML_STOICHIOMETRY_MATH);

    createUnitsDataFromMath(unitFormatter, fud,
                            sr->getStoichiometryMath()->getMath());
  }
  else if (sr->getLevel() > 2 && sr->isSetId())
  {
    fud = createFormulaUnitsData(sr->getId(), SBML_SPECIES_REFERENCE);
    //fud->setUnitReferenceId(sr->getId());
    //fud->setComponentTypecode(SBML_SPECIES_REFERENCE);

    /* units will be dimensionless */
    UnitDefinition* ud;
    try
    {
      ud = new UnitDefinition(getSBMLNamespaces());
    }
    catch ( ... )
    {
      ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
        SBMLDocument::getDefaultVersion());
    }
    Unit* u = ud->createUnit();
    u->setKind(UNIT_KIND_DIMENSIONLESS);
    u->initDefaults();

    fud->setUnitDefinition(ud);
    fud->setContainsParametersWithUndeclaredUnits(false);
    fud->setCanIgnoreUndeclaredUnits(true);

    populatePerTimeUnitDefinition(fud);
  }
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
/**
  * Populates the ListFormulaDataUnits with the units of each
  * set of math encountered in the model
  */
void
Model::populateListFormulaUnitsData()
{
  removeListFormulaUnitsData();

  UnitFormulaFormatter *unitFormatter = new UnitFormulaFormatter(this);

  /* create the model wide units data */
  createSubstanceUnitsData();
  createVolumeUnitsData();
  createAreaUnitsData();
  createLengthUnitsData();
  createTimeUnitsData();
  createExtentUnitsData();
  createSubstancePerTimeUnitsData();

  /* create the units data for 'variables' */
  createCompartmentUnitsData();
  createSpeciesUnitsData();
  createParameterUnitsData();
  if (getLevel() > 2)
  {
    createL3SpeciesUnitsData();
  }

  /* create the units data from math elements */

  // pass the unitFormatter as this will save data
  // for math expressions already evaluated

  createInitialAssignmentUnitsData(unitFormatter);
  createConstraintUnitsData(unitFormatter);
  createRuleUnitsData(unitFormatter);
  createReactionUnitsData(unitFormatter);
  createEventUnitsData(unitFormatter);

  delete unitFormatter;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::removeListFormulaUnitsData()
{
  if (mFormulaUnitsData != NULL)
  {
    unsigned int size = mFormulaUnitsData->getSize();
    while (size--)
      delete static_cast<FormulaUnitsData*>( mFormulaUnitsData->remove(0) );
    delete mFormulaUnitsData;
    mFormulaUnitsData = NULL;
  }

  mUnitsDataMap.clear();
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createSubstanceUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("substance", SBML_MODEL);

  //fud->setUnitReferenceId("substance");
  //fud->setComponentTypecode(SBML_MODEL);

  if (getLevel() < 3)
  {
    ud = getSubstanceUD();
  }
  else
  {
    ud = getL3SubstanceUD();

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getSubstanceUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  // units will be mole unless substance has been overridden
  if (getUnitDefinition("substance") != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition("substance")->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition("substance")->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }
  else
  {
    Unit* u = ud->createUnit();
    u->setKind(UNIT_KIND_MOLE);
    u->initDefaults();
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3SubstanceUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  /* in L3 the units will be possibly not declared at all !
   */
  std::string substanceUnits = getSubstanceUnits();
  if (UnitKind_isValidUnitKindString(substanceUnits.c_str(),
                                     getLevel(), getVersion()))
  {
    Unit* u = ud->createUnit();
    u->setKind(UnitKind_forName(substanceUnits.c_str()));
    u->initDefaults();
  }
  else if (getUnitDefinition(substanceUnits) != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition(substanceUnits)->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition(substanceUnits)->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createTimeUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("time", SBML_MODEL);

  //fud->setUnitReferenceId("time");
  //fud->setComponentTypecode(SBML_MODEL);

  if (getLevel() < 3)
  {
    ud = getTimeUD();
  }
  else
  {
    ud = getL3TimeUD();

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getTimeUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  // units are second unless time has been overridden
  if (getUnitDefinition("time") != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition("time")->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition("time")->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }
  else
  {
    Unit* u = ud->createUnit();
    u->setKind(UNIT_KIND_SECOND);
    u->initDefaults();
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3TimeUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  /* in L3 the units will be possibly not declared at all !
   */
  std::string timeUnits = getTimeUnits();
  if (UnitKind_isValidUnitKindString(timeUnits.c_str(),
                                     getLevel(), getVersion()))
  {
    Unit* u = ud->createUnit();
    u->setKind(UnitKind_forName(timeUnits.c_str()));
    u->initDefaults();
  }
  else if (getUnitDefinition(timeUnits) != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition(timeUnits)->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition(timeUnits)->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createVolumeUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("volume", SBML_MODEL);

  //fud->setUnitReferenceId("volume");
  //fud->setComponentTypecode(SBML_MODEL);

  if (getLevel() < 3)
  {
    ud = getVolumeUD();
  }
  else
  {
    ud = getL3VolumeUD();

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getVolumeUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  // units will be litre unless volume has been overridden
  if (getUnitDefinition("volume") != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition("volume")->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition("volume")->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }
  else
  {
    Unit* u = ud->createUnit();
    u->setKind(UNIT_KIND_LITRE);
    u->initDefaults();
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3VolumeUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  /* in L3 the units will be possibly not declared at all !
   */
  std::string volumeUnits = getVolumeUnits();
  if (UnitKind_isValidUnitKindString(volumeUnits.c_str(),
                                     getLevel(), getVersion()))
  {
    Unit* u = ud->createUnit();
    u->setKind(UnitKind_forName(volumeUnits.c_str()));
    u->initDefaults();
  }
  else if (getUnitDefinition(volumeUnits) != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition(volumeUnits)->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition(volumeUnits)->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createAreaUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("area", SBML_MODEL);

  //fud->setUnitReferenceId("area");
  //fud->setComponentTypecode(SBML_MODEL);

  if (getLevel() < 3)
  {
    ud = getAreaUD();
  }
  else
  {
    ud = getL3AreaUD();

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getAreaUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  // units will be metre squared unless area has been overridden
  if (getUnitDefinition("area") != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition("area")->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition("area")->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }
  else
  {
    Unit* u = ud->createUnit();
    u->setKind(UNIT_KIND_METRE);
    u->initDefaults();
    u->setExponent(2);
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3AreaUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }


  /* in L3 the units will be possibly not declared at all !
   */
  std::string areaUnits = getAreaUnits();
  if (UnitKind_isValidUnitKindString(areaUnits.c_str(),
                                     getLevel(), getVersion()))
  {
    Unit* u = ud->createUnit();
    u->setKind(UnitKind_forName(areaUnits.c_str()));
    u->initDefaults();
  }
  else if (getUnitDefinition(areaUnits) != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition(areaUnits)->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition(areaUnits)->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createLengthUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("length", SBML_MODEL);

  //fud->setUnitReferenceId("length");
  //fud->setComponentTypecode(SBML_MODEL);

  if (getLevel() < 3)
  {
    ud = getLengthUD();
  }
  else
  {
    ud = getL3LengthUD();

