CTimeSensMethod Class Reference

#include <CTimeSensMethod.h>

Inheritance diagram for CTimeSensMethod:

Public Types
enum	Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 }
Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator
typedef std::vector< CCopasiParameter * >	elements
typedef elements::iterator	index_iterator
typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator
Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }
enum class	Type {   DOUBLE = 0 , UDOUBLE , INT , UINT ,   BOOL , GROUP , STRING , CN ,   KEY , FILE , EXPRESSION , INVALID ,   __SIZE }
typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag
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 Member Functions
virtual void	copySensitivitiesToResultMatrix ()=0
	CTimeSensMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
	CTimeSensMethod (const CTimeSensMethod &src, const CDataContainer *pParent)
const CVectorCore< C_INT > &	getRoots () const
void	initializeDerivativesCalculations (bool reduced)
virtual void	initResult ()
const bool &	integrateReducedModel () const
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
void	setProblem (CTimeSensProblem *problem)
virtual void	start ()
virtual void	stateChange (const CMath::StateChange &change)
virtual Status	step (const double &deltaT, const bool &final=false)
	~CTimeSensMethod ()
Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)
virtual void	clearCallBack ()
const CProcessReportLevel &	getCallBack () const
CMathContainer *	getMathContainer () const
const CTaskEnum::Method &	getSubType () const
const CTaskEnum::Task &	getType () const
virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
CCopasiMethod &	operator= (const CCopasiMethod &rhs)
virtual void	print (std::ostream *ostream) const
virtual void	printResult (std::ostream *ostream) const
virtual bool	setCallBack (CProcessReportLevel callBack)
void	setMathContainer (CMathContainer *pContainer)
virtual	~CCopasiMethod ()
Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)
void	addParameter (CCopasiParameter *pParameter)
bool	addParameter (const CCopasiParameter &parameter)
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)
index_iterator	beginIndex () const
const_name_iterator	beginName () const
	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)
	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")
void	clear ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
virtual bool	elevateChildren ()
index_iterator	endIndex () const
const_name_iterator	endName () const
CCopasiParameterGroup &	getElementTemplates ()
const CCopasiParameterGroup &	getElementTemplates () const
CCopasiParameterGroup *	getGroup (const size_t &index)
const CCopasiParameterGroup *	getGroup (const size_t &index) const
CCopasiParameterGroup *	getGroup (const std::string &name)
const CCopasiParameterGroup *	getGroup (const std::string &name) const
virtual size_t	getIndex (const CDataObject *pObject) const
size_t	getIndex (const std::string &name) const
std::string	getKey (const size_t &index) const
std::string	getKey (const std::string &name) const
virtual const std::string &	getName (const size_t &index) const
virtual const CObjectInterface *	getObject (const CCommonName &cn) const
CCopasiParameter *	getParameter (const size_t &index)
const CCopasiParameter *	getParameter (const size_t &index) const
CCopasiParameter *	getParameter (std::string name)
const CCopasiParameter *	getParameter (std::string name) const
CCopasiParameter::Type	getType (const size_t &index) const
CCopasiParameter::Type	getType (const std::string &name) const
std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const
template<class CType >
CType &	getValue (const size_t &index)
template<class CType >
const CType &	getValue (const size_t &index) const
template<class CType >
CType &	getValue (const std::string &name)
template<class CType >
const CType &	getValue (const std::string &name) const
bool	haveTemplate () const
virtual CUndoObjectInterface *	insert (const CData &data)
CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)
virtual bool	remove (CDataObject *pObject)
bool	removeParameter (CCopasiParameter *pParameter)
bool	removeParameter (const size_t &index)
bool	removeParameter (const std::string &name)
virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)
template<class CType >
bool	setValue (const size_t &index, const CType &value)
template<class CType >
bool	setValue (const std::string &name, const CType &value)
size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const
bool	swap (const size_t &iFrom, const size_t &iTo)
bool	swap (index_iterator &from, index_iterator &to)
virtual CData	toData () const
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CCopasiParameterGroup ()
Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)
	CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="Parameter")
virtual CCommonName	getCN () const override
template<class CType >
const CType &	getDefault () const
virtual const std::string &	getKey () const override
virtual std::string	getObjectDisplayName () const override
const CCopasiParameter::Type &	getType () const
const UserInterfaceFlag &	getUserInterfaceFlag () const
template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()
template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const
void *	getValidValuesPointer () const
template<class CType >
CType &	getValue ()
template<class CType >
const CType &	getValue () const
virtual void *	getValuePointer () const override
CDataObject *	getValueReference () const
bool	hasValidValues () const
bool	isBasic () const
bool	isDefault () const
bool	isEditable () const
bool	isUnsupported () const
bool	isValidValue (const bool &value) const
bool	isValidValue (const C_FLOAT64 &value) const
bool	isValidValue (const C_INT32 &value) const
bool	isValidValue (const CCommonName &value) const
template<class CType >
bool	isValidValue (const CType &) const
bool	isValidValue (const std::string &value) const
bool	isValidValue (const std::vector< CCopasiParameter * > &value) const
bool	isValidValue (const unsigned C_INT32 &value) const
CCopasiParameter &	operator= (const CCopasiParameter &rhs)
template<class CType >
bool	setDefault (const CType &defaultValue)
bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)
virtual bool	setObjectParent (const CDataContainer *pParent) override
template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)
template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)
template<class CType >
bool	setValue (const CType &value)
bool	setValue (const std::vector< CCopasiParameter * > &value)
virtual	~CCopasiParameter ()
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 objectMap &	getObjects ()
virtual const objectMap &	getObjects () const
virtual const std::string	getUnits () const override
virtual const CDataObject *	getValueObject () const override
void	objectRenamed (CDataObject *pObject, const std::string &oldName)
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 const CDataObject *	getDataObject () const override
CDataContainer *	getObjectAncestor (const std::string &type) const
CDataModel *	getObjectDataModel () const
const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const
const std::string &	getObjectName () const
CDataContainer *	getObjectParent () const
const std::string &	getObjectType () const
virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override
virtual const CValidity &	getValidity () const override
bool	hasFlag (const Flag &flag) const
virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
bool	prerequisitsContains (const DataObjectSet &objects) const
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	~CUndoObjectInterface ()

