Interface Summary Interface Description AccessionedIndicates an entity is accessioned ComplementCompound Compound CompoundSet<C extends Compound> CompoundTranslator<F extends Compound,T extends Compound> LightweightProfile<S extends Sequence<C>,C extends Compound>Defines a minimal data structure for reading and writing a sequence alignment. ProxySequenceReader<C extends Compound> Sequence<C extends Compound>Main interface for defining a collection of Compounds and accessing them using biological indexes SequenceReader<C extends Compound> SequenceView<C extends Compound>
Class Summary Class Description AbstractCompoundThe details of a Compound AbstractCompoundSet<C extends Compound> AbstractCompoundTranslator<F extends Compound,T extends Compound> AbstractNucleotideCompoundSet<C extends NucleotideCompound> AbstractSequence<C extends Compound>The base class for DNA, RNA and Protein sequences. SequenceMixinProvides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way. SequenceMixin.SequenceIterator<C extends Compound>A basic sequence iterator which iterates over the given Sequence by biological index. SequenceProxyView<C extends Compound>
Enum Summary Enum Description AbstractSequence.AnnotationType LightweightProfile.StringFormatList of output formats.