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NetworkMinimizable Class Reference

#include <NetworkMinimizable.h>

Inheritance diagram for NetworkMinimizable:

[legend]Collaboration diagram for NetworkMinimizable:

[legend]List of all members.

Public Methods
	NetworkMinimizable ()
virtual	~NetworkMinimizable ()
virtual 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 void	Initialize (Experiment *experiment, CReactionMover *reactionMover, int nCells, bool rateConstantsOptimizable, bool initialChemConcOptimizable, bool logsInObjectiveFunction, double timeSeriesWeight, double rateConstantsWeight, double initialChemConcWeight)
int	GetNCells ()
bool	GetRateConstantsOptimizable () const
bool	GetInitialChemConcOptimizable () const
bool	GetLogsInObjectiveFunction () const
double	GetTimeSeriesWeight ()
double	GetRateConstantsWeight ()
double	GetInitialChemConcWeight ()
void	SetTimeSeriesWeight (double timeSeriesWeight)
void	SetRateConstantsWeight (double rateConstantsWeight)
void	SetInitialChemConcWeight (double initialChemConcWeight)
CConversionFactor *	GetConversionFactor (int factorIndex)
virtual double	GetParameter (int parIndex)=0
virtual Experiment *	GetExperiment ()
virtual Experiment *	GetExperiment (int expNum)
virtual int	GetNParameters ()=0
virtual double	ComputeResiduals (double *parameters)=0
virtual double	ComputeES (double *parameters, double T)=0
double	EntropyShift (double T)
virtual double	F (double *parameters, double T)=0
virtual double	F0 (double *parameters, double T)=0
int	GetNBFactors ()
Protected Attributes
bool	rateConstantsOptimizable
bool	initialChemConcOptimizable
bool	logsInObjectiveFunction
int	nCells
double	timeSeriesWeight
double	rateConstantsWeight
double	initialChemConcWeight
std::vector< CConversionFactor * >	m_pConversionFactors
int	m_iNBFactors

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Constructor & Destructor Documentation

NetworkMinimizable::NetworkMinimizable (    )

Definition at line 11 of file NetworkMinimizable.cpp.

NetworkMinimizable::~NetworkMinimizable (    )  [virtual]

Definition at line 16 of file NetworkMinimizable.cpp.

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Member Function Documentation

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

Reimplemented from NLLSMinimizable. Implemented in SharedBFactorNetworkMinimizable.

virtual double NetworkMinimizable::ComputeResiduals (  double *    parameters )  [pure virtual]

Implements NLLSMinimizable. Implemented in SharedBFactorNetworkMinimizable.

double NetworkMinimizable::EntropyShift (  double    T )  [virtual]

Implements NLLSMinimizable. Reimplemented in SingleNetworkMinimizable. Definition at line 36 of file NetworkMinimizable.cpp. References m_iNBFactors. Referenced by SharedBFactorNetworkMinimizable::ComputeES, and SharedBFactorNetworkMinimizable::F0.

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

Implements NLLSMinimizable. Implemented in SharedBFactorNetworkMinimizable.

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

Implements NLLSMinimizable. Implemented in SharedBFactorNetworkMinimizable.

CConversionFactor* NetworkMinimizable::GetConversionFactor (  int    factorIndex )  [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 41 of file NetworkMinimizable.h. References m_pConversionFactors. Referenced by GnuPlotterTimeSeriesSharedBFactorObserver::Update.

Experiment * NetworkMinimizable::GetExperiment (  int    expNum )  [virtual]

Reimplemented in SharedBFactorNetworkMinimizable. Definition at line 73 of file NetworkMinimizable.cpp.

Experiment * NetworkMinimizable::GetExperiment (    )  [virtual]

Reimplemented in SingleNetworkMinimizable. Definition at line 67 of file NetworkMinimizable.cpp.

bool NetworkMinimizable::GetInitialChemConcOptimizable (    )  const [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 33 of file NetworkMinimizable.h. References initialChemConcOptimizable.

double NetworkMinimizable::GetInitialChemConcWeight (    )  [inline]

Definition at line 37 of file NetworkMinimizable.h. References initialChemConcWeight.

bool NetworkMinimizable::GetLogsInObjectiveFunction (    )  const [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 34 of file NetworkMinimizable.h. References logsInObjectiveFunction.

int NetworkMinimizable::GetNBFactors (    )  [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 56 of file NetworkMinimizable.h. References m_iNBFactors.

