Package org.biojava.nbio.core.sequence.features

Interface Summary

Interface	Description
DatabaseReferenceInterface	If a SequenceProxyReader implements this interface then that external source has a list of cross reference id(s)
FeatureInterface<S extends AbstractSequence<C>,C extends Compound>	Interface class to handle describing arbitrary features.
FeatureRetriever	If a SequenceProxyReader implements this interface then that external source has a list features
FeaturesKeyWordInterface	Models the keywords that are annotated for a protein sequence at Uniprot.

Class Summary

Class	Description
AbstractFeature<S extends AbstractSequence<C>,C extends Compound>	A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
DBReferenceInfo	If you have a uniprot ID then it is possible to get a collection of other id(s) that the protein is known by.
FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound>	It is DBReferenceInfo which implements FeatureInterface.
Qualifier
QualityFeature<S extends AbstractSequence<C>,C extends Compound>	DNA Sequences produced by modern sequencers usually have quality informaion attached to them.
QuantityFeature<S extends AbstractSequence<C>,C extends Compound>	It is common to have a numerical value or values associated with a feature.
TextFeature<S extends AbstractSequence<C>,C extends Compound>	A implmentation of AbstractFeature