Version 1.2 (June 2013)
 All Classes Namespaces Files Functions Variables Pages
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
simulator.agent.zoo.Bacterium Class Reference

Creates an object of the Bacterium Species. Acts as a superclass for all current species with the exception of ParticulateEPS. More...

Inheritance diagram for simulator.agent.zoo.Bacterium:
simulator.agent.LocatedAgent simulator.agent.ActiveAgent simulator.agent.SpecialisedAgent simulator.agent.HasReaction simulator.agent.Agent simulator.agent.HasSpecies simulator.agent.zoo.BactEPS simulator.agent.zoo.BactAdaptable

Public Member Functions

 Bacterium ()
 Constructor used to generate progenitor and initialise an object to store relevant parameters. More...
 
Object clone () throws CloneNotSupportedException
 Used by makeKid method to create a daughter Bacterium agent by cloning this agent and parameter objects. More...
 
void initFromProtocolFile (Simulator aSim, XMLParser aSpeciesRoot)
 Creates a Bacterium agent from the parameters specified in the XML protocol file. More...
 
void initFromResultFile (Simulator aSim, String[] singleAgentData)
 Create an agent using information in a previous state or initialisation file. More...
 
void init ()
 Initialises any new agent (progenitor or daughter cell), setting cell radius, generation, and geneology. More...
 
Bacterium sendNewAgent () throws CloneNotSupportedException
 Called by Bacterium.createAgent and to obtain another instance of the same species (totally independent). The returned agent is NOT registered. More...
 
void createNewAgent (ContinuousVector position)
 Create a new Bacterium agent (who a priori is registered in at least one container) More...
 
void mutatePop ()
 Mutates inherited parameters and distributes particle mass - either exponentially or normally, dependent on value of distMethod. More...
 
void mutateAgent ()
 
void makeKid () throws CloneNotSupportedException
 Used by Bacterium.divide() method to create a daughter cell of this agent. More...
 
void die (boolean isStarving)
 Converts the agent into particle EPS and inert on agent death. More...
 
void manageEPS ()
 Excretes EPS particle with 75% of initial mass if the EPS capsule is too thick. More...
 
void excreteEPS (double ratio)
 Excretes part of the agents bound EPS as slime EPS. More...
 
boolean willDie ()
 Determines if this agent has reached either the radius size limit at which it will die, or a state of zero mass. More...
 
void guessMass ()
 Sets the mass of the primary particle of the progenitor to half the mass at-division. 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 ()
 Update the volume of this agent by examining the particle density. More...
 
BacteriumParam getSpeciesParam ()
 Return the set of parameters that is associated with the object of this species. More...
 
boolean hasEPS ()
 Determine whether this bacterium contains any eps particles (capsule in the protocol file) More...
 
boolean hasInert ()
 Determine whether this bacterium contains any inert particles. More...
 
double getBirthday ()
 Return the simulation time at which this agent was created. More...
 
double getActiveFrac ()
 Compute the active fraction of the bacterium, ignoring EPS (i.e. only compare active and inert compartments) More...
 
Color getColorCapsule ()
 Send the colour associated to the species to the defined EPS capsule (if appropriate) More...
 
Color getColor ()
 Used for POV-Ray output, defines the colour that this species of Bacterium has been assigned. More...
 
- Public Member Functions inherited from simulator.agent.LocatedAgent
 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...
 
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...
 

Protected Member Functions

void internalStep ()
 Called at each time step of the simulation to compute mass growth and update radius, mass, and volume. More...
 

Protected Attributes

boolean _hasEps = false
 
boolean _hasInert = false
 
Species _epsSpecies
 
- Protected Attributes inherited from simulator.agent.LocatedAgent
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
 

Additional Inherited Members

- Public Attributes inherited from simulator.agent.LocatedAgent
double detPriority = 0
 
double _timeSinceLastDivisionCheck = Double.MAX_VALUE
 
double _distProb = 0
 
double _distCumProb = 0
 
- Static Protected Attributes inherited from simulator.agent.LocatedAgent
static ContinuousVector _diff = new ContinuousVector()
 
static ContinuousVector _newLoc = new ContinuousVector()
 

Detailed Description

Creates an object of the Bacterium Species. Acts as a superclass for all current species with the exception of ParticulateEPS.

