Uses of Package
org.biojava.bio.symbol

Packages that use org.biojava.bio.symbol

Package	Description
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.fastq	FASTQ and variants sequence format I/O.
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.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	Interface between biojava and biosql databases
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

Class	Description
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

Class	Description
AbstractSymbolList	Abstract helper implementation of the SymbolList core interface.
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

Class	Description
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

Class	Description
Symbol	A single symbol.

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

Class	Description
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

Class	Description
AbstractSymbol	The base-class for Symbol implementations.
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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.program

Class	Description
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

Class	Description
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.fastq

Class	Description
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.program.hmmer

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
FiniteAlphabet	An alphabet over a finite set of Symbols.

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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
AbstractSymbolList	Abstract helper implementation of the SymbolList core interface.
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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.symbol

Class	Description
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.
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.
SimpleManyToOneTranslationTable	A no-frills implementation of a translation table that maps between two alphabets.
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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

Class	Description
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.