de.jstacs.data.sequences
Class IntSequence

java.lang.Object
  de.jstacs.data.sequences.Sequence<int[]>
      de.jstacs.data.sequences.SimpleDiscreteSequence
          de.jstacs.data.sequences.IntSequence

All Implemented Interfaces:

Comparable<Sequence<int[]>>

public class IntSequence
extends SimpleDiscreteSequence

This class is for sequences with the alphabet symbols encoded as ints and can therefore be used for discrete AlphabetContainers with alphabets that use a huge number of 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

IntSequence(AlphabetContainer alphabetContainer, int... content)
Creates a new IntSequence from an array of int- encoded alphabet symbols.

IntSequence(AlphabetContainer alphabetContainer, int[] content, int start, int length)
Creates a new IntSequence from a part of the array of int- encoded alphabet symbols.

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

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

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

Method Summary

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

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

IntSequence

public IntSequence(AlphabetContainer alphabetContainer,
                   int... content)
            throws WrongAlphabetException,
                   WrongSequenceTypeException

Creates a new IntSequence from an array of int- 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 ints

See Also:

StatisticalModel.emitDataSet(int, int...), IntSequence(AlphabetContainer, int[], int, int)

IntSequence

public IntSequence(AlphabetContainer alphabetContainer,
                   int[] content,
                   int start,
                   int length)
            throws WrongAlphabetException,
                   WrongSequenceTypeException

Creates a new IntSequence from a part of the array of int- encoded alphabet symbols.

Parameters:

alphabetContainer - the AlphabetContainer for the sequence

content - an array containing the encoded symbols

start - the start index in content

length - the length of the part of the array

Throws:

WrongAlphabetException - if the sequence is not defined over alphabetContainer

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

See Also:

SimpleDiscreteSequence.SimpleDiscreteSequence(AlphabetContainer, SequenceAnnotation[])

IntSequence

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

Creates a new IntSequence 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 ints

See Also:

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

IntSequence

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

Creates a new IntSequence 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 ints

See Also:

IntSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

IntSequence

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

Creates a new IntSequence 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 ints

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 IntSequence 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