#include <CModel.h>

Inheritance diagram for CModel:

Public Types
enum	DependencyType { initial = 0 , transient , physical }

enum class	ModelType { deterministic , stochastic , __SIZE }

enum	UnitType { volume = 0 , area , length , time , quantity }

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

Public Member Functions
void	addModelEntity (const CModelEntity *pModelEntity)

bool	appendAllDependents (const CDataContainer &container, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const

bool	appendAllDependents (const ObjectSet &objects, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const

bool	appendDirectDependents (const CDataContainer &container, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const

bool	appendDirectDependents (const ObjectSet &objects, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const

void	applyActiveParameterSet ()

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

void	applyInitialValues ()

bool	buildDependencyGraphs ()

CCore::CUpdateSequence	buildInitialRefreshSequence (std::set< const CDataObject * > &changedObjects)

void	buildLinkZero ()

void	buildMoieties ()

void	buildRedStoi ()

void	buildStoi ()

void	changeUnitExpressionSymbols (std::string oldSymbol, std::string newSymbol)

void	clearSbmlIds ()

	CModel (CDataContainer *pParent)

bool	compileIfNecessary (CProcessReport *pProcessReport)

bool	convert2NonReversible ()

CCompartment *	createCompartment (const std::string &name, const C_FLOAT64 &volume=1.0)

CEvent *	createEvent (const std::string &name)

bool	createEventsForTimeseries (CExperiment *experiment=NULL)

CMetab *	createMetabolite (const std::string &name, const std::string &compartment, const C_FLOAT64 &iconc=1.0, const CModelEntity::Status &status=CModelEntity::Status::REACTIONS)

CModelValue *	createModelValue (const std::string &name, const C_FLOAT64 &value=0.0)

CReaction *	createReaction (const std::string &name)

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

CMetab *	findMetabByName (const std::string &name) const

size_t	findMoiety (const std::string &Target) const

bool	forceCompile (CProcessReport *pProcessReport)

void	functionDefinitionChanged (const CFunction *pFunction)

CModelParameterSet &	getActiveModelParameterSet ()

const CModelParameterSet &	getActiveModelParameterSet () const

const std::string &	getAreaUnit () const

std::string	getAreaUnitName () const

const C_FLOAT64 &	getAvogadro () const

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

CDataVectorNS< CCompartment > &	getCompartments ()

const CDataVectorNS< CCompartment > &	getCompartments () const

CDataObject *	getCorrespondingTransientObject (const CDataObject *pObject) const

CDataVectorN< CEvent > &	getEvents ()

const CDataVectorN< CEvent > &	getEvents () const

const C_FLOAT64 &	getInitialTime () const

const std::string &	getKey () const

const CLinkMatrixView &	getL () const

const CLinkMatrix &	getL0 () const

const CDataArray *	getLAnnotation () const

const std::string &	getLengthUnit () const

std::string	getLengthUnitName () const

CMathContainer &	getMathContainer ()

const CMathContainer &	getMathContainer () const

CDataVector< CMetab > &	getMetabolites ()

const CDataVector< CMetab > &	getMetabolites () const

CDataVector< CMetab > &	getMetabolitesX ()

const CDataVector< CMetab > &	getMetabolitesX () const

CDataVectorN< CModelParameterSet > &	getModelParameterSets ()

const CDataVectorN< CModelParameterSet > &	getModelParameterSets () const

const ModelType &	getModelType () const

CDataVectorN< CModelValue > &	getModelValues ()

const CDataVectorN< CModelValue > &	getModelValues () const

const CDataVector< CMoiety > &	getMoieties () const

size_t	getNumAssignmentMetabs () const

const C_FLOAT64 &	getNumber2QuantityFactor () const

size_t	getNumDependentReactionMetabs () const

size_t	getNumIndependentReactionMetabs () const

size_t	getNumMetabs () const

size_t	getNumModelValues () const

size_t	getNumODEMetabs () const

size_t	getNumVariableMetabs () const

const CVector< C_FLOAT64 > &	getParticleFlux () const

const C_FLOAT64 &	getQuantity2NumberFactor () const

const std::string	getQuantityUnit () const

std::string	getQuantityUnitName () const

CDataVectorNS< CReaction > &	getReactions ()

const CDataVectorNS< CReaction > &	getReactions () const

const std::set< std::pair< const CReaction *, C_FLOAT64 > > &	getReactionsPerSpecies (const CMetab *) const

const CMatrix< C_FLOAT64 > &	getRedStoi () const

const CDataArray *	getRedStoiAnnotation () const

const CStateTemplate &	getStateTemplate () const

const CMatrix< C_FLOAT64 > &	getStoi () const

const CDataArray *	getStoiAnnotation () const

const C_FLOAT64 &	getTime () const

const std::string &	getTimeUnit () const

std::string	getTimeUnitName () const

size_t	getTotSteps () const

std::vector< const CEvaluationTree * >	getTreesWithDiscontinuities () const

virtual const std::string	getUnits () const

CDataObject::DataObjectSet	getUnitSymbolUsage (std::string symbol) const

std::map< std::string, CUnit >	getUsedUnits () const

const std::string &	getVolumeUnit () const

std::string	getVolumeUnitName () const

bool	hasReversibleReaction () const

CVector< C_FLOAT64 >	initializeAtolVector (const C_FLOAT64 &baseTolerance, const bool &reducedModel) const

void	initializeMetabolites ()

const bool &	isAutonomous () const

const bool &	isCompileNecessary () const

bool	isStateVariable (const CDataObject *pObject) const

C_INT32	load (CReadConfig &configBuffer)

CEvaluationNode *	prepareElasticity (const CReaction pReaction, const CModelEntity pVar, bool simplify)

void	refreshActiveParameterSet ()

bool	removeCompartment (const CCompartment *pCompartment, const bool &recursive=true)

bool	removeCompartment (const size_t index, const bool &recursive=true)

bool	removeCompartment (const std::string &key, const bool &recursive=true)

void	removeDependentModelObjects (const ObjectSet &deletedObjects, const bool &onlyStructural=false)

bool	removeEvent (const CEvent *pEvent, const bool &recursive=true)

bool	removeEvent (const size_t index, const bool &recursive=true)

bool	removeEvent (const std::string &key, const bool &recursive=true)

bool	removeFunction (const CFunction *pFunction, const bool &recursive=true)

bool	removeLocalReactionParameter (const std::string &key, const bool &recursive=true)

bool	removeMetabolite (const CMetab *pMetabolite, const bool &recursive=true)

bool	removeMetabolite (const size_t index, const bool &recursive=true)

bool	removeMetabolite (const std::string &key, const bool &recursive=true)

void	removeModelEntity (const CModelEntity *pModelEntity)

bool	removeModelValue (const CModelValue *pModelValue, const bool &recursive=true)

bool	removeModelValue (const size_t index, const bool &recursive=true)

bool	removeModelValue (const std::string &key, const bool &recursive=true)

bool	removeReaction (const CReaction *pReaction, const bool &recursive=true)

bool	removeReaction (const size_t index, const bool &recursive=true)

bool	removeReaction (const std::string &key, const bool &recursive=true)

bool	setAreaUnit (const std::string &name)

void	setAvogadro (const C_FLOAT64 &avogadro, const CCore::Framework &frameWork)

void	setCompileFlag (bool flag=true)

void	setInitialTime (const C_FLOAT64 &time)

bool	setLengthUnit (const std::string &name)

void	setModelType (const ModelType &modelType)

virtual bool	setObjectParent (const CDataContainer *pParent)

bool	setQuantityUnit (const std::string &name, const CCore::Framework &frameWork)

void	setTime (const C_FLOAT64 &time)

bool	setTimeUnit (const std::string &name)

bool	setVolumeUnit (const std::string &name)

void	stateToIntialState ()

std::string	suitableForStochasticSimulation () const

virtual CData	toData () const

bool	updateInitialValues (const CCore::Framework &framework)

void	updateInitialValues (const CDataObject *changedObject)

void	updateInitialValues (std::set< const CDataObject * > &changedObjects)

	~CModel ()

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)

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

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)

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 CModel *	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)

Static Public Attributes
static const CEnumAnnotation< std::string, ModelType >	ModelTypeNames

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

Private Member Functions
bool	buildStateTemplate ()

bool	buildUserOrder ()

void	clearMoieties ()

	CModel (const CModel &src)

CIssue	compile ()

CIssue	compileEvents ()

bool	handleUnusedMetabolites ()

void	initObjects ()

CModel &	operator= (const CModel &src)

void	removeDataObject (const CDataObject *pObject)

void	replaceInExpressions (const std::string &oldStr, const std::string &newStr)

void	updateMatrixAnnotations ()

void	updateMoietyValues ()

Private Attributes
std::string	mActiveParameterSetKey

std::string	mAreaUnit

C_FLOAT64	mAvogadro

bool	mBuildInitialSequence

CDataVectorNS< CCompartment >	mCompartments

bool	mCompileIsNecessary

CMatrix< C_FLOAT64 >	mElasticities

CDataVectorN< CEvent >	mEvents

bool	mIsAutonomous

CVector< size_t >	mJacobianPivot

CLinkMatrix	mL

std::string	mLengthUnit

CLinkMatrixView	mLView

CDataVector< CMetab >	mMetabolites

CDataVector< CMetab >	mMetabolitesX

CDataVector< CMoiety >	mMoieties

C_FLOAT64	mNumber2QuantityFactor

size_t	mNumMetabolitesAssignment

size_t	mNumMetabolitesODE

size_t	mNumMetabolitesReaction

size_t	mNumMetabolitesReactionIndependent

size_t	mNumMetabolitesUnused

CModelParameterSet	mParameterSet

CDataVectorN< CModelParameterSet >	mParameterSets

CVector< C_FLOAT64 >	mParticleFluxes

CDataObject *	mpAvogadroReference

CDataArray *	mpLinkMatrixAnnotation

CMathContainer *	mpMathContainer

CProcessReport *	mpProcessReport

CDataObject *	mpQuantity2NumberFactorReference

CDataArray *	mpRedStoiAnnotation

CDataArray *	mpStoiAnnotation

C_FLOAT64	mQuantity2NumberFactor

std::string	mQuantityUnit

std::map< const CMetab , std::set< std::pair< const CReaction , C_FLOAT64 > > >	mReactionsPerSpecies

CMatrix< C_FLOAT64 >	mRedStoi

bool	mReorderNeeded

CStateTemplate	mStateTemplate

CDataVectorNS< CReaction >	mSteps

CMatrix< C_FLOAT64 >	mStoi

CMathDependencyGraph	mStructuralDependencies

std::string	mTimeUnit

ModelType	mType

CDataVectorN< CModelValue >	mValues

std::string	mVolumeUnit

Friends
class	CFunctionDB

Additional Inherited Members
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 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

Member Enumeration Documentation

◆ DependencyType

enum CModel::DependencyType

Enumerator
initial
transient
physical

◆ ModelType

enum CModel::ModelType

strong

Enum of valid model types.

Enumerator
deterministic
stochastic
__SIZE

◆ UnitType

enum CModel::UnitType

Enumerator
volume
area
length
time
quantity

Constructor & Destructor Documentation

◆ CModel() [1/2]

CModel::CModel ( const CModel & src )

private

Copy constructor

Parameters

const CModel & src

Referenced by fromData().

◆ CModel() [2/2]

CModel::CModel ( CDataContainer * pParent )

constructor

References forceCompile(), initializeMetabolites(), initObjects(), CModelEntity::mIValue, mQuantityUnit, CCore::ParticleNumbers, setQuantityUnit(), CModelEntity::setStatus(), CModelEntity::setUsed(), and CModelEntity::TIME.

◆ ~CModel()

CModel::~CModel ( )

Destructor

References DESTRUCTOR_TRACE, CRootContainer::getKeyFactory(), CAnnotation::mKey, mpLinkMatrixAnnotation, mpMathContainer, CModelEntity::mpModel, mpRedStoiAnnotation, mpStoiAnnotation, pdelete, and CKeyFactory::remove().

Member Function Documentation

◆ addModelEntity()

void CModel::addModelEntity ( const CModelEntity * pModelEntity )

Add a model entity to the model

Parameters

const CModelEntity * pModelEntity

References CStateTemplate::add(), and mStateTemplate.

