org.biojava   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.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.chromatogram.graphic

Tools for displaying chromatograms.

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.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.

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

Java wrappers for interacting with external bioinformatics tools.

org.biojava.bio.program.abi

ABI Trace Handling.

org.biojava.bio.program.blast2html

Code for generating HTML reports from blast output

org.biojava.bio.program.fastq

FASTQ and variants sequence format I/O.

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

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.scf

Support for the SCF chromatogram format.

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.program.xml

Utility classes for the org.biojava.bio.program.sax package.

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.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.distributed

Sequences and SequenceDBs which are composed from data taken from a number of data sources.

org.biojava.bio.seq.filter   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.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).

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.naming   org.biojava.ontology

A general-purpose API for ontologies.

org.biojava.ontology.io

Tools for loading and saving ontologies.

org.biojava.ontology.obo   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

Miscellaneous utility classes used by other BioJava components.

org.biojava.utils.automata   org.biojava.utils.bytecode

A Java object-model for a Java Bytecode Macro-Assembler.

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.lsid

Life Science Identifier (LSID) package.

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.

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.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.phylo

Classes to support phlylogeny objects.

org.biojavax.bio.phylo.io.nexus

Classes to support the I/O of Nexus files.

org.biojavax.bio.phylo.io.phylip

Classes to support the reading and writing of PHYLIP format.

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.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

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.