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Packages that use EmptyDataSetException | |
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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 |
Uses of EmptyDataSetException in de.jstacs.data |
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Methods in de.jstacs.data that throw EmptyDataSetException | |
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static DataSet |
DataSet.diff(DataSet data,
DataSet... samples)
This method computes the difference between the DataSet data and
the DataSet s samples . |
DataSet |
DataSet.getPartialDataSet(int[]... indexes)
Returns a new DataSet that contains all elements of this DataSet that are specified
by the supplied pairs of start and end indexes in indexes . |
DataSet |
DataSet.getPartialDataSet(int start,
int end)
Returns a new DataSet that contains all elements of this DataSet that are specified
by the supplied start (inclusive) and end (exclusive) indexes. |
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. |
DataSet |
DataSet.subSampling(double number)
Randomly samples elements, i.e. |
Pair<DataSet,double[]> |
DataSet.subSampling(double number,
double[] weights)
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static DataSet |
DataSet.union(DataSet[] s,
boolean[] in)
This method unites all DataSet s of the array s
regarding the array in . |
static Pair<DataSet,double[]> |
DataSet.union(DataSet[] s,
double[][] weights,
boolean[] in)
This method unites all DataSet s of the array s
regarding the array in and sets the element length in the
united DataSet to subsequenceLength . |
Constructors in de.jstacs.data that throw EmptyDataSetException | |
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DataSet(AlphabetContainer abc,
AbstractStringExtractor se)
Creates a new DataSet from a StringExtractor
using the given AlphabetContainer . |
|
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(String annotation,
Collection<Sequence> seqs)
Creates a new DataSet from a Collection of Sequence s and a
given annotation. |
|
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 . |
Uses of EmptyDataSetException in de.jstacs.data.sequences |
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Methods in de.jstacs.data.sequences that throw EmptyDataSetException | |
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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. |
Uses of EmptyDataSetException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw EmptyDataSetException | |
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DataSet |
HomogeneousTrainSM.emitDataSet(int no,
int... length)
Creates a DataSet of a given number of Sequence s from a
trained homogeneous model. |
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