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NetworkMinimizableDirector Class Reference

#include <NetworkMinimizableDirector.h>

Inheritance diagram for NetworkMinimizableDirector:

[legend]Collaboration diagram for NetworkMinimizableDirector:

[legend]List of all members.

Public Methods
	NetworkMinimizableDirector ()
virtual	~NetworkMinimizableDirector ()
virtual int	GetNParameters ()=0
virtual double	ObjectiveFunction (double *parameters)
virtual double	ComputeResiduals (double *parameters)
virtual double	ComputeES (double *parameters, double T)
virtual double	EntropyShift (double T)
virtual double	F (double *parameters, double T)
virtual double	F0 (double *parameters, double T)
virtual double	GetParameter (int parIndex)=0
virtual CReactionMover *	GetMover (int moverIndex)
virtual int	GetNExperiments () const
virtual ReactionNetwork *	GetReactionNetwork (int networkIndex)
virtual void	DumpResidualInfo ()
Protected Attributes
std::vector< NetworkMinimizable * >	_minimizableList
std::vector< Experiment * >	_experimentList
std::vector< ReactionNetwork * >	_networkList
std::vector< CReactionMover * >	_moverList
std::vector< int >	m_iPriorList
double	m_dGammaSquared
Private Methods
virtual void	DefineExperiments ()=0

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Constructor & Destructor Documentation

NetworkMinimizableDirector::NetworkMinimizableDirector (    )

Definition at line 11 of file NetworkMinimizableDirector.cpp.

NetworkMinimizableDirector::~NetworkMinimizableDirector (    )  [virtual]

Definition at line 16 of file NetworkMinimizableDirector.cpp. References _experimentList, _minimizableList, _moverList, and _networkList.

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Member Function Documentation

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

Reimplemented from NLLSMinimizable. Definition at line 65 of file NetworkMinimizableDirector.cpp. References _minimizableList, ComputeResiduals, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

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

Implements NLLSMinimizable. Reimplemented in CEGFRTraffickingCHOMinimizableDirector. Definition at line 112 of file NetworkMinimizableDirector.cpp. References _minimizableList, _moverList, _networkList, m_dGammaSquared, m_iPriorList, NLLSMinimizable::nResiduals, and NLLSMinimizable::residuals. Referenced by ComputeES, F, F0, and ObjectiveFunction.

virtual void NetworkMinimizableDirector::DefineExperiments (    )  [private, pure virtual]

Implemented in CCombinatorialNetworkMinimizableDirector.

void NetworkMinimizableDirector::DumpResidualInfo (    )  [virtual]

Definition at line 37 of file NetworkMinimizableDirector.cpp. References _experimentList. Referenced by PC12EGFNGFMinimizableDirector::PC12EGFNGFMinimizableDirector.

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

Implements NLLSMinimizable. Definition at line 77 of file NetworkMinimizableDirector.cpp. References _minimizableList.

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

Implements NLLSMinimizable. Definition at line 88 of file NetworkMinimizableDirector.cpp. References _minimizableList, ComputeResiduals, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

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

Implements NLLSMinimizable. Definition at line 100 of file NetworkMinimizableDirector.cpp. References _minimizableList, ComputeResiduals, Minimizable::m_dEnergyLastComputed, and Minimizable::m_dEntropyLastComputed.

virtual CReactionMover* NetworkMinimizableDirector::GetMover (  int    moverIndex )  [inline, virtual]

Definition at line 36 of file NetworkMinimizableDirector.h. References _moverList.

virtual int NetworkMinimizableDirector::GetNExperiments (    )  const [inline, virtual]

Definition at line 38 of file NetworkMinimizableDirector.h. References _experimentList.

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

Implements Minimizable. Implemented in CCombinatorialNetworkMinimizableDirector. Referenced by CSharedParametersMinimizableDirector::ComputeResiduals, CCoupledReplicasMinimizableDirector::ComputeResiduals, CSharedParametersMinimizableDirector::GetNParameters, CCoupledReplicasMinimizableDirector::GetNParameters, CSharedParametersMinimizableDirector::GetParameter, CCoupledReplicasMinimizableDirector::GetParameter, and main.

