Package org.biojava.bio.symbol

Class SimpleCodonPref

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.symbol.SimpleCodonPref

All Implemented Interfaces:

CodonPref, Changeable

public class SimpleCodonPref
extends AbstractChangeable
implements CodonPref

a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.

Since:

1.3

Author:

David Huen, gwaldon pyrrolysine

Constructor Summary

Constructors

Constructor	Description
SimpleCodonPref(String geneticCodeName, Distribution codonPref, String name)

Method Summary

Modifier and Type	Method	Description
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.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleCodonPref

public SimpleCodonPref(String geneticCodeName,
                       Distribution codonPref,
                       String name)
                throws IllegalAlphabetException

Throws:

IllegalAlphabetException

Method Detail

getName

public String getName()

Description copied from interface: CodonPref

get name of object

Specified by:

getName in interface CodonPref

getGeneticCodeName

public String getGeneticCodeName()

Description copied from interface: CodonPref

get the name of the genetic code

Specified by:

getGeneticCodeName in interface CodonPref

getGeneticCode

public ManyToOneTranslationTable getGeneticCode()

Description copied from interface: CodonPref

the genetic code that this codon preference is based on.

Specified by:

getGeneticCode in interface CodonPref

getFrequency

public Distribution getFrequency()

Description copied from interface: CodonPref

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

Specified by:

getFrequency in interface CodonPref

getFrequencyForSynonyms

public Distribution getFrequencyForSynonyms(Symbol residue)
                                     throws IllegalSymbolException

Description copied from interface: CodonPref

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

Specified by:

getFrequencyForSynonyms in interface CodonPref

Throws:

IllegalSymbolException

getWobbleDistributionForSynonyms

public WobbleDistribution getWobbleDistributionForSynonyms(Symbol residue)
                                                    throws IllegalSymbolException

Description copied from interface: CodonPref

returns a WobbleDistribution for a specified residue.

Specified by:

getWobbleDistributionForSynonyms in interface CodonPref

Throws:

IllegalSymbolException