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See:
Description
Interface Summary | |
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RecyclableSequenceEnumerator | This interface extends Enumeration of Sequence s by declaring an additional method that allows to reuse the Enumeration. |
Class Summary | |
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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 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. |
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. |
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 | |
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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 | |
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EmptyDataSetException | An EmptyDataSetException will be thrown if no Sequence is in a
DataSet (i.e. the DataSet is empty). |
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. |
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 samples comprising a set of sequences.
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