Uses of Package
org.biojava.bio

Packages that use org.biojava.bio

Package	Description
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.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.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 The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio	Classes to represent biological entities and their relationships.
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.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Classes in org.biojava.bio used by org.biojava.bio

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dist

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dp

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.dp.twohead

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.gui

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.molbio

Class and Description
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

Class and Description
BioError A nestable biological error.

Classes in org.biojava.bio used by org.biojava.bio.program.formats

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.gff3

Class and Description
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

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.indexdb

Class and Description
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

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.ssaha

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.program.ssbind

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.proteomics.aaindex

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.search

Class and Description
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

Class and Description
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

Class and Description
BioException A nestable biological exception.
BioRuntimeException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.db.biofetch

Class and Description
BioException A nestable biological exception.

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

Class and Description
BioException A nestable biological exception.
BioRuntimeException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.db.flat

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.distributed

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.seq.homol

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
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

Class and Description
Annotatable Indicates that an object has an associated annotation.
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.bio.symbol

Class and Description
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

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.ontology

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.utils.math

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.utils.regex

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojava.utils.walker

Class and Description
BioException A nestable biological exception.

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

Class and Description
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

Class and Description
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.alignment

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojavax.bio.alignment.blast

Class and Description
BioException A nestable biological exception.

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

Class and Description
BioException A nestable biological exception.

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

Class and Description
BioException A nestable biological exception.

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

Class and Description
BioException A nestable biological exception.

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

Class and Description
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

Class and Description
BioException A nestable biological exception.

Classes in org.biojava.bio used by org.biojavax.ontology

Class and Description
Annotatable Indicates that an object has an associated annotation.
Annotation Arbitrary annotation associated with one or more objects.