Package pal.datatype

Class SpecificAminoAcids

java.lang.Object
pal.datatype.SimpleDataType
pal.datatype.AminoAcids
pal.datatype.SpecificAminoAcids
All Implemented Interfaces:
Serializable, DataType, MolecularDataType
public class SpecificAminoAcids extends AminoAcids implements MolecularDataType
implements a MolecularDataType for amino acids, where we specifiy the Codon Table basis of amino acid by supplying the CodonTable which is/was used for converting Nucleotide sequences to Amino Acids. We need this table to do conversion between Nucleotides and Amino Acids (and vice versa)
Version:
$Id: SpecificAminoAcids.java,v 1.8 2004/10/29 01:13:37 matt Exp $
Author:
Matthew Goode
See Also:

  • Constructor Details

    • SpecificAminoAcids

      public SpecificAminoAcids()
      Creates with Universal Codon Table

    • SpecificAminoAcids

      public SpecificAminoAcids(CodonTable translationTable)

    • SpecificAminoAcids

      public SpecificAminoAcids(int organismTypeID)

  • Method Details

    • getOrganismTypeID

      public int getOrganismTypeID()
      Returns:
      Organism TypeID as for CodonTable

    • getNucleotideStates

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

    • getMolecularStatesFromIUPACNucleotides

      public final int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
      Specified by:
      getMolecularStatesFromIUPACNucleotides in interface MolecularDataType

    • getMolecularStatesFromSimpleNucleotides

      public final int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
      Specified by:
      getMolecularStatesFromSimpleNucleotides in interface MolecularDataType

    • isCreatesIUPACNuecleotides

      public boolean isCreatesIUPACNuecleotides()
      Specified by:
      isCreatesIUPACNuecleotides in interface MolecularDataType
      Returns:
      false

    • getNucleotideLength

      public final int getNucleotideLength()
      Specified by:
      getNucleotideLength in interface MolecularDataType
      Returns:
      3