Protected Member Functions
void	calculate_dAssignments_dPar (CMatrix< C_FLOAT64 > &s)
void	calculate_dAssignments_dState (CMatrix< C_FLOAT64 > &s, bool reduced)
void	calculate_dInitialState_dPar (CMatrix< C_FLOAT64 > &s)
void	calculate_dRate_dPar (CMatrix< C_FLOAT64 > &s, bool reduced)
void	output (const bool &useMoieties)
virtual void	signalMathContainerChanged ()
Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src)
	CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)
Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()
Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &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)

Static Protected Member Functions
static void	printObjectSet (const std::string &s, const CObjectInterface::ObjectSet &os)
	some methods for doing debug output More...
static void	printUpdateSeq (const std::string &s, const CCore::CUpdateSequence &us)

Protected Attributes
CMatrix< C_FLOAT64 >	mAssignmentJacobian
CVector< C_FLOAT64 * >	mAssTargetValuePointers
CVectorCore< C_FLOAT64 >	mContainerState
CMatrix< C_FLOAT64 >	mdAssignment_dPar
CMatrix< C_FLOAT64 >	mdRate_dPar
CMatrix< C_FLOAT64 >	mJacobian
size_t	mNumAssTargets
	Number of assignment targets for which sensitivities are calculated. More...
unsigned C_INT32	mNumParameters
CVector< C_FLOAT64 * >	mParameterInitialValuePointers
	the pointers to the values of the objects as provided by the problem (generally initial values) More...
CVector< bool >	mParameterIsInitialConcentration
CVector< C_FLOAT64 * >	mParameterTransientValuePointers
	the pointers as used during the simulation, initial values of fixed quantities are replaced by their transient counterparts. More...
C_FLOAT64 *	mpContainerStateTime
CTimeSensProblem *	mpProblem
const bool *	mpReducedModel
CTimeSensTask *	mpTask
CVectorCore< C_INT >	mRootsFound
CCore::CUpdateSequence	mSeq1
CCore::CUpdateSequence	mSeq2
CCore::CUpdateSequence	mSeq3
size_t	mSystemSize
Protected Attributes inherited from CCopasiMethod
CMathContainer *	mpContainer
CProcessReportLevel	mProcessReport
Protected Attributes inherited from CCopasiParameter
std::string	mKey
void *	mpDefault
void *	mpValidValues
void *	mpValue
CDataObject *	mpValueReference
UserInterfaceFlag	mUserInterfaceFlag
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

