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
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
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
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.
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
PropertyConstraints 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
PropertyConstraints 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.