Package de.jstacs.data

Provides classes for the representation of data.

See:
Description

Interface Summary

RecyclableSequenceEnumerator

This interface extends Enumeration of Sequences 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 Alphabets 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 Alphabets of defined length.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet	Class for the parameter set of an array of Alphabets 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 Sequences of a specific AlphabetContainer and length.
DNASample	This class exist for convenience to allow the user an easy creation of Samples of DNA Sequences.
Sample	This is the class for any sample of Sequences.
Sample.ElementEnumerator	This class can be used to have a fast sequential access to a Sample.
Sample.WeightedSampleFactory	This class enables you to eliminate Sequences that occur more than once in one or more Samples.
SampleKMerEnumerator	Class for an RecyclableSequenceEnumerator of Sequences 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 Sequences.
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 Sequences.

Enum Summary

AlphabetContainer.AlphabetContainerType	This enum defines types of AlphabetContainers.
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.