## Uses of Package
org.biojava.bio

Packages that use org.biojava.bio
org.biojava.bio: The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment: Implementation of the `Alignment` interface.
org.biojava.bio.chromatogram: Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist: Probability distributions over Alphabets.
org.biojava.bio.dp: HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead
org.biojava.bio.gui: Graphical interfaces for biojava objects.
org.biojava.bio.molbio: The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.abi: ABI Trace Handling.
org.biojava.bio.program.das: Development client for the Distributed Annotation System.
org.biojava.bio.program.gff: GFF manipulation.
org.biojava.bio.program.hmmer: Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.indexdb: A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.phred: Parser for Phred output
org.biojava.bio.program.ssaha: SSAHA sequence searching API.
org.biojava.bio.program.ssbind: Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.tagvalue: Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene: Objects for representing Unigene clusters.
org.biojava.bio.program.xff: Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.proteomics: Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.search: Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq: Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db: Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch: Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql: General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.flat: Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed: Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.homol: The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl: Standard in-memory implementations of `Sequence` and `Feature`.
org.biojava.bio.seq.io: Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave: Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.filterxml: Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.projection: Code for projecting Feature objects into alternate coordinate systems.
org.biojava.bio.seq.ragbag: The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.
org.biojava.bio.symbol: Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa: Taxonomy object for representing species information.
org.biojava.directory: Open Bio Sequence Database Access (OBDA) registry support.
org.biojava.utils.math: Mathematical utility classes.

Classes in org.biojava.bio used by org.biojava.bio
AbstractAnnotation A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
Annotation Arbitrary annotation associated with one or more objects.
AnnotationType A set of constraints on the data contained in an `Annotation`.
AnnotationType.Abstract An abstract base class useful for implementing AnnotationType instances.
CollectionConstraint Used by `AnnotationType` to represent the constraint on the collection of values in a property-slot.
PropertyConstraint `PropertyConstraint`s describes a constraint applied to the members of an annotation bundle.

Classes in org.biojava.bio used by org.biojava.bio.alignment
BioError A nestable biological error.
BioException A nestable biological exception.
BioRuntimeException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.chromatogram
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dist
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dp
Annotatable Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dp.onehead
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dp.twohead
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.gui
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.molbio
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.abi
BioError A nestable biological error.

Classes in org.biojava.bio used by org.biojava.bio.program.das
Annotatable.AnnotationForwarder A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.gff
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.hmmer
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.

Classes in org.biojava.bio used by org.biojava.bio.program.indexdb
Annotation Arbitrary annotation associated with one or more objects.
AnnotationType A set of constraints on the data contained in an `Annotation`.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.phred
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.ssaha
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.ssbind
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.tagvalue
Annotation Arbitrary annotation associated with one or more objects.
AnnotationType A set of constraints on the data contained in an `Annotation`.

Classes in org.biojava.bio used by org.biojava.bio.program.unigene
Annotatable Indicates that an object has an associated annotation.
AnnotationType A set of constraints on the data contained in an `Annotation`.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.xff
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.proteomics
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.search
Annotatable Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq
Annotatable Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
Annotation Arbitrary annotation associated with one or more objects.
AnnotationType A set of constraints on the data contained in an `Annotation`.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.db
BioException A nestable biological exception.
BioRuntimeException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.db.biofetch
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.db.biosql
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.db.flat
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.distributed
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.homol
Annotatable Indicates that an object has an associated annotation.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.impl
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.io
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.io.agave
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
SimpleAnnotation A no-frills implementation of Annotation that is just a wrapper around a Map.

Classes in org.biojava.bio used by org.biojava.bio.seq.io.filterxml
AnnotationType A set of constraints on the data contained in an `Annotation`.
CollectionConstraint Used by `AnnotationType` to represent the constraint on the collection of values in a property-slot.
PropertyConstraint `PropertyConstraint`s describes a constraint applied to the members of an annotation bundle.

Classes in org.biojava.bio used by org.biojava.bio.seq.projection
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.ragbag
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.symbol
Annotatable Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder A helper class so that you don't have to worry about forwarding events from the Annotation object to the Annotatable one.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.taxa
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.directory
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.utils.math
BioException A nestable biological exception.