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getLengthUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  // units will be metre unless length has been overridden
  if (getUnitDefinition("length") != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition("length")->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition("length")->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }
  else
  {
    Unit* u = ud->createUnit();
    u->setKind(UNIT_KIND_METRE);
    u->initDefaults();
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3LengthUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  /* in L3 the units will be possibly not declared at all !
   */
  std::string lengthUnits = getLengthUnits();
  if (UnitKind_isValidUnitKindString(lengthUnits.c_str(),
                                     getLevel(), getVersion()))
  {
    Unit* u = ud->createUnit();
    u->setKind(UnitKind_forName(lengthUnits.c_str()));
    u->initDefaults();
  }
  else if (getUnitDefinition(lengthUnits) != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition(lengthUnits)->getNumUnits(); n++)
    {
      Unit* uFromModel = getUnitDefinition(lengthUnits)->getUnit(n);
      if (uFromModel  != NULL)
      {
        ud->addUnit(uFromModel);
      }
    }
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createExtentUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("extent", SBML_MODEL);

  //fud->setUnitReferenceId("extent");
  //fud->setComponentTypecode(SBML_MODEL);

  if (getLevel() < 3)
  {
    // create a unitDefinition with no children
    try
    {
      ud = new UnitDefinition(getSBMLNamespaces());
    }
    catch ( ... )
    {
      ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
        SBMLDocument::getDefaultVersion());
    }
    fud->setContainsParametersWithUndeclaredUnits(true);
    fud->setCanIgnoreUndeclaredUnits(false);

  }
  else
  {
    ud = getL3ExtentUD();

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3ExtentUD()
{
  UnitDefinition* ud;
  try
  {
    ud = new UnitDefinition(getSBMLNamespaces());
  }
  catch ( ... )
  {
    ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
      SBMLDocument::getDefaultVersion());
  }

  /* in L3 the units will be possibly not declared at all !
   */
  std::string extentUnits = getExtentUnits();
  if (UnitKind_isValidUnitKindString(extentUnits.c_str(),
                                     getLevel(), getVersion()))
  {
    Unit* u = ud->createUnit();
    u->setKind(UnitKind_forName(extentUnits.c_str()));
    u->initDefaults();
  }
  else if (getUnitDefinition(extentUnits) != NULL)
  {
    for (unsigned int n = 0; n < getUnitDefinition(extentUnits)->getNumUnits(); n++)
    {
      // need to prevent level/version mismatches
      // ud will have default level and veersion
      Unit* uFromModel = getUnitDefinition(extentUnits)->getUnit(n);
      if (uFromModel  != NULL)
      {
        Unit* u = ud->createUnit();
        u->setKind(uFromModel->getKind());
        u->setExponent(uFromModel->getExponent());
        u->setScale(uFromModel->getScale());
        u->setMultiplier(uFromModel->getMultiplier());
      }
    }
  }

  return ud;
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void
Model::createSubstancePerTimeUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData("subs_per_time", SBML_UNKNOWN);

  //fud->setUnitReferenceId("subs_per_time");
  //fud->setComponentTypecode(SBML_UNKNOWN);

  if (getLevel() < 3)
  {
    ud = getSubstancePerTimeUD();
  }
  else
  {
    //need to pass the formulaUnitsData object
    // as we need to log whether extent or time has undeclared
    // one might be
    ud = getL3SubstancePerTimeUD(fud);

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getSubstancePerTimeUD()
{
  UnitDefinition *ud = getFormulaUnitsData("substance", SBML_MODEL)
                                        ->getUnitDefinition()->clone();

  UnitDefinition * temp = getFormulaUnitsData("time", SBML_MODEL)
                                                      ->getUnitDefinition();

  for (unsigned int n = 0; n < temp->getNumUnits(); n++)
  {
    Unit * u = temp->getUnit(n)->clone();
    u->setExponent(u->getExponent() * -1);
    ud->addUnit(u);
    delete u;
  }

  return ud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
UnitDefinition *
Model::getL3SubstancePerTimeUD(FormulaUnitsData * fud)
{
  FormulaUnitsData * tempFUD = getFormulaUnitsData("extent", SBML_MODEL);

  // extent is undeclared
  if (tempFUD->getContainsUndeclaredUnits() == true)
  {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
  }


  UnitDefinition *ud = tempFUD->getUnitDefinition()->clone();

  tempFUD = getFormulaUnitsData("time", SBML_MODEL);

  // time is undeclared
  if (tempFUD->getContainsUndeclaredUnits() == true)
  {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
  }

  UnitDefinition * temp = tempFUD->getUnitDefinition();

  for (unsigned int n = 0; n < temp->getNumUnits(); n++)
  {
    Unit * u = temp->getUnit(n)->clone();
    u->setExponent(u->getExponent() * -1);
    ud->addUnit(u);
    delete u;
  }

  return ud;
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void
Model::createCompartmentUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = NULL;
  UnitFormulaFormatter unitFormatter = this;

  for (unsigned int n = 0; n < getNumCompartments(); n++)
  {
    Compartment* c = getCompartment(n);

    fud = createFormulaUnitsData(c->getId(), SBML_COMPARTMENT);
    //fud->setUnitReferenceId(c->getId());
    //fud->setComponentTypecode(SBML_COMPARTMENT);

    ud = unitFormatter.getUnitDefinitionFromCompartment(c);

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }

    fud->setUnitDefinition(ud);
    populatePerTimeUnitDefinition(fud);
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createSpeciesUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = NULL;
  UnitFormulaFormatter unitFormatter = this;

  for (unsigned int n=0; n < getNumSpecies(); n++)
  {
    Species* s = getSpecies(n);

    fud = createFormulaUnitsData(s->getId(), SBML_SPECIES);
    //fud->setUnitReferenceId(s->getId());
    //fud->setComponentTypecode(SBML_SPECIES);

    /* TO DO - sort out getUDFromSpecies
     */
    if (getCompartment(s->getCompartment()) == NULL)
    {
      try
      {
        ud = new UnitDefinition(getSBMLNamespaces());
      }
      catch ( ... )
      {
        ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
          SBMLDocument::getDefaultVersion());
      }
    }
    else
    {
      ud = unitFormatter.getUnitDefinitionFromSpecies(s);
    }

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }

    fud->setUnitDefinition(ud);
    populatePerTimeUnitDefinition(fud);
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createL3SpeciesUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = NULL;
  UnitFormulaFormatter unitFormatter = this;

  for (unsigned int n=0; n < getNumSpecies(); n++)
  {
    Species* s = getSpecies(n);

    /* create the substance unit */
    unitFormatter.resetFlags();

    fud = createFormulaUnitsData(s->getId() + "subs", SBML_SPECIES);
    //fud->setUnitReferenceId(s->getId()+"subs");
    //fud->setComponentTypecode(SBML_SPECIES);

    ud = unitFormatter.getSpeciesSubstanceUnitDefinition(s);

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
    else
    {
      fud->setContainsParametersWithUndeclaredUnits
                              (unitFormatter.getContainsUndeclaredUnits());
      fud->setCanIgnoreUndeclaredUnits
                                (unitFormatter.canIgnoreUndeclaredUnits());
    }

    fud->setSpeciesSubstanceUnitDefinition(ud);

