Package org.biojava.bio.symbol

Representation of the Symbols that make up a sequence, and locations within them.

This package is not intended to have strong biological ties. It is here to make programming things like dynamic-programming much easier. It also handles serialization of well-known alphabets so that applicable singleton properties of alphabets and Symbols are maintained.

All coordinates are in 'bio-coordinates' - that is - legal indexes start from 1 and a range is inclusive (4 to 7 includes 4, 5, 6 and 7).

A Symbol is a single token. The Symbol maintains a name, a token (char), and an Annotation bundle. A set of Symbols is represented by an Alphabet instance. If the Alphabet can guarantee that there are only ever a finite number of Symbols contained with in it, then it must implement FiniteAlphabet. The Symbol objects within a FiniteAlphabet can be tested for equality by comparing their references directly. A SymbolList is a string over the Symbols from a single Alphabet instance. This allows you to represent a sequence of tokens, such as DNA nucleotides, or stock-market prices.

CrossProductAlphabet and CrossProductSymbol allow alphabets and symbols to be represented that are the combination of two or more alphabets and symbols under cross-product. For example, the CrossProduct alphabet DNA x DNA would contain all di-nucleotides. DNA x DNA x DNA x Protein would contain all combinations of three nucleotides and a single amino-acid. Dice x Coin would contain every possible combination of dice roles (1..6) and of coin flips (Heads, Tails) as the Symbol objects (1, Heads), (1, Tails), (2, Heads) ... (6, Tails). If any one of the Alphabets that make up the source of a CrossProductAlphabet is not finite, then the resulting CrossProductAlphabet will not be finite either.

Locations within a SymbolList can be represented by a Location object. This interface defines a sub-set of points that are within the Location. This uses bio-coordinates, and defines all the operations that you are likely to need to build your own Locations (union, intersection and the like).

Interface Summary

Interface	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.
BasisSymbol	A symbol that can be represented as a string of Symbols.
CodonPref
CodonPrefFilter
FiniteAlphabet	An alphabet over a finite set of Symbols.
FuzzyLocation.RangeResolver	Determines how a FuzzyLocation should be treated when used as a normal Location.
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.
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.
Packing	An encapsulation of the way symbols map to bit-patterns.
ReversibleTranslationTable	A translation table that can also translate from the target to source alphabet.
SoftMaskedAlphabet.MaskingDetector	Implementations will define how soft masking looks.
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.
WobbleDistribution	an object to return statistics about the frequency of the wobble base in a set of synonymous codons.

Class Summary

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.
AlphabetManager	Utility methods for working with Alphabets.
BetweenLocation	Between view onto an underlying Location instance.
ChunkedSymbolList	SymbolList implementation using constant-size chunks.
CircularLocation	Circular view onto an underlying Location instance.
CodonPrefFilter.AcceptAll
CodonPrefFilter.ByName
CodonPrefFilter.EverythingToXML
CodonPrefTools	An utility class for codon preferences
DNAAmbPack	Packing utility class for DNA.
DNANoAmbPack	A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols.
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.
DummySymbolList	Symbol list which just consists of non-informative symbols.
Edit	Encapsulates an edit operation on a SymbolList.
FundamentalAtomicSymbol	An atomic symbol consisting only of itself.
FuzzyLocation	A 'fuzzy' location a-la Embl fuzzy locations.
FuzzyPointLocation	FuzzyPointLocation represents two types of EMBL-style partially-defined locations.
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
LocationTools	Tools class containing a number of operators for working with Location objects.
MergeLocation	Produced by LocationTools as a result of union operations.
MotifTools	MotifTools contains utility methods for sequence motifs.
PackedSymbolList	A SymbolList that stores symbols as bit-patterns in an array of longs.
PackedSymbolListFactory	This class makes PackedSymbolLists.
PackingFactory	A factory that is used to maintain associations between alphabets and preferred bit-packings for them.
PointLocation	A location representing a single point.
RangeLocation	A simple implementation of Location that contains all points between getMin and getMax inclusive.
RelabeledAlignment	An alignment that relabels another alignment.
SimpleAlphabet	A simple no-frills implementation of the FiniteAlphabet interface.
SimpleAtomicSymbol	A basic implementation of AtomicSymbol.
SimpleCodonPref	a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
SimpleGappedSymbolList	This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
SimpleGappedSymbolList.Block	An aligned block.
SimpleGeneticCodeTable	A genetic code translation table representing a translation table in the DDBJ/EMBL/GenBank Feature Table (appendix V).
SimpleManyToOneTranslationTable	A no-frills implementation of a translation table that maps between two alphabets.
SimpleReversibleTranslationTable	A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleSymbolList	Basic implementation of SymbolList.
SimpleSymbolListFactory	This class makes SimpleSymbolLists.
SimpleSymbolPropertyTable	Class that implements the SymbolPropertyTable interface
SimpleTranslationTable	A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SingletonAlphabet	An alphabet that contains a single atomic symbol.
SoftMaskedAlphabet	Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
SuffixTree	Suffix tree implementation.
SuffixTree.SuffixNode	A node in the suffix tree.
SymbolListViews	Tools class for constructing views of SymbolList objects.
UkkonenSuffixTree	A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence.
UkkonenSuffixTree.SuffixNode	end Tree modification methods

Exception Summary

Exception	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.