Uses of Package
org.biojavax.bio.seq

Packages that use org.biojavax.bio.seq

org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql
org.biojavax.bio.db.ncbi
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Classes in org.biojavax.bio.seq used by org.biojavax

PositionResolver
Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.

RichLocation
Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.

RichSequenceHandler
An interface for classes that know how to handle subsequence operations.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.db

RichSequence
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

RichSequenceIterator
Essentially the same as SequenceIterator.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.db.biosql

DummyRichSequenceHandler

RichLocation
Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.

RichLocation.Strand
This class represents a strand on which a location may lie.

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.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.db.ncbi

RichSequence
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.seq

CompoundRichLocation
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.

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.

RichLocation.Strand
This class represents a strand on which a location may lie.

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.

SimpleRichLocation
A simple implementation of RichLocation.

ThinRichSequence
A simple implementation of RichSequence.

Classes in org.biojavax.bio.seq used by org.biojavax.bio.seq.io

RichFeature
Represents a feature that can be given name and rank and be moved from one sequence to another.

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.

RichSequence.Terms
Stores a number of useful terms used across many sequence formats for consistency's sake.

RichSequenceIterator
Essentially the same as SequenceIterator.