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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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Creates an object of the Bacterium EPS Species: a bacterium with a permanent hydrolytic activity of its EPS capsule. More...
Public Member Functions | |
| BactEPS () | |
| Constructor used to generate progenitor and initialise an object to store relevant parameters. More... | |
| void | manageEPS () |
| Manages EPS hydrolyse by the agent and distribution between neighbouring agents. More... | |
| BactEPSParam | getSpeciesParam () |
| Return the set of parameters that is associated with the object of this species. More... | |
 Public Member Functions inherited from simulator.agent.zoo.Bacterium | |
| 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. In this case also manages EPS hydrolysis. More... | |
| Protected Member Functions inherited from simulator.agent.zoo.Bacterium | |
| void | internalStep () |
| Called at each time step of the simulation to compute mass growth and update radius, mass, and volume. More... | |
Additional Inherited Members | |
| Public Attributes inherited from simulator.agent.LocatedAgent | |
| double | detPriority = 0 |
| double | _timeSinceLastDivisionCheck = Double.MAX_VALUE |
| double | _distProb = 0 |
| double | _distCumProb = 0 |
| Protected Attributes inherited from simulator.agent.zoo.Bacterium | |
| boolean | _hasEps = false |
| boolean | _hasInert = false |
| Species | _epsSpecies |
| Static Protected Attributes inherited from simulator.agent.LocatedAgent | |
| static ContinuousVector | _diff = new ContinuousVector() |
| static ContinuousVector | _newLoc = new ContinuousVector() |
Creates an object of the Bacterium EPS Species: a bacterium with a permanent hydrolytic activity of its EPS capsule.
The BactEPS species behaves just like the Bacterium species, with one small change: capsular EPS is excreted continuously at a defined rate rather than during discrete events like for a Bacterium. During excretion, an agent will distribute any excreted EPS to neighbouring EPS agents of that type, or will create a new EPS agent if none are nearby. This new functionality requires specification of one additional parameter: the hydrolysis rate kHyd, which controls the rate at which capsular EPS is excreted to neighboring EPS particles.
| simulator.agent.zoo.BactEPS.BactEPS | ( | ) |
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
| BactEPSParam simulator.agent.zoo.BactEPS.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
Implements simulator.agent.HasSpecies.
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protectedvirtual |
Called at each time step of the simulation to compute mass growth and update radius, mass, and volume. In this case also manages EPS hydrolysis.
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. In this case also manages EPS hydrolysis
Reimplemented from simulator.agent.LocatedAgent.
| void simulator.agent.zoo.BactEPS.manageEPS | ( | ) |
Manages EPS hydrolyse by the agent and distribution between neighbouring agents.
Manages EPS hydrolyse by the agent and distribution between neighbouring agents
1.8.3.1