Referenced by CModelEntity::initObjects(), and CModelEntity::setObjectParent().

◆ appendAllDependents() [1/2]

bool CModel::appendAllDependents	(	const CDataContainer &	container,
		DataObjectSet &	dependentReactions,
		DataObjectSet &	dependentMetabolites,
		DataObjectSet &	dependentCompartments,
		DataObjectSet &	dependentModelValues,
		DataObjectSet &	dependentEvents,
		DataObjectSet &	dependentEventAssignments,
		const bool &	onlyStructural = `false`
	)		const

Appends pointers to compartments, species, model values, reactions, events, and event assignments which dependent on the container. list.

Parameters

const	CDataContainer & container
CDataObject::DataObjectSet	& dependentReactions
CDataObject::DataObjectSet	& dependentMetabolites
CDataObject::DataObjectSet	& dependentCompartments
CDataObject::DataObjectSet	& dependentModelValues
CDataObject::DataObjectSet	& dependentEvents
CDataObject::DataObjectSet	& dependentEventAssignments
const	bool & onlyStructural (default: false)

Returns: bool objectsAppended

Referenced by CDataContainer::appendDeletedDependentData(), SBMLImporter::createCModelFromSBMLDocument(), CModelExpansion::SetOfModelElements::fillDependencies(), CFunctionDB::getUsedFunctions(), and removeDependentModelObjects().

◆ appendAllDependents() [2/2]

bool CModel::appendAllDependents	(	const ObjectSet &	objects,
		DataObjectSet &	dependentReactions,
		DataObjectSet &	dependentMetabolites,
		DataObjectSet &	dependentCompartments,
		DataObjectSet &	dependentModelValues,
		DataObjectSet &	dependentEvents,
		DataObjectSet &	dependentEventAssignments,
		const bool &	onlyStructural = `false`
	)		const

Appends pointers to compartments, species, model values, reactions, events, and event assignments which dependent on any of the objets. list.

Parameters

const	ObjectSet & objects
CDataObject::DataObjectSet	& dependentReactions
CDataObject::DataObjectSet	& dependentMetabolites
CDataObject::DataObjectSet	& dependentCompartments
CDataObject::DataObjectSet	& dependentModelValues
CDataObject::DataObjectSet	& dependentEvents
CDataObject::DataObjectSet	& dependentEventAssignments
const	bool & onlyStructural (default: false)

Returns: bool objectsAppended

References CMathDependencyGraph::appendAllDependents(), CDataVector< CType >::begin(), CDataVector< CType >::end(), CChemEq::getBalances(), CDataObject::getDataObject(), CDataContainer::getDescendants(), CMathContainer::getInitialDependencies(), CMathContainer::getInitialValueObject(), CMathContainer::getMathObject(), CDataObject::getObjectAncestor(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CModelEntity::getRateReference(), CModelEntity::getStatus(), CMathContainer::getTransientDependencies(), CMetab::getTransitionTimeReference(), CUndoObjectInterface::insert(), CDataContainer::insert(), mpMathContainer, mStructuralDependencies, and CModelEntity::REACTIONS.

◆ appendDirectDependents() [1/2]

bool CModel::appendDirectDependents	(	const CDataContainer &	container,
		CDataObject::DataObjectSet &	dependentReactions,
		CDataObject::DataObjectSet &	dependentMetabolites,
		CDataObject::DataObjectSet &	dependentCompartments,
		CDataObject::DataObjectSet &	dependentModelValues,
		CDataObject::DataObjectSet &	dependentEvents,
		CDataObject::DataObjectSet &	dependentEventAssignments,
		const bool &	onlyStructural = `false`
	)		const

Appends pointers to compartments, species, model values, reactions, events, and event assignments which directly dependent on the container. list.

Parameters

const	CDataContainer & container
CDataObject::DataObjectSet	& dependentReactions
CDataObject::DataObjectSet	& dependentMetabolites
CDataObject::DataObjectSet	& dependentCompartments
CDataObject::DataObjectSet	& dependentModelValues
CDataObject::DataObjectSet	& dependentEvents
CDataObject::DataObjectSet	& dependentEventAssignments
const	bool & onlyStructural (default: false)

Returns: bool objectsAppended

Referenced by CMetab::getCountOfDependentReactions().

◆ appendDirectDependents() [2/2]

bool CModel::appendDirectDependents	(	const ObjectSet &	objects,
		CDataObject::DataObjectSet &	dependentReactions,
		CDataObject::DataObjectSet &	dependentMetabolites,
		CDataObject::DataObjectSet &	dependentCompartments,
		CDataObject::DataObjectSet &	dependentModelValues,
		CDataObject::DataObjectSet &	dependentEvents,
		CDataObject::DataObjectSet &	dependentEventAssignments,
		const bool &	onlyStructural = `false`
	)		const

Appends pointers to compartments, species, model values, reactions, events, and event assignments which directly dependent on any of the objets. list.

Parameters

const	ObjectSet & objects
CDataObject::DataObjectSet	& dependentReactions
CDataObject::DataObjectSet	& dependentMetabolites
CDataObject::DataObjectSet	& dependentCompartments
CDataObject::DataObjectSet	& dependentModelValues
CDataObject::DataObjectSet	& dependentEvents
CDataObject::DataObjectSet	& dependentEventAssignments
const	bool & onlyStructural (default: false)

Returns: bool objectsAppended

References CMathDependencyGraph::appendDirectDependents(), CDataVector< CType >::begin(), CDataVector< CType >::end(), CEvent::getAssignments(), CDataObject::getDataObject(), CDataContainer::getDescendants(), CMathContainer::getInitialDependencies(), CMathContainer::getMathObject(), CDataObject::getObjectAncestor(), CMathContainer::getTransientDependencies(), CUndoObjectInterface::insert(), CDataContainer::insert(), mpMathContainer, and mStructuralDependencies.

◆ applyActiveParameterSet()

void CModel::applyActiveParameterSet ( )

Update the model initial values from the active parameter set.

References CModelParameterSet::createFromModel(), CKeyFactory::get(), CModelParameterSet::getKey(), CRootContainer::getKeyFactory(), mActiveParameterSetKey, mParameterSet, and CModelParameterSet::updateModel().

◆ applyData()

bool CModel::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 CModelEntity::applyData(), CData::AREA_UNIT, CData::AVOGADRO_NUMBER, deterministic, CData::FRAMEWORK, CCore::FrameworkNames, CData::getProperty(), CData::isSetProperty(), CData::LENGTH_UNIT, CData::MODEL_TYPE, ModelTypeNames, CCore::ParticleNumbers, CData::QUANTITY_UNIT, setAreaUnit(), setAvogadro(), setLengthUnit(), setModelType(), setQuantityUnit(), setTimeUnit(), setVolumeUnit(), CData::TIME_UNIT, CDataValue::toData(), CDataValue::toDouble(), CEnumAnnotation< Type, Enum >::toEnum(), CDataValue::toString(), CData::VALUE, and CData::VOLUME_UNIT.

◆ applyInitialValues()

void CModel::applyInitialValues ( )

initialize all values of the model with their initial values

References CMathContainer::applyInitialValues(), CMathContainer::fetchInitialState(), mpMathContainer, CCore::ParticleNumbers, CMathContainer::pushAllTransientValues(), CMathContainer::updateInitialValues(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().

◆ buildDependencyGraphs()

bool CModel::buildDependencyGraphs ( )

References CMathDependencyGraph::addObject(), CDataVector< CType >::begin(), CMathDependencyGraph::clear(), CDataVector< CType >::end(), CMathDependencyGraph::exportDOTFormat(), mCompartments, mEvents, mMetabolites, mSteps, mStructuralDependencies, and mValues.

Referenced by compile().

◆ buildInitialRefreshSequence()

CCore::CUpdateSequence CModel::buildInitialRefreshSequence ( std::set< const CDataObject * > & changedObjects )

Build the update sequence used to calculate all initial values depending on the changed objects. For metabolites the initial particle number is updated by default unless itself is in the list of changed objects. In that case the initial concentration is updated.

Parameters

std::set< const CDataObject * > & changedObjects

Returns: CCore::CUpdateSequence initialRefreshSequence

References CMathUpdateSequence::begin(), CMathContainer::getInitialDependencies(), CMathContainer::getInitialStateObjects(), CMathContainer::getMathObject(), CMathDependencyGraph::getUpdateSequence(), mpMathContainer, and CCore::UpdateMoieties.

Referenced by CSlider::setSliderObject(), and updateInitialValues().

◆ buildLinkZero()

void CModel::buildLinkZero ( )

Build the core of the link matrix L

Parameters

const CMatrix< C_FLOAT64 > & LU

References CLinkMatrix::build(), CLinkMatrix::doRowPivot(), CLinkMatrix::getNumIndependent(), mL, mNumMetabolitesReactionIndependent, and mStoi.

Referenced by compile().

◆ buildMoieties()

void CModel::buildMoieties ( )

Build the moieties based on the LU decomposition

References CMoiety::add(), CDataVector< CType >::add(), CMatrix< CType >::array(), CDataVector< CType >::begin(), C_FLOAT64, CDataVector< CType >::cleanup(), CDataObject::getObjectName(), mL, mMetabolitesX, mMoieties, mNumMetabolitesODE, MNumMetabolitesReactionDependent, mNumMetabolitesReactionIndependent, and updateMoietyValues().

Referenced by compile().

◆ buildRedStoi()

void CModel::buildRedStoi ( )

Build the Reduced Stoichiometry Matrix from the LU decomposition

References CLinkMatrix::applyRowPivot(), CVectorCore< CType >::array(), CDataVector< CType >::begin(), mL, mMetabolitesX, mNumMetabolitesODE, mNumMetabolitesReaction, mNumMetabolitesReactionIndependent, mRedStoi, mStoi, CMatrix< CType >::numCols(), and CMatrix< CType >::resize().

Referenced by compile().

◆ buildStateTemplate()

bool CModel::buildStateTemplate ( )

private

Build the state template for the model.

Returns: bool success

References CVectorCore< CType >::array(), CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), CDataVector< CType >::end(), mCompartments, mMetabolitesX, mReorderNeeded, mStateTemplate, mSteps, mValues, CModelEntity::ODE, CStateTemplate::reorder(), CDataVector< CType >::size(), and CVectorCore< CType >::size().

Referenced by compile().

◆ buildStoi()

void CModel::buildStoi ( )

Build the Stoichiometry Matrix from the chemical equations of the steps

References CProcessReport::addItem(), CMatrix< CType >::array(), CDataVector< CType >::begin(), C_FLOAT64, C_INT32, CDataVector< CType >::end(), CCopasiMessage::ERROR, CProcessReport::finishItem(), CDataObject::getKey(), handleUnusedMetabolites(), initializeMetabolites(), MCReaction, mMetabolitesX, mNumMetabolitesODE, mNumMetabolitesReaction, mParticleFluxes, mpProcessReport, mReactionsPerSpecies, mSteps, mStoi, CProcessReport::progressItem(), CMatrix< CType >::resize(), CVector< CType >::resize(), and CDataVector< CType >::size().

Referenced by compile().

◆ buildUserOrder()

bool CModel::buildUserOrder ( )

private

Build the user order for the state template

Returns: bool success

References CVectorCore< CType >::array(), CDataVector< CType >::begin(), CDataVector< CType >::end(), CStateTemplate::getEntities(), CStateTemplate::getNumIndependent(), CStateTemplate::getUserOrder(), CModelEntity::isUsed(), mCompartments, mJacobianPivot, mMetabolites, mMetabolitesX, MNumMetabolitesReactionDependent, mStateTemplate, mValues, CModelEntity::ODE, CModelEntity::REACTIONS, CVector< CType >::resize(), CStateTemplate::setUserOrder(), CDataVector< CType >::size(), and CVectorCore< CType >::size().

Referenced by compile().

◆ changeUnitExpressionSymbols()

void CModel::changeUnitExpressionSymbols	(	std::string	oldSymbol,
		std::string	newSymbol
	)

References CDataVector< CType >::begin(), CDataVector< CType >::end(), getModelValues(), mAreaUnit, mLengthUnit, mQuantityUnit, mTimeUnit, mVolumeUnit, and CUnit::replaceSymbol().

