Extension of Agent and SpecialisedAgent - adds reaction information to model agent involvement in reactions. More...

Inheritance diagram for simulator.agent.ActiveAgent:

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

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

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

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

void	createNewAgent ()
	Create a new agent with mutated parameters based on species default values. Agent is not located. More...

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

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

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

void	updateSize ()
	Update size of agent to take growth into account. More...

void	updateMass ()
	Update mass of agent, summing the particle mass. More...

void	addReaction (Reaction aReaction, boolean useDefaultParam)
	Add the reaction to the list of known reactions. More...

void	addActiveReaction (Reaction aReaction, boolean useDefaultParam)
	Adds an active reaction to the list of known reactions and switches the reaction on. More...

void	removeReaction (Reaction aPathway)
	Remove a reaction from the list of known reactions. More...

void	switchOffreaction (Reaction aPathway)
	Switches off a reaction by removing it from the active reaction array. More...

void	switchOnReaction (Reaction aReaction)
	Switches on a reaction by adding it to the active reaction array. More...

void	registerOnAllActiveReaction ()
	Register the agent on each guild of its activated pathways. Called by makeKid. More...

void	unregisterFromAllActiveReactions ()
	Called by the die method, to unregister the agent from all active reactions. More...

void	fitMassOnGrid (SpatialGrid aSpG, int catalystIndex)
	Add the reacting concentration of an agent to the received grid. More...

void	fitReacRateOnGrid (SpatialGrid aRateGrid, int reactionIndex)
	Add the reaction/growth rate of an agent on received grid, for a specified reaction. More...

void	fitMassOnGrid (SpatialGrid aSpG)
	Add the total concentration of an agent on received grid. 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...

double	getTotalMass ()
	Return total mass of this agent. More...

double	getParticleMass (int particleIndex)
	Return particle mass of this agent. More...

double	getNetGrowth ()
	Return net growth rate of this agent. More...

double	getVolGrowth ()
	Return volume growth rate of this agent. More...

void	setNetGrowth (double value)
	Set net growth rate of this agent. More...

double[]	getSoluteYield (int indexReaction)
	Return solute yield for a particular reaction. More...

double[]	getReactionKinetic (int indexReaction)
	Return the reaction kinetic parameters for a particular reaction. More...

ActiveParam	getSpeciesParam ()
	Return the parameters associated with this agent (speciesParam) More...

Public Member Functions inherited from simulator.agent.SpecialisedAgent
	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 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 Attributes
Reaction[]	allReactions

double[][]	soluteYield

double[][]	reactionKinetic

double[][]	particleYield

double[]	particleMass

Public Attributes inherited from simulator.agent.SpecialisedAgent
int	speciesIndex

boolean	isDead = false

String	death

Protected Member Functions
void	internalStep ()
	Called at each time step of the simulation to compute cell growth, update size, and monitor cell death and division. More...

void	grow ()

Protected Attributes
ArrayList< Integer >	reactionActive

ArrayList< Integer >	reactionKnown

double	_netGrowthRate = 0

double	_netVolumeRate = 0

double[]	growthRate

double	_totalMass

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

Detailed Description

Extension of Agent and SpecialisedAgent - adds reaction information to model agent involvement in reactions.

Extension of Agent and SpecialisedAgent - adds reaction information to model agent involvement in reactions

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; 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.ActiveAgent.ActiveAgent ( )

Creates an ActiveAgent object and initialises the object in which associated parameters are stored.

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

Member Function Documentation

void simulator.agent.ActiveAgent.addActiveReaction	(	Reaction	aReaction,
		boolean	useDefaultParam
	)

Adds an active reaction to the list of known reactions and switches the reaction on.

Adds an active reaction to the list of known reactions and switches the reaction on

Parameters

aReaction	The reaction to add to the list
useDefaultParam	Whether to use default reaction parameters or bespoke parameters have been specified in the protocol file

Implements simulator.agent.HasReaction.

void simulator.agent.ActiveAgent.addReaction	(	Reaction	aReaction,
		boolean	useDefaultParam
	)

Add the reaction to the list of known reactions.

Add the reaction to the list of known reactions

Parameters

aReaction	The reaction to add to the list
useDefaultParam	Whether to use default reaction parameters or bespoke parameters have been specified in the protocol file

Implements simulator.agent.HasReaction.

Object simulator.agent.ActiveAgent.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

void simulator.agent.ActiveAgent.createNewAgent ( )

virtual

Create a new agent with mutated parameters based on species default values. Agent is not located.

Create a new agent with mutated parameters based on species default values. Agent is not located

Implements simulator.agent.SpecialisedAgent.

void simulator.agent.ActiveAgent.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

void simulator.agent.ActiveAgent.fitMassOnGrid	(	SpatialGrid	aSpG,
		int	catalystIndex
	)

Add the reacting concentration of an agent to the received grid.

Add the reacting concentration of an agent to the received grid

Parameters

aSpG	Spatial grid used to sum catalysing mass
catalystIndex	Index of the compartment of the cell supporting the reaction

void simulator.agent.ActiveAgent.fitMassOnGrid ( SpatialGrid aSpG )

Add the total concentration of an agent on received grid.

Add the total concentration of an agent on received grid

Parameters

aSpG	Spatial grid used to sum total mass

void simulator.agent.ActiveAgent.fitReacRateOnGrid	(	SpatialGrid	aRateGrid,
		int	reactionIndex
	)

Add the reaction/growth rate of an agent on received grid, for a specified reaction.

Add the total reaction/growth rate of an agent on received grid, for a specified reaction

Parameters

aRateGrid	Spatial grid used to store total reaction rate
reactionIndex	Index of this declared reaction in the simulation dictionary

double simulator.agent.ActiveAgent.getNetGrowth ( )

Return net growth rate of this agent.

Return net growth rate of this agent

Returns: Double stating the net growth rate of this agent

double simulator.agent.ActiveAgent.getParticleMass ( int particleIndex )

Return particle mass of this agent.

Return particle mass of this agent

Returns: Double stating the particle mass of this agent

double [] simulator.agent.ActiveAgent.getReactionKinetic ( int indexReaction )

Return the reaction kinetic parameters for a particular reaction.

Return rection kinetic parameters for a particular reaction

Parameters

indexReaction Index to a reaction in the simulation dictionary

Returns: Double array of the rection kinetic parameters for that reaction

double [] simulator.agent.ActiveAgent.getSoluteYield ( int indexReaction )

Return solute yield for a particular reaction.

Return solute yield for a particular reaction

Parameters

indexReaction Index to a reaction in the simulation dictionary

Returns: Double array of the solute yields for that reaction

ActiveParam simulator.agent.ActiveAgent.getSpeciesParam ( )

Return the parameters associated with this agent (speciesParam)

Returns: ActiveParam object containing the species associated with this agent

Implements simulator.agent.HasSpecies.

double simulator.agent.ActiveAgent.getTotalMass ( )

Return total mass of this agent.

Return total mass of this agent

Returns: Double stating the total mass of this agent

double simulator.agent.ActiveAgent.getVolGrowth ( )

Return volume growth rate of this agent.

Return volume growth rate of this agent

Returns: Double stating the volume growth rate of this agent

void simulator.agent.ActiveAgent.grow ( )

protected

Perform agent growth by calling all active reaction pathways.

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

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
xmlMarkUp	A species mark-up within the specified protocol file

void simulator.agent.ActiveAgent.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

void simulator.agent.ActiveAgent.internalStep ( )

protectedvirtual

Called at each time step of the simulation to compute cell growth, update size, and monitor cell death and division.

Called at each time step of the simulation to compute cell growth, update size, and monitor cell death. Also determines whether the agent has reached the size at which it must divide

Implements simulator.agent.Agent.

Reimplemented in simulator.agent.LocatedAgent, simulator.agent.zoo.Bacterium, simulator.agent.zoo.ParticulateEPS, simulator.agent.zoo.BactAdaptable, and simulator.agent.zoo.BactEPS.

void simulator.agent.ActiveAgent.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.ActiveAgent.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.ActiveAgent.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.LocatedAgent.

void simulator.agent.ActiveAgent.registerOnAllActiveReaction ( )

Register the agent on each guild of its activated pathways. Called by makeKid.

Register the agent on each guild of its activated pathways. Called by makeKid

void simulator.agent.ActiveAgent.removeReaction ( Reaction aPathway )

Remove a reaction from the list of known reactions.

Remove a reaction from the list of known reactions

Parameters

aPathway The reaction to remove from the list

Implements simulator.agent.HasReaction.

String simulator.agent.ActiveAgent.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.

void simulator.agent.ActiveAgent.setNetGrowth ( double value )

Set net growth rate of this agent.

Set net growth rate of this agent

Parameters

value Double stating the net growth rate of this agent

void simulator.agent.ActiveAgent.switchOffreaction ( Reaction aPathway )

Switches off a reaction by removing it from the active reaction array.

Switches off a reaction by removing it from the active reaction array. BVM 27.11.08: added the '.reactionIndex' calls to the two lines below in order to get this function to work correctly

Parameters

aPathway The reaction to switch off

Implements simulator.agent.HasReaction.

void simulator.agent.ActiveAgent.switchOnReaction ( Reaction aReaction )

Switches on a reaction by adding it to the active reaction array.

Switches off a reaction by adding it to the active reaction array. BVM 27.11.08: added the if statement to prevent adding a reaction if it is already present

Parameters

aReaction The reaction to switch on

Implements simulator.agent.HasReaction.

void simulator.agent.ActiveAgent.unregisterFromAllActiveReactions ( )

Called by the die method, to unregister the agent from all active reactions.

Called by the die method, to unregister the agent from all active reactions

void simulator.agent.ActiveAgent.updateMass ( )

Update mass of agent, summing the particle mass.

Update mass of agent, summing the particle mass

void simulator.agent.ActiveAgent.updateSize ( )

Update size of agent to take growth into account.

Update mass of agent to take growth into account

String simulator.agent.ActiveAgent.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.ActiveAgent._netGrowthRate = 0

protected

Net growth rate of this agent due to reactions

double simulator.agent.ActiveAgent._netVolumeRate = 0

protected

Net volume change rate of this agent due to reactions

double simulator.agent.ActiveAgent._totalMass

protected

Sum of masses of all particles

Reaction [] simulator.agent.ActiveAgent.allReactions

Array of all the reactions this agent is involved in

double [] simulator.agent.ActiveAgent.growthRate

protected

Growth rate of this agent due to reactions

double [] simulator.agent.ActiveAgent.particleMass

Mass of the agent (table for all particles belonging to the agent)

double [][] simulator.agent.ActiveAgent.particleYield

Particle yield for reactions involving this agent

ArrayList<Integer> simulator.agent.ActiveAgent.reactionActive

protected

Array of the reactions that are active

double [][] simulator.agent.ActiveAgent.reactionKinetic

Array of the kinetic factor parameters for the reactions this agent is involved in

ArrayList<Integer> simulator.agent.ActiveAgent.reactionKnown

protected

Array of all reactions (even those not active on this agent)

double [][] simulator.agent.ActiveAgent.soluteYield

Solute yield for reactions involving this agent

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

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

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation