src/sbml/FunctionDefinition.cpp

/**
 * @file    FunctionDefinition.cpp
 * @brief   Implementation of FunctionDefinition and ListOfFunctionDefinitions.
 * @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 <cstring>

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

#include <sbml/math/FormulaParser.h>
#include <sbml/math/ASTNode.h>
#include <sbml/math/MathML.h>

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

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

LIBSBML_CPP_NAMESPACE_BEGIN
#ifdef __cplusplus

FunctionDefinition::FunctionDefinition (unsigned int level, unsigned int version) :
   SBase ( level, version )
 , mMath ( NULL  )
{
  if (!hasValidLevelVersionNamespaceCombination())
    throw SBMLConstructorException();
}


FunctionDefinition::FunctionDefinition (SBMLNamespaces * sbmlns) :
   SBase ( sbmlns )
 , mMath ( NULL  )
{
  if (!hasValidLevelVersionNamespaceCombination())
  {
    throw SBMLConstructorException(getElementName(), sbmlns);
  }

  loadPlugins(sbmlns);
}


/*
 * Destroys this FunctionDefinition.
 */
FunctionDefinition::~FunctionDefinition ()
{
  delete mMath;
}


/*
 * Copy constructor. Creates a copy of this FunctionDefinition.
 */
FunctionDefinition::FunctionDefinition (const FunctionDefinition& orig) :
   SBase             ( orig         )
 , mMath             ( NULL            )
{

  if (orig.mMath != NULL)
  {
    mMath = orig.mMath->deepCopy();
    mMath->setParentSBMLObject(this);
  }
}


/*
 * Assignment operator
 */
FunctionDefinition& FunctionDefinition::operator=(const FunctionDefinition& rhs)
{
  if(&rhs!=this)
  {
    this->SBase::operator =(rhs);

    delete mMath;
    if (rhs.mMath != NULL)
    {
      mMath = rhs.mMath->deepCopy();
      mMath->setParentSBMLObject(this);
    }
    else
    {
      mMath = NULL;
    }
  }

  return *this;
}


/** @cond doxygenLibsbmlInternal */
bool
FunctionDefinition::accept (SBMLVisitor& v) const
{
  return v.visit(*this);
}
/** @endcond */


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


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


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


/*
 * @return the math of this FunctionDefinition.
 */
const ASTNode*
FunctionDefinition::getMath () const
{
  return mMath;
}


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


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


/*
 * @return @c true if the math of this FunctionDefinition is set, false
 * otherwise.
 */
bool
FunctionDefinition::isSetMath () const
{
  return (mMath != NULL);
}

/*
 * Sets the id of this SBML object to a copy of @p sid.
 */
int
FunctionDefinition::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
FunctionDefinition::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 math of this FunctionDefinition to the given ASTNode.
 */
int
FunctionDefinition::setMath (const ASTNode* math)
{
  if (mMath == math)
  {
    return LIBSBML_OPERATION_SUCCESS;
  }
  else if (math == NULL)
  {
    delete mMath;
    mMath = NULL;
    return LIBSBML_OPERATION_SUCCESS;
  }
  else if (!(math->isWellFormedASTNode()))
  {
    return LIBSBML_INVALID_OBJECT;
  }
  else
  {
    delete mMath;
    mMath = (math != NULL) ? math->deepCopy() : NULL;
    if (mMath != NULL) mMath->setParentSBMLObject(this);
    return LIBSBML_OPERATION_SUCCESS;
  }
}


/*
 * Unsets the name of this SBML object.
 */
int
FunctionDefinition::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;
  }
}


/*
 * @return the nth argument (bound variable) passed to this
 * FunctionDefinition.
 */
const ASTNode*
FunctionDefinition::getArgument (unsigned int n) const
{
  if (mMath == NULL) return NULL;

  /* if the math is not a lambda this function can cause issues
   * elsewhere, technically if the math is not a lambda
   * function the body is NULL
   */
  ASTNode * lambda = NULL;

  if (mMath->isLambda() == true)
  {
    lambda = mMath;
  }
  else
  {
    if ((getLevel() == 2 && getVersion() > 2) || getLevel() > 2)
    {
      if (mMath->isSemantics() == true && mMath->getNumChildren() == 1
        && mMath->getChild(0)->isLambda() == true)
      {
        lambda = mMath->getChild(0);
      }
    }
  }

  if (lambda == NULL)
  {
    return NULL;
  }
  else if (n < getNumArguments())
  {
    return lambda->getChild(n);
  }
  else
  {
    return NULL;
  }
}


