Package org.biojava.nbio.core.sequence.template

Interface Summary

Interface	Description
Accessioned	Indicates 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
AbstractCompound	The 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.
SequenceMixin	Provides 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.StringFormat	List of output formats.