biojava-legacy 1.9.1 API

Package Description
The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
Databases of generic structured data (annotation) objects.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Tools for displaying chromatograms.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
Glyphs implementations that draw shapes into SequenceRenderers
Graphical displays of biological sequences and associated annotations.
Classes for the handling of the layout of a WrappedSequencePanel.
The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
Java wrappers for interacting with external bioinformatics tools.
ABI Trace Handling.
Code for generating HTML reports from blast output
FASTQ and variants sequence format I/O.
Experimental parsers using the tagvalue framework.
GFF manipulation.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
Support classes for Homologene data.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Parser for Phred output
Parsers which offer XML representations of the output from common bioinformatics tools.
Parsers for the XML output from NCBI blast.
Support for the SCF chromatogram format.
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Process files as streams of records, each with tags with values.
Objects for representing Unigene clusters.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utility classes for the package.
Utilities to aid in performing various physical analysis of proteins.
Classes and interfaces to load Amino Acid Index database files.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken from a number of data sources.
The classes and interfaces for defining sequence similarity and honology.
Standard in-memory implementations of Sequence and Feature.
Classes and interfaces for processing and producing flat-file representations of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Code for projecting Feature objects and systematically altering their properties.
Representation of the Symbols that make up a sequence, and locations within them.
Taxonomy object for representing species information.
Open Bio Sequence Database Access (OBDA) registry support.
A general-purpose API for ontologies.
Tools for loading and saving ontologies.
Support Vector Machine classification and regression.
Tools for use of the SVM package.
Miscellaneous utility classes used by other BioJava components.
A Java object-model for a Java Bytecode Macro-Assembler.
A simple cache system with pluggable caching behaviours.
The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.
I/O utility classes.
Life Science Identifier (LSID) package.
Mathematical utility classes.
Network programming utility classes.
Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
The Stack API for XML (StAX).
Utility classes for handling and generating XML documents.
The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
Classes to represent biological entities and their relationships.
This package contains the interfaces that need to be implemented by discrete alignment services.
This package holds implementations of the interfaces for the NCBI remote QBlast services through the WWW.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Classes to support phlylogeny objects.
Classes to support the I/O of Nexus files.
Classes to support the reading and writing of PHYLIP format.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and Bioentry objects.
Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
Classes to provide a genetic algorithm framework
Exceptions related to the GA framework
GA functions A genetic algorithm requires a number of functions.
Default implementations and abstract classes.
Utility functions and helper classes
Extensions to the biojava ontology model that represent BioSQL ontology.
Utility classes that are used by biojavax objects but could have wider utility to other applications.

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