CMetab Class Reference

#include <CMetab.h>

Inheritance diagram for CMetab:

Public Member Functions
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes) override
virtual void	calculate () override
void	cleanup ()
	CMetab (const CMetab &src, const CDataContainer *pParent)
	CMetab (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT)
virtual CIssue	compile () override
void	compileIsInitialValueChangeAllowed ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const override
virtual std::string	getChildObjectUnits (const CDataObject *pObject) const override
const CCompartment *	getCompartment () const
const C_FLOAT64 &	getConcentration () const
C_FLOAT64	getConcentrationRate () const
CDataObject *	getConcentrationRateReference () const
CDataObject *	getConcentrationReference () const
size_t	getCountOfDependentReactions () const
const C_FLOAT64 &	getInitialConcentration () const
CDataObject *	getInitialConcentrationReference () const
CDataObject *	getIntensiveNoiseReference () const
const CMoiety *	getMoiety () const
virtual std::string	getObjectDisplayName () const override
const C_FLOAT64 &	getTransitionTime () const
CDataObject *	getTransitionTimeReference () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
virtual void *	getValuePointer () const override
void	initCompartment (const CCompartment *pCompartment=NULL)
bool	isDependent () const
const bool &	isInitialValueChangeAllowed (CCore::Framework framework) const
C_INT32	load (CReadConfig &configbuffer)
CMetab &	operator= (const CMetabOld &rhs)
bool	setCompartment (const std::string &compName)
void	setConcentration (const C_FLOAT64 concentration)
void	setDependsOnMoiety (const CMoiety *pMoiety)
void	setInitialConcentration (const C_FLOAT64 &initialConcentration)
virtual bool	setObjectParent (const CDataContainer *pParent) override
void	setTransitionTime (const C_FLOAT64 &transitionTime)
virtual CData	toData () const override
	~CMetab ()
Public Member Functions inherited from CModelEntity
	CModelEntity (const CModelEntity &src, const CDataContainer *pParent)
	CModelEntity (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT, const std::string &type="ModelEntity", const CFlags< Flag > &flag=CFlags< Flag >::None)
std::string	getDefaultNoiseExpression () const
std::string	getExpression () const
CExpression *	getExpressionPtr ()
const CExpression *	getExpressionPtr () const
std::string	getInitialExpression () const
CExpression *	getInitialExpressionPtr ()
const CExpression *	getInitialExpressionPtr () const
const C_FLOAT64 &	getInitialValue () const
CDataObject *	getInitialValueReference () const
virtual const std::string &	getKey () const override
CModel *	getModel () const
std::string	getNoiseExpression () const
CExpression *	getNoiseExpressionPtr ()
const CExpression *	getNoiseExpressionPtr () const
CDataObject *	getNoiseReference () const
const C_FLOAT64 &	getRate () const
CDataObject *	getRateReference () const
const std::string &	getSBMLId () const
const CModelEntity::Status &	getStatus () const
virtual const std::string &	getUnitExpression () const
const C_FLOAT64 &	getValue () const
CDataObject *	getValueReference () const
const bool &	hasNoise () const
bool	isFixed () const
const bool &	isUsed () const
CIssue	setExpression (const std::string &expression)
bool	setExpressionPtr (CExpression *pExpression)
void	setHasNoise (const bool &hasNoise)
CIssue	setInitialExpression (const std::string &expression)
bool	setInitialExpressionPtr (CExpression *pExpression)
virtual void	setInitialValue (const C_FLOAT64 &initialValue)
bool	setNoiseExpression (const std::string &expression)
bool	setNoiseExpressionPtr (CExpression *pExpression)
void	setRate (const C_FLOAT64 &rate)
void	setSBMLId (const std::string &id) const
bool	setStatus (const CModelEntity::Status &status)
virtual CIssue	setUnitExpression (std::string unitExpression)
void	setUsed (const bool &used)
virtual void	setValue (const C_FLOAT64 &value)
	~CModelEntity ()
Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)
virtual bool	appendDeletedDependentData (CUndoData &undoData) const
	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)
	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
virtual size_t	getIndex (const CDataObject *pObject) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const override
virtual objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual CUndoObjectInterface *	insert (const CData &data) override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
virtual bool	remove (CDataObject *pObject)
virtual	~CDataContainer ()
Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)
void	addReference (const CDataContainer *pReference)
virtual void	calculateValue () override
	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)
virtual void	destruct () override
virtual CCommonName	getCN () const override
virtual const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const
const std::string &	getObjectName () const
CDataContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override
virtual const CValidity &	getValidity () const override
bool	hasFlag (const Flag &flag) const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
bool	prerequisitsContains (const DataObjectSet &objects) const
virtual void	print (std::ostream *ostream) const override
void	removeIssue (const CIssue &issue)
void	removeReference (const CDataContainer *pReference)
bool	setObjectName (const std::string &name)
void	validityChanged (const CValidity &changedValidity) override
void	validityRemoved (const CValidity &changedValidity)
virtual	~CDataObject ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
	CObjectInterface (const CObjectInterface &src)
virtual	~CObjectInterface ()
Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()
	CUndoObjectInterface (const CUndoObjectInterface &src)
bool	generateUuid ()
const xg::Guid &	getUuid () const
bool	setUuid (const std::string &uuid)
bool	setUuid (const xg::Guid &uuid)
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CUndoObjectInterface ()
Public Member Functions inherited from CAnnotation
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)
bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CAnnotation ()
	CAnnotation (const CAnnotation &src)
void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
const std::string &	getMiriamAnnotation () const
const std::string &	getNotes () const
UnsupportedAnnotation &	getUnsupportedAnnotations ()
const UnsupportedAnnotation &	getUnsupportedAnnotations () const
void	initMiriamAnnotation (const std::string &newId)
bool	operator== (const CAnnotation &rhs) const
bool	removeUnsupportedAnnotation (const std::string &name)
bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
void	setNotes (const std::string &notes)
CData	toData () const
virtual	~CAnnotation ()

