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See:
Description
Class Summary | |
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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
byte s and can therefore be used for discrete
AlphabetContainer s with alphabets that use only few symbols. |
IntSequence | This class is for sequences with the alphabet symbols encoded as
int s and can therefore be used for discrete
AlphabetContainer s with alphabets that use a huge number of symbols. |
MappedDiscreteSequence | This class allows to map a discrete Sequence to an new Sequence using some DiscreteAlphabetMapping s. |
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 Sequence s. |
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
shorts s and can therefore be used for discrete
AlphabetContainer s 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 | |
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WrongSequenceTypeException | This Exception indicates that the type of the sequence (
ByteSequence , ShortSequence , ...) is not suitable for a given
AlphabetContainer . |
Provides classes for representing sequences.
The implementations of sequences currently include DiscreteSequence
s prepared for alphabets of different sizes, and ArbitrarySequence
s that may
contain continuous values as well.
As sub-package provides the facilities to annotate Sequence
s.
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