Rich implementations of Sequences, Locations and Features.
Interface Summary Interface Description PositionHolds info about base positions. PositionResolverResolves a position that is fuzzy or covers a range of bases by converting it to a single base. RichFeatureRepresents a feature that can be given name and rank and be moved from one sequence to another. RichFeatureRelationshipRepresents the relation between two features. RichFeatureRelationshipHolderHolds feature relationships. RichLocationDescribes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases. RichSequenceA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence. RichSequenceHandlerAn interface for classes that know how to handle subsequence operations. RichSequenceIteratorEssentially the same as SequenceIterator.
Class Summary Class Description CompoundRichLocationAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence. DummyRichSequenceHandler EmptyRichLocationAn Empty implementation of RichLocation. InfinitelyAmbiguousSymbolListA symbol list that is
Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
MultiSourceCompoundRichLocationAn implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences. PositionResolver.AverageResolverThe minimal resolver returns the base which provides the average range, halfway between maximal and minimal. PositionResolver.MaximalResolverThe maximal resolver returns the base which provides the largest possible range. PositionResolver.MinimalResolverThe minimal resolver returns the base which provides the smallest possible range. RichFeature.TemplateAdded-value extension of Feature.Template including bits we're interested in, eg. featureRelationshipSet for relationships with other features, and rankedCrossRefs for lookups into other databases. RichFeature.ToolsSome useful tools for working with features. RichLocation.StrandThis class represents a strand on which a location may lie. RichLocation.ToolsSome useful tools for working with Locations. RichSequence.IOToolsA set of convenience methods for handling common file formats. RichSequence.IOTools.SingleRichSeqIteratorUsed to iterate over a single rich sequence RichSequence.TermsStores a number of useful terms used across many sequence formats for consistency's sake. RichSequence.ToolsSome useful tools for working with RichSequence objects. SimplePositionA simple implementation of the Position interface. SimpleRichFeatureA simple implementation of RichFeature. SimpleRichFeatureRelationshipRepresents a relationship between two features that is described by a term. SimpleRichLocationA simple implementation of RichLocation. SimpleRichSequenceA simple implementation of RichSequence. ThinRichSequenceA simple implementation of RichSequence.