Static Public Member Functions
static C_FLOAT64	convertToConcentration (const C_FLOAT64 &number, const CCompartment &compartment)
static C_FLOAT64	convertToNumber (const C_FLOAT64 &concentration, const CCompartment &compartment)
static CMetab *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CModelEntity
static CModelEntity *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)
static void	sanitizeObjectName (std::string &name)
Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)
static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)
Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)
Static Public Member Functions inherited from CAnnotation
static CMIRIAMInfo *	allocateMiriamInfo (CDataContainer *pParent)
static CAnnotation *	castObject (CDataObject *pObject)
static const CAnnotation *	castObject (const CDataObject *pObject)
static void	freeMiriamInfo (CDataContainer *pParent)

Protected Member Functions
	CMetab (const CMetab &src)
Protected Member Functions inherited from CModelEntity
	CModelEntity (const CModelEntity &src)
Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
	CDataContainer (const CDataContainer &src)
void	initObjects ()
Protected Member Functions inherited from CDataObject
	CDataObject ()
	CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes
CDataObjectReference< C_FLOAT64 > *	mpConcRateReference
CDataObjectReference< C_FLOAT64 > *	mpConcReference
CDataObjectReference< C_FLOAT64 > *	mpIConcReference
CDataObjectReference< C_FLOAT64 > *	mpIntensiveNoiseReference
CDataObjectReference< C_FLOAT64 > *	mpTTReference
Protected Attributes inherited from CModelEntity
bool	mHasNoise
C_FLOAT64	mIValue
C_FLOAT64	mNoise
CExpression *	mpExpression
CExpression *	mpInitialExpression
CDataObjectReference< C_FLOAT64 > *	mpIValueReference
CModel *	mpModel
CExpression *	mpNoiseExpression
CDataObjectReference< C_FLOAT64 > *	mpNoiseReference
CDataObjectReference< C_FLOAT64 > *	mpRateReference
CDataObjectReference< C_FLOAT64 > *	mpValueReference
C_FLOAT64	mRate
std::string	mSBMLId
std::string	mUnitExpression
C_FLOAT64	mValue
Protected Attributes inherited from CDataContainer
objectMap	mObjects
Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits
std::set< CDataContainer * >	mReferences
Protected Attributes inherited from CObjectInterface
CValidity	mValidity
Protected Attributes inherited from CAnnotation
std::string	mKey

Private Member Functions
void	initObjects ()

Private Attributes
C_FLOAT64	mConc
C_FLOAT64	mConcRate
C_FLOAT64	mIConc
C_FLOAT64	mIntensiveNoise
bool	mIsInitialConcentrationChangeAllowed
bool	mIsInitialParticleNumberChangeAllowed
const CCompartment *	mpCompartment
const CMoiety *	mpMoiety
C_FLOAT64	mTT