Referenced by CCopasiXML::mergeUnitDefinitions().

◆ clearMoieties()

void CModel::clearMoieties ( )

private

Clear all references to moieties

References CDataVector< CType >::clear(), and mMoieties.

Referenced by removeEvent(), removeMetabolite(), and removeReaction().

◆ clearSbmlIds()

void CModel::clearSbmlIds ( )

clears all SBML ids in the model

References getCompartments(), getEvents(), getMetabolites(), getModelValues(), and getReactions().

◆ compile()

CIssue CModel::compile ( )

privatevirtual

Compile the model value. This is only needed for status ASIGNMENT and ODE.

Returns: CIssue issue

Reimplemented from CModelEntity.

References CProcessReport::addItem(), CDataVector< CType >::begin(), buildDependencyGraphs(), buildLinkZero(), buildMoieties(), buildRedStoi(), buildStateTemplate(), buildStoi(), buildUserOrder(), C_INT32, CLinkMatrix::clearPivoting(), CMathContainer::compile(), compileEvents(), CModelParameterSet::createFromModel(), CDataVector< CType >::end(), CIssue::Error, CMathContainer::fetchInitialState(), CProcessReport::finishItem(), CMathContainer::isAutonomous(), CRegisteredCommonName::isEnabled(), mCompileIsNecessary, mIsAutonomous, mL, mMetabolitesX, mParameterSet, mpMathContainer, mpProcessReport, CCore::ParticleNumbers, CProcessReport::progressItem(), CMathContainer::pushInitialState(), CRegisteredCommonName::setEnabled(), CProcessReport::setName(), CMathContainer::updateInitialValues(), and updateMatrixAnnotations().

Referenced by compileIfNecessary(), and load().

◆ compileEvents()

CIssue CModel::compileEvents ( )

private

Compile the events

Returns: CIssue issue

References CDataVector< CType >::begin(), CDataVector< CType >::end(), and mEvents.

Referenced by compile().

◆ compileIfNecessary()

bool CModel::compileIfNecessary ( CProcessReport * pProcessReport )

◆ convert2NonReversible()

bool CModel::convert2NonReversible ( )

Converts the set of reactions to a set of reactions where all reactions are irreversible.

References CFunctionDB::addAndAdaptName(), CReaction::addModifier(), CReaction::addProduct(), CReaction::addSubstrate(), CReaction::compile(), createReaction(), CCopasiMessage::ERROR, findFunction(), CFunctionParameter::FLOAT64, CReaction::getChemEq(), CDataObject::getCN(), CReaction::getFluxReference(), CReaction::getFunction(), CRootContainer::getFunctionList(), CReaction::getFunctionParameters(), CDataObject::getObjectName(), CCopasiParameterGroup::getParameter(), CReaction::getParameterCNs(), CReaction::getParameterObjects(), CReaction::getParameters(), CReaction::getParameterValue(), CReaction::getParticleFluxReference(), CChemEq::getProducts(), getReactions(), CChemEq::getSubstrates(), CFunctionParameter::getType(), CFunctionParameter::getUsage(), CCopasiParameter::getValueReference(), CReaction::isLocalParameter(), MCReaction, CFunctionParameter::MODIFIER, CFunctionParameter::PARAMETER, pdelete, CFunctionParameter::PRODUCT, replaceInExpressions(), setCompileFlag(), CReaction::setFunction(), CReaction::setParameterCNs(), CReaction::setParameterValue(), CReaction::setReversible(), CDataVector< CType >::size(), CFunctionParameters::size(), CFunction::splitFunction(), and CFunctionParameter::SUBSTRATE.

◆ createCompartment()

CCompartment * CModel::createCompartment	(	const std::string &	name,
		const C_FLOAT64 &	volume = `1.0`
	)

Add a compartment to the model

Parameters

const	std::string &name
const	C_FLOAT64 & volume (default 1.0)

Returns: bool success (false if failed)

References CDataVectorN< CType >::add(), C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), mCompartments, mCompileIsNecessary, CModelEntity::setInitialValue(), and volume.

Referenced by CModelAdd::addCompartments(), SBMLImporter::createCCompartmentFromCompartment(), CChemEqInterface::createNonExistingMetabs(), CReactionInterface::createOtherObjects(), and CModelExpansion::duplicateCompartment().

◆ createEvent()

CEvent * CModel::createEvent ( const std::string & name )

Add a new event to the model

Parameters

const std::string &name

Returns: bool success (false if failed)

References CDataVectorN< CType >::add(), C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), mCompileIsNecessary, and mEvents.

Referenced by CModelAdd::addEvents(), createEventsForTimeseries(), CModelExpansion::duplicateEvent(), and SBMLImporter::importEvent().

◆ createEventsForTimeseries()

bool CModel::createEventsForTimeseries ( CExperiment * experiment = NULL )

Creates events for all elements of an parameter estimation time course experiment

References CDataVectorN< CType >::add(), CLocaleString::c_str(), CExpression::compile(), CExperiment::compile(), createEvent(), CCopasiMessage::ERROR, CLocaleString::fromUtf8(), CEvent::getAssignments(), CObjectInterface::getCN(), CDataObject::getCN(), CObjectInterface::getDataObject(), CExperiment::getDependentData(), CExperiment::getDependentObjectsMap(), getDependentOrNull(), CExperimentSet::getExperiment(), CFitProblem::getExperimentSet(), CExperiment::getExperimentType(), CEventAssignment::getExpressionPtr(), CExperiment::getFileName(), getNextId(), CExperiment::getNumDataRows(), CDataContainer::getObject(), CDataObject::getObjectDataModel(), CDataObject::getObjectDisplayName(), CDataObject::getObjectParent(), CCopasiTask::getProblem(), CDataModel::getTaskList(), CExperiment::getTimeData(), CEvent::getTriggerExpressionPtr(), mpMathContainer, CMatrix< CType >::numCols(), CExperiment::read(), CEventAssignment::setExpression(), CEvent::setTriggerExpression(), CCopasiParameterGroup::size(), time, CTaskEnum::timeCourse, and CCopasiMessage::WARNING.

◆ createMetabolite()

CMetab * CModel::createMetabolite	(	const std::string &	name,
		const std::string &	compartment,
		const C_FLOAT64 &	iconc = `1.0`,
		const CModelEntity::Status &	status = `CModelEntity::Status::REACTIONS`
	)

Add a metabolite to the model

Parameters

const	std::string & name
const	std::string & compartment
const	C_FLOAT64 & iconc (default 1.0)
const	CMetab::Status & status (default CMetab::METAB_VARIABL)

Returns: bool success (false if failed)

See also: CMetab for more information

References CDataVector< CType >::add(), C_INVALID_INDEX, CDataContainer::getIndex(), CDataVectorN< CType >::getIndex(), CModelEntity::getInitialValue(), getMetabolites(), getQuantity2NumberFactor(), mCompartments, mCompileIsNecessary, mMetabolites, CModelEntity::mpModel, CMetab::setInitialConcentration(), CModelEntity::setInitialValue(), CModelEntity::setStatus(), and CDataVector< CType >::size().

Referenced by CModelAdd::addMetabolites(), SBMLImporter::createCMetabFromSpecies(), CChemEqInterface::createNonExistingMetabs(), and CModelExpansion::duplicateMetab().

◆ createModelValue()

CModelValue * CModel::createModelValue	(	const std::string &	name,
		const C_FLOAT64 &	value = `0.0`
	)

Add a non concentration value to the model

Parameters

const	std::string &name
const	C_FLOAT64 & value (default 0.0)

References CDataVectorN< CType >::add(), C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), mCompileIsNecessary, mValues, and CModelEntity::setInitialValue().

Referenced by CModelAdd::addModelValues(), CFixLocalReactionParameters::changeModel(), SEDMLUtils::createAmountMV(), SBMLImporter::createCModelValueFromParameter(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::createLinearArray(), CReactionInterface::createOtherObjects(), CModelExpansion::createRectangularArray(), CModelExpansion::duplicateGlobalQuantity(), and CModelExpansion::simpleCall().

◆ createReaction()

CReaction * CModel::createReaction ( const std::string & name )

Add a new reaction to the model

Parameters

const std::string &name

Returns: bool success (false if failed)

References CDataVectorN< CType >::add(), C_INVALID_INDEX, CDataVectorN< CType >::getIndex(), mCompileIsNecessary, and mSteps.

Referenced by CModelAdd::addReactions(), convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::createDiffusionReaction(), and CModelExpansion::duplicateReaction().

◆ createUndoData()

void CModel::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(), CData::AREA_UNIT, CData::AVOGADRO_NUMBER, CUndoData::CHANGE, CModelEntity::createUndoData(), CData::FRAMEWORK, CCore::FrameworkNames, CData::getProperty(), CData::LENGTH_UNIT, mAreaUnit, mAvogadro, mLengthUnit, CData::MODEL_TYPE, ModelTypeNames, mQuantityUnit, mTimeUnit, mVolumeUnit, CData::QUANTITY_UNIT, CData::TIME_UNIT, CDataValue::toData(), CData::VALUE, and CData::VOLUME_UNIT.

◆ findMetabByName()

CMetab * CModel::findMetabByName ( const std::string & name ) const

Returns the pointer to the species with the given name

Parameters

const std::string & name

Returns: CMetab * pSpecies

Returns the index of the metab

References CDataObjectMap::equal_range(), CDataContainer::getObjects(), mMetabolites, and unQuote().

Referenced by CMetabNameInterface::getMetabolite(), and CReaction::loadOneRole().

◆ findMoiety()

size_t CModel::findMoiety ( const std::string & Target ) const

Returns the index of the moiety

Parameters

const std::string & Target

Returns: index

Returns the index of the Moiety

References C_INVALID_INDEX, CDataObject::getObjectName(), mMoieties, and CDataVector< CType >::size().

◆ forceCompile()

bool CModel::forceCompile ( CProcessReport * pProcessReport )

Force a compile the model.

Parameters

CProcessReport * pProcessReport

Returns: bool success

References compileIfNecessary(), and setCompileFlag().

Referenced by CModel(), and CModelExpansion::replaceInModel().

◆ fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const CData & data

Returns: CModel * pDataObject

References CModel(), CData::getProperty(), NO_PARENT, CData::OBJECT_NAME, CDataObject::setObjectName(), and CDataValue::toString().

◆ functionDefinitionChanged()

void CModel::functionDefinitionChanged ( const CFunction * pFunction )

Trigger a model compile in the case the function is used in the model

References CMathDependencyGraph::appendDirectDependents(), mStructuralDependencies, and setCompileFlag().

◆ getActiveModelParameterSet() [1/2]

CModelParameterSet & CModel::getActiveModelParameterSet ( )

References mParameterSet.

◆ getActiveModelParameterSet() [2/2]

const CModelParameterSet & CModel::getActiveModelParameterSet ( ) const

Retrieve the parameter set

Returns: const CModelParameterSet & modelParameterSet

References mParameterSet.

Referenced by CDataModel::commonAfterLoad(), SEDMLImporter::importModel(), CModelParameterSet::isActive(), ModelHandler::processEnd(), CDataModel::saveModel(), CCopasiXML::saveModelParameterSets(), and CDataModel::saveModelToString().

◆ getAreaUnit()

const std::string & CModel::getAreaUnit ( ) const

Get the current area unit of the model

Returns: const CUnit & areaunit

References mAreaUnit.

Referenced by CSBMLExporter::createAreaUnit(), and CCompartment::getUnits().

◆ getAreaUnitName()

std::string CModel::getAreaUnitName ( ) const

Get the unit for areas

Returns: std::string areaUnit

References mAreaUnit.

Referenced by CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ getAvogadro()

const C_FLOAT64 & CModel::getAvogadro ( ) const

Retrieve the Avogadro number.

References mAvogadro.

Referenced by CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ getChildObjectUnits()

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

virtual

Retrieve the units of the child object.

Returns: std::string units

Reimplemented from CModelEntity.

References CModelEntity::getChildObjectUnits(), mpAvogadroReference, mpQuantity2NumberFactorReference, and mQuantityUnit.