    /* create the extent unit */
    unitFormatter.resetFlags();

    fud = createFormulaUnitsData(s->getId() + "extent", SBML_SPECIES);
    //fud->setUnitReferenceId(s->getId()+"extent");
    //fud->setComponentTypecode(SBML_SPECIES);

    ud = unitFormatter.getSpeciesExtentUnitDefinition(s);

    if (ud->getNumUnits() == 0)
    {
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
    else
    {
      fud->setContainsParametersWithUndeclaredUnits
                              (unitFormatter.getContainsUndeclaredUnits());
      fud->setCanIgnoreUndeclaredUnits
                                (unitFormatter.canIgnoreUndeclaredUnits());
    }

    fud->setSpeciesExtentUnitDefinition(ud);
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createParameterUnitsData()
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = NULL;
  UnitFormulaFormatter unitFormatter = this;

  for (unsigned int n=0; n < getNumParameters(); n++)
  {
    Parameter* p = getParameter(n);

    unitFormatter.resetFlags();

    fud = createFormulaUnitsData(p->getId(), SBML_PARAMETER);
    //fud->setUnitReferenceId(p->getId());
    //fud->setComponentTypecode(SBML_PARAMETER);

    unitFormatter.resetFlags();
    ud = unitFormatter.getUnitDefinitionFromParameter(p);

    fud->setUnitDefinition(ud);
    fud->setContainsParametersWithUndeclaredUnits
                                (unitFormatter.getContainsUndeclaredUnits());
    fud->setCanIgnoreUndeclaredUnits
                                  (unitFormatter.canIgnoreUndeclaredUnits());

    populatePerTimeUnitDefinition(fud);
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createUnitsDataFromMath(UnitFormulaFormatter * unitFormatter,
                               FormulaUnitsData *fud, const ASTNode * math)
{
  UnitDefinition * ud = NULL;

  if (math != NULL)
  {
    unitFormatter->resetFlags();
    ud = unitFormatter->getUnitDefinition(math);

    fud->setContainsParametersWithUndeclaredUnits
                              (unitFormatter->getContainsUndeclaredUnits());
    fud->setCanIgnoreUndeclaredUnits
                                (unitFormatter->canIgnoreUndeclaredUnits());
    fud->setContainsInconsistency(unitFormatter->getContainsInconsistentUnits());
  }

  fud->setUnitDefinition(ud);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createInitialAssignmentUnitsData(UnitFormulaFormatter * unitFormatter)
{
  FormulaUnitsData *fud = NULL;

  for (unsigned int n=0; n < getNumInitialAssignments(); n++)
  {
    InitialAssignment* ia = getInitialAssignment(n);

    fud = createFormulaUnitsData(ia->getSymbol(), SBML_INITIAL_ASSIGNMENT);
    //fud->setUnitReferenceId(ia->getSymbol());
    //fud->setComponentTypecode(SBML_INITIAL_ASSIGNMENT);

    createUnitsDataFromMath(unitFormatter, fud, ia->getMath());
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createConstraintUnitsData(UnitFormulaFormatter * unitFormatter)
{
  FormulaUnitsData *fud = NULL;
  char newId[15];
  std::string newID;

  for (unsigned int n = 0; n < getNumConstraints(); n++)
  {
    Constraint* c = getConstraint(n);
    sprintf(newId, "constraint_%u", n);
    newID.assign(newId);
    c->setInternalId(newID);

    fud = createFormulaUnitsData(newID, SBML_CONSTRAINT);
    //fud->setUnitReferenceId(newID);
    //fud->setComponentTypecode(SBML_CONSTRAINT);

    createUnitsDataFromMath(unitFormatter, fud, c->getMath());
  }
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void
Model::createRuleUnitsData(UnitFormulaFormatter * unitFormatter)
{
  FormulaUnitsData *fud = NULL;
  char newId[12];
  std::string newID;
  unsigned int countAlg = 0;

  for (unsigned int n=0; n < getNumRules(); n++)
  {
    Rule* r = getRule(n);

    //fud = createFormulaUnitsData();
    // need to create an id for an algebbraic rule
    if (r->getTypeCode() == SBML_ALGEBRAIC_RULE)
    {
      sprintf(newId, "alg_rule_%u", countAlg);
      newID.assign(newId);
      r->setInternalId(newID);
      static_cast <AlgebraicRule *> (r)->setInternalIdOnly();
      countAlg++;

      fud = createFormulaUnitsData(newID, r->getTypeCode());
      //fud->setUnitReferenceId(newID);
    }
    else
    {
      fud = createFormulaUnitsData(r->getVariable(), r->getTypeCode());
      //fud->setUnitReferenceId(r->getVariable());
    }
    //fud->setComponentTypecode(r->getTypeCode());

    createUnitsDataFromMath(unitFormatter, fud, r->getMath());
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createReactionUnitsData(UnitFormulaFormatter * unitFormatter)
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = NULL;

  for (unsigned int n=0; n < getNumReactions(); n++)
  {
    Reaction* react = getReaction(n);

    /* get units returned by kineticLaw formula */
    if (react->isSetKineticLaw())
    {
      fud = createFormulaUnitsData(react->getId(), SBML_KINETIC_LAW);
      //fud->setUnitReferenceId(react->getId());

      /* set the id of the kinetic law
       * normally a kinetic law doesnt have an id
       * but since it is an sbase object it can
       * so we set it to be the reaction id so
       * that searching the listFormulaUnitsData can find it
       */
      react->getKineticLaw()->setInternalId(react->getId());

      //fud->setComponentTypecode(SBML_KINETIC_LAW);

      // have to use the old way for now as unitFormatter needs to know
      // if we are in a reaction so it can access localParameters
      unitFormatter->resetFlags();
      if(react->getKineticLaw()->isSetMath())
      {
        ud = unitFormatter->getUnitDefinition
                                  (react->getKineticLaw()->getMath(), true, (int)n);
        fud->setContainsParametersWithUndeclaredUnits
                                 (unitFormatter->getContainsUndeclaredUnits());
        fud->setCanIgnoreUndeclaredUnits
                                   (unitFormatter->canIgnoreUndeclaredUnits());
      }

      fud->setUnitDefinition(ud);

      createLocalParameterUnitsData(react->getKineticLaw(), unitFormatter);
    }

    ///* get units returned by any stoichiometryMath set */
    for (unsigned int j = 0; j < react->getNumReactants(); j++)
    {
      SpeciesReference* sr = react->getReactant(j);
      createSpeciesReferenceUnitsData(sr, unitFormatter);
    }

    for (unsigned int j = 0; j < react->getNumProducts(); j++)
    {
      SpeciesReference* sr = react->getProduct(j);
      createSpeciesReferenceUnitsData(sr, unitFormatter);
    }
  }

}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createLocalParameterUnitsData(KineticLaw * kl,
                                     UnitFormulaFormatter*)
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = NULL;

  for (unsigned int n=0; n < kl->getNumParameters(); n++)
  {
    Parameter * lp = kl->getParameter(n);
    std::string lpId = lp->getId() + '_' + kl->getInternalId();

    fud = createFormulaUnitsData(lpId, SBML_LOCAL_PARAMETER);