Friends
void	CMoiety::add (C_FLOAT64 value, CMetab *pMetabolite)
std::ostream &	operator<< (std::ostream &os, const CMetab &d)

Additional Inherited Members
Public Types inherited from CModelEntity
enum class	Status {   FIXED = 0 , ASSIGNMENT , REACTIONS , ODE ,   TIME , __SIZE }
Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap
Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet
enum	Flag {   Container , Vector , Matrix , NameVector ,   Reference , ValueBool , ValueInt , ValueInt64 ,   ValueDbl , NonUniqueName , StaticString , ValueString ,   Separator , DisplayName , ModelEntity , Array ,   DataModel , Root , Gui , __SIZE }
Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList
typedef std::set< const CObjectInterface * >	ObjectSet
Public Types inherited from CAnnotation
typedef std::map< std::string, std::string >	UnsupportedAnnotation
Static Public Attributes inherited from CModelEntity
static const CEnumAnnotation< std::string, Status >	StatusName
static const CEnumAnnotation< std::string, Status >	XMLStatus
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Constructor & Destructor Documentation

CMetab() [1/3]

CMetab::CMetab ( const CMetab &  src )

protected

Referenced by fromData().

CMetab() [2/3]

CMetab::CMetab	(	const std::string &	name = "NoName",
		const CDataContainer *	pParent = NO_PARENT
	)

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CDataContainer * pParent (default: NULL)

References CONSTRUCTOR_TRACE, CDataObject::getObjectParent(), initCompartment(), initObjects(), CModelEntity::REACTIONS, setConcentration(), setInitialConcentration(), and CModelEntity::setStatus().

CMetab() [3/3]

CMetab::CMetab	(	const CMetab &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const	CMetab & src
const	CDataContainer * pParent (default: NULL)

References CONSTRUCTOR_TRACE, initCompartment(), initObjects(), and mpCompartment.

~CMetab()

CMetab::~CMetab

(

)

Destructor.

References DESTRUCTOR_TRACE, CRootContainer::getKeyFactory(), CAnnotation::mKey, and CKeyFactory::remove().

Member Function Documentation

applyData()

bool CMetab::applyData ( const CData &  data, CUndoData::CChangeSet &  changes  )

overridevirtual

Apply the provided data to the object

Parameters

const

CData & data

Returns

bool success

Reimplemented from CModelEntity.

References CModelEntity::applyData(), CData::getProperty(), CData::INITIAL_INTENSIVE_VALUE, CData::isSetProperty(), mIConc, and CDataValue::toDouble().

calculate()

void CMetab::calculate ( void  )

overridevirtual

Calculate the value or the rate depending whether we have an ASIGNMENT or ODE

Reimplemented from CModelEntity.

References CModelEntity::ASSIGNMENT, CExpression::calcValue(), CModelEntity::FIXED, CMoiety::getDependentNumber(), CModel::getQuantity2NumberFactor(), CModelEntity::getStatus(), CModelEntity::getValue(), isDependent(), mConc, mpCompartment, CModelEntity::mpExpression, CModelEntity::mpModel, mpMoiety, CModelEntity::mRate, CModelEntity::mValue, CModelEntity::ODE, and CModelEntity::REACTIONS.

cleanup()

void CMetab::cleanup

(

)

Cleanup

compile()

CIssue CMetab::compile ( )

overridevirtual

Compile the model value.

Returns

CIssue firstWorstIssue

Reimplemented from CModelEntity.

References CDataContainer::add(), CValidity::add(), CModelEntity::ASSIGNMENT, CExpression::calcValue(), CValidity::clear(), CExpression::compile(), convertToNumber(), CExpression::createInitialExpression(), CIssue::ExpressionEmpty, CModelEntity::FIXED, CModelEntity::getExpression(), CValidity::getFirstWorstIssue(), CEvaluationTree::getInfix(), CModelEntity::getNoiseExpression(), CDataObject::getObjectAncestor(), CDataObject::getObjectDataModel(), CDataObject::getPrerequisites(), CModelEntity::getStatus(), CDataObject::getValidity(), initCompartment(), mConcRate, CModelEntity::mHasNoise, mIConc, mIntensiveNoise, CModelEntity::mIValue, mpCompartment, CModelEntity::mpExpression, CModelEntity::mpInitialExpression, CModelEntity::mpNoiseExpression, CDataObject::mPrerequisits, CModelEntity::mRate, mTT, CObjectInterface::mValidity, CModelEntity::ODE, pdelete, CModelEntity::REACTIONS, CDataObject::setObjectName(), and CIssue::Warning.

