de.jstacs.data.sequences
Class ByteSequence

java.lang.Object
  de.jstacs.data.Sequence
      de.jstacs.data.sequences.DiscreteSequence
          de.jstacs.data.sequences.ByteSequence

All Implemented Interfaces:

Comparable<Sequence>

public class ByteSequence
extends DiscreteSequence

This class can be used for discrete AlphabetContainer with alphabets that use only few symbols.

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

ByteSequence(AlphabetContainer alphabetContainer, byte[] content)
This constructor is designed for the emitSample( int n ) of AbstractModel.

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

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

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

Method Summary

int	discreteVal(int pos) Returns the discrete value of position pos.
protected Sequence	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.DiscreteSequence

continuousVal

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, 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

ByteSequence

public ByteSequence(AlphabetContainer alphabetContainer,
                    byte[] content)
             throws WrongAlphabetException,
                    WrongSequenceTypeException

This constructor is designed for the emitSample( int n ) of AbstractModel.

Parameters:

alphabetContainer - the alphabet container for the sequence

content - an array containing the encoded symbols

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

WrongSequenceTypeException - if the alphabetContainer contains alphabets that can not be encoded with bytes.

See Also:

AbstractModel.emitSample(int, int[])

ByteSequence

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

Creates a new sequence from a string representation using the default delimiter.

Parameters:

alphabetContainer - the alphabet container for the sequence

sequence - a string representation of the sequence

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

WrongSequenceTypeException - if the alphabetContainer contains alphabets that can not be encoded with bytes.

ByteSequence

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

Creates a new sequence from a string representation using the delimiter delim.

Parameters:

alphabetContainer - the alphabet container 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 the alphabetContainer contains alphabets that can not be encoded with bytes.

ByteSequence

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

Creates a new sequence from a SymbolExctractor.

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 the alphabetContainer contains alphabets that can not be encoded with bytes.

Method Detail

discreteVal

public int discreteVal(int pos)

Description copied from class: Sequence

Returns the discrete value of position pos.

Specified by:

discreteVal in class Sequence

Parameters:

pos - the position

Returns:

the discrete value of position pos

getLength

public int getLength()

Description copied from class: Sequence

Returns the length of the sequence

Specified by:

getLength in class Sequence

Returns:

the length

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