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Packages that use WrongSequenceTypeException | |
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de.jstacs.data | Provides classes for the representation of data. |
de.jstacs.data.sequences | Provides classes for representing sequences. |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
Uses of WrongSequenceTypeException in de.jstacs.data |
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Methods in de.jstacs.data that throw WrongSequenceTypeException | |
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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)
Creates a new DataSet by converting each Sequence in original to the 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. |
Sequence |
DinucleotideProperty.getPropertyAsSequence(Sequence original)
Computes this dinucleotide property for all overlapping twomers in original
and returns the result as a Sequence of length original.getLength()-1 |
Sequence |
DinucleotideProperty.getPropertyAsSequence(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 Sequence . |
Uses of WrongSequenceTypeException in de.jstacs.data.sequences |
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Methods in de.jstacs.data.sequences that throw WrongSequenceTypeException | |
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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. |
Constructors in de.jstacs.data.sequences that throw WrongSequenceTypeException | |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
float[] content)
Creates a new ArbitraryFloatSequence from an array of
float -encoded alphabet symbols. |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ArbitraryFloatSequence from a String
representation using the delimiter delim . |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ArbitraryFloatSequence from a SymbolExtractor . |
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ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ArbitraryFloatSequence from a String
representation using the default delimiter. |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
double[] content)
Creates a new ArbitrarySequence from an array of
double -encoded alphabet symbols. |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ArbitrarySequence from a String
representation using the delimiter delim . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ArbitrarySequence from a SymbolExtractor . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ArbitrarySequence from a String
representation using the default delimiter. |
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ByteSequence(AlphabetContainer alphabetContainer,
byte[] content)
Creates a new ByteSequence from an array of byte -
encoded alphabet symbols. |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ByteSequence from a String representation
using the delimiter delim . |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ByteSequence from a SymbolExtractor . |
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ByteSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ByteSequence from a String representation
using the default delimiter. |
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IntSequence(AlphabetContainer alphabetContainer,
int... content)
Creates a new IntSequence from an array of int -
encoded alphabet symbols. |
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IntSequence(AlphabetContainer alphabetContainer,
int[] content,
int start,
int length)
Creates a new IntSequence from a part of the array of
int - encoded alphabet symbols. |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new IntSequence from a String representation
using the delimiter delim . |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new IntSequence from a SymbolExtractor . |
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IntSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new IntSequence from a String representation
using the default delimiter. |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new ShortSequence from a String representation
using the delimiter delim . |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new ShortSequence from a SymbolExtractor . |
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ShortSequence(AlphabetContainer alphabetContainer,
short[] content)
Creates a new ShortSequence from an array of short -
encoded alphabet symbols. |
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ShortSequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new ShortSequence from a String representation
using the default delimiter. |
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SparseSequence(AlphabetContainer alphCon,
String seq)
Creates a new SparseSequence from a String
representation. |
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SparseSequence(AlphabetContainer alphCon,
SymbolExtractor se)
Creates a new SparseSequence from a SymbolExtractor . |
Uses of WrongSequenceTypeException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw WrongSequenceTypeException | |
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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. |
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)
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