/*
 * @return the argument (bound variable) in this FunctionDefinition with
 * the given name or @c NULL if no such argument exists.
 */
const ASTNode*
FunctionDefinition::getArgument (const std::string& name) const
{
  const char*    cname = name.c_str();
  const ASTNode* found = NULL;


  for (unsigned int n = 0; n < getNumArguments(); ++n)
  {
    const ASTNode* node = getArgument(n);

    if (node != NULL && node->isName() && !strcmp(node->getName(), cname))
    {
      found = node;
      break;
    }
  }

  return found;
}


/*
 * @return the body of this FunctionDefinition, or @c NULL if no body is
 * defined.
 */
const ASTNode*
FunctionDefinition::getBody () const
{
  if (mMath == NULL) return NULL;

  /* if the math is not a lambda this function can cause issues
   * elsewhere, technically if the math is not a lambda
   * function the body is NULL
   */
  ASTNode * lambda = NULL;

  if (mMath->isLambda() == true)
  {
    lambda = mMath;
  }
  else
  {
    if ((getLevel() == 2 && getVersion() > 2) || getLevel() > 2)
    {
      if (mMath->isSemantics() == true && mMath->getNumChildren() == 1
        && mMath->getChild(0)->isLambda() == true)
      {
        lambda = mMath->getChild(0);
      }
    }
  }

  if (lambda == NULL)
  {
    return NULL;
  }


  unsigned int nc = lambda->getNumChildren();
  /* here we do actually need to look at whether something is a bvar
   * and not just assume that the last child is a function body
   * it should be BUT it might not be
   */

  if (nc > 0 && lambda->getNumBvars() < nc)
  {
    return lambda->getChild(nc-1);
  }
  else
  {
    return NULL;
  }
}


/*
 * @return the body of this FunctionDefinition, or @c NULL if no body is
 * defined.
 */
ASTNode*
FunctionDefinition::getBody ()
{
  if (mMath == NULL) return NULL;

  /* if the math is not a lambda this function can cause issues
   * elsewhere, technically if the math is not a lambda
   * function the body is NULL
   */
  ASTNode * lambda = NULL;

  if (mMath->isLambda() == true)
  {
    lambda = mMath;
  }
  else
  {
    if ((getLevel() == 2 && getVersion() > 2) || getLevel() > 2)
    {
      if (mMath->isSemantics() == true && mMath->getNumChildren() == 1
        && mMath->getChild(0)->isLambda() == true)
      {
        lambda = mMath->getChild(0);
      }
    }
  }

  if (lambda == NULL)
  {
    return NULL;
  }


  unsigned int nc = lambda->getNumChildren();
  /* here we do actually need to look at whether something is a bvar
   * and not just assume that the last child is a function body
   * it should be BUT it might not be
   */

  if (nc > 0 && lambda->getNumBvars() < nc)
  {
    return lambda->getChild(nc-1);
  }
  else
  {
    return NULL;
  }
}


/*
 * @return the true if the body of this FunctionDefinition is set
 */
bool
FunctionDefinition::isSetBody () const
{
  return (getBody() == NULL) ? false : true;
}


/*
 * @return the number of arguments (bound variables) that must be passed
 * to this FunctionDefinition.
 */
unsigned int
FunctionDefinition::getNumArguments () const
{
  if (isSetMath() == false)
  {
    return 0;
  }

  /* if the math is not a lambda this function can cause issues
   * elsewhere, technically if the math is not a lambda
   * function there are no arguments
   */
  ASTNode * lambda = NULL;

  if (mMath->isLambda() == true)
  {
    lambda = mMath;
  }
  else
  {
    if ((getLevel() == 2 && getVersion() > 2) || getLevel() > 2)
    {
      if (mMath->isSemantics() == true && mMath->getNumChildren() == 1
        && mMath->getChild(0)->isLambda() == true)
      {
        lambda = mMath->getChild(0);
      }
    }
  }

  if ( lambda == NULL)
  {
    return 0;
  }
  else
  {
    return lambda->getNumBvars();
  }
}


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


/*
 * @return the name of this element ie "functionDefinition".
 */
const string&
FunctionDefinition::getElementName () const
{
  static const string name = "functionDefinition";
  return name;
}


bool
FunctionDefinition::hasRequiredAttributes() const
{
  bool allPresent = true;

