## 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: Classes to generate and describe sequence alignments.
org.biojava.bio.annodb: Databases of generic structured data (annotation) objects.
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.das.dasalignment: request alignments via DAS
org.biojava.bio.program.formats: Experimental parsers using the tagvalue framework.
org.biojava.bio.program.gff: GFF manipulation.
org.biojava.bio.program.gff3: Support for reading and writing GFF3.
org.biojava.bio.program.hmmer: Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.homologene: Support classes for Homologene data.
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.sax.blastxml: Parsers for the XML output from NCBI blast.
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.proteomics.aaindex: Classes and interfaces to load Amino Acid Index database files.
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 and systematically altering their properties.
org.biojava.bio.structure: Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.io: Input and Output of Structures
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.ontology: A general-purpose API for ontologies.
org.biojava.utils.automata
org.biojava.utils.math: Mathematical utility classes.
org.biojava.utils.regex: This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojava.utils.walker
org.biojavax: The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio: Classes to represent biological entities and their relationships.
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.
org.biojavax.ontology: Extensions to the biojava ontology model that represent BioSQL ontology.

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.
EcNumber An ec (enzyme classification) number.
EcNumber.Impl A simple implementation of EcNumber.
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.annodb
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.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.
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
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.das.dasalignment
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.formats
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.gff
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.gff3
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.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.homologene
BioException A nestable biological exception.

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.sax.blastxml
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
Annotation Arbitrary annotation associated with one or more objects.
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.proteomics.aaindex
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.
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.
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.
BioRuntimeException 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
AbstractAnnotation A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
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 `LinkedHashMap`.

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.
BioException A nestable biological exception.

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

Classes in org.biojava.bio used by org.biojava.bio.structure.io
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.
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.ontology
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.utils.automata
BioException A nestable biological exception.

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

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

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

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

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

Classes in org.biojava.bio used by org.biojavax.bio.db.ncbi
BioException A nestable biological exception.

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

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