The SequenceWithQualityTools static class. More...

#include <Bpp/Seq/SequenceWithQualityTools.h>

Collaboration diagram for bpp::SequenceWithQualityTools:

Static Public Member Functions
static SequenceWithQuality *	subseq (const SequenceWithQuality &sequence, unsigned int begin, unsigned int end) throw (IndexOutOfBoundsException, Exception)
	Get a sub-sequence.
static SequenceWithQuality *	concatenate (const SequenceWithQuality &seqwq1, const SequenceWithQuality &seqwq2) throw (AlphabetMismatchException, Exception)
	Concatenate two sequences.
static SequenceWithQuality *	complement (const SequenceWithQuality &sequence) throw (AlphabetException)
	Get the complementary sequence of a nucleotide sequence.
static SequenceWithQuality *	transcript (const SequenceWithQuality &sequence) throw (AlphabetException)
	Get the transcription sequence of a DNA sequence.
static SequenceWithQuality *	reverseTranscript (const SequenceWithQuality &sequence) throw (AlphabetException)
	Get the reverse-transcription sequence of a RNA sequence.
static SequenceWithQuality *	invert (const SequenceWithQuality &sequence)
	Inverse a sequence from 5'->3' to 3'->5' and vice-versa.
static SequenceWithQuality *	removeGaps (const SequenceWithQuality &seq)
	Remove gaps from a SequenceWithQuality.
static SequenceWithQuality &	trimLeft (SequenceWithQuality &seq)
	Trim the left part of the sequence according to quality.
Static Private Attributes
static DNA	_DNA
static RNA	_RNA
static NucleicAcidsReplication	_DNARep
static NucleicAcidsReplication	_RNARep
static NucleicAcidsReplication	_transc

Detailed Description

The SequenceWithQualityTools static class.

Implement methods to manipulate SequencesWithQuality

Todo:

does complement, transcript and reverseTranscript have a meaning on SequenceWithQuality as the quality is not transferable

Author:: Cahais Vincent

Definition at line 60 of file SequenceWithQualityTools.h.

Member Function Documentation

SequenceWithQuality * SequenceWithQualityTools::complement ( const SequenceWithQuality & sequence ) throw (AlphabetException) [static]

Get the complementary sequence of a nucleotide sequence.

See also:: DNAReplication

Returns:: sequence A new SequenceWithQuality object with the complementary sequence.

Parameters:

sequence The sequence to complement.

Exceptions:

AlphabetException If the sequence is not a nucleotide sequence.

Definition at line 100 of file SequenceWithQualityTools.cpp.

References bpp::SymbolList::getContent(), and bpp::NucleicAcidsReplication::translate().

SequenceWithQuality * SequenceWithQualityTools::concatenate	(	const SequenceWithQuality &	seqwq1,
		const SequenceWithQuality &	seqwq2
	)		throw (AlphabetMismatchException, Exception) `[static]`

Concatenate two sequences.

Sequences must have the same name and alphabets. Only first sequence's commentaries are kept.

Parameters:

seqwq1	The first SequenceWithQuality.
seqwq2	The second SequenceWithQuality.

Returns:: A new SequenceWithQuality object with the concatenation of the two sequences.

Exceptions:

AlphabetMismatchException	If the two alphabets do not match.
Exception	If the sequence names do not match.

Definition at line 77 of file SequenceWithQualityTools.cpp.

SequenceWithQuality * SequenceWithQualityTools::invert ( const SequenceWithQuality & sequence ) [static]

Inverse a sequence from 5'->3' to 3'->5' and vice-versa.

ABCDEF becomes FEDCBA, and the sense attribute is changed (may be inhibited).

Returns:: A new SequenceWithQuality object containing the inverted sequence.

Parameters:

sequence The SequenceWithQuality to inverse.

Definition at line 155 of file SequenceWithQualityTools.cpp.

References bpp::SequenceWithQuality::clone(), bpp::EdSymbolList::getContent(), and bpp::SequenceWithQuality::getQualities().

SequenceWithQuality * SequenceWithQualityTools::removeGaps ( const SequenceWithQuality & seq ) [static]

Remove gaps from a SequenceWithQuality.

Parameters:

seq	The sequence to analyse.

Returns:: A new SequenceWithQuality object without gaps.

Definition at line 168 of file SequenceWithQualityTools.cpp.

References bpp::SequenceWithQuality::clone(), bpp::EdSymbolList::getAlphabet(), bpp::SequenceWithQuality::getQualities(), bpp::Alphabet::isGap(), bpp::SequenceWithAnnotation::setContent(), bpp::SequenceWithQuality::setQualities(), and bpp::EdSymbolList::size().

SequenceWithQuality * SequenceWithQualityTools::reverseTranscript ( const SequenceWithQuality & sequence ) throw (AlphabetException) [static]

Get the reverse-transcription sequence of a RNA sequence.

See also:: DNAReplication

Returns:: sequence A new SequenceWithQuality object with the reverse- transcription sequence.

Parameters:

sequence The SequenceWithQuality to reverse-transcript.

Exceptions:

AlphabetException If the sequence is not a RNA sequence.

Definition at line 139 of file SequenceWithQualityTools.cpp.

References bpp::SymbolList::getContent().

SequenceWithQuality * SequenceWithQualityTools::subseq	(	const SequenceWithQuality &	sequence,
		unsigned int	begin,
		unsigned int	end
	)		throw (IndexOutOfBoundsException, Exception) `[static]`