Class GeneticCode

java.lang.Object
jebl.evolution.sequences.GeneticCode

public final class GeneticCode extends Object
A set of standard genetic codes.
Version:
$Id: GeneticCode.java 1044 2009-12-09 03:33:54Z stevensh $
Author:
Andrew Rambaut, Alexei Drummond
  • Field Details

    • UNIVERSAL

      public static final GeneticCode UNIVERSAL
    • VERTEBRATE_MT

      public static final GeneticCode VERTEBRATE_MT
    • YEAST

      public static final GeneticCode YEAST
    • MOLD_PROTOZOAN_MT

      public static final GeneticCode MOLD_PROTOZOAN_MT
    • MYCOPLASMA

      public static final GeneticCode MYCOPLASMA
    • INVERTEBRATE_MT

      public static final GeneticCode INVERTEBRATE_MT
    • CILIATE

      public static final GeneticCode CILIATE
    • ECHINODERM_MT

      public static final GeneticCode ECHINODERM_MT
    • EUPLOTID_NUC

      public static final GeneticCode EUPLOTID_NUC
    • BACTERIAL

      public static final GeneticCode BACTERIAL
    • ALT_YEAST

      public static final GeneticCode ALT_YEAST
    • ASCIDIAN_MT

      public static final GeneticCode ASCIDIAN_MT
    • FLATWORM_MT

      public static final GeneticCode FLATWORM_MT
    • BLEPHARISMA_NUC

      public static final GeneticCode BLEPHARISMA_NUC
    • GENETIC_CODES

      @Deprecated public static final GeneticCode[] GENETIC_CODES
      Deprecated.
      use getGeneticCodes() instead
      Use of this field is deprecated because being an array it is mutable, i.e. an attacker could potentially replace values in this array.
  • Method Details

    • getGeneticCodes

      public static Iterable<GeneticCode> getGeneticCodes()
      Returns an iterable that allows you to iterate over all the standard genetic codes
      Returns:
      An iterable over the genetic codes
    • getGeneticCodesArray

      public static GeneticCode[] getGeneticCodesArray()
    • valueOf

      public static GeneticCode valueOf(String name)
      Parameters:
      name - the name of the genetic code
      Returns:
      the genetic code such that getDescription() equals name
    • valueOf

      public static GeneticCode valueOf(int NCBITranslationTableNumber)
      Parameters:
      NCBITranslationTableNumber - the name of the genetic code
      Returns:
      the genetic code such that getNcbiTranslationTableNumber() equals NCBITranslationTableNumber
    • getName

      public String getName()
      Returns the name of the genetic code
      Returns:
      the name of this genetic code
    • getDescription

      public String getDescription()
      Returns the description of the genetic code
      Returns:
      the description of this genetic code
    • getCodeTable

      public String getCodeTable()
      Returns a length-64 string that for each nucleotide triplet contains the single-character amino acid code (see AminoAcids to which that triplet is translated in this genetic code.
      Returns:
      the string passed to the constructor as the codeTable argument.
    • getTranslation

      public AminoAcidState getTranslation(CodonState codonState)
      Returns the state associated with AminoAcid represented by codonState. Note that the state is the canonical state (generated combinatorially)
      Returns:
      '?' if codon unknown
      See Also:
    • getTranslation

      public AminoAcidState getTranslation(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)
      Returns the state associated with AminoAcid represented by the three nucleotides. If one or more of the nucleotides are ambiguous, and all combinations translate to the same protein, then this method will return that protein
      Returns:
      '?' if codon unknown
      See Also:
    • getTranslation

      public AminoAcidState getTranslation(String nucleotides)
      Returns the state associated with AminoAcid represented by the three nucleotides. If one or more of the nucleotides are ambiguous, and all combinations translate to the same protein, then this method will return that protein
      Parameters:
      nucleotides - a string consisting of exactly 3 residues in any case.
      Returns:
      '?' if codon unknown
      See Also:
    • isStartCodonString

      public MaybeBoolean isStartCodonString(String tripletString) throws IllegalArgumentException
      Checks whether all possible disambiguations of a given nucleotide triplet string represents a start codon.
      Parameters:
      tripletString - A string of length 3, with each character representing one nucleotide or ambiguity symbol
      Returns:
      Whether all possible disambiguations of tripletString represent a start codon.
      Throws:
      IllegalArgumentException - if tripletString doesn't consist of 3 nucleotide or ambiguity symbols
      NullPointerException - if tripletString is null
    • isStartCodon

      @Deprecated public boolean isStartCodon(CodonState codonState)
      Deprecated.
      As of 2007-07-30, CodonStates exist only for nonambiguous nucleotide triplets. Therefore, this method cannot be used to check if an ambiguous triplet of nucleotides codes for a transcription, start and therefore this method is deprecated.
      Parameters:
      codonState -
      Returns:
      True if the specified codonState codes for a transcription start under this genetic code.
    • isStopCodon

      @Deprecated public boolean isStopCodon(CodonState codonState)
      Deprecated.
      As of 2007-07-30, CodonStates exist only for nonambiguous nucleotide triplets. Therefore, this method cannot be used to check if an ambiguous triplet of nucleotides codes for a stop, and therefore this method is deprecated.
      Parameters:
      codonState -
      Returns:
      True if the specified codonState codes for a stop under this genetic code.
    • isStopCodonString

      public MaybeBoolean isStopCodonString(String tripletString) throws IllegalArgumentException
      Checks whether a given String represents a stop codon.
      Parameters:
      tripletString - A string of length 3, with each character representing one nucleotide or ambiguity symbol
      Returns:
      true if tripletString represents a stop codon.
      Throws:
      IllegalArgumentException - if tripletString doesn't consist of 3 nucleotide or ambiguity symbols
      NullPointerException - if tripletString is null
    • getCodonsForAminoAcid

      public Set<CodonState> getCodonsForAminoAcid(AminoAcidState aminoAcidState)
      Returns:
      all the possible codons for a given amino acid
    • getStartCodons

      public Set<CodonState> getStartCodons()
      Returns:
      the codon states of starts
    • getStopCodons

      public Set<CodonState> getStopCodons()
      Returns:
      the codon states of stops.
    • getStopCodonCount

      public int getStopCodonCount()
      Returns the number of terminator amino acids.
    • getNcbiTranslationTableNumber

      public int getNcbiTranslationTableNumber()
      Returns:
      the number used by NCBI to represent this genetic code or -1 if none. Eg. 1 = Standard...
    • toString

      public String toString()
      Same as getDescription() (so that GeneticCode objects can be used e.g. in a JComboBox).
      Overrides:
      toString in class Object
      Returns:
      the description of this genetic code