Package pal.datatype

Class Codons

  • All Implemented Interfaces:
    java.io.Serializable, DataType, MolecularDataType
    public class Codons
extends SimpleDataType
implements MolecularDataType
    implements DataType for all Codons (including terminators). Characters are defined as 'A-Z' followed by 'a-z' followed by '0-9' followed by '@' and '%' Now incorporates the ungeneral code from GeneralizedCodons (which has died due to it's limited use)
    Version:
    $Id: Codons.java,v 1.21 2004/03/10 04:42:54 matt Exp $
    Author:
    Matthew Goode, Alexei Drummond
    See Also:
    Serialized Form

    • Field Detail

      • DEFAULT_INSTANCE

        public static final Codons DEFAULT_INSTANCE

    • Constructor Detail

      • Codons

        public Codons()

    • Method Detail

      • getNumStates

        public int getNumStates()
        Description copied from interface: DataType
        get number of unique states
        Specified by:
        getNumStates in interface DataType
        Returns:
        number of unique states

      • getStateImpl

        public int getStateImpl​(char c)
        Description copied from class: SimpleDataType
        For sub classes to implement main functionality of getState. Gaps do not need to be considered
        Specified by:
        getStateImpl in class SimpleDataType

      • getCharImpl

        protected char getCharImpl​(int state)
        Get character corresponding to a given state
        Specified by:
        getCharImpl in class SimpleDataType

      • getDescription

        public java.lang.String getDescription()
        Description copied from interface: DataType
        description of data type
        Specified by:
        getDescription in interface DataType
        Returns:
        string describing the data type

      • isUnknownStateImpl

        protected final boolean isUnknownStateImpl​(int state)
        Description copied from class: SimpleDataType
        For subclasses to handle, without regard for gaps
        Specified by:
        isUnknownStateImpl in class SimpleDataType

      • getTypeID

        public int getTypeID()
        Description copied from interface: DataType
        get numerical code describing the data type
        Specified by:
        getTypeID in interface DataType
        Returns:
        numerical code

      • getNucleotideStates

        public int[] getNucleotideStates​(int[] residueStates)
        Specified by:
        getNucleotideStates in interface MolecularDataType
        Parameters:
        residue - states an array of states corresponding to states of this datatype
        Returns:
        the corresponding IUPAC states

      • getTLA

        public static final java.lang.String getTLA​(int state)
        Returns:
        a three letter acronym for an AminoAcid, according to state

      • getCodonIndexFromNucleotides

        public static final int getCodonIndexFromNucleotides​(char[] codon)
        The codon index is a number between 0 and 64 assigned to each different codon type
        Parameters:
        codon - a 3 element array of characters which contain Nucleotide characters
        Returns:
        -1 if the codon has unknowns, or gaps in it, or is length is less than 3

      • getCodonIndexFromNucleotideStates

        public static final int getCodonIndexFromNucleotideStates​(int[] codon)
        The codon index is a number between 0 and 64 assigned to each different codon type
        Parameters:
        codon - a 3 element array of characters which contain Nucleotide states
        Returns:
        -1 if the codon has unknowns, or gaps in it, or is length is less than 3

      • getCodonIndexFromNucleotideStates

        public static final int getCodonIndexFromNucleotideStates​(int[] codon,
                                                          int startingPosition)
        The codon index is a number between 0 and 64 assigned to each different codon type
        Parameters:
        codon - a 3 element array of characters which contain Nucleotide states
        startingPosition - an offset into the array to start examining
        Returns:
        -1 if the codon has unknowns, or gaps in it, or is length is less than 3

      • getCodonIndexFromIUPACNucleotideStates

        public static final int getCodonIndexFromIUPACNucleotideStates​(int[] codon)
        The codon index is a number between 0 and 64 assigned to each different codon type
        Parameters:
        codon - a 3 element array of characters which contain Nucleotide states
        startingPosition - an offset into the array to start examining
        Returns:
        -1 if the codon has unknowns, or gaps in it, or is length is less than 3

      • getCodonIndexFromIUPACNucleotideStates

        public static final int getCodonIndexFromIUPACNucleotideStates​(int[] codon,
                                                               int startingPosition)
        The codon index is a number between 0 and 64 assigned to each different codon type
        Parameters:
        codon - a 3 element array of characters which contain Nucleotide states
        startingPosition - an offset into the array to start examining
        Returns:
        -1 if the codon has unknowns, or gaps in it, or is length is less than 3

      • getNucleotidesFromCodonIndex

        public static final char[] getNucleotidesFromCodonIndex​(int index)
        Translates an index into a codon
        Parameters:
        index - the codon index
        Returns:
        a char array contain 3 nucleotide characters

      • getNucleotideStatesFromCodonIndex

        public static final int[] getNucleotideStatesFromCodonIndex​(int codonIndex)
        Translates an index into a codon
        Parameters:
        index - the codon index
        Returns:
        an int array contain 3 nucleotide states

      • getF1X4CodonFrequencies

        public static final double[] getF1X4CodonFrequencies​(double[] nucleotideFrequencies)

      • getF3X4CodonFrequencies

        public static final double[] getF3X4CodonFrequencies​(double[][] nucleotideTripletFrequencies)