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BioJava-1.7.1

Core biological packages 
Package Description
org.biojava.bibliography
The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
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.dist
Probability distributions over Alphabets.
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.filter  
org.biojava.bio.seq.io
Classes and interfaces for processing and producing flat-file representations of sequences.
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.
User interface components 
Package Description
org.biojava.bio.gui
Graphical interfaces for biojava objects.
org.biojava.bio.gui.glyph
Glyphs implementations that draw shapes into SequenceRenderers
org.biojava.bio.gui.sequence
Graphical displays of biological sequences and associated annotations.
org.biojava.bio.gui.sequence.tracklayout
Classes for the handling of the layout of a WrappedSequencePanel.
Sequence databases and formats 
Package Description
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.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.xff
Event-driven parsing system for the Extensible Feature Format (XFF).
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.emblcd
Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.
org.biojava.bio.seq.db.flat
Support for OBDA flatfile databases.
org.biojava.bio.seq.io.agave
Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.game
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Handling output from external tools 
Package Description
org.biojava.bio.program
Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.blast2html
Code for generating HTML reports from blast output
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.phred
Parser for Phred output
org.biojava.bio.program.sax
Parsers which offer XML representations of the output from common bioinformatics tools.
org.biojava.bio.program.sax.blastxml
Parsers for the XML output from NCBI blast.
org.biojava.bio.program.ssbind
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.xml
Utility classes for the org.biojava.bio.program.sax package.
Dynamic programming packages 
Package Description
org.biojava.bio.dp
HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead  
org.biojava.bio.dp.twohead  
Chromatogram and trace file support 
Package Description
org.biojava.bio.chromatogram
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.chromatogram.graphic
Tools for displaying chromatograms.
org.biojava.bio.program.abi
ABI Trace Handling.
org.biojava.bio.program.scf
Support for the SCF chromatogram format.
Macromolecular structure (PDB) 
Package Description
org.biojava.bio.program.das.dasstructure
request a protein structure via DAS
org.biojava.bio.structure
Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align
Classes for the super-imposition of structures.
org.biojava.bio.structure.align.helper
Helper classes for structural alignment.
org.biojava.bio.structure.align.pairwise
Classes for the pairwise alignment of structures.
org.biojava.bio.structure.gui
A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.bio.structure.io
Input and Output of Structures
org.biojava.bio.structure.jama
Matrix package for from JAMA
org.biojava.bio.structure.server
classes for easier management of PDB installations
Utilities and developers' packages 
Package Description
org.biojava.bio.program.tagvalue
Process files as streams of records, each with tags with values.
org.biojava.bio.seq.impl
Standard in-memory implementations of Sequence and Feature.
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.naming  
org.biojava.ontology
A general-purpose API for ontologies.
org.biojava.ontology.io
Tools for loading and saving ontologies.
org.biojava.utils
Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.automata  
org.biojava.utils.cache
A simple cache system with pluggable caching behaviours.
org.biojava.utils.candy
The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.
org.biojava.utils.io
I/O utility classes.
org.biojava.utils.math
Mathematical utility classes.
org.biojava.utils.net
Network programming utility classes.
org.biojava.utils.process
Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
org.biojava.utils.regex
This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojava.utils.stax
The Stack API for XML (StAX).
org.biojava.utils.walker  
org.biojava.utils.xml
Utility classes for handling and generating XML documents.
Molecular biology packages 
Package Description
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.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.
Experimental packages 
Package Description
org.biojava.bio.annodb
Databases of generic structured data (annotation) objects.
org.biojava.bio.program.formats
Experimental parsers using the tagvalue framework.
org.biojava.bio.program.ssaha
SSAHA sequence searching API.
org.biojava.bio.program.unigene
Objects for representing Unigene clusters.
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.stats.svm
Support Vector Machine classification and regression.
org.biojava.stats.svm.tools
Tools for use of the SVM package.
org.biojava.utils.lsid
Life Science Identifier (LSID) package.
Biojava extension (biojavax) packages 
Package Description
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.bio.taxa
Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
org.biojavax.bio.taxa.io  
org.biojavax.ontology
Extensions to the biojava ontology model that represent BioSQL ontology.
org.biojavax.utils
Utility classes that are used by biojavax objects but could have wider utility to other applications.
Genetic Algorithm Framework 
Package Description
org.biojavax.ga
Classes to provide a genetic algorithm framework
org.biojavax.ga.exception
Exceptions related to the GA framework
org.biojavax.ga.functions
GA functions
org.biojavax.ga.impl
Default implementations and abstract classes.
org.biojavax.ga.util
Utility functions and helper classes
Experimental Phylogeny packages 
Package Description
org.biojavax.bio.phylo
Classes to support phlylogeny objects.
org.biojavax.bio.phylo.io.phylip
Classes to support the reading and writing of PHYLIP format.
Other Packages 
Package Description
org.biojava.bio.program.fastq
FASTQ and variants sequence format IO.
org.biojava.bio.structure.gui.events
Some event classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util
Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.io.mmcif
Input and Output of mmcif files
org.biojava.bio.structure.io.mmcif.chem  
org.biojava.bio.structure.io.mmcif.model
Datamodel objects used for processing mmcif files.
org.biojava.ontology.obo  
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