simulator.agent.zoo.MultiEpisome Class Reference

Inheritance diagram for simulator.agent.zoo.MultiEpisome:

Public Member Functions
	MultiEpisome ()
Object	clone () throws CloneNotSupportedException
void	setHost (MultiEpiBac anHost)
void	initFromProtocolFile (Simulator aSim, XMLParser xmlMarkUp)
MultiEpisome	reset (MultiEpisome aPlasmid)
void	init ()
MultiEpisome	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 (double elapsedHGTtime)
void	replication ()
void	die ()
double	getPilusLength ()
void	givePlasmid (double elapsedHGTtime)
void	receivedPlasmid ()
void	segregation (MultiEpisome aPlasmid)
MultiEpisomeParam	getSpeciesParam ()
	Return the set of parameters that is associated with the object of this species. More...
int	getCopyNumber ()
void	setCopyNumber (int value)
void	increaseCopyNumber ()
void	setDefaultCopyNumber ()
void	setInitialCopyNumber ()
boolean	isTransConjugant ()
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
MultiEpiBac	_host
double	_nCopy
double	lastExchange =0
double	_newT =0
boolean	isHot = false
Reaction[]	allReactions

Protected Attributes
ArrayList< Integer >	reactionActive
ArrayList< Integer >	reactionKnown
LinkedList< LocatedAgent >	nbhList = new LinkedList<LocatedAgent>()

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.MultiEpisome.MultiEpisome

(

)

Member Function Documentation

Object simulator.agent.zoo.MultiEpisome.clone

(

)

throws CloneNotSupportedException

void simulator.agent.zoo.MultiEpisome.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.MultiEpisome.die

(

)

int simulator.agent.zoo.MultiEpisome.getCopyNumber

(

)

double simulator.agent.zoo.MultiEpisome.getPilusLength

(

)

MultiEpisomeParam simulator.agent.zoo.MultiEpisome.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.MultiEpisome.givePlasmid

(

double

elapsedHGTtime

)

You are doing a conjugation ! Update your parameters

void simulator.agent.zoo.MultiEpisome.increaseCopyNumber

(

)

sonia: to be used in increasing the copy number of a plasmid when this is received by a cell that already contains a plasmid of this type. - which will never happen due to entry exclusion systems...

void simulator.agent.zoo.MultiEpisome.init

(

)

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

See Also

sendNewAgent()

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

void simulator.agent.zoo.MultiEpisome.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.MultiEpisome.isReadyToConjugate

(

double

elapsedHGTtime

)

Test if the episome can be transfered

boolean simulator.agent.zoo.MultiEpisome.isTransConjugant

(

)

void simulator.agent.zoo.MultiEpisome.makeKid

(

)

throws CloneNotSupportedException

void simulator.agent.zoo.MultiEpisome.mutateAgent

(

)

void simulator.agent.zoo.MultiEpisome.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.MultiEpisome.receivedPlasmid

(

)

sonia:14-05-09 Set the lastReception field to the current time which corresponds to the time the cell received the plasmid.

void simulator.agent.zoo.MultiEpisome.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.MultiEpisome.replication

(

)

NOT BEING USED Number of plasmid copies is doubled at the doubling speed rate until the maximal value is reached

MultiEpisome simulator.agent.zoo.MultiEpisome.reset

(

MultiEpisome

aPlasmid

)

void simulator.agent.zoo.MultiEpisome.segregation

(

MultiEpisome

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

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

String simulator.agent.zoo.MultiEpisome.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.

MultiEpisome simulator.agent.zoo.MultiEpisome.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.MultiEpisome.setCopyNumber

(

int

value

)

void simulator.agent.zoo.MultiEpisome.setDefaultCopyNumber

(

)

void simulator.agent.zoo.MultiEpisome.setHost

(

MultiEpiBac

anHost

)

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

Parameters

anHost

void simulator.agent.zoo.MultiEpisome.setInitialCopyNumber

(

)

sonia: used in conjugation events: when a cell receives a plasmid, it will start off with just one copy

String simulator.agent.zoo.MultiEpisome.writeOutput

(

)

Member Data Documentation

MultiEpiBac simulator.agent.zoo.MultiEpisome._host

double simulator.agent.zoo.MultiEpisome._nCopy

double simulator.agent.zoo.MultiEpisome._newT =0

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

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

double simulator.agent.zoo.MultiEpisome.lastExchange =0

LinkedList<LocatedAgent> simulator.agent.zoo.MultiEpisome.nbhList = new LinkedList<LocatedAgent>()

protected

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

protected

ArrayList<Integer> simulator.agent.zoo.MultiEpisome.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/MultiEpisome.java