de.jstacs.data
Class Sequence.RecursiveSequence<T>

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

Type Parameters:

T - the type of each position

All Implemented Interfaces:

Comparable<Sequence<T>>

Direct Known Subclasses:

PermutedSequence, Sequence.CompositeSequence, Sequence.SubSequence

Enclosing class:

Sequence<T>

public abstract static class Sequence.RecursiveSequence<T>
extends Sequence<T>

This is the main class for subsequences, composite sequences, ... . All these sequences are defined on an existing Sequence. After creating an Sequence.RecursiveSequence, no SequenceAnnotation of the internally Sequence is returned by Sequence.getAnnotation(), ...

Author:

Jens Keilwagen

Nested Class Summary

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

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

Field Summary

protected Sequence<T>

content The internal sequence.

Fields inherited from class de.jstacs.data.Sequence

alphabetCon, annotation, rc

Constructor Summary

Sequence.RecursiveSequence(AlphabetContainer alphabet, Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.

Sequence.RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence<T> seq)
Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

Method Summary

protected void	addToRepresentation(Object representation, int pos, String delim) This method adds the information of one position to the representation using the specified delimiter
int	compareTo(T t1, T t2) This method compares to container and is used in Sequence.compareTo(Sequence).
double	continuousVal(int pos) Returns the continuous value at position pos of the Sequence.
int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.
void	fillContainer(T container, int pos) The method fills the content of a specific position in to the container.
T	getEmptyContainer() The method returns a container that can be used for accessing the symbols for each position.
protected Object	getEmptyRepresentation() Returns an empty representation which is used to create the String representation of this instance in the method Sequence.toString(String, int, int).
protected abstract int	getIndex(int pos) Returns the index in the internal sequence.
protected String	getStringRepresentation(Object representation) This method creates a String representation from the given representation.
protected int	hashCodeForPos(int pos) This method is used in Sequence.hashCode() and the hash code for one specific position.
boolean	isMultiDimensional() The method returns true if the sequence is multidimensional, otherwise .

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, complement, create, create, create, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, 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

Field Detail

content

protected Sequence<T> content

The internal sequence.

Constructor Detail

Sequence.RecursiveSequence

public Sequence.RecursiveSequence(AlphabetContainer alphabet,
                                  SequenceAnnotation[] annotation,
                                  Sequence<T> seq)

Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.

Parameters:

alphabet - the AlphabetContainer

annotation - the annotation of the Sequence.RecursiveSequence

seq - the sequence

See Also:

Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

Sequence.RecursiveSequence

public Sequence.RecursiveSequence(AlphabetContainer alphabet,
                                  Sequence<T> seq)

Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet using the annotation of the given Sequence.

Parameters:

alphabet - the AlphabetContainer

seq - the sequence

Method Detail

continuousVal

public double continuousVal(int pos)

Description copied from class: Sequence

Returns the continuous value at position pos of the Sequence.

Specified by:

continuousVal in class Sequence<T>

Parameters:

pos - the position of the Sequence

Returns:

the continuous value at position pos of the Sequence

discreteVal

public int discreteVal(int pos)

Description copied from class: Sequence

Returns the discrete value at position pos of the Sequence.

Specified by:

discreteVal in class Sequence<T>

Parameters:

pos - the position of the Sequence

Returns:

the discrete value at position pos of the Sequence

getIndex

protected abstract int getIndex(int pos)

Returns the index in the internal sequence.

Parameters:

pos - the index in the external sequence

Returns:

the index in the internal sequence

isMultiDimensional

public boolean isMultiDimensional()

Description copied from class: Sequence

The method returns true if the sequence is multidimensional, otherwise .

Specified by:

isMultiDimensional in class Sequence<T>

Returns:

true if the sequence is multidimensional, otherwise

getEmptyContainer

public T getEmptyContainer()

Description copied from class: Sequence

The method returns a container that can be used for accessing the symbols for each position. This is especially of interest for multidimensional sequences.

Specified by:

getEmptyContainer in class Sequence<T>

Returns:

a container that can be used for accessing the symbols for each position

See Also:

Sequence.fillContainer(Object, int), Sequence.isMultiDimensional()

fillContainer

public void fillContainer(T container,
                          int pos)

Description copied from class: Sequence

The method fills the content of a specific position in to the container. This is especially of interest for multidimensional sequences.

Specified by:

fillContainer in class Sequence<T>

Parameters:

container - the container which is used for filling the content.

pos - the position

See Also:

Sequence.getEmptyContainer(), Sequence.isMultiDimensional()

compareTo

public int compareTo(T t1,
                     T t2)

Description copied from class: Sequence

This method compares to container and is used in Sequence.compareTo(Sequence).

Specified by:

compareTo in class Sequence<T>

Parameters:

t1 - the first container

t2 - the second container

Returns:

zero if arguments are equal

See Also:

Sequence.getEmptyContainer(), Sequence.fillContainer(Object, int), Comparable.compareTo(java.lang.Object)

getEmptyRepresentation

protected Object getEmptyRepresentation()

Description copied from class: Sequence

Returns an empty representation which is used to create the String representation of this instance in the method Sequence.toString(String, int, int).

Specified by:

getEmptyRepresentation in class Sequence<T>

Returns:

an empty representation which is used to create the String representation

See Also:

Sequence.toString(String, int, int)

addToRepresentation

protected void addToRepresentation(Object representation,
                                   int pos,
                                   String delim)

Description copied from class: Sequence

This method adds the information of one position to the representation using the specified delimiter

Specified by:

addToRepresentation in class Sequence<T>

Parameters:

representation - the representation

pos - the position

delim - the delimiter separating the information for different positions

See Also:

Sequence.getEmptyRepresentation(), Sequence.toString(String, int, int)

getStringRepresentation

protected String getStringRepresentation(Object representation)

Description copied from class: Sequence

This method creates a String representation from the given representation.

Specified by:

getStringRepresentation in class Sequence<T>

Parameters:

representation - the representation instance (which should be created by Sequence.getEmptyContainer() and filled by Sequence.addToRepresentation(Object, int, String))

Returns:

a String representation

See Also:

Sequence.getEmptyRepresentation(), Sequence.addToRepresentation(Object, int, String), Sequence.toString(String, int, int)

hashCodeForPos

protected int hashCodeForPos(int pos)

Description copied from class: Sequence

This method is used in Sequence.hashCode() and the hash code for one specific position.

Specified by:

hashCodeForPos in class Sequence<T>

Parameters:

pos - the position

Returns:

the hash code for the position