    //fud->setUnitReferenceId(lpId);
    //fud->setComponentTypecode(SBML_LOCAL_PARAMETER);

    std::string units = lp->getUnits();
    if (units.empty() == false)
    {
      char * charUnits = safe_strdup(units.c_str());
      fud->setContainsParametersWithUndeclaredUnits(false);

      if (UnitKind_isValidUnitKindString(units.c_str(),
                            getLevel(), getVersion()))
      {
        try
        {
          ud = new UnitDefinition(getSBMLNamespaces());
        }
        catch ( ... )
        {
          ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
            SBMLDocument::getDefaultVersion());
        }
        Unit * unit = ud->createUnit();
        unit->setKind(UnitKind_forName(charUnits));
        unit->initDefaults();
      }
      else
      {
        /* must be a unit definition */
        UnitDefinition * existingUD = getUnitDefinition(units);
        if (existingUD != NULL)
        {
          ud = new UnitDefinition(*(getUnitDefinition(units)));
          ud->setId("");
        }
        else
        {
          try
          {
            ud = new UnitDefinition(getSBMLNamespaces());
          }
          catch ( ... )
          {
            ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
              SBMLDocument::getDefaultVersion());
          }
          fud->setContainsParametersWithUndeclaredUnits(true);
        }
      }

      safe_free(charUnits);
      fud->setUnitDefinition(ud);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
    else
    {
      // here we have none but for consistency return a unitDefinition
      // with no units
      try
      {
        ud = new UnitDefinition(getSBMLNamespaces());
      }
      catch ( ... )
      {
        ud = new UnitDefinition(SBMLDocument::getDefaultLevel(),
          SBMLDocument::getDefaultVersion());
      }
      fud->setUnitDefinition(ud);
      fud->setContainsParametersWithUndeclaredUnits(true);
      fud->setCanIgnoreUndeclaredUnits(false);
    }
  }
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
void
Model::createEventUnitsData(UnitFormulaFormatter * unitFormatter)
{
  char newId[12];
  std::string newID;
  unsigned int countEvents = 0;

  for (unsigned int n=0; n < getNumEvents(); n++)
  {
    Event* e = getEvent(n);

    sprintf(newId, "event_%u", countEvents);
    newID.assign(newId);
    e->setInternalId(newID);
    countEvents++;

    /* dont need units returned by trigger formula -
     * should be boolean
     * but we might want to check they are defined
     */
    if (e->isSetTrigger())
    {
      createTriggerUnitsData(unitFormatter, e, newID);
    }


    /* get units returned by dely */
    if (e->isSetDelay())
    {
      createDelayUnitsData(unitFormatter, e, newID);
    }

    /* get units returned by priority */
    if (e->isSetPriority())
    {
      createPriorityUnitsData(unitFormatter, e->getPriority(), newID);
    }

    /* get units returned by any event assignments */
    for (unsigned int j = 0; j < e->getNumEventAssignments(); j++)
    {
      createEventAssignmentUnitsData(unitFormatter,
                                     e->getEventAssignment(j), newID);
    }
  }
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void
Model::createDelayUnitsData(UnitFormulaFormatter* unitFormatter, Event * e,
                            const std::string& eventId)
{
  UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData(eventId, SBML_EVENT);

  Delay * d = e->getDelay();

  //fud->setUnitReferenceId(eventId);
  d->setInternalId(eventId);

  //fud->setComponentTypecode(SBML_EVENT);

  createUnitsDataFromMath(unitFormatter, fud, d->getMath());

  /* get event time definition */
  unitFormatter->resetFlags();
  ud = unitFormatter->getUnitDefinitionFromEventTime(e);
  if (ud->getNumUnits() == 0)
  {
    fud->setContainsParametersWithUndeclaredUnits(true);
    fud->setCanIgnoreUndeclaredUnits(false);
  }
  fud->setEventTimeUnitDefinition(ud);
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void
Model::createTriggerUnitsData(UnitFormulaFormatter* unitFormatter, Event * e,
  const std::string& eventId)
{
  //UnitDefinition *ud = NULL;
  FormulaUnitsData *fud = createFormulaUnitsData(eventId, SBML_TRIGGER);

  Trigger * d = e->getTrigger();

  //fud->setUnitReferenceId(eventId);
  d->setInternalId(eventId);

  //fud->setComponentTypecode(SBML_TRIGGER);

  createUnitsDataFromMath(unitFormatter, fud, d->getMath());

  fud->setEventTimeUnitDefinition(NULL);
}
/** @endcond */
/** @cond doxygenLibsbmlInternal */
void
Model::createPriorityUnitsData(UnitFormulaFormatter* unitFormatter,
                               Priority * p, const std::string& eventId)
{
  FormulaUnitsData *fud = createFormulaUnitsData(eventId, SBML_PRIORITY);

  //fud->setUnitReferenceId(eventId);
  p->setInternalId(eventId);

  //fud->setComponentTypecode(SBML_PRIORITY);

  createUnitsDataFromMath(unitFormatter, fud, p->getMath());
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
void
Model::createEventAssignmentUnitsData(UnitFormulaFormatter* unitFormatter,
                            EventAssignment * ea, const std::string& eventId)
{
  std::string eaId = ea->getVariable() + eventId;
  FormulaUnitsData *fud = createFormulaUnitsData(eaId, SBML_EVENT_ASSIGNMENT);

  //fud->setUnitReferenceId(eaId);
  //fud->setComponentTypecode(SBML_EVENT_ASSIGNMENT);

  createUnitsDataFromMath(unitFormatter, fud, ea->getMath());
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * Adds a copy of the given FormulaUnitsData to this Model.
 */
void
Model::addFormulaUnitsData (const FormulaUnitsData* fud)
{
  if (mFormulaUnitsData == NULL)
  {
    mFormulaUnitsData = new List();
  }

  FormulaUnitsData *newFud = fud->clone();
  mFormulaUnitsData->add((void *)newFud);
  std::string id =  fud->getUnitReferenceId();
  int typecode = fud->getComponentTypecode();

  KeyValue key(id, typecode);
  mUnitsDataMap.insert(make_pair(key, newFud));
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/**
  * Creates a new FormulaUnitsData inside this Model and returns it.
  */
FormulaUnitsData*
Model::createFormulaUnitsData ()
{
  FormulaUnitsData* fud = new FormulaUnitsData();
  if (mFormulaUnitsData == NULL)
  {
    mFormulaUnitsData = new List();
  }
  mFormulaUnitsData->add(fud);

  return fud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/**
* Creates a new FormulaUnitsData inside this Model and returns it.
*/
FormulaUnitsData*
Model::createFormulaUnitsData(const std::string& id, int typecode)
{
  FormulaUnitsData* fud = new FormulaUnitsData();
  if (mFormulaUnitsData == NULL)
  {
    mFormulaUnitsData = new List();
  }
  fud->setUnitReferenceId(id);
  fud->setComponentTypecode(typecode);

