de.jstacs.data.sequences

Class ShortSequence

java.lang.Object

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

de.jstacs.data.sequences.SimpleDiscreteSequence

de.jstacs.data.sequences.ShortSequence

All Implemented Interfaces:

Comparable<Sequence<int[]>>

public class ShortSequence
extends SimpleDiscreteSequence

This class is for sequences with the alphabet symbols encoded as shortss and can therefore be used for discrete AlphabetContainers with alphabets that use many different symbols.

Author:

Jens Keilwagen, Jan Grau

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

alphabetCon, annotation, rc

Constructor Summary

Constructors

Constructor and Description
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ShortSequence from a String representation using the delimiter delim.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ShortSequence from a SymbolExtractor.
ShortSequence(AlphabetContainer alphabetContainer, short[] content) Creates a new ShortSequence from an array of short- encoded alphabet symbols.
ShortSequence(AlphabetContainer alphabetContainer, String sequence) Creates a new ShortSequence from a String representation using the default delimiter.

Method Summary

Modifier and Type	Method and Description
int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.
protected ShortSequence	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
int	getLength() Returns the length of the Sequence.

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

addToRepresentation, compareTo, continuousVal, fillContainer, getEmptyContainer, 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

Constructor Detail

ShortSequence

public ShortSequence(AlphabetContainer alphabetContainer,
                     short[] content)
              throws WrongAlphabetException,
                     WrongSequenceTypeException

Creates a new ShortSequence from an array of short- encoded alphabet symbols. This constructor is designed for the method StatisticalModel.emitDataSet(int, int...).

Parameters:

alphabetContainer - the AlphabetContainer for the sequence

content - an array containing the encoded symbols

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

WrongSequenceTypeException - if alphabetContainer contains alphabets that can not be encoded with shorts

See Also:

StatisticalModel.emitDataSet(int, int...), SimpleDiscreteSequence.SimpleDiscreteSequence(AlphabetContainer, SequenceAnnotation[])

ShortSequence

public ShortSequence(AlphabetContainer alphabetContainer,
                     String sequence)
              throws WrongAlphabetException,
                     WrongSequenceTypeException

Creates a new ShortSequence from a String representation using the default delimiter.

Parameters:

alphabetContainer - the AlphabetContainer for the sequence

sequence - a String representation of the sequence

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

WrongSequenceTypeException - if alphabetContainer contains alphabets that can not be encoded with shorts

See Also:

ShortSequence(AlphabetContainer, SequenceAnnotation[], String, String)

ShortSequence

public ShortSequence(AlphabetContainer alphabetContainer,
                     SequenceAnnotation[] annotation,
                     String sequence,
                     String delim)
              throws WrongAlphabetException,
                     WrongSequenceTypeException

Creates a new ShortSequence from a String representation using the delimiter delim. Annotations for this sequence are considered by annotation.

Parameters:

alphabetContainer - the AlphabetContainer for the sequence

annotation - the annotation for this sequence

sequence - a String representation of the sequence

delim - the delimiter, a String that separates the symbols

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

WrongSequenceTypeException - if alphabetContainer contains alphabets that can not be encoded with shorts

See Also:

ShortSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

ShortSequence

public ShortSequence(AlphabetContainer alphabetContainer,
                     SequenceAnnotation[] annotation,
                     SymbolExtractor extractor)
              throws WrongAlphabetException,
                     WrongSequenceTypeException

Creates a new ShortSequence from a SymbolExtractor. Annotations for this sequence are considered by annotation.

Parameters:

alphabetContainer - the AlphabetContainer for the sequence

annotation - the annotation for this sequence

extractor - the SymbolExtractor

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

WrongSequenceTypeException - if alphabetContainer contains alphabets that can not be encoded with shorts

See Also:

SimpleDiscreteSequence.SimpleDiscreteSequence(AlphabetContainer, SequenceAnnotation[])

Method Detail

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

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

flatCloneWithoutAnnotation

protected ShortSequence 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