  /* required attributes for functionDefinition: id */

  if (!isSetId())
    allPresent = false;

  return allPresent;
}


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

  /* required attributes for functionDefinition: math */
  /* l3v2 removed that requirement */

  if ((getLevel() < 3 ) || (getLevel() == 3 && getVersion() == 1))
  {
    if (!isSetMath())
      allPresent = false;
  }

  return allPresent;
}

void
FunctionDefinition::renameUnitSIdRefs(const std::string& oldid, const std::string& newid)
{
  SBase::renameUnitSIdRefs(oldid, newid);
  if (isSetMath()) {
    mMath->renameUnitSIdRefs(oldid, newid);
  }
}

/** @cond doxygenLibsbmlInternal */

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

  return return_value;
}

/** @endcond */


/** @cond doxygenLibsbmlInternal */

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

/** @endcond */


/** @cond doxygenLibsbmlInternal */

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

  return value;
}

/** @endcond */


/** @cond doxygenLibsbmlInternal */

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

  return return_value;
}

/** @endcond */


/** @cond doxygenLibsbmlInternal */

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

/** @endcond */


/** @cond doxygenLibsbmlInternal */

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

  return value;
}

/** @endcond */


/** @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
FunctionDefinition::readOtherXML (XMLInputStream& stream)
{
  bool          read = false;
  const string& name = stream.peek().getName();

  if (name == "math")
  {
    // if this is level 1 there shouldnt be any math!!!
    if (getLevel() == 1)
    {
      logError(NotSchemaConformant, getLevel(), getVersion(),
	       "SBML Level 1 does not support MathML.");
      delete mMath;
      return false;
    }


    if (mMath != NULL)
    {
      if (getLevel() < 3)
      {
        logError(NotSchemaConformant, getLevel(), getVersion(),
	        "Only one <math> element is permitted inside a "
	        "particular containing element.");
      }
      else
      {
        logError(OneMathElementPerFunc, getLevel(), getVersion(),
          "The <functionDefinition> with id '" + getId() + "' contains "
          "more than one <math> element.");
      }
    }
    /* check for MathML namespace
     * this may be explicitly declared here
     * or implicitly declared on the whole document
     */
    const XMLToken elem = stream.peek();
    const std::string prefix = checkMathMLNamespace(elem);

    delete mMath;
    mMath = readMathML(stream, prefix);
    if (mMath != NULL) mMath->setParentSBMLObject(this);
    read  = true;
  }

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

  return read;
}
/** @endcond */


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

  attributes.add("name");
  attributes.add("id");

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

  if (level == 2 && version == 2)
  {
    attributes.add("sboTerm");
  }

}

/*
 * 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
FunctionDefinition::readAttributes (const XMLAttributes& attributes,
                                    const ExpectedAttributes& expectedAttributes)
{
  const unsigned int level   = getLevel  ();
  const unsigned int version = getVersion();

  SBase::readAttributes(attributes, expectedAttributes);

  switch (level)
  {
  case 1:
    logError(NotSchemaConformant, level, version,
	      "FunctionDefinition is not a valid component for this level/version.");
    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
FunctionDefinition::readL2Attributes (const XMLAttributes& attributes)
{
  const unsigned int level = getLevel();
  const unsigned int version = getVersion();

  //
  // id: SId  { use="required" }  (L2v1 ->)
  //
  bool assigned;
  assigned = attributes.readInto("id", mId, getErrorLog(), true, getLine(), getColumn());
  if (assigned && mId.size() == 0)
  {
    logEmptyString("id", level, version, "<functionDefinition>");
  }
  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
FunctionDefinition::readL3Attributes (const XMLAttributes& attributes)
{
  const unsigned int level = getLevel();
  const unsigned int version = getVersion();

  //
  // id: SId  { use="required" }  (L2v1 ->)
  //
  bool assigned;
  // 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)
    {
      logError(AllowedAttributesOnFunc, level, version,
        "The required attribute 'id' is missing.");
    }
    if (assigned && mId.size() == 0)
    {
      logEmptyString("id", level, version, "<functionDefinition>");
    }
    if (!SyntaxChecker::isValidInternalSId(mId))
      logError(InvalidIdSyntax, level, version, "The id '" + mId + "' does not conform to the syntax.");
  }
  else
  {
    // need to check that id was present
    // it has already been read and checked for syntax/emptyness
    if (attributes.hasAttribute("id") == false)
    {
      logError(AllowedAttributesOnFunc, level, version,
        "The required attribute 'id' is missing.");
    }
  }

