org.biojava.bio.symbol
Interface CodonPref

All Known Implementing Classes:

SimpleCodonPref

public interface CodonPref

Method Summary

Distribution	getFrequency() returns a Distribution giving the frequency of codons (sums to one over the totality of codons).
Distribution	getFrequencyForSynonyms(Symbol residue) returns a Distribution giving the frequency of synonymous codons.
ManyToOneTranslationTable	getGeneticCode() the genetic code that this codon preference is based on.
String	getGeneticCodeName() get the name of the genetic code
String	getName() get name of object
WobbleDistribution	getWobbleDistributionForSynonyms(Symbol residue) returns a WobbleDistribution for a specified residue.

Method Detail

getName

public String getName()

get name of object

getGeneticCodeName

public String getGeneticCodeName()

get the name of the genetic code

getGeneticCode

public ManyToOneTranslationTable getGeneticCode()

the genetic code that this codon preference is based on.

getFrequency

public Distribution getFrequency()

returns a Distribution giving the frequency of codons (sums to one over the totality of codons).

getFrequencyForSynonyms

public Distribution getFrequencyForSynonyms(Symbol residue)
                                     throws IllegalSymbolException

returns a Distribution giving the frequency of synonymous codons. (sums to one over the total number of codons that encode that residue).

Throws:

IllegalSymbolException

getWobbleDistributionForSynonyms

public WobbleDistribution getWobbleDistributionForSynonyms(Symbol residue)
                                                    throws IllegalSymbolException

returns a WobbleDistribution for a specified residue.

Throws:

IllegalSymbolException