Package pal.datatype

Interface CodonTable

All Superinterfaces:
Serializable
public interface CodonTable extends 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 Details

    • UNIVERSAL

      static final int UNIVERSAL
      TypeID for Universal
      See Also:

    • VERTEBRATE_MITOCHONDRIAL

      static final int VERTEBRATE_MITOCHONDRIAL
      TypeID for Vertebrate Mitochondrial
      See Also:

    • YEAST

      static final int YEAST
      TypeID for Yeast
      See Also:

    • MOLD_PROTOZOAN_MITOCHONDRIAL

      static final int MOLD_PROTOZOAN_MITOCHONDRIAL
      TypeID for Mold Protozoan Mitochondrial
      See Also:

    • MYCOPLASMA

      static final int MYCOPLASMA
      TypeID for Mycoplasma
      See Also:

    • INVERTEBRATE_MITOCHONDRIAL

      static final int INVERTEBRATE_MITOCHONDRIAL
      TypeID for Invertebrate Mitochondrial
      See Also:

    • CILATE

      static final int CILATE
      TypeID for Cilate
      See Also:

    • ECHINODERM_MITOCHONDRIAL

      static final int ECHINODERM_MITOCHONDRIAL
      TypeID for Echinoderm Mitochondrial
      See Also:

    • EUPLOTID_NUCLEAR

      static final int EUPLOTID_NUCLEAR
      TypeID for Euplotid Nuclear
      See Also:

    • ASCIDIAN_MITOCHONDRIAL

      static final int ASCIDIAN_MITOCHONDRIAL
      TypeID for Ascidian Mitochondrial
      See Also:

    • FLATWORM_MITOCHONDRIAL

      static final int FLATWORM_MITOCHONDRIAL
      TypeID for Flatworm Mitochondrial
      See Also:

    • BLEPHARISMA_NUCLEAR

      static final int BLEPHARISMA_NUCLEAR
      TypeID for Blepharisma Nuclear
      See Also:

    • BACTERIAL

      static final int BACTERIAL
      TypeID for Bacterial
      See Also:

    • ALTERNATIVE_YEAST

      static final int ALTERNATIVE_YEAST
      TypeID for Alternative Yeast
      See Also:

    • ORGANISM_TYPE_NAMES

      static final String[] ORGANISM_TYPE_NAMES
      A textual version of an organism type - type is index into array

  • Method Details

    • 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:

    • getAminoAcidState

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

    • 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