public class ByteSequence extends SimpleDiscreteSequence
byte
s and can therefore be used for discrete
AlphabetContainer
s with alphabets that use only few symbols.Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>
alphabetCon, annotation, rc
Constructor and Description |
---|
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. |
Modifier and Type | Method and Description |
---|---|
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 . |
addToRepresentation, compareTo, continuousVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional, shuffle
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
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 symbolsWrongAlphabetException
- 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 sequenceWrongAlphabetException
- 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 symbolsWrongAlphabetException
- 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[])
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
.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