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## 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)`

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