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## de.jstacs.data.sequences
Class PermutedSequence<T>

    java.lang.Object
      de.jstacs.data.Sequence<T>
          de.jstacs.data.Sequence.RecursiveSequence<T>
              de.jstacs.data.sequences.PermutedSequence<T>

Type Parameters:
  `T` - the type of each position

All Implemented Interfaces:
  Comparable<Sequence<T>>

    public class PermutedSequence<T>

extends Sequence.RecursiveSequence<T>

This class is for permuted sequences.

Author:
  Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.Sequence
`Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>`

Field Summary

Fields inherited from class de.jstacs.data.Sequence.RecursiveSequence
`content`

Fields inherited from class de.jstacs.data.Sequence
`alphabetCon, annotation, rc`

Constructor Summary
`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

Method Summary
`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`.

Methods inherited from class de.jstacs.data.Sequence.RecursiveSequence
`addToRepresentation, compareTo, continuousVal, discreteVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional`

Methods inherited from class de.jstacs.data.Sequence
`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`

Methods inherited from class java.lang.Object
`clone, finalize, getClass, notify, notifyAll, wait, wait, wait`

Constructor Detail

### PermutedSequence

    public PermutedSequence(Sequence<T> seq)
                     throws WrongAlphabetException

  Creates a new `PermutedSequence` by shuffling the symbols of a given `Sequence`.

  Parameters:
    `seq` - the initial sequence
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer` is not simple
  See Also:
    `Sequence.RecursiveSequence.Sequence.RecursiveSequence(de.jstacs.data.AlphabetContainer, de.jstacs.data.Sequence)`

### PermutedSequence

    public PermutedSequence(Sequence<T> seq,
                            int[] permutation)
                     throws WrongAlphabetException,
                            Exception

  Creates a new `PermutedSequence` for a given permutation

  Parameters:
    `seq` - the original sequence
    `permutation` - the permutation of the sequence
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer` is not simple
    `Exception` - if the length of the permutation does not match that of the sequence
  See Also:
    `Sequence.RecursiveSequence.Sequence.RecursiveSequence(de.jstacs.data.AlphabetContainer, de.jstacs.data.Sequence)`

Method Detail

### getIndex

    protected int getIndex(int pos)

  Description copied from class: `Sequence.RecursiveSequence`
  Returns the index in the internal sequence.

  Specified by:
    `getIndex` in class `Sequence.RecursiveSequence<T>`
  Parameters:
    `pos` - the index in the external sequence
  Returns:
    the index in the internal sequence

### getLength

    public int getLength()

  Description copied from class: `Sequence`
  Returns the length of the `Sequence`.

  Specified by:
    `getLength` in class `Sequence<T>`
  Returns:
    the length of the `Sequence`

### flatCloneWithoutAnnotation

    protected PermutedSequence<T> flatCloneWithoutAnnotation()

  Description copied from class: `Sequence`
  Works in analogy to `Object.clone()`, but does not clone the annotation. This method is used in `Sequence.annotate(boolean, SequenceAnnotation...)`.

  Specified by:
    `flatCloneWithoutAnnotation` in class `Sequence<T>`
  Returns:
    the cloned `Sequence` without annotation

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