Creates an object of the Bacterium Species. Acts as a superclass for all current species with the exception of ParticulateEPS. The first part of the Bacterium species mark-up in the XML file lists the different particles composing this species; these particles form ‘compartments’ within the agent that signify the types of biomass that the agent contains. The possible particle types that may be used are taken from the particle mark-ups defined early in the protocol file, generally consisting of ‘biomass’, ‘inert’, and ‘capsule’. The initial mass of each particle may be given (in units of femtograms, 1 fg = 10-15 g), but if you set the value to zero the simulator will assign a reasonable random initial value for the mass. For this Bacterium species, only one particle type is actually necessary to include, but it is common to include several types. In this species, inert and capsule compartments exhibit special behaviour: inert biomass will accumulate in the agent, while a capsule will be excreted if it accumulates to take up too much of the agent’s mass. Note that the ‘capsule’ particle also requires you to specify its type via the class attribute; when the capsule has become too large and needs to be excreted, an agent of that class will be created (this means that it is necessary to have previously defined a species with that name.

Author
Andreas Dotsch (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)
Sonia Martins (SCM80.nosp@m.8@bh.nosp@m.am.ac.nosp@m..uk), Centre for Systems Biology, University of Birmingham (UK)

Constructor & Destructor Documentation

simulator.agent.zoo.Bacterium.Bacterium ( )

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

Object simulator.agent.zoo.Bacterium.clone ( ) throws CloneNotSupportedException

Used by makeKid method to create a daughter Bacterium agent by cloning this agent and parameter objects.

Used by makeKid method to create a daughter Bacterium agent by cloning this agent and parameter objects

Exceptions
CloneNotSupportedExceptionThrown if the agent cannot be cloned
void simulator.agent.zoo.Bacterium.createNewAgent ( ContinuousVector  position)

Create a new Bacterium agent (who a priori is registered in at least one container)

Create a new Bacterium agent (who a priori is registered in at least one container). This agent is located on the relevant grid

void simulator.agent.zoo.Bacterium.die ( boolean  isStarving)

Converts the agent into particle EPS and inert on agent death.

Converts the agent into particle EPS and inert on agent death

Parameters
isStarvingBoolean noting whether the agent currently has access to any resources
void simulator.agent.zoo.Bacterium.excreteEPS ( double  ratio)

Excretes part of the agents bound EPS as slime EPS.

Excretes part of the agents bound EPS as slime EPS

Parameters
ratioRatio of EPS that should be excreted
double simulator.agent.zoo.Bacterium.getActiveFrac ( )

Compute the active fraction of the bacterium, ignoring EPS (i.e. only compare active and inert compartments)

Compute the active fraction of the bacterium, ignoring EPS (i.e. only compare active and inert compartments)

Returns
Double noting the fraction of the bacterium that is active
double simulator.agent.zoo.Bacterium.getBirthday ( )

Return the simulation time at which this agent was created.

Return the simulation time at which this agent was created

Returns
Double noting the simulation time at which this agent was created
Color simulator.agent.zoo.Bacterium.getColor ( )

Used for POV-Ray output, defines the colour that this species of Bacterium has been assigned.

Used for POV-Ray output, defines the colour that this species of Bacterium has been assigned

Returns
Color object that this species of Bacterium has been assigned
Color simulator.agent.zoo.Bacterium.getColorCapsule ( )

Send the colour associated to the species to the defined EPS capsule (if appropriate)

Send the colour associated to the species to the defined EPS capsule (if appropriate)

Returns
Color object that this species of Bacterium has been assigned
BacteriumParam simulator.agent.zoo.Bacterium.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.Bacterium.guessMass ( )

Sets the mass of the primary particle of the progenitor to half the mass at-division.

This sets the mass of the primary particle of the progenitor to half the mass at-division (i.e. the average mass after division, regardless of babyMassFrac). The mass-at-division is determined by the particle density and the volume-at-division; volume is determined by the divRadius, or the divRadius and the z-resolution if in a 2D simulation.

boolean simulator.agent.zoo.Bacterium.hasEPS ( )

Determine whether this bacterium contains any eps particles (capsule in the protocol file)

Determine whether this bacterium contains any eps particles (capsule in the protocol file)

Returns
Boolean noting whether this bacterium object contains eps particles
boolean simulator.agent.zoo.Bacterium.hasInert ( )

Determine whether this bacterium contains any inert particles.

Determine whether this bacterium contains any inert particles.

Returns
Boolean noting whether this bacterium object contains inert particles
void simulator.agent.zoo.Bacterium.init ( )

Initialises any new agent (progenitor or daughter cell), setting cell radius, generation, and geneology.

Initialises any new agent (progenitor or daughter cell), setting cell radius, generation, and geneology

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

Creates a Bacterium agent from the parameters specified in the XML protocol file.

Creates a Bacterium agent from the parameters specified in the XML protocol file

Parameters
aSimThe simulation object used to simulate the conditions specified in the protocol file
aSpeciesRootA species mark-up within the specified protocol file
void simulator.agent.zoo.Bacterium.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
aSimThe simulation object used to simulate the conditions specified in the protocol file
singleAgentDataData from the result or initialisation file that is used to recreate this agent
void simulator.agent.zoo.Bacterium.internalStep ( )
protectedvirtual

Called at each time step of the simulation to compute mass growth and update radius, mass, and volume.

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 of the simulation (under the control of the method Step of the class Agent) to compute mass growth and update radius, mass, and volume. Also determines whether the agent has reached the size at which it must divide, and monitors agent death

Reimplemented from simulator.agent.LocatedAgent.

void simulator.agent.zoo.Bacterium.makeKid ( ) throws CloneNotSupportedException

Used by Bacterium.divide() method to create a daughter cell of this agent.

Used by Bacterium.divide() method to create a daughter cell of this agent

Exceptions
CloneNotSupportedExceptionException thrown if the object cannot be cloned
void simulator.agent.zoo.Bacterium.manageEPS ( )

Excretes EPS particle with 75% of initial mass if the EPS capsule is too thick.

Excretes EPS particle with 75% of initial mass if the EPS capsule is too thick

void simulator.agent.zoo.Bacterium.mutateAgent ( )

Mutate inherited agent parameters after agent division.

void simulator.agent.zoo.Bacterium.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.

String simulator.agent.zoo.Bacterium.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.

Bacterium simulator.agent.zoo.Bacterium.sendNewAgent ( ) throws CloneNotSupportedException
virtual

Called by Bacterium.createAgent and to obtain another instance of the same species (totally independent). The returned agent is NOT registered.

Called by Bacterium.createAgent and to obtain another instance of the same species (totally independent). The returned agent is NOT registered

Exceptions
CloneNotSupportedExceptionException thrown if the object cannot be cloned

Implements simulator.agent.SpecialisedAgent.

void simulator.agent.zoo.Bacterium.updateVolume ( )

Update the volume of this agent by examining the particle density.

Update the volume of this agent by examining the particle density

boolean simulator.agent.zoo.Bacterium.willDie ( )

Determines if this agent has reached either the radius size limit at which it will die, or a state of zero mass.

Determines if this agent has reached either the radius size limit at which it will die, or a state of zero mass

Returns
Boolean value noting whether the cell will die (true) or not (false)
String simulator.agent.zoo.Bacterium.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

Species simulator.agent.zoo.Bacterium._epsSpecies
protected

Previously declared species object of the type of agent that will be created when the capsule is excreted

boolean simulator.agent.zoo.Bacterium._hasEps = false
protected

Boolean noting whether any EPS particles have been declared as part of this Bacterium

boolean simulator.agent.zoo.Bacterium._hasInert = false
protected

Boolean noting whether any inert particles have been declared as part of this Bacterium


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