Static Protected Attributes
static const bool	ReducedModel

Private Member Functions
	CTimeSensMethod ()

Additional Inherited Members
Static Public Member Functions inherited from CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)
static void	allocateValue (const Type &type, void *&pValue)
static void	assignValue (const Type &type, void *&pValue, const void *pNewValue)
static void	deleteValidValues (const Type &type, void *&pValidValues)
static void	deleteValue (const Type &type, void *&pValue)
static CCopasiParameter *	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 Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName
static const CEnumAnnotation< std::string, Type >	XMLType
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Member Enumeration Documentation

Status

enum CTimeSensMethod::Status

Enumeration value for the return value

Enumerator
FAILURE
NORMAL
ROOT

Constructor & Destructor Documentation

CTimeSensMethod() [1/3]

CTimeSensMethod::CTimeSensMethod ( )

private

Default constructor.

CTimeSensMethod() [2/3]

CTimeSensMethod::CTimeSensMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType,
		const CTaskEnum::Task &	taskType = CTaskEnum::Task::timeCourse
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType
const	CTaskEnum::Task & taskType (default: timeCourse)

Default constructor.

References CDataObject::getObjectParent(), and mpTask.

CTimeSensMethod() [3/3]

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

Copy constructor.

Parameters

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

Copy constructor.

Parameters

const CTimeSensMethod &

src

References CDataObject::getObjectParent(), and mpTask.

~CTimeSensMethod()

CTimeSensMethod::~CTimeSensMethod

(

)

Destructor.

References DESTRUCTOR_TRACE.

Member Function Documentation

calculate_dAssignments_dPar()

void CTimeSensMethod::calculate_dAssignments_dPar ( CMatrix< C_FLOAT64 > &  s )

protected

This calculates the derivatives of the assignments with respect to the requested parameters

References CMathContainer::applyUpdateSequence(), CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, mAssTargetValuePointers, mNumAssTargets, mNumParameters, mParameterTransientValuePointers, CCopasiMethod::mpContainer, mSeq2, and CMatrix< CType >::resize().

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix().

calculate_dAssignments_dState()

void CTimeSensMethod::calculate_dAssignments_dState ( CMatrix< C_FLOAT64 > &  s, bool  reduced  )

protected

This calculates the derivatives of the assignments with respect to the state variables

References CMathContainer::applyUpdateSequence(), CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, CMathContainer::getCountFixedEventTargets(), CMathContainer::getState(), mAssTargetValuePointers, mNumAssTargets, CCopasiMethod::mpContainer, mSeq3, mSystemSize, and CMatrix< CType >::resize().

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix().

calculate_dInitialState_dPar()

void CTimeSensMethod::calculate_dInitialState_dPar ( CMatrix< C_FLOAT64 > &  s )

protected

This calculates the derivatives of the initial state with respect to the requested parameters

References CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, CCore::Concentration, CMathContainer::getCountFixed(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getInitialState(), CVectorCore< CType >::initialize(), mNumParameters, mParameterInitialValuePointers, mParameterIsInitialConcentration, CCopasiMethod::mpContainer, mSystemSize, CCore::ParticleNumbers, CMatrix< CType >::resize(), and CMathContainer::updateInitialValues().

Referenced by CTimeSensLsodaMethod::start().

calculate_dRate_dPar()

void CTimeSensMethod::calculate_dRate_dPar ( CMatrix< C_FLOAT64 > &  s, bool  reduced  )

protected

This calculates the derivatives of the RHS with respect to the requested parameters

References CMathContainer::applyUpdateSequence(), CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, CMathContainer::getCountFixedEventTargets(), CMathContainer::getRate(), mNumParameters, mParameterTransientValuePointers, CCopasiMethod::mpContainer, mSeq1, mSystemSize, and CMatrix< CType >::resize().

Referenced by CTimeSensLsodaMethod::evalF().

copySensitivitiesToResultMatrix()

virtual void CTimeSensMethod::copySensitivitiesToResultMatrix ( )

pure virtual

This updates the result matrices from the internal calculations. To be called before output.