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

Implemented in CCombinatorialNetworkMinimizableDirector. Referenced by CSharedParametersMinimizableDirector::GetParameter, CCoupledReplicasMinimizableDirector::GetParameter, and main.

virtual ReactionNetwork* NetworkMinimizableDirector::GetReactionNetwork (  int    networkIndex )  [inline, virtual]

Definition at line 40 of file NetworkMinimizableDirector.h. References _networkList. Referenced by CSharedParametersMinimizableDirector::SetIntersectionLists, and CCoupledReplicasMinimizableDirector::SetIntersectionLists.

double NetworkMinimizableDirector::ObjectiveFunction (  double *    parameters )  [virtual]

Reimplemented from NLLSMinimizable. Definition at line 58 of file NetworkMinimizableDirector.cpp. References ComputeResiduals. Referenced by CSharedParametersMinimizableDirector::ComputeResiduals, and CCoupledReplicasMinimizableDirector::ComputeResiduals.

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Member Data Documentation

std::vector<Experiment *> NetworkMinimizableDirector::_experimentList [protected]

Definition at line 49 of file NetworkMinimizableDirector.h. Referenced by CAlternateOneGeneInhibitoryNetworkMinimizableDirector::CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector::CCombinatorialNetworkMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector::CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector::CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingMinimizableDirector::CEGFRTraffickingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::CEGFRTraffickingNIH3T3MinimizableDirector, CExampleNetworkMinimizableDirector::CExampleNetworkMinimizableDirector, CForestNitrogenCyclingMinimizableDirector::CForestNitrogenCyclingMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector::CLaubLoomisDictyNetworkMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector::CMartielGoldbeterDictyNetworkMinimizableDirector, COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector::COneGeneReplicaMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector::COneGeneStochasticNetworkMinimizableDirector, CPC12AlternateMinimizableDirector::CPC12AlternateMinimizableDirector, CPC12RapMinusMinimizableDirector::CPC12RapMinusMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::CQuorumSensingNetworkMinimizableDirector, DumpResidualInfo, GetNExperiments, PC12EGFNGFMinimizableDirector::PC12EGFNGFMinimizableDirector, and ~NetworkMinimizableDirector.

std::vector<NetworkMinimizable *> NetworkMinimizableDirector::_minimizableList [protected]

