de.jstacs.data.sequences
Class PermutedSequence

java.lang.Object
  de.jstacs.data.Sequence
      de.jstacs.data.sequences.RecursiveSequence
          de.jstacs.data.sequences.PermutedSequence

All Implemented Interfaces:

Comparable<Sequence>

public class PermutedSequence
extends RecursiveSequence

This class is for permuted sequences.

Author:

Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.Sequence

Sequence.CompositeSequence, Sequence.SubSequence

Field Summary

Fields inherited from class de.jstacs.data.sequences.RecursiveSequence

content

Fields inherited from class de.jstacs.data.Sequence

alphabetCon, annotation, rc

Constructor Summary

PermutedSequence(Sequence seq)
Creates a new PermutedSequence by shuffling the symbols of a given Sequence.

Method Summary

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.CompositeSequence.

Methods inherited from class de.jstacs.data.sequences.RecursiveSequence

continuousVal, discreteVal

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, 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 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:

RecursiveSequence.RecursiveSequence(de.jstacs.data.AlphabetContainer, Sequence)

Method Detail

getIndex

protected int getIndex(int pos)

Description copied from class: RecursiveSequence

Returns the index in the internal sequence.

Specified by:

getIndex in class RecursiveSequence

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.CompositeSequence.

Specified by:

getLength in class Sequence

Returns:

the length of the Sequence.CompositeSequence

flatCloneWithoutAnnotation

protected Sequence 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

Returns:

the cloned Sequence.CompositeSequence without annotation