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SimpleCodonPref (biojava-legacy 1.9.5 API)

  • 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

      All Methods Instance Methods Concrete Methods 
      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