  //
  // name: string  { use="optional" }  (L2v1 ->)
  //
  // for l3v2 sbase will read this
  if (version == 1)
  {
    attributes.readInto("name", mName, 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
FunctionDefinition::writeAttributes (XMLOutputStream& stream) const
{
  const unsigned int level = getLevel();
  const unsigned int version = getVersion();

  /* invalid level/version */
  if (level < 2)
  {
    return;
  }

  SBase::writeAttributes(stream);

  //
  // 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))
  {
    //
    // id: SId  { use="required" }  (L2v1 ->)
    //
    stream.writeAttribute("id", mId);

    //
    // name: string  { use="optional" }  (L2v1 ->)
    //
    stream.writeAttribute("name", mName);
  }

  //
  // (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
FunctionDefinition::writeElements (XMLOutputStream& stream) const
{
  SBase::writeElements(stream);

  if (mMath) writeMathML(mMath, stream, getSBMLNamespaces());

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


/*
 * Creates a new ListOfFunctionDefinitions items.
 */
ListOfFunctionDefinitions::ListOfFunctionDefinitions (unsigned int level, unsigned int version)
: ListOf(level,version)
{
}


/*
 * Creates a new ListOfFunctionDefinitions items.
 */
ListOfFunctionDefinitions::ListOfFunctionDefinitions (SBMLNamespaces* sbmlns)
: ListOf(sbmlns)
{
  loadPlugins(sbmlns);
}


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


/*
 * @return the typecode (int) of SBML objects contained in this ListOf or
 * SBML_UNKNOWN (default).
 */
int
ListOfFunctionDefinitions::getItemTypeCode () const
{
  return SBML_FUNCTION_DEFINITION;
}


/*
 * @return the name of this element ie "listOfFunctionDefinitions".
 */
const string&
ListOfFunctionDefinitions::getElementName () const
{
  static const string name = "listOfFunctionDefinitions";
  return name;
}


/* return nth item in list */
FunctionDefinition *
ListOfFunctionDefinitions::get(unsigned int n)
{
  return static_cast<FunctionDefinition*>(ListOf::get(n));
}


/* return nth item in list */
const FunctionDefinition *
ListOfFunctionDefinitions::get(unsigned int n) const
{
  return static_cast<const FunctionDefinition*>(ListOf::get(n));
}


/**
 * Used by ListOf::get() to lookup an SBase based by its id.
 */
struct IdEqFD : public unary_function<SBase*, bool>
{
  const string& mId;

  IdEqFD (const string& id) : mId(id) { }
  bool operator() (SBase* sb)
       { return static_cast <FunctionDefinition *> (sb)->getId() == mId; }
};


/* return item by id */
FunctionDefinition*
ListOfFunctionDefinitions::get (const std::string& sid)
{
  return const_cast<FunctionDefinition*>(
    static_cast<const ListOfFunctionDefinitions&>(*this).get(sid) );
}


/* return item by id */
const FunctionDefinition*
ListOfFunctionDefinitions::get (const std::string& sid) const
{
  vector<SBase*>::const_iterator result;

  result = find_if( mItems.begin(), mItems.end(), IdEqFD(sid) );
  return (result == mItems.end()) ? NULL :
                             static_cast <FunctionDefinition*> (*result);

}


/* Removes the nth item from this list */
FunctionDefinition*
ListOfFunctionDefinitions::remove (unsigned int n)
{
   return static_cast<FunctionDefinition*>(ListOf::remove(n));
}


/* Removes item in this list by id */
FunctionDefinition*
ListOfFunctionDefinitions::remove (const std::string& sid)
{
  SBase* item = NULL;
  vector<SBase*>::iterator result;

  result = find_if( mItems.begin(), mItems.end(), IdEqFD(sid) );

  if (result != mItems.end())
  {
    item = *result;
    mItems.erase(result);
  }

  return static_cast <FunctionDefinition*> (item);
}


/** @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
ListOfFunctionDefinitions::getElementPosition () const
{
  return 1;
}
/** @endcond */


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


  if (name == "functionDefinition")
  {
    try
    {
      object = new FunctionDefinition(getSBMLNamespaces());
    }
    catch (SBMLConstructorException*)
    {
      object = new FunctionDefinition(SBMLDocument::getDefaultLevel(),
        SBMLDocument::getDefaultVersion());
    }
    catch ( ... )
    {
      object = new FunctionDefinition(SBMLDocument::getDefaultLevel(),
        SBMLDocument::getDefaultVersion());
    }

    if (object != NULL) mItems.push_back(object);
  }

  return object;
}
/** @endcond */


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


LIBSBML_EXTERN
FunctionDefinition_t *
FunctionDefinition_createWithNS (SBMLNamespaces_t* sbmlns)
{
  try
  {
    FunctionDefinition* obj = new FunctionDefinition(sbmlns);
    return obj;
  }
  catch (SBMLConstructorException)
  {
    return NULL;
  }
}


