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<!DOCTYPE HTML>

<head>

<title>All Packages (biojava-legacy 1.9.5 API)</title>

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<h1 title="All&nbsp;Packages" class="title">All Packages</h1>

</div>

<caption><span>Package Summary</span><span class="tabEnd"> </span></caption>

<tr>

<th class="colFirst" scope="col">Package</th>

<th class="colLast" scope="col">Description</th>

</tr>

<tbody>

<th class="colFirst" scope="row"><a href="org/biojava/package-summary.html">org.biojava</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></th>

<div class="block">The data structures and interfaces included in this package define an

interoperable framework for bibliographic searches.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/package-summary.html">org.biojava.bio</a></th>

<div class="block">The core classes that will be used throughout the bio packages.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></th>

Classes to generate and describe sequence alignments.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></th>

Databases of generic structured data (annotation) objects.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></th>

Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></th>

Tools for displaying chromatograms.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></th>

Probability distributions over Alphabets.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></th>

<div class="block">HMM and Dynamic Programming Algorithms.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></th>

<div class="block">Graphical interfaces for biojava objects.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></th>

<div class="block">Glyphs implementations that draw shapes into SequenceRenderers</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></th>

Graphical displays of biological sequences and associated annotations.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/gui/sequence/tracklayout/package-summary.html">org.biojava.bio.gui.sequence.tracklayout</a></th>

<div class="block">Classes for the handling of the layout of a WrappedSequencePanel.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></th>

<div class="block">The classes and interfaces in this package cover common molecular

biological techniques such as restriction digests and PCR.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/package-summary.html">org.biojava.bio.program</a></th>

Java wrappers for interacting with external bioinformatics tools.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></th>

<div class="block">ABI Trace Handling.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></th>

<div class="block">Code for generating HTML reports from blast output</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></th>

<div class="block">FASTQ and variants sequence format I/O.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></th>

Experimental parsers using the tagvalue framework.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></th>

<div class="block">GFF manipulation.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a></th>

Support for reading and writing GFF3.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a></th>

Tools for working with profile Hidden Markov Models from the HMMer package.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></th>

Support classes for Homologene data.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></th>

<div class="block">A flat-file ascii index of ascii flat files as per the OBDA specification.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a></th>

<div class="block">Parser for Phred output</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></th>

<div class="block">Parsers which offer XML representations of the output from common

bioinformatics tools.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/sax/blastxml/package-summary.html">org.biojava.bio.program.sax.blastxml</a></th>

Parsers for the XML output from NCBI blast.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/scf/package-summary.html">org.biojava.bio.program.scf</a></th>

Support for the SCF chromatogram format.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></th>

<div class="block">SSAHA sequence searching API.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></th>

Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></th>

<div class="block"> Process files as streams of records, each with tags with values.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></th>

<div class="block">Objects for representing Unigene clusters.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></th>

<div class="block">Event-driven parsing system for the Extensible Feature Format (XFF).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/program/xml/package-summary.html">org.biojava.bio.program.xml</a></th>

<div class="block">Utility classes for the <code>org.biojava.bio.program.sax</code>

package.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></th>

<div class="block">Utilities to aid in performing various physical analysis of proteins.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></th>

<div class="block">Classes and interfaces to load Amino Acid Index database files.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></th>

Interfaces and classes for representing sequence similarity search results.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></th>

<div class="block">Classes and interfaces for defining biological sequences and informatics

objects.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></th>

Collections of biological sequence data.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/db/biofetch/package-summary.html">org.biojava.bio.seq.db.biofetch</a></th>

<div class="block">Client for the OBDA BioFetch protocol.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></th>

<div class="block">General purpose Sequence storage in a relational database.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></th>

Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/db/flat/package-summary.html">org.biojava.bio.seq.db.flat</a></th>

Support for OBDA flatfile databases.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a></th>

<div class="block">Sequences and SequenceDBs which are composed from data taken

from a number of data sources.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/filter/package-summary.html">org.biojava.bio.seq.filter</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></th>

<div class="block">The classes and interfaces for defining sequence similarity and

honology.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></th>

<div class="block">Standard in-memory implementations of <code>Sequence</code> and

<code>Feature</code>.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></th>

<div class="block">Classes and interfaces for processing and producing flat-file representations

of sequences.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></th>

<div class="block">Classes for converting between AGAVE XML and BioJava objects.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></th>

<div class="block">Tools for reading and writing an XML representation of BioJava's FeatureFilter language.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></th>

<div class="block">Event-driven parsing system for the Gene Annotation Markup Elements (GAME).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></th>

