Package org.biojava.bio.seq.impl

Standard in-memory implementations of Sequence and Feature.

Many classes in this package have been extended by biojavax interfaces and implemenations. These alternatives offer more functionality and better persistence to biosql. Where possible it would be preferable to use these alternatives.

Class Summary

Class	Description
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.