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## 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

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 an instance with the `AlphabetContainer` and the annotation, but without the content.

Method Summary
`double` | `continuousVal(int pos)` Returns the continuous value of position `pos`.

Methods inherited from class de.jstacs.data.Sequence
`annotate, compareTo, complement, complement, create, create, create, discreteVal, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getLength, 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 an instance with the `AlphabetContainer` and the 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

Method Detail

### continuousVal

    public final double continuousVal(int pos)

  Description copied from class: `Sequence`
  Returns the continuous value of position `pos`.

  Specified by:
    `continuousVal` in class `Sequence`
  Parameters:
    `pos` - the position
  Returns:
    the continuous value of position `pos`

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