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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 AlpahbetContainer 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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