Definition at line 48 of file NetworkMinimizableDirector.h. Referenced by CAlternateOneGeneInhibitoryNetworkMinimizableDirector::CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector::CCombinatorialNetworkMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector::CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector::CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingMinimizableDirector::CEGFRTraffickingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::CEGFRTraffickingNIH3T3MinimizableDirector, CExampleNetworkMinimizableDirector::CExampleNetworkMinimizableDirector, CForestNitrogenCyclingMinimizableDirector::CForestNitrogenCyclingMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector::CLaubLoomisDictyNetworkMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector::CMartielGoldbeterDictyNetworkMinimizableDirector, ComputeES, CReplicaMinimizableDirector::ComputeResiduals, ComputeResiduals, CEGFRTraffickingNIH3T3MinimizableDirector::ComputeResiduals, CEGFRTraffickingCHOMinimizableDirector::ComputeResiduals, COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector::COneGeneReplicaMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector::COneGeneStochasticNetworkMinimizableDirector, CPC12AlternateMinimizableDirector::CPC12AlternateMinimizableDirector, CPC12RapMinusMinimizableDirector::CPC12RapMinusMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::CQuorumSensingNetworkMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::DefineExperiments, CPC12RapMinusMinimizableDirector::DefineExperiments, PC12EGFNGFMinimizableDirector::DefineExperiments, CPC12AlternateMinimizableDirector::DefineExperiments, COneGeneStochasticNetworkMinimizableDirector::DefineExperiments, COneGeneReplicaMinimizableDirector::DefineExperiments, COneGeneInhibitoryNetworkMinimizableDirector::DefineExperiments, CLaubLoomisDictyNetworkMinimizableDirector::DefineExperiments, CExampleNetworkMinimizableDirector::DefineExperiments, CEGFRTraffickingNIH3T3MinimizableDirector::DefineExperiments, CEGFRTraffickingMinimizableDirector::DefineExperiments, CEGFRTraffickingIdealCellMinimizableDirector::DefineExperiments, CEGFRTraffickingCHOMinimizableDirector::DefineExperiments, CCombinatorialNetworkMinimizableDirector::DefineExperiments, CAlternateOneGeneInhibitoryNetworkMinimizableDirector::DefineExperiments, EntropyShift, F, F0, CReplicaMinimizableDirector::GetNParameters, CQuorumSensingNetworkMinimizableDirector::GetNParameters, CPC12RapMinusMinimizableDirector::GetNParameters, PC12EGFNGFMinimizableDirector::GetNParameters, CPC12AlternateMinimizableDirector::GetNParameters, COneGeneStochasticNetworkMinimizableDirector::GetNParameters, COneGeneInhibitoryNetworkMinimizableDirector::GetNParameters, CMartielGoldbeterDictyNetworkMinimizableDirector::GetNParameters, CLaubLoomisDictyNetworkMinimizableDirector::GetNParameters, CForestNitrogenCyclingMinimizableDirector::GetNParameters, CExampleNetworkMinimizableDirector::GetNParameters, CEGFRTraffickingNIH3T3MinimizableDirector::GetNParameters, CEGFRTraffickingMinimizableDirector::GetNParameters, CEGFRTraffickingIdealCellMinimizableDirector::GetNParameters, CEGFRTraffickingCHOMinimizableDirector::GetNParameters, CCombinatorialNetworkMinimizableDirector::GetNParameters, CAlternateOneGeneInhibitoryNetworkMinimizableDirector::GetNParameters, CReplicaMinimizableDirector::GetParameter, CQuorumSensingNetworkMinimizableDirector::GetParameter, CPC12RapMinusMinimizableDirector::GetParameter, PC12EGFNGFMinimizableDirector::GetParameter, CPC12AlternateMinimizableDirector::GetParameter, COneGeneStochasticNetworkMinimizableDirector::GetParameter, COneGeneInhibitoryNetworkMinimizableDirector::GetParameter, CMartielGoldbeterDictyNetworkMinimizableDirector::GetParameter, CLaubLoomisDictyNetworkMinimizableDirector::GetParameter, CForestNitrogenCyclingMinimizableDirector::GetParameter, CExampleNetworkMinimizableDirector::GetParameter, CEGFRTraffickingNIH3T3MinimizableDirector::GetParameter, CEGFRTraffickingMinimizableDirector::GetParameter, CEGFRTraffickingIdealCellMinimizableDirector::GetParameter, CEGFRTraffickingCHOMinimizableDirector::GetParameter, CCombinatorialNetworkMinimizableDirector::GetParameter, CAlternateOneGeneInhibitoryNetworkMinimizableDirector::GetParameter, PC12EGFNGFMinimizableDirector::PC12EGFNGFMinimizableDirector, CAlternateOneGeneInhibitoryNetworkMinimizableDirector::~CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector::~CCombinatorialNetworkMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector::~CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector::~CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingMinimizableDirector::~CEGFRTraffickingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::~CEGFRTraffickingNIH3T3MinimizableDirector, CExampleNetworkMinimizableDirector::~CExampleNetworkMinimizableDirector, CForestNitrogenCyclingMinimizableDirector::~CForestNitrogenCyclingMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector::~CLaubLoomisDictyNetworkMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector::~CMartielGoldbeterDictyNetworkMinimizableDirector, COneGeneInhibitoryNetworkMinimizableDirector::~COneGeneInhibitoryNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector::~COneGeneReplicaMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector::~COneGeneStochasticNetworkMinimizableDirector, CPC12AlternateMinimizableDirector::~CPC12AlternateMinimizableDirector, CPC12RapMinusMinimizableDirector::~CPC12RapMinusMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::~CQuorumSensingNetworkMinimizableDirector, ~NetworkMinimizableDirector, and PC12EGFNGFMinimizableDirector::~PC12EGFNGFMinimizableDirector.

std::vector<CReactionMover *> NetworkMinimizableDirector::_moverList [protected]

Definition at line 51 of file NetworkMinimizableDirector.h. Referenced by CAlternateOneGeneInhibitoryNetworkMinimizableDirector::CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector::CCombinatorialNetworkMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector::CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector::CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingMinimizableDirector::CEGFRTraffickingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::CEGFRTraffickingNIH3T3MinimizableDirector, CExampleNetworkMinimizableDirector::CExampleNetworkMinimizableDirector, CForestNitrogenCyclingMinimizableDirector::CForestNitrogenCyclingMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector::CLaubLoomisDictyNetworkMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector::CMartielGoldbeterDictyNetworkMinimizableDirector, CReplicaMinimizableDirector::ComputeResiduals, ComputeResiduals, CEGFRTraffickingNIH3T3MinimizableDirector::ComputeResiduals, CEGFRTraffickingCHOMinimizableDirector::ComputeResiduals, COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector::COneGeneReplicaMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector::COneGeneStochasticNetworkMinimizableDirector, CPC12AlternateMinimizableDirector::CPC12AlternateMinimizableDirector, CPC12RapMinusMinimizableDirector::CPC12RapMinusMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::CQuorumSensingNetworkMinimizableDirector, GetMover, PC12EGFNGFMinimizableDirector::PC12EGFNGFMinimizableDirector, and ~NetworkMinimizableDirector.

