Uses of Package
org.biojava.bio.symbol

Packages that use org.biojava.bio.symbol
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
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.
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.
FASTQ and variants sequence format I/O.
Tools for working with profile Hidden Markov Models from the HMMer package.
Parser for Phred output
Support for the SCF chromatogram format.
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Event-driven parsing system for the Extensible Feature Format (XFF).
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.
General purpose Sequence storage in a relational database.
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.
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.
 
This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
The Biojava extensions packages, classes that extend the core biojava functionality
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and Bioentry objects.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Utility functions and helper classes