Standard in-memory implementations of
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 AssembledSymbolListSupport class for applications which need to patch together sections of sequence into a single SymbolList. DummySequenceA Sequence implementation that has a name and URI but no features, and a zero length symbol list. FeatureImplWrap up default sets of Feature implementations. LazyFilterFeatureHolderFeatureHolder which lazily applies a specified filter to another FeatureHolder. NewAssembledSymbolListSupport class for applications which need to patch together sections of sequence into a single SymbolList. RevCompSequenceA reverse complement view onto
SimpleFeatureA no-frills implementation of a feature. SimpleFramedFeatureTitle: SimpleFramedFeature. SimpleGappedSequenceSimple implementation of GappedSequence. SimpleHomologyFeature SimpleRemoteFeatureA no-frills implementation of a remote feature. SimpleRemoteFeature.DBResolver SimpleRestrictionSite
SimpleRestrictionSiterepresents the recognition site of a restriction enzyme.
SimpleSequenceA basic implementation of the
SimpleSequenceFactoryA no-frills implementation of SequenceFactory that produces SimpleSequence objects. SimpleSimilarityPairFeature
SimpleSimilarityPairFeaturerepresents a similarity between a query sequence and a subject sequence as produced by a search program.
SimpleStrandedFeatureA no-frills implementation of StrandedFeature. SubSequenceView a sub-section of a given sequence object, including all the features intersecting that region. SubSequence.SubProjectedFeatureContextTargetContext that implements the mapping between the parent sequence and this sub-sequence. TemplateUtilsCommon things you may want to do with feature templates. ViewSequenceA view onto another Sequence object.