  KeyValue key(id, typecode);
  mUnitsDataMap.insert(make_pair(key, fud));
  mFormulaUnitsData->add(fud);

  return fud;
}
/** @endcond */

/** @cond doxygenLibsbmlInternal */
/*
 * @return the nth FormulaUnitsData of this Model.
 */
const FormulaUnitsData*
Model::getFormulaUnitsData (unsigned int n) const
{
  if (mFormulaUnitsData == NULL) return NULL;
  return static_cast<const FormulaUnitsData*>( mFormulaUnitsData->get(n) );
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the nth FormulaUnitsData of this Model.
 */
FormulaUnitsData*
Model::getFormulaUnitsData (unsigned int n)
{
  if (mFormulaUnitsData == NULL) return NULL;
  return static_cast<FormulaUnitsData*>( mFormulaUnitsData->get(n) );
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the FormulaUnitsData in this Model with the given @p id
 * or @c NULL if no such
 * FormulaUnitsData exists.
 */
const FormulaUnitsData*
Model::getFormulaUnitsData (const std::string& sid,
                            int typecode) const
{
  return const_cast<Model*>(this)->getFormulaUnitsData(sid,typecode);
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the FormulaUnitsData in this Model with the given @p id  and typecode
 * or @c NULL if no such FormulaUnitsData exists.
 */
FormulaUnitsData*
Model::getFormulaUnitsData (const std::string& sid, int typecode)
{
  FormulaUnitsData * fud = NULL;

  //for (unsigned int n = 0; n < getNumFormulaUnitsData(); n++)
  //{
  //  fud = static_cast <FormulaUnitsData*> (mFormulaUnitsData->get(n));
  //  if (!strcmp(fud->getUnitReferenceId().c_str(), sid.c_str()))
  //  {
  //    if (fud->getComponentTypecode() == typecode)
  //    {
  //      return fud;
  //    }
  //  }
  //}

  KeyValue key(sid, typecode);
  UnitsValueIter it = mUnitsDataMap.find(key);
  if (it != mUnitsDataMap.end())
  {
    fud = it->second;
  }
  return fud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the FormulaUnitsData in this Model with the given @p id  and typecode
 * or @c NULL if no such FormulaUnitsData exists.
 */
FormulaUnitsData*
Model::getFormulaUnitsDataForVariable (const std::string& sid)
{
  FormulaUnitsData * fud = NULL;

  if (getParameter(sid) != NULL)
  {
    fud = getFormulaUnitsData(sid, SBML_PARAMETER);
  }
  else if (getCompartment(sid) != NULL)
  {
    fud = getFormulaUnitsData(sid, SBML_COMPARTMENT);
  }
  else if (getSpecies(sid) != NULL)
  {
    fud = getFormulaUnitsData(sid, SBML_SPECIES);
  }
  else if (getSpeciesReference(sid) != NULL)
  {
    fud = getFormulaUnitsData(sid, SBML_SPECIES_REFERENCE);
  }

  return fud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the FormulaUnitsData in this Model with the given @p id  and typecode
 * or @c NULL if no such FormulaUnitsData exists.
 */
FormulaUnitsData*
Model::getFormulaUnitsDataForAssignment(const std::string& sid)
{
  FormulaUnitsData * fud = NULL;

  if (getInitialAssignment(sid) != NULL)
  {
    fud = getFormulaUnitsData(sid, SBML_INITIAL_ASSIGNMENT);
  }
  else if (getAssignmentRule(sid) != NULL)
  {
    fud = getFormulaUnitsData(sid, SBML_ASSIGNMENT_RULE);
  }

  return fud;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * @return the number of FormulaUnitsDatas in this Model.
 */
unsigned int
Model::getNumFormulaUnitsData () const
{
  if (mFormulaUnitsData == NULL) return 0;
  return mFormulaUnitsData->getSize();
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/**
  * Get the list of FormulaUnitsData object in this Model.
  *
  * @return the list of FormulaUnitsData for this Model.
  */
List*
Model::getListFormulaUnitsData ()
{
  return mFormulaUnitsData;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/**
  * Get the list of FormulaUnitsData object in this Model.
  *
  * @return the list of FormulaUnitsData for this Model.
  */
const List*
Model::getListFormulaUnitsData () const
{
  return mFormulaUnitsData;
}
/** @endcond */


/** @cond doxygenLibsbmlInternal */
/*
 * returns true if the list has been populated, false otherwise
 */
bool
Model::isPopulatedListFormulaUnitsData()
{
  if (mFormulaUnitsData != NULL)
    return true;
  else
    return false;
}
/** @endcond */


/**
 * Populates the internal list of the identifiers of all elements within this Model object.
 */
void
Model::populateAllElementIdList()
{
  mIdList.clear();
  IdFilter filter;
  List* allElements = this->getAllElements(&filter);

  //for (unsigned int i = 0; i < allElements->getSize(); i++)
  //{
  //  mIdList.append(static_cast<SBase*>(allElements->get(i))->getId());
  //}

  for (ListIterator iter = allElements->begin(); iter != allElements->end(); ++iter)
  {
    mIdList.append(static_cast<SBase*>(*iter)->getId());
  }

  delete allElements;
}


/**
  * @return @c true if the id list has already been populated, @c false
  * otherwise.
  */
bool
Model::isPopulatedAllElementIdList() const
{
  return (mIdList.size() != 0);
}


/**
  * Returns the internal list of the identifiers of all elements within this Model object.
  */
IdList
Model::getAllElementIdList() const
{
  return mIdList;
}


/**
  * Clears the internal list of the identifiers of all elements within this Model object.
  */
void
Model::clearAllElementIdList()
{
  mIdList.clear();
}


/**
 * Populates the internal list of the metaids of all elements within this Model object.
 */
void
Model::populateAllElementMetaIdList()
{
  mMetaidList.clear();
  MetaIdFilter filter;
  List* allElements = this->getAllElements(&filter);

  for (ListIterator iter = allElements->begin(); iter != allElements->end(); ++iter)
  {
    mMetaidList.append(static_cast<SBase*>(*iter)->getMetaId());
  }

  delete allElements;
}


/**
  * @return @c true if the metaid list has already been populated, @c false
  * otherwise.
  */
bool
Model::isPopulatedAllElementMetaIdList() const
{
  return (mMetaidList.size() != 0);
}


/**
  * Returns the internal list of the metaids of all elements within this Model object.
  */
IdList
Model::getAllElementMetaIdList() const
{
  return mMetaidList;
}


/**
  * Clears the internal list of the metaids of all elements within this Model object.
  */
void
Model::clearAllElementMetaIdList()
{
  mMetaidList.clear();
}


#endif /* __cplusplus */
/** @cond doxygenIgnored */
LIBSBML_EXTERN
Model_t *
Model_create (unsigned int level, unsigned int version)
{
  try
  {
    Model* obj = new Model(level,version);
    return obj;
  }
  catch (SBMLConstructorException)
  {
    return NULL;
  }
}


LIBSBML_EXTERN
Model_t *
Model_createWithNS (SBMLNamespaces_t* sbmlns)
{
  try
  {
    Model* obj = new Model(sbmlns);
    return obj;
  }
  catch (SBMLConstructorException)
  {
    return NULL;
  }
}


LIBSBML_EXTERN
Model_t *
Model_clone (const Model_t *m)
{
  return (m != NULL) ? static_cast<Model*>( m->clone() ) : NULL;
}