compileIsInitialValueChangeAllowed()

void CMetab::compileIsInitialValueChangeAllowed

(

)

Determine whether changing the initial concentration is allowed

References CDataObject::Container, CModel::getMathContainer(), mIsInitialConcentrationChangeAllowed, mIsInitialParticleNumberChangeAllowed, mpCompartment, mpIConcReference, CModelEntity::mpIValueReference, and CModelEntity::mpModel.

convertToConcentration()

C_FLOAT64 CMetab::convertToConcentration ( const C_FLOAT64 &  number, const CCompartment &  compartment  )

static

Converts the number to concentration

Parameters

const	C_FLOAT64 & number
const	CCompartment & compartment
const	CModel & model

Returns

C_FLOAT64 concentration

References CModelEntity::getInitialValue(), CModelEntity::getModel(), and CModel::getNumber2QuantityFactor().

convertToNumber()

C_FLOAT64 CMetab::convertToNumber ( const C_FLOAT64 &  concentration, const CCompartment &  compartment  )

static

Converts the concentration to number

Parameters

const	C_FLOAT64 & concentration
const	CCompartment & compartment
const	CModel & model

Returns

C_FLOAT64 number

References CModelEntity::getInitialValue(), CModelEntity::getModel(), and CModel::getQuantity2NumberFactor().

Referenced by compile(), and operator=().

createUndoData()

void CMetab::createUndoData ( CUndoData &  undoData, const CUndoData::Type &  type, const CData &  oldData = CData(), const CCore::Framework &  framework = CCore::Framework::ParticleNumbers  ) const

overridevirtual

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

CUndoData	& undoData
const	CUndoData::Type & type
const	CData & oldData (default: empty data)
const	CCore::Framework & framework (default: CCore::Framework::ParticleNumbers)

Returns

CUndoData undoData

Reimplemented from CModelEntity.

References CUndoData::addProperty(), CUndoData::CHANGE, CModelEntity::createUndoData(), CData::getProperty(), CData::INITIAL_INTENSIVE_VALUE, CUndoData::isChangedProperty(), mIConc, and CData::OBJECT_PARENT_CN.

fromData()

CMetab * CMetab::fromData ( const CData &  data, CUndoObjectInterface *  pParent  )

static

Static method to create a CDataObject based on the provided data

Parameters

const

CData & data

Returns

CMetab * pDataObject

References CMetab(), CData::getProperty(), NO_PARENT, CData::OBJECT_NAME, and CDataValue::toString().

getChildObjectUnits()

std::string CMetab::getChildObjectUnits ( const CDataObject *  pObject ) const

overridevirtual

Retrieve the units of the child object.

Returns

const & CUnit units

Reimplemented from CModelEntity.

References CModelEntity::getChildObjectUnits(), CModelEntity::getInitialValueReference(), CModel::getQuantityUnit(), CModel::getTimeUnit(), CDataObject::getUnits(), mpCompartment, mpConcRateReference, mpConcReference, mpIConcReference, CModelEntity::mpModel, and mpTTReference.

Referenced by CModelParameter::getUnit().

getCompartment()

const CCompartment * CMetab::getCompartment

(

)

const

References mpCompartment.

Referenced by CSBMLExporter::addInitialAssignmentsToModel(), CModelAdd::addMetabolites(), CChemEqInterface::addModifier(), addParticleNumberToInitialValueMap(), CMathObject::compile(), CTimeSeries::compile(), CMathEvent::CAssignment::compile(), CChemEqInterface::completeCompartments(), SEDMLUtils::createAmountMV(), CMathObject::createExtensiveValueExpression(), CSBMLExporter::createInitialAssignment(), CMathObject::createIntensiveRateExpression(), CCopasiSpringLayout::createLayout(), CModelExpansion::createLinearArray(), CSBMLExporter::createMetabolite(), CModelExpansion::createRectangularArray(), CSBMLExporter::createRule(), CMetabNameInterface::createUniqueDisplayName(), CCSPMethod::cspstep(), CMetabNameInterface::doesExist(), CModelExpansion::duplicateMetab(), CSBMLExporter::exportEventAssignments(), CODEExporter::exportMetabolites(), CODEExporter::exportModelEntityExpression(), CChemEqInterface::getCompartment(), CMathContainer::getCompartment(), CMetabNameInterface::getDisplayName(), SBMLImporter::importEvent(), SBMLImporter::importInitialAssignments(), CChemEqInterface::init(), CCopasiSpringLayout::initFromLayout(), CMathContainer::initializeAtolVector(), CModel::initializeAtolVector(), MetaboliteHandler::processStart(), CCopasiSpringLayout::randomize(), CModelExpansion::replaceInMetab(), CSBMLExporter::replaceSpeciesReferences(), CCopasiXML::saveModel(), setCompartment(), and CReaction::setScalingFactor().

