Package pal.datatype

Interface CodonTable

  • All Superinterfaces:
    java.io.Serializable

    public interface CodonTable
    extends java.io.Serializable
    Describes a device for translating Nucleotide triplets or codon indices into amino acid codes. Codon Indexes (or states) are defined as in GeneralizedCodons
    Version:
    $Id: CodonTable.java,v 1.10 2003/09/04 03:22:34 matt Exp $
    Author:
    Matthew Goode, Alexei Drummond
    • Field Detail

      • VERTEBRATE_MITOCHONDRIAL

        static final int VERTEBRATE_MITOCHONDRIAL
        TypeID for Vertebrate Mitochondrial
        See Also:
        Constant Field Values
      • MOLD_PROTOZOAN_MITOCHONDRIAL

        static final int MOLD_PROTOZOAN_MITOCHONDRIAL
        TypeID for Mold Protozoan Mitochondrial
        See Also:
        Constant Field Values
      • INVERTEBRATE_MITOCHONDRIAL

        static final int INVERTEBRATE_MITOCHONDRIAL
        TypeID for Invertebrate Mitochondrial
        See Also:
        Constant Field Values
      • ECHINODERM_MITOCHONDRIAL

        static final int ECHINODERM_MITOCHONDRIAL
        TypeID for Echinoderm Mitochondrial
        See Also:
        Constant Field Values
      • EUPLOTID_NUCLEAR

        static final int EUPLOTID_NUCLEAR
        TypeID for Euplotid Nuclear
        See Also:
        Constant Field Values
      • ASCIDIAN_MITOCHONDRIAL

        static final int ASCIDIAN_MITOCHONDRIAL
        TypeID for Ascidian Mitochondrial
        See Also:
        Constant Field Values
      • FLATWORM_MITOCHONDRIAL

        static final int FLATWORM_MITOCHONDRIAL
        TypeID for Flatworm Mitochondrial
        See Also:
        Constant Field Values
      • BLEPHARISMA_NUCLEAR

        static final int BLEPHARISMA_NUCLEAR
        TypeID for Blepharisma Nuclear
        See Also:
        Constant Field Values
      • ALTERNATIVE_YEAST

        static final int ALTERNATIVE_YEAST
        TypeID for Alternative Yeast
        See Also:
        Constant Field Values
      • ORGANISM_TYPE_NAMES

        static final java.lang.String[] ORGANISM_TYPE_NAMES
        A textual version of an organism type - type is index into array
    • Method Detail

      • getAminoAcidChar

        char getAminoAcidChar​(char[] codon)
        Returns the char associated with AminoAcid represented by 'codon'
        Returns:
        state for '?' if codon unknown or wrong length
        See Also:
        AminoAcids
      • getAminoAcidState

        int getAminoAcidState​(char[] codon)
        Returns the state associated with AminoAcid represented by 'codon'
        Returns:
        '?' if codon unknown or wrong length
        See Also:
        AminoAcids
      • getCodonsFromAminoAcidState

        char[][] getCodonsFromAminoAcidState​(int aminoAcidState)
        Returns:
        all the possible codons for a given amino acid
      • getCodonsFromAminoAcidChar

        char[][] getCodonsFromAminoAcidChar​(char aminoAcidChar)
      • getAminoAcidCharFromCodonIndex

        char getAminoAcidCharFromCodonIndex​(int codonIndex)
        Returns the amino acid char at the corresponding codonIndex
      • getAminoAcidStateFromCodonIndex

        int getAminoAcidStateFromCodonIndex​(int codonIndex)
        Returns the amino acid state at the corresponding codonIndex
      • getIUPACStatesFromAminoAcidState

        int[] getIUPACStatesFromAminoAcidState​(int aminoAcid)
      • getStatesFromAminoAcidState

        int[] getStatesFromAminoAcidState​(int aminoAcid)
      • getAminoAcidStateFromStates

        int getAminoAcidStateFromStates​(int[] states)
        Returns:
        The AminoAcid states given the nucleotides states (array should be of size 3)
      • getTerminatorIndexes

        int[] getTerminatorIndexes()
        Returns:
        the codon states of terminator amino acids.
      • getNumberOfTerminatorIndexes

        int getNumberOfTerminatorIndexes()
        Returns the number of terminator amino acids.
      • getOrganismTypeID

        int getOrganismTypeID()
        Returns:
        the type of this organism (see defined type constants)
      • isSynonymous

        boolean isSynonymous​(int codonIndexOne,
                             int codonIndexTwo)
        Returns:
        true if the amino acids that map to two codons are the same (synonymous). False otherwise