de.jstacs.data.sequences
Class Sequence.CompositeSequence<T>

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

Type Parameters:

T - the type of each position

All Implemented Interfaces:

Comparable<Sequence<T>>

Enclosing class:

Sequence<T>

protected static class Sequence.CompositeSequence<T>
extends Sequence.RecursiveSequence<T>

The class handles composite Sequences. A Sequence.CompositeSequence consists of several (partial) Sequence s. A biological example are promoters like in eukaryotes (-10 and -35 box).

Author:

Jens Keilwagen

Nested Class Summary

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

Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>

Field Summary

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

content

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

alphabetCon, annotation, rc

Constructor Summary

Sequence.CompositeSequence(AlphabetContainer abc, Sequence<T> seq, int[] starts, int[] lengths)
This constructor should be used if one wants to create a DataSet of Sequence.CompositeSequences.

Sequence.CompositeSequence(Sequence seq, int[] starts, int[] lengths)
This is a very efficient way to create a Sequence.CompositeSequence for Sequences with a simple AlphabetContainer.

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.

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

addToRepresentation, compareTo, continuousVal, discreteVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional

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

Sequence.CompositeSequence

public Sequence.CompositeSequence(Sequence seq,
                                  int[] starts,
                                  int[] lengths)

This is a very efficient way to create a Sequence.CompositeSequence for Sequences with a simple AlphabetContainer.

Parameters:

seq - the original Sequence

starts - the start positions of the junks

lengths - the length of each junk

Sequence.CompositeSequence

public Sequence.CompositeSequence(AlphabetContainer abc,
                                  Sequence<T> seq,
                                  int[] starts,
                                  int[] lengths)

This constructor should be used if one wants to create a DataSet of Sequence.CompositeSequences. With this constructor you are enabled to create a DataSet where every Sequence has the same AlphabetContainer instance.

Internally it is checked that the AlphabetContainer matches with the one of the subsequence.

Parameters:

abc - the new AlphabetContainer

seq - the original Sequence

starts - the start positions of the junks

lengths - the length of each junk

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 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<T>

Returns:

the cloned Sequence without annotation