Package de.jstacs.data.sequences

Provides classes for representing sequences.
The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well.
As sub-package provides the facilities to annotate Sequences.

See: Description

Class Summary

Class	Description
ArbitraryFloatSequence	This class is for any continuous or hybrid sequence.
ArbitrarySequence	This class is for any continuous or hybrid sequence.
ByteSequence	This class is for sequences with the alphabet symbols encoded as bytes and can therefore be used for discrete AlphabetContainers with alphabets that use only few symbols.
CyclicSequenceAdaptor<T>	This class is an adapter for sequence to mimic cyclic sequences.
IntSequence	This class is for sequences with the alphabet symbols encoded as ints and can therefore be used for discrete AlphabetContainers with alphabets that use a huge number of symbols.
MappedDiscreteSequence	This class allows to map a discrete Sequence to an new Sequence using some DiscreteAlphabetMappings.
MultiDimensionalArbitrarySequence	This class is for multidimensional arbitrary sequences.
MultiDimensionalDiscreteSequence	This class is for multidimensional discrete sequences that can be used, for instance, for phylogenetic footprinting.
MultiDimensionalSequence<T>	This class is for multidimensional sequences that can be used, for instance, for phylogenetic footprinting.
PermutedSequence<T>	This class is for permuted sequences.
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.
ShortSequence	This class is for sequences with the alphabet symbols encoded as shortss and can therefore be used for discrete AlphabetContainers with alphabets that use many different symbols.
SimpleDiscreteSequence	This is the main class for any discrete sequence.
SparseSequence	This class is an implementation for sequences on one alphabet with length 4.

Exception Summary

Exception	Description
WrongSequenceTypeException	This Exception indicates that the type of the sequence ( ByteSequence, ShortSequence, ...) is not suitable for a given AlphabetContainer.

Package de.jstacs.data.sequences Description

Provides classes for representing sequences.
The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well.
As sub-package provides the facilities to annotate Sequences.