Class Summary Class Description ArrayListSequenceReader<C extends Compound>Stores a Sequence as a collection of compounds in an ArrayList BitSequenceReader<C extends Compound>An implementation of the popular bit encodings. BitSequenceReader.BitArrayWorker<C extends Compound>The logic of working with a bit has been separated out into this class to help developers create the bit data structures without having to put the code into an intermediate format and to also use the format without the need to copy this code. FourBitSequenceReader<C extends Compound>Four bit encoding of the bit formats. FourBitSequenceReader.FourBitArrayWorker<C extends Compound>A four bit per compound implementation of the bit array worker code. JoiningSequenceReader<C extends Compound>This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence. SequenceAsStringHelper<C extends Compound>This is a common method that can be used across multiple storage/proxy implementations to handle Negative strand and other interesting elements of sequence data. SingleCompoundSequenceReader<C extends Compound>An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet). TwoBitSequenceReader<C extends NucleotideCompound>Implementation of the 2bit encoding. TwoBitSequenceReader.TwoBitArrayWorker<C extends NucleotideCompound>Extension of the BitArrayWorker which provides the 2bit implementation code.