CChemEqInterface.h

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// Begin CVS Header
//   $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/model/CChemEqInterface.h,v $
//   $Revision: 1.21 $
//   $Name:  $
//   $Author: shoops $
//   $Date: 2011/03/07 19:30:49 $
// End CVS Header

// Copyright (C) 2011 - 2010 by Pedro Mendes, Virginia Tech Intellectual
// Properties, Inc., University of Heidelberg, and The University
// of Manchester.
// All rights reserved.

// Copyright (C) 2008 by Pedro Mendes, Virginia Tech Intellectual
// Properties, Inc., EML Research, gGmbH, University of Heidelberg,
// and The University of Manchester.
// All rights reserved.

// Copyright (C) 2001 - 2007 by Pedro Mendes, Virginia Tech Intellectual
// Properties, Inc. and EML Research, gGmbH.
// All rights reserved.

#ifndef CCHEMEQINTERFACE_H
#define CCHEMEQINTERFACE_H

#include <string>
#include <vector>
#include <set>

#include "function/CFunctionParameter.h"

class CChemEq;
class CModel;
class CReaction;
class CCompartment;

/**
 * This class describes a chemical equation based on metabolite names
 * It supports parsing and generating string representations.
 * Note that this class handles only metab names without caring about whether
 * these metabs exist in the model. There is however a method to create
 * the missing metabs.
 */
class CChemEqInterface
{
private:
  CModel * mpModel;

  std::vector< std::string > mSubstrateNames;
  std::vector< std::string > mProductNames;
  std::vector< std::string > mModifierNames;

  std::vector< C_FLOAT64 > mSubstrateMult;
  std::vector< C_FLOAT64 > mProductMult;
  std::vector< C_FLOAT64 > mModifierMult;

  std::vector< std::string > mSubstrateCompartments;
  std::vector< std::string > mProductCompartments;
  std::vector< std::string > mModifierCompartments;

  std::vector< std::string > mSubstrateDisplayNames;
  std::vector< std::string > mProductDisplayNames;
  std::vector< std::string > mModifierDisplayNames;

  bool mReversibility;

private:
  CChemEqInterface();

public:
  CChemEqInterface(CModel * pModel);

  ~CChemEqInterface();

  std::string getChemEqString(bool expanded) const;
  bool setChemEqString(const std::string & ces);

  bool loadFromChemEq(const CChemEq & ce);
  bool writeToChemEq(CChemEq & ce) const;

  const std::vector<C_FLOAT64> & getListOfMultiplicities(CFunctionParameter::Role role) const;
  const std::vector<std::string> & getListOfDisplayNames(CFunctionParameter::Role role) const;

  /**
   * add a modifier to the chemical equation. It is only added if it is not alreay in there.
   */
  void addModifier(const std::string & name);
  void clearModifiers();

  bool getReversibility() const {return mReversibility;};
  void setReversibility(bool rev) {mReversibility = rev;};

  /**
   * this method tries to find out if the chemical equation involves several compartments
   * in a given model. It only takes into account the metabs that
   * actually exist in the model. A non existing metabolite is assumed
   * not to be in a different compartment
   */
  bool isMulticompartment() const;

  /**
   * convenience method. If the reaction is single compartment the
   * compartment is returned, else NULL.
   */
  const CCompartment * getCompartment() const;

  void reverse();

  size_t getMolecularity(CFunctionParameter::Role role) const;

  std::set<std::string> listOfNonUniqueMetabNames() const;
  std::set< std::pair< std::string, std::string > > listOfNonExistingMetabNames() const;

  bool createNonExistingMetabs();

  //convenience methods:
  static std::string getChemEqString(CModel * model, const CReaction & rea, bool expanded);
  static void setChemEqFromString(CModel * model, CReaction & rea, const std::string & ces);
  static bool isValidEq(const std::string & eq);

private:
  void buildDisplayNames();
  void completeCompartments();
  static std::string writeElement(const std::string & name, C_FLOAT64 mult, bool expanded);
};

#endif