de.jstacs.data.sequences

Class MultiDimensionalSequence<T>

java.lang.Object

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

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

Type Parameters:

T - the type of this MultiDimensionalSequence

All Implemented Interfaces:

Comparable<Sequence<T>>

Direct Known Subclasses:

MultiDimensionalArbitrarySequence, MultiDimensionalDiscreteSequence

public abstract class MultiDimensionalSequence<T>
extends Sequence<T>

This class is for multidimensional sequences that can be used, for instance, for phylogenetic footprinting.

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

Modifier and Type	Field and Description
protected Sequence[]	content The internally used sequences.

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

alphabetCon, annotation, rc

Constructor Summary

Constructors

Constructor and Description
MultiDimensionalSequence(SequenceAnnotation[] seqAn, Sequence... sequence) This constructor creates an MultiDimensionalSequence from a set of individual Sequences.

Method Summary

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
MultiDimensionalSequence<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.
protected MultiDimensionalSequence<T>	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
SequenceAnnotation[][]	getAnnotations() This method returns the SequenceAnnotation[] for each dimension of this multidimensional sequence.
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 MultiDimensionalSequence<T>	getInstance(SequenceAnnotation[] seqAn, Sequence... seqs) Returns a new instance of a MultiDimensionalSequence with given SequenceAnnotations and given Sequences.
int	getLength() Returns the length of the Sequence.
int	getNumberOfSequences() This method returns the number of internal sequences.
Sequence	getSequence(int index) This method returns the internal sequence with index index.
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 false.
MultiDimensionalSequence<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, compareTo, compareTo, complement, create, create, create, equals, fillContainer, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getEmptyContainer, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, reverse, reverse, 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[] content

The internally used sequences.

Constructor Detail

MultiDimensionalSequence

public MultiDimensionalSequence(SequenceAnnotation[] seqAn,
                                Sequence... sequence)
                         throws WrongLengthException,
                                WrongAlphabetException

This constructor creates an MultiDimensionalSequence from a set of individual Sequences.

Parameters:

seqAn - the annotations for the aligned sequences

sequence - the individual sequences that have been aligned

Throws:

WrongLengthException - if the sequences have different lengths

WrongAlphabetException - if the sequences have different AlphabetContainers

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

getInstance

protected abstract MultiDimensionalSequence<T> getInstance(SequenceAnnotation[] seqAn,
                                                           Sequence... seqs)
                                                    throws WrongLengthException,
                                                           WrongAlphabetException

Returns a new instance of a MultiDimensionalSequence with given SequenceAnnotations and given Sequences.

Parameters:

seqAn - the sequence annotations

seqs - the sequence buidl9ing the new MultiDimensionalSequence

Returns:

a new instance of a MultiDimensionalSequence with given SequenceAnnotations and given Sequences

Throws:

WrongLengthException - if the sequences have different lengths

WrongAlphabetException - if the sequences have different AlphabetContainers

See Also:

flatCloneWithoutAnnotation(), Sequence.complement(), Sequence.reverseComplement()

flatCloneWithoutAnnotation

protected MultiDimensionalSequence<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

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)

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

isMultiDimensional

public boolean isMultiDimensional()

Description copied from class: Sequence

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

Specified by:

isMultiDimensional in class Sequence<T>

Returns:

true if the sequence is multidimensional, otherwise false

complement

public MultiDimensionalSequence<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 MultiDimensionalSequence<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

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

getAnnotations

public SequenceAnnotation[][] getAnnotations()

This method returns the SequenceAnnotation[] for each dimension of this multidimensional sequence.

Returns:

the SequenceAnnotation array for each dimension of this multidimensional sequence

See Also:

Sequence.getAnnotation()

getNumberOfSequences

public int getNumberOfSequences()

This method returns the number of internal sequences.

Returns:

the number of internal sequences

See Also:

content

getSequence

public Sequence getSequence(int index)

This method returns the internal sequence with index index.

Parameters:

index - the index of the internal sequence

Returns:

the internal sequence with index index