de.jstacs.data.sequences
Class DiscreteSequence

java.lang.Object
  de.jstacs.data.Sequence
      de.jstacs.data.sequences.DiscreteSequence

All Implemented Interfaces:

Comparable<Sequence>

Direct Known Subclasses:

ByteSequence, IntSequence, ShortSequence, SparseSequence

public abstract class DiscreteSequence
extends Sequence

This is the main class for any discrete sequence.

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.Sequence

Sequence.CompositeSequence, Sequence.SubSequence

Field Summary

Fields inherited from class de.jstacs.data.Sequence

alphabetCon, annotation, rc

Constructor Summary

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

double

continuousVal(int pos) Returns the continuous value at position pos of the Sequence.CompositeSequence.

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, complement, create, create, create, discreteVal, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, 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

public DiscreteSequence(AlphabetContainer container,
                        SequenceAnnotation[] annotation)
                 throws WrongAlphabetException

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 extending class.

Parameters:

container - the AlphabetContainer of the sequence

annotation - the annotation of the sequence

Throws:

WrongAlphabetException - if the AlphabetContainer is not discrete

See Also:

Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

Method Detail

continuousVal

public final double continuousVal(int pos)

Description copied from class: Sequence

Returns the continuous value at position pos of the Sequence.CompositeSequence.

Specified by:

continuousVal in class Sequence

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the continuous value at position pos of the Sequence.CompositeSequence