#include <CEFMTask.h>

Inheritance diagram for CEFMTask:

Public Member Functions
	CEFMTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::fluxMode)

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

std::string	getFluxModeDescription (const CFluxMode &fluxMode) const

const std::vector< CFluxMode > &	getFluxModes () const

std::string	getInternalSpecies (const CFluxMode &fluxMode) const

std::string	getNetReaction (const CFluxMode &fluxMode) const

std::string	getReactionEquation (const std::map< size_t, C_FLOAT64 >::const_iterator &itReaction) const

std::pair< C_FLOAT64, C_FLOAT64 >	getSpeciesChanges (const CFluxMode &fluxMode, const CMetab &metab) const

virtual const CTaskEnum::Method *	getValidMethods () const

virtual bool	initialize (const OutputFlag &of, COutputHandler pOutputHandler, std::ostream pOstream)

virtual bool	process (const bool &useInitialValues)

virtual bool	setCallBack (CProcessReportLevel callBack)

virtual	~CEFMTask ()

Public Member Functions inherited from CCopasiTask
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

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

	CCopasiTask (const CDataContainer *pParent, const CTaskEnum::Task &taskType, const std::string &type="Task")

void	cleanup ()

virtual void	clearCallBack ()

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

const CProcessReportLevel &	getCallBack () const

const CDescription &	getDescription () const

virtual const std::string &	getKey () const

CMathContainer *	getMathContainer () const

CCopasiMethod *	getMethod ()

const CCopasiMethod *	getMethod () const

COutputHandler *	getOutputHandler () const

const OutputFlag &	getOutputMode () const

CCopasiProblem *	getProblem ()

const CCopasiProblem *	getProblem () const

CReport &	getReport ()

const CReport &	getReport () const

const CResult &	getResult () const

CCopasiParameterGroup *	getSliders ()

CTaskEnum::Task	getType () const

const bool &	isScheduled () const

const bool &	isUpdateModel () const

virtual void	output (const COutputInterface::Activity &activity)

virtual bool	restore (const bool &updateModel=true)

virtual void	separate (const COutputInterface::Activity &activity)

void	setIgnoreProblemData (const bool &ignoreProblemData)

void	setMathContainer (CMathContainer *pContainer)

bool	setMethodType (const CTaskEnum::Method &type)

void	setScheduled (const bool &scheduled)

void	setType (const CTaskEnum::Task &type)

virtual void	setUpdateModel (const bool &updateModel)

virtual CData	toData () const

virtual bool	updateMatrices ()

virtual	~CCopasiTask ()

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)

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

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 const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

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

virtual void *	getValuePointer () 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)

virtual bool	setObjectParent (const CDataContainer *pParent)

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 ()

Private Member Functions
	CEFMTask ()

std::map< const CMetab *, C_FLOAT64 >	getNetReactionData (const CFluxMode &fluxMode) const

Additional Inherited Members
Public Types inherited from CCopasiTask
enum	eOutputFlagBase { INITIALIZE = 0x01 , STREAM = 0x02 , FINISH = 0x04 , REPORT = 0x10 , PLOT = 0x20 , TIME_SERIES = 0x40 }

enum	OutputFlag { NO_OUTPUT = 0 , OUTPUT_BEFORE = INITIALIZE , OUTPUT_DURING = STREAM , OUTPUT_AFTER = FINISH , OUTPUT = REPORT \| PLOT \| STREAM , OUTPUT_SE = REPORT \| PLOT \| INITIALIZE \| STREAM \| FINISH , OUTPUT_UI = REPORT \| PLOT \| TIME_SERIES \| INITIALIZE \| STREAM \| FINISH , ONLY_TIME_SERIES = TIME_SERIES \| INITIALIZE \| STREAM \| FINISH }

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

Static Public Member Functions inherited from CCopasiTask
static CCopasiTask *	fromData (const CData &data, CUndoObjectInterface *pParent)

static bool	isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)

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 *)

Public Attributes inherited from CCopasiTask
std::string	Error

std::string	Warning

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CCopasiTask
bool	isTaskValid () const

virtual void	signalMathContainerChanged ()

virtual void	signalMethodChanged ()

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 CCopasiTask
CDescription	mDescription

OutputFlag	mDoOutput

bool	mIgnoreProblemData

CVector< C_FLOAT64 >	mInitialState

std::string	mKey

unsigned C_INT32	mOutputCounter

CMathContainer *	mpContainer

CCopasiMethod *	mpMethod

COutputHandler *	mpOutputHandler

CCopasiProblem *	mpProblem

CProcessReportLevel	mProcessReport

CCopasiParameterGroup *	mpSliders

CReport	mReport

CResult	mResult

bool	mScheduled

CTaskEnum::Task	mType

bool	mUpdateModel

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

Constructor & Destructor Documentation

◆ CEFMTask() [1/3]

CEFMTask::CEFMTask ( )

private

Default constructor

◆ CEFMTask() [2/3]

CEFMTask::CEFMTask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = `CTaskEnum::Task::fluxMode`
	)

Specific constructor

Parameters

const CDataContainer * pParent

CEFMTask class.

This class implements a optimization task which is comprised of a of a problem and a method.

References CMethodFactory::create(), CTaskEnum::EFMAlgorithm, CCopasiTask::getType(), and CCopasiTask::mpMethod.

◆ CEFMTask() [3/3]

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

Copy constructor

Parameters

const COptTask & src

◆ ~CEFMTask()

CEFMTask::~CEFMTask ( )

virtual

Destructor

Member Function Documentation

◆ getFluxModeDescription()

std::string CEFMTask::getFluxModeDescription ( const CFluxMode & fluxMode ) const

Retrieve the description of the flux mode

Parameters

const CFluxMode & fluxMode

Returns: std::string fluxModeDescription

References CFluxMode::begin(), C_INT32, CFluxMode::end(), CDataObject::getObjectName(), getReactionIndex(), CCopasiMethod::getSubType(), CSSAMethod::isReactionReversed(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

Referenced by CEFMProblem::printResult().

◆ getFluxModes()

const std::vector< CFluxMode > & CEFMTask::getFluxModes ( ) const

Retrieve the Flux Modes

Returns: const std::vector< CFluxMode > &

References CCopasiTask::mpProblem.

Referenced by CEFMProblem::printResult().

◆ getInternalSpecies()

std::string CEFMTask::getInternalSpecies ( const CFluxMode & fluxMode ) const

Retrieve the internal species for the given flux mode.

Parameters

const CFluxMode & fluxMode

Returns: std::string species

References CMetabNameInterface::getDisplayName(), CMathContainer::getModel(), getNetReactionData(), and CCopasiTask::mpContainer.

Referenced by CEFMProblem::printResult().

◆ getNetReaction()

std::string CEFMTask::getNetReaction ( const CFluxMode & fluxMode ) const

Retrieve the net reaction for the given flux mode.

Parameters

const CFluxMode & fluxMode

Returns: std::string netReaction

References CMetabNameInterface::getDisplayName(), CMathContainer::getModel(), getNetReactionData(), CFluxMode::isReversible(), and CCopasiTask::mpContainer.

Referenced by CEFMProblem::printResult().

◆ getNetReactionData()

std::map< const CMetab *, C_FLOAT64 > CEFMTask::getNetReactionData ( const CFluxMode & fluxMode ) const

private

Retrieve the net reaction data for the given flux mode.

Parameters

const CFluxMode & fluxMode

Returns: std::map< const CMetab *, C_FLOAT64 >g netReactionData

References CDataVector< CType >::begin(), CFluxMode::begin(), CDataVector< CType >::end(), CFluxMode::end(), CReaction::getChemEq(), CChemEq::getProducts(), getSpeciesChanges(), CChemEq::getSubstrates(), and CCopasiTask::mpProblem.

Referenced by getInternalSpecies(), and getNetReaction().

◆ getReactionEquation()

std::string CEFMTask::getReactionEquation ( const std::map< size_t, C_FLOAT64 >::const_iterator & itReaction ) const

Retrieve the reaction equation of the part of the flux mode pointed at by itReaction

Parameters

const std::map< size_t, C_FLOAT64 >::const_iterator & itReaction

Returns: std::string reactionEquation

References CChemEqInterface::getChemEqString(), CEFMProblem::getReorderedReactions(), CCopasiMethod::getSubType(), CSSAMethod::isReactionReversed(), CReaction::isReversible(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

Referenced by CEFMProblem::printResult().

◆ getSpeciesChanges()

std::pair< C_FLOAT64, C_FLOAT64 > CEFMTask::getSpeciesChanges	(	const CFluxMode &	fluxMode,
		const CMetab &	metab
	)		const

Retrieve the species changes for the given flux mode and species

Parameters

const	CFluxMode & fluxMode
const	CMetab & pMetab

Returns: std::pair< C_FLOAT64, C_FLOAT64 > changes

References CDataVector< CType >::begin(), CFluxMode::begin(), C_FLOAT64, CDataVector< CType >::end(), CFluxMode::end(), CReaction::getChemEq(), CModelEntity::getKey(), CChemEq::getProducts(), CChemEq::getSubstrates(), and CCopasiTask::mpProblem.

Referenced by getNetReactionData(), and CEFMProblem::printResult().

◆ getValidMethods()

const CTaskEnum::Method * CEFMTask::getValidMethods ( ) const

virtual

Retrieve the list of valid methods

Returns: const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References CTaskEnum::EFMAlgorithm, CTaskEnum::EFMBitPatternAlgorithm, CTaskEnum::EFMBitPatternTreeAlgorithm, and CTaskEnum::UnsetMethod.

◆ initialize()

bool CEFMTask::initialize	(	const OutputFlag &	of,
		COutputHandler *	pOutputHandler,
		std::ostream *	pOstream
	)

virtual

Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler
std::ostream	* pOstream (default: NULL)

Returns: bool success

Reimplemented from CCopasiTask.

References CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

◆ process()

bool CEFMTask::process ( const bool & useInitialValues )

virtual

Process the task with or without initializing to the initial state.

Parameters

const bool & useInitialValues

Returns: bool success

Reimplemented from CCopasiTask.

References COutputInterface::AFTER, COutputInterface::BEFORE, CCopasiTask::mpMethod, and CCopasiTask::output().

◆ setCallBack()

bool CEFMTask::setCallBack ( CProcessReportLevel callBack )

virtual

Set the call back of the task

Parameters

CProcessReport * pCallBack

Returns: bool success

Reimplemented from CCopasiTask.

References CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, CCopasiMethod::setCallBack(), CCopasiProblem::setCallBack(), and CCopasiTask::setCallBack().

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

Public Member Functions

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ CEFMTask() [1/3]

◆ CEFMTask() [2/3]

◆ CEFMTask() [3/3]

◆ ~CEFMTask()

Member Function Documentation

◆ getFluxModeDescription()

◆ getFluxModes()

◆ getInternalSpecies()

◆ getNetReaction()

◆ getNetReactionData()

◆ getReactionEquation()

◆ getSpeciesChanges()

◆ getValidMethods()

◆ initialize()

◆ process()

◆ setCallBack()