de.jstacs.data.sequences

Class MappedDiscreteSequence

java.lang.Object

de.jstacs.data.sequences.Sequence<int[]>

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 DiscreteAlphabetMappings.

Author:

Jens Keilwagen

Nested Class Summary

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

Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>

Field Summary

Fields

Modifier and Type	Field and Description
protected SimpleDiscreteSequence	original The original Sequence.
protected AlphabetContainer	originalAlphabetContainer The original AlphabetContainer.
protected DiscreteAlphabetMapping[]	transformation The DiscreteAlphabetMappings used for mapping the original Sequence.

Fields inherited from class de.jstacs.data.sequences.Sequence

alphabetCon, annotation, rc

Constructor Summary

Constructors

Modifier	Constructor and Description
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 DiscreteAlphabetMappings.

Method Summary

Modifier and Type	Method and Description
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 MappedDiscreteSequence	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 Sequences that yield the same mapped Sequence.
double	getLogNumberOfPossibleOriginalSequences(int start, int end) This method returns the logarithm of the number of original Sequences 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 DiscreteAlphabetMappings.

Methods inherited from class de.jstacs.data.sequences.SimpleDiscreteSequence

addToRepresentation, compareTo, continuousVal, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional, shuffle

Methods inherited from class de.jstacs.data.sequences.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 DiscreteAlphabetMappings 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 SequenceAnnotations 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 DiscreteAlphabetMappings.

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 DiscreteAlphabetMappings.

Parameters:

original - the original AlphabetContainer

transformation - the DiscreteAlphabetMappings 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 MappedDiscreteSequence 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 Sequences that yield the same mapped Sequence.

Returns:

the logarithm of the number of original Sequences that yield the same mapped Sequence

getLogNumberOfPossibleOriginalSequences

public double getLogNumberOfPossibleOriginalSequences(int start,
                                                      int end)

This method returns the logarithm of the number of original Sequences 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 Sequences 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()