Creates a parameter object for BactAdaptable, a Bacterium agent object that can change its reaction based on local conditions. More...

Inheritance diagram for simulator.agent.zoo.BactAdaptableParam:

Public Member Functions
	BactAdaptableParam ()
	Creates a parameter storage object for the BactAdaptable species type. More...

void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Initialises BactAdaptable Species parameters, calling the relevant superclasses to initialise common parameters and then setting up the reaction switch. More...

Public Member Functions inherited from simulator.agent.zoo.BactEPSParam
	BactEPSParam ()
	Creates a parameter storage object for the Bacterium EPS species type. More...

void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Initialises Bacterium EPS Species parameters, calling the relevant superclasses to initialise common parameters and reading in the hydrolysis speed. More...

Public Member Functions inherited from simulator.agent.zoo.BacteriumParam
	BacteriumParam ()
	Constructor to create a BacteriumParam parameter storage object. More...

void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Initialises Bacterium species parameters, calling the relevant superclasses to initialise common parameters for Bacterium derived species. More...

Public Member Functions inherited from simulator.agent.LocatedParam
	LocatedParam ()
	Create a new LocatedParam parameter storage object, calling the relevant extended class constructors. More...

void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Assigns values to each of the location and behavioural specific parameters, reading these from the protocol file. More...

double	getCellRunSpeed ()
	Return the cell run speed. Used in agent self-attachment scenarios. More...

double	getStickinessRadius ()
	Return the cell stickiness radius. Used in agent self-attachment scenarios. More...

Public Member Functions inherited from simulator.agent.ActiveParam
void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction. More...

Public Member Functions inherited from simulator.agent.SpeciesParam
void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Read in specific parameters for this species, changing the default if required. More...

Public Attributes
Color	onColor

Color	offColor

Public Attributes inherited from simulator.agent.zoo.BactEPSParam
double	kHyd = 0.007

Public Attributes inherited from simulator.agent.zoo.BacteriumParam
double	epsMax = .15

Color	epsColor = Color.lightGray

Boolean	distMethod = false

Public Attributes inherited from simulator.agent.LocatedParam
double	divRadius = .97

double	divRadiusCV = .1

double	babyMassFrac = .5

double	babyMassFracCV = .1

double	deathRadius = .2

double	deathRadiusCV = .1

double	shoveFactor = 1.15

double	shoveLimit = 0

double	cellRunSpeed

double	tumbleInterval

double	stickinessAddition

Public Attributes inherited from simulator.agent.ActiveParam
double[]	particleDensity

double[][]	soluteYield

double[][]	particleYield

double[][]	reactionKinetic

double[]	lysisYield

Public Attributes inherited from simulator.agent.SpeciesParam
double	initialMassCV = .1

Protected Attributes
SoluteGrid[]	_soluteList

ArrayList< Integer >	onStateReactions

ArrayList< Integer >	offStateReactions

String	switchType

String	switchControl

int	switchControlIndex

String	switchCondition

double	switchValue

double	lagSwitchOn = 1.0

double	lagSwitchOff = 1.0

Detailed Description

Creates a parameter object for BactAdaptable, a Bacterium agent object that can change its reaction based on local conditions.

Creates a parameter object for BactAdaptable, a Bacterium agent object that can change its reaction based on local conditions

Author: Brian Merkey (brim@.nosp@m.env..nosp@m.dtu.d.nosp@m.k, bvm@n.nosp@m.orth.nosp@m.weste.nosp@m.rn.e.nosp@m.du), Department of Engineering Sciences and Applied Mathematics, Northwestern University (USA)

Constructor & Destructor Documentation

simulator.agent.zoo.BactAdaptableParam.BactAdaptableParam ( )

Creates a parameter storage object for the BactAdaptable species type.

Creates a parameter storage object for the BactAdaptable species type

Member Function Documentation

void simulator.agent.zoo.BactAdaptableParam.init	(	Simulator	aSim,
		XMLParser	aSpeciesRoot
	)

Initialises BactAdaptable Species parameters, calling the relevant superclasses to initialise common parameters and then setting up the reaction switch.

Initialises Bacterium EPS Species parameters, calling the relevant superclasses to initialise common parameters and then setting up the reaction switch

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
aSpeciesRoot	A species mark-up within the specified protocol file

Member Data Documentation

SoluteGrid [] simulator.agent.zoo.BactAdaptableParam._soluteList

protected

Array used to read the solute concentrations

double simulator.agent.zoo.BactAdaptableParam.lagSwitchOff = 1.0

protected

Lag time before switch actually changes after a request to change it, to capture microbial metabolic delays

double simulator.agent.zoo.BactAdaptableParam.lagSwitchOn = 1.0

protected

Lag time before switch actually changes after a request to change it, to capture microbial metabolic delays

Color simulator.agent.zoo.BactAdaptableParam.offColor

Colour to be used by POV-Ray to show objects of this species when the reaction switch is off

ArrayList<Integer> simulator.agent.zoo.BactAdaptableParam.offStateReactions

protected

Subsets of all known reactions which take place when the switch is set to off. Contains indices to be used in referencing the allReactions array

Color simulator.agent.zoo.BactAdaptableParam.onColor

Colour to be used by POV-Ray to show objects of this species when the reaction switch is on

ArrayList<Integer> simulator.agent.zoo.BactAdaptableParam.onStateReactions

protected

Subsets of all known reactions which take place when the switch is set to on. Contains indices to be used in referencing the allReactions array

String simulator.agent.zoo.BactAdaptableParam.switchCondition

protected

Used in the onCondtion reaction mark-up - tests switch changing thresholds. Can be lessThan or greaterThan

String simulator.agent.zoo.BactAdaptableParam.switchControl

protected

The name of the component that is controlling the value of this switch (e.g. o2d)

int simulator.agent.zoo.BactAdaptableParam.switchControlIndex

protected

Integer index of the particle or reaction in the simulation dictionary

String simulator.agent.zoo.BactAdaptableParam.switchType

protected

The factor controlling what changes the value of this switch - the local solute concentration or agents biomass amount

double simulator.agent.zoo.BactAdaptableParam.switchValue

protected

The value (concentration or mass) that will prompt the changing of the reaction switch

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/agent/zoo/BactAdaptableParam.java

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation