#include <CModelParameter.h>

Inheritance diagram for CModelParameterSpecies:

Collaboration diagram for CModelParameterSpecies:

Public Member Functions
	CModelParameterSpecies (CModelParameterGroup *pParent, const CModelParameter::Type &type=CModelParameter::Species)

	CModelParameterSpecies (const CModelParameterSpecies &src, CModelParameterGroup *pParent)

virtual void	compile ()

virtual std::string	getName () const

virtual const C_FLOAT64 &	getValue (const Framework &framework) const

virtual void	setCN (const CCopasiObjectName &cn)

virtual void	setValue (const C_FLOAT64 &value, const Framework &framework)

virtual	~CModelParameterSpecies ()

Public Member Functions inherited from CModelParameter
	CModelParameter (CModelParameterGroup *pParent, const CModelParameter::Type &type)

	CModelParameter (const CModelParameter &src, CModelParameterGroup *pParent)

virtual const CompareResult &	diff (const CModelParameter &other, const CModelParameter::Framework &framework=ParticleNumbers, const bool &createMissing=false)

virtual const CModelParameter *	getChild (const size_t &index) const

const CCopasiObjectName &	getCN () const

const CompareResult &	getCompareResult () const

size_t	getIndex () const

std::string	getInitialExpression () const

const CExpression *	getInitialExpressionPtr () const

CModel *	getModel () const

virtual size_t	getNumChildren () const

CCopasiObject *	getObject () const

CModelParameterGroup *	getParent () const

CModelParameterSet *	getSet () const

const CModelEntity::Status &	getSimulationType () const

const Type &	getType () const

const std::string	getUnit (const Framework &framework) const

bool	isInitialExpressionValid () const

bool	isReadOnly () const

virtual bool	refreshFromModel (const bool &modifyExistence)

void	setCompareResult (const CompareResult &compareResult)

void	setInitialExpression (const std::string &initialExpression)

void	setParent (CModelParameterGroup *pParent)

bool	setSimulationType (const CModelEntity::Status &simulationType)

virtual void	setValue (const double &value, const Framework &framework)

virtual bool	updateModel ()

virtual	~CModelParameter ()

Private Member Functions
friend	CModelParameterCompartment::~CModelParameterCompartment ()

CCopasiObjectName	getCompartmentCN () const

Private Attributes
CRegisteredObjectName	mCompartmentCN

C_FLOAT64	mConcentration

CModelParameterCompartment *	mpCompartment

Additional Inherited Members
Public Types inherited from CModelParameter
enum	CompareResult { Obsolete, Missing, Modified, Conflict, Identical }

enum	Framework { Concentration = 0, ParticleNumbers }

enum	Type { Model, Compartment, Species, ModelValue, ReactionParameter, Reaction, Group, Set, unknown }

Static Public Attributes inherited from CModelParameter
static const char *	TypeNames []

Static Protected Member Functions inherited from CModelParameter
static std::string	nameFromCN (const CCopasiObjectName &cn)

Protected Attributes inherited from CModelParameter
CRegisteredObjectName	mCN

CompareResult	mCompareResult

bool	mIsInitialExpressionValid

CExpression *	mpInitialExpression

CCopasiObject *	mpObject

CModelParameterGroup *	mpParent

CModelEntity::Status	mSimulationType

Type	mType

double	mValue

Detailed Description

Definition at line 353 of file CModelParameter.h.

Constructor & Destructor Documentation

CModelParameterSpecies::CModelParameterCompartment::~CModelParameterCompartment ( )

private

CModelParameterSpecies::CModelParameterSpecies	(	CModelParameterGroup *	pParent,
		const CModelParameter::Type &	type = `CModelParameter::Species`
	)

Constructor

Definition at line 737 of file CModelParameter.cpp.

                                                                                                               :
   CModelParameter(pParent, type),
   mCompartmentCN(),
   mpCompartment(NULL),
   mConcentration(std::numeric_limits< C_FLOAT64 >::quiet_NaN())
 {}

CModelParameterSpecies::CModelParameterSpecies	(	const CModelParameterSpecies &	src,
		CModelParameterGroup *	pParent
	)

Copy constructor

Definition at line 744 of file CModelParameter.cpp.

                                                                                                                 :
   CModelParameter(src, pParent),
   mCompartmentCN(src.mCompartmentCN),
   mpCompartment(NULL),
   mConcentration(src.mConcentration)
 {}

CModelParameterSpecies::~CModelParameterSpecies ( )

virtual

Destructor

Definition at line 752 of file CModelParameter.cpp.

References mpCompartment, and CModelParameterCompartment::removeSpecies().

 {
   if (mpCompartment != NULL)
     {
       mpCompartment->removeSpecies(this);
     }
 }

Member Function Documentation

void CModelParameterSpecies::compile ( )

virtual

Compile the parameter

Reimplemented from CModelParameter.

Definition at line 774 of file CModelParameter.cpp.

References CModelParameterCompartment::addSpecies(), CModelParameter::compile(), CModelParameterGroup::getModelParameter(), CModelParameter::getSet(), mCompartmentCN, mpCompartment, CModelParameter::mValue, CModelParameter::ParticleNumbers, and setValue().

