|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.jstacs.data.Sequence
de.jstacs.data.sequences.ArbitrarySequence
public class ArbitrarySequence
The class for any continuous or hybrid sequence.
Nested Class Summary |
---|
Nested classes/interfaces inherited from class de.jstacs.data.Sequence |
---|
Sequence.CompositeSequence, Sequence.SubSequence |
Field Summary |
---|
Fields inherited from class de.jstacs.data.Sequence |
---|
alphabetCon, annotation, rc |
Constructor Summary | |
---|---|
ArbitrarySequence(AlphabetContainer alphabetContainer,
double[] content)
This constructor is designed for the emitSample( int n ) of AbstractModel . |
|
ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
|
ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
|
ArbitrarySequence(AlphabetContainer alphabetContainer,
String sequence)
Creates a new sequence from a string representation using the default delimiter. |
Method Summary | |
---|---|
double |
continuousVal(int pos)
Returns the continuous value of position pos . |
int |
discreteVal(int pos)
Returns the discrete value of position pos . |
protected Sequence |
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.Sequence |
---|
annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString |
Methods inherited from class java.lang.Object |
---|
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
---|
public ArbitrarySequence(AlphabetContainer alphabetContainer, double[] content) throws WrongAlphabetException, WrongSequenceTypeException
emitSample( int n )
of AbstractModel
.
alphabetContainer
- the alphabet container for the sequencecontent
- an array containing the encoded symbols
WrongAlphabetException
- if the sequence
is not defined over alphabetContainer
WrongSequenceTypeException
- if the alphabetContainer
contains alphabets that can not be encoded with doubles.AbstractModel.emitSample(int, int[])
public ArbitrarySequence(AlphabetContainer alphabetContainer, String sequence) throws WrongAlphabetException, WrongSequenceTypeException
alphabetContainer
- the alphabet container for the sequencesequence
- a string representation of the sequence
WrongAlphabetException
- if the sequence
is not defined over alphabetContainer
WrongSequenceTypeException
- if the alphabetContainer
contains alphabets that can not be encoded with doubles.public ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) throws WrongAlphabetException, WrongSequenceTypeException, IllegalArgumentException
delim
.
alphabetContainer
- the alphabet container 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 the alphabetContainer
contains alphabets that can not be encoded with doubles.
IllegalArgumentException
- if the delimiter is empty and the alphabetContainer is not discretepublic ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) throws WrongAlphabetException, WrongSequenceTypeException
alphabetContainer
- the alphabet container for the sequenceannotation
- the annotation for this sequenceextractor
- the SymbolExtractor
WrongAlphabetException
- if the sequence
is not defined over alphabetContainer
WrongSequenceTypeException
- if the alphabetContainer
contains alphabets that can not be encoded with doubles.Method Detail |
---|
public double continuousVal(int pos)
Sequence
pos
.
continuousVal
in class Sequence
pos
- the position
pos
public int discreteVal(int pos)
Sequence
pos
.
discreteVal
in class Sequence
pos
- the position
pos
public int getLength()
Sequence
getLength
in class Sequence
protected Sequence flatCloneWithoutAnnotation()
Sequence
Object.clone()
, but does not clone the annotation. This method is used in Sequence.annotate(boolean, SequenceAnnotation...)
.
flatCloneWithoutAnnotation
in class Sequence
Sequence.CompositeSequence
without annotation
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |