org.biojava.bio.symbol
Interface WobbleDistribution

public interface WobbleDistribution

an object to return statistics about the frequency of the wobble base in a set of synonymous codons.

Since:

1.3

Author:

David Huen

Method Summary

Distribution	getFrequencyOfNonWobbleBases() returns the frequency with which synonymous codons start with a specified pair of bases.
Set	getNonWobbleBases() returns Set containing the nonWobbleBases that occur in codons that encode this residue
Symbol	getResidue() returns the residue encoded by this WobbleDistribution
Distribution	getWobbleFrequency(Symbol nonWobbleBases) returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases.

Method Detail

getResidue

public Symbol getResidue()

returns the residue encoded by this WobbleDistribution

getNonWobbleBases

public Set getNonWobbleBases()

returns Set containing the nonWobbleBases that occur in codons that encode this residue

getFrequencyOfNonWobbleBases

public Distribution getFrequencyOfNonWobbleBases()

returns the frequency with which synonymous codons start with a specified pair of bases.

getWobbleFrequency

public Distribution getWobbleFrequency(Symbol nonWobbleBases)

returns the frequency of a specific wobble base in a set of synonymous codons that start with the same two bases. (sums to one over this set).