Class FourBitSequenceReader<C extends Compound>

  • All Implemented Interfaces:
    Iterable<C>, Accessioned, ProxySequenceReader<C>, Sequence<C>, SequenceReader<C>

    public class FourBitSequenceReader<C extends Compound>
    extends BitSequenceReader<C>
    Four bit encoding of the bit formats. This can support up to 16 compounds from a compound set. To allow us to support the redundant set of Nucleotide compounds this class will use case-insensitive encoding. The values assigned to these compounds is also done at runtime; if you want a predictable ordering then override and use your own encodings. However all encodings are calculated using lexographical ordering of the compounds so if a CompoundSet does not change then this encoding should not cauuse a problem.