T - the type of each positionpublic static class Sequence.SubSequence<T> extends Sequence.RecursiveSequence<T>
Sequence.SubSequences 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.SubSequences.Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>contentalphabetCon, annotation, rc| Constructor and Description |
|---|
SubSequence(AlphabetContainer abc,
Sequence seq,
int start,
int length)
This constructor should be used if one wants to create a
DataSet of Sequence.SubSequences of defined length. |
SubSequence(Sequence seq,
int start,
int length)
This is a very efficient way to create a
Sequence.SubSequence of
defined length for Sequences with a simple
AlphabetContainer. |
| Modifier and Type | Method and Description |
|---|---|
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<T> |
getOriginal()
Returns the original sequence, this sequence is a sub-sequence of.
|
int |
getStart()
Returns the start of this sub-sequence in the original sequence.
|
Sequence |
reverseComplement(int start,
int end)
|
addToRepresentation, compareTo, continuousVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensionalannotate, 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, toStringpublic SubSequence(AlphabetContainer abc, Sequence seq, int start, int length)
DataSet of Sequence.SubSequences 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 AlphabetContainerseq - the original Sequencestart - the index of the start positionlength - the length of the new sequencepublic SubSequence(Sequence seq, int start, int length)
Sequence.SubSequence of
defined length for Sequences with a simple
AlphabetContainer.public Sequence reverseComplement(int start, int end) throws OperationNotSupportedException
SequenceSequence 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
Sequenceend - the end position (exclusive) in the original SequenceSequence of the partOperationNotSupportedException - if the current Sequence is not discrete and simple
((not based on a ComplementableDiscreteAlphabet)Sequence.reverse(),
Sequence.complement(),
ComplementableDiscreteAlphabetprotected final int getIndex(int pos)
Sequence.RecursiveSequencegetIndex in class Sequence.RecursiveSequence<T>pos - the index in the external sequencepublic Sequence<T> getOriginal()
public int getStart()
public final int discreteVal(int pos)
Sequencepos of the
Sequence.discreteVal in class Sequence.RecursiveSequence<T>pos - the position of the Sequencepos of the
Sequencepublic int getLength()
SequenceSequence.protected Sequence flatCloneWithoutAnnotation()
SequenceObject.clone(), but does not clone the
annotation. This method is used in
Sequence.annotate(boolean, SequenceAnnotation...).flatCloneWithoutAnnotation in class Sequence<T>Sequence without annotation