int NetworkMinimizable::GetNCells (    )  [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 31 of file NetworkMinimizable.h. References nCells.

virtual int NetworkMinimizable::GetNParameters (    )  [pure virtual]

Implements Minimizable. Implemented in SharedBFactorNetworkMinimizable.

virtual double NetworkMinimizable::GetParameter (  int    parIndex )  [pure virtual]

Implemented in SharedBFactorNetworkMinimizable.

bool NetworkMinimizable::GetRateConstantsOptimizable (    )  const [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 32 of file NetworkMinimizable.h. References rateConstantsOptimizable.

double NetworkMinimizable::GetRateConstantsWeight (    )  [inline]

Definition at line 36 of file NetworkMinimizable.h. References rateConstantsWeight.

double NetworkMinimizable::GetTimeSeriesWeight (    )  [inline]

Definition at line 35 of file NetworkMinimizable.h. References timeSeriesWeight.

void NetworkMinimizable::Initialize (  Experiment *    experiment, CReactionMover *    reactionMover, int    nCells, bool    rateConstantsOptimizable, bool    initialChemConcOptimizable, bool    logsInObjectiveFunction, double    timeSeriesWeight, double    rateConstantsWeight, double    initialChemConcWeight )  [virtual]

Reimplemented in SingleNetworkMinimizable. Definition at line 26 of file NetworkMinimizable.cpp.

void NetworkMinimizable::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 in SharedBFactorNetworkMinimizable. Definition at line 21 of file NetworkMinimizable.cpp.

void NetworkMinimizable::SetInitialChemConcWeight (  double    initialChemConcWeight )  [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 40 of file NetworkMinimizable.h. References initialChemConcWeight. Referenced by SharedBFactorNetworkMinimizable::Initialize.

void NetworkMinimizable::SetRateConstantsWeight (  double    rateConstantsWeight )  [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 39 of file NetworkMinimizable.h. References rateConstantsWeight. Referenced by SharedBFactorNetworkMinimizable::Initialize.

void NetworkMinimizable::SetTimeSeriesWeight (  double    timeSeriesWeight )  [inline]

Reimplemented in SingleNetworkMinimizable. Definition at line 38 of file NetworkMinimizable.h. References timeSeriesWeight. Referenced by SharedBFactorNetworkMinimizable::Initialize.

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Member Data Documentation

bool NetworkMinimizable::initialChemConcOptimizable [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 59 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, GetInitialChemConcOptimizable, SharedBFactorNetworkMinimizable::GetNParameters, SharedBFactorNetworkMinimizable::Initialize, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

double NetworkMinimizable::initialChemConcWeight [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 64 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, GetInitialChemConcWeight, SharedBFactorNetworkMinimizable::Initialize, SetInitialChemConcWeight, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

bool NetworkMinimizable::logsInObjectiveFunction [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 60 of file NetworkMinimizable.h. Referenced by GetLogsInObjectiveFunction, SharedBFactorNetworkMinimizable::Initialize, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

int NetworkMinimizable::m_iNBFactors [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 69 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, EntropyShift, GetNBFactors, and SharedBFactorNetworkMinimizable::Initialize.

std::vector<CConversionFactor *> NetworkMinimizable::m_pConversionFactors [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 67 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, GetConversionFactor, SharedBFactorNetworkMinimizable::Initialize, and SharedBFactorNetworkMinimizable::~SharedBFactorNetworkMinimizable.

int NetworkMinimizable::nCells [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 61 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, GetNCells, SharedBFactorNetworkMinimizable::Initialize, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

bool NetworkMinimizable::rateConstantsOptimizable [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 58 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, SharedBFactorNetworkMinimizable::GetNParameters, GetRateConstantsOptimizable, SharedBFactorNetworkMinimizable::Initialize, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

double NetworkMinimizable::rateConstantsWeight [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 63 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, GetRateConstantsWeight, SharedBFactorNetworkMinimizable::Initialize, SetRateConstantsWeight, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

double NetworkMinimizable::timeSeriesWeight [protected]

Reimplemented in SingleNetworkMinimizable. Definition at line 62 of file NetworkMinimizable.h. Referenced by SharedBFactorNetworkMinimizable::ComputeResiduals, GetTimeSeriesWeight, SharedBFactorNetworkMinimizable::Initialize, SetTimeSeriesWeight, and SharedBFactorNetworkMinimizable::SharedBFactorNetworkMinimizable.

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

• NetworkMinimizable.h
• NetworkMinimizable.cpp

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