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. More...

static SequenceWithQuality *	concatenate (const SequenceWithQuality &seqwq1, const SequenceWithQuality &seqwq2) throw (AlphabetMismatchException, Exception)
	Concatenate two sequences. More...

static SequenceWithQuality *	complement (const SequenceWithQuality &sequence) throw (AlphabetException)
	Get the complementary sequence of a nucleotide sequence. More...

static SequenceWithQuality *	transcript (const SequenceWithQuality &sequence) throw (AlphabetException)
	Get the transcription sequence of a DNA sequence. More...

static SequenceWithQuality *	reverseTranscript (const SequenceWithQuality &sequence) throw (AlphabetException)
	Get the reverse-transcription sequence of a RNA sequence. More...

static SequenceWithQuality *	invert (const SequenceWithQuality &sequence)
	Inverse a sequence from 5'->3' to 3'->5' and vice-versa. More...

static SequenceWithQuality *	removeGaps (const SequenceWithQuality &seq)
	Remove gaps from a SequenceWithQuality. More...

static SequenceWithQuality &	trimLeft (SequenceWithQuality &seq)
	Trim the left part of the sequence according to quality. More...

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

◆ complement()

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().

◆ concatenate()

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.

◆ invert()

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().

◆ removeGaps()

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().

◆ reverseTranscript()

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().

◆ subseq()

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

static

Get a sub-sequence.

Parameters

sequence	The sequence to trunc.
begin	The first position of the subsequence.
end	The last position of the subsequence.

Returns: A new SequenceWithQuality object with the given subsequence.

Exceptions

IndexOutOfBoundsException,Exception In case of bad indices.

Definition at line 54 of file SequenceWithQualityTools.cpp.

◆ transcript()

SequenceWithQuality * SequenceWithQualityTools::transcript	(	const SequenceWithQuality &	sequence	)
throw	(	AlphabetException
	)

static

Get the transcription sequence of a DNA sequence.

See also: DNAReplication

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

Parameters

sequence The sequence to transcript.

Exceptions

AlphabetException If the sequence is not a DNA sequence.

Definition at line 124 of file SequenceWithQualityTools.cpp.

References bpp::SymbolList::getContent().

◆ trimLeft()

SequenceWithQuality & SequenceWithQualityTools::trimLeft ( SequenceWithQuality & seq )

static

Trim the left part of the sequence according to quality.

Parameters

seq	The sequence to analyse.

Returns: The modified sequence.

Definition at line 189 of file SequenceWithQualityTools.cpp.

Member Data Documentation

◆ _DNA

DNA SequenceWithQualityTools::_DNA

staticprivate

Definition at line 62 of file SequenceWithQualityTools.h.

◆ _DNARep

NucleicAcidsReplication bpp::SequenceWithQualityTools::_DNARep

staticprivate

Definition at line 64 of file SequenceWithQualityTools.h.

◆ _RNA

RNA SequenceWithQualityTools::_RNA

staticprivate

Definition at line 63 of file SequenceWithQualityTools.h.

◆ _RNARep

NucleicAcidsReplication bpp::SequenceWithQualityTools::_RNARep

staticprivate

Definition at line 65 of file SequenceWithQualityTools.h.

◆ _transc

NucleicAcidsReplication bpp::SequenceWithQualityTools::_transc

staticprivate

Definition at line 66 of file SequenceWithQualityTools.h.

The documentation for this class was generated from the following files:

Bpp/Seq/SequenceWithQualityTools.h
Bpp/Seq/SequenceWithQualityTools.cpp

Static Public Member Functions

Static Private Attributes

Detailed Description

Member Function Documentation

◆ complement()

◆ concatenate()

◆ invert()

◆ removeGaps()

◆ reverseTranscript()

◆ subseq()

◆ transcript()

◆ trimLeft()

Member Data Documentation

◆ _DNA

◆ _DNARep

◆ _RNA

◆ _RNARep

◆ _transc