simulator.agent.zoo.Episome Class Reference

Inheritance diagram for simulator.agent.zoo.Episome:

Public Member Functions
	Episome ()
Object	clone () throws CloneNotSupportedException
void	setHost (EpiBac anHost)
EpiBac	getHost ()
void	initFromProtocolFile (Simulator aSim, XMLParser xmlMarkUp)
void	initFromResultFile (Simulator aSim, String[] singleAgentData)
void	init ()
Episome	sendNewAgent () throws CloneNotSupportedException
	Obtain another instance of the same species (totally independent). The returned agent is NOT registered. More...
void	createNewAgent ()
	Create a new progenitor with random deviation of the parameters. More...
void	mutatePop ()
	Mutates inherited parameters and distributes particle mass - either exponentially or normally, dependent on value of distMethod. More...
void	registerBirth ()
	Registers a created agent into a respective container. Each agent must be referenced by one such container. More...
void	makeKid () throws CloneNotSupportedException
void	mutateAgent ()
void	internalStep ()
	Called at each time step of the simulation to compute agent characteristics. More...
boolean	isReadyToConjugate ()
void	die ()
double	getPilusRange ()
void	givePlasmid (Episome baby)
void	segregation (Episome aPlasmid)
EpisomeParam	getSpeciesParam ()
	Return the set of parameters that is associated with the object of this species. More...
int	getCopyNumber ()
void	setDefaultCopyNumber ()
boolean	testProficiency ()
boolean	isCompatible (Episome aPlasmid)
int	giveStatus ()
String	sendHeader ()
	Used in creation of results files - specifies the header of the columns of output information for this agent. More...
String	writeOutput ()

Public Attributes
double	lastExchange
boolean	isHot = false
Reaction[]	allReactions

Protected Attributes
EpiBac	_host
double	_nCopy
double	_pilusLength
boolean	_isRepressed = false
ArrayList< Integer >	reactionActive
ArrayList< Integer >	reactionKnown

Additional Inherited Members
Protected Member Functions inherited from simulator.agent.Agent
void	recordGenealogy (Agent baby)
	Called when creating an agent : updates _generation and _genealogy field. More...
Static Protected Attributes inherited from simulator.agent.Agent
static int	nextFamily = 0

Constructor & Destructor Documentation

simulator.agent.zoo.Episome.Episome

(

)

Member Function Documentation

Object simulator.agent.zoo.Episome.clone

(

)

throws CloneNotSupportedException

void simulator.agent.zoo.Episome.createNewAgent

(

)

Create a new progenitor with random deviation of the parameters.

Create a new progenitor with random deviation of the parameters

Exceptions

CloneNotSupportedException

Exception thrown if the object cannot be cloned

Implements simulator.agent.HasSpecies.

void simulator.agent.zoo.Episome.die

(

)

int simulator.agent.zoo.Episome.getCopyNumber

(

)

EpiBac simulator.agent.zoo.Episome.getHost

(

)

double simulator.agent.zoo.Episome.getPilusRange

(

)

EpisomeParam simulator.agent.zoo.Episome.getSpeciesParam

(

)

Return the set of parameters that is associated with the object of this species.

Return the set of parameters that is associated with the object of this species

Returns

Object of BacteriumParam that stores the parameters associated with this species

Implements simulator.agent.HasSpecies.

void simulator.agent.zoo.Episome.givePlasmid

(

Episome

baby

)

You are doing a conjugation ! Update your parameters

int simulator.agent.zoo.Episome.giveStatus

(

)

void simulator.agent.zoo.Episome.init

(

)

Used to initialize any new agent (progenitor or daughter cell)

See Also

sendNewAgent()

void simulator.agent.zoo.Episome.initFromProtocolFile	(	Simulator	aSim,
		XMLParser	xmlMarkUp
	)

void simulator.agent.zoo.Episome.initFromResultFile	(	Simulator	aSim,
		String[]	singleAgentData
	)

void simulator.agent.zoo.Episome.internalStep ( )

virtual

Called at each time step of the simulation to compute agent characteristics.

Called at each time step of the simulation to compute agent characteristics

Implements simulator.agent.InfoAgent.

boolean simulator.agent.zoo.Episome.isCompatible

(

Episome

aPlasmid

)

boolean simulator.agent.zoo.Episome.isReadyToConjugate

(

)

test if the episome can be transfered

void simulator.agent.zoo.Episome.makeKid

(

)

throws CloneNotSupportedException

void simulator.agent.zoo.Episome.mutateAgent

(

)

void simulator.agent.zoo.Episome.mutatePop

(

)

Mutates inherited parameters and distributes particle mass - either exponentially or normally, dependent on value of distMethod.

Mutates inherited parameters and distributes particle mass - either exponentially or normally, dependent on value of distMethod

Implements simulator.agent.HasSpecies.

void simulator.agent.zoo.Episome.registerBirth ( )

virtual

Registers a created agent into a respective container. Each agent must be referenced by one such container.

Registers a created agent into a respective container. Each agent must be referenced by one such container. In this case, the species is registered into the agent grid

Reimplemented from simulator.agent.SpecialisedAgent.

void simulator.agent.zoo.Episome.segregation

(

Episome

aPlasmid

)

Called during the division of an EpiBac ; apply the segregation of plasmids, modify the number for the plasmid calling the method and sends the number for the other one

Returns

String simulator.agent.zoo.Episome.sendHeader

(

)

Used in creation of results files - specifies the header of the columns of output information for this agent.

Used in creation of results files - specifies the header of the columns of output information for this agent

Returns

String specifying the header of each column of results associated with this agent

Implements simulator.agent.HasSpecies.

Episome simulator.agent.zoo.Episome.sendNewAgent

(

)

throws CloneNotSupportedException

Obtain another instance of the same species (totally independent). The returned agent is NOT registered.

Obtain another instance of the same species (totally independent). The returned agent is NOT registered

Exceptions

CloneNotSupportedException

Exception thrown if the object cannot be cloned

Implements simulator.agent.HasSpecies.

void simulator.agent.zoo.Episome.setDefaultCopyNumber

(

)

void simulator.agent.zoo.Episome.setHost

(

EpiBac

anHost

)

Attributes the plasmid to an host (used for conjugation events)

Parameters

anHost

boolean simulator.agent.zoo.Episome.testProficiency

(

)

String simulator.agent.zoo.Episome.writeOutput

(

)

Member Data Documentation

EpiBac simulator.agent.zoo.Episome._host

protected

boolean simulator.agent.zoo.Episome._isRepressed = false

protected

double simulator.agent.zoo.Episome._nCopy

protected

double simulator.agent.zoo.Episome._pilusLength

protected

Reaction [] simulator.agent.zoo.Episome.allReactions

boolean simulator.agent.zoo.Episome.isHot = false

double simulator.agent.zoo.Episome.lastExchange

ArrayList<Integer> simulator.agent.zoo.Episome.reactionActive

protected

ArrayList<Integer> simulator.agent.zoo.Episome.reactionKnown

protected

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

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