biojava-legacy 1.9.1 API

Packages 
Package Description
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 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.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 A genetic algorithm requires a number of 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.

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