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

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object --+
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        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.

Instance Methods [hide private]
 
__init__(self, ambig_finder, num_ambiguous)
Initialize the repair class.
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repair(self, organism)
Perform a repair to remove excess ambiguous genes.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, ambig_finder, num_ambiguous)
(Constructor)

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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.

Overrides: object.__init__