LIBSBML_EXTERN
void
Model_free (Model_t *m)
{
  if (m != NULL)
  delete m;
}


LIBSBML_EXTERN
const XMLNamespaces_t *
Model_getNamespaces(Model_t *m)
{
  return (m != NULL) ? m->getNamespaces() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getId (const Model_t *m)
{
  return (m != NULL && m->isSetId()) ? m->getId().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getName (const Model_t *m)
{
  return (m != NULL && m->isSetName()) ? m->getName().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getSubstanceUnits (const Model_t *m)
{
  return (m != NULL && m->isSetSubstanceUnits()) ?
                       m->getSubstanceUnits().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getTimeUnits (const Model_t *m)
{
  return (m != NULL && m->isSetTimeUnits()) ? m->getTimeUnits().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getVolumeUnits (const Model_t *m)
{
  return (m != NULL && m->isSetVolumeUnits()) ?
                       m->getVolumeUnits().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getAreaUnits (const Model_t *m)
{
  return (m != NULL && m->isSetAreaUnits()) ? m->getAreaUnits().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getLengthUnits (const Model_t *m)
{
  return (m != NULL && m->isSetLengthUnits()) ?
                       m->getLengthUnits().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getExtentUnits (const Model_t *m)
{
  return (m != NULL && m->isSetExtentUnits()) ?
                       m->getExtentUnits().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
Model_getConversionFactor (const Model_t *m)
{
  return (m != NULL && m->isSetConversionFactor()) ?
                       m->getConversionFactor().c_str() : NULL;
}


LIBSBML_EXTERN
int
Model_isSetId (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetId() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetName (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetName() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetSubstanceUnits (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetSubstanceUnits() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetTimeUnits (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetTimeUnits() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetVolumeUnits (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetVolumeUnits() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetAreaUnits (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetAreaUnits() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetLengthUnits (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetLengthUnits() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetExtentUnits (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetExtentUnits() ) : 0;
}


LIBSBML_EXTERN
int
Model_isSetConversionFactor (const Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetConversionFactor() ) : 0;
}


LIBSBML_EXTERN
int
Model_setId (Model_t *m, const char *sid)
{
  if (m != NULL)
    return (sid == NULL) ? m->unsetId() : m->setId(sid);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setName (Model_t *m, const char *name)
{
  if (m != NULL)
    return (name == NULL) ? m->unsetName() : m->setName(name);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setSubstanceUnits (Model_t *m, const char *units)
{
  if (m != NULL)
    return (units == NULL) ? m->unsetSubstanceUnits() :
                                     m->setSubstanceUnits(units);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setTimeUnits (Model_t *m, const char *units)
{
  if (m != NULL)
    return (units == NULL) ? m->unsetTimeUnits() :
                                     m->setTimeUnits(units);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setVolumeUnits (Model_t *m, const char *units)
{
  if (m != NULL)
    return (units == NULL) ? m->unsetVolumeUnits() :
                                     m->setVolumeUnits(units);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setAreaUnits (Model_t *m, const char *units)
{
  if (m != NULL)
    return (units == NULL) ? m->unsetAreaUnits() :
                                     m->setAreaUnits(units);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setLengthUnits (Model_t *m, const char *units)
{
  if (m != NULL)
    return (units == NULL) ? m->unsetLengthUnits() :
                                     m->setLengthUnits(units);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setExtentUnits (Model_t *m, const char *units)
{
  if (m != NULL)
    return (units == NULL) ? m->unsetExtentUnits() :
                                     m->setExtentUnits(units);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_setConversionFactor (Model_t *m, const char *sid)
{
  if (m != NULL)
    return (sid == NULL) ? m->unsetConversionFactor() :
                                     m->setConversionFactor(sid);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetId (Model_t *m)
{
  if (m != NULL)
    return m->unsetId();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetName (Model_t *m)
{
  if (m != NULL)
    return m->unsetName();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetSubstanceUnits (Model_t *m)
{
  if (m != NULL)
    return m->unsetSubstanceUnits();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetTimeUnits (Model_t *m)
{
  if (m != NULL)
    return m->unsetTimeUnits();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetVolumeUnits (Model_t *m)
{
  if (m != NULL)
    return m->unsetVolumeUnits();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetAreaUnits (Model_t *m)
{
  if (m != NULL)
    return m->unsetAreaUnits();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetLengthUnits (Model_t *m)
{
  if (m != NULL)
    return m->unsetLengthUnits();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetExtentUnits (Model_t *m)
{
  if (m != NULL)
    return m->unsetExtentUnits();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_unsetConversionFactor (Model_t *m)
{
  if (m != NULL)
    return m->unsetConversionFactor();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
ModelHistory_t *
Model_getModelHistory(Model_t *m)
{
  return (m != NULL) ? m->getModelHistory() : NULL;
}


LIBSBML_EXTERN
int
Model_isSetModelHistory(Model_t *m)
{
  return (m != NULL) ? static_cast<int>( m->isSetModelHistory() ) : 0;
}


LIBSBML_EXTERN
int
Model_setModelHistory(Model_t *m, ModelHistory_t *history)
{
  return (m != NULL) ? m->setModelHistory(history) : LIBSBML_INVALID_OBJECT;
}

LIBSBML_EXTERN
int
Model_unsetModelHistory(Model_t *m)
{
  return (m != NULL) ? m->unsetModelHistory() : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addFunctionDefinition (Model_t *m, const FunctionDefinition_t *fd)
{
  return  (m != NULL) ? m->addFunctionDefinition(fd) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addUnitDefinition (Model_t *m, const UnitDefinition_t *ud)
{
  return (m != NULL) ? m->addUnitDefinition(ud) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addCompartmentType (Model_t *m, const CompartmentType_t *ct)
{
  return (m != NULL) ? m->addCompartmentType(ct) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addSpeciesType (Model_t *m, const SpeciesType_t *st)
{
  return (m != NULL) ? m->addSpeciesType(st) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addCompartment (Model_t *m, const Compartment_t *c)
{
  return (m != NULL) ? m->addCompartment(c) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addSpecies (Model_t *m, const Species_t *s)
{
  return (m != NULL) ? m->addSpecies(s) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addParameter (Model_t *m, const Parameter_t *p)
{
  return (m != NULL) ? m->addParameter(p) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addInitialAssignment (Model_t *m, const InitialAssignment_t *ia)
{
  return (m != NULL) ? m->addInitialAssignment(ia) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addRule (Model_t *m, const Rule_t *r)
{
  return (m != NULL) ? m->addRule(r) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addConstraint (Model_t *m, const Constraint_t *c)
{
  return (m != NULL) ? m->addConstraint(c) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addReaction (Model_t *m, const Reaction_t *r)
{
  return (m != NULL) ? m->addReaction(r) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
Model_addEvent (Model_t *m, const Event_t *e)
{
  return (m != NULL) ? m->addEvent(e) : LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
FunctionDefinition_t *
Model_createFunctionDefinition (Model_t *m)
{
  return (m != NULL) ? m->createFunctionDefinition() : NULL;
}


LIBSBML_EXTERN
UnitDefinition_t *
Model_createUnitDefinition (Model_t *m)
{
  return (m != NULL) ? m->createUnitDefinition() : NULL;
}


