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Version 1.2 (June 2013)
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Version 1.2 (June 2013)
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Extends LocatedParam to create an object that can store all common parameters for Bacteria-based species. More...
Public Member Functions | |
| BacteriumParam () | |
| Constructor to create a BacteriumParam parameter storage object. More... | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Initialises Bacterium species parameters, calling the relevant superclasses to initialise common parameters for Bacterium derived species. More... | |
 Public Member Functions inherited from simulator.agent.LocatedParam | |
| LocatedParam () | |
| Create a new LocatedParam parameter storage object, calling the relevant extended class constructors. More... | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Assigns values to each of the location and behavioural specific parameters, reading these from the protocol file. More... | |
| double | getCellRunSpeed () |
| Return the cell run speed. Used in agent self-attachment scenarios. More... | |
| double | getStickinessRadius () |
| Return the cell stickiness radius. Used in agent self-attachment scenarios. More... | |
| Public Member Functions inherited from simulator.agent.ActiveParam | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction. More... | |
| Public Member Functions inherited from simulator.agent.SpeciesParam | |
| void | init (Simulator aSim, XMLParser aSpeciesRoot) |
| Read in specific parameters for this species, changing the default if required. More... | |
Public Attributes | |
| double | epsMax = .15 |
| Color | epsColor = Color.lightGray |
| Boolean | distMethod = false |
| Public Attributes inherited from simulator.agent.LocatedParam | |
| double | divRadius = .97 |
| double | divRadiusCV = .1 |
| double | babyMassFrac = .5 |
| double | babyMassFracCV = .1 |
| double | deathRadius = .2 |
| double | deathRadiusCV = .1 |
| double | shoveFactor = 1.15 |
| double | shoveLimit = 0 |
| double | cellRunSpeed |
| double | tumbleInterval |
| double | stickinessAddition |
| Public Attributes inherited from simulator.agent.ActiveParam | |
| double[] | particleDensity |
| double[][] | soluteYield |
| double[][] | particleYield |
| double[][] | reactionKinetic |
| double[] | lysisYield |
| Public Attributes inherited from simulator.agent.SpeciesParam | |
| double | initialMassCV = .1 |
Extends LocatedParam to create an object that can store all common parameters for Bacteria-based species.
Extends LocatedParam to create an object that can store all common parameters for Bacteria-based species
| simulator.agent.zoo.BacteriumParam.BacteriumParam | ( | ) |
Constructor to create a BacteriumParam parameter storage object.
Constructor to create a BacteriumParam parameter storage object. Simply calls the LocatedAgent super constructor
Initialises Bacterium species parameters, calling the relevant superclasses to initialise common parameters for Bacterium derived species.
Initialises Bacterium species parameters, calling the relevant superclasses to initialise common parameters for Bacterium derived species
| aSim | The simulation object used to simulate the conditions specified in the protocol file |
| aSpeciesRoot | A species mark-up within the specified protocol file |
| Boolean simulator.agent.zoo.BacteriumParam.distMethod = false |
How particle mass is distributed: false -> normal/gaussian, true -> exponential (power of 2)
| Color simulator.agent.zoo.BacteriumParam.epsColor = Color.lightGray |
Colour assigned to eps when visualising results in POV-Ray
| double simulator.agent.zoo.BacteriumParam.epsMax = .15 |
Maximal fraction of eps volume before excretion
1.8.3.1
