de.jstacs.data

Interface Summary
Interface Description

RecyclableSequenceEnumerator
This interface extends Enumeration of Sequences by declaring an additional method that allows to reuse the Enumeration.

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

Class Summary
Class	Description
AlphabetContainer	The container for `Alphabet`s used in a `Sequence`, `DataSet`, `AbstractTrainableStatisticalModel` or ...
AlphabetContainer.AbstractAlphabetContainerParameterSet<T extends AlphabetContainer>	This class is the super class of any `InstanceParameterSet` for `AlphabetContainer`.
AlphabetContainerParameterSet	Class for the `ParameterSet` 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.
DataSet	This is the class for any data set of `Sequence`s.
DataSet.ElementEnumerator	This class can be used to have a fast sequential access to a `DataSet`.
DataSet.WeightedDataSetFactory	This class enables you to eliminate `Sequence`s that occur more than once in one or more `DataSet`s.
DataSetKMerEnumerator	Class for an `RecyclableSequenceEnumerator` of `Sequence`s that enumerates all k-mers that exist in a given `DataSet`, optionally ignoring reverse complements.
DeBruijnGraphSequenceGenerator	Class for creating De Bruin sequences using explicit De Bruijn graphs.
DeBruijnSequenceGenerator	Generates De Buijn sequences using the algorithm from Frank Ruskey's Combinatorial Generation.
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.
DNADataSet	This class exist for convenience to allow the user an easy creation of `DataSet`s of DNA `Sequence`s.
SequenceEnumeration	This class implements a `RecyclableSequenceEnumerator` on user-specified `Sequence`s.

Enum Summary
Enum	Description
AlphabetContainer.AlphabetContainerType	This `enum` defines types of `AlphabetContainer`s.
DataSet.PartitionMethod	This `enum` defines different partition methods for a `DataSet`.
DataSet.WeightedDataSetFactory.SortOperation	This `enum` defines the different types of sort operations that can be performed while creating a `DataSet.WeightedDataSetFactory`.
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.

Exception Summary
Exception	Description
EmptyDataSetException	An `EmptyDataSetException` will be thrown if no `Sequence` is in a `DataSet` (i.e.
WrongAlphabetException	A `WrongAlphabetException` is thrown if the given `Alphabet` or `AlphabetContainer` does not support some data.
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 DataSet to represent data sets comprising a set of sequences.