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java.lang.Objectde.jstacs.data.sequences.Sequence<int[]>
de.jstacs.data.sequences.SimpleDiscreteSequence
de.jstacs.data.sequences.ByteSequence
public 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.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.data.sequences.Sequence |
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Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T> |
Field Summary |
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Fields inherited from class de.jstacs.data.sequences.Sequence |
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alphabetCon, annotation, rc |
Constructor Summary | |
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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. |
Method Summary | |
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int |
discreteVal(int pos)
Returns the discrete value at position pos of the
Sequence . |
protected ByteSequence |
flatCloneWithoutAnnotation()
Works in analogy to Object.clone() , but does not clone the
annotation. |
int |
getLength()
Returns the length of the Sequence . |
Methods inherited from class de.jstacs.data.sequences.SimpleDiscreteSequence |
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addToRepresentation, compareTo, continuousVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional |
Methods inherited from class de.jstacs.data.sequences.Sequence |
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annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public ByteSequence(AlphabetContainer alphabetContainer, byte[] content) throws WrongAlphabetException, WrongSequenceTypeException
ByteSequence
from an array of byte
-
encoded alphabet symbols. This constructor is designed for the method
StatisticalModel.emitDataSet(int, int...)
.
alphabetContainer
- the AlphabetContainer
for the sequencecontent
- an array containing the encoded symbols
WrongAlphabetException
- if the sequence is not defined over
alphabetContainer
WrongSequenceTypeException
- if alphabetContainer
contains alphabets that can
not be encoded with byte
sStatisticalModel.emitDataSet(int, int...)
,
SimpleDiscreteSequence.SimpleDiscreteSequence(AlphabetContainer, SequenceAnnotation[])
public ByteSequence(AlphabetContainer alphabetContainer, String sequence) throws WrongAlphabetException, WrongSequenceTypeException
ByteSequence
from a String
representation
using the default delimiter.
alphabetContainer
- the AlphabetContainer
for the sequencesequence
- a String
representation of the sequence
WrongAlphabetException
- if the sequence is not defined over
alphabetContainer
WrongSequenceTypeException
- if alphabetContainer
contains alphabets that can
not be encoded with byte
sByteSequence(AlphabetContainer, SequenceAnnotation[],
String, String)
public ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) throws WrongAlphabetException, WrongSequenceTypeException
ByteSequence
from a String
representation
using the delimiter delim
. Annotations for this sequence are
considered by annotation
.
alphabetContainer
- the AlphabetContainer
for the sequenceannotation
- the annotation for this sequencesequence
- a String
representation of the sequencedelim
- the delimiter, a String
that separates the symbols
WrongAlphabetException
- if the sequence is not defined over
alphabetContainer
WrongSequenceTypeException
- if alphabetContainer
contains alphabets that can
not be encoded with byte
sByteSequence(AlphabetContainer, SequenceAnnotation[],
SymbolExtractor)
public ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) throws WrongAlphabetException, WrongSequenceTypeException
ByteSequence
from a SymbolExtractor
.
Annotations for this sequence are considered by annotation
.
alphabetContainer
- the AlphabetContainer
for the sequenceannotation
- the annotation for this sequenceextractor
- the SymbolExtractor
WrongAlphabetException
- if the sequence is not defined over
alphabetContainer
WrongSequenceTypeException
- if alphabetContainer
contains alphabets that can
not be encoded with byte
sSimpleDiscreteSequence.SimpleDiscreteSequence(AlphabetContainer, SequenceAnnotation[])
Method Detail |
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public int discreteVal(int pos)
Sequence
pos
of the
Sequence
.
discreteVal
in class Sequence<int[]>
pos
- the position of the Sequence
pos
of the
Sequence
public int getLength()
Sequence
Sequence
.
getLength
in class Sequence<int[]>
Sequence
protected ByteSequence flatCloneWithoutAnnotation()
Sequence
Object.clone()
, but does not clone the
annotation. This method is used in
Sequence.annotate(boolean, SequenceAnnotation...)
.
flatCloneWithoutAnnotation
in class Sequence<int[]>
Sequence
without annotation
|
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