Package pal.datatype

Interface MolecularDataType

All Superinterfaces:
DataType, Serializable
All Known Implementing Classes:
Codons, GapBalanced, IUPACNucleotides, Nucleotides, SpecificAminoAcids

public interface MolecularDataType extends DataType
An extension to the generic DataType class for DataTypes related to genetic residues (by this it is meant Nucleotides, AminoAcids, and Codons).
Version:
1.1
Author:
Matthew Goode
  • Method Details

    • getNucleotideStates

      int[] getNucleotideStates(int[] molecularStates)
      Parameters:
      molecularStates - an array of states corresponding to states of this datatype
      Returns:
      the corresponding IUPAC states
    • getMolecularStatesFromIUPACNucleotides

      int[] getMolecularStatesFromIUPACNucleotides(int[] nucleotideStates, int startingIndex)
      Parameters:
      the - IUPAC nucleotidestates
    • getMolecularStatesFromSimpleNucleotides

      int[] getMolecularStatesFromSimpleNucleotides(int[] nucleotideStates, int startingIndex)
      Parameters:
      the - Simple nucleotide states (eg 0,1,2,3 or A,C,G,T)
    • isCreatesIUPACNuecleotides

      boolean isCreatesIUPACNuecleotides()
      Returns:
      true if this data type will create Nucleotide states using IUPAC states (for example if this DataType is AminoAcid based, IUPAC states are needed to maintain information on different possible values for a state)
    • getNucleotideLength

      int getNucleotideLength()
      Returns:
      the number of nucleotides required for a single character of this data typedata