The SequenceWithQualityTools static class. More...

#include <Bpp/Seq/SequenceWithQualityTools.h>

Collaboration diagram for