Package org.biojava.bio.seq.impl

Standard in-memory implementations of Sequence and Feature.

See:
Description

Class Summary

AssembledSymbolList	Support class for applications which need to patch together sections of sequence into a single SymbolList.
DummySequence	A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
FeatureImpl	Wrap up default sets of Feature implementations.
LazyFilterFeatureHolder	FeatureHolder which lazily applies a specified filter to another FeatureHolder.
NewAssembledSymbolList	Support class for applications which need to patch together sections of sequence into a single SymbolList.
RevCompSequence	A reverse complement view onto Sequence interface.
SimpleFeature	A no-frills implementation of a feature.
SimpleFramedFeature	Title: SimpleFramedFeature.
SimpleGappedSequence	Simple implementation of GappedSequence.
SimpleHomologyFeature
SimpleRemoteFeature	A no-frills implementation of a remote feature.
SimpleRemoteFeature.DBResolver
SimpleRestrictionSite	SimpleRestrictionSite represents the recognition site of a restriction enzyme.
SimpleSequence	A basic implementation of the Sequence interface.
SimpleSequenceFactory	A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
SimpleSimilarityPairFeature	SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
SimpleStrandedFeature	A no-frills implementation of StrandedFeature.
SubSequence	View a sub-section of a given sequence object, including all the features intersecting that region.
SubSequence.SubProjectedFeatureContext	TargetContext that implements the mapping between the parent sequence and this sub-sequence.
TemplateUtils	Common things you may want to do with feature templates.
ViewSequence	A view onto another Sequence object.

Package org.biojava.bio.seq.impl Description

Standard in-memory implementations of Sequence and Feature.