◆ getCompartments() [1/2]

CDataVectorNS< CCompartment > & CModel::getCompartments ( )

Return the compartments of this model

Returns: CDataVectorNS < CCompartment > *

References mCompartments.

Referenced by CModelAdd::addCompartments(), CModelAdd::addCompartmentsExpressions(), CModelAdd::addReactions(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForPiecewiseFunctions(), CModelAnalyzer::checkReaction(), clearSbmlIds(), CSBMLExporter::collectIds(), CChemEqInterface::completeCompartments(), SBMLImporter::createCCompartmentFromCompartment(), CSBMLExporter::createCompartments(), CModelParameterSet::createFromModel(), CChemEqInterface::createNonExistingMetabs(), CSBMLExporter::createSBMLDocument(), CReactionInterface::createUndoData(), CMathContainer::createValueChangeProhibited(), CODEExporter::exportCompartments(), CODEExporter::exportModelValuesExpressions(), CODEExporterC::exportTitleData(), CModelExpansion::SetOfModelElements::fillComplete(), CDataModel::findObjectByDisplayName(), CReactionInterface::getConcentrationRateUnit(), CMetabNameInterface::getDisplayName(), CObjectLists::getListOfConstObjects(), CMetabNameInterface::getMetabolite(), SEDMLUtils::getObjectForSbmlId(), CExpressionGenerator::getObjectsForSelection(), CReactionInterface::getUnit(), CReactionInterface::getUnitVector(), CSBMLExporter::hasVolumeAssignment(), CLsodaMethod::initializeParameter(), CReactionInterface::isLocked(), CSBMLExporter::isModelSBMLCompatible(), CLNAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CTSSAMethod::isValidProblem(), CModelMerging::mergeMetabolites(), CODEExporter::preprocess(), CODEExporterC::preprocess(), CompartmentHandler::processStart(), removeCompartment(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModel(), CCopasiXML::saveModel(), CMetab::setCompartment(), SBMLImporter::setInitialValues(), CTSSAMethod::start(), CReactionInterface::writeBackToReaction(), and CMMLOutput::writeDifferentialEquations().

◆ getCompartments() [2/2]

const CDataVectorNS< CCompartment > & CModel::getCompartments ( ) const

Return the compartments of this model

Returns: const CDataVectorNS < CCompartment > *

References mCompartments.

◆ getCorrespondingTransientObject()

CDataObject * CModel::getCorrespondingTransientObject ( const CDataObject * pObject ) const

Retrieve the corresponding transient state object of the given object

Parameters

const CDataObject * pObject

Returns: CDataObject * correspondingTransientObject

References CMetab::getConcentrationReference(), CMetab::getInitialConcentrationReference(), CDataObject::getObjectParent(), and CModelEntity::getValueReference().

◆ getEvents() [1/2]

CDataVectorN< CEvent > & CModel::getEvents ( )

◆ getEvents() [2/2]

const CDataVectorN< CEvent > & CModel::getEvents ( ) const

Return the vector of events

References mEvents.

◆ getInitialTime()

const C_FLOAT64 & CModel::getInitialTime ( ) const

Retrieve the initial time

Returns: const C_FLOAT64 & time

References CModelEntity::mIValue.

Referenced by CModelParameterSet::createFromModel(), CSEDMLExporter::createTimeCourseTask(), and CEvaluationNodeObject::toAST().

◆ getKey()

const std::string & CModel::getKey ( ) const

virtual

Return the key of this model

Returns: string key

Reimplemented from CModelEntity.

References CAnnotation::mKey.

Referenced by ModelHandler::processEnd(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameterSets(), and CModelAdd::simpleCall().

◆ getL()

const CLinkMatrixView & CModel::getL ( ) const

Get the LU decomposition matrix of this model

Returns: const TNT::Matrix < C_FLOAT64 > & LU Get the link matrix L of the relation: Stoi = L * RedStoi; const CLinkMatrixView L

References mLView.

Referenced by CODEExporter::exportMetabolites().

◆ getL0()

const CLinkMatrix & CModel::getL0 ( ) const

Get the relevant portion of the link matrix L.

Returns: const CLinkMatrix & L0

References mL.

Referenced by CLNAMethod::calculateCovarianceMatrixFull(), and CMCAMethod::createLinkMatrix().

◆ getLAnnotation()

const CDataArray * CModel::getLAnnotation ( ) const

Returns: get the annotated link matrix

References mpLinkMatrixAnnotation.

◆ getLengthUnit()

const std::string & CModel::getLengthUnit ( ) const

Get the current length unit of the model

Returns: const CUnit & lengthunit

References mLengthUnit.

Referenced by CSBMLExporter::createLengthUnit(), and CCompartment::getUnits().

◆ getLengthUnitName()

std::string CModel::getLengthUnitName ( ) const

Get the unit for lengths

Returns: std::string lengthUnit

References mLengthUnit.

Referenced by CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ getMathContainer() [1/2]

CMathContainer & CModel::getMathContainer ( )

Retrieve the container of all mathematical objects

Returns: CMathContainer & mathContainer

References mpMathContainer.

◆ getMathContainer() [2/2]

const CMathContainer & CModel::getMathContainer ( ) const

Retrieve the container of all mathematical objects

Returns: const CMathContainer & mathContainer

References mpMathContainer.

Referenced by CDataModel::commonAfterLoad(), CMetab::compileIsInitialValueChangeAllowed(), CODEExporter::exportObjectNodesFromModel(), CModelParameterGroup::getObjectUnit(), CCopasiTask::initObjects(), TaskHandler::processStart(), CCopasiProblem::setModel(), SEDMLImporter::updateCopasiTaskForSimulation(), and CSlider::writeToObject().

◆ getMetabolites() [1/2]

CDataVector< CMetab > & CModel::getMetabolites ( )

References mMetabolites.

◆ getMetabolites() [2/2]

const CDataVector< CMetab > & CModel::getMetabolites ( ) const

Return the metabolites of this model

Returns: CDataVectorN< CMetab > & metabolites

References mMetabolites.

Referenced by CModelAdd::addMetabolites(), CModelAdd::addMetabolitesExpressions(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CSBMLExporter::checkForPiecewiseFunctions(), SBMLUnitSupport::checkForSpatialSizeUnits(), clearSbmlIds(), CSBMLExporter::collectIds(), CPlotSpecification::createDefaultPlot(), CModelParameterSet::createFromModel(), createMetabolite(), CSBMLExporter::createMetabolites(), CSBMLExporter::createSBMLDocument(), CReactionInterface::createUndoData(), CMetabNameInterface::doesExist(), CObjectLists::existsFixedMetab(), CODEExporter::exportModelValuesExpressions(), CModelExpansion::SetOfModelElements::fillComplete(), CDataModel::findObjectByDisplayName(), CObjectLists::getListOfConstObjects(), SEDMLUtils::getObjectForSbmlId(), CExpressionGenerator::getObjectsForSelection(), CSBMLExporter::isModelSBMLCompatible(), CMetabNameInterface::isUnique(), CTSSAMethod::isValidProblem(), CModelMerging::mergeMetabolites(), CEFMProblem::printResult(), MetaboliteHandler::processStart(), removeMetabolite(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModel(), CCopasiXML::saveModel(), SBMLImporter::setInitialValues(), CModelMerging::simpleCall(), and CMMLOutput::writeDifferentialEquations().

◆ getMetabolitesX() [1/2]

CDataVector< CMetab > & CModel::getMetabolitesX ( )

References mMetabolitesX.

◆ getMetabolitesX() [2/2]

const CDataVector< CMetab > & CModel::getMetabolitesX ( ) const

Retrieves the vector of metabolites at it is used in the reduced model.

Returns: const CDataVectorN< CMetab > &metabolites

References mMetabolitesX.

Referenced by CSSAMethod::buildKineticMatrix(), CReactionInterface::createUndoData(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportODEs(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CODEExporter::preprocess(), CODEExporterC::preprocess(), CILDMMethod::printResult(), CILDMModifiedMethod::printResult(), CLNAMethod::resizeAllMatrices(), CMCAMethod::resizeAllMatrices(), CILDMMethod::setAnnotationM(), and CILDMModifiedMethod::setAnnotationM().

◆ getModelParameterSets() [1/2]

CDataVectorN< CModelParameterSet > & CModel::getModelParameterSets ( )

References mParameterSets.

◆ getModelParameterSets() [2/2]

const CDataVectorN< CModelParameterSet > & CModel::getModelParameterSets ( ) const

Return the non model parameter sets

Returns: CDataVectorN< CModelParameterSet > & modelParameterSets

References mParameterSets.

Referenced by CFitProblem::createParameterSet(), CDataModel::loadModelParameterSets(), ModelHandler::processStart(), ModelParameterSetHandler::processStart(), and CCopasiXML::saveModelParameterSets().

◆ getModelType()

const CModel::ModelType & CModel::getModelType ( ) const

Retrieve the type of the model.

Returns: const ModelType & modelType

References mType.

Referenced by CMathObject::compilePropensity(), CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ getModelValues() [1/2]

CDataVectorN< CModelValue > & CModel::getModelValues ( )

References mValues.

◆ getModelValues() [2/2]

const CDataVectorN< CModelValue > & CModel::getModelValues ( ) const

Return the non concentration values of this model

Returns: CDataVectorN< CModelValue > & values

References mValues.

Referenced by CModelAdd::addModelValues(), CModelAdd::addModelValuesExpressions(), changeUnitExpressionSymbols(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForPiecewiseFunctions(), CModelAnalyzer::checkReaction(), clearSbmlIds(), CSBMLExporter::collectIds(), CReactionInterface::connectNonMetabolites(), SEDMLUtils::createAmountMV(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCModelValueFromParameter(), CModelParameterSet::createFromModel(), CSBMLExporter::createParameters(), CSBMLExporter::createSBMLDocument(), CReactionInterface::createUndoData(), CDataModel::exportMathModel(), CDataModel::exportMathModelToString(), CODEExporter::exportModelValues(), CODEExporter::exportModelValuesExpressions(), CODEExporterC::exportTitleData(), CModelExpansion::SetOfModelElements::fillComplete(), CSBMLExporter::findAvogadro(), CDataModel::findObjectByDisplayName(), CObjectLists::getListOfConstObjects(), SEDMLUtils::getObjectForSbmlId(), CExpressionGenerator::getObjectsForSelection(), getQuantityParameterOrValue(), CReactionInterface::getUnit(), getUnitSymbolUsage(), getUsedUnits(), CReactionInterface::isLocked(), CSBMLExporter::isModelSBMLCompatible(), CTSSAMethod::isValidProblem(), CModelMerging::mergeMetabolites(), CODEExporter::preprocess(), CODEExporterC::preprocess(), ModelValueHandler::processStart(), removeModelValue(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModel(), CCopasiXML::saveModel(), SBMLImporter::setInitialValues(), CReactionInterface::writeBackToReaction(), and CMMLOutput::writeDifferentialEquations().

◆ getMoieties()

const CDataVector< CMoiety > & CModel::getMoieties ( ) const

Return the mMoieties of this model

Returns: CDataVectorN < CMoiety > &

References mMoieties.

Referenced by CMathContainer::allocate(), CMathContainer::initializeObjects(), and CMoietiesProblem::printResult().

◆ getNumAssignmentMetabs()

size_t CModel::getNumAssignmentMetabs ( ) const

Get the number of metabolites determined by assignments

Returns: size_t dimension

References mNumMetabolitesAssignment.

Referenced by CLNAMethod::isValidProblem(), and CTSSAMethod::isValidProblem().

◆ getNumber2QuantityFactor()

const C_FLOAT64 & CModel::getNumber2QuantityFactor ( ) const

Get the conversion factor number -> quantity

References mNumber2QuantityFactor.

Referenced by CTimeSeries::compile(), CMetab::convertToConcentration(), CReactionInterface::createUndoData(), CILDMMethod::deuflhard(), CMoiety::initConversionFactor(), CILDMMethod::newton(), CModelParameterSpecies::setValue(), CCSPMethod::start(), and CTSSAMethod::start().

