de.jstacs.data.sequences

Class ArbitraryFloatSequence

java.lang.Object

de.jstacs.data.sequences.Sequence<float[]>

de.jstacs.data.sequences.ArbitraryFloatSequence

All Implemented Interfaces:

Comparable<Sequence<float[]>>

public class ArbitraryFloatSequence
extends Sequence<float[]>

This class is for any continuous or hybrid sequence. In contrast to ArbitrarySequences, the numeric values are represented by floats instead of doubles. This may be useful if either the represented data are known to be only of float precision or if double precision is dispensible for the sake of memory consumption.

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

Constructors

Constructor and Description
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, float[] content) Creates a new ArbitraryFloatSequence from an array of float-encoded alphabet symbols.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ArbitraryFloatSequence from a String representation using the delimiter delim.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ArbitraryFloatSequence from a SymbolExtractor.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, String sequence) Creates a new ArbitraryFloatSequence from a String representation using the default delimiter.

Method Summary

Modifier and Type	Method and Description
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(float[] t1, float[] 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.
int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.
void	fillContainer(float[] container, int pos) The method fills the content of a specific position in to the container.
protected ArbitraryFloatSequence	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
static DataSet	getDataSet(AlphabetContainer con, AbstractStringExtractor... se) This method allows to create a DataSet containing ArbitraryFloatSequences.
static DataSet	getDataSet(AlphabetContainer con, String filename) This method allows to create a DataSet containing ArbitraryFloatSequences using a file name.
static DataSet	getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) This method allows to create a DataSet containing ArbitraryFloatSequences using a file name.
float[]	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).
int	getLength() Returns the length of the Sequence.
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 false.

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

ArbitraryFloatSequence

public ArbitraryFloatSequence(AlphabetContainer alphabetContainer,
                              float[] content)
                       throws WrongAlphabetException,
                              WrongSequenceTypeException

Creates a new ArbitraryFloatSequence from an array of float-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 floats

See Also:

StatisticalModel.emitDataSet(int, int...), Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])

ArbitraryFloatSequence

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

Creates a new ArbitraryFloatSequence 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 floats

See Also:

ArbitraryFloatSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

ArbitraryFloatSequence

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

Creates a new ArbitraryFloatSequence 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 floats

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

See Also:

ArbitraryFloatSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor)

ArbitraryFloatSequence

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

Creates a new ArbitraryFloatSequence 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 floats

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.

Specified by:

continuousVal in class Sequence<float[]>

Parameters:

pos - the position of the Sequence

Returns:

the continuous value at position pos of the Sequence

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<float[]>

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<float[]>

Returns:

the length of the Sequence

flatCloneWithoutAnnotation

protected ArbitraryFloatSequence 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<float[]>

Returns:

the cloned Sequence without annotation

isMultiDimensional

public boolean isMultiDimensional()

Description copied from class: Sequence

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

Specified by:

isMultiDimensional in class Sequence<float[]>

Returns:

true if the sequence is multidimensional, otherwise false

getEmptyContainer

public float[] 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<float[]>

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(float[] 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<float[]>

Parameters:

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

pos - the position

See Also:

Sequence.getEmptyContainer(), Sequence.isMultiDimensional()

compareTo

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

Description copied from class: Sequence

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

Specified by:

compareTo in class Sequence<float[]>

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)

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<float[]>

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<float[]>

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<float[]>

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<float[]>

Parameters:

pos - the position

Returns:

the hash code for the position

getDataSet

public static DataSet getDataSet(AlphabetContainer con,
                                 String filename,
                                 SequenceAnnotationParser parser)
                          throws FileNotFoundException,
                                 WrongAlphabetException,
                                 WrongSequenceTypeException,
                                 EmptyDataSetException,
                                 IOException

This method allows to create a DataSet containing ArbitraryFloatSequences using a file name. Annotations are parsed by the supplied SequenceAnnotationParser. The file is assumed to be in FastA format.

Parameters:

con - the AlphabetContainer for the DataSet and ArbitraryFloatSequences

filename - the file name

parser - a parser for the annotations of the ArbitraryFloatSequences

Returns:

a DataSet containing ArbitraryFloatSequences

Throws:

FileNotFoundException - if the file filename could not be found

WrongAlphabetException - if the alphabet does not fit the data

WrongSequenceTypeException - if the data can not be represented as floats

EmptyDataSetException - if not sequences exist in filename

IOException - if the file could not be read

getDataSet

public static DataSet getDataSet(AlphabetContainer con,
                                 String filename)
                          throws FileNotFoundException,
                                 WrongAlphabetException,
                                 WrongSequenceTypeException,
                                 EmptyDataSetException,
                                 IOException

This method allows to create a DataSet containing ArbitraryFloatSequences using a file name.

Parameters:

con - the AlphabetContainer for the DataSet and ArbitraryFloatSequences

filename - the file name

Returns:

a DataSet containing ArbitraryFloatSequences

Throws:

FileNotFoundException - if the file filename could not be found

WrongAlphabetException - if the alphabet does not fit the data

WrongSequenceTypeException - if the data can not be represented as floats

EmptyDataSetException - if not sequences exist in filename

IOException - if the file could not be read

getDataSet

public static DataSet getDataSet(AlphabetContainer con,
                                 AbstractStringExtractor... se)
                          throws WrongAlphabetException,
                                 WrongSequenceTypeException,
                                 EmptyDataSetException

This method allows to create a DataSet containing ArbitraryFloatSequences.

Parameters:

con - the AlphabetContainer for the DataSet and ArbitraryFloatSequences

se - the AbstractStringExtractors that handle the DataSet as String

Returns:

a DataSet containing ArbitraryFloatSequences

Throws:

WrongAlphabetException - if the alphabet does not fit the data

WrongSequenceTypeException - if the data can not be represented as floats

EmptyDataSetException - if a DataSet with 0 (zero) ArbitraryFloatSequences should be created