Package org.biojava.bio.symbol
Class SimpleCodonPref
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.SimpleCodonPref
- All Implemented Interfaces:
CodonPref
,Changeable
a simple no-frills implementation of the
CodonPref object that encapsulates
codon preference data.
- Since:
- 1.3
- Author:
- David Huen, gwaldon pyrrolysine
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Constructor Summary
ConstructorsConstructorDescriptionSimpleCodonPref
(String geneticCodeName, Distribution codonPref, String name) -
Method Summary
Modifier and TypeMethodDescriptionreturns a Distribution giving the frequency of codons (sums to one over the totality of codons).getFrequencyForSynonyms
(Symbol residue) returns a Distribution giving the frequency of synonymous codons.the genetic code that this codon preference is based on.get the name of the genetic codegetName()
get name of objectgetWobbleDistributionForSynonyms
(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
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Constructor Details
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SimpleCodonPref
public SimpleCodonPref(String geneticCodeName, Distribution codonPref, String name) throws IllegalAlphabetException - Throws:
IllegalAlphabetException
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Method Details
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getName
Description copied from interface:CodonPref
get name of object -
getGeneticCodeName
Description copied from interface:CodonPref
get the name of the genetic code- Specified by:
getGeneticCodeName
in interfaceCodonPref
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getGeneticCode
Description copied from interface:CodonPref
the genetic code that this codon preference is based on.- Specified by:
getGeneticCode
in interfaceCodonPref
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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 interfaceCodonPref
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getFrequencyForSynonyms
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 interfaceCodonPref
- Throws:
IllegalSymbolException
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getWobbleDistributionForSynonyms
public WobbleDistribution getWobbleDistributionForSynonyms(Symbol residue) throws IllegalSymbolException Description copied from interface:CodonPref
returns a WobbleDistribution for a specified residue.- Specified by:
getWobbleDistributionForSynonyms
in interfaceCodonPref
- Throws:
IllegalSymbolException
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