See: Description
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 manytoone mappings
that you see, for example, with genetic codes.

Packing 
An encapsulation of the way symbols map to bitpatterns.

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  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 baseclass 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 constantsize 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 noninformative symbols.

Edit 
Encapsulates an edit operation on a SymbolList.

FundamentalAtomicSymbol 
An atomic symbol consisting only of itself.

FuzzyLocation 
A 'fuzzy' location ala Embl fuzzy locations.

FuzzyPointLocation 
FuzzyPointLocation represents two types of EMBLstyle
partiallydefined 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 bitpatterns in an array of longs.

PackedSymbolListFactory 
This class makes PackedSymbolLists.

PackingFactory 
A factory that is used to maintain associations between alphabets and
preferred bitpackings 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 nofrills implementation of the FiniteAlphabet interface.

SimpleAtomicSymbol 
A basic implementation of AtomicSymbol.

SimpleCodonPref 
a simple nofrills 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 nofrills implementation of a translation table that
maps between two alphabets.

SimpleReversibleTranslationTable 
A nofrills 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 nofrills 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  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.

This package is not intended to have strong biological ties. It is here to make programming things like dynamicprogramming much easier. It also handles serialization of wellknown alphabets so that applicable singleton properties of alphabets and Symbols are maintained.
All coordinates are in 'biocoordinates'  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 stockmarket prices.
CrossProductAlphabet and CrossProductSymbol allow alphabets and symbols to be represented that are the combination of two or more alphabets and symbols under crossproduct. For example, the CrossProduct alphabet DNA x DNA would contain all dinucleotides. DNA x DNA x DNA x Protein would contain all combinations of three nucleotides and a single aminoacid. 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 subset of points that are within the Location. This uses biocoordinates, and defines all the operations that you are likely to need to build your own Locations (union, intersection and the like).
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