Uses of Package
org.biojava.bio.symbol

Packages that use org.biojava.bio.symbol

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.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.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.das	Development client for the Distributed Annotation System.
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.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.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
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.biosql	General purpose Sequence storage in a relational database.
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.game	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.structure	Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.io
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.utils.automata
org.biojava.utils.regex	This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio.db.biosql
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.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.functions	GA functions
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ga.util	Utility functions and helper classes

Classes in org.biojava.bio.symbol used by org.biojava.bio

Location
A set of integers, often used to represent positions on biological sequences.

Classes in org.biojava.bio.symbol used by org.biojava.bio.alignment

AbstractSymbolList
Abstract helper implementation of the SymbolList core interface.

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Edit
Encapsulates an edit operation on a SymbolList.

FiniteAlphabet
An alphabet over a finite set of Symbols.

GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps.

Location
A set of integers, often used to represent positions on biological sequences.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.chromatogram

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AtomicSymbol
A symbol that is not ambiguous.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.chromatogram.graphic

Symbol
A single symbol.

Classes in org.biojava.bio.symbol used by org.biojava.bio.dist

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AlphabetIndex
Map between Symbols and index numbers.

AtomicSymbol
A symbol that is not ambiguous.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

ReversibleTranslationTable
A translation table that can also translate from the target to source alphabet.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.dp

AbstractSymbol
The base-class for Symbol implementations.

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AtomicSymbol
A symbol that is not ambiguous.

BasisSymbol
A symbol that can be represented as a string of Symbols.

Edit
Encapsulates an edit operation on a SymbolList.

FiniteAlphabet
An alphabet over a finite set of Symbols.

FundamentalAtomicSymbol
An atomic symbol consisting only of itself.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Location
A set of integers, often used to represent positions on biological sequences.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.dp.onehead

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.dp.twohead

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.gui

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AtomicSymbol
A symbol that is not ambiguous.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

Classes in org.biojava.bio.symbol used by org.biojava.bio.gui.sequence

Location
A set of integers, often used to represent positions on biological sequences.

RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.gui.sequence.tracklayout

RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive.

Classes in org.biojava.bio.symbol used by org.biojava.bio.molbio

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.abi

Alignment
An alignment containing multiple SymbolLists.

AtomicSymbol
A symbol that is not ambiguous.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.das

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Edit
Encapsulates an edit operation on a SymbolList.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.hmmer

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AtomicSymbol
A symbol that is not ambiguous.

BasisSymbol
A symbol that can be represented as a string of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.phred

Alignment
An alignment containing multiple SymbolLists.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

IntegerAlphabet.IntegerSymbol
A single int value.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.scf

IntegerAlphabet.SubIntegerAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabet

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.ssaha

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

Packing
An encapsulation of the way symbols map to bit-patterns.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.ssbind

FiniteAlphabet
An alphabet over a finite set of Symbols.

Classes in org.biojava.bio.symbol used by org.biojava.bio.program.xff

FiniteAlphabet
An alphabet over a finite set of Symbols.

Location
A set of integers, often used to represent positions on biological sequences.

Classes in org.biojava.bio.symbol used by org.biojava.bio.proteomics

AtomicSymbol
A symbol that is not ambiguous.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.proteomics.aaindex

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

SimpleSymbolPropertyTable
Class that implements the SymbolPropertyTable interface

SymbolPropertyTable
class for maintaining properties associated with a symbol

Classes in org.biojava.bio.symbol used by org.biojava.bio.search

Alignment
An alignment containing multiple SymbolLists.

AtomicSymbol
A symbol that is not ambiguous.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AtomicSymbol
A symbol that is not ambiguous.

Edit
Encapsulates an edit operation on a SymbolList.

FiniteAlphabet
An alphabet over a finite set of Symbols.

GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Location
A set of integers, often used to represent positions on biological sequences.

ManyToOneTranslationTable
A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.

RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive.

ReversibleTranslationTable
A translation table that can also translate from the target to source alphabet.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

SymbolPropertyTable
class for maintaining properties associated with a symbol

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.db

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.db.biosql

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.homol

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Edit
Encapsulates an edit operation on a SymbolList.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

Location
A set of integers, often used to represent positions on biological sequences.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.impl

AbstractSymbolList
Abstract helper implementation of the SymbolList core interface.

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Edit
Encapsulates an edit operation on a SymbolList.

GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

Location
A set of integers, often used to represent positions on biological sequences.

SimpleGappedSymbolList
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

IntegerAlphabet.SubIntegerAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabet

Location
A set of integers, often used to represent positions on biological sequences.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

SymbolListFactory
This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io.agave

Location
A set of integers, often used to represent positions on biological sequences.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io.game

Location
A set of integers, often used to represent positions on biological sequences.

RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive.

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.projection

Location
A set of integers, often used to represent positions on biological sequences.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.bio.structure

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

Classes in org.biojava.bio.symbol used by org.biojava.bio.structure.io

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Classes in org.biojava.bio.symbol used by org.biojava.bio.symbol

AbstractAlphabet
An abstract implementation of Alphabet.

AbstractLocation
An abstract implementation of Location.

AbstractLocationDecorator
Abstract Location decorator (wrapper).

AbstractManyToOneTranslationTable
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.

AbstractRangeLocation
Base class for simple contiguous Location implementations.

AbstractReversibleTranslationTable
an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.

AbstractSymbol
The base-class for Symbol implementations.

AbstractSymbolList
Abstract helper implementation of the SymbolList core interface.

AbstractSymbolList.EditScreener
This adapter screens all edit events to see if they overlap with a window of interest.

Alignment
An alignment containing multiple SymbolLists.

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

AlphabetIndex
Map between Symbols and index numbers.

AlphabetManager
Utility methods for working with Alphabets.

AtomicSymbol
A symbol that is not ambiguous.

BasisSymbol
A symbol that can be represented as a string of Symbols.

CircularLocation
Circular view onto an underlying Location instance.

CodonPref

CodonPrefFilter

DoubleAlphabet
An efficient implementation of an Alphabet over the infinite set of double values.

DoubleAlphabet.DoubleRange
A range of double values.

DoubleAlphabet.DoubleSymbol
A single double value.

DoubleAlphabet.SubDoubleAlphabet
A class to represent a contiguous range of double symbols.

Edit
Encapsulates an edit operation on a SymbolList.

FiniteAlphabet
An alphabet over a finite set of Symbols.

FuzzyLocation
A 'fuzzy' location a-la Embl fuzzy locations.

FuzzyLocation.RangeResolver
Determines how a FuzzyLocation should be treated when used as a normal Location.

FuzzyPointLocation
FuzzyPointLocation represents two types of EMBL-style partially-defined locations.

FuzzyPointLocation.PointResolver
Determines how a FuzzyPointLocation should be treated when used as a normal Location.

GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

IntegerAlphabet
An efficient implementation of an Alphabet over the infinite set of integer values.

IntegerAlphabet.IntegerSymbol
A single int value.

IntegerAlphabet.SubIntegerAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabet

Location
A set of integers, often used to represent positions on biological sequences.

ManyToOneTranslationTable
A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.

MergeLocation
Produced by LocationTools as a result of union operations.

Packing
An encapsulation of the way symbols map to bit-patterns.

RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive.

ReversibleTranslationTable
A translation table that can also translate from the target to source alphabet.

SimpleGappedSymbolList.Block
An aligned block.

SoftMaskedAlphabet
Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.

SoftMaskedAlphabet.MaskingDetector
Implementations will define how soft masking looks.

SuffixTree.SuffixNode
A node in the suffix tree.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

SymbolListFactory
This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.

SymbolPropertyTable
class for maintaining properties associated with a symbol

TranslationTable
Encapsulates the mapping from a source to a destination alphabet.

UkkonenSuffixTree.SuffixNode
end Tree modification methods

WobbleDistribution
an object to return statistics about the frequency of the wobble base in a set of synonymous codons.

Classes in org.biojava.bio.symbol used by org.biojava.utils.automata

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojava.utils.regex

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax.bio.db.biosql

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Edit
Encapsulates an edit operation on a SymbolList.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax.bio.seq

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

Edit
Encapsulates an edit operation on a SymbolList.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Location
A set of integers, often used to represent positions on biological sequences.

Symbol
A single symbol.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax.bio.seq.io

Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

Symbol
A single symbol.

SymbolListFactory
This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.

Classes in org.biojava.bio.symbol used by org.biojavax.ga

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax.ga.functions

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

PointLocation
A location representing a single point.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax.ga.impl

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

SymbolList
A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol used by org.biojavax.ga.util

AtomicSymbol
A symbol that is not ambiguous.

FiniteAlphabet
An alphabet over a finite set of Symbols.

IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used.

IllegalSymbolException
The exception to indicate that a symbol is not valid within a context.

SymbolList
A sequence of symbols that belong to an alphabet.