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 Implementation of the Alignment interface. 
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.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.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 into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
org.biojava.bio.symbol Representation of the Symbols that make up a sequence, and locations within them. 
 

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.
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.
 

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.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.search
Alignment
          An alignment containing multiple SymbolLists.
SymbolList
          A sequence of symbols that belong to an alphabet.
 

Classes in org.biojava.bio.symbol used by org.biojava.bio.seq
AbstractSymbolList
           Abstract helper implementation of the SymbolList core interface.
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.
ReversibleTranslationTable
          A translation table that can also translate from the target to source alphabet.
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.
SymbolPropertyTable
          class for maintaining properties associated with a symbol
TranslationTable
          Encapsulates the mapping from a source to a destination alphabet.
 

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.
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.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.
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.seq.ragbag
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.
RangeLocation
          A simple implementation of Location that contains all points between getMin and getMax inclusive.
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.symbol
AbstractAlphabet
           An abstract implementation of Alphabet.
AbstractLocation
          An abstract implementation of Location.
AbstractLocationDecorator
          Abstract Location decorator (wrapper).
AbstractRangeLocation
          Base class for simple contiguous Location implementations.
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.
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.
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.
SimpleTranslationTable
          A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
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.