de.jstacs.data.sequences
Class SparseSequence

java.lang.Object
  de.jstacs.data.Sequence
      de.jstacs.data.sequences.DiscreteSequence
          de.jstacs.data.sequences.SparseSequence

All Implemented Interfaces:

Comparable<Sequence>

public final class SparseSequence
extends DiscreteSequence

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 DiscreteSequence, 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.Sequence

Sequence.CompositeSequence, Sequence.SubSequence

Field Summary

Fields inherited from class de.jstacs.data.Sequence

alphabetCon, annotation, rc

Constructor Summary

SparseSequence(AlphabetContainer alphCon, String seq)
This constructor creates an instance from a String.

SparseSequence(AlphabetContainer alphCon, SymbolExtractor se)
This constructor creates an instance from a SymbolExtractor.

Method Summary

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 of position pos.
protected Sequence	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
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 sequence instance containing a part of the complementary current sequence.

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

continuousVal

Methods inherited from class de.jstacs.data.Sequence

annotate, compareTo, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, 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

This constructor creates an instance from a String.

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

SparseSequence

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

This constructor creates an instance 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

Method Detail

discreteVal

public int discreteVal(int pos)

Description copied from class: Sequence

Returns the discrete value of position pos.

Specified by:

discreteVal in class Sequence

Parameters:

pos - the position

Returns:

the discrete value of position pos

getLength

public int getLength()

Description copied from class: Sequence

Returns the length of the sequence

Specified by:

getLength in class Sequence

Returns:

the length

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 for instance invoking this method on the sequence "TAATA" with an AlphabetContainer on DNAAlphabet returns "ATTAT".

Overrides:

complement in class Sequence

Parameters:

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

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

Returns:

the complementary sequence

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

Parameters:

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

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

Returns:

the reverse sequence

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 sequence instance containing a part of the complementary current sequence. For more details see the methods reverse() and complement().

Overrides:

reverseComplement in class Sequence

Parameters:

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

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

Returns:

the reverse complementary sequence

Throws:

OperationNotSupportedException - if the current sequence is not discrete and simple

See Also:

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

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