de.jstacs.data.sequences

Class CyclicSequenceAdaptor<T>

java.lang.Object

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

de.jstacs.data.sequences.CyclicSequenceAdaptor<T>

Type Parameters:

T - the type of the internal sequence

All Implemented Interfaces:

Comparable<Sequence<T>>

public class CyclicSequenceAdaptor<T>
extends Sequence<T>

This class is an adapter for sequence to mimic cyclic sequences.

Author:

Jens Keilwagen, Jan Grau

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

alphabetCon, annotation, rc

Constructor Summary

Constructors

Constructor and Description
CyclicSequenceAdaptor(Sequence<T> seq) Creates a new cyclic sequence of the length of the original sequence.
CyclicSequenceAdaptor(Sequence<T> seq, int extLength) Creates a new cyclic sequence of given virtual length (i.e., the length reported by getLength()).

Method Summary

Methods

Modifier and Type	Method and Description
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(Sequence<T> s)
protected int	compareTo(T t1, T t2) This method compares to container and is used in Sequence.compareTo(Sequence).
CyclicSequenceAdaptor<T>	complement() This method returns a new instance of Sequence containing the complementary current Sequence.
CyclicSequenceAdaptor<T>	complement(int start, int end) This method returns a new instance of Sequence containing a part of the complementary current 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.
protected CyclicSequenceAdaptor<T>	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
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).
int	getLength() Returns the length of the Sequence.
protected String	getStringRepresentation(Object representation) This method creates a String representation from the given representation.
CyclicSequenceAdaptor<T>	getSuperSequence(int length) Returns a new cyclic sequence using the internal sequence of this CyclicSequenceAdaptor but with the supplied virtual length
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 .
CyclicSequenceAdaptor<T>	reverse(int start, int end) This method returns a new instance of Sequence containing a part of the reverse current Sequence.
CyclicSequenceAdaptor<T>	reverseComplement() This method returns a new instance of Sequence containing the reverse complementary current Sequence.
CyclicSequenceAdaptor<T>	reverseComplement(int start, int end) This method returns a new instance of Sequence containing a reverse part of the complementary current Sequence.

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

annotate, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, reverse, toDiscrete, toString, toString, toString, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

CyclicSequenceAdaptor

public CyclicSequenceAdaptor(Sequence<T> seq,
                     int extLength)

Creates a new cyclic sequence of given virtual length (i.e., the length reported by getLength()).

Parameters:

seq - the original sequence

extLength - the virtual length

CyclicSequenceAdaptor

public CyclicSequenceAdaptor(Sequence<T> seq)

Creates a new cyclic sequence of the length of the original sequence.

Parameters:

seq - the original sequence

Method Detail

compareTo

public int compareTo(Sequence<T> s)

Specified by:

compareTo in interface Comparable<Sequence<T>>

Overrides:

compareTo in class Sequence<T>

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

flatCloneWithoutAnnotation

protected CyclicSequenceAdaptor<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

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

compareTo

protected 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

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()

reverse

public CyclicSequenceAdaptor<T> reverse(int start,
                               int end)
                                 throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing a part of the reverse current Sequence.

Overrides:

reverse in class Sequence<T>

Parameters:

start - the start position (inclusive) in the original Sequence

end - the end position (exclusive) in the original Sequence

Returns:

the reverse Sequence of the part

Throws:

OperationNotSupportedException - if the current Sequence is based on an AlphabetContainer that is not simple

complement

public CyclicSequenceAdaptor<T> complement()
                                    throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing the complementary current Sequence.
So invoking this method, for instance, on the sequence "TAATA" with an AlphabetContainer on DNAAlphabet returns "ATTAT".

Overrides:

complement in class Sequence<T>

Returns:

the complementary Sequence

Throws:

OperationNotSupportedException - if the current Sequence is not based on a ComplementableDiscreteAlphabet

See Also:

ComplementableDiscreteAlphabet, Sequence.complement(int, int)

reverseComplement

public CyclicSequenceAdaptor<T> reverseComplement()
                                           throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing the reverse complementary current Sequence. For more details see the methods Sequence.reverse() and Sequence.complement().

Overrides:

reverseComplement in class Sequence<T>

Returns:

the reverse complementary Sequence

Throws:

OperationNotSupportedException - if the current Sequence is not discrete and simple (not based on a ComplementableDiscreteAlphabet)

See Also:

Sequence.reverse(), Sequence.complement(), Sequence.reverseComplement(int, int), ComplementableDiscreteAlphabet

complement

public CyclicSequenceAdaptor<T> complement(int start,
                                  int end)
                                    throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing a part of the complementary current Sequence.
So invoking this method, for instance, on the sequence "TAATA" with an AlphabetContainer on DNAAlphabet returns "ATTAT".

Overrides:

complement in class Sequence<T>

Parameters:

start - the start position (inclusive) in the original Sequence

end - the end position (exclusive) in the original Sequence

Returns:

the complementary Sequence of the part

Throws:

OperationNotSupportedException - if the current Sequence is not based on a ComplementableDiscreteAlphabet

See Also:

ComplementableDiscreteAlphabet

reverseComplement

public CyclicSequenceAdaptor<T> reverseComplement(int start,
                                         int end)
                                           throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing a reverse part of the complementary current Sequence. For more details see the methods Sequence.reverse() and Sequence.complement().

Overrides:

reverseComplement in class Sequence<T>

Parameters:

start - the start position (inclusive) in the original Sequence

end - the end position (exclusive) in the original Sequence

Returns:

the reverse complementary Sequence of the part

Throws:

OperationNotSupportedException - if the current Sequence is not discrete and simple ((not based on a ComplementableDiscreteAlphabet)

See Also:

Sequence.reverse(), Sequence.complement(), ComplementableDiscreteAlphabet

getSuperSequence

public CyclicSequenceAdaptor<T> getSuperSequence(int length)

Returns a new cyclic sequence using the internal sequence of this CyclicSequenceAdaptor but with the supplied virtual length

Parameters:

length - the virtual length

Returns:

the cyclic sequence

See Also:

CyclicSequenceAdaptor(Sequence, int)