Package pal.datatype

Interface MolecularDataType

    • Method Detail

      • 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