Package jebl.evolution.sequences

Class Codons

java.lang.Object
jebl.evolution.sequences.Codons
public final class Codons extends Object
Version:
$Id: Codons.java 744 2007-07-30 02:57:11Z twobeers $
Author:
Andrew Rambaut, Alexei Drummond

  • Field Details

  • Constructor Details

    • Codons

      public Codons()

  • Method Details

    • getStateCount

      public static int getStateCount()

    • getStates

      public static List<State> getStates()

    • getCanonicalStateCount

      public static int getCanonicalStateCount()

    • getCanonicalStates

      public static List<State> getCanonicalStates()

    • getState

      public static CodonState getState(NucleotideState nucleotide1, NucleotideState nucleotide2, NucleotideState nucleotide3)

    • getState

      public static CodonState getState(String code)
      Gets the state object for the given code. Returns null if the code is illegal or contains ambiguous nucleotides.
      Parameters:
      code - a three-character string of non-ambiguous nucleotides in uppercase
      Returns:
      the state

    • getState

      public static CodonState getState(int index)

    • getUnknownState

      public static CodonState getUnknownState()

    • getGapState

      public static CodonState getGapState()

    • isUnknown

      public static boolean isUnknown(CodonState state)

    • isGap

      public static boolean isGap(CodonState state)

    • toNucleotides

      public static NucleotideState[] toNucleotides(State[] states)

    • toNucleotides

      public static NucleotideState[] toNucleotides(CodonState state)

    • toStateArray

      public static CodonState[] toStateArray(String sequenceString)

    • toStateArray

      public static CodonState[] toStateArray(byte[] indexArray)