Event-driven parsing system for the Gene Annotation Markup Elements (GAME).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></th>

<div class="block">Code for projecting Feature objects and systematically altering their

properties.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></th>

<div class="block">Representation of the Symbols that make up a sequence, and locations within

them.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></th>

<div class="block">Taxonomy object for representing species information.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/directory/package-summary.html">org.biojava.directory</a></th>

<div class="block">Open Bio Sequence Database Access (OBDA) registry support.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/naming/package-summary.html">org.biojava.naming</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/ontology/package-summary.html">org.biojava.ontology</a></th>

A general-purpose API for ontologies.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/ontology/io/package-summary.html">org.biojava.ontology.io</a></th>

Tools for loading and saving ontologies.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></th>

Support Vector Machine classification and regression.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></th>

<div class="block">Tools for use of the SVM package.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/package-summary.html">org.biojava.utils</a></th>

Miscellaneous utility classes used by other BioJava components.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/bytecode/package-summary.html">org.biojava.utils.bytecode</a></th>

<div class="block">A Java object-model for a Java Bytecode Macro-Assembler.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></th>

<div class="block">A simple cache system with pluggable caching behaviours.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a></th>

<div class="block">The data structures and interfaces included in this package define an

interoperable framework for simple controlled vocabularies.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></th>

<div class="block">I/O utility classes.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/lsid/package-summary.html">org.biojava.utils.lsid</a></th>

<div class="block">Life Science Identifier (LSID) package.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/math/package-summary.html">org.biojava.utils.math</a></th>

Mathematical utility classes.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/net/package-summary.html">org.biojava.utils.net</a></th>

Network programming utility classes.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></th>

<div class="block">Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></th>

<div class="block">This package is used to perform regular expression searches of

SymbolLists defined in arbitrary Alphabets.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></th>

<div class="block">The Stack API for XML (StAX).</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/walker/package-summary.html">org.biojava.utils.walker</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></th>

Utility classes for handling and generating XML documents.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/package-summary.html">org.biojavax</a></th>

<div class="block">The Biojava extensions packages, classes that extend the core biojava

functionality</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/package-summary.html">org.biojavax.bio</a></th>

<div class="block">Classes to represent biological entities and their relationships.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/alignment/package-summary.html">org.biojavax.bio.alignment</a></th>

<div class="block">This package contains the interfaces that need to be implemented by discrete alignment services.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/alignment/blast/package-summary.html">org.biojavax.bio.alignment.blast</a></th>

<div class="block">This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services

through the WWW.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></th>

<div class="block">Interactions between biojavax objects and a DB.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></th>

<div class="block">Interface between biojava and biosql databases</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/db/ncbi/package-summary.html">org.biojavax.bio.db.ncbi</a></th>

<div class="block">Interfaces to NCBI data.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/phylo/package-summary.html">org.biojavax.bio.phylo</a></th>

<div class="block">Classes to support phlylogeny objects.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/phylo/io/nexus/package-summary.html">org.biojavax.bio.phylo.io.nexus</a></th>

<div class="block">Classes to support the I/O of Nexus files.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/phylo/io/phylip/package-summary.html">org.biojavax.bio.phylo.io.phylip</a></th>

<div class="block">Classes to support the reading and writing of PHYLIP format.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></th>

<div class="block">Rich implementations of Sequences, Locations and Features.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></th>

<div class="block">Classes to support the I/O of RichSequence and

Bioentry objects.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/taxa/package-summary.html">org.biojavax.bio.taxa</a></th>

<div class="block">Objects that model the NCBI taxonomy schema as described in the BioSQL

schema.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/bio/taxa/io/package-summary.html">org.biojavax.bio.taxa.io</a></th>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/ga/package-summary.html">org.biojavax.ga</a></th>

<div class="block">Classes to provide a genetic algorithm framework</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/ga/exception/package-summary.html">org.biojavax.ga.exception</a></th>

<div class="block">Exceptions related to the GA framework</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></th>

<div class="block">GA functions</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></th>

<div class="block">Default implementations and abstract classes.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/ga/util/package-summary.html">org.biojavax.ga.util</a></th>

<div class="block">Utility functions and helper classes</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></th>

<div class="block">Extensions to the biojava ontology model that represent BioSQL ontology.</div>

</td>

</tr>

<th class="colFirst" scope="row"><a href="org/biojavax/utils/package-summary.html">org.biojavax.utils</a></th>

<div class="block">Utility classes that are used by biojavax objects but could have wider utility

to other applications.</div>

</td>

</tr>

</tbody>

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