CCompartment.h

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// Begin CVS Header
//   $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/model/CCompartment.h,v $
//   $Revision: 1.51 $
//   $Name:  $
//   $Author: ssahle $
//   $Date: 2009/05/04 14:51:12 $
// End CVS Header

// 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.

/**
 * CCompartment
 *
 * Derived from Gepasi's ccompart.cpp
 * (C) Pedro Mendes 1995-2000
 *
 *  Converted for COPASI by Pedro Mendes
 */
#ifndef COPASI_CCompartment
#define COPASI_CCompartment

#include <string>

#include "model/CModelValue.h"
#include "utilities/CCopasiVector.h"
#include "model/CMetab.h"

class CReadConfig;

class CCompartment : public CModelEntity
{
private:
  /**
   * Metabolites located in the compartment.
   * @supplierCardinality 0..*
   * @associates <{CMetab}>
   */
  CCopasiVectorNS < CMetab > mMetabolites;

public:
  /**
   * Default constructor.
   * @param const std::string & name (default: "NoName")
   * @param const CCopasiContainer * pParent (default: NULL)
   */
  CCompartment(const std::string & name = "NoName",
               const CCopasiContainer * pParent = NULL);

  /**
   * Copy constructor.
   * @param "const CCompartment &" src
   * @param const CCopasiContainer * pParent (default: NULL)
   */
  CCompartment(const CCompartment & src,
               const CCopasiContainer * pParent = NULL);

  /**
   * Destructor.
   * The destructor does nothing.
   */
  virtual ~CCompartment();

  /**
   * Retrieve the units of the child object.
   * @return std::string units
   */
  virtual std::string getChildObjectUnits(const CCopasiObject * pObject) const;

  /**
   * Cleanup
   */
  void cleanup();

  /**
   * Retrieve the list of deleted numeric child objects;
   * @return std::set< const CCopasiObject * > deletedObjects
   */
  virtual std::set< const CCopasiObject * > getDeletedObjects() const;

  /**
   * Loads an object with data coming from a CReadConfig object.
   * (CReadConfig object reads an input stream)
   * @param pconfigbuffer reference to a CReadConfig object.
   * @return mFail
   * @see mFail
   */
  C_INT32 load(CReadConfig & configbuffer);

  /**
   * Retrieve the vector of contained metabolites
   * @return CCopasiVectorNS < CMetab > & metabolites
   */
  CCopasiVectorNS < CMetab > & getMetabolites();

  /**
   * Retrieve the vector of contained metabolites
   * @return const CCopasiVectorNS < CMetab > & metabolites
   */
  const CCopasiVectorNS < CMetab > & getMetabolites() const;

  /**
   *  Adds a metabolite to the compartment. Only the concentration is taken from
   *  the metabolite, the number of particles is calculated according to the
   *  volume of the compartment
   *  @param const CMetab & metabolite;
   *  @return bool success
   */
  bool createMetabolite(const CMetab & metabolite);

  /**
   *  Adds a metabolite to the compartment. Only the concentration is taken from
   *  the metabolite, the number of particles is calculated according to the
   *  volume of the compartment
   *  @param CMetab * metabolite;
   *  @return bool success
   */
  bool addMetabolite(CMetab * metabolite);

  /**
   *  Set the dimensionality of the compartment. May be 0, 1, 2, or 3.
   *  If the value is not valid it will be ignored and the return value will be false
   */
  bool setDimensionality(unsigned C_INT32 dim);

  /**
   *  Get the dimensionality of the compartment
   */
  unsigned C_INT32 getDimensionality() const;

  /**
   * Friend declaration for ostream operator <<
   * @param std::ostream & os
   * @param const CCompartment & d
   * @return std::ostream & os
   */
  friend std::ostream & operator<<(std::ostream &os, const CCompartment & d);

private:
  /**
   * Initialize the contained CCopasiObjects
   */
  void initObjects();

protected:
  /**
   * The dimensionality of the compartment. Can be 0, 1, 2, or 3
   */
  unsigned C_INT32 mDimensionality;
};

#endif // COPASI_CCompartment