org.aisb.bio.things.evolution
Class AsexualOrganism

java.lang.Object
  org.aisb.bio.things.evolution.AsexualOrganism

public class AsexualOrganism

extends java.lang.Object

This is an "organism" for the purpose of running evolutionary experiments. There's a Sequence representing the "genotype", and a unitless floating point number representing how much time until the organisim reproduces. There's also an integer value representing "fitness".

For convenience, there's also a floating point number representing "birthday", so we can fit the organism's entire lifespan into a timeline if we wish.

There's also a "parent" of type AsexualOrganism, so we can trace the organism's family tree if we wish.

Author:

Doug DeJulio

Constructor Summary

AsexualOrganism()

Method Summary

double	getBirthday()
int	getFitness()
Sequence	getGenotype()
Mutator	getMutator()
AsexualOrganism	getParent()
double	getTimeToReproduce()
AsexualOrganism	haveMutantBaby(double now) Create a new AsexualOrganism with a specified birthday.
void	loadFromFile(java.io.File file) Load the organism's gene sequence from a file.
void	loadFromFile(java.lang.String fileName) Load the organism's gene sequence from a file.
void	setBirthday(double birthday)
void	setFitness(int fitness)
void	setGenotype(Sequence genotype)
void	setMutator(Mutator mutator)
void	setParent(AsexualOrganism parent)
void	setTimeToReproduce(double timeToReproduce)
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AsexualOrganism

public AsexualOrganism()

Method Detail

getBirthday

public double getBirthday()

Returns:

Returns the birthday.

setBirthday

public void setBirthday(double birthday)

Parameters:

birthday - The birthday to set.

getFitness

public int getFitness()

Returns:

Returns the fitness.

setFitness

public void setFitness(int fitness)

Parameters:

fitness - The fitness to set.

getGenotype

public Sequence getGenotype()

Returns:

Returns the genotype.

setGenotype

public void setGenotype(Sequence genotype)

Parameters:

genotype - The genotype to set.

getTimeToReproduce

public double getTimeToReproduce()

Returns:

Returns the timeToReproduce.

setTimeToReproduce

public void setTimeToReproduce(double timeToReproduce)

Parameters:

timeToReproduce - The timeToReproduce to set.

getParent

public AsexualOrganism getParent()

Returns:

Returns the parent.

setParent

public void setParent(AsexualOrganism parent)

Parameters:

parent - The parent to set.

haveMutantBaby

public AsexualOrganism haveMutantBaby(double now)

Create a new AsexualOrganism with a specified birthday. The offspring will be mutated as per the mutator assigned to the parent, and will inherit that mutator.

To simulate the budding of an organism, keep the parent around and call this method once. To simulate cell division, call this method twice on the parent and then throw the parent away.

Parameters:

now - The offspring's "birthday".

Returns:

The child organism.

loadFromFile

public void loadFromFile(java.io.File file)
                  throws java.io.IOException

Load the organism's gene sequence from a file.

Parameters:

file - A file containing exactly one line consisting only of nucleotide code letters.

Throws:

java.io.IOException

loadFromFile

public void loadFromFile(java.lang.String fileName)
                  throws java.io.IOException

Load the organism's gene sequence from a file.

Parameters:

fileName - The name of a file containing exactly one line consisting only of nucleotide code letters.

Throws:

java.io.IOException

getMutator

public Mutator getMutator()

Returns:

Returns the mutator.

setMutator

public void setMutator(Mutator mutator)

Parameters:

mutator - The mutator to use.

toString

public java.lang.String toString()