__init__ ( self,  alphabet=SchemaDNAAlphabet() )

Initialize a finder to get schemas using Genetic Algorithms.

Arguments:

• alphabet -- The alphabet which specifies the contents of the schemas we'll be generating. This alphabet must contain the attribute alphabet_matches, which is a dictionary specifying the potential ambiguities of each letter in the alphabet. These ambiguities will be used in building up the schema.

_set_up_genetic_algorithm ( self )

Overrideable function to set up the genetic algorithm parameters.

This functions sole job is to set up the different genetic algorithm functionality. Since this can be quite complicated, this allows cusotmizablity of all of the parameters. If you want to customize specially, you can inherit from this class and override this function.

find_schemas (
        self,
        fitness,
        num_schemas,
        )

Find the given number of unique schemas using a genetic algorithm

Arguments:

• fitness - A callable object (ie. function) which will evaluate the fitness of a motif.

• num_schemas - The number of unique schemas with good fitness that we want to generate.