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java.lang.Objectde.jstacs.data.sequences.Sequence<T>
de.jstacs.data.sequences.Sequence.RecursiveSequence<T>
T
- the type of each positionpublic abstract static class Sequence.RecursiveSequence<T>
This is the main class for subsequences, composite sequences, ... . All these
sequences are defined on an existing Sequence
. After creating an
Sequence.RecursiveSequence
, no SequenceAnnotation
of the internally Sequence
is returned by Sequence.getAnnotation()
, ...
Nested Class Summary |
---|
Nested classes/interfaces inherited from class de.jstacs.data.sequences.Sequence |
---|
Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T> |
Field Summary | |
---|---|
protected Sequence<T> |
content
The internal sequence. |
Fields inherited from class de.jstacs.data.sequences.Sequence |
---|
alphabetCon, annotation, rc |
Constructor Summary | |
---|---|
Sequence.RecursiveSequence(AlphabetContainer alphabet,
Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
using the annotation of the given Sequence . |
|
Sequence.RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
and the annotation annotation . |
Method Summary | |
---|---|
protected void |
addToRepresentation(Object representation,
int pos,
String delim)
This method adds the information of one position to the representation using the specified delimiter |
int |
compareTo(T t1,
T t2)
This method compares to container and is used in Sequence.compareTo(Sequence) . |
double |
continuousVal(int pos)
Returns the continuous value at position pos of the
Sequence . |
int |
discreteVal(int pos)
Returns the discrete value at position pos of the
Sequence . |
void |
fillContainer(T container,
int pos)
The method fills the content of a specific position in to the container. |
T |
getEmptyContainer()
The method returns a container that can be used for accessing the symbols for each position. |
protected Object |
getEmptyRepresentation()
Returns an empty representation which is used to create the String representation of this instance in the method Sequence.toString(String, int, int) . |
protected abstract int |
getIndex(int pos)
Returns the index in the internal sequence. |
protected String |
getStringRepresentation(Object representation)
This method creates a String representation from the given representation. |
protected int |
hashCodeForPos(int pos)
This method is used in Sequence.hashCode() and the hash code for one specific position. |
boolean |
isMultiDimensional()
The method returns true if the sequence is multidimensional, otherwise . |
Methods inherited from class de.jstacs.data.sequences.Sequence |
---|
annotate, compareTo, complement, complement, create, create, create, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, 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 |
---|
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Field Detail |
---|
protected Sequence<T> content
Constructor Detail |
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public Sequence.RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence<T> seq)
Sequence.RecursiveSequence
on the Sequence
seq
with the AlphabetContainer
alphabet
and the annotation annotation
.
alphabet
- the AlphabetContainer
annotation
- the annotation of the Sequence.RecursiveSequence
seq
- the sequenceSequence.Sequence(AlphabetContainer, SequenceAnnotation[])
public Sequence.RecursiveSequence(AlphabetContainer alphabet, Sequence<T> seq)
Sequence.RecursiveSequence
on the Sequence
seq
with the AlphabetContainer
alphabet
using the annotation of the given Sequence
.
alphabet
- the AlphabetContainer
seq
- the sequenceMethod Detail |
---|
public double continuousVal(int pos)
Sequence
pos
of the
Sequence
.
continuousVal
in class Sequence<T>
pos
- the position of the Sequence
pos
of the
Sequence
public int discreteVal(int pos)
Sequence
pos
of the
Sequence
.
discreteVal
in class Sequence<T>
pos
- the position of the Sequence
pos
of the
Sequence
protected abstract int getIndex(int pos)
pos
- the index in the external sequence
public boolean isMultiDimensional()
Sequence
true
if the sequence is multidimensional, otherwise .
isMultiDimensional
in class Sequence<T>
true
if the sequence is multidimensional, otherwise
public T getEmptyContainer()
Sequence
getEmptyContainer
in class Sequence<T>
Sequence.fillContainer(Object, int)
,
Sequence.isMultiDimensional()
public void fillContainer(T container, int pos)
Sequence
fillContainer
in class Sequence<T>
container
- the container which is used for filling the content.pos
- the positionSequence.getEmptyContainer()
,
Sequence.isMultiDimensional()
public int compareTo(T t1, T t2)
Sequence
Sequence.compareTo(Sequence)
.
compareTo
in class Sequence<T>
t1
- the first containert2
- the second container
Sequence.getEmptyContainer()
,
Sequence.fillContainer(Object, int)
,
Comparable.compareTo(java.lang.Object)
protected Object getEmptyRepresentation()
Sequence
String
representation of this instance in the method Sequence.toString(String, int, int)
.
getEmptyRepresentation
in class Sequence<T>
String
representationSequence.toString(String, int, int)
protected void addToRepresentation(Object representation, int pos, String delim)
Sequence
addToRepresentation
in class Sequence<T>
representation
- the representationpos
- the positiondelim
- the delimiter separating the information for different positionsSequence.getEmptyRepresentation()
,
Sequence.toString(String, int, int)
protected String getStringRepresentation(Object representation)
Sequence
getStringRepresentation
in class Sequence<T>
representation
- the representation instance (which should be created by Sequence.getEmptyContainer()
and filled by Sequence.addToRepresentation(Object, int, String)
)
Sequence.getEmptyRepresentation()
,
Sequence.addToRepresentation(Object, int, String)
,
Sequence.toString(String, int, int)
protected int hashCodeForPos(int pos)
Sequence
Sequence.hashCode()
and the hash code for one specific position.
hashCodeForPos
in class Sequence<T>
pos
- the position
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