de.jstacs.data.sequences

Class SparseSequence

java.lang.Object

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

de.jstacs.data.sequences.SimpleDiscreteSequence

de.jstacs.data.sequences.SparseSequence

All Implemented Interfaces:

Comparable<Sequence<int[]>>

public final class SparseSequence
extends SimpleDiscreteSequence

This class is an implementation for sequences on one alphabet with length 4. This implementation can be used, for instance, for DNA sequences.

The symbols are encoded in the bits of the primitive type long, which allows to save 32 symbols in one long. On the one hand an instance of this class is more memory efficient than any other SimpleDiscreteSequence, e.g. ByteSequence. But on the other hand this class will be a little bit slower when accessing single positions.

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

Constructors

Constructor and Description
SparseSequence(AlphabetContainer alphCon, String seq) Creates a new SparseSequence from a String representation.
SparseSequence(AlphabetContainer alphCon, SymbolExtractor se) Creates a new SparseSequence from a SymbolExtractor.

Method Summary

Modifier and Type	Method and Description
SparseSequence	complement(int start, int end) This method returns a new instance of Sequence containing a part of the complementary current Sequence.
int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.
protected SparseSequence	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 SparseSequences.
static DataSet	getDataSet(AlphabetContainer con, String filename) This method allows to create a DataSet containing SparseSequences using a file name.
static DataSet	getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) This method allows to create a DataSet containing SparseSequences using a file name.
int	getLength() Returns the length of the Sequence.
SparseSequence	reverse(int start, int end) This method returns a new instance of Sequence containing a part of the reverse current Sequence.
SparseSequence	reverseComplement(int start, int end) This method returns a new instance of Sequence containing a reverse part of the complementary current Sequence.

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

addToRepresentation, compareTo, continuousVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional, shuffle

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

annotate, compareTo, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, reverse, reverseComplement, toDiscrete, toString, toString, toString, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

SparseSequence

public SparseSequence(AlphabetContainer alphCon,
                      String seq)
               throws WrongSequenceTypeException,
                      WrongAlphabetException

Creates a new SparseSequence from a String representation.

Parameters:

alphCon - the AlphabetContainer

seq - the sequence as String

Throws:

WrongSequenceTypeException - if the AlphabetContainer is not simple or the internal Alphabet has more than 4 symbols

WrongAlphabetException - if the AlphabetContainer is not discrete

See Also:

SparseSequence(AlphabetContainer, SymbolExtractor)

SparseSequence

public SparseSequence(AlphabetContainer alphCon,
                      SymbolExtractor se)
               throws WrongSequenceTypeException,
                      WrongAlphabetException

Creates a new SparseSequence from a SymbolExtractor.

Parameters:

alphCon - the AlphabetContainer

se - the SymbolExtractor

Throws:

WrongSequenceTypeException - if the AlphabetContainer is not simple or the internal Alphabet has more than 4 symbols

WrongAlphabetException - if the AlphabetContainer is not discrete

See Also:

SparseSequence(AlphabetContainer, int, 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

complement

public SparseSequence complement(int start,
                                 int end)
                          throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing a part of the complementary current Sequence.
So invoking this method, for instance, on the sequence "TAATA" with an AlphabetContainer on DNAAlphabet returns "ATTAT".

Overrides:

complement in class Sequence<int[]>

Parameters:

start - the start position (inclusive) in the original Sequence

end - the end position (exclusive) in the original Sequence

Returns:

the complementary Sequence of the part

Throws:

OperationNotSupportedException - if the current Sequence is not based on a ComplementableDiscreteAlphabet

See Also:

ComplementableDiscreteAlphabet

reverse

public SparseSequence reverse(int start,
                              int end)
                       throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing a part of the reverse current Sequence.

Overrides:

reverse in class Sequence<int[]>

Parameters:

start - the start position (inclusive) in the original Sequence

end - the end position (exclusive) in the original Sequence

Returns:

the reverse Sequence of the part

Throws:

OperationNotSupportedException - if the current Sequence is based on an AlphabetContainer that is not simple

reverseComplement

public SparseSequence reverseComplement(int start,
                                        int end)
                                 throws OperationNotSupportedException

Description copied from class: Sequence

This method returns a new instance of Sequence containing a reverse part of the complementary current Sequence. For more details see the methods Sequence.reverse() and Sequence.complement().

Overrides:

reverseComplement in class Sequence<int[]>

Parameters:

start - the start position (inclusive) in the original Sequence

end - the end position (exclusive) in the original Sequence

Returns:

the reverse complementary Sequence of the part

Throws:

OperationNotSupportedException - if the current Sequence is not discrete and simple ((not based on a ComplementableDiscreteAlphabet)

See Also:

Sequence.reverse(), Sequence.complement(), ComplementableDiscreteAlphabet

flatCloneWithoutAnnotation

protected SparseSequence 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

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 SparseSequences 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 SparseSequences

filename - the file name

parser - a parser for the annotations of the SparseSequences

Returns:

a DataSet containing SparseSequences

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 SparseSequences using a file name.

Parameters:

con - the AlphabetContainer for the DataSet and SparseSequences

filename - the file name

Returns:

a DataSet containing SparseSequences

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

This method allows to create a DataSet containing SparseSequences.

Parameters:

con - the AlphabetContainer for the DataSet and Sequences

se - the AbstractStringExtractors that handle the DataSet as String

Returns:

a DataSet containing SparseSequences

Throws:

WrongSequenceTypeException - if the AlphabetContainer is not simple or the internal Alphabet has more than 4 symbols

WrongAlphabetException - if the AlphabetContainer is not discrete

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