Class ABITools

  • public class ABITools
    extends Object
    Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
    Matthew Pocock
    • Field Detail

      • QUALITY

        public static final FiniteAlphabet QUALITY
        The quality alphabet. This is equivalent to DNA x [0,1] where 0 represents poorly supported (lower case) and 1 represents strongly supported (upper case).
      • _0

        public static final AtomicSymbol _0
        The poorly supported symbol.
      • SEQUENCE

        public static final Object SEQUENCE
        Alignment label for the DNA sequence row.
      • SUPPORT

        public static final Object SUPPORT
        Alignment label for the support row.
    • Method Detail

      • getAlignment

        public static Alignment getAlignment​(SymbolList abiSeq)
                                      throws IllegalAlphabetException

        View a symbol list over the QUALITY alphabet as an alignment.

        The alignment will have labels of SEQUENCE and SUPPORT that retrieve the DNA sequence and the binary support values respectively.

        abiSeq - the SymbolList over the QUALITY alphabet to view
        an Alignment view of abiSeq
        IllegalAlphabetException - if abiSeq is not over QUALITY