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 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 | 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 | 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 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).
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