de.jstacs.data.sequences
Class ByteSequence

java.lang.Object
  extended by de.jstacs.data.Sequence
      extended by de.jstacs.data.sequences.DiscreteSequence
          extended by de.jstacs.data.sequences.ByteSequence
All Implemented Interfaces:
Comparable<Sequence>

public class ByteSequence
extends DiscreteSequence

This class is for sequences with the alphabet symbols encoded as bytes and can therefore be used for discrete AlphabetContainers 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)
          Creates a new ByteSequence from an array of byte- encoded alphabet symbols.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new ByteSequence from a String representation using the delimiter delim.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new ByteSequence from a SymbolExtractor.
ByteSequence(AlphabetContainer alphabetContainer, String sequence)
          Creates a new ByteSequence from a String representation using the default delimiter.
 
Method Summary
 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.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
Creates a new ByteSequence from an array of byte- 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 bytes
See Also:
AbstractModel.emitSample(int, int...), DiscreteSequence.DiscreteSequence(AlphabetContainer, SequenceAnnotation[])

ByteSequence

public ByteSequence(AlphabetContainer alphabetContainer,
                    String sequence)
             throws WrongAlphabetException,
                    WrongSequenceTypeException
Creates a new ByteSequence 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 bytes
See Also:
ByteSequence(AlphabetContainer, SequenceAnnotation[], String, String)

ByteSequence

public ByteSequence(AlphabetContainer alphabetContainer,
                    SequenceAnnotation[] annotation,
                    String sequence,
                    String delim)
             throws WrongAlphabetException,
                    WrongSequenceTypeException
Creates a new ByteSequence 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 bytes
See Also:
ByteSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

ByteSequence

public ByteSequence(AlphabetContainer alphabetContainer,
                    SequenceAnnotation[] annotation,
                    SymbolExtractor extractor)
             throws WrongAlphabetException,
                    WrongSequenceTypeException
Creates a new ByteSequence 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 bytes
See Also:
DiscreteSequence.DiscreteSequence(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.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