◆ getNumDependentReactionMetabs()

size_t CModel::getNumDependentReactionMetabs ( ) const

Get the number of dependent metabolites determined by reactions

Returns: size_t dimension

References mNumMetabolitesReaction, and mNumMetabolitesReactionIndependent.

Referenced by CMathContainer::allocate(), initializeAtolVector(), CCSPMethod::initializeOutput(), and CCSPMethod::setAnnotationM().

◆ getNumIndependentReactionMetabs()

size_t CModel::getNumIndependentReactionMetabs ( ) const

Get the number of independent metabolites determined by reactions

Returns: size_t dimension

References mNumMetabolitesReactionIndependent.

Referenced by CMathContainer::allocate(), CSSAMethod::buildKineticMatrix(), CMCAMethod::createLinkMatrix(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportODEs(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CCSPMethod::initializeOutput(), and CCSPMethod::setAnnotationM().

◆ getNumMetabs()

size_t CModel::getNumMetabs ( ) const

Get the number of total metabolites

Returns: C_INT32 totMetab

References mMetabolitesX, and CDataVector< CType >::size().

Referenced by CMathContainer::allocate(), and CODEExporter::exportModelValuesExpressions().

◆ getNumModelValues()

size_t CModel::getNumModelValues ( ) const

Get the number of non concentration values

Returns: C_INT32

References mValues, and CDataVector< CType >::size().

Referenced by CODEExporter::exportModelValuesExpressions().

◆ getNumODEMetabs()

size_t CModel::getNumODEMetabs ( ) const

Get the number of metabolites determined by ODEs

Returns: size_t dimension

References mNumMetabolitesODE.

Referenced by CMathContainer::allocate(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportODEs(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CLNAMethod::isValidProblem(), and CTSSAMethod::isValidProblem().

◆ getNumVariableMetabs()

size_t CModel::getNumVariableMetabs ( ) const

Get the number of variable metabolites

Returns: size_t totMetab

References mNumMetabolitesAssignment, mNumMetabolitesODE, and mNumMetabolitesReaction.

◆ getParticleFlux()

const CVector< C_FLOAT64 > & CModel::getParticleFlux ( ) const

Retrieve the vector of particle fluxes from the model

Returns: const CVector< C_FLOAT64 > & particleFlux

References mParticleFluxes.

◆ getQuantity2NumberFactor()

const C_FLOAT64 & CModel::getQuantity2NumberFactor ( ) const

Get the conversion factor quantity -> number

References mQuantity2NumberFactor.

Referenced by addParticleNumberToInitialValueMap(), CSteadyStateMethod::allPositive(), CMetab::calculate(), CMetab::convertToNumber(), CSBMLExporter::createAvogadroIfNeeded(), SBMLImporter::createCModelFromSBMLDocument(), createMetabolite(), CReactionInterface::createUndoData(), CSBMLExporter::exportEventAssignments(), CODEExporter::exportExpression(), CSBMLExporter::findAvogadro(), getQuantityParameterOrValue(), CLsodaMethod::initializeParameter(), SBMLImporter::preprocessNode(), CSBMLExporter::replaceSpeciesReferences(), SBMLImporter::setInitialValues(), CModelParameterSpecies::setValue(), and CTSSAMethod::start().

◆ getQuantityUnit()

const std::string CModel::getQuantityUnit ( ) const

Get the current quantity unit of the model

Returns: const CUnit & quantityunit

References mQuantityUnit.

Referenced by CSBMLExporter::createSubstanceUnit(), CCopasiXML::fixBuild18(), CReactionInterface::getAmountRateUnit(), CReaction::getChildObjectUnits(), CMetab::getChildObjectUnits(), CReactionInterface::getConcentrationRateUnit(), CReaction::getKineticLawUnit(), CReactionInterface::getUnit(), CReactionInterface::getUnitVector(), and CSBMLExporter::replaceSpeciesReferences().

◆ getQuantityUnitName()

std::string CModel::getQuantityUnitName ( ) const

Get the unit for quantities

Returns: std::string quantityUnit

References mQuantityUnit.

Referenced by CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ getReactions() [1/2]

CDataVectorNS< CReaction > & CModel::getReactions ( )

Return the vector of reactions

Returns: CDataVectorNS <CReaction> & reactions

References mSteps.

Referenced by CModelAdd::addReactions(), CMathContainer::allocate(), CSBMLExporter::assignSBMLIdsToReactions(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSBMLExporter::checkForPiecewiseFunctions(), CFixLocalReactionParameters::checkModel(), CHybridMethod::checkModel(), CHybridMethodODE45::checkModel(), CModelAnalyzer::checkModel(), clearSbmlIds(), CSBMLExporter::collectIds(), CMathContainer::compile(), convert2NonReversible(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCReactionFromReaction(), CModelParameterSet::createFromModel(), CSBMLExporter::createReactions(), CSBMLExporter::createSBMLDocument(), CCSPMethod::CSPOutput(), CODEExporter::exportExpression(), CODEExporterC::exportKineticFunctionGroup(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CModelExpansion::SetOfModelElements::fillComplete(), CDataModel::findObjectByDisplayName(), CCopasiXML::fixBuild113(), CObjectLists::getListOfConstObjects(), SEDMLUtils::getObjectForSbmlId(), CExpressionGenerator::getObjectsForSelection(), CEFMAlgorithm::initialize(), CSSAMethod::initialize(), CMathContainer::initializeObjects(), CCSPMethod::initializeOutput(), CEFMMethod::isValidProblem(), CLNAMethod::isValidProblem(), CMMLOutput::listReactionsForMetab(), CModelMerging::mergeMetabolites(), CODEExporter::preprocess(), CODEExporterC::preprocess(), CCSPMethod::printResult(), CILDMMethod::printResult(), ReactionHandler::processStart(), removeReaction(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModel(), CMCAMethod::resizeAllMatrices(), CCopasiXML::saveModel(), CCSPMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), and CLLayoutRenderer::update_associations().

◆ getReactions() [2/2]

const CDataVectorNS< CReaction > & CModel::getReactions ( ) const

Return the vector of reactions

Returns: const CDataVectorS <CReaction> & reactions

References mSteps.

◆ getReactionsPerSpecies()

const std::set< std::pair< const CReaction *, C_FLOAT64 > > & CModel::getReactionsPerSpecies ( const CMetab * pSpecies ) const

Return the vector of reaction indices for a species

Returns: const std::vector <size_t> mReactionsPerSpecies

References mReactionsPerSpecies.

Referenced by CMathObject::compileTransitionTime(), CMathObject::createExtensiveReactionNoiseExpression(), and CMathObject::createExtensiveReactionRateExpression().

◆ getRedStoi()

const CMatrix< C_FLOAT64 > & CModel::getRedStoi ( ) const

Get the Reduced Stoichiometry Matrix of this Model

References mRedStoi.

Referenced by CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CMCAMethod::createLinkMatrix(), CODEExporter::exportExpression(), CODEExporter::exportReacParamsAndFuncs(), CMathContainer::getStoichiometry(), CSSAMethod::initialize(), CEFMMethod::isValidProblem(), and CILDMMethod::step().

◆ getRedStoiAnnotation()

const CDataArray * CModel::getRedStoiAnnotation ( ) const

Returns: Get the matrix annotation to the reduced stoichiometry matrix.

References mpRedStoiAnnotation.

◆ getStateTemplate()

const CStateTemplate & CModel::getStateTemplate ( ) const

Retrieve the state template

Returns: const CModel::CStateTemplate & stateTemplate

References mStateTemplate.

Referenced by CMathContainer::allocate(), CFixLocalReactionParameters::checkModel(), CCSPMethod::CSPOutput(), CMathContainer::initializeObjects(), CCSPMethod::initializeOutput(), CCSPMethod::printResult(), CCopasiXML::saveModel(), and CCSPMethod::setAnnotationM().

◆ getStoi()

const CMatrix< C_FLOAT64 > & CModel::getStoi ( ) const

Get the stoichiometry matrix of this model

Get the reordered stoichiometry matrix of this model

References mStoi.

Referenced by CHybridMethod::checkModel(), CHybridMethodODE45::checkModel(), CMCAMethod::createLinkMatrix(), CMathContainer::getStoichiometry(), and CEFMAlgorithm::initialize().

◆ getStoiAnnotation()

const CDataArray * CModel::getStoiAnnotation ( ) const

Returns: Get the matrix annotation to the stoichiometry matrix.

References mpStoiAnnotation.

◆ getTime()

const C_FLOAT64 & CModel::getTime ( ) const

Retrieve the actual model time

Returns: const C_FLOAT64 & time

References CModelEntity::mValue.

Referenced by CExperiment::calculateStatistics().

◆ getTimeUnit()

const std::string & CModel::getTimeUnit ( ) const

Get the current time unit of the model

Returns: const CUnit & timeunit

References mTimeUnit.

Referenced by CSBMLExporter::createTimeUnit(), CCopasiXML::fixBuildBefore104(), CReactionInterface::getAmountRateUnit(), CReaction::getChildObjectUnits(), CMetab::getChildObjectUnits(), CModelEntity::getChildObjectUnits(), CReactionInterface::getConcentrationRateUnit(), CReaction::getKineticLawUnit(), CEvaluationNodeDelay::getUnit(), and CEvaluationNodeDelay::setUnit().

◆ getTimeUnitName()

std::string CModel::getTimeUnitName ( ) const

Get the unit for time

Returns: std::string timeUnit

References mTimeUnit.

Referenced by CCSPMethod::printResult(), CILDMMethod::printResult(), CILDMModifiedMethod::printResult(), CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ getTotSteps()

size_t CModel::getTotSteps ( ) const

Get the total steps

Returns: size_t total steps;

References mSteps, and CDataVector< CType >::size().

Referenced by CModelAnalyzer::checkModel().

◆ getTreesWithDiscontinuities()

std::vector< const CEvaluationTree * > CModel::getTreesWithDiscontinuities ( ) const

generates a string that contains a text description of all model parameters (initial values and reaction parameters) List all trees which introduce discrete changes.

Returns: std::vector< const CEvaluationTree * > treesWithDiscontinuities

References CVectorCore< CType >::array(), CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), CDataVector< CType >::end(), CStateTemplate::getEntities(), mEvents, mStateTemplate, mSteps, CModelEntity::ODE, and CStateTemplate::size().

Referenced by CMathContainer::createDiscontinuityEvents().

◆ getUnits()

const std::string CModel::getUnits ( ) const

virtual

Retrieve the units of the object.

Returns: std::string units

Reimplemented from CDataContainer.

References mTimeUnit.

Referenced by CReactionInterface::getUnit().

◆ getUnitSymbolUsage()

CDataObject::DataObjectSet CModel::getUnitSymbolUsage ( std::string symbol ) const

References CDataVector< CType >::begin(), CDataVector< CType >::end(), getModelValues(), getUsedSymbolCount(), CUnit::getUsedSymbols(), mAreaUnit, mLengthUnit, mQuantityUnit, mTimeUnit, mVolumeUnit, and CUnit::setExpression().

Referenced by CCopasiXML::saveUnitDefinitionList().

◆ getUsedUnits()

std::map< std::string, CUnit > CModel::getUsedUnits ( ) const

References CDataVector< CType >::begin(), CDataVector< CType >::end(), getModelValues(), mAreaUnit, mLengthUnit, mQuantityUnit, mTimeUnit, and mVolumeUnit.

◆ getVolumeUnit()

const std::string & CModel::getVolumeUnit ( ) const

Get the current volume unit of the model

Returns: const CUnit & volumeunit

References mVolumeUnit.

Referenced by CSBMLExporter::createVolumeUnit(), CReactionInterface::getConcentrationRateUnit(), CReaction::getKineticLawUnit(), CReactionInterface::getUnit(), CCompartment::getUnits(), and CReactionInterface::getUnitVector().

◆ getVolumeUnitName()

std::string CModel::getVolumeUnitName ( ) const

Get the unit for volumes

Returns: std::string volumeUnit

References mVolumeUnit.

Referenced by CCopasiXML::saveModel(), and CCopasiXML::saveModelParameterSets().

◆ handleUnusedMetabolites()

bool CModel::handleUnusedMetabolites ( )

private

Handles unused metabolites and moves them to the end of mMetabolites. Rows of the stoichiometry matrix dealing with unused metabolites are removed.

