| 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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