getConcentration()

const C_FLOAT64 & CMetab::getConcentration

(

)

const

References mConc.

getConcentrationRate()

C_FLOAT64 CMetab::getConcentrationRate

(

)

const

Return rate of production of this metaboLite

References mConcRate.

getConcentrationRateReference()

CDataObject * CMetab::getConcentrationRateReference

(

)

const

Retrieve object referencing the concentration

Returns

CDataObject * concentrationRateReference

References mpConcRateReference.

Referenced by CDataModel::findObjectByDisplayName(), CMathContainer::initializeMathObjects(), and SEDMLUtils::resolveVariable().

getConcentrationReference()

CDataObject * CMetab::getConcentrationReference

(

)

const

Retrieve object referencing the concentration

Returns

CConcentrationReference * concentrationReference

References mpConcReference.

Referenced by CMathObject::compileValue(), SEDMLUtils::createAmountMV(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), CMathObject::createIntensiveRateExpression(), CDataModel::findObjectByDisplayName(), CModel::getCorrespondingTransientObject(), CReactionInterface::getUnit(), CReactionInterface::getUnitVector(), CMathContainer::initializeMathObjects(), CModel::prepareElasticity(), CSBMLExporter::replaceSpeciesReferences(), SEDMLUtils::resolveVariable(), and VariableInfo::VariableInfo().

getCountOfDependentReactions()

size_t CMetab::getCountOfDependentReactions

(

)

const

Retrieve the count of structural dependent reactions

Returns

const size_t countOfDependentReactions

References CModel::appendDirectDependents(), and CModelEntity::mpModel.

getInitialConcentration()

const C_FLOAT64 & CMetab::getInitialConcentration

(

)

const

References mIConc.

Referenced by CModelAdd::addMetabolites(), CSBMLExporter::createMetabolite(), CModelExpansion::duplicateMetab(), CODEExporter::exportExpression(), and CODEExporter::exportMetabolites().

getInitialConcentrationReference()

CDataObject * CMetab::getInitialConcentrationReference

(

)

const

Retrieve object referencing the initial concentration

Returns

CConcentrationReference * initialConcentrationReference

References mpIConcReference.

Referenced by CMathObject::compileInitialValue(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), CDataModel::findObjectByDisplayName(), CModel::getCorrespondingTransientObject(), getInitialCNForSBase(), CModelParameter::getUnit(), CMathContainer::initializeMathObjects(), and CModelParameterSet::saveToStream().

getIntensiveNoiseReference()

CDataObject * CMetab::getIntensiveNoiseReference

(

)

const

Retrieve object referencing the concentration

Returns

CDataObject * concentrationRateReference

References mpIntensiveNoiseReference.

Referenced by CMathContainer::initializeMathObjects().

getMoiety()

const CMoiety * CMetab::getMoiety

(

)

const

Retrieve a pointer to the moiety the species depends on

Returns

const CMoiety * pMoiety;

References mpMoiety.

Referenced by CMathObject::compileValue().

getObjectDisplayName()

std::string CMetab::getObjectDisplayName ( ) const

overridevirtual

Retrieve the display name of the object

Parameters

bool	regular (default: true)
bool	richtext (default: false)

Returns

std::string objectDisplayName

Reimplemented from CDataObject.

References CMetabNameInterface::getDisplayName(), CDataObject::getObjectAncestor(), and CDataObject::getObjectDisplayName().

Referenced by CReaction::createFunctionFromExpression(), CSBMLExporter::createMetabolite(), and CDataModel::findObjectByDisplayName().

getTransitionTime()

const C_FLOAT64 & CMetab::getTransitionTime

(

)

const

Retrieves the transition time

Returns

"const C_FLOAT64 &" transitionTime

References mTT.

getTransitionTimeReference()

CDataObject * CMetab::getTransitionTimeReference

(

)

const

Retrieve object referencing the Transition Time

Returns

CDataObject * transitionTimeReference

References mpTTReference.

