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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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Abstract class used for declaring Episome and MultiEpisome objects. More...
Public Member Functions | |
| abstract void | internalStep () |
| Called at each time step of the simulation to compute agent characteristics. 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 void | createNewAgent () |
| Create a new agent with mutated parameters based on species default values. More... | |
| abstract SpecialisedAgent | sendNewAgent () throws CloneNotSupportedException |
| void | mutateAgent () |
| Mutate any inherited parameters for this particular agent. More... | |
| void | mutatePop () |
| Mutate any inherited parameters for a population of agents. More... | |
| void | registerBirth () |
| Registers a created agent into a respective container. Each agent must be referenced by one such container. More... | |
| void | die (boolean isStarving) |
| Notifies the simulation that this agent has become too small and is then counted as dead. More... | |
| double | move () |
| Used in the calculation of delta move in Agent Container class. Will investigate further why this class returns 0. More... | |
| void | setSpeciesParam (SpeciesParam aSpeciesParam) |
| Set the species parameters to a specified Species Parameter object. More... | |
| SpeciesParam | getSpeciesParam () |
| Species | getSpecies () |
| Returns the species object that is represented by this agent. More... | |
| void | setSpecies (Species aSpecies) |
| Set the progenitor Specialised agent to a specified species. More... | |
| String | getName () |
| Return the name of the species represented by this agent. More... | |
| boolean | willDetach () |
| Returns a boolean noting whether this agent is detached and may be removed in sloughing. Implemented by extending classes. More... | |
| int | getGridIndex () |
| Returns the integer grid index where this agent resides. Implemented by extending classes. More... | |
| double | interact (boolean MUTUAL, boolean pull, boolean seq, double gain) |
| Models a mechanical interaction between two located agents. Implemented by extending classes (LocatedAgent) More... | |
| boolean | isMoving () |
| Returns a boolean noting whether this agent is moving due to growth and sloughing. Implemented by extending classes. More... | |
| void | writePOVColorDefinition (FileWriter fr) throws IOException |
| Used in POV-Ray output to display this species - writes a colour definition to the passed-in file. More... | |
| Public Member Functions inherited from simulator.agent.Agent | |
| Agent () | |
| Initialise an agent object, setting its time of creation and thus the time it was last stepped. More... | |
| void | initFromProtocolFile (Simulator aSimulator, XMLParser aSpeciesRoot) |
| Initialise the agent from the protocol file. Implemented by classes that extend this class. More... | |
| void | initFromResultFile (Simulator aSim, String[] singleAgentData) |
| Create an agent using information in a previous state or initialisation file. More... | |
| void | mutateAgent () |
| Mutates agent parameters. Implemented by classes that extend this class. More... | |
| void | makeKid () throws CloneNotSupportedException |
| Creates a new agent from an existing one, and registers this new agent in the simulation. More... | |
| Object | clone () throws CloneNotSupportedException |
| Clones this agent object, creating a new progeny of this agent. More... | |
| void | step () |
| Perform the next timestep of the simulation for this agent. More... | |
| String | sendHeader () |
| Used in creation of results files - specifies the header of the columns of output information for this agent. More... | |
| String | writeOutput () |
| Used in creation of results files - creates an output string of information generated on this particular agent. More... | |
| String | sendName () |
| Returns a string containing the family name and genealogy of this agent. More... | |
| void | giveName () |
| Set the family for this agent, based on the next family. More... | |
| Public Member Functions inherited from simulator.agent.HasSpecies | |
| String | sendHeader () |
| Used in creation of results files - specifies the header of the columns of output information for this agent. More... | |
Additional Inherited Members | |
| Public Attributes inherited from simulator.agent.SpecialisedAgent | |
| int | speciesIndex |
| boolean | isDead = false |
| String | death |
| Protected Member Functions inherited from simulator.agent.Agent | |
| void | recordGenealogy (Agent baby) |
| Called when creating an agent : updates _generation and _genealogy field. More... | |
| Protected Attributes inherited from simulator.agent.SpecialisedAgent | |
| Species | _species |
| SpeciesParam | _speciesParam |
| AgentContainer | _agentGrid |
| Static Protected Attributes inherited from simulator.agent.Agent | |
| static int | nextFamily = 0 |
Abstract class used for declaring Episome and MultiEpisome objects.
Abstract class used for declaring Episome and MultiEpisome objects
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pure virtual |
Called at each time step of the simulation to compute agent characteristics.
Called at each time step of the simulation to compute agent characteristics
Implements simulator.agent.Agent.
Implemented in simulator.agent.zoo.MultiEpisome, and simulator.agent.zoo.Episome.
1.8.3.1