Implemented in CTimeSensLsodaMethod.

Referenced by CFitProblem::calculate(), and CTimeSensTask::output().

getRoots()

const CVectorCore< C_INT > & CTimeSensMethod::getRoots

(

)

const

Retrieve the roots.

Returns

const CVectorCore< C_INT > & roots

References mRootsFound.

Referenced by CTimeSensTask::processStep().

initializeDerivativesCalculations()

void CTimeSensMethod::initializeDerivativesCalculations

(

bool

reduced

)

Initialize everything that is needed for the various derivatives, e.g. lists of value pointers, update sequences, etc.

References C_FLOAT64, CCore::Default, CMath::Fixed, CMathObject::getDataObject(), CMathContainer::getMathObject(), CMathContainer::getObject(), CDataObject::getObjectParent(), CTimeSensProblem::getParameterCN(), CMathObject::getSimulationType(), CMathContainer::getSimulationUpToDateObjects(), CMathContainer::getStateObjects(), CTimeSensProblem::getTargetCN(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CDataContainer::getValueObject(), CMathObject::getValuePointer(), CMathObject::isIntensiveProperty(), mAssTargetValuePointers, mNumAssTargets, mNumParameters, mParameterInitialValuePointers, mParameterIsInitialConcentration, mParameterTransientValuePointers, CCopasiMethod::mpContainer, mpProblem, mSeq1, mSeq2, mSeq3, printObjectSet(), printUpdateSeq(), and CVector< CType >::resize().

initResult()

void CTimeSensMethod::initResult ( )

virtual

This initializes the Matrix for the results

References CVectorCore< CType >::array(), CMathContainer::getCountFixedEventTargets(), CMathObject::getDataObject(), CMathContainer::getMathObject(), CTimeSensProblem::getNumParameters(), CTimeSensProblem::getNumTargets(), CMathContainer::getObject(), CTimeSensProblem::getParameterCN(), CTimeSensProblem::getScaledStateResult(), CTimeSensProblem::getScaledStateResultAnnotated(), CTimeSensProblem::getScaledTargetsResult(), CTimeSensProblem::getScaledTargetsResultAnnotated(), CMathContainer::getState(), CTimeSensProblem::getStateResult(), CTimeSensProblem::getStateResultAnnotated(), CTimeSensProblem::getTargetCN(), CTimeSensProblem::getTargetsResult(), CTimeSensProblem::getTargetsResultAnnotated(), CVectorCore< CType >::initialize(), mContainerState, mNumAssTargets, mNumParameters, CCopasiMethod::mpContainer, mpContainerStateTime, mpProblem, mpReducedModel, mSystemSize, CDataArray::resize(), CArray::resize(), CDataArray::setAnnotation(), CDataArray::setDimensionDescription(), and CVectorCore< CType >::size().

Referenced by CTimeSensTask::updateMatrices().

integrateReducedModel()

const bool & CTimeSensMethod::integrateReducedModel

(

)

const

Check whether to integrate the reduced model

Returns

const bool & integrateReducedModel

References mpReducedModel.

Referenced by CTimeSensTask::initialize().

isValidProblem()

bool CTimeSensMethod::isValidProblem ( const CCopasiProblem *  pProblem )

virtual

Check if the method is suitable for this problem

Returns

bool suitability of the method

Reimplemented from CCopasiMethod.

References CCopasiMessage::EXCEPTION, CCopasiMethod::isValidProblem(), and MCTrajectoryMethod.

output()

void CTimeSensMethod::output ( const bool &  useMoieties )

protected

References COutputInterface::DURING, mContainerState, CCopasiMethod::mpContainer, mpTask, CTimeSensTask::output(), CMathContainer::setState(), and CMathContainer::updateSimulatedValues().

printObjectSet()

void CTimeSensMethod::printObjectSet ( const std::string &  s, const CObjectInterface::ObjectSet &  os  )

staticprotected

some methods for doing debug output

Referenced by initializeDerivativesCalculations().

printUpdateSeq()

void CTimeSensMethod::printUpdateSeq ( const std::string &  s, const CCore::CUpdateSequence &  us  )

staticprotected

References CMathUpdateSequence::begin(), CObjectInterface::DataObject(), CMathUpdateSequence::end(), CDataObject::getObjectDisplayName(), and CMathObject::getObjectDisplayName().

