Package | Description |
---|---|
de.jstacs.data.sequences |
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. |
Modifier and Type | Class and Description |
---|---|
class |
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. |
class |
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. |
class |
MappedDiscreteSequence
This class allows to map a discrete
Sequence to an new Sequence using some DiscreteAlphabetMapping s. |
class |
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. |
class |
SparseSequence
This class is an implementation for sequences on one alphabet with length 4.
|
Modifier and Type | Field and Description |
---|---|
protected SimpleDiscreteSequence |
MappedDiscreteSequence.original
The original
Sequence . |
Modifier and Type | Method and Description |
---|---|
static SimpleDiscreteSequence |
SimpleDiscreteSequence.shuffle(SimpleDiscreteSequence original,
int k)
This method implements the algorithm of D.
|
Modifier and Type | Method and Description |
---|---|
static SimpleDiscreteSequence |
SimpleDiscreteSequence.shuffle(SimpleDiscreteSequence original,
int k)
This method implements the algorithm of D.
|
Constructor and Description |
---|
MappedDiscreteSequence(SimpleDiscreteSequence original,
DiscreteAlphabetMapping... transformation)
This method allows to create a
MappedDiscreteSequence from a given Sequence and some given DiscreteAlphabetMapping s. |
MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAn,
SimpleDiscreteSequence... sequence)
This constructor creates an
MultiDimensionalDiscreteSequence from a set of individual Sequence s. |