Class AbstractNucleotideCompoundSet<C extends NucleotideCompound>

    • Constructor Detail

      • AbstractNucleotideCompoundSet

        public AbstractNucleotideCompoundSet()
    • Method Detail

      • addNucleotideCompound

        protected void addNucleotideCompound​(java.lang.String base,
                                             java.lang.String complement,
                                             java.lang.String... equivalents)
      • newNucleotideCompound

        protected abstract C newNucleotideCompound​(java.lang.String base,
                                                   java.lang.String complement,
                                                   java.lang.String... equivalents)
      • calculateIndirectAmbiguities

        protected void calculateIndirectAmbiguities()
        Loops through all known nucleotides and attempts to find which are equivalent to each other. Also takes into account lower casing nucleotides as well as upper-cased ones.
      • getAmbiguity

        public NucleotideCompound getAmbiguity​(NucleotideCompound... compounds)
        Calculates the best symbol for a collection of compounds. For example if you gave this method a AC it will return a M which is the ambiguity symbol for these compounds.
        Parameters:
        compounds - Compounds to calculate ambiguity for
        Returns:
        The ambiguity symbol which represents this set of nucleotides best