Referenced by initializeDerivativesCalculations().

setProblem()

void CTimeSensMethod::setProblem

(

CTimeSensProblem *

problem

)

Set a pointer to the problem. This method is used by CTrajectory

Parameters

CTimeSensProblem *

problem

Set a pointer to the problem. This method is used by CTimeSens

Parameters

CTimeSensProblem *

problem

References mpProblem.

Referenced by CTimeSensTask::initialize().

signalMathContainerChanged()

void CTimeSensMethod::signalMathContainerChanged ( )

protectedvirtual

Signal that the math container has changed

Reimplemented from CCopasiMethod.

References CVectorCore< CType >::array(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mContainerState, CCopasiMethod::mpContainer, mpContainerStateTime, and mpReducedModel.

start()

void CTimeSensMethod::start ( )

virtual

This instructs the method to prepare for integration

Reimplemented in CTimeSensLsodaMethod.

Referenced by CTimeSensTask::processStart(), and CTimeSensLsodaMethod::start().

stateChange()

void CTimeSensMethod::stateChange ( const CMath::StateChange &  change )

virtual

Inform the trajectory method that the state has changed outside its control

Parameters

const

CMath::StateChange & change

Reimplemented in CTimeSensLsodaMethod.

Referenced by CTimeSensTask::process(), and CTimeSensTask::processStep().

step()

CTimeSensMethod::Status CTimeSensMethod::step ( const double &  deltaT, const bool &  final = false  )

virtual

This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.

Parameters

const	double & deltaT
const	bool & final (default: false)

Returns

Status status

This instructs the method to calculate a a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.

Parameters

const double &

deltaT

Reimplemented in CTimeSensLsodaMethod.

References FAILURE.

Referenced by CTimeSensTask::processStep().

Member Data Documentation

mAssignmentJacobian

CMatrix<C_FLOAT64> CTimeSensMethod::mAssignmentJacobian

protected

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix().

mAssTargetValuePointers

CVector< C_FLOAT64* > CTimeSensMethod::mAssTargetValuePointers

protected

pointers to the values of the assignment targets

Referenced by calculate_dAssignments_dPar(), calculate_dAssignments_dState(), CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), and initializeDerivativesCalculations().

mContainerState

CVectorCore< C_FLOAT64 > CTimeSensMethod::mContainerState

protected

A reference to the current state. This is set from outside with the setState() method and never changed anywhere else. It's used to report the results to the calling TrajectoryTask

Referenced by CTimeSensLsodaMethod::hasStateChanged(), initResult(), output(), CTimeSensLsodaMethod::resetState(), CTimeSensLsodaMethod::saveState(), signalMathContainerChanged(), CTimeSensLsodaMethod::start(), CTimeSensLsodaMethod::stateChange(), and CTimeSensLsodaMethod::step().

mdAssignment_dPar

CMatrix<C_FLOAT64> CTimeSensMethod::mdAssignment_dPar

protected

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix().

mdRate_dPar

CMatrix<C_FLOAT64> CTimeSensMethod::mdRate_dPar

protected

Referenced by CTimeSensLsodaMethod::evalF(), and CTimeSensLsodaMethod::start().

mJacobian

CMatrix<C_FLOAT64> CTimeSensMethod::mJacobian

protected

Referenced by CTimeSensLsodaMethod::evalF(), and CTimeSensLsodaMethod::start().

mNumAssTargets

size_t CTimeSensMethod::mNumAssTargets

protected

Number of assignment targets for which sensitivities are calculated.

Referenced by calculate_dAssignments_dPar(), calculate_dAssignments_dState(), initializeDerivativesCalculations(), and initResult().

mNumParameters

unsigned C_INT32 CTimeSensMethod::mNumParameters

protected

Number of parameters for the sensitivities to calculate

Referenced by calculate_dAssignments_dPar(), calculate_dInitialState_dPar(), calculate_dRate_dPar(), CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), CTimeSensLsodaMethod::evalF(), initializeDerivativesCalculations(), initResult(), and CTimeSensLsodaMethod::start().

