T
- the type of each positionpublic class PermutedSequence<T> extends Sequence.RecursiveSequence<T>
Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>
content
alphabetCon, annotation, rc
Constructor and Description |
---|
PermutedSequence(Sequence<T> seq)
Creates a new
PermutedSequence by shuffling the symbols of a
given Sequence . |
PermutedSequence(Sequence<T> seq,
int[] permutation)
Creates a new
PermutedSequence for a given permutation |
Modifier and Type | Method and Description |
---|---|
protected PermutedSequence<T> |
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 . |
addToRepresentation, compareTo, continuousVal, discreteVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional
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 PermutedSequence(Sequence<T> seq) throws WrongAlphabetException
PermutedSequence
by shuffling the symbols of a
given Sequence
.seq
- the initial sequenceWrongAlphabetException
- if the AlphabetContainer
is not simpleSequence.RecursiveSequence.Sequence.RecursiveSequence(de.jstacs.data.AlphabetContainer, de.jstacs.data.sequences.Sequence)
public PermutedSequence(Sequence<T> seq, int[] permutation) throws WrongAlphabetException, Exception
PermutedSequence
for a given permutationseq
- the original sequencepermutation
- the permutation of the sequenceWrongAlphabetException
- if the AlphabetContainer
is not simpleException
- if the length of the permutation does not match that of the sequenceSequence.RecursiveSequence.Sequence.RecursiveSequence(de.jstacs.data.AlphabetContainer, de.jstacs.data.sequences.Sequence)
protected int getIndex(int pos)
Sequence.RecursiveSequence
getIndex
in class Sequence.RecursiveSequence<T>
pos
- the index in the external sequencepublic int getLength()
Sequence
Sequence
.protected PermutedSequence<T> 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