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 | Description |
---|---|
RecyclableSequenceEnumerator |
This interface extends
Enumeration of Sequence s by declaring an additional method that allows to reuse the Enumeration. |
Class | Description |
---|---|
AlphabetContainer | |
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 | |
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 | |
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 | |
SequenceEnumeration |
This class implements a
RecyclableSequenceEnumerator on user-specified Sequence s. |
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 | Description |
---|---|
EmptyDataSetException | |
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. |
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.