biojava 1.30

Core biological packages
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 Implementation of the Alignment interface.
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.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
org.biojava.bio.gui Graphical interfaces for biojava objects.
org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations.

 

Sequence databases and formats
org.biojava.bio.program.das Development client for the Distributed Annotation System.
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).
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.

 

Handling output from external tools
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.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
org.biojava.bio.dp HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead  
org.biojava.bio.dp.twohead  

 

Chromatogram and trace file support
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.

 

Utilities and developers' packages
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 into alternate coordinate systems.
org.biojava.utils Miscellaneous utility classes used by other BioJava components.
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.stax The Stack API for XML (StAX).
org.biojava.utils.xml Utility classes for handling and generating XML documents.

 

Experimental and new packages
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.ssaha SSAHA sequence searching API.
org.biojava.bio.program.unigene Objects for representing Unigene clusters.
org.biojava.bio.proteomics Utilities to aid in performing various physical analysis of proteins.
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.