#include <CCompartment.h>

Inheritance diagram for CCompartment:

Public Member Functions
bool	addMetabolite (CMetab *metabolite)

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

	CCompartment (const CCompartment &src, const CDataContainer *pParent)

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

void	cleanup ()

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

unsigned C_INT32	getDimensionality () const

CDataVectorNS< CMetab > &	getMetabolites ()

const CDataVectorNS< CMetab > &	getMetabolites () const

virtual const std::string	getUnits () const

C_INT32	load (CReadConfig &configbuffer)

bool	setDimensionality (unsigned C_INT32 dim)

virtual CData	toData () const

virtual	~CCompartment ()

Public Member Functions inherited from CModelEntity
virtual void	calculate ()

	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)

virtual CIssue	compile ()

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const override

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

virtual const CDataObject *	getValueObject () const override

virtual void *	getValuePointer () const override

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)

virtual bool	setObjectParent (const CDataContainer *pParent) override

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

virtual std::string	getObjectDisplayName () const override

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 CCompartment *	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 Attributes
unsigned C_INT32	mDimensionality

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
CDataVectorNS< CMetab >	mMetabolites

Friends
std::ostream &	operator<< (std::ostream &os, const CCompartment &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

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)

Constructor & Destructor Documentation

◆ CCompartment() [1/2]

CCompartment::CCompartment	(	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, CModelEntity::FIXED, initObjects(), CModelEntity::mIValue, and CModelEntity::setStatus().

Referenced by fromData().

◆ CCompartment() [2/2]

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

Copy constructor.

Parameters

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

References CONSTRUCTOR_TRACE, and initObjects().

◆ ~CCompartment()

CCompartment::~CCompartment ( )

virtual

Destructor. The destructor does nothing.

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

Member Function Documentation

◆ addMetabolite()

bool CCompartment::addMetabolite ( 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

Parameters

CMetab * metabolite;

Returns: bool success

References CDataVectorN< CType >::add(), CDataObject::getCN(), CDataObject::getObjectParent(), CRegisteredCommonName::handle(), and mMetabolites.

Referenced by MetaboliteHandler::processStart(), CModelExpansion::replaceInMetab(), and CMetab::setCompartment().

◆ applyData()

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

virtual

Apply the provided data to the object

Parameters

const CData & data

Returns: bool success

Reimplemented from CModelEntity.

References CUndoData::CChangeSet::add(), CModelEntity::applyData(), CUndoData::CHANGE, CData::FRAMEWORK, CCore::FrameworkNames, CDataObject::getCN(), CData::getProperty(), CData::INITIAL_VALUE, CData::isSetProperty(), CModelEntity::mIValue, CModelEntity::mpModel, CCore::ParticleNumbers, setDimensionality(), CData::SPATIAL_DIMENSION, CDataValue::toData(), CDataValue::toDouble(), toEnum(), CDataValue::toString(), CDataValue::toUint(), CModel::updateInitialValues(), and CData::VALUE.

◆ cleanup()

void CCompartment::cleanup ( )

Cleanup

References CDataVector< CType >::cleanup(), and mMetabolites.

◆ createUndoData()

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

virtual

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(), CData::addProperty(), CUndoData::CHANGE, CModelEntity::createUndoData(), CData::FRAMEWORK, CCore::FrameworkNames, CData::getProperty(), CData::INITIAL_VALUE, mDimensionality, CModelEntity::mIValue, CData::SPATIAL_DIMENSION, CDataValue::toData(), and CData::VALUE.

◆ fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const CData & data

Returns: CCompartment * pDataObject

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

◆ getDimensionality()

unsigned C_INT32 CCompartment::getDimensionality ( ) const

Get the dimensionality of the compartment

References mDimensionality.

Referenced by CModelAdd::addCompartments(), CSBMLExporter::createCompartment(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::duplicateCompartment(), SBMLImporter::importInitialAssignments(), SBMLImporter::importRuleForModelEntity(), and CCopasiXML::saveModel().

◆ getMetabolites() [1/2]

CDataVectorNS< CMetab > & CCompartment::getMetabolites ( )

Retrieve the vector of contained metabolites

Returns: CDataVectorNS < CMetab > & metabolites

References mMetabolites.

Referenced by SBMLImporter::createCMetabFromSpecies(), CMetabNameInterface::getMetabolite(), CModelExpansion::replaceInMetab(), and CMetab::setCompartment().

◆ getMetabolites() [2/2]

const CDataVectorNS< CMetab > & CCompartment::getMetabolites ( ) const

Retrieve the vector of contained metabolites

Returns: const CDataVectorNS < CMetab > & metabolites

References mMetabolites.

◆ getUnits()

const std::string CCompartment::getUnits ( ) const

virtual

Retrieve the units of the object.

Returns: std::string units

Reimplemented from CDataContainer.

References CModel::getAreaUnit(), CModel::getLengthUnit(), CModel::getVolumeUnit(), mDimensionality, and CModelEntity::mpModel.

Referenced by SBMLImporter::createCCompartmentFromCompartment(), and CReactionInterface::getConcentrationRateUnit().

◆ initObjects()

void CCompartment::initObjects ( )

private

Initialize the contained CDataObjects

References CModelEntity::mpIValueReference, CModelEntity::mpValueReference, and CDataObject::setObjectName().

Referenced by CCompartment().

◆ load()

C_INT32 CCompartment::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: mFail

See also: mFail

References C_FLOAT64, C_INT32, CReadConfig::getVariable(), CReadConfig::SEARCH, CModelEntity::setInitialValue(), and CDataObject::setObjectName().

◆ setDimensionality()

bool CCompartment::setDimensionality ( unsigned C_INT32 dim )

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

References mDimensionality.

Referenced by CModelAdd::addCompartments(), applyData(), SBMLImporter::createCCompartmentFromCompartment(), CModelExpansion::duplicateCompartment(), and CompartmentHandler::processStart().

◆ toData()

CData CCompartment::toData ( ) const

virtual

Retrieve the data describing the object

Returns: CData data

Reimplemented from CModelEntity.

References CData::addProperty(), CData::FRAMEWORK, CCore::FrameworkNames, CData::INITIAL_VALUE, mDimensionality, CModelEntity::mIValue, CCore::ParticleNumbers, CData::SPATIAL_DIMENSION, CModelEntity::toData(), and CData::VALUE.

Friends And Related Function Documentation

◆ operator<<

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

friend

Friend declaration for ostream operator <<

Parameters

std::ostream	& os
const	CCompartment & d

Returns: std::ostream & os

Member Data Documentation

◆ mDimensionality

unsigned C_INT32 CCompartment::mDimensionality

protected

The dimensionality of the compartment. Can be 0, 1, 2, or 3

Referenced by createUndoData(), getDimensionality(), getUnits(), setDimensionality(), and toData().

◆ mMetabolites

CDataVectorNS< CMetab > CCompartment::mMetabolites

private

Metabolites located in the compartment. @supplierCardinality 0..* @associates <{CMetab}>

Referenced by addMetabolite(), cleanup(), and getMetabolites().

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ CCompartment() [1/2]

◆ CCompartment() [2/2]

◆ ~CCompartment()

Member Function Documentation

◆ addMetabolite()

◆ applyData()

◆ cleanup()

◆ createUndoData()

◆ fromData()

◆ getDimensionality()

◆ getMetabolites() [1/2]

◆ getMetabolites() [2/2]

◆ getUnits()

◆ initObjects()

◆ load()

◆ setDimensionality()

◆ toData()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ mDimensionality

◆ mMetabolites