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## 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 | Input and Output of Structures
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.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.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.
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
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
FiniteAlphabet An alphabet over a finite set of Symbols.

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.
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
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.phylo.io.phylip
Alignment An alignment containing multiple SymbolLists.

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.

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