Package org.biojavax.bio.seq

Rich implementations of Sequences, Locations and Features.

Interface Summary

Interface	Description
Position	Holds info about base positions.
PositionResolver	Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.
RichFeature	Represents a feature that can be given name and rank and be moved from one sequence to another.
RichFeatureRelationship	Represents the relation between two features.
RichFeatureRelationshipHolder	Holds feature relationships.
RichLocation	Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichSequence	A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequenceHandler	An interface for classes that know how to handle subsequence operations.
RichSequenceIterator	Essentially the same as SequenceIterator.

Class Summary

Class	Description
CompoundRichLocation	An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
DummyRichSequenceHandler
EmptyRichLocation	An Empty implementation of RichLocation.
InfinitelyAmbiguousSymbolList	A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
MultiSourceCompoundRichLocation	An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
PositionResolver.AverageResolver	The minimal resolver returns the base which provides the average range, halfway between maximal and minimal.
PositionResolver.MaximalResolver	The maximal resolver returns the base which provides the largest possible range.
PositionResolver.MinimalResolver	The minimal resolver returns the base which provides the smallest possible range.
RichFeature.Template	Added-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.Tools	Some useful tools for working with features.
RichLocation.Strand	This class represents a strand on which a location may lie.
RichLocation.Tools	Some useful tools for working with Locations.
RichSequence.IOTools	A set of convenience methods for handling common file formats.
RichSequence.IOTools.SingleRichSeqIterator	Used to iterate over a single rich sequence
RichSequence.Terms	Stores a number of useful terms used across many sequence formats for consistency's sake.
RichSequence.Tools	Some useful tools for working with RichSequence objects.
SimplePosition	A simple implementation of the Position interface.
SimpleRichFeature	A simple implementation of RichFeature.
SimpleRichFeatureRelationship	Represents a relationship between two features that is described by a term.
SimpleRichLocation	A simple implementation of RichLocation.
SimpleRichSequence	A simple implementation of RichSequence.
ThinRichSequence	A simple implementation of RichSequence.