Returns: bool found

References CMatrix< CType >::array(), CDataVector< CType >::begin(), C_FLOAT64, min, mMetabolitesX, mNumMetabolitesAssignment, mNumMetabolitesODE, mNumMetabolitesReaction, mNumMetabolitesUnused, mStoi, CMatrix< CType >::numCols(), and CMatrix< CType >::numRows().

Referenced by buildStoi().

◆ hasReversibleReaction()

bool CModel::hasReversibleReaction ( ) const

Check whether the model contains reversible reactions

Returns: bool hasReversibleReaction

References mSteps, and CDataVector< CType >::size().

◆ initializeAtolVector()

CVector< C_FLOAT64 > CModel::initializeAtolVector	(	const C_FLOAT64 &	baseTolerance,
		const bool &	reducedModel
	)		const

Initialize a vector of individual absolute tolerances

Parameters

const	C_FLOAT64 & baseTolerance
const	bool & reducedModel

Returns: CVector< C_FLOAT64 > absoluteTolerances

References CVectorCore< CType >::array(), CStateTemplate::beginIndependent(), C_FLOAT64, CMetab::getCompartment(), CModelEntity::getInitialValue(), getNumDependentReactionMetabs(), CStateTemplate::getNumIndependent(), max, min, mQuantity2NumberFactor, mStateTemplate, CVector< CType >::resize(), and CVectorCore< CType >::size().

◆ initializeMetabolites()

void CModel::initializeMetabolites ( )

This function must be called to initialize the vector of Metabolites after finishing adding metabolites to compartments.

References CDataVector< CType >::add(), CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), CDataVector< CType >::clear(), CDataVector< CType >::end(), fatalError, CModelEntity::FIXED, mCompartments, mMetabolitesX, mNumMetabolitesAssignment, mNumMetabolitesODE, mNumMetabolitesReaction, mNumMetabolitesUnused, CModelEntity::ODE, and CModelEntity::REACTIONS.

Referenced by buildStoi(), CModel(), load(), CModelExpansion::replaceInMetab(), and CMetab::setCompartment().

◆ initObjects()

void CModel::initObjects ( )

private

◆ isAutonomous()

const bool & CModel::isAutonomous ( ) const

Check whether the model is autonomous

Returns: const bool &isAutonomous

References mIsAutonomous.

◆ isCompileNecessary()

const bool & CModel::isCompileNecessary ( ) const

Check whether a model compile is necessary.

Returns: const bool & isCompileNecessary

References mCompileIsNecessary.

◆ isStateVariable()

bool CModel::isStateVariable ( const CDataObject * pObject ) const

Check whether the given object is a part of state variable

Parameters

const CDataObject * pObject

Returns: bool isStateVariable

References CStateTemplate::beginIndependent(), CStateTemplate::endDependent(), CObjectLists::getEventTargets(), CDataObject::getObjectParent(), and mStateTemplate.

◆ load()

C_INT32 CModel::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 CDataVector< CType >::add(), C_INT32, CDataVector< CType >::cleanup(), compile(), CRootContainer::getFunctionList(), CDataContainer::getIndex(), CCopasiMessage::getLastMessage(), CCopasiException::getMessage(), CCopasiMessage::getNumber(), CDataObject::getObjectDataModel(), CReadConfig::getVariable(), initializeMetabolites(), CDataVectorS< CType >::load(), CDataVectorNS< CType >::load(), CReadConfig::LOOP, mCompartments, MCReadConfig, CModelEntity::mIValue, mMetabolites, mSteps, CCore::ParticleNumbers, CDataModel::pOldMetabolites, CReadConfig::SEARCH, setCompileFlag(), CAnnotation::setNotes(), CDataObject::setObjectName(), setQuantityUnit(), setTimeUnit(), setVolumeUnit(), CCopasiMessage::size(), and CDataVector< CType >::size().

Referenced by CDataModel::loadModel().

◆ operator=()

CModel& CModel::operator= ( const CModel & src )

private

◆ prepareElasticity()

CEvaluationNode * CModel::prepareElasticity	(	const CReaction *	pReaction,
		const CModelEntity *	pVar,
		bool	simplify
	)

References CCopasiNode< _Data >::addChild(), CEvaluationNode::CN, CEvaluationNodeObject::compile(), CExpression::compile(), CDerive::compileTree(), CDerive::deleteBranch(), CDerive::deriveBranch(), CDataObject::getCN(), CMetab::getConcentrationReference(), CReaction::getFunction(), CReaction::getMap(), CFunctionParameterMap::getObjects(), CDataContainer::getObjects(), CEvaluationTree::getRoot(), CReaction::isReversible(), CEvaluationNode::MINUS, CDerive::multiply(), CEvaluationTree::setRoot(), and CCallParameters< Type >::size().

◆ refreshActiveParameterSet()

void CModel::refreshActiveParameterSet ( )

refresh the active parameter set from the model initial values

References mParameterSet, and CModelParameterSet::refreshFromModel().

Referenced by stateToIntialState(), and updateInitialValues().

◆ removeCompartment() [1/3]

bool CModel::removeCompartment	(	const CCompartment *	pCompartment,
		const bool &	recursive = `true`
	)

Remove a Compartment from the model

References C_INVALID_INDEX, mCompartments, mCompileIsNecessary, removeDataObject(), and removeDependentModelObjects().

◆ removeCompartment() [2/3]

bool CModel::removeCompartment	(	const size_t	index,
		const bool &	recursive = `true`
	)

Remove a Compartment from the model

References getCompartments().

Referenced by removeCompartment(), removeDependentModelObjects(), and CModelExpansion::replaceInModel().

◆ removeCompartment() [3/3]

bool CModel::removeCompartment	(	const std::string &	key,
		const bool &	recursive = `true`
	)

Remove a Compartment from the model

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and removeCompartment().

◆ removeDataObject()

void CModel::removeDataObject ( const CDataObject * pObject )

private

Remove a data container from the model

Parameters

const CDataObject * pObject

References mpMathContainer, mStructuralDependencies, CMathContainer::removeDataObject(), and CMathDependencyGraph::removeObject().

Referenced by removeCompartment(), removeDependentModelObjects(), removeEvent(), removeFunction(), removeMetabolite(), removeModelValue(), and removeReaction().

◆ removeDependentModelObjects()

void CModel::removeDependentModelObjects	(	const ObjectSet &	deletedObjects,
		const bool &	onlyStructural = `false`
	)

Remove all model objects which depend on the deleted objects

Parameters

const	CDataObject::ObjectSet & deletedObjects
const	bool & onlyStructural (default: false)

References appendAllDependents(), removeCompartment(), removeDataObject(), removeEvent(), removeMetabolite(), removeModelValue(), and removeReaction().

Referenced by removeCompartment(), removeFunction(), removeLocalReactionParameter(), removeMetabolite(), removeModelValue(), and removeReaction().

◆ removeEvent() [1/3]

bool CModel::removeEvent	(	const CEvent *	pEvent,
		const bool &	recursive = `true`
	)

Remove an event from the model

Parameters

const	CEvent * pEvent
const	bool & recursive (default: true)

Returns: bool success

References C_INVALID_INDEX, clearMoieties(), mCompileIsNecessary, mEvents, and removeDataObject().

◆ removeEvent() [2/3]

bool CModel::removeEvent	(	const size_t	index,
		const bool &	recursive = `true`
	)

Remove an event from the model

Parameters

const	size_t index
const	bool & recursive (default: true)

Returns: bool success

References mEvents.

Referenced by removeDependentModelObjects(), removeEvent(), and CModelExpansion::replaceInModel().

◆ removeEvent() [3/3]

bool CModel::removeEvent	(	const std::string &	key,
		const bool &	recursive = `true`
	)

Remove an event from the model

Parameters

const	std::string & key
const	bool & recursive (default: true)

Returns: bool success

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and removeEvent().

◆ removeFunction()

bool CModel::removeFunction	(	const CFunction *	pFunction,
		const bool &	recursive = `true`
	)

References mCompileIsNecessary, removeDataObject(), and removeDependentModelObjects().

◆ removeLocalReactionParameter()

bool CModel::removeLocalReactionParameter	(	const std::string &	key,
		const bool &	recursive = `true`
	)

Remove a local reaction parameter from the model

References CKeyFactory::get(), CRootContainer::getKeyFactory(), CDataContainer::insert(), and removeDependentModelObjects().

◆ removeMetabolite() [1/3]

bool CModel::removeMetabolite	(	const CMetab *	pMetabolite,
		const bool &	recursive = `true`
	)

References clearMoieties(), CKeyFactory::get(), CModelEntity::getKey(), CRootContainer::getKeyFactory(), mCompileIsNecessary, mMetabolites, mMetabolitesX, pdelete, CDataVector< CType >::remove(), removeDataObject(), and removeDependentModelObjects().

◆ removeMetabolite() [2/3]

bool CModel::removeMetabolite	(	const size_t	index,
		const bool &	recursive = `true`
	)

References getMetabolites(), and removeMetabolite().

◆ removeMetabolite() [3/3]

bool CModel::removeMetabolite	(	const std::string &	key,
		const bool &	recursive = `true`
	)

References CKeyFactory::get(), and CRootContainer::getKeyFactory().

Referenced by removeDependentModelObjects(), removeMetabolite(), CModelExpansion::replaceInModel(), and CModelMerging::simpleCall().

◆ removeModelEntity()

void CModel::removeModelEntity ( const CModelEntity * pModelEntity )

Remove a model entity to the model

Parameters

const CModelEntity * pModelEntity

References mStateTemplate, and CStateTemplate::remove().

Referenced by CModelEntity::setObjectParent(), and CModelEntity::~CModelEntity().

◆ removeModelValue() [1/3]

bool CModel::removeModelValue	(	const CModelValue *	pModelValue,
		const bool &	recursive = `true`
	)

References C_INVALID_INDEX, mCompileIsNecessary, mValues, removeDataObject(), and removeDependentModelObjects().

Referenced by SBMLImporter::createCModelFromSBMLDocument(), CSBMLExporter::createSBMLDocument(), removeDependentModelObjects(), removeModelValue(), and CModelExpansion::replaceInModel().

◆ removeModelValue() [2/3]

bool CModel::removeModelValue	(	const size_t	index,
		const bool &	recursive = `true`
	)

References getModelValues(), and removeModelValue().

◆ removeModelValue() [3/3]

bool CModel::removeModelValue	(	const std::string &	key,
		const bool &	recursive = `true`
	)

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and removeModelValue().

◆ removeReaction() [1/3]

bool CModel::removeReaction	(	const CReaction *	pReaction,
		const bool &	recursive = `true`
	)

Remove a reaction from the model using its pointer

References C_INVALID_INDEX, clearMoieties(), mCompileIsNecessary, mSteps, removeDataObject(), and removeDependentModelObjects().

Referenced by removeDependentModelObjects(), removeReaction(), and CModelExpansion::replaceInModel().

◆ removeReaction() [2/3]

bool CModel::removeReaction	(	const size_t	index,
		const bool &	recursive = `true`
	)

Remove a reaction from the model using its index

References getReactions(), and removeReaction().

◆ removeReaction() [3/3]

bool CModel::removeReaction	(	const std::string &	key,
		const bool &	recursive = `true`
	)

Remove a reaction from the model using its key

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and removeReaction().

◆ replaceInExpressions()

void CModel::replaceInExpressions	(	const std::string &	oldStr,
		const std::string &	newStr
	)

private

Replace the old string with the new string in all expressions in the model

Parameters

const	std::string & oldStr
const	std::string & newStr

References CDataVector< CType >::begin(), CDataVector< CType >::end(), mCompartments, mEvents, mMetabolitesX, mValues, and stringReplace().

Referenced by convert2NonReversible().

◆ setAreaUnit()

bool CModel::setAreaUnit ( const std::string & name )

Set the unit for areas.

Parameters

const std::string & name

Returns: bool success

References mAreaUnit, and CUnit::prettyPrint().

Referenced by applyData(), SBMLUnitSupport::checkElementUnits(), SBMLImporter::createCModelFromSBMLDocument(), SBMLUnitSupport::importUnitsFromSBMLDocument(), and ModelHandler::processStart().

