de.jstacs.data.sequences

Class MultiDimensionalArbitrarySequence

java.lang.Object

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

de.jstacs.data.sequences.MultiDimensionalSequence<double[]>

de.jstacs.data.sequences.MultiDimensionalArbitrarySequence

All Implemented Interfaces:

Comparable<Sequence<double[]>>

public class MultiDimensionalArbitrarySequence
extends MultiDimensionalSequence<double[]>

This class is for multidimensional arbitrary sequences.

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.MultiDimensionalSequence

content

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

alphabetCon, annotation, rc

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
int	compareTo(double[] t1, double[] t2) This method compares to container and is used in Sequence.compareTo(Sequence).
void	fillContainer(double[] container, int pos) The method fills the content of a specific position in to the container.
double[]	getEmptyContainer() The method returns a container that can be used for accessing the symbols for each position.
protected MultiDimensionalArbitrarySequence	getInstance(SequenceAnnotation[] seqAn, Sequence... seqs) Returns a new instance of a MultiDimensionalSequence with given SequenceAnnotations and given Sequences.

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

addToRepresentation, complement, continuousVal, discreteVal, flatCloneWithoutAnnotation, getAnnotations, getEmptyRepresentation, getLength, getNumberOfSequences, getSequence, getStringRepresentation, hashCodeForPos, isMultiDimensional, reverseComplement

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

annotate, compareTo, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, 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

Constructor Detail

MultiDimensionalArbitrarySequence

public MultiDimensionalArbitrarySequence(SequenceAnnotation[] seqAn,
                                         ArbitrarySequence... sequence)
                                  throws WrongLengthException,
                                         WrongAlphabetException

This constructor creates an MultiDimensionalDiscreteSequence 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

fillContainer

public void fillContainer(double[] 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<double[]>

Parameters:

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

pos - the position

See Also:

Sequence.getEmptyContainer(), Sequence.isMultiDimensional()

getEmptyContainer

public double[] 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<double[]>

Returns:

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

See Also:

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

getInstance

protected MultiDimensionalArbitrarySequence getInstance(SequenceAnnotation[] seqAn,
                                                        Sequence... seqs)
                                                 throws WrongLengthException,
                                                        WrongAlphabetException

Description copied from class: MultiDimensionalSequence

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

Specified by:

getInstance in class MultiDimensionalSequence<double[]>

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:

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

compareTo

public int compareTo(double[] t1,
                     double[] t2)

Description copied from class: Sequence

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

Specified by:

compareTo in class Sequence<double[]>

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)