de.jstacs.data.sequences
Class SimpleDiscreteSequence

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

All Implemented Interfaces:

Comparable<Sequence<int[]>>

Direct Known Subclasses:

ByteSequence, IntSequence, MappedDiscreteSequence, ShortSequence, SparseSequence

public abstract class SimpleDiscreteSequence
extends Sequence<int[]>

This is the main class for any discrete sequence.

Author:

Jens Keilwagen

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

SimpleDiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)
This constructor creates a new SimpleDiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content.

Method Summary

protected void	addToRepresentation(Object representation, int pos, String delim) This method adds the information of one position to the representation using the specified delimiter
int	compareTo(int[] t1, int[] t2) This method compares to container and is used in Sequence.compareTo(Sequence).
double	continuousVal(int pos) Returns the continuous value at position pos of the Sequence.
void	fillContainer(int[] container, int pos) The method fills the content of a specific position in to the container.
int[]	getEmptyContainer() The method returns a container that can be used for accessing the symbols for each position.
protected Object	getEmptyRepresentation() Returns an empty representation which is used to create the String representation of this instance in the method Sequence.toString(String, int, int).
protected String	getStringRepresentation(Object representation) This method creates a String representation from the given representation.
protected int	hashCodeForPos(int pos) This method is used in Sequence.hashCode() and the hash code for one specific position.
boolean	isMultiDimensional() The method returns true if the sequence is multidimensional, otherwise .

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

annotate, compareTo, complement, complement, create, create, create, discreteVal, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, 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

SimpleDiscreteSequence

public SimpleDiscreteSequence(AlphabetContainer container,
                              SequenceAnnotation[] annotation)
                       throws WrongAlphabetException

This constructor creates a new SimpleDiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content. The content has to be set by the constructor of the subclass.

Parameters:

container - the AlphabetContainer of the sequence

annotation - the annotation of the sequence

Throws:

WrongAlphabetException - if the AlphabetContainer is not discrete

See Also:

Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

Method Detail

continuousVal

public final double continuousVal(int pos)

Description copied from class: Sequence

Returns the continuous value at position pos of the Sequence.

Specified by:

continuousVal in class Sequence<int[]>

Parameters:

pos - the position of the Sequence

Returns:

the continuous value at position pos of the Sequence

isMultiDimensional

public boolean isMultiDimensional()

Description copied from class: Sequence

The method returns true if the sequence is multidimensional, otherwise .

Specified by:

isMultiDimensional in class Sequence<int[]>

Returns:

true if the sequence is multidimensional, otherwise

getEmptyContainer

public int[] getEmptyContainer()

Description copied from class: Sequence

The method returns a container that can be used for accessing the symbols for each position. This is especially of interest for multidimensional sequences.

Specified by:

getEmptyContainer in class Sequence<int[]>

Returns:

a container that can be used for accessing the symbols for each position

See Also:

Sequence.fillContainer(Object, int), Sequence.isMultiDimensional()

fillContainer

public void fillContainer(int[] container,
                          int pos)

Description copied from class: Sequence

The method fills the content of a specific position in to the container. This is especially of interest for multidimensional sequences.

Specified by:

fillContainer in class Sequence<int[]>

Parameters:

container - the container which is used for filling the content.

pos - the position

See Also:

Sequence.getEmptyContainer(), Sequence.isMultiDimensional()

getEmptyRepresentation

protected Object getEmptyRepresentation()

Description copied from class: Sequence

Returns an empty representation which is used to create the String representation of this instance in the method Sequence.toString(String, int, int).

Specified by:

getEmptyRepresentation in class Sequence<int[]>

Returns:

an empty representation which is used to create the String representation

See Also:

Sequence.toString(String, int, int)

addToRepresentation

protected void addToRepresentation(Object representation,
                                   int pos,
                                   String delim)

Description copied from class: Sequence

This method adds the information of one position to the representation using the specified delimiter

Specified by:

addToRepresentation in class Sequence<int[]>

Parameters:

representation - the representation

pos - the position

delim - the delimiter separating the information for different positions

See Also:

Sequence.getEmptyRepresentation(), Sequence.toString(String, int, int)

getStringRepresentation

protected String getStringRepresentation(Object representation)

Description copied from class: Sequence

This method creates a String representation from the given representation.

Specified by:

getStringRepresentation in class Sequence<int[]>

Parameters:

representation - the representation instance (which should be created by Sequence.getEmptyContainer() and filled by Sequence.addToRepresentation(Object, int, String))

Returns:

a String representation

See Also:

Sequence.getEmptyRepresentation(), Sequence.addToRepresentation(Object, int, String), Sequence.toString(String, int, int)

hashCodeForPos

protected int hashCodeForPos(int pos)

Description copied from class: Sequence

This method is used in Sequence.hashCode() and the hash code for one specific position.

Specified by:

hashCodeForPos in class Sequence<int[]>

Parameters:

pos - the position

Returns:

the hash code for the position

compareTo

public int compareTo(int[] t1,
                     int[] t2)

Description copied from class: Sequence

This method compares to container and is used in Sequence.compareTo(Sequence).

Specified by:

compareTo in class Sequence<int[]>

Parameters:

t1 - the first container

t2 - the second container

Returns:

zero if arguments are equal

See Also:

Sequence.getEmptyContainer(), Sequence.fillContainer(Object, int), Comparable.compareTo(java.lang.Object)