Package Bio :: Package NeuralNetwork :: Package Gene :: Module Schema :: Class MostCountSchemaFitness
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Class MostCountSchemaFitness


Calculate a fitness giving weight to schemas that match many times.

This fitness function tries to maximize schemas which are found many times in a group of sequences.
Method Summary
  __init__(self, seq_records, schema_evaluator)
Initialize with sequences to evaluate.
  calculate_fitness(self, genome)
Calculate the fitness of a genome based on schema matches.

Method Details

__init__(self, seq_records, schema_evaluator)
(Constructor)

Initialize with sequences to evaluate.

Arguments:

o seq_records -- A set of SeqRecord objects which we use to calculate the fitness.

o schema_evaluator - An Schema class which can be used to evaluate find motif matches in sequences.

calculate_fitness(self, genome)

Calculate the fitness of a genome based on schema matches.

This bases the fitness of a genome completely on the number of times it matches in the set of seq_records. Matching more times gives a better fitness

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