lm::cme::SelfRegulatingGeneSwitch Class Reference

#include <SelfRegulatingGeneSwitch.h>

Inheritance diagram for lm::cme::SelfRegulatingGeneSwitch:

Collaboration diagram for lm::cme::SelfRegulatingGeneSwitch:

Classes
struct	OUKHillPropensityArgs

Public Member Functions
	SelfRegulatingGeneSwitch ()
virtual	~SelfRegulatingGeneSwitch ()
virtual bool	needsReactionModel ()
	Tells whether the solver needs a reaction model.
virtual bool	needsDiffusionModel ()
	Tells whether the solver needs a reaction model.
virtual void	generateTrajectory ()
	Actually run the simulation.
Public Member Functions inherited from lm::cme::NextReactionSolver
	NextReactionSolver ()
	NextReactionSolver (RandomGenerator::Distributions neededDists)
virtual	~NextReactionSolver ()
virtual void	buildModel (const uint numberSpecies, const uint numberReactions, const uint *initialSpeciesCounts, const uint *reactionType, const double *k, const int *S, const uint *D, const uint kCols=1)
Public Member Functions inherited from lm::cme::CMESolver
	CMESolver (RandomGenerator::Distributions neededDists)
virtual	~CMESolver ()
virtual void	initialize (unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)
	Initialize the simulation.
virtual void	setReactionModel (lm::io::ReactionModel *reactionModel)
virtual void	setModelPropensityFunction (uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg)
virtual void	setSpeciesUpperLimit (uint species, uint limit)
virtual void	setSpeciesLowerLimit (uint species, uint limit)
virtual void	setFptTrackingList (list< uint > speciesList)
virtual void	addToParameterTrackingList (pair< string, double * >parameter)
virtual void	setReactionRateCME (unsigned int reactionId, double rate)
virtual void	getSpeciesCountView (uint **counts, int *number)
virtual void	getReactionRateConstantsView (int reactionNumber, double **rates, int *rateConstantCount)
Public Member Functions inherited from lm::me::MESolver
	MESolver ()
	Create the MESolver.
virtual	~MESolver ()

Static Protected Member Functions
static double	ouKHillPropensity (double time, uint *speciesCounts, void *pargs)
Static Protected Member Functions inherited from lm::cme::CMESolver
static double	zerothOrderPropensity (double time, uint *speciesCounts, void *pargs)
static double	firstOrderPropensity (double time, uint *speciesCounts, void *pargs)
static double	secondOrderPropensity (double time, uint *speciesCounts, void *pargs)
static double	secondOrderSelfPropensity (double time, uint *speciesCounts, void *pargs)
static double	kHillPropensity (double time, uint *speciesCounts, void *pargs)
static double	kHillTransportPropensity (double time, uint *speciesCounts, void *pargs)
static double	zerothOrderHeavisidePropensity (double time, uint *speciesCounts, void *pargs)
static double	michaelisMentenPropensity (double time, uint *speciesCounts, void *pargs)
static double	competitiveMMPropensity (double time, uint *speciesCounts, void *pargs)
static double	uncompetitiveMMPropensity (double time, uint *speciesCounts, void *pargs)
static double	noncompetitiveMMPropensity (double time, uint *speciesCounts, void *pargs)

Additional Inherited Members
Protected Member Functions inherited from lm::cme::NextReactionSolver
virtual void	destroyModel ()
int	updateAllReactionEvents (double time, int rngNext, double *expRngValues)
int	updateReactionEvents (uint sourceReaction, double time, int rngNext, double *expRngValues)
virtual int	hookSimulation (double time)
Protected Member Functions inherited from lm::cme::CMESolver
virtual void	allocateModel (uint numberSpecies, uint numberReactions)
virtual double	recordParameters (double nextRecordTime, double recordInterval, double simulationTime)
virtual void	queueRecordedParameters (bool flush=false)
void	updateSpeciesCounts (uint r)
bool	reachedSpeciesLimit ()
virtual int	onBeginTrajectory ()
virtual int	onEndTrajectory ()
Protected Attributes inherited from lm::cme::NextReactionSolver
ReactionQueue *	reactionQueue
Protected Attributes inherited from lm::cme::CMESolver
RandomGenerator::Distributions	neededDists
unsigned int	replicate
map< string, string > *	parameters
ResourceAllocator::ComputeResources *	resources
RandomGenerator *	rng
uint	numberSpecies
uint	numberSpeciesToTrack
uint	numberReactions
uint *	initialSpeciesCounts
uint *	speciesCounts
uint *	reactionTypes
int *	S
uint *	D
void **	propensityFunctions
void **	propensityFunctionArgs
list< PropensityArgs * >	propensityArgs
uint	numberSpeciesLimits
SpeciesLimit *	speciesLimits
uint	numberFptTrackedSpecies
FPTTracking *	fptTrackedSpecies
list< TrackedParameter >	trackedParameters
uint *	numberDependentSpecies
uint **	dependentSpecies
int **	dependentSpeciesChange
uint *	numberDependentReactions
uint **	dependentReactions

Constructor & Destructor Documentation

SelfRegulatingGeneSwitch()

lm::cme::SelfRegulatingGeneSwitch::SelfRegulatingGeneSwitch

(

)

~SelfRegulatingGeneSwitch()

lm::cme::SelfRegulatingGeneSwitch::~SelfRegulatingGeneSwitch ( )

virtual

Member Function Documentation

generateTrajectory()

void lm::cme::SelfRegulatingGeneSwitch::generateTrajectory ( )

virtual

Actually run the simulation.

Reimplemented from lm::cme::NextReactionSolver.

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needsDiffusionModel()

virtual bool lm::cme::SelfRegulatingGeneSwitch::needsDiffusionModel ( )

inlinevirtual

Tells whether the solver needs a reaction model.

Reimplemented from lm::cme::NextReactionSolver.

needsReactionModel()

virtual bool lm::cme::SelfRegulatingGeneSwitch::needsReactionModel ( )

inlinevirtual

Tells whether the solver needs a reaction model.

Reimplemented from lm::cme::NextReactionSolver.

ouKHillPropensity()

double lm::cme::SelfRegulatingGeneSwitch::ouKHillPropensity ( double time, uint * speciesCounts, void * pargs )

staticprotected

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

• /data2/LM_zls_github/Lattice-Microbes/src/cme/SelfRegulatingGeneSwitch.h
• /data2/LM_zls_github/Lattice-Microbes/src/cme/SelfRegulatingGeneSwitch.cpp