mParameterInitialValuePointers

CVector< C_FLOAT64* > CTimeSensMethod::mParameterInitialValuePointers

protected

the pointers to the values of the objects as provided by the problem (generally initial values)

pointers to the values of the parameters

Referenced by calculate_dInitialState_dPar(), and initializeDerivativesCalculations().

mParameterIsInitialConcentration

CVector<bool> CTimeSensMethod::mParameterIsInitialConcentration

protected

Referenced by calculate_dInitialState_dPar(), and initializeDerivativesCalculations().

mParameterTransientValuePointers

CVector< C_FLOAT64* > CTimeSensMethod::mParameterTransientValuePointers

protected

the pointers as used during the simulation, initial values of fixed quantities are replaced by their transient counterparts.

Referenced by calculate_dAssignments_dPar(), calculate_dRate_dPar(), CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), and initializeDerivativesCalculations().

mpContainerStateTime

C_FLOAT64* CTimeSensMethod::mpContainerStateTime

protected

A pointer to the time value of the current state.

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), CTimeSensLsodaMethod::evalF(), CTimeSensLsodaMethod::evalR(), initResult(), CTimeSensLsodaMethod::resetState(), CTimeSensLsodaMethod::saveState(), signalMathContainerChanged(), CTimeSensLsodaMethod::start(), CTimeSensLsodaMethod::stateChange(), and CTimeSensLsodaMethod::step().

mpProblem

CTimeSensProblem* CTimeSensMethod::mpProblem

protected

A pointer to the trajectory problem.

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), initializeDerivativesCalculations(), initResult(), setProblem(), and CTimeSensLsodaMethod::start().

mpReducedModel

const bool* CTimeSensMethod::mpReducedModel

protected

Pointer to the value indicating whether to integrate the reduced model.

Referenced by CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), CTimeSensLsodaMethod::createRootMask(), CTimeSensLsodaMethod::evalF(), CTimeSensLsodaMethod::evalR(), CTimeSensLsodaMethod::initializeParameter(), initResult(), integrateReducedModel(), CTimeSensLsodaMethod::setRootMaskType(), signalMathContainerChanged(), CTimeSensLsodaMethod::start(), CTimeSensLsodaMethod::stateChange(), and CTimeSensLsodaMethod::step().

mpTask

CTimeSensTask* CTimeSensMethod::mpTask

protected

The task calling the method

Referenced by CTimeSensMethod(), and output().

mRootsFound

CVectorCore< C_INT > CTimeSensMethod::mRootsFound

protected

Vector containing information on the current roots

Referenced by CTimeSensLsodaMethod::createRootMask(), getRoots(), CTimeSensLsodaMethod::peekAhead(), CTimeSensLsodaMethod::resetState(), CTimeSensLsodaMethod::saveState(), CTimeSensLsodaMethod::start(), CTimeSensLsodaMethod::step(), and CTimeSensLsodaMethod::~CTimeSensLsodaMethod().

mSeq1

CCore::CUpdateSequence CTimeSensMethod::mSeq1

protected

Referenced by calculate_dRate_dPar(), and initializeDerivativesCalculations().

mSeq2

CCore::CUpdateSequence CTimeSensMethod::mSeq2

protected

Referenced by calculate_dAssignments_dPar(), and initializeDerivativesCalculations().

mSeq3

CCore::CUpdateSequence CTimeSensMethod::mSeq3

protected

Referenced by calculate_dAssignments_dState(), and initializeDerivativesCalculations().

mSystemSize

size_t CTimeSensMethod::mSystemSize

protected

Number of variables in the model

Referenced by calculate_dAssignments_dState(), calculate_dInitialState_dPar(), calculate_dRate_dPar(), CTimeSensLsodaMethod::copySensitivitiesToResultMatrix(), CTimeSensLsodaMethod::evalF(), initResult(), CTimeSensLsodaMethod::start(), CTimeSensLsodaMethod::stateChange(), and CTimeSensLsodaMethod::step().

ReducedModel

const bool CTimeSensMethod::ReducedModel

staticprotected

Default value indicating whether to integrate the reduced model initialized to false.

CTimeSensMethod class. This class describes the interface to all integration methods. The various method like LSODA or Gillespie have to be derived from this class.

Created for COPASI by Stefan Hoops 2002

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

• CTimeSensMethod.h
• CTimeSensMethod.cpp