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.

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.