◆ setAvogadro()

void CModel::setAvogadro	(	const C_FLOAT64 &	avogadro,
		const CCore::Framework &	frameWork
	)

Set the Avogadro number used for the model.

Parameters

const C_FLOAT64 & avogadro

References mAvogadro, mQuantityUnit, and setQuantityUnit().

Referenced by applyData(), SBMLUnitSupport::importUnitsFromSBMLDocument(), and ModelHandler::processStart().

◆ setCompileFlag()

void CModel::setCompileFlag ( bool flag = true )

This must be called whenever something is changed in the model that would make it necessary to recalculate the matrix decomposition

References mCompileIsNecessary.

Referenced by CStateTemplate::add(), CReaction::addParameterObject(), CEventAssignment::applyData(), CEvent::applyData(), CReaction::applyData(), CModelEntity::applyData(), CEventAssignment::CEventAssignment(), convert2NonReversible(), forceCompile(), functionDefinitionChanged(), CEvent::initObjects(), load(), ModelHandler::processEnd(), CStateTemplate::remove(), CDataModel::reparameterizeFromIniFile(), CModelExpansion::replaceInMetab(), CMetab::setCompartment(), CEvent::setDelayAssignment(), CEvent::setDelayExpression(), CEvent::setDelayExpressionPtr(), CEventAssignment::setExpression(), CModelEntity::setExpression(), CEventAssignment::setExpressionPtr(), CModelEntity::setExpressionPtr(), CEvent::setFireAtInitialTime(), CModelEntity::setHasNoise(), CReaction::setHasNoise(), CModelEntity::setInitialExpression(), CModelEntity::setInitialExpressionPtr(), CModelEntity::setNoiseExpression(), CReaction::setNoiseExpression(), CModelEntity::setNoiseExpressionPtr(), CReaction::setNoiseExpressionPtr(), CEventAssignment::setObjectParent(), CEvent::setObjectParent(), CReaction::setParameterObjects(), CEvent::setPersistentTrigger(), CEvent::setPriorityExpression(), CEvent::setPriorityExpressionPtr(), CModelEntity::setStatus(), CEventAssignment::setTargetCN(), CEvent::setTriggerExpression(), CEvent::setTriggerExpressionPtr(), CEvent::~CEvent(), CEventAssignment::~CEventAssignment(), and CReaction::~CReaction().

◆ setInitialTime()

void CModel::setInitialTime ( const C_FLOAT64 & time )

Return a pointer to the current time Set the start time for modeling

Parameters

const C_FLOAT64 & time

References CModelEntity::mIValue, and time.

Referenced by SEDMLImporter::updateCopasiTaskForSimulation().

◆ setLengthUnit()

bool CModel::setLengthUnit ( const std::string & name )

Set the unit for lengths.

Parameters

const std::string & name

Returns: bool success

References mLengthUnit, and CUnit::prettyPrint().

Referenced by applyData(), SBMLUnitSupport::checkElementUnits(), SBMLImporter::createCModelFromSBMLDocument(), SBMLUnitSupport::importUnitsFromSBMLDocument(), and ModelHandler::processStart().

◆ setModelType()

void CModel::setModelType ( const ModelType & modelType )

Get the unit for quantities

Returns: CModel::QuantityUnit quantityUnit Set the type of the model

Parameters

const ModelType & modelType

References mType.

Referenced by applyData(), SBMLImporter::createCModelFromSBMLDocument(), and ModelHandler::processStart().

◆ setObjectParent()

bool CModel::setObjectParent ( const CDataContainer * pParent )

virtual

Set the object parent

Parameters

const CDataContainer * pParent

Returns: bool success

Reimplemented from CModelEntity.

References CDataObject::setObjectParent().

Referenced by CDataModel::commonAfterLoad().

◆ setQuantityUnit()

bool CModel::setQuantityUnit	(	const std::string &	name,
		const CCore::Framework &	frameWork
	)

Set the unit for quantities. If COPASI recognizes the unit the conversion factors are set accordingly and true is returned.

Parameters

const std::string & name

Returns: bool success

References CBaseUnit::avogadro, CBaseUnit::dimensionless, CUnit::getComponents(), CUnit::isDimensionless(), CUnit::isUndefined(), mAvogadro, mNumber2QuantityFactor, mQuantity2NumberFactor, mQuantityUnit, CUnit::prettyPrint(), and updateInitialValues().

Referenced by applyData(), SBMLUnitSupport::checkElementUnits(), CModel(), SBMLImporter::createCModelFromSBMLDocument(), CCopasiXML::fixBuild18(), SBMLUnitSupport::importUnitsFromSBMLDocument(), load(), ModelHandler::processStart(), and setAvogadro().

◆ setTime()

void CModel::setTime ( const C_FLOAT64 & time )

Set the actual model time

Parameters

const C_FLOAT64 & time

References CModelEntity::mValue, and time.

◆ setTimeUnit()

bool CModel::setTimeUnit ( const std::string & name )

Set the unit for time. If COPASI recognizes the unit the conversion factors are set accordingly and true is returned.

Parameters

const std::string & name

Returns: bool success

References mTimeUnit, and CUnit::prettyPrint().

Referenced by applyData(), SBMLUnitSupport::checkElementUnits(), SBMLImporter::createCModelFromSBMLDocument(), CCopasiXML::fixBuildBefore104(), SBMLUnitSupport::importUnitsFromSBMLDocument(), load(), and ModelHandler::processStart().

◆ setVolumeUnit()

bool CModel::setVolumeUnit ( const std::string & name )

Set the unit for volumes. If COPASI recognizes the unit the conversion factors are set accordingly and true is returned.

Parameters

const std::string & name

Returns: bool success

References mVolumeUnit, and CUnit::prettyPrint().

Referenced by applyData(), SBMLUnitSupport::checkElementUnits(), SBMLImporter::createCModelFromSBMLDocument(), SBMLUnitSupport::importUnitsFromSBMLDocument(), load(), and ModelHandler::processStart().

◆ stateToIntialState()

void CModel::stateToIntialState ( )

Copy the current state value to the initial state

References CMathContainer::fetchState(), CMathContainer::getState(), mpMathContainer, CCore::ParticleNumbers, CMathContainer::pushInitialState(), refreshActiveParameterSet(), CMathContainer::setInitialState(), and CMathContainer::updateInitialValues().

◆ suitableForStochasticSimulation()

std::string CModel::suitableForStochasticSimulation ( ) const

check if the model is suitable for stochastic simulation

References C_FLOAT64, C_INT32, CModelEntity::getInitialValue(), max, mMetabolites, mSteps, mStoi, CMatrix< CType >::numRows(), and CDataVector< CType >::size().

Referenced by CHybridMethod::isValidProblem(), CStochDirectMethod::isValidProblem(), CStochMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), and CTrajectoryMethodDsaLsodar::isValidProblem().

◆ toData()

CData CModel::toData ( ) const

virtual

Retrieve the data describing the object

Returns: CData data

Reimplemented from CModelEntity.

References CData::addProperty(), CData::AREA_UNIT, CData::AVOGADRO_NUMBER, CData::FRAMEWORK, CCore::FrameworkNames, CData::LENGTH_UNIT, mAreaUnit, mAvogadro, mLengthUnit, CData::MODEL_TYPE, ModelTypeNames, mQuantityUnit, mTimeUnit, mType, mVolumeUnit, CCore::ParticleNumbers, CData::QUANTITY_UNIT, CData::TIME_UNIT, CModelEntity::toData(), CData::VALUE, and CData::VOLUME_UNIT.

◆ updateInitialValues() [1/3]

bool CModel::updateInitialValues ( const CCore::Framework & framework )

Update all initial values.

Parameters

const CCore::Framework & framework

Returns: bool success

References compileIfNecessary(), CMathContainer::fetchInitialState(), mpMathContainer, CMathContainer::pushInitialState(), refreshActiveParameterSet(), and CMathContainer::updateInitialValues().

Referenced by CCompartment::applyData(), CDataModel::changeModelParameter(), CDataModel::commonAfterLoad(), SBMLImporter::setInitialValues(), setQuantityUnit(), SEDMLImporter::updateCopasiTaskForSimulation(), updateInitialValues(), and CModelParameterSet::updateModel().

◆ updateInitialValues() [2/3]

void CModel::updateInitialValues ( const CDataObject * changedObject )

Builds and executes the the update sequence used to calculate all initial values depending on the changed objects For metabolites the initial particle number is updated by default unless itself is in the list of changed objects. In that case the initial concentration is updated.

Parameters

std::set< const CDataObject * > & changedObjects

See also: updateInitialValues(std::set< const CDataObject * > & changedObjects)

References updateInitialValues().

◆ updateInitialValues() [3/3]

void CModel::updateInitialValues ( std::set< const CDataObject * > & changedObjects )

Builds and executes the the update sequence used to calculate all initial values depending on the changed objects. For metabolites the initial particle number is updated by default unless itself is in the list of changed objects. In that case the initial concentration is updated.

Parameters

std::set< const CDataObject * > & changedObjects

See also: buildInitialRefreshSequence(std::set< const CDataObject * > & changedObjects)

References CMathContainer::applyUpdateSequence(), buildInitialRefreshSequence(), compileIfNecessary(), CMathContainer::fetchInitialState(), mpMathContainer, CMathContainer::pushInitialState(), and refreshActiveParameterSet().

◆ updateMatrixAnnotations()

void CModel::updateMatrixAnnotations ( )

private

This updates the annotations of the link matrix and the stoichiometry matrix

References CDataVector< CType >::begin(), mMetabolitesX, mNumMetabolitesODE, MNumMetabolitesReactionDependent, mNumMetabolitesReactionIndependent, mpLinkMatrixAnnotation, mpRedStoiAnnotation, mpStoiAnnotation, mSteps, CDataArray::resize(), CDataArray::setAnnotation(), and CDataArray::setCopasiVector().

Referenced by compile().

◆ updateMoietyValues()

void CModel::updateMoietyValues ( )

private

compute the actual initial value of all moieties (from the initial values of the metabolites).

References CDataVector< CType >::begin(), CDataVector< CType >::end(), and mMoieties.

Referenced by buildMoieties().

Friends And Related Function Documentation

◆ CFunctionDB

friend class CFunctionDB

friend

Member Data Documentation

◆ mActiveParameterSetKey

std::string CModel::mActiveParameterSetKey

private

The key of the currently active parameter set.

Referenced by applyActiveParameterSet().

◆ mAreaUnit

std::string CModel::mAreaUnit

private

The volume unit used in the Model

Referenced by changeUnitExpressionSymbols(), createUndoData(), getAreaUnit(), getAreaUnitName(), getUnitSymbolUsage(), getUsedUnits(), setAreaUnit(), and toData().

◆ mAvogadro

C_FLOAT64 CModel::mAvogadro

private

The Avogadro number used for this model.

Referenced by createUndoData(), getAvogadro(), setAvogadro(), setQuantityUnit(), and toData().

◆ mBuildInitialSequence

bool CModel::mBuildInitialSequence

private

A Boolean value indicating whether we need to rebuild the initial value refresh sequence

◆ mCompartments

CDataVectorNS< CCompartment > CModel::mCompartments

private

for array of compartments

Referenced by buildDependencyGraphs(), buildStateTemplate(), buildUserOrder(), createCompartment(), createMetabolite(), getCompartments(), initializeMetabolites(), load(), removeCompartment(), and replaceInExpressions().

◆ mCompileIsNecessary

bool CModel::mCompileIsNecessary

private

indicates whether a recalculation of the stoichiometry matrix decomposition is necessary

Referenced by compile(), compileIfNecessary(), createCompartment(), createEvent(), createMetabolite(), createModelValue(), createReaction(), isCompileNecessary(), removeCompartment(), removeEvent(), removeFunction(), removeMetabolite(), removeModelValue(), removeReaction(), and setCompileFlag().

◆ mElasticities

CMatrix< C_FLOAT64 > CModel::mElasticities

private

The elasticity matrix d(Flux_i)/dx_j

◆ mEvents

CDataVectorN< CEvent > CModel::mEvents

private

for array of events

Referenced by buildDependencyGraphs(), compileEvents(), createEvent(), getEvents(), getTreesWithDiscontinuities(), removeEvent(), and replaceInExpressions().

