---

SharedBFactorNetworkMinimizable Class Reference

#include <SharedBFactorNetworkMinimizable.h>

Inheritance diagram for SharedBFactorNetworkMinimizable:

[legend]Collaboration diagram for SharedBFactorNetworkMinimizable:

[legend]List of all members.

Public Methods
	SharedBFactorNetworkMinimizable ()
	SharedBFactorNetworkMinimizable (std::vector< Experiment * > experiments, std::vector< CReactionMover * > reactionMovers, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight, int nCells=1)
void	Initialize (std::vector< Experiment * > experiments, std::vector< CReactionMover * > reactionMovers, int nCells, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight)
virtual	~SharedBFactorNetworkMinimizable ()
Experiment *	GetExperiment (int expNum)
CellAverageObserver *	GetCellObserver (int coNum)
double	GetParameter (int parIndex)
int	GetNExp ()
int	GetNParameters ()
double	ComputeResiduals (double *parameters)
virtual double	ComputeES (double *parameters, double T)
virtual double	F (double *parameters, double T)
virtual double	F0 (double *parameters, double T)
Private Attributes
std::vector< Experiment * >	experiments
std::vector< CReactionMover * >	reactionMovers
std::vector< CellAverageObserver * >	cellObservers
std::vector< std::vector< double * > * >	initialNetworkData
std::vector< std::vector< double * > * >	currentNetworkData
int	nExp

---

Constructor & Destructor Documentation

SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable (    )

Definition at line 11 of file SharedBFactorNetworkMinimizable.cpp.

SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable (  std::vector< Experiment * >    experiments, std::vector< CReactionMover * >    reactionMovers, bool    rateConstantsOptimizable, bool    initialChemConcOptimizable, bool    logsInObjectiveFunction, double    timeSeriesWeight, double    rateConstantsWeight, double    initialChemConcWeight, int    nCells = 1 )

Definition at line 16 of file SharedBFactorNetworkMinimizable.cpp. References experiments, NetworkMinimizable::initialChemConcOptimizable, NetworkMinimizable::initialChemConcWeight, Initialize, NetworkMinimizable::logsInObjectiveFunction, NetworkMinimizable::nCells, NetworkMinimizable::rateConstantsOptimizable, NetworkMinimizable::rateConstantsWeight, reactionMovers, and NetworkMinimizable::timeSeriesWeight.

SharedBFactorNetworkMinimizable::~SharedBFactorNetworkMinimizable (    )  [virtual]

Definition at line 22 of file SharedBFactorNetworkMinimizable.cpp. References cellObservers, NetworkMinimizable::m_pConversionFactors, nExp, and reactionMovers.

---

Member Function Documentation

double SharedBFactorNetworkMinimizable::ComputeES (  double *    parameters, double    T )  [virtual]

Implements NetworkMinimizable. Definition at line 146 of file SharedBFactorNetworkMinimizable.cpp. References ComputeResiduals, NetworkMinimizable::EntropyShift, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

double SharedBFactorNetworkMinimizable::ComputeResiduals (  double *    parameters )  [virtual]

Implements NetworkMinimizable. Definition at line 175 of file SharedBFactorNetworkMinimizable.cpp. References cellObservers, currentNetworkData, experiments, NetworkMinimizable::initialChemConcOptimizable, NetworkMinimizable::initialChemConcWeight, initialNetworkData, Minimizable::m_dEntropyLastComputed, NetworkMinimizable::m_iNBFactors, NetworkMinimizable::m_pConversionFactors, NetworkMinimizable::nCells, nExp, Subject::Notify, NetworkMinimizable::rateConstantsOptimizable, NetworkMinimizable::rateConstantsWeight, reactionMovers, NLLSMinimizable::residuals, stop, and NetworkMinimizable::timeSeriesWeight. Referenced by ComputeES, F, and F0.

double SharedBFactorNetworkMinimizable::F (  double *    parameters, double    T )  [virtual]

Implements NetworkMinimizable. Definition at line 159 of file SharedBFactorNetworkMinimizable.cpp. References ComputeResiduals, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

double SharedBFactorNetworkMinimizable::F0 (  double *    parameters, double    T )  [virtual]

Implements NetworkMinimizable. Definition at line 167 of file SharedBFactorNetworkMinimizable.cpp. References ComputeResiduals, NetworkMinimizable::EntropyShift, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

CellAverageObserver* SharedBFactorNetworkMinimizable::GetCellObserver (  int    coNum )  [inline]

Definition at line 33 of file SharedBFactorNetworkMinimizable.h. References cellObservers. Referenced by GnuPlotterTimeSeriesSharedBFactorObserver::Update.

