org.biojava.bio.seq.impl (BioJava-1.5-beta API)
Keywords: org.biojava.bio.seq.impl package

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## 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.

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