Referenced by CModel::appendAllDependents(), and CMathContainer::initializeMathObjects().

getUnits()

const std::string CMetab::getUnits ( ) const

overridevirtual

Retrieve the units of the object.

Returns

std::string units

Reimplemented from CDataContainer.

getValueObject()

const CDataObject * CMetab::getValueObject ( ) const

overridevirtual

Retrieve the object representing the value;

Reimplemented from CModelEntity.

References mpConcReference.

getValuePointer()

void * CMetab::getValuePointer ( ) const

overridevirtual

Retrieve a pointer to the value;

Reimplemented from CModelEntity.

References C_FLOAT64, and mConc.

initCompartment()

void CMetab::initCompartment

(

const CCompartment *

pCompartment = NULL

)

References CDataObject::getObjectAncestor(), mpCompartment, and CDataObject::mPrerequisits.

Referenced by CMetab(), compile(), and setObjectParent().

initObjects()

void CMetab::initObjects ( )

private

Initialize the contained CDataObjects

References CDataContainer::addObjectReference(), mConc, mConcRate, mIConc, mIntensiveNoise, mpConcRateReference, mpConcReference, mpIConcReference, mpIntensiveNoiseReference, CModelEntity::mpIValueReference, CModelEntity::mpRateReference, mpTTReference, CModelEntity::mpValueReference, mTT, CDataObject::setObjectName(), and CDataObject::ValueDbl.

Referenced by CMetab().

isDependent()

bool CMetab::isDependent

(

)

const

Retrieve whether the metabolite dependent

Returns

bool dependent

References mpMoiety.

Referenced by calculate(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CODEExporter::preprocess(), CODEExporterC::preprocess(), and CStateTemplate::reorder().

isInitialValueChangeAllowed()

const bool & CMetab::isInitialValueChangeAllowed

(

CCore::Framework

framework

)

const

Check whether changing the initial concentration is allowed

Returns

const bool & allowed

References CCore::Concentration, mIsInitialConcentrationChangeAllowed, and mIsInitialParticleNumberChangeAllowed.

load()

C_INT32 CMetab::load

(

CReadConfig &

configbuffer

)

Loads an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

pconfigbuffer

reference to a CReadConfig object.

Returns

Fail

References C_INT32, CDataObject::getObjectName(), CReadConfig::getVariable(), METAB_MOIETY, mIConc, CModelEntity::REACTIONS, CReadConfig::SEARCH, setConcentration(), setInitialConcentration(), CDataObject::setObjectName(), CModelEntity::setStatus(), and CCopasiMessage::WARNING.

operator=()

CMetab & CMetab::operator=

(

const CMetabOld &

rhs

)

Assignment operator.

References C_FLOAT64, convertToNumber(), CDataObject::getObjectName(), mConcRate, CMetabOld::mIConc, mpCompartment, CModelEntity::mRate, CMetabOld::mStatus, mTT, CModelEntity::setInitialValue(), CDataObject::setObjectName(), and CModelEntity::setStatus().

setCompartment()

bool CMetab::setCompartment

(

const std::string &

compName

)

moves the species to the compartment with the given name, removes it from the old compartment (if there was one), and updates references to the species if needed

References CCompartment::addMetabolite(), CDataObject::getCN(), getCompartment(), CModel::getCompartments(), CCompartment::getMetabolites(), CDataObject::getObjectName(), CRegisteredCommonName::handle(), CModel::initializeMetabolites(), CRegisteredCommonName::isEnabled(), CModelEntity::mpModel, CDataVectorN< CType >::remove(), CModel::setCompileFlag(), and CRegisteredCommonName::setEnabled().

setConcentration()

void CMetab::setConcentration

(

const C_FLOAT64

concentration

)

References CModelEntity::isFixed(), and mConc.

Referenced by CMetab(), and load().

setDependsOnMoiety()

void CMetab::setDependsOnMoiety

(

const CMoiety *

pMoiety

)

Set whether the metabolite is dependent, i.e., calculated by a moiety

Parameters

const

CMoiety * pMoiety

References mpMoiety.

Referenced by CMoiety::add().

setInitialConcentration()

void CMetab::setInitialConcentration

(

const C_FLOAT64 &

initialConcentration

)

References mIConc.