std::vector<ReactionNetwork *> NetworkMinimizableDirector::_networkList [protected]

Definition at line 50 of file NetworkMinimizableDirector.h. Referenced by CAlternateOneGeneInhibitoryNetworkMinimizableDirector::CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector::CCombinatorialNetworkMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector::CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector::CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingMinimizableDirector::CEGFRTraffickingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::CEGFRTraffickingNIH3T3MinimizableDirector, CExampleNetworkMinimizableDirector::CExampleNetworkMinimizableDirector, CForestNitrogenCyclingMinimizableDirector::CForestNitrogenCyclingMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector::CLaubLoomisDictyNetworkMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector::CMartielGoldbeterDictyNetworkMinimizableDirector, ComputeResiduals, CEGFRTraffickingNIH3T3MinimizableDirector::ComputeResiduals, CEGFRTraffickingCHOMinimizableDirector::ComputeResiduals, COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector::COneGeneReplicaMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector::COneGeneStochasticNetworkMinimizableDirector, CPC12AlternateMinimizableDirector::CPC12AlternateMinimizableDirector, CPC12RapMinusMinimizableDirector::CPC12RapMinusMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::CQuorumSensingNetworkMinimizableDirector, GetReactionNetwork, PC12EGFNGFMinimizableDirector::PC12EGFNGFMinimizableDirector, CReplicaMinimizableDirector::SetIntersectionLists, and ~NetworkMinimizableDirector.

double NetworkMinimizableDirector::m_dGammaSquared [protected]

Definition at line 56 of file NetworkMinimizableDirector.h. Referenced by CAlternateOneGeneInhibitoryNetworkMinimizableDirector::CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector::CCombinatorialNetworkMinimizableDirector, CCoupledOneGeneNetworksMinimizableDirector::CCoupledOneGeneNetworksMinimizableDirector, CCoupledPC12NetworksMinimizableDirector::CCoupledPC12NetworksMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector::CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingCoupledMinimizableDirector::CEGFRTraffickingCoupledMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector::CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingMinimizableDirector::CEGFRTraffickingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::CEGFRTraffickingNIH3T3MinimizableDirector, CForestNitrogenCyclingMinimizableDirector::CForestNitrogenCyclingMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector::CLaubLoomisDictyNetworkMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector::CMartielGoldbeterDictyNetworkMinimizableDirector, CReplicaMinimizableDirector::ComputeResiduals, ComputeResiduals, CEGFRTraffickingNIH3T3MinimizableDirector::ComputeResiduals, CEGFRTraffickingCHOMinimizableDirector::ComputeResiduals, COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector::COneGeneReplicaMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector::COneGeneStochasticNetworkMinimizableDirector, CPC12AlternateMinimizableDirector::CPC12AlternateMinimizableDirector, CPC12RapMinusMinimizableDirector::CPC12RapMinusMinimizableDirector, CQuorumSensingNetworkMinimizableDirector::CQuorumSensingNetworkMinimizableDirector, CSharedPC12NetworksMinimizableDirector::CSharedPC12NetworksMinimizableDirector, and PC12EGFNGFMinimizableDirector::PC12EGFNGFMinimizableDirector.

std::vector<int> NetworkMinimizableDirector::m_iPriorList [protected]

Definition at line 53 of file NetworkMinimizableDirector.h. Referenced by CEGFRTraffickingCHOMinimizableDirector::CEGFRTraffickingCHOMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector::CEGFRTraffickingNIH3T3MinimizableDirector, ComputeResiduals, CEGFRTraffickingNIH3T3MinimizableDirector::ComputeResiduals, CEGFRTraffickingCHOMinimizableDirector::ComputeResiduals, COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector, and CEGFRTraffickingNIH3T3MinimizableDirector::~CEGFRTraffickingNIH3T3MinimizableDirector.

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

• NetworkMinimizableDirector.h
• NetworkMinimizableDirector.cpp

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