Extension of Agent class, adds location and parameter information for an object of a particular species in the simulation. More...

Inheritance diagram for simulator.agent.SpecialisedAgent:

Public Member Functions
	SpecialisedAgent ()
	Creates a SpecialisedAgent object and initialises the object in which associated parameters are stored. More...

void	initFromProtocolFile (Simulator aSim, XMLParser aSpeciesRoot)
	Creates an agent of the specified species and notes the grid in which this is assigned. More...

Object	clone () throws CloneNotSupportedException
	Clones this agent object, creating a new progeny of this agent. Ensures new clone inherits same parameters as parents. More...

abstract void	createNewAgent ()
	Create a new agent with mutated parameters based on species default values. More...

abstract SpecialisedAgent	sendNewAgent () throws CloneNotSupportedException

void	mutateAgent ()
	Mutate any inherited parameters for this particular agent. More...

void	mutatePop ()
	Mutate any inherited parameters for a population of agents. More...

void	registerBirth ()
	Registers a created agent into a respective container. Each agent must be referenced by one such container. More...

void	die (boolean isStarving)
	Notifies the simulation that this agent has become too small and is then counted as dead. More...

double	move ()
	Used in the calculation of delta move in Agent Container class. Will investigate further why this class returns 0. More...

void	setSpeciesParam (SpeciesParam aSpeciesParam)
	Set the species parameters to a specified Species Parameter object. More...

SpeciesParam	getSpeciesParam ()

Species	getSpecies ()
	Returns the species object that is represented by this agent. More...

void	setSpecies (Species aSpecies)
	Set the progenitor Specialised agent to a specified species. More...

String	getName ()
	Return the name of the species represented by this agent. More...

boolean	willDetach ()
	Returns a boolean noting whether this agent is detached and may be removed in sloughing. Implemented by extending classes. More...

int	getGridIndex ()
	Returns the integer grid index where this agent resides. Implemented by extending classes. More...

double	interact (boolean MUTUAL, boolean pull, boolean seq, double gain)
	Models a mechanical interaction between two located agents. Implemented by extending classes (LocatedAgent) More...

boolean	isMoving ()
	Returns a boolean noting whether this agent is moving due to growth and sloughing. Implemented by extending classes. More...

void	writePOVColorDefinition (FileWriter fr) throws IOException
	Used in POV-Ray output to display this species - writes a colour definition to the passed-in file. More...

Public Member Functions inherited from simulator.agent.Agent
	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...

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...

Public Member Functions inherited from simulator.agent.HasSpecies
String	sendHeader ()
	Used in creation of results files - specifies the header of the columns of output information for this agent. More...

Public Attributes
int	speciesIndex

boolean	isDead = false

String	death

Protected Attributes
Species	_species

SpeciesParam	_speciesParam

AgentContainer	_agentGrid

Protected Attributes inherited from simulator.agent.Agent
int	_lastStep

int	_generation = 0

long	_genealogy = 0

int	_family = 0

double	_birthday

Additional Inherited Members
Protected Member Functions inherited from simulator.agent.Agent
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...

Static Protected Attributes inherited from simulator.agent.Agent
static int	nextFamily = 0

Detailed Description

Extension of Agent class, adds location and parameter information for an object of a particular species in the simulation.

Extension of Agent class, adds location and parameter information for an object of a particular species in the simulation

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.SpecialisedAgent.SpecialisedAgent ( )

Creates a SpecialisedAgent object and initialises the object in which associated parameters are stored.

Creates a SpecialisedAgent object and initialises the object in which associated parameters are stored

Member Function Documentation

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

Clones this agent object, creating a new progeny of this agent. Ensures new clone inherits same parameters as parents.

Clones this agent object, creating a new progeny of this agent. Ensures new clone inherits same parameters as parents

Exceptions

CloneNotSupportedException Exception should the class not implement Cloneable

abstract void simulator.agent.SpecialisedAgent.createNewAgent ( )

pure virtual

Create a new agent with mutated parameters based on species default values.

Create a new agent with mutated parameters based on species default values

Implements simulator.agent.HasSpecies.

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

void simulator.agent.SpecialisedAgent.die ( boolean isStarving )

Notifies the simulation that this agent has become too small and is then counted as dead.

Notifies the simulation that this agent has become too small and is then counted as dead. Decreases the population of this species

Parameters

isStarving Boolean noting whether the agent currently has access to any resources

int simulator.agent.SpecialisedAgent.getGridIndex ( )

Returns the integer grid index where this agent resides. Implemented by extending classes.

Returns the integer grid index where this agent resides. Implemented by extending classes

Returns: Integer grid index where this agent is located within

String simulator.agent.SpecialisedAgent.getName ( )

Return the name of the species represented by this agent.

Return the name of the species represented by this agent

Returns: Name of the species represented

Species simulator.agent.SpecialisedAgent.getSpecies ( )

Returns the species object that is represented by this agent.

