Uses of Package
org.biojavax.bio.seq

Packages that use org.biojavax.bio.seq

Package	Description
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojavax.bio.alignment.blast	This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services through the WWW.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.
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

Class	Description
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.alignment

Class	Description
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.alignment.blast

Class	Description
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.db

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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.
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.
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

Class	Description
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.