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java.lang.Objectde.jstacs.data.sequences.Sequence<T>
de.jstacs.data.sequences.Sequence.RecursiveSequence<T>
de.jstacs.data.sequences.Sequence.SubSequence<T>
T
- the type of each positionprotected static class Sequence.SubSequence<T>
This class handles subsequences. Sequence.SubSequence
s are often used to
extract the Sequence
of a sliding window on a long
Sequence
. The class is implemented in such a way that it avoids
chains of Sequence.SubSequence
s.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.data.sequences.Sequence |
---|
Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T> |
Field Summary |
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Fields inherited from class de.jstacs.data.sequences.Sequence.RecursiveSequence |
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content |
Fields inherited from class de.jstacs.data.sequences.Sequence |
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alphabetCon, annotation, rc |
Constructor Summary | |
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Sequence.SubSequence(AlphabetContainer abc,
Sequence seq,
int start,
int length)
This constructor should be used if one wants to create a DataSet of Sequence.SubSequence s of defined length. |
|
Sequence.SubSequence(Sequence seq,
int start,
int length)
This is a very efficient way to create a Sequence.SubSequence of
defined length for Sequence s with a simple
AlphabetContainer . |
Method Summary | |
---|---|
int |
discreteVal(int pos)
Returns the discrete value at position pos of the
Sequence . |
protected Sequence |
flatCloneWithoutAnnotation()
Works in analogy to Object.clone() , but does not clone the
annotation. |
protected int |
getIndex(int pos)
Returns the index in the internal sequence. |
int |
getLength()
Returns the length of the Sequence . |
Sequence |
reverseComplement(int start,
int end)
This method returns a new instance of Sequence containing a
reverse part of the complementary current Sequence . |
Methods inherited from class de.jstacs.data.sequences.Sequence.RecursiveSequence |
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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, 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 Sequence.SubSequence(AlphabetContainer abc, Sequence seq, int start, int length)
DataSet
of Sequence.SubSequence
s of defined length. With this
constructor you are enabled to create a DataSet
where every
Sequence
has the same AlphabetContainer
instance.
AlphabetContainer
matches
with the one of the Sequence.SubSequence
.
abc
- the new AlphabetContainer
seq
- the original Sequence
start
- the index of the start positionlength
- the length of the new sequencepublic Sequence.SubSequence(Sequence seq, int start, int length)
Sequence.SubSequence
of
defined length for Sequence
s with a simple
AlphabetContainer
.
seq
- the original Sequence
start
- the index of the start positionlength
- the length of the new Sequence
Method Detail |
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public Sequence reverseComplement(int start, int end) throws OperationNotSupportedException
Sequence
Sequence
containing a
reverse part of the complementary current Sequence
. For more
details see the methods Sequence.reverse()
and Sequence.complement()
.
reverseComplement
in class Sequence<T>
start
- the start position (inclusive) in the original
Sequence
end
- the end position (exclusive) in the original Sequence
Sequence
of the part
OperationNotSupportedException
- if the current Sequence
is not discrete and simple
((not based on a ComplementableDiscreteAlphabet
)Sequence.reverse()
,
Sequence.complement()
,
ComplementableDiscreteAlphabet
protected final int getIndex(int pos)
Sequence.RecursiveSequence
getIndex
in class Sequence.RecursiveSequence<T>
pos
- the index in the external sequence
public final int discreteVal(int pos)
Sequence
pos
of the
Sequence
.
discreteVal
in class Sequence.RecursiveSequence<T>
pos
- the position of the Sequence
pos
of the
Sequence
public int getLength()
Sequence
Sequence
.
getLength
in class Sequence<T>
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<T>
Sequence
without annotation
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