Package Bio :: Package GA :: Package Repair :: Module Stabilizing :: Class AmbiguousRepair
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Class AmbiguousRepair


Perform repair to reduce the number of Ambiguous genes in a genome.

In cases where ambiguous genes are allowed in a genome (for example, where you have a wild card character like '*' that will match anything), these can come to dominate a genome since, really, the best fitness is someting like '*******'. This repair protects against that by changing ambiguous characters into some non-ambiguous gene.
Method Summary
  __init__(self, ambig_finder, num_ambiguous)
Initialize the repair class.
  repair(self, organism)
Perform a repair to remove excess ambiguous genes.

Method Details

__init__(self, ambig_finder, num_ambiguous)
(Constructor)

Initialize the repair class.

Arguments:

o ambig_finder - A class implementing the function find_ambiguous which will return a list of all ambiguous positions in a sequence. It also must have the function all_unambiguous, which will return all allowed unambiguous letters.

o num_ambiguous - The minimum number of ambiguous items that are allowed in a genome. If there are more than this present, repair will be performed.

repair(self, organism)

Perform a repair to remove excess ambiguous genes.

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