Referenced by CMetab(), CModel::createMetabolite(), CReactionInterface::createUndoData(), load(), and CModelParameterSpecies::updateModel().

setObjectParent()

bool CMetab::setObjectParent ( const CDataContainer *  pParent )

overridevirtual

Sets the parent of the metabolite;

Parameters

const

CDataContainer * pParent

Returns

bool success

Reimplemented from CModelEntity.

References CModelEntity::FIXED, CModelEntity::getExpression(), CModelEntity::getStatus(), initCompartment(), CModelEntity::REACTIONS, CModelEntity::setExpression(), CModelEntity::setObjectParent(), and CModelEntity::setStatus().

setTransitionTime()

void CMetab::setTransitionTime

(

const C_FLOAT64 &

transitionTime

)

Set transition time

Parameters

const C_FLOAT64 &

transitionTime

References mTT.

toData()

CData CMetab::toData ( ) const

overridevirtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CModelEntity.

References CData::addProperty(), CData::INITIAL_INTENSIVE_VALUE, mIConc, and CModelEntity::toData().

Friends And Related Function Documentation

CMoiety::add

void CMoiety::add ( C_FLOAT64  value, CMetab *  pMetabolite  )

friend

operator<<

std::ostream& operator<< ( std::ostream &  os, const CMetab &  d  )

friend

ostream operator

Member Data Documentation

mConc

C_FLOAT64 CMetab::mConc

private

Concentration of the metabolite as double.

Referenced by calculate(), getConcentration(), getValuePointer(), initObjects(), and setConcentration().

mConcRate

C_FLOAT64 CMetab::mConcRate

private

The rate of concentration change

Referenced by compile(), getConcentrationRate(), initObjects(), and operator=().

mIConc

C_FLOAT64 CMetab::mIConc

private

Initial concentration of the metabolite as double

Referenced by applyData(), compile(), createUndoData(), getInitialConcentration(), initObjects(), load(), setInitialConcentration(), and toData().

mIntensiveNoise

C_FLOAT64 CMetab::mIntensiveNoise

private

The intensive noise

Referenced by compile(), and initObjects().

mIsInitialConcentrationChangeAllowed

bool CMetab::mIsInitialConcentrationChangeAllowed

private

Referenced by compileIsInitialValueChangeAllowed(), and isInitialValueChangeAllowed().

mIsInitialParticleNumberChangeAllowed

bool CMetab::mIsInitialParticleNumberChangeAllowed

private

Referenced by compileIsInitialValueChangeAllowed(), and isInitialValueChangeAllowed().

mpCompartment

const CCompartment* CMetab::mpCompartment

private

pointer to the compartment the metabolite is located in. The metab needs to know about volumes.

Referenced by calculate(), CMetab(), compile(), compileIsInitialValueChangeAllowed(), getChildObjectUnits(), getCompartment(), initCompartment(), and operator=().

mpConcRateReference

CDataObjectReference< C_FLOAT64 >* CMetab::mpConcRateReference

protected

Referenced by getChildObjectUnits(), getConcentrationRateReference(), and initObjects().

mpConcReference

CDataObjectReference< C_FLOAT64 >* CMetab::mpConcReference

protected

Referenced by getChildObjectUnits(), getConcentrationReference(), getValueObject(), and initObjects().

mpIConcReference

CDataObjectReference< C_FLOAT64 >* CMetab::mpIConcReference

protected

Referenced by compileIsInitialValueChangeAllowed(), getChildObjectUnits(), getInitialConcentrationReference(), and initObjects().

mpIntensiveNoiseReference

CDataObjectReference< C_FLOAT64 >* CMetab::mpIntensiveNoiseReference

protected

Referenced by getIntensiveNoiseReference(), and initObjects().

mpMoiety

const CMoiety* CMetab::mpMoiety

private

If dependent the moiety the metabolite is calculated from

Referenced by calculate(), getMoiety(), isDependent(), and setDependsOnMoiety().

mpTTReference

CDataObjectReference< C_FLOAT64 >* CMetab::mpTTReference

protected

Referenced by getChildObjectUnits(), getTransitionTimeReference(), and initObjects().

mTT

C_FLOAT64 CMetab::mTT

private

Transition time of the metabolite

Referenced by compile(), getTransitionTime(), initObjects(), operator=(), and setTransitionTime().

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

• CMetab.h
• CMetab.cpp