◆ mIsAutonomous

bool CModel::mIsAutonomous

private

A flag indicating whether the model is autonomous.

Referenced by compile(), and isAutonomous().

◆ mJacobianPivot

CVector< size_t > CModel::mJacobianPivot

private

Vector for storing the row interchanges during LU-Decomposition Vector for storing the row and column interchanges needed to calculate the full Jacobian in user order.

Referenced by buildUserOrder().

◆ mL

CLinkMatrix CModel::mL

private

This matrix stores L

Referenced by buildLinkZero(), buildMoieties(), buildRedStoi(), compile(), and getL0().

◆ mLengthUnit

std::string CModel::mLengthUnit

private

The volume unit used in the Model

Referenced by changeUnitExpressionSymbols(), createUndoData(), getLengthUnit(), getLengthUnitName(), getUnitSymbolUsage(), getUsedUnits(), setLengthUnit(), and toData().

◆ mLView

CLinkMatrixView CModel::mLView

private

This is used to return a view to L

Referenced by getL(), and initObjects().

◆ mMetabolites

CDataVector< CMetab > CModel::mMetabolites

private

Vector of reference to metabolites

Referenced by buildDependencyGraphs(), buildUserOrder(), createMetabolite(), findMetabByName(), getMetabolites(), load(), removeMetabolite(), and suitableForStochasticSimulation().

◆ mMetabolitesX

CDataVector< CMetab > CModel::mMetabolitesX

private

Vector of reference to metabolites in reduced model representation

Referenced by buildMoieties(), buildRedStoi(), buildStateTemplate(), buildStoi(), buildUserOrder(), compile(), getMetabolitesX(), getNumMetabs(), handleUnusedMetabolites(), initializeMetabolites(), removeMetabolite(), replaceInExpressions(), and updateMatrixAnnotations().

◆ mMoieties

CDataVector< CMoiety > CModel::mMoieties

private

for array of conserved moieties

Referenced by buildMoieties(), clearMoieties(), findMoiety(), getMoieties(), and updateMoietyValues().

◆ mNumber2QuantityFactor

C_FLOAT64 CModel::mNumber2QuantityFactor

private

Factor to convert from particle number to quantity taking into account the unit for substance quantities

Referenced by getNumber2QuantityFactor(), and setQuantityUnit().

◆ mNumMetabolitesAssignment

size_t CModel::mNumMetabolitesAssignment

private

The number of metabs determined by assignments in the model

Referenced by getNumAssignmentMetabs(), getNumVariableMetabs(), handleUnusedMetabolites(), and initializeMetabolites().

◆ mNumMetabolitesODE

size_t CModel::mNumMetabolitesODE

private

The number of metabs determined by ODEs in the model

Referenced by buildMoieties(), buildRedStoi(), buildStoi(), getNumODEMetabs(), getNumVariableMetabs(), handleUnusedMetabolites(), initializeMetabolites(), and updateMatrixAnnotations().

◆ mNumMetabolitesReaction

size_t CModel::mNumMetabolitesReaction

private

The number of metabs determined by reactions in the model

Referenced by buildRedStoi(), buildStoi(), getNumDependentReactionMetabs(), getNumVariableMetabs(), handleUnusedMetabolites(), and initializeMetabolites().

◆ mNumMetabolitesReactionIndependent

size_t CModel::mNumMetabolitesReactionIndependent

private

The number of metabs determined by reactions which can be calculated through moieties

Referenced by buildLinkZero(), buildMoieties(), buildRedStoi(), getNumDependentReactionMetabs(), getNumIndependentReactionMetabs(), and updateMatrixAnnotations().

◆ mNumMetabolitesUnused

size_t CModel::mNumMetabolitesUnused

private

The number of unused metabs in the model

Referenced by handleUnusedMetabolites(), and initializeMetabolites().

◆ ModelTypeNames

const CEnumAnnotation< std::string, CModel::ModelType > CModel::ModelTypeNames

static

String representation of the valid model types.

Referenced by applyData(), createUndoData(), ModelHandler::processStart(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameterSets(), and toData().

◆ mParameterSet

CModelParameterSet CModel::mParameterSet

private

The parameter set of the model itself

Referenced by applyActiveParameterSet(), compile(), getActiveModelParameterSet(), and refreshActiveParameterSet().

◆ mParameterSets

CDataVectorN< CModelParameterSet > CModel::mParameterSets

private

Vector of parameter sets

Referenced by getModelParameterSets().

◆ mParticleFluxes

CVector< C_FLOAT64 > CModel::mParticleFluxes

private

Vectors of fluxes of the reactions.

Referenced by buildStoi(), and getParticleFlux().

◆ mpAvogadroReference

CDataObject* CModel::mpAvogadroReference

private

Referenced by getChildObjectUnits().

◆ mpLinkMatrixAnnotation

CDataArray* CModel::mpLinkMatrixAnnotation

private

Column and Row Annotation for the Link Matrix

Referenced by getLAnnotation(), initObjects(), updateMatrixAnnotations(), and ~CModel().

◆ mpMathContainer

CMathContainer* CModel::mpMathContainer

private

The container of the mathematical model.

Referenced by appendAllDependents(), appendDirectDependents(), applyInitialValues(), buildInitialRefreshSequence(), compile(), createEventsForTimeseries(), getMathContainer(), initObjects(), removeDataObject(), stateToIntialState(), updateInitialValues(), and ~CModel().

◆ mpProcessReport

CProcessReport* CModel::mpProcessReport

private

A pointer to the process report. If not NULL the compile progress is reported to it.

Referenced by buildStoi(), compile(), and compileIfNecessary().

◆ mpQuantity2NumberFactorReference

CDataObject* CModel::mpQuantity2NumberFactorReference

private

Referenced by getChildObjectUnits().

◆ mpRedStoiAnnotation

CDataArray* CModel::mpRedStoiAnnotation

private

Column and Row Annotation for the reduced Stoichiometry Matrix

Referenced by getRedStoiAnnotation(), initObjects(), updateMatrixAnnotations(), and ~CModel().

◆ mpStoiAnnotation

CDataArray* CModel::mpStoiAnnotation

private

Column and Row Annotation for the reduced Stoichiometry Matrix

Referenced by getStoiAnnotation(), initObjects(), updateMatrixAnnotations(), and ~CModel().

◆ mQuantity2NumberFactor

C_FLOAT64 CModel::mQuantity2NumberFactor

private

Factor to convert from quantity to particle number taking into account the unit for substance quantities

Referenced by getQuantity2NumberFactor(), initializeAtolVector(), and setQuantityUnit().

◆ mQuantityUnit

std::string CModel::mQuantityUnit

private

The quantity unit used in the Model

Referenced by changeUnitExpressionSymbols(), CModel(), createUndoData(), getChildObjectUnits(), getQuantityUnit(), getQuantityUnitName(), getUnitSymbolUsage(), getUsedUnits(), setAvogadro(), setQuantityUnit(), and toData().

◆ mReactionsPerSpecies

std::map< const CMetab *, std::set< std::pair< const CReaction *, C_FLOAT64 > > > CModel::mReactionsPerSpecies

private

Vector of species that contains associated reactions

Referenced by buildStoi(), and getReactionsPerSpecies().

◆ mRedStoi

CMatrix< C_FLOAT64 > CModel::mRedStoi

private

Reduced Stoichiometry Matrix

Referenced by buildRedStoi(), getRedStoi(), and initObjects().

◆ mReorderNeeded

bool CModel::mReorderNeeded

private

A flag indicating whether the state template has to be reordered

Referenced by buildStateTemplate().

◆ mStateTemplate

CStateTemplate CModel::mStateTemplate

private

The state template for the model

Referenced by addModelEntity(), buildStateTemplate(), buildUserOrder(), getStateTemplate(), getTreesWithDiscontinuities(), initializeAtolVector(), initObjects(), isStateVariable(), and removeModelEntity().

◆ mSteps

CDataVectorNS< CReaction > CModel::mSteps

private

for array of steps

Referenced by buildDependencyGraphs(), buildStateTemplate(), buildStoi(), createReaction(), getReactions(), getTotSteps(), getTreesWithDiscontinuities(), hasReversibleReaction(), initObjects(), load(), removeReaction(), suitableForStochasticSimulation(), and updateMatrixAnnotations().

◆ mStoi

CMatrix< C_FLOAT64 > CModel::mStoi

private

Stoichiometry Matrix

Referenced by buildLinkZero(), buildRedStoi(), buildStoi(), getStoi(), handleUnusedMetabolites(), initObjects(), and suitableForStochasticSimulation().

◆ mStructuralDependencies

CMathDependencyGraph CModel::mStructuralDependencies

private

The structural dependencies

Referenced by appendAllDependents(), appendDirectDependents(), buildDependencyGraphs(), functionDefinitionChanged(), and removeDataObject().

◆ mTimeUnit

std::string CModel::mTimeUnit

private

The time unit used in the Model

Referenced by changeUnitExpressionSymbols(), createUndoData(), getTimeUnit(), getTimeUnitName(), getUnits(), getUnitSymbolUsage(), getUsedUnits(), setTimeUnit(), and toData().

◆ mType

ModelType CModel::mType

private

The type of the model

Referenced by getModelType(), setModelType(), and toData().

◆ mValues

CDataVectorN< CModelValue > CModel::mValues

private

vector of non concentration values in the model

Referenced by buildDependencyGraphs(), buildStateTemplate(), buildUserOrder(), createModelValue(), getModelValues(), getNumModelValues(), removeModelValue(), and replaceInExpressions().

◆ mVolumeUnit

std::string CModel::mVolumeUnit

private

The volume unit used in the Model

Referenced by changeUnitExpressionSymbols(), createUndoData(), getUnitSymbolUsage(), getUsedUnits(), getVolumeUnit(), getVolumeUnitName(), setVolumeUnit(), and toData().

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Member Enumeration Documentation

◆ DependencyType

◆ ModelType

◆ UnitType

Constructor & Destructor Documentation

◆ CModel() [1/2]

◆ CModel() [2/2]

◆ ~CModel()

Member Function Documentation

◆ addModelEntity()

◆ appendAllDependents() [1/2]

◆ appendAllDependents() [2/2]

◆ appendDirectDependents() [1/2]

◆ appendDirectDependents() [2/2]

◆ applyActiveParameterSet()

◆ applyData()

◆ applyInitialValues()

◆ buildDependencyGraphs()

◆ buildInitialRefreshSequence()

◆ buildLinkZero()

◆ buildMoieties()

◆ buildRedStoi()

◆ buildStateTemplate()

◆ buildStoi()

◆ buildUserOrder()

◆ changeUnitExpressionSymbols()

◆ clearMoieties()

◆ clearSbmlIds()

◆ compile()

◆ compileEvents()

◆ compileIfNecessary()

◆ convert2NonReversible()

◆ createCompartment()

◆ createEvent()

◆ createEventsForTimeseries()

◆ createMetabolite()

◆ createModelValue()

◆ createReaction()

◆ createUndoData()

◆ findMetabByName()

◆ findMoiety()

◆ forceCompile()

◆ fromData()

◆ functionDefinitionChanged()

◆ getActiveModelParameterSet() [1/2]

◆ getActiveModelParameterSet() [2/2]

◆ getAreaUnit()

◆ getAreaUnitName()

◆ getAvogadro()

◆ getChildObjectUnits()

◆ getCompartments() [1/2]

◆ getCompartments() [2/2]

◆ getCorrespondingTransientObject()

◆ getEvents() [1/2]

◆ getEvents() [2/2]

◆ getInitialTime()

◆ getKey()

◆ getL()

◆ getL0()

◆ getLAnnotation()

◆ getLengthUnit()

◆ getLengthUnitName()

◆ getMathContainer() [1/2]

◆ getMathContainer() [2/2]

◆ getMetabolites() [1/2]

◆ getMetabolites() [2/2]

◆ getMetabolitesX() [1/2]

◆ getMetabolitesX() [2/2]

◆ getModelParameterSets() [1/2]

◆ getModelParameterSets() [2/2]

◆ getModelType()

◆ getModelValues() [1/2]