LIBSBML_EXTERN
void
FunctionDefinition_free (FunctionDefinition_t *fd)
{
  if (fd != NULL)
  delete fd;
}


LIBSBML_EXTERN
FunctionDefinition_t *
FunctionDefinition_clone (const FunctionDefinition_t* fd)
{
  return (fd != NULL) ? static_cast<FunctionDefinition*>( fd->clone() ) : NULL;
}


LIBSBML_EXTERN
const XMLNamespaces_t *
FunctionDefinition_getNamespaces(FunctionDefinition_t *fd)
{
  return (fd != NULL) ? fd->getNamespaces() : NULL;
}


LIBSBML_EXTERN
const char *
FunctionDefinition_getId (const FunctionDefinition_t *fd)
{
  return (fd != NULL && fd->isSetId()) ? fd->getId().c_str() : NULL;
}


LIBSBML_EXTERN
const char *
FunctionDefinition_getName (const FunctionDefinition_t *fd)
{
  return (fd != NULL && fd->isSetName()) ? fd->getName().c_str() : NULL;
}


LIBSBML_EXTERN
const ASTNode_t *
FunctionDefinition_getMath (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? fd->getMath() : NULL;
}


LIBSBML_EXTERN
int
FunctionDefinition_isSetId (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? static_cast<int>( fd->isSetId() ) : 0;
}


LIBSBML_EXTERN
int
FunctionDefinition_isSetName (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? static_cast<int>( fd->isSetName() ) : 0;
}


LIBSBML_EXTERN
int
FunctionDefinition_isSetMath (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? static_cast<int>( fd->isSetMath() ) : 0;
}


LIBSBML_EXTERN
int
FunctionDefinition_setId (FunctionDefinition_t *fd, const char *sid)
{
  if (fd != NULL)
    return (sid == NULL) ? fd->setId("") : fd->setId(sid);
  else
    return LIBSBML_INVALID_OBJECT;
}


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


LIBSBML_EXTERN
int
FunctionDefinition_setMath (FunctionDefinition_t *fd, const ASTNode_t *math)
{
  if (fd != NULL)
    return fd->setMath(math);
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
int
FunctionDefinition_unsetName (FunctionDefinition_t *fd)
{
  if (fd != NULL)
    return fd->unsetName();
  else
    return LIBSBML_INVALID_OBJECT;
}


LIBSBML_EXTERN
const ASTNode_t *
FunctionDefinition_getArgument (const FunctionDefinition_t *fd, unsigned int n)
{
  return (fd != NULL) ? fd->getArgument(n) : NULL;
}


LIBSBML_EXTERN
const ASTNode_t *
FunctionDefinition_getArgumentByName ( FunctionDefinition_t *fd,
                                       const char *name )
{
  return (fd != NULL) ? fd->getArgument(name != NULL ? name : "") : NULL;
}


LIBSBML_EXTERN
const ASTNode_t *
FunctionDefinition_getBody (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? fd->getBody() : NULL;
}


LIBSBML_EXTERN
int
FunctionDefinition_isSetBody (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? static_cast<int>( fd->isSetBody() ) : 0;
}


LIBSBML_EXTERN
unsigned int
FunctionDefinition_getNumArguments (const FunctionDefinition_t *fd)
{
  return (fd != NULL) ? fd->getNumArguments() : SBML_INT_MAX;
}


LIBSBML_EXTERN
FunctionDefinition_t *
ListOfFunctionDefinitions_getById (ListOf_t *lo, const char *sid)
{
  if (lo != NULL)
    return (sid != NULL) ?
      static_cast <ListOfFunctionDefinitions *> (lo)->get(sid) : NULL;
  else
    return NULL;
}


LIBSBML_EXTERN
FunctionDefinition_t *
ListOfFunctionDefinitions_removeById (ListOf_t *lo, const char *sid)
{
  if (lo != NULL)
    return (sid != NULL) ?
      static_cast <ListOfFunctionDefinitions *> (lo)->remove(sid) : NULL;
  else
    return NULL;
}
/** @endcond */

LIBSBML_CPP_NAMESPACE_END