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

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## Package org.biojavax.bio.seq

Rich implementations of Sequences, Locations and Features.

See:
Description

Interface Summary
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.
RichFeatureHolder | Holds feature relationships.
RichFeatureRelationship | Represents the relation between two bioentries.
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
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_VALUE`long, 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.
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.

## Package org.biojavax.bio.seq Description

Rich implementations of Sequences, Locations and Features.

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