de.jstacs.data.sequences

Class MultiDimensionalDiscreteSequence

java.lang.Object

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

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

de.jstacs.data.sequences.MultiDimensionalDiscreteSequence

All Implemented Interfaces:

Comparable<Sequence<int[]>>

public class MultiDimensionalDiscreteSequence
extends MultiDimensionalSequence<int[]>

This class is for multidimensional discrete 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 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
MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAn, SimpleDiscreteSequence... sequence) This constructor creates an MultiDimensionalDiscreteSequence from a set of individual Sequences.

Method Summary

Methods

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

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

MultiDimensionalDiscreteSequence

public MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAn,
                                SimpleDiscreteSequence... 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(int[] 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<int[]>

Parameters:

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

pos - the position

See Also:

Sequence.getEmptyContainer(), Sequence.isMultiDimensional()

getEmptyContainer

public int[] 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<int[]>

Returns:

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

See Also:

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

getInstance

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

Specified by:

getInstance in class MultiDimensionalSequence<int[]>

Throws:

WrongLengthException

WrongAlphabetException

compareTo

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

Description copied from class: Sequence

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

Specified by:

compareTo in class Sequence<int[]>

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)