LIBSBML_EXTERN
Unit_t *
Model_createUnit (Model_t *m)
{
  return (m != NULL) ? m->createUnit() : NULL;
}


LIBSBML_EXTERN
CompartmentType_t *
Model_createCompartmentType (Model_t *m)
{
  return (m != NULL) ? m->createCompartmentType() : NULL;
}


LIBSBML_EXTERN
SpeciesType_t *
Model_createSpeciesType (Model_t *m)
{
  return (m != NULL) ? m->createSpeciesType() : NULL;
}


LIBSBML_EXTERN
Compartment_t *
Model_createCompartment (Model_t *m)
{
  return (m != NULL) ? m->createCompartment() : NULL;
}


LIBSBML_EXTERN
Species_t *
Model_createSpecies (Model_t *m)
{
  return (m != NULL) ? m->createSpecies() : NULL;
}


LIBSBML_EXTERN
Parameter_t *
Model_createParameter (Model_t *m)
{
  return (m != NULL) ? m->createParameter() : NULL;
}


LIBSBML_EXTERN
InitialAssignment_t *
Model_createInitialAssignment (Model_t *m)
{
  return (m != NULL) ? m->createInitialAssignment() : NULL;
}


LIBSBML_EXTERN
Rule_t *
Model_createAlgebraicRule (Model_t *m)
{
  return (m != NULL) ? m->createAlgebraicRule() : NULL;
}


LIBSBML_EXTERN
Rule_t *
Model_createAssignmentRule (Model_t *m)
{
  return (m != NULL) ? m->createAssignmentRule() : NULL;
}


LIBSBML_EXTERN
Rule_t *
Model_createRateRule (Model_t *m)
{
  return (m != NULL) ? m->createRateRule() : NULL;
}


LIBSBML_EXTERN
Constraint_t *
Model_createConstraint (Model_t *m)
{
  return (m != NULL) ? m->createConstraint() : NULL;
}

LIBSBML_EXTERN
Reaction_t *
Model_createReaction (Model_t *m)
{
  return (m != NULL) ? m->createReaction() : NULL;
}


LIBSBML_EXTERN
SpeciesReference_t *
Model_createReactant (Model_t *m)
{
  return (m != NULL) ? m->createReactant() : NULL;
}


LIBSBML_EXTERN
SpeciesReference_t *
Model_createProduct (Model_t *m)
{
  return (m != NULL) ? m->createProduct() : NULL;
}


LIBSBML_EXTERN
SpeciesReference_t *
Model_createModifier (Model_t *m)
{
  return (m != NULL) ?
          static_cast<SpeciesReference_t*>( m->createModifier() ) : NULL;
}


LIBSBML_EXTERN
KineticLaw_t *
Model_createKineticLaw (Model_t *m)
{
  return (m != NULL) ? m->createKineticLaw() : NULL;
}


LIBSBML_EXTERN
Parameter_t *
Model_createKineticLawParameter (Model_t *m)
{
  return (m != NULL) ? m->createKineticLawParameter() : NULL;
}


LIBSBML_EXTERN
LocalParameter_t *
Model_createKineticLawLocalParameter (Model_t *m)
{
  return (m != NULL) ? m->createKineticLawLocalParameter() : NULL;
}


LIBSBML_EXTERN
Event_t *
Model_createEvent (Model_t *m)
{
  return (m != NULL) ? m->createEvent() : NULL;
}


LIBSBML_EXTERN
EventAssignment_t *
Model_createEventAssignment (Model_t *m)
{
  return (m != NULL) ? m->createEventAssignment() : NULL;
}


LIBSBML_EXTERN
Trigger_t *
Model_createTrigger (Model_t *m)
{
  return (m != NULL) ? m->createTrigger() : NULL;
}


LIBSBML_EXTERN
Delay_t *
Model_createDelay (Model_t *m)
{
  return (m != NULL) ? m->createDelay() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfFunctionDefinitions (Model_t *m)
{
  return (m != NULL) ? m->getListOfFunctionDefinitions() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfUnitDefinitions (Model_t *m)
{
  return (m != NULL) ? m->getListOfUnitDefinitions() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfCompartmentTypes (Model_t *m)
{
  return (m != NULL) ? m->getListOfCompartmentTypes() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfSpeciesTypes (Model_t *m)
{
  return (m != NULL) ? m->getListOfSpeciesTypes() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfCompartments (Model_t *m)
{
  return (m != NULL) ? m->getListOfCompartments() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfSpecies (Model_t *m)
{
  return (m != NULL) ? m->getListOfSpecies() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfParameters (Model_t *m)
{
  return (m != NULL) ? m->getListOfParameters() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfInitialAssignments (Model_t* m)
{
  return (m != NULL) ? m->getListOfInitialAssignments() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfRules (Model_t *m)
{
  return (m != NULL) ? m->getListOfRules() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfConstraints (Model_t* m)
{
  return (m != NULL) ? m->getListOfConstraints() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfReactions (Model_t *m)
{
  return (m != NULL) ? m->getListOfReactions() : NULL;
}


LIBSBML_EXTERN
ListOf_t *
Model_getListOfEvents (Model_t *m)
{
  return (m != NULL) ? m->getListOfEvents() : NULL;
}


LIBSBML_EXTERN
FunctionDefinition_t *
Model_getFunctionDefinition (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getFunctionDefinition(n) : NULL;
}


LIBSBML_EXTERN
FunctionDefinition_t *
Model_getFunctionDefinitionById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getFunctionDefinition(sid) : NULL;
}


LIBSBML_EXTERN
UnitDefinition_t *
Model_getUnitDefinition (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getUnitDefinition(n) : NULL;
}


LIBSBML_EXTERN
UnitDefinition_t *
Model_getUnitDefinitionById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getUnitDefinition(sid) : NULL;
}


LIBSBML_EXTERN
CompartmentType_t *
Model_getCompartmentType (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getCompartmentType(n) : NULL;
}


LIBSBML_EXTERN
CompartmentType_t *
Model_getCompartmentTypeById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getCompartmentType(sid) : NULL;
}


LIBSBML_EXTERN
SpeciesType_t *
Model_getSpeciesType (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getSpeciesType(n) : NULL;
}


LIBSBML_EXTERN
SpeciesType_t *
Model_getSpeciesTypeById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getSpeciesType(sid) : NULL;
}


LIBSBML_EXTERN
Compartment_t *
Model_getCompartment (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getCompartment(n) : NULL;
}


LIBSBML_EXTERN
Compartment_t *
Model_getCompartmentById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getCompartment(sid) : NULL;
}


LIBSBML_EXTERN
Species_t *
Model_getSpecies (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getSpecies(n) : NULL;
}


LIBSBML_EXTERN
Species_t *
Model_getSpeciesById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getSpecies(sid) : NULL;
}


LIBSBML_EXTERN
Parameter_t *
Model_getParameter (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getParameter(n) : NULL;
}


LIBSBML_EXTERN
Parameter_t *
Model_getParameterById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getParameter(sid) : NULL;
}


LIBSBML_EXTERN
InitialAssignment_t *
Model_getInitialAssignment (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getInitialAssignment(n) : NULL;
}


