Bio.GA.Organism.Organism

Class Organism

object --+ | Organism

Represent a single individual in a population. Attributes: o genome -- The genome of the organism. This is a Bio.MutableSeq object that has the sequence of the genome, and the alphabet describing all elements that can be a part of the genome. o fitness -- The calculate fitness of the organism. This fitness is based on the last time it was calculated using the fitness_calculator. So... the fitness could potentially be out of date with the real genome if you are not careful to recalculate it after changes with recalculate_fitness()

Instance Methods

[hide private]

__init__(self, genome, fitness_calculator, start_fitness=None)
Initialize an organism

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__str__(self)
Provide a string output for debugging.

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__eq__(self, other)
Compare organisms by their genomes (as strings of letters).

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__ne__(self, other)
Compare organisms by their genomes (as strings of letters).

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__lt__(self, other)
Compare organisms by their genomes (as strings of letters).

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__le__(self, other)
Compare organisms by their genomes (as strings of letters).

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__gt__(self, other)
Compare organisms by their genomes (as strings of letters).

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__ge__(self, other)
Compare organisms by their genomes (as strings of letters).

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copy(self)
Return a copy of the organism.

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recalculate_fitness(self)
Calculate and reset the fitness of the current genome

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__

Properties

[hide private]

Inherited from object: __class__

init(self, genome, fitness_calculator, start_fitness=None)
(Constructor)

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Initialize an organism

Arguments:

o genome -- A MutableSeq object representing the sequence of the
genome.

o fitness_calculator -- A function that will calculate the fitness
of the organism when given the organisms genome.

o start_fitness - the starting fitness corresponding with the
given genome. If not supplied, the fitness will be calculated
using fitness_calculator.

Overrides: object.__init__

str(self)
(Informal representation operator)

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Provide a string output for debugging.

Overrides: object.__str__

copy(self)

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Return a copy of the organism.

This makes it easy to duplicate an organism before changing it.

recalculate_fitness(self)

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Calculate and reset the fitness of the current genome

This should be called after the genome is updated to ensure that
fitness always stays in sync with the current genome.

Class Organism

__init__(self, genome, fitness_calculator, start_fitness=None) (Constructor)

__str__(self) (Informal representation operator)

copy(self)

recalculate_fitness(self)

init(self, genome, fitness_calculator, start_fitness=None)
(Constructor)

str(self)
(Informal representation operator)