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