#include <CLNATask.h>

Inheritance diagram for CLNATask:

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

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

virtual const CTaskEnum::Method *	getValidMethods () const override

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

void	load (CReadConfig &configBuffer)

void	printResult (std::ostream *ostream) const

virtual bool	process (const bool &useInitialValues) override

virtual bool	setCallBack (CProcessReportLevel callBack) override

virtual bool	updateMatrices () override

virtual	~CLNATask ()

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	~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
void	cleanup ()

	CLNATask ()

Friends
std::ostream &	operator<< (std::ostream &os, const CLNATask &A)

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

◆ CLNATask() [1/3]

CLNATask::CLNATask ( )

private

Default constructor

◆ CLNATask() [2/3]

CLNATask::CLNATask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = `CTaskEnum::Task::lna`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Task & type (default: lna)

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

◆ CLNATask() [3/3]

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

Copy constructor

Parameters

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

◆ ~CLNATask()

CLNATask::~CLNATask ( )

virtual

Destructor

Member Function Documentation

◆ cleanup()

void CLNATask::cleanup ( )

private

cleanup()

◆ getValidMethods()

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

overridevirtual

Retrieve the list of valid methods

Returns: const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References CTaskEnum::linearNoiseApproximation, and CTaskEnum::UnsetMethod.

◆ initialize()

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

overridevirtual

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 CReport::getStream(), CLNAProblem::getSubTask(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mReport, CCopasiTask::NO_OUTPUT, and updateMatrices().

◆ load()

void CLNATask::load ( CReadConfig & configBuffer )

Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

configbuffer reference to a CReadConfig object.

References CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiTask::mScheduled.

◆ printResult()

void CLNATask::printResult ( std::ostream * ostream ) const

This functionality is expected from the problem but has to be implemented here for the moment. This is called from the corresponding method of the problem

References CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, CSteadyStateMethod::foundNegative, CLNAMethod::getCovarianceMatrixAnn(), CLNAMethod::getSteadyStateStatus(), CLNAProblem::getSubTask(), CLNAProblem::isSteadyStateRequested(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CSteadyStateMethod::notFound.

Referenced by CLNAProblem::printResult().

◆ process()

bool CLNATask::process ( const bool & useInitialValues )

overridevirtual

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

Parameters

const bool & useInitialValues

Returns: bool success

Reimplemented from CCopasiTask.

References COutputInterface::AFTER, CLNAMethod::allNeg, CMathContainer::applyInitialValues(), COutputInterface::BEFORE, COutputInterface::DURING, CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, CSteadyStateTask::getEigenValuesReduced(), CEigen::getNimag(), CEigen::getNposreal(), CEigen::getNzero(), CCopasiTask::getProblem(), CSteadyStateTask::getResult(), CCopasiProblem::getSubTask(), CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, CLNAMethod::nonNegEigenvaluesExist, CSteadyStateMethod::notFound, CCopasiTask::output(), CLNAMethod::process(), CSteadyStateTask::process(), CCopasiTask::setCallBack(), CLNAMethod::setEigenValueStatus(), CSteadyStateProblem::setStabilityAnalysisRequested(), and CLNAMethod::setSteadyStateStatus().

◆ setCallBack()

bool CLNATask::setCallBack ( CProcessReportLevel callBack )

overridevirtual

Set the call back of the task

Parameters

CProcessReport * pCallBack

Returns: bool success

Reimplemented from CCopasiTask.

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

◆ updateMatrices()

bool CLNATask::updateMatrices ( )

overridevirtual

Resizes result matrices and updates array annotations for a specific task. This is used when we need to know about the data structures of a task result without actually performing the task, e.g. when selecting objects for output. For now we assume that this functionality is also performed when initialize() is called.

Reimplemented from CCopasiTask.

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

Referenced by initialize().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const CLNATask &	A
	)

friend

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

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ CLNATask() [1/3]

◆ CLNATask() [2/3]

◆ CLNATask() [3/3]

◆ ~CLNATask()

Member Function Documentation

◆ cleanup()

◆ getValidMethods()

◆ initialize()

◆ load()

◆ printResult()

◆ process()

◆ setCallBack()

◆ updateMatrices()

Friends And Related Function Documentation

◆ operator<<