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## Package de.jstacs.data

Provides classes for the representation of data.

See:
Description

Interface Summary
RecyclableSequenceEnumerator | This interface extends `Enumeration` of `Sequence`s by declaring an additional method that allows to reuse the Enumeration.

Class Summary
Alphabet | Class for a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet | The super class for the `InstanceParameterSet` of any `Alphabet`.
AlphabetContainer | The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
AlphabetContainerParameterSet | Class for the `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` of an `AlphabetContainer`.
AlphabetContainerParameterSet.AlphabetArrayParameterSet | Class for the parameters of an array of `Alphabet`s of defined length.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet | Class for the parameter set of an array of `Alphabet`s where each `Alphabet` may be used for one or more sections of positions.
DinucleotideProperty.MeanSmoothing | Smoothing by mean using a pre-defined window width.
DinucleotideProperty.MedianSmoothing | Smoothing by median using a pre-defined window width.
DinucleotideProperty.NoSmoothing | Implementation of `DinucleotideProperty.Smoothing` that conducts no smoothing.
DinucleotideProperty.Smoothing | Abstract class for methods that smooth a series of real values.
DiscreteSequenceEnumerator | This class enumerates over all `Sequence`s of a specific `AlphabetContainer` and length.
DNASample | This class exist for convenience to allow the user an easy creation of `Sample`s of DNA `Sequence`s.
Sample | This is the class for any sample of `Sequence`s.
Sample.ElementEnumerator | This class can be used to have a fast sequential access to a `Sample`.
Sample.WeightedSampleFactory | This class enables you to eliminate `Sequence`s that occur more than once in one or more `Sample`s.
SampleKMerEnumerator | Class for an `RecyclableSequenceEnumerator` of `Sequence`s that enumerates all k-mers that exist in a given `Sample`, optionally ignoring reverse complements.
Sequence<T> | This is the main class for all sequences.
Sequence.CompositeSequence<T> | The class handles composite `Sequence`s.
Sequence.RecursiveSequence<T> | This is the main class for subsequences, composite sequences, ... .
Sequence.SubSequence<T> | This class handles subsequences.
SequenceEnumeration | This class implements a `RecyclableSequenceEnumerator` on user-specified `Sequence`s.

Enum Summary
AlphabetContainer.AlphabetContainerType | This `enum` defines types of `AlphabetContainer`s.
DinucleotideProperty | This `enum` defines physicochemical, conformational, and letter-based dinucleotide properties of nucleotide sequences.
DinucleotideProperty.HowCreated | This enum defines the origins of nucleotide properties
DinucleotideProperty.Type | This enum defines the types of dinucleotide properties.
Sample.PartitionMethod | This `enum` defines different partition methods for a `Sample`.
Sample.WeightedSampleFactory.SortOperation | This `enum` defines the different types of sort operations that can be performed while creating a `Sample.WeightedSampleFactory`.

Exception Summary
EmptySampleException | An `EmptySampleException` will be thrown if no `Sequence` is in a `Sample` (i.e. the `Sample` is empty).
WrongLengthException | A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

## Package de.jstacs.data Description

Provides classes for the representation of data.
The base classes to represent data are `Alphabet` and `AlphabetContainer` for representing alphabets, `Sequence` and its sub-classes to represent continuous and discrete sequences, and `Sample` to represent samples comprising a set of sequences.

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