LIBSBML_EXTERN
InitialAssignment_t *
Model_getInitialAssignmentBySym (Model_t *m, const char *symbol)
{
  return (symbol != NULL) ? m->getInitialAssignment(symbol) : NULL;
}


LIBSBML_EXTERN
Rule_t *
Model_getRule (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getRule(n) : NULL;
}


LIBSBML_EXTERN
Rule_t *
Model_getRuleByVar (Model_t *m, const char *variable)
{
  return (variable != NULL) ? m->getRule(variable) : NULL;
}


LIBSBML_EXTERN
Constraint_t *
Model_getConstraint (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getConstraint(n) : NULL;
}


LIBSBML_EXTERN
Reaction_t *
Model_getReaction (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getReaction(n) : NULL;
}


LIBSBML_EXTERN
Reaction_t *
Model_getReactionById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getReaction(sid) : NULL;
}

LIBSBML_EXTERN
SpeciesReference_t *
Model_getSpeciesReferenceById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getSpeciesReference(sid) : NULL;
}



LIBSBML_EXTERN
Event_t *
Model_getEvent (Model_t *m, unsigned int n)
{
  return (m != NULL) ? m->getEvent(n) : NULL;
}


LIBSBML_EXTERN
Event_t *
Model_getEventById (Model_t *m, const char *sid)
{
  return (m != NULL && sid != NULL) ? m->getEvent(sid) : NULL;
}


LIBSBML_EXTERN
unsigned int
Model_getNumFunctionDefinitions (const Model_t *m)
{
  return (m != NULL) ? m->getNumFunctionDefinitions() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumUnitDefinitions (const Model_t *m)
{
  return (m != NULL) ? m->getNumUnitDefinitions() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumCompartmentTypes (const Model_t *m)
{
  return (m != NULL) ? m->getNumCompartmentTypes() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumSpeciesTypes (const Model_t *m)
{
  return (m != NULL) ? m->getNumSpeciesTypes() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumCompartments (const Model_t *m)
{
  return (m != NULL) ? m->getNumCompartments() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumSpecies (const Model_t *m)
{
  return (m != NULL) ? m->getNumSpecies() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumSpeciesWithBoundaryCondition (const Model_t *m)
{
  return (m != NULL) ? m->getNumSpeciesWithBoundaryCondition() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumParameters (const Model_t *m)
{
  return (m != NULL) ? m->getNumParameters() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumInitialAssignments (const Model_t *m)
{
  return (m != NULL) ? m->getNumInitialAssignments() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumRules (const Model_t *m)
{
  return (m != NULL) ? m->getNumRules() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumConstraints (const Model_t *m)
{
  return (m != NULL) ? m->getNumConstraints() : SBML_INT_MAX;
}

LIBSBML_EXTERN
unsigned int
Model_getNumReactions (const Model_t *m)
{
  return (m != NULL) ? m->getNumReactions() : SBML_INT_MAX;
}


LIBSBML_EXTERN
unsigned int
Model_getNumEvents (const Model_t *m)
{
  return (m != NULL) ? m->getNumEvents() : SBML_INT_MAX;
}


LIBSBML_EXTERN
void
Model_populateListFormulaUnitsData(Model_t *m)
{
  if (m != NULL)
    m->populateListFormulaUnitsData();
}


LIBSBML_EXTERN
int
Model_isPopulatedListFormulaUnitsData(Model_t *m)
{
  return (m != NULL) ?
    static_cast<int>( m->isPopulatedListFormulaUnitsData()) : 0;
}


LIBSBML_EXTERN
FunctionDefinition_t*
Model_removeFunctionDefinition (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeFunctionDefinition(n);
  else
    return NULL;
}


LIBSBML_EXTERN
FunctionDefinition_t*
Model_removeFunctionDefinitionById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeFunctionDefinition(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
UnitDefinition_t*
Model_removeUnitDefinition (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeUnitDefinition(n);
  else
    return NULL;
}


LIBSBML_EXTERN
UnitDefinition_t*
Model_removeUnitDefinitionById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeUnitDefinition(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
CompartmentType_t*
Model_removeCompartmentType (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeCompartmentType(n);
  else
    return NULL;
}


LIBSBML_EXTERN
CompartmentType_t*
Model_removeCompartmentTypeById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeCompartmentType(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
SpeciesType_t*
Model_removeSpeciesType (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeSpeciesType(n);
  else
    return NULL;
}


LIBSBML_EXTERN
SpeciesType_t*
Model_removeSpeciesTypeById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeSpeciesType(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
Compartment_t*
Model_removeCompartment (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeCompartment(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Compartment_t*
Model_removeCompartmentById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeCompartment(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
Species_t*
Model_removeSpecies (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeSpecies(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Species_t*
Model_removeSpeciesById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeSpecies(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
Parameter_t*
Model_removeParameter (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeParameter(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Parameter_t*
Model_removeParameterById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeParameter(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
InitialAssignment_t*
Model_removeInitialAssignment (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeInitialAssignment(n);
  else
    return NULL;
}


LIBSBML_EXTERN
InitialAssignment_t*
Model_removeInitialAssignmentBySym (Model_t *m, const char* symbol)
{
  if (m != NULL)
    return (symbol != NULL) ? m->removeInitialAssignment(symbol) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
Rule_t*
Model_removeRule (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeRule(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Rule_t*
Model_removeRuleByVar (Model_t *m, const char* variable)
{
  if (m != NULL)
    return (variable != NULL) ? m->removeRule(variable) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
Constraint_t*
Model_removeConstraint (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeConstraint(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Reaction_t*
Model_removeReaction (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeReaction(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Reaction_t*
Model_removeReactionById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeReaction(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
Event_t*
Model_removeEvent (Model_t *m, unsigned int n)
{
  if (m != NULL)
    return m->removeEvent(n);
  else
    return NULL;
}


LIBSBML_EXTERN
Event_t*
Model_removeEventById (Model_t *m, const char* sid)
{
  if (m != NULL)
    return (sid != NULL) ? m->removeEvent(sid) : NULL;
  else
    return NULL;
}


/* NOT YET USED but leave in case of future need

LIBSBML_EXTERN
void
Model_addFormulaUnitsData (Model_t *m, FormulaUnitsData_t* fud)
{
  m->addFormulaUnitsData(fud);
}


LIBSBML_EXTERN
FormulaUnitsData_t*
Model_createFormulaUnitsData (Model_t *m)
{
  return m->createFormulaUnitsData();
}


LIBSBML_EXTERN
FormulaUnitsData_t*
Model_getFormulaUnitsData (Model_t *m, unsigned int n)
{
  return m->getFormulaUnitsData(n);
}


LIBSBML_EXTERN
FormulaUnitsData_t*
Model_getFormulaUnitsDataById(Model_t *m, const char* sid,
                                          int typecode)
{
  return m->getFormulaUnitsData(sid, typecode);
}


LIBSBML_EXTERN
unsigned int
Model_getNumFormulaUnitsData (Model_t *m)
{
  return m->getNumFormulaUnitsData();
}


LIBSBML_EXTERN
List_t*
Model_getListFormulaUnitsData (Model_t *m)
{
  return m->getListFormulaUnitsData();
}

*/
/** @endcond */
LIBSBML_CPP_NAMESPACE_END