Package | Description |
---|---|
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 DataSet |
DataSet.diff(DataSet data,
DataSet... samples)
|
DataSet |
DataSet.getPartialDataSet(int[]... indexes)
|
DataSet |
DataSet.getPartialDataSet(int start,
int end)
|
static DataSet |
DataSet.intersection(DataSet... samples)
This method computes the intersection between all elements/
DataSet
s of the array, i.e. |
DataSet[] |
DataSet.partition(DataSet.PartitionMethod method,
double... percentage)
This method partitions the elements, i.e.
|
DataSet[] |
DataSet.partition(DataSet.PartitionMethod method,
int k)
This method partitions the elements, i.e.
|
Pair<DataSet[],double[][]> |
DataSet.partition(double[] sequenceWeights,
DataSet.PartitionMethod method,
double... percentage)
This method partitions the elements, i.e.
|
Pair<DataSet[],double[][]> |
DataSet.partition(double[] sequenceWeights,
DataSet.PartitionMethod method,
int k)
This method partitions the elements, i.e.
|
Pair<DataSet,double[]> |
DataSet.subSampling(double number,
double[] weights)
Sub-samples sequences and corresponding weights from this
DataSet . |
DataSet |
DataSet.subSampling(int number)
Randomly samples elements, i.e.
|
static DataSet |
DataSet.union(DataSet[] s,
boolean[] in)
|
static Pair<DataSet,double[]> |
DataSet.union(DataSet[] s,
double[][] weights,
boolean[] in)
|
Constructor and Description |
---|
DataSet(AlphabetContainer abc,
AbstractStringExtractor se)
|
DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
int subsequenceLength)
Creates a new
DataSet from a StringExtractor
using the given AlphabetContainer and all overlapping windows of
length subsequenceLength . |
DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
String delim)
Creates a new
DataSet from a StringExtractor
using the given AlphabetContainer and a delimiter
delim . |
DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
String delim,
int subsequenceLength)
Creates a new
DataSet from a StringExtractor
using the given AlphabetContainer , the given delimiter
delim and all overlapping windows of length
subsequenceLength . |
DataSet(AlphabetContainer abc,
AbstractStringExtractor se,
String delim,
int subsequenceLength,
double percentage)
Creates a new
DataSet from a StringExtractor
using the given AlphabetContainer , the given delimiter
delim and all overlapping windows of length
subsequenceLength . |
DataSet(String annotation,
Collection<Sequence> seqs)
|
DataSet(String annotation,
Sequence... seqs)
Creates a new
DataSet from an array of Sequence s and a
given annotation.This constructor is specially designed for the method StatisticalModel.emitDataSet(int, int...) |
DNADataSet(String fName)
Creates a new data set of DNA sequence from a FASTA file with file name
fName . |
DNADataSet(String fName,
char ignore)
Creates a new data set of DNA sequence from a file with file name
fName . |
DNADataSet(String fName,
char ignore,
SequenceAnnotationParser parser)
Creates a new data set of DNA sequence from a file with file name
fName using the given parser . |
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. |
Modifier and Type | Method and Description |
---|---|
DataSet |
HomogeneousTrainSM.emitDataSet(int no,
int... length)
|