Class SimpleAtomicSymbol

    • Field Detail

      • symbols

        protected List symbols
    • Method Detail

      • getSymbols

        public final List getSymbols()
        Description copied from interface: BasisSymbol

        The list of symbols that this symbol is composed from.

        In the usual case, this list will contain just this single symbol. In the case where a symbol represents an ordered combination of other symbols, the list will contain each of these BasisSymbols.

        Specified by:
        getSymbols in interface BasisSymbol
        the List of Symbols that this Symbol is built from
      • createSymbols

        protected List createSymbols()
      • getAnnotation

        public Annotation getAnnotation()
        Description copied from interface: Annotatable
        Should return the associated annotation object.
        Specified by:
        getAnnotation in interface Annotatable
        an Annotation object, never null
      • getMatches

        public Alphabet getMatches()
        Description copied from interface: Symbol
        The alphabet containing the symbols matched by this ambiguity symbol.

        This alphabet contains all of, and only, the symbols matched by this symbol. For example, the symbol representing the DNA ambiguity code for W would contain the symbol for A and T from the DNA alphabet.

        Specified by:
        getMatches in interface Symbol
        the Alphabet of symbols matched by this symbol
      • getName

        public String getName()
        Description copied from interface: Symbol
        The long name for the symbol.
        Specified by:
        getName in interface Symbol
        the long name