Package de.jstacs.data

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.

See:
          Description

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

Class Summary
AlphabetContainer The container for Alphabets 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 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.
DataSet This is the class for any data set of Sequences.
DataSet.ElementEnumerator This class can be used to have a fast sequential access to a DataSet.
DataSet.WeightedDataSetFactory This class enables you to eliminate Sequences that occur more than once in one or more DataSets.
DataSetKMerEnumerator Class for an RecyclableSequenceEnumerator of Sequences that enumerates all k-mers that exist in a given DataSet, optionally ignoring reverse complements.
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.
DNADataSet This class exist for convenience to allow the user an easy creation of DataSets of DNA Sequences.
SequenceEnumeration This class implements a RecyclableSequenceEnumerator on user-specified Sequences.
 

Enum Summary
AlphabetContainer.AlphabetContainerType This enum defines types of AlphabetContainers.
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
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.