Package | Description |
---|---|
de.jstacs.clustering.distances | |
de.jstacs.data |
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 data sets comprising a set of sequences. |
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. |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
Modifier and Type | Method and Description |
---|---|
static CyclicSequenceAdaptor[] |
RandomSequenceScoreDistance.createSequences(DiscreteAlphabet alphabet,
int n)
Creates a new random sequence of the given length and alphabet.
|
Constructor and Description |
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RandomSequenceScoreDistance(DiscreteAlphabet alphabet,
int n,
boolean exp)
Creates a distance using a random sequence of length
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SequenceScoreDistance(DiscreteAlphabet alphabet,
int n,
boolean exp)
Creates a new distance.
|
Modifier and Type | Method and Description |
---|---|
static CyclicSequenceAdaptor[] |
DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet,
int n)
Generates a De Bruijn sequence of length
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static CyclicSequenceAdaptor[] |
DeBruijnGraphSequenceGenerator.generate(DiscreteAlphabet alphabet,
int n)
Generates a De Bruijn sequence of length
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static CyclicSequenceAdaptor |
DeBruijnSequenceGenerator.generate(DiscreteAlphabet alphabet,
int n,
int alphabetShift)
Generates a De Bruijn sequence using the supplied alphabet and the given alphabet shift, i.e., for a cyclic shift of the symbols
of the alphabet.
|
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty... properties)
Creates a new
DataSet by converting each Sequence in original to the DinucleotideProperty s properties and setting these as ReferenceSequenceAnnotation of each original sequence. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty.Smoothing smoothing,
boolean addToAnnotation,
DinucleotideProperty... properties)
Creates a new
DataSet by converting each Sequence in original to the DinucleotideProperty s properties and adding or setting these as ReferenceSequenceAnnotation of each original sequence. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty.Smoothing smoothing,
boolean originalAsAnnotation,
DinucleotideProperty property)
Creates a new
DataSet by converting each Sequence in original to the DinucleotideProperty property using the DinucleotideProperty.Smoothing smoothing. |
static DataSet |
DinucleotideProperty.getDataSetForProperty(DataSet original,
DinucleotideProperty property)
|
double[] |
DinucleotideProperty.getProperty(Sequence original)
Computes this dinucleotide property for all overlapping twomers in
original
and returns the result as a double array of length original.getLength()-1 |
double[] |
DinucleotideProperty.getProperty(Sequence original,
DinucleotideProperty.Smoothing smoothing)
Computes this dinucleotide property for all overlapping twomers in
original , smoothes the result using smoothing ,
and returns the smoothed property as a double array. |
ArbitrarySequence |
DinucleotideProperty.getPropertyAsSequence(Sequence original)
Computes this dinucleotide property for all overlapping dimers in
original
and returns the result as a Sequence of length original.getLength()-1 |
ArbitrarySequence |
DinucleotideProperty.getPropertyAsSequence(Sequence original,
DinucleotideProperty.Smoothing smoothing)
Computes this dinucleotide property for all overlapping dimers in
original , smoothes the result using smoothing ,
and returns the smoothed property as a Sequence . |
Modifier and Type | Method and Description |
---|---|
static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
AbstractStringExtractor... se)
This method allows to create a
DataSet containing SparseSequence s. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
AbstractStringExtractor... se)
This method allows to create a
DataSet containing ArbitraryFloatSequence s. |
static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
String filename)
This method allows to create a
DataSet containing SparseSequence s using
a file name. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
String filename)
This method allows to create a
DataSet containing ArbitraryFloatSequence s using
a file name. |
static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a
DataSet containing SparseSequence s using
a file name. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a
DataSet containing ArbitraryFloatSequence s using
a file name. |
Constructor and Description |
---|
ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
float[] content)
Creates a new
ArbitraryFloatSequence from an array of
float -encoded alphabet symbols. |
ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
|
ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new
ArbitraryFloatSequence from a SymbolExtractor . |
ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new
ArbitraryFloatSequence from a String
representation using the default delimiter. |
ArbitrarySequence(AlphabetContainer alphabetContainer,
double... content)
Creates a new
ArbitrarySequence from an array of
double -encoded alphabet symbols. |
ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
|
ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new
ArbitrarySequence from a SymbolExtractor . |
ArbitrarySequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new
ArbitrarySequence from a String
representation using the default delimiter. |
ByteSequence(AlphabetContainer alphabetContainer,
byte[] content)
Creates a new
ByteSequence from an array of byte -
encoded alphabet symbols. |
ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
|
ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new
ByteSequence from a SymbolExtractor . |
ByteSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new
ByteSequence from a String representation
using the default delimiter. |
IntSequence(AlphabetContainer alphabetContainer,
int... content)
Creates a new
IntSequence from an array of int -
encoded alphabet symbols. |
IntSequence(AlphabetContainer alphabetContainer,
int[] content,
int start,
int length)
Creates a new
IntSequence from a part of the array of
int - encoded alphabet symbols. |
IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
|
IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new
IntSequence from a SymbolExtractor . |
IntSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new
IntSequence from a String representation
using the default delimiter. |
ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
|
ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new
ShortSequence from a SymbolExtractor . |
ShortSequence(AlphabetContainer alphabetContainer,
short[] content)
Creates a new
ShortSequence from an array of short -
encoded alphabet symbols. |
ShortSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new
ShortSequence from a String representation
using the default delimiter. |
SparseSequence(AlphabetContainer alphCon,
String seq)
Creates a new
SparseSequence from a String
representation. |
SparseSequence(AlphabetContainer alphCon,
SymbolExtractor se)
Creates a new
SparseSequence from a SymbolExtractor . |
Modifier and Type | Method and Description |
---|---|
DataSet |
HomogeneousTrainSM.emitDataSet(int no,
int... length)
|
protected abstract Sequence |
HomogeneousTrainSM.getRandomSequence(Random r,
int length)
This method creates a random
Sequence from a trained homogeneous
model. |
protected Sequence |
HomogeneousMM.getRandomSequence(Random r,
int length) |