Experiment* SharedBFactorNetworkMinimizable::GetExperiment (  int    expNum )  [inline, virtual]

Reimplemented from NetworkMinimizable. Definition at line 32 of file SharedBFactorNetworkMinimizable.h. References experiments. Referenced by GnuPlotterTimeSeriesSharedBFactorObserver::Update.

int SharedBFactorNetworkMinimizable::GetNExp (    )  [inline]

Definition at line 36 of file SharedBFactorNetworkMinimizable.h. References nExp. Referenced by GnuPlotterTimeSeriesSharedBFactorObserver::Update.

int SharedBFactorNetworkMinimizable::GetNParameters (    )  [virtual]

Implements NetworkMinimizable. Definition at line 478 of file SharedBFactorNetworkMinimizable.cpp. References experiments, NetworkMinimizable::initialChemConcOptimizable, and NetworkMinimizable::rateConstantsOptimizable. Referenced by GetParameter.

double SharedBFactorNetworkMinimizable::GetParameter (  int    parIndex )  [virtual]

Implements NetworkMinimizable. Definition at line 509 of file SharedBFactorNetworkMinimizable.cpp. References currentNetworkData, and GetNParameters.

void SharedBFactorNetworkMinimizable::Initialize (  std::vector< Experiment * >    experiments, std::vector< CReactionMover * >    reactionMovers, int    nCells, bool    rateConstantsOptimizable, bool    initialChemConcOptimizable, bool    logsInObjectiveFunction, double    timeSeriesWeight, double    rateConstantsWeight, double    initialChemConcWeight )  [virtual]

Reimplemented from NetworkMinimizable. Definition at line 36 of file SharedBFactorNetworkMinimizable.cpp. References NLLSMinimizable::Allocate, cellObservers, currentNetworkData, experiments, NetworkMinimizable::initialChemConcOptimizable, NetworkMinimizable::initialChemConcWeight, initialNetworkData, NetworkMinimizable::logsInObjectiveFunction, NetworkMinimizable::m_iNBFactors, NetworkMinimizable::m_pConversionFactors, NetworkMinimizable::nCells, nExp, NetworkMinimizable::rateConstantsOptimizable, NetworkMinimizable::rateConstantsWeight, reactionMovers, NetworkMinimizable::SetInitialChemConcWeight, NetworkMinimizable::SetRateConstantsWeight, NetworkMinimizable::SetTimeSeriesWeight, and NetworkMinimizable::timeSeriesWeight. Referenced by SharedBFactorNetworkMinimizable.

---

Member Data Documentation

std::vector<CellAverageObserver *> SharedBFactorNetworkMinimizable::cellObservers [private]

Definition at line 47 of file SharedBFactorNetworkMinimizable.h. Referenced by ComputeResiduals, GetCellObserver, Initialize, and ~SharedBFactorNetworkMinimizable.

std::vector<std::vector<double *> *> SharedBFactorNetworkMinimizable::currentNetworkData [private]

Definition at line 49 of file SharedBFactorNetworkMinimizable.h. Referenced by ComputeResiduals, GetParameter, and Initialize.

std::vector<Experiment *> SharedBFactorNetworkMinimizable::experiments [private]

Definition at line 45 of file SharedBFactorNetworkMinimizable.h. Referenced by ComputeResiduals, GetExperiment, GetNParameters, Initialize, and SharedBFactorNetworkMinimizable.

std::vector<std::vector<double *> *> SharedBFactorNetworkMinimizable::initialNetworkData [private]

Definition at line 48 of file SharedBFactorNetworkMinimizable.h. Referenced by ComputeResiduals, and Initialize.

int SharedBFactorNetworkMinimizable::nExp [private]

Definition at line 50 of file SharedBFactorNetworkMinimizable.h. Referenced by ComputeResiduals, GetNExp, Initialize, and ~SharedBFactorNetworkMinimizable.

std::vector<CReactionMover *> SharedBFactorNetworkMinimizable::reactionMovers [private]

Definition at line 46 of file SharedBFactorNetworkMinimizable.h. Referenced by ComputeResiduals, Initialize, SharedBFactorNetworkMinimizable, and ~SharedBFactorNetworkMinimizable.

---

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

• SharedBFactorNetworkMinimizable.h
• SharedBFactorNetworkMinimizable.cpp

---