Major class of iDynoMiCS - defines the agents that are involved in an iDynoMiCS simulation. Extended by a number of agent types. More...

Inheritance diagram for simulator.agent.Agent:

Public Member Functions
	Agent ()
	Initialise an agent object, setting its time of creation and thus the time it was last stepped. More...

void	initFromProtocolFile (Simulator aSimulator, XMLParser aSpeciesRoot)
	Initialise the agent from the protocol file. Implemented by classes that extend this class. More...

void	initFromResultFile (Simulator aSim, String[] singleAgentData)
	Create an agent using information in a previous state or initialisation file. More...

void	mutateAgent ()
	Mutates agent parameters. Implemented by classes that extend this class. More...

void	makeKid () throws CloneNotSupportedException
	Creates a new agent from an existing one, and registers this new agent in the simulation. More...

Object	clone () throws CloneNotSupportedException
	Clones this agent object, creating a new progeny of this agent. More...

abstract void	registerBirth ()
	Registers a created agent into a respective container. Each agent must be referenced by one such container. Implemented by classes that extend Agent. More...

void	step ()
	Perform the next timestep of the simulation for this agent. More...

String	sendHeader ()
	Used in creation of results files - specifies the header of the columns of output information for this agent. More...

String	writeOutput ()
	Used in creation of results files - creates an output string of information generated on this particular agent. More...

String	sendName ()
	Returns a string containing the family name and genealogy of this agent. More...

void	giveName ()
	Set the family for this agent, based on the next family. More...

Protected Member Functions
abstract void	internalStep ()
	Called at each time step (under the control of the method Step of the class Agent to avoid multiple calls) More...

void	recordGenealogy (Agent baby)
	Called when creating an agent : updates _generation and _genealogy field. More...

Protected Attributes
int	_lastStep

int	_generation = 0

long	_genealogy = 0

int	_family = 0

double	_birthday

Static Protected Attributes
static int	nextFamily = 0

Detailed Description

Major class of iDynoMiCS - defines the agents that are involved in an iDynoMiCS simulation. Extended by a number of agent types.

Major class of iDynoMiCS - defines the agents that are involved in an iDynoMiCS simulation. Extended by a number of agent types

Author: Andreas Dötsch (andre.nosp@m.as.d.nosp@m.oetsc.nosp@m.h@he.nosp@m.lmhol.nosp@m.tz-h.nosp@m.zi.de), Helmholtz Centre for Infection Research (Germany); Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France

Constructor & Destructor Documentation

simulator.agent.Agent.Agent ( )

Initialise an agent object, setting its time of creation and thus the time it was last stepped.

Initialise an agent object, setting its time of creation and thus the time it was last stepped

Member Function Documentation

Object simulator.agent.Agent.clone ( ) throws CloneNotSupportedException

Clones this agent object, creating a new progeny of this agent.

Clones this agent object, creating a new progeny of this agent

Exceptions

CloneNotSupportedException Exception should the class not implement Cloneable

void simulator.agent.Agent.giveName ( )

Set the family for this agent, based on the next family.

Set the family for this agent, based on the next family

void simulator.agent.Agent.initFromProtocolFile	(	Simulator	aSimulator,
		XMLParser	aSpeciesRoot
	)

Initialise the agent from the protocol file. Implemented by classes that extend this class.

Initialise the agent from the protocol file. Implemented by classes that extend this class

Parameters

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

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

Create an agent using information in a previous state or initialisation file.

Create an agent using information in a previous state or initialisation file

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
singleAgentData	Data from the result or initialisation file that is used to recreate this agent

abstract void simulator.agent.Agent.internalStep ( )

protectedpure virtual

Called at each time step (under the control of the method Step of the class Agent to avoid multiple calls)

Called at each time step (under the control of the method Step of the class Agent to avoid multiple calls). Implemented by classes that extend Agent

Implemented in simulator.agent.ActiveAgent, simulator.agent.LocatedAgent, simulator.agent.zoo.Bacterium, simulator.agent.zoo.ParticulateEPS, simulator.agent.zoo.MultiEpisome, simulator.agent.zoo.Episome, simulator.agent.zoo.BactAdaptable, simulator.agent.zoo.BactEPS, and simulator.agent.InfoAgent.

void simulator.agent.Agent.makeKid ( ) throws CloneNotSupportedException

Creates a new agent from an existing one, and registers this new agent in the simulation.

Creates a new agent from an existing one, and registers this new agent in the simulation

Exceptions

CloneNotSupportedException Exception should the class not implement Cloneable

void simulator.agent.Agent.mutateAgent ( )

Mutates agent parameters. Implemented by classes that extend this class.

Implemented by classes that extend this class

void simulator.agent.Agent.recordGenealogy ( Agent baby )

protected

Called when creating an agent : updates _generation and _genealogy field.

Called when creating an agent : updates _generation and _genealogy field

Parameters

baby	The newly created agent that is the next generation of this agent

abstract void simulator.agent.Agent.registerBirth ( )

pure virtual

Registers a created agent into a respective container. Each agent must be referenced by one such container. Implemented by classes that extend Agent.

Registers a created agent into a respective container. Each agent must be referenced by one such container. Implemented by classes that extend Agent

Implemented in simulator.agent.ActiveAgent, simulator.agent.LocatedAgent, simulator.agent.zoo.MultiEpisome, simulator.agent.zoo.Episome, and simulator.agent.SpecialisedAgent.

String simulator.agent.Agent.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

String simulator.agent.Agent.sendName ( )

Returns a string containing the family name and genealogy of this agent.

Returns a string containing the family name and genealogy of this agent

Returns: String containing the family name and genealogy of this agent

void simulator.agent.Agent.step ( )

Perform the next timestep of the simulation for this agent.

Perform the next timestep of the simulation for this agent. _lastStep is implemented to note that the agent has been stepped. Implemented fully by agent types that extend Agent

String simulator.agent.Agent.writeOutput ( )

Used in creation of results files - creates an output string of information generated on this particular agent.

Used in creation of results files - creates an output string of information generated on this particular agent

Returns: String containing results associated with this agent

Member Data Documentation

double simulator.agent.Agent._birthday

protected

Timestep at which this agent was created

int simulator.agent.Agent._family = 0

protected

Integer noting the family which this agent belongs to

long simulator.agent.Agent._genealogy = 0

protected

Integer for the binary reading of the 0 and 1 coding the lineage. When a cells divides, one daughter has the index value 1, the other the index value 0, then this index is added on the left of the lineage description

int simulator.agent.Agent._generation = 0

protected

The number of generations between the progenitor and the current agent

int simulator.agent.Agent._lastStep

protected

Integer noting the last simulation timestep when this agent was stepped

int simulator.agent.Agent.nextFamily = 0

staticprotected

Integer noting the next family that any newly created agent will belong to

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/agent/Agent.java

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation