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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 the fitness could potentially be out of date with the real genome if you are not careful to recalculate it after changes with recalculate_fitness()
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Initialize an organism Arguments: o genome -- A MutableSeq object representing the sequence of the genome. o fitness_calculator -- A funtion 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. |
Define comparisons for organisms. Compare organisms by their genomes (as strings of letters). |
Return a copy of the organism. This makes it easy to duplicate an organism before changing it. |
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. |
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Generated by Epydoc 3.0.1 on Wed Jul 14 01:35:50 2010 | http://epydoc.sourceforge.net |