Class simMoran
- All Implemented Interfaces:
Runnable
,IBS.HasIBS
,MilestoneListener
,ODE.HasDE
,ODE.HasODE
,PDE.HasPDE
,SDE.HasSDE
,Features
,Features.Static
,HasHistogram
,HasHistogram.Degree
,HasHistogram.Fitness
,HasHistogram.StatisticsProbability
,HasHistogram.StatisticsStationary
,HasHistogram.StatisticsTime
,HasMean
,HasMean.Fitness
,HasMean.Strategy
,HasPop2D
,HasPop2D.Fitness
,HasPop2D.Strategy
,HasPop3D
,HasPop3D.Fitness
,HasPop3D.Strategy
,CLOProvider
- Author:
- Christoph Hauert
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface Features
Features.Groups, Features.Pairs, Features.Static
Nested classes/interfaces inherited from interface HasHistogram
HasHistogram.Degree, HasHistogram.Fitness, HasHistogram.StatisticsProbability, HasHistogram.StatisticsStationary, HasHistogram.StatisticsTime, HasHistogram.Strategy
Nested classes/interfaces inherited from interface HasMean
HasMean.Fitness, HasMean.Strategy
Nested classes/interfaces inherited from interface HasPop2D
HasPop2D.Fitness, HasPop2D.Strategy
Nested classes/interfaces inherited from interface HasPop3D
HasPop3D.Fitness, HasPop3D.Strategy
Nested classes/interfaces inherited from interface IBS.HasIBS
IBS.HasIBS.CGroups, IBS.HasIBS.CPairs, IBS.HasIBS.DGroups, IBS.HasIBS.DPairs, IBS.HasIBS.MCGroups, IBS.HasIBS.MCPairs
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Field Summary
FieldsModifier and TypeFieldDescription(package private) final CLOption
Command line option to show the simulation progress.(package private) EvoLudoJRE
The EvoLudoJRE engine for running the simulation.(package private) PrintStream
The output stream.(package private) boolean
The flag to indicate whether to show progress.Fields inherited from class Moran
cloFitness, MUTANT, RESIDENT, typeScores
Fields inherited from class Discrete
cloMonoStop, monoStop, mutation
Fields inherited from class Module
cloDeathRate, cloGeometry, cloNGroup, cloNPopulation, cloPhase2DAxis, cloSpeciesUpdateRate, cloTraitColors, cloTraitDisable, cloTraitNames, competition, deathRate, defaultColor, engine, interaction, logger, map2fitness, markers, model, nActive, name, nGroup, nPopulation, nTraits, playerUpdate, speciesUpdateRate, structure, traitColor, trajectoryColor, VACANT
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Constructor Summary
ConstructorsConstructorDescriptionsimMoran
(EvoLudoJRE engine) Create a new simulation to investigate fixation probabilities and times in the Moran process. -
Method Summary
Modifier and TypeMethodDescriptionvoid
collectCLO
(CLOParser parser) All providers of command line options must implement this method to collect their options.Type[]
Return array of Model types that this Module supports.static void
Main method to run the simulation.private String
msecToString
(long msec) Helper method to convert milliseconds to a more readable string representation in the format 'HH:mm:ss.ss'.void
run()
Methods inherited from class Moran
avgScores, getAuthors, getCustomLevels, getDependent, getFitness, getFitness, getMaxGameScore, getMinGameScore, getMonoGameScore, getStaticScores, getTitle, load, modelSettings, rhoA, setFitness, setFitness, t1, tA1, tAi, ti, unload
Methods inherited from class Discrete
add, getMaxMonoGameScore, getMinMonoGameScore, getMonoStop, getMutation, setMonoStop
Methods inherited from class Module
check, createGeometry, createIBSPop, getActiveTraits, getCompetitionGeometry, getDeathRate, getGeometry, getIBSPopulation, getID, getInteractionGeometry, getKey, getMapToFitness, getMarkers, getMeanColors, getNActive, getName, getNGroup, getNPopulation, getNRoles, getNSpecies, getNTraits, getOpponent, getPlayerUpdate, getSpecies, getSpecies, getSpeciesUpdateRate, getTraitColor, getTraitColors, getTraitName, getTraitNames, getTrajectoryColor, getVacant, init, isNeutral, processColorMap, reset, setActiveTraits, setDeathRate, setGeometries, setIBSPopulation, setModel, setName, setNGroup, setNPopulation, setNTraits, setOpponent, setSpeciesUpdateRate, setTraitColors, setTraitNames, setTrajectoryColor
Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface CLOProvider
adjustCLO
Methods inherited from interface Features
isPairwise
Methods inherited from interface Features.Static
isStatic
Methods inherited from interface HasHistogram
getNTraits, getTraitColors
Methods inherited from interface IBS.HasIBS
createIBS
Methods inherited from interface MilestoneListener
modelDidInit, modelDidReset, modelLoaded, modelRelaxed, modelRunning, modelStopped, modelUnloaded, moduleLoaded, moduleRestored, moduleUnloaded
Methods inherited from interface ODE.HasODE
createODE
Methods inherited from interface PDE.HasPDE
createPDE
Methods inherited from interface SDE.HasSDE
createSDE
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Field Details
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progress
boolean progressThe flag to indicate whether to show progress. -
out
PrintStream outThe output stream. Defaults toSystem.out
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jrengine
EvoLudoJRE jrengineThe EvoLudoJRE engine for running the simulation. This is a convenience field that saves us casting engine to EvoLudoJRE every time we need to access its methods. -
cloProgress
Command line option to show the simulation progress.
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Constructor Details
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simMoran
public simMoran(EvoLudoJRE engine) Create a new simulation to investigate fixation probabilities and times in the Moran process.- Parameters:
engine
- the pacemaker for running the model
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Method Details
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getModelTypes
Description copied from class:Module
Return array of Model types that this Module supports.- Overrides:
getModelTypes
in classModule
- Returns:
- the array of supported Model types
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run
public void run()Description copied from class:Module
Default run-loop for modules. Opportunity to override in subclasses for running customized simulations. Currently only called from
EvoLudoJRE.simulation()
if custom simulation class is specified injar
file. -
msecToString
Helper method to convert milliseconds to a more readable string representation in the format 'HH:mm:ss.ss'.- Parameters:
msec
- the time in milliseconds- Returns:
- the formatted string
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collectCLO
Description copied from interface:CLOProvider
All providers of command line options must implement this method to collect their options.Each command line option is (uniquely) identified by it's name (see
CLOption.getName()
), which corresponds to the long version of the option. If an attempt is made to add an option with a name that already exists, theparser
issues a warning and ignores the option. Thus, in general, implementing subclasses should first register their options and callsuper.collectCLO(CLOParser)
at the end such that subclasses are able to override command line options specified in a parental class.Override this method in subclasses to add further command line options. Subclasses must make sure that they include a call to super.
- Specified by:
collectCLO
in interfaceCLOProvider
- Overrides:
collectCLO
in classMoran
- Parameters:
parser
- the reference to parser that manages command line options- See Also:
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main
Main method to run the simulation.- Parameters:
args
- the array of command line arguments
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