/**
 * @cond doxygenLibsbmlInternal
 *
 * @file    StoichiometryMathVars.cpp
 * @brief   Ensures FunctionDefinitions contain no undefined variables.
 * @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) 2013-2015 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/Model.h>
#include <sbml/Reaction.h>
#include <sbml/util/List.h>
#include <sbml/math/ASTNode.h>

#include <sbml/ModifierSpeciesReference.h>

#include "StoichiometryMathVars.h"

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

LIBSBML_CPP_NAMESPACE_BEGIN
#ifdef __cplusplus
/*
 * Creates a new Constraint with the given @p id.
 */
StoichiometryMathVars::StoichiometryMathVars (unsigned int id, Validator& v) :
  TConstraint<Reaction>(id, v)
{
}


/*
 * Destroys this Constraint.
 */
StoichiometryMathVars::~StoichiometryMathVars ()
{
}


/*
 * Checks that all variables referenced in FunctionDefinition bodies are
 * bound variables (function arguments).
 */
void
StoichiometryMathVars::check_ (const Model& m, const Reaction& r)
{
  if (r.getLevel() == 1) return;

  unsigned int n, ns;
  
  for (n = 0; n < r.getNumReactants(); n++)
  {
    mSpecies.append(r.getReactant(n)->getSpecies());
  }
  for (n = 0; n < r.getNumProducts(); n++)
  {
    mSpecies.append(r.getProduct(n)->getSpecies());
  }
  for (n = 0; n < r.getNumModifiers(); n++)
  {
    mSpecies.append(r.getModifier(n)->getSpecies());
  }

  for (n = 0; n < r.getNumReactants(); n++)
  {
    const SpeciesReference *sr = r.getReactant(n);

    if (sr->isSetStoichiometryMath())
    {
      List* variables = sr->getStoichiometryMath()->getMath()
        ->getListOfNodes( ASTNode_isName );
      for (ns = 0; ns < variables->getSize(); ns++)
      {
        ASTNode* node = static_cast<ASTNode*>( variables->get(ns) );
        string   name = node->getName() ? node->getName() : "";
       
        if (m.getSpecies(name) != NULL && !mSpecies.contains(name))
          logUndefined(r, name);
      }

      delete variables;
      
    }
  }
  for (n = 0; n < r.getNumProducts(); n++)
  {
    const SpeciesReference *sr = r.getProduct(n);

    if (sr->isSetStoichiometryMath())
    {
      List* variables = sr->getStoichiometryMath()->getMath()
        ->getListOfNodes( ASTNode_isName );
      for (ns = 0; ns < variables->getSize(); ns++)
      {
        ASTNode* node = static_cast<ASTNode*>( variables->get(ns) );
        string   name = node->getName() ? node->getName() : "";
       
        if (m.getSpecies(name) != NULL && !mSpecies.contains(name))
          logUndefined(r, name);
      }

      delete variables;

    }
  }
}


/*
 * Logs a message about an undefined variable in the given
 * FunctionDefinition.
 */
void
StoichiometryMathVars::logUndefined ( const Reaction& r,
                                       const string& varname )
{
  msg =
    //"All species referenced in the <stoichiometryMath> formula of a given "
    //"reaction must first be declared using <speciesReference> or "
    //"<modifierSpeciesReference>. More formally, if a <species> identifier "
    //"appears in a <ci> element of a <reaction>'s <stoichiometryMath> "
    //"formula, that same identifier must also appear in at least one "
    //"<speciesReference> or <modifierSpeciesReference> in the <reaction> "
    //"definition. (References: L2V2 Sections 4.13.2 and 4.13.4; L2V3 Sections "
    //"4.13.2 and 4.13.4.)"
    "The species '";

  msg += varname;
  msg += "' is not listed as a product, reactant, or modifier of reaction '";
  msg += r.getId();
  msg += "'.";
  
  logFailure(r);
}

#endif /* __cplusplus */

LIBSBML_CPP_NAMESPACE_END
/** @endcond */