 {
   CModelParameter::compile();
 
   mpCompartment = static_cast< CModelParameterCompartment * >(getSet()->getModelParameter(mCompartmentCN));
 
   if (mpCompartment != NULL)
     {
       mpCompartment->addSpecies(this);
     }
 
   // Update the concentration if possible
   setValue(mValue, ParticleNumbers);
 }

CCopasiObjectName CModelParameterSpecies::getCompartmentCN ( ) const

private

Retrieve the CN of the compartment the species is contained in.

Returns: CCopasiObjectName compartmentCN

Definition at line 857 of file CModelParameter.cpp.

References mCompartmentCN.

 {
   return mCompartmentCN;
 }

std::string CModelParameterSpecies::getName ( ) const

virtual

Retrieve the name.

Returns: std::string name

Reimplemented from CModelParameter.

Definition at line 761 of file CModelParameter.cpp.

References CMetabNameInterface::getDisplayName(), CModelParameterSet::getModel(), CModelParameter::getSet(), CModelParameter::mCN, mCompartmentCN, CModelParameter::mpObject, and CModelParameter::nameFromCN().

 {
   CModel * pModel = getSet()->getModel();
 
   if (mpObject != NULL)
     {
       return CMetabNameInterface::getDisplayName(pModel, *static_cast< CMetab * >(mpObject), false);
     }
 
   return nameFromCN(mCN) + '{' + nameFromCN(mCompartmentCN) + '}';
 }

const C_FLOAT64 & CModelParameterSpecies::getValue ( const Framework & framework ) const

virtual

Retrieve the value of the parameter based on the current framework

Parameters

const Framework & framework

Returns: const double & value

Reimplemented from CModelParameter.

Definition at line 847 of file CModelParameter.cpp.

References CModelParameter::Concentration, mConcentration, and CModelParameter::mValue.

 {
   if (framework == Concentration)
     {
       return mConcentration;
     }
 
   return mValue;
 }

void CModelParameterSpecies::setCN ( const CCopasiObjectName & cn )

virtual

Set the CN of the object represented by the parameter

Parameters

const CCopasiObjectName & cn

Reimplemented from CModelParameter.

Definition at line 790 of file CModelParameter.cpp.

References CCopasiObjectName::getPrimary(), CCopasiObjectName::getRemainder(), CModelParameter::mCN, mCompartmentCN, and CModelParameter::setCN().

 {
   CModelParameter::setCN(cn);
 
   // Determine the CN for the compartment.
   // "CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[A]"
   CCopasiObjectName Tmp = mCN;
   std::string Separator = "";
 
   for (; Tmp != ""; Tmp = Tmp.getRemainder())
     {
       CCopasiObjectName Primary = Tmp.getPrimary();
       mCompartmentCN += Separator + Primary;
       Separator = ",";
 
       if (Primary.getObjectType() == "Vector" &&
           Primary.getObjectName() == "Compartments")
         {
           break;
         }
     }
 }

void CModelParameterSpecies::setValue	(	const C_FLOAT64 &	value,
		const Framework &	framework
	)

virtual

Set the value of the parameter based on the current framework

Parameters

const	double & value
const	Framework & framework

Definition at line 814 of file CModelParameter.cpp.

References CModelParameter::Concentration, CModelParameter::getModel(), CModel::getNumber2QuantityFactor(), CModel::getQuantity2NumberFactor(), CModelParameter::getValue(), mConcentration, mpCompartment, CModelParameter::mValue, and CModelParameter::ParticleNumbers.

Referenced by compile().

 {
   CModel * pModel = getModel();
 
   if (framework == Concentration)
     {
       mConcentration = value;
 
       if (mpCompartment != NULL && pModel != NULL)
         {
           mValue = mConcentration * mpCompartment->getValue(ParticleNumbers) * pModel->getQuantity2NumberFactor();
         }
       else
         {
           mValue = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
         }
     }
   else
     {
       mValue = value;
 
       if (mpCompartment != NULL && pModel != NULL)
         {
           mConcentration = mValue / mpCompartment->getValue(ParticleNumbers) * pModel->getNumber2QuantityFactor();
         }
       else
         {
           mConcentration = std::numeric_limits< C_FLOAT64 >::quiet_NaN();
         }
     }
 }

Member Data Documentation

CRegisteredObjectName CModelParameterSpecies::mCompartmentCN

private

The CN of the compartment the species is contained in.

Definition at line 415 of file CModelParameter.h.

Referenced by compile(), getCompartmentCN(), getName(), and setCN().

C_FLOAT64 CModelParameterSpecies::mConcentration

private

The concentration value of the species.

Definition at line 425 of file CModelParameter.h.

Referenced by getValue(), and setValue().

CModelParameterCompartment* CModelParameterSpecies::mpCompartment

private

A pointer to the parameter representing the compartment the species is contained in.

Definition at line 420 of file CModelParameter.h.

Referenced by compile(), setValue(), and ~CModelParameterSpecies().

The documentation for this class was generated from the following files:

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation