de.jstacs.data.sequences
Class ArbitrarySequence

java.lang.Object
  de.jstacs.data.Sequence
      de.jstacs.data.sequences.ArbitrarySequence

All Implemented Interfaces:

Comparable<Sequence>

public class ArbitrarySequence
extends Sequence

This class is for any continuous or hybrid 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

ArbitrarySequence(AlphabetContainer alphabetContainer, double[] content)
Creates a new ArbitrarySequence from an array of double-encoded alphabet symbols.

ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
Creates a new ArbitrarySequence from a String representation using the delimiter delim.

ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
Creates a new ArbitrarySequence from a SymbolExtractor.

ArbitrarySequence(AlphabetContainer alphabetContainer, String sequence)
Creates a new ArbitrarySequence from a String representation using the default delimiter.

Method Summary

double	continuousVal(int pos) Returns the continuous value at position pos of the Sequence.CompositeSequence.
int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.CompositeSequence.
protected Sequence	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
int	getLength() Returns the length of the Sequence.CompositeSequence.

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, 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

ArbitrarySequence

public ArbitrarySequence(AlphabetContainer alphabetContainer,
                         double[] content)
                  throws WrongAlphabetException,
                         WrongSequenceTypeException

Creates a new ArbitrarySequence from an array of double-encoded alphabet symbols. This constructor is designed for the method AbstractModel.emitSample(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 doubles

See Also:

AbstractModel.emitSample(int, int...), Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

ArbitrarySequence

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

Creates a new ArbitrarySequence 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 doubles

See Also:

ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

ArbitrarySequence

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

Creates a new ArbitrarySequence 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 doubles

IllegalArgumentException - if the delimiter is empty and the alphabet container is not discrete

See Also:

ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

ArbitrarySequence

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

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

Parameters:

alphabetContainer - the alphabet container 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 doubles

See Also:

Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

Method Detail

continuousVal

public double continuousVal(int pos)

Description copied from class: Sequence

Returns the continuous value at position pos of the Sequence.CompositeSequence.

Specified by:

continuousVal in class Sequence

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the continuous value at position pos of the Sequence.CompositeSequence

discreteVal

public int discreteVal(int pos)

Description copied from class: Sequence

Returns the discrete value at position pos of the Sequence.CompositeSequence.

Specified by:

discreteVal in class Sequence

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the discrete value at position pos of the Sequence.CompositeSequence

getLength

public int getLength()

Description copied from class: Sequence

Returns the length of the Sequence.CompositeSequence.

Specified by:

getLength in class Sequence

Returns:

the length of the Sequence.CompositeSequence

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

Returns:

the cloned Sequence.CompositeSequence without annotation