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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.symbol.SimpleCodonPref
public class SimpleCodonPref
a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
Constructor Summary | |
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SimpleCodonPref(java.lang.String geneticCodeName,
Distribution codonPref,
java.lang.String name)
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Method Summary | |
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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. |
java.lang.String |
getGeneticCodeName()
get the name of the genetic code |
java.lang.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 |
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addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SimpleCodonPref(java.lang.String geneticCodeName, Distribution codonPref, java.lang.String name) throws IllegalAlphabetException
IllegalAlphabetException
Method Detail |
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public java.lang.String getName()
CodonPref
getName
in interface CodonPref
public java.lang.String getGeneticCodeName()
CodonPref
getGeneticCodeName
in interface CodonPref
public ManyToOneTranslationTable getGeneticCode()
CodonPref
getGeneticCode
in interface CodonPref
public Distribution getFrequency()
CodonPref
getFrequency
in interface CodonPref
public Distribution getFrequencyForSynonyms(Symbol residue) throws IllegalSymbolException
CodonPref
getFrequencyForSynonyms
in interface CodonPref
IllegalSymbolException
public WobbleDistribution getWobbleDistributionForSynonyms(Symbol residue) throws IllegalSymbolException
CodonPref
getWobbleDistributionForSynonyms
in interface CodonPref
IllegalSymbolException
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