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## de.jstacs.data.sequences
Class MappedDiscreteSequence

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

All Implemented Interfaces:
  Comparable<Sequence<int[]>>

    public class MappedDiscreteSequence

extends SimpleDiscreteSequence

This class allows to map a discrete `Sequence` to an new `Sequence` using some `DiscreteAlphabetMapping`s.

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
`protected SimpleDiscreteSequence` | `original` The original `Sequence`.
`protected AlphabetContainer` | `originalAlphabetContainer` The original `AlphabetContainer`.
`protected DiscreteAlphabetMapping[]` | `transformation` The `DiscreteAlphabetMapping`s used for mapping the original `Sequence`.

Fields inherited from class de.jstacs.data.Sequence
`alphabetCon, annotation, rc`

Constructor Summary
`protected` | `MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer, SequenceAnnotation[] seqAn, DiscreteAlphabetMapping... transformation)` This method allows to create an empty `MappedDiscreteSequence`.
`` | `MappedDiscreteSequence(SimpleDiscreteSequence original, DiscreteAlphabetMapping... transformation)` This method allows to create a `MappedDiscreteSequence` from a given `Sequence` and some given `DiscreteAlphabetMapping`s.

Method Summary
`int` | `discreteVal(int pos)` Returns the discrete value at position `pos` of the `Sequence`.
`void` | `fillContainer(int[] container, int pos)` The method fills the content of a specific position in to the container.
`protected Sequence` | `flatCloneWithoutAnnotation()` Works in analogy to `Object.clone()`, but does not clone the annotation.
`int[]` | `getEmptyContainer()` The method returns a container that can be used for accessing the symbols for each position.
`int` | `getLength()` Returns the length of the `Sequence`.
`double` | `getLogNumberOfPossibleOriginalSequences()` This method returns the logarithm of the number of original `Sequence`s that yield the same mapped `Sequence`.
`double` | `getLogNumberOfPossibleOriginalSequences(int start, int end)` This method returns the logarithm of the number of original `Sequence`s that yield the same mapped `Sequence`.
`static AlphabetContainer` | `getNewAlphabetContainer(AlphabetContainer original, DiscreteAlphabetMapping... transformation)` This method allows to create a new `AlphabetContainer` given an old `AlphabetContainer` and some `DiscreteAlphabetMapping`s.

Methods inherited from class de.jstacs.data.sequences.SimpleDiscreteSequence
`addToRepresentation, continuousVal, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional`

Methods inherited from class de.jstacs.data.sequences.DiscreteSequence
`compareTo`

Methods inherited from class de.jstacs.data.Sequence
`annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, 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`

Field Detail

### original

    protected SimpleDiscreteSequence original

  The original `Sequence`.

### originalAlphabetContainer

    protected AlphabetContainer originalAlphabetContainer

  The original `AlphabetContainer`.

### transformation

    protected DiscreteAlphabetMapping[] transformation

  The `DiscreteAlphabetMapping`s used for mapping the original `Sequence`.

Constructor Detail

### MappedDiscreteSequence

    protected MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer,
                                     SequenceAnnotation[] seqAn,
                                     DiscreteAlphabetMapping... transformation)
                              throws WrongAlphabetException

  This method allows to create an empty `MappedDiscreteSequence`. That is a `MappedDiscreteSequence` that contains no original `Sequence`.

  Parameters:
    `originalAlphabetContainer` - the original `AlphabetContainer`
    `seqAn` - the `SequenceAnnotation`s for the `MappedDiscreteSequence`
    `transformation` - the `DiscreteAlphabetMapping` defining the mapping
  Throws:
    `WrongAlphabetException` - if the mapped `AlphabetContainer` is not discrete (should never happen)

### MappedDiscreteSequence

    public MappedDiscreteSequence(SimpleDiscreteSequence original,
                                  DiscreteAlphabetMapping... transformation)
                           throws WrongAlphabetException

  This method allows to create a `MappedDiscreteSequence` from a given `Sequence` and some given `DiscreteAlphabetMapping`s.

  Parameters:
    `original` - the original `Sequence`
    `transformation` - the `DiscreteAlphabetMapping` defining the mapping
  Throws:
    `WrongAlphabetException` - if the mapped `AlphabetContainer` is not discrete (should never happen)

Method Detail

### getNewAlphabetContainer

    public static final AlphabetContainer getNewAlphabetContainer(AlphabetContainer original,
                                                                  DiscreteAlphabetMapping... transformation)

  This method allows to create a new `AlphabetContainer` given an old `AlphabetContainer` and some `DiscreteAlphabetMapping`s.

  Parameters:
    `original` - the original `AlphabetContainer`
    `transformation` - the `DiscreteAlphabetMapping`s defining the mapping
  Returns:
    a new `AlphabetContainer`

### discreteVal

    public int discreteVal(int pos)

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

  Specified by:
    `discreteVal` in class `Sequence<int[]>`
  Parameters:
    `pos` - the position of the `Sequence`
  Returns:
    the discrete value at position `pos` of the `Sequence`

### flatCloneWithoutAnnotation

    protected Sequence flatCloneWithoutAnnotation()

  Description copied from class: `Sequence`
  Works in analogy to `Object.clone()`, but does not clone the annotation. This method is used in `Sequence.annotate(boolean, SequenceAnnotation...)`.

  Specified by:
    `flatCloneWithoutAnnotation` in class `Sequence<int[]>`
  Returns:
    the cloned `Sequence` without annotation

### getLength

    public int getLength()

  Description copied from class: `Sequence`
  Returns the length of the `Sequence`.

  Specified by:
    `getLength` in class `Sequence<int[]>`
  Returns:
    the length of the `Sequence`

### getLogNumberOfPossibleOriginalSequences

    public double getLogNumberOfPossibleOriginalSequences()

  This method returns the logarithm of the number of original `Sequence`s that yield the same mapped `Sequence`.

  Returns:
    the logarithm of the number of original `Sequence`s that yield the same mapped `Sequence`

### getLogNumberOfPossibleOriginalSequences

    public double getLogNumberOfPossibleOriginalSequences(int start,
                                                          int end)

  This method returns the logarithm of the number of original `Sequence`s that yield the same mapped `Sequence`.

  Parameters:
    `start` - the start position (inclusive)
    `end` - the end position (exclusive)
  Returns:
    the logarithm of the number of original `Sequence`s that yield the same mapped `Sequence`

### getEmptyContainer

    public final int[] getEmptyContainer()

  Description copied from class: `Sequence`
  The method returns a container that can be used for accessing the symbols for each position. This is especially of interest for multidimensional sequences.

  Overrides:
    `getEmptyContainer` in class `SimpleDiscreteSequence`
  Returns:
    a container that can be used for accessing the symbols for each position
  See Also:
    `Sequence.fillContainer(Object, int)`, `Sequence.isMultiDimensional()`

### fillContainer

    public final void fillContainer(int[] container,
                                    int pos)

  Description copied from class: `Sequence`
  The method fills the content of a specific position in to the container. This is especially of interest for multidimensional sequences.

  Overrides:
    `fillContainer` in class `SimpleDiscreteSequence`
  Parameters:
    `container` - the container which is used for filling the content.
    `pos` - the position
  See Also:
    `Sequence.getEmptyContainer()`, `Sequence.isMultiDimensional()`

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