de.jstacs.data.sequences
Class DiscreteSequence

java.lang.Object
  de.jstacs.data.Sequence<int[]>
      de.jstacs.data.sequences.DiscreteSequence

All Implemented Interfaces:

Comparable<Sequence<int[]>>

Direct Known Subclasses:

MultiDimensionalDiscreteSequence, SimpleDiscreteSequence

public abstract class DiscreteSequence
extends Sequence<int[]>

This is the super class of discrete sequences.

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

Fields inherited from class de.jstacs.data.Sequence

alphabetCon, annotation, rc

Constructor Summary

protected

DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation) This constructor creates a new DiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content.

Method Summary

int	compareTo(int[] t1, int[] t2) This method compares to container and is used in Sequence.compareTo(Sequence).

Methods inherited from class de.jstacs.data.Sequence

addToRepresentation, annotate, compareTo, complement, complement, continuousVal, create, create, create, discreteVal, equals, fillContainer, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getEmptyContainer, getEmptyRepresentation, getHammingDistance, getLength, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getStringRepresentation, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, hashCodeForPos, isMultiDimensional, 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

Constructor Detail

DiscreteSequence

protected DiscreteSequence(AlphabetContainer container,
                           SequenceAnnotation[] annotation)

This constructor creates a new DiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content. The content has to be set by the constructor of the subclass.

Parameters:

container - the AlphabetContainer of the sequence

annotation - the annotation of the sequence

See Also:

Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

Method Detail

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)