Returns the species object that is represented by this agent

Returns: Object of the Species class that this agent is representing

SpeciesParam simulator.agent.SpecialisedAgent.getSpeciesParam ( )

Returns the object containing a set of parameters associated with a particular agent (species)

Implements simulator.agent.HasSpecies.

void simulator.agent.SpecialisedAgent.initFromProtocolFile	(	Simulator	aSim,
		XMLParser	aSpeciesRoot
	)

Creates an agent of the specified species and notes the grid in which this is assigned.

Creates an agent of the specified species and notes the grid in which this is assigned

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

double simulator.agent.SpecialisedAgent.interact	(	boolean	MUTUAL,
		boolean	pull,
		boolean	seq,
		double	gain
	)

Models a mechanical interaction between two located agents. Implemented by extending classes (LocatedAgent)

Parameters

MUTUAL	Whether movement is shared between two agents or applied only to this one
pull	Boolean noting whether this action is shoving (false) or pulling (shrinking biofilm) (true)
seq	Whether the move should be applied immediately or wait until the end of the step
gain	Double noting change in position

Returns: The move to be applied once the shoving or pull calculations have been performed

boolean simulator.agent.SpecialisedAgent.isMoving ( )

Returns a boolean noting whether this agent is moving due to growth and sloughing. Implemented by extending classes.

Returns a boolean noting whether this agent is moving due to growth and sloughing. Implemented by extending classes

Returns: Boolean noting whether or not this agent is moving

double simulator.agent.SpecialisedAgent.move ( )

Used in the calculation of delta move in Agent Container class. Will investigate further why this class returns 0.

Used in the calculation of delta move in Agent Container class. Will investigate further why this class returns 0

Returns: 0

void simulator.agent.SpecialisedAgent.mutateAgent ( )

Mutate any inherited parameters for this particular agent.

Mutate any inherited parameters for this particular agent. KA June 2013 - not sure this action is implemented

void simulator.agent.SpecialisedAgent.mutatePop ( )

Mutate any inherited parameters for a population of agents.

Mutate any inherited parameters for a population of agents. KA June 2013 - not sure this action is implemented

Implements simulator.agent.HasSpecies.

void simulator.agent.SpecialisedAgent.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

Implements simulator.agent.Agent.

Reimplemented in simulator.agent.zoo.MultiEpisome, and simulator.agent.zoo.Episome.

abstract SpecialisedAgent simulator.agent.SpecialisedAgent.sendNewAgent ( ) throws CloneNotSupportedException

pure virtual

Implemented by classes that extend this class - obtain another instance of the same species (totally independent)

Implements simulator.agent.HasSpecies.

Implemented in simulator.agent.zoo.Bacterium, simulator.agent.zoo.MultiEpisome, simulator.agent.zoo.Episome, and simulator.agent.zoo.ParticulateEPS.

void simulator.agent.SpecialisedAgent.setSpecies ( Species aSpecies )

Set the progenitor Specialised agent to a specified species.

Set the progenitor Specialised agent to a specified species. New agents of this species are created using this information

Parameters

aSpecies A species object to use as the progenitor

Implements simulator.agent.HasSpecies.

void simulator.agent.SpecialisedAgent.setSpeciesParam ( SpeciesParam aSpeciesParam )

Set the species parameters to a specified Species Parameter object.

Set the species parameters to a specified Species Parameter object

Parameters

aSpeciesParam

boolean simulator.agent.SpecialisedAgent.willDetach ( )

Returns a boolean noting whether this agent is detached and may be removed in sloughing. Implemented by extending classes.

Returns a boolean noting whether this agent is detached and may be removed in sloughing. Implemented by extending classes

Returns: Boolean value noting whether this agent will be detached

void simulator.agent.SpecialisedAgent.writePOVColorDefinition ( FileWriter fr ) throws IOException

Used in POV-Ray output to display this species - writes a colour definition to the passed-in file.

Used in POV-Ray output to display this species. This writes a color definition to the passed-in file. Meant for later use in macros. Note that this routine is put here and not in Species to allow derived agents to use different colors for different states; EpiBac is one example, with different colors for donor, recipient, and transconjugant states

Parameters

fr	POV-Ray output file where the colour definition should be applied

Member Data Documentation

AgentContainer simulator.agent.SpecialisedAgent._agentGrid

protected

Grid in which this agent is contained

Species simulator.agent.SpecialisedAgent._species

protected

Type of species that this agent is representing

SpeciesParam simulator.agent.SpecialisedAgent._speciesParam

protected

Set of parameters associated with this specialised agent

String simulator.agent.SpecialisedAgent.death

Reason for agent's death. Added by Sonia Martins April 2010

boolean simulator.agent.SpecialisedAgent.isDead = false

Boolean noting whether this agent is still active in the simulation

int simulator.agent.SpecialisedAgent.speciesIndex

Integer index to that species within the simulation dictionary

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

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

Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation