Extends ActiveAgent by adding functionality to control agent grid location, agent shoving, agent death and division, and agent movement. More...

Inheritance diagram for simulator.agent.LocatedAgent:

Classes
class	detPriorityComparator
	Comparator used by AgentContainer.erodeBorder()

class	totalMassComparator
	Comparator used by AgentContainer.erodeBorder()

Public Member Functions
	LocatedAgent ()
	Constructor used to generate progenitor and initialise an object to store relevant parameters. More...

Object	clone () throws CloneNotSupportedException
	Creates a daughter Located Agent by cloning this agent and parameter objects. More...

void	createNewAgent (ContinuousVector position)
	Create a new agent in a specified position. More...

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

void	divide ()
	Captures cell division by making a clone of this agent using the makeKid method. More...

boolean	willDivide ()
	Determines whether or not a cell has reached the radius where cell division can be triggered. More...

boolean	willDie ()
	Determines whether or not a cell has reached the radius where cell death can be triggered. More...

void	die (boolean isStarving)
	Kills an agent. Called by detachment and starving test. More...

void	makeKid () throws CloneNotSupportedException
	With it determined that cell division will occur, create a new agent from the existing one. More...

void	divideCompounds (LocatedAgent baby, double babyMassFrac)
	On agent division, divides the mass between the old and new agent, at a specified fraction. More...

void	transferCompounds (LocatedAgent baby, double splitRatio)
	On agent division, transfers EPS between the old and new agent, at a specified ratio. More...

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

void	setDivisionDirection (double distance)
	Set the movement vector that states where to put a newly-created particle. More...

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

boolean	addPushMovement (LocatedAgent aNeighbour, boolean isMutual, double gain)
	Mutual shoving : The movement by shoving of an agent is calculated based on the cell overlap and added to the agents movement vector. More...

boolean	addSpringMovement (LocatedAgent aNeighbor, boolean isMutual, double gain)
	Pulling : The movement of agents by a shrinking biofilm. Move calculated and added to the agents movement vector. More...

double	computeDifferenceVector (ContinuousVector me, ContinuousVector him)
	Computes the shortest distance between this agent and another, stored as ContinuousVectors. This may be around the cyclic boundary. More...

void	getPotentialShovers (double radius)
	Find neighbouring agents in a range around you. More...

LocatedAgent	pickNeighbor ()
	Pick a random neighbour from the _myNeigbors collection. More...

void	findCloseSiblings (int indexSpecies)
	Find a sibling of this agent. More...

double	move ()
	With the agent move calculated, apply this movement, taking care to respect boundary conditions. More...

void	checkBoundaries ()
	Used by the move method to determine if an agents move crosses any of the domain's boundaries. More...

void	mutateAgent ()
	Mutate inherited agent parameters after agent division. More...

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

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

void	fitVolRateOnGrid (SpatialGrid aSpG)
	Add the total volume rate of an agent on 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...

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...

void	updateVolume ()
	Compute the volume on the basis of the mass and density of different compounds defined in the cell. More...

void	updateRadius ()

AllBC	updateAttachment ()
	Update the attachment, determining if an agent location crosses any boundaries. More...

void	addMovement (ContinuousVector aMove)
	Add movement to the ContinuousVector storing the agents move. More...

LocatedParam	getSpeciesParam ()
	Return the set of parameters associated with this agent (LocatedParam object) More...

double	getVolume (boolean withCapsule)
	Return the volume of this agent, with or without the capsule. More...

double	getRadius (boolean withCapsule)
	Return the radius of this agent, with or without the capsule. More...

double	getMass (boolean withCapsule)
	Return the mass of this agent, with or without the capsule. More...

double	getMaximumRadius ()

boolean	hasEPS ()
	Determine whether this cell has any EPS. More...

boolean	hasInert ()
	Determine whether this agent contains any inert particles. More...

double	getShoveFactor ()
	Return the shove factor to be used in shoving for this species of agent. More...

double	getShoveRadius ()
	Return the shove radius to be used in shoving for this species of agent. More...

double	getInteractDistance ()
	Return the shoving interaction distance to be used in shoving for this species of agent. More...

double	getInteractDistance (LocatedAgent baby)
	Return the shoving interaction distance to be used in shoving against a specified agent. More...

double	getBabyMassFrac ()
	Return the fraction of mass that is transferred to the new agent on cell division. More...

double	getDivRadius ()
	Return the agent radius at which cell division is triggered. More...

double	getDeathRadius ()
	Return the agent radius at which cell death is triggered. More...

boolean	isMoving ()
	Determine if an agent has a move to perform. More...

boolean	isAttached ()
	Determine if an agent is attached to a surface. More...

double	getActiveFrac ()
	Return the active fraction of this agent. More...

Color	getColor ()
	Return the colour assigned to this agent in POV-Ray output. More...

Color	getColorCapsule ()
	Return the colour assigned to any capsules contained in this agent in POV-Ray output. More...

ContinuousVector	getLocation ()
	Return the location of this agent. More...

double	getDistance (LocatedAgent aLoc)
	Return the distance between two agents. More...

void	setLocation (ContinuousVector cc)
	Set the location of this agent to the supplied continuous vector. More...

ContinuousVector	getMovement ()
	Return the continuous vector that states this agents move. More...

int	getGridIndex ()
	Return the index of the grid on which this agent is placed. More...

LocatedGroup	getGridElement ()
	Return the LocatedGroup of agents that are present in the location where this agent is placed. More...

void	setGridIndex (int aGridIndex)
	Move this agent to another grid index. More...

Domain	getDomain ()
	Return the domain where this agent is contained. More...

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

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
double	detPriority = 0

double	_timeSinceLastDivisionCheck = Double.MAX_VALUE

double	_distProb = 0

double	_distCumProb = 0

Public Attributes inherited from simulator.agent.ActiveAgent
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...

Protected Member Functions inherited from simulator.agent.ActiveAgent
void	grow ()

Protected Attributes
double	_radius

double	_totalRadius

double	_myDivRadius

double	_myDeathRadius

double	_volume

double	_totalVolume

ContinuousVector	_location = new ContinuousVector()

ContinuousVector	_movement = new ContinuousVector()

ContinuousVector	_divisionDirection = new ContinuousVector()

LinkedList< LocatedAgent >	_myNeighbors = new LinkedList<LocatedAgent>()

int	_agentGridIndex

boolean	_isAttached = false

Protected Attributes inherited from simulator.agent.ActiveAgent
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

Static Protected Attributes
static ContinuousVector	_diff = new ContinuousVector()

static ContinuousVector	_newLoc = new ContinuousVector()

Detailed Description

Extends ActiveAgent by adding functionality to control agent grid location, agent shoving, agent death and division, and agent movement.

Extends ActiveAgent by adding functionality to control agent grid location, agent shoving, agent death and division, and agent movement. During each global timestep, agent divisions and agent growth lead to many cases where neighbouring agents will overlap. A relaxation algorithm is used to find iteratively the new overlap-minimising steady state configuration of agent locations at the end of each timestep.

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; Sónia Martins (SCM80.nosp@m.8@bh.nosp@m.am.ac.nosp@m..uk), Centre for Systems Biology, University of Birmingham (UK); Rob Clegg (rjc09.nosp@m.6@bh.nosp@m.am.ac.nosp@m..uk), Centre for Systems Biology, University of Birmingham (UK)

Constructor & Destructor Documentation

simulator.agent.LocatedAgent.LocatedAgent ( )

Constructor used to generate progenitor and initialise an object to store relevant parameters.

Constructor used to generate progenitor and initialise an object to store relevant parameters

Member Function Documentation

void simulator.agent.LocatedAgent.addMovement ( ContinuousVector aMove )

Add movement to the ContinuousVector storing the agents move.

Add movement to the ContinuousVector storing the agents move

Parameters

aMove ContinuousVector to add to the movement vector

boolean simulator.agent.LocatedAgent.addPushMovement	(	LocatedAgent	aNeighbour,
		boolean	isMutual,
		double	gain
	)

Mutual shoving : The movement by shoving of an agent is calculated based on the cell overlap and added to the agents movement vector.

Mutual shoving : The movement by shoving of an agent is calculated based on the cell overlap and added to the agents movement vector. Both agents are moved of half the overlapping distance in opposite directions.

Parameters

aNeighbour	Reference to the potentially shoving neighbour
isMutual	Whether movement is shared between two agents or applied only to this one
gain	Double noting change in position

Returns: Boolean stating whether shoving is detected (true) or not (false)

boolean simulator.agent.LocatedAgent.addSpringMovement	(	LocatedAgent	aNeighbor,
		boolean	isMutual,
		double	gain
	)

Pulling : The movement of agents by a shrinking biofilm. Move calculated and added to the agents movement vector.

The movement of agents by a shrinking biofilm. Move calculated and added to the agents movement vector.

Parameters

aNeighbor	Reference to the potentially shoving neighbour
isMutual	Whether movement is shared between two agents or applied only to this one
gain	Double noting change in position

Returns: Boolean stating whether pulling is detected (true) or not (false)

void simulator.agent.LocatedAgent.checkBoundaries ( )

Used by the move method to determine if an agents move crosses any of the domain's boundaries.

Used by the move method to determine if an agents move crosses any of the domain's boundaries

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

Creates a daughter Located Agent by cloning this agent and parameter objects.

Creates a daughter Located Agent by cloning this agent and parameter objects

Exceptions

CloneNotSupportedException Thrown if the agent cannot be cloned

double simulator.agent.LocatedAgent.computeDifferenceVector	(	ContinuousVector	me,
		ContinuousVector	him
	)

Computes the shortest distance between this agent and another, stored as ContinuousVectors. This may be around the cyclic boundary.

Computes the distance between this agent and another, stored as ContinuousVectors. This may be around the cyclic boundary

Parameters

me	ContinuousVector stating first agent location
him	ContinuousVector stating other agent location

Returns: the shortest movement vector to go from a to b, take into account the cyclic boundary

See Also: addOverlapMovement; addPullMovement works in 2 and 3D

void simulator.agent.LocatedAgent.createNewAgent ( ContinuousVector position )

Create a new agent in a specified position.

Create a new agent in a specified position

Parameters

position Vector stating where this agent should be located

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

Kills an agent. Called by detachment and starving test.

Kills an agent. Called by detachment and starving test

void simulator.agent.LocatedAgent.divide ( )

Captures cell division by making a clone of this agent using the makeKid method.

Captures cell division by making a clone of this agent using the makeKid method

void simulator.agent.LocatedAgent.divideCompounds	(	LocatedAgent	baby,
		double	babyMassFrac
	)

On agent division, divides the mass between the old and new agent, at a specified fraction.

On agent division, divides the mass between the old and new agent, at a specified fraction

Parameters

baby	The new agent, which is inheriting mass
babyMassFrac	The fraction of this agents mass that should be transferred to the new agent

void simulator.agent.LocatedAgent.findCloseSiblings ( int indexSpecies )

Find a sibling of this agent.

Find a sibling of this agent

Parameters

indexSpecies The index used to reference this species in the simulation dictionary

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

void simulator.agent.LocatedAgent.fitVolRateOnGrid ( SpatialGrid aSpG )

Add the total volume rate of an agent on received grid.

Add the total volume rate of an agent on received grid

Parameters

aSpG	Spatial grid used to sum volume

double simulator.agent.LocatedAgent.getActiveFrac ( )

Return the active fraction of this agent.

Return the active fraction of this agent

Returns: Double value stating the active fraction of this agent

double simulator.agent.LocatedAgent.getBabyMassFrac ( )

Return the fraction of mass that is transferred to the new agent on cell division.

Return the fraction of mass that is transferred to the new agent on cell division

Returns: Double stating the fraction of mass that is transferred to the new agent on cell division

Color simulator.agent.LocatedAgent.getColor ( )

Return the colour assigned to this agent in POV-Ray output.

Return the colour assigned to this agent in POV-Ray output

Returns: Colour assigned to this agent as specified in the protocol file

Color simulator.agent.LocatedAgent.getColorCapsule ( )

Return the colour assigned to any capsules contained in this agent in POV-Ray output.

Return the colour assigned to any capsules contained in this agent in POV-Ray output

Returns: Colour assigned to this agent capsules as specified in the protocol file

double simulator.agent.LocatedAgent.getDeathRadius ( )

Return the agent radius at which cell death is triggered.

Return the agent radius at which cell death is triggered

Returns: Double stating the agent radius at which cell death is triggered

double simulator.agent.LocatedAgent.getDistance ( LocatedAgent aLoc )

Return the distance between two agents.

Return the distance between two agents

Parameters

aLoc	LocatedAgent to find distance to

Returns: distance between two agents (assuming cyclic boundaries)

double simulator.agent.LocatedAgent.getDivRadius ( )

Return the agent radius at which cell division is triggered.

Return the agent radius at which cell division is triggered

Returns: Double stating the agent radius at which cell division is triggered

Domain simulator.agent.LocatedAgent.getDomain ( )

Return the domain where this agent is contained.

Return the domain where this agent is contained

Returns: The domain where this agent is contained (Domain object)

LocatedGroup simulator.agent.LocatedAgent.getGridElement ( )

Return the LocatedGroup of agents that are present in the location where this agent is placed.

Return the LocatedGroup of agents that are present in the location where this agent is placed

Returns: LocatedGroup containing all agents present in the same grid space as this agent

int simulator.agent.LocatedAgent.getGridIndex ( )

Return the index of the grid on which this agent is placed.

Return the index of the grid on which this agent is placed

Returns: Integer grid index of where this agent is placed

double simulator.agent.LocatedAgent.getInteractDistance ( )

Return the shoving interaction distance to be used in shoving for this species of agent.

Return the shoving interaction distance to be used in shoving for this species of agent

Returns: Double specifying the shoving interaction distance that will be applied

double simulator.agent.LocatedAgent.getInteractDistance ( LocatedAgent baby )

Return the shoving interaction distance to be used in shoving against a specified agent.

Return the shoving interaction distance to be used in shoving against a specified agent

Returns: Double specifying the shoving interaction distance that will be applied

ContinuousVector simulator.agent.LocatedAgent.getLocation ( )

Return the location of this agent.

Return the location of this agent

Returns: ContinuousVector stating the location of this agent

double simulator.agent.LocatedAgent.getMass ( boolean withCapsule )

Return the mass of this agent, with or without the capsule.

Return the mass of this agent, with or without the capsule

Parameters

withCapsule Boolean noting whether any capsule should be included in this calculation

Returns: Double specifying the mass of this agent

double simulator.agent.LocatedAgent.getMaximumRadius ( )

ContinuousVector simulator.agent.LocatedAgent.getMovement ( )

Return the continuous vector that states this agents move.

Return the continuous vector that states this agents move

Returns: continuous vector that states this agents move

void simulator.agent.LocatedAgent.getPotentialShovers ( double radius )

Find neighbouring agents in a range around you.

Find neighbouring agents in a range around you

Parameters

radius The distance to search around the agent location

double simulator.agent.LocatedAgent.getRadius ( boolean withCapsule )

Return the radius of this agent, with or without the capsule.

Return the radius of this agent, with or without the capsule

Parameters

withCapsule Boolean noting whether any capsule should be included in this calculation

Returns: Double specifying the radius of this agent

double simulator.agent.LocatedAgent.getShoveFactor ( )

Return the shove factor to be used in shoving for this species of agent.

Return the shove factor to be used in shoving for this species of agent

Returns: Double specifying the shove factor that will be applied

double simulator.agent.LocatedAgent.getShoveRadius ( )

Return the shove radius to be used in shoving for this species of agent.

Return the shove radius to be used in shoving for this species of agent

Returns: Double specifying the shove radius that will be applied

LocatedParam simulator.agent.LocatedAgent.getSpeciesParam ( )

Return the set of parameters associated with this agent (LocatedParam object)

Returns: LocatedParam object of parameters associated with this agent

Implements simulator.agent.HasSpecies.

double simulator.agent.LocatedAgent.getVolume ( boolean withCapsule )

Return the volume of this agent, with or without the capsule.

Return the volume of this agent, with or without the capsule

Parameters

withCapsule Boolean noting whether any capsule should be included in this calculation

Returns: Double specifying the volume of this agent

boolean simulator.agent.LocatedAgent.hasEPS ( )

Determine whether this cell has any EPS.

Determine whether this cell has any EPS

Returns: Boolean noting whether this cell has any EPS

boolean simulator.agent.LocatedAgent.hasInert ( )

Determine whether this agent contains any inert particles.

Determine whether this agent contains any inert particles

Returns: Boolean noting whether this agent contains any inert particles

void simulator.agent.LocatedAgent.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.LocatedAgent.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

double simulator.agent.LocatedAgent.interact	(	boolean	MUTUAL,
		boolean	shoveOnly,
		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
shoveOnly	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

void simulator.agent.LocatedAgent.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

Reimplemented from simulator.agent.ActiveAgent.

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

boolean simulator.agent.LocatedAgent.isAttached ( )

Determine if an agent is attached to a surface.

Determine if an agent is attached to a surface

Returns: Boolean noting whether the agent is attached to a surface

boolean simulator.agent.LocatedAgent.isMoving ( )

Determine if an agent has a move to perform.

Determine if an agent has a move to perform

Returns: Boolean noting whether the agent has a move to perform

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

With it determined that cell division will occur, create a new agent from the existing one.

With it determined that cell division will occur, create a new agent from the existing one

Exceptions

CloneNotSupportedException Thrown if the agent cannot be cloned

double simulator.agent.LocatedAgent.move ( )

With the agent move calculated, apply this movement, taking care to respect boundary conditions.

With the agent move calculated, apply this movement, taking care to respect boundary conditions

void simulator.agent.LocatedAgent.mutateAgent ( )

Mutate inherited agent parameters after agent division.

Mutation Function. If you don't want apply a mutation in a specified class, do not redefine this method. If you want, you are free to choose which fields to mutate for each different class by a simple redefinition

void simulator.agent.LocatedAgent.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.

LocatedAgent simulator.agent.LocatedAgent.pickNeighbor ( )

Pick a random neighbour from the _myNeigbors collection.

Pick a random neighbour from the _myNeigbors collection

Returns: A randomly picked neighbour (LocatedAgent object) from the list of neighbours

void simulator.agent.LocatedAgent.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.ActiveAgent.

String simulator.agent.LocatedAgent.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.LocatedAgent.setDivisionDirection ( double distance )

Set the movement vector that states where to put a newly-created particle.

Set the movement vector that states where to put a newly-created particle

Parameters

distance Distance between the this agent and the new agent

void simulator.agent.LocatedAgent.setGridIndex ( int aGridIndex )

Move this agent to another grid index.

Move this agent to another grid index

Parameters

aGridIndex Grid index in which this agent should now be placed

void simulator.agent.LocatedAgent.setLocation ( ContinuousVector cc )

Set the location of this agent to the supplied continuous vector.

Set the location of this agent to the supplied continuous vector

Parameters

cc	Location which this agent should be assigned to

void simulator.agent.LocatedAgent.transferCompounds	(	LocatedAgent	baby,
		double	splitRatio
	)

On agent division, transfers EPS between the old and new agent, at a specified ratio.

On agent division, transfers EPS between the old and new agent, at a specified ratio

Parameters

baby	The new agent, which is inheriting mass
splitRatio	The ratio of the EPS that should be transferred to the new agent

AllBC simulator.agent.LocatedAgent.updateAttachment ( )

Update the attachment, determining if an agent location crosses any boundaries.

Update the attachment, determining if an agent location crosses any boundaries

Returns: Boundary that has been crossed

void simulator.agent.LocatedAgent.updateRadius ( )

Compute the radius on the basis of the volume The radius evolution is stored in deltaRadius (used for shrinking)

void simulator.agent.LocatedAgent.updateSize ( )

Update the radius of the agent from the current mass (and then the volume) of the agent (EPS included)

void simulator.agent.LocatedAgent.updateVolume ( )

Compute the volume on the basis of the mass and density of different compounds defined in the cell.

Compute the volume on the basis of the mass and density of different compounds defined in the cell

boolean simulator.agent.LocatedAgent.willDie ( )

Determines whether or not a cell has reached the radius where cell death can be triggered.

Determines whether or not a cell has reached the radius where cell death can be triggered

Returns: Boolean stating whether cell death should be triggered (true) or not (false)

boolean simulator.agent.LocatedAgent.willDivide ( )

Determines whether or not a cell has reached the radius where cell division can be triggered.

Determines whether or not a cell has reached the radius where cell division can be triggered

Returns: Boolean stating whether cell division should be triggered (true) or not (false)

String simulator.agent.LocatedAgent.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

int simulator.agent.LocatedAgent._agentGridIndex

protected

Index of the agent position on the vectorized grid

ContinuousVector simulator.agent.LocatedAgent._diff = new ContinuousVector()

staticprotected

Temporary variable storing the distance between two agents

double simulator.agent.LocatedAgent._distCumProb = 0

Cumulative probability as to whether the plasmid will be transferred

double simulator.agent.LocatedAgent._distProb = 0

Distance based probability from a given neighbour (used in HGT). Sonia 8-12-2010

ContinuousVector simulator.agent.LocatedAgent._divisionDirection = new ContinuousVector()

protected

Direction in which this cell divides

boolean simulator.agent.LocatedAgent._isAttached = false

protected

Boolean noting whether this agent is interacting with a surface (true) or not (false)

ContinuousVector simulator.agent.LocatedAgent._location = new ContinuousVector()

protected

Agent position - continuous coordinates

ContinuousVector simulator.agent.LocatedAgent._movement = new ContinuousVector()

protected

ContinuousVector noting the move that will be applied to the agents position

double simulator.agent.LocatedAgent._myDeathRadius

protected

Radius at which agent death is triggered

double simulator.agent.LocatedAgent._myDivRadius

protected

Radius at which this agent will divide

LinkedList<LocatedAgent> simulator.agent.LocatedAgent._myNeighbors = new LinkedList<LocatedAgent>()

protected

List of neighbouring agents in this agents vicinity

ContinuousVector simulator.agent.LocatedAgent._newLoc = new ContinuousVector()

staticprotected

Temporary store of the new location this cell will move to

double simulator.agent.LocatedAgent._radius

protected

Radius of this agent

double simulator.agent.LocatedAgent._timeSinceLastDivisionCheck = Double.MAX_VALUE

Stores the simulation time since the last division check

double simulator.agent.LocatedAgent._totalRadius

protected

Cell radius including any capsules

double simulator.agent.LocatedAgent._totalVolume

protected

Cell volume including any capsules

double simulator.agent.LocatedAgent._volume

protected

Volume of this agent

double simulator.agent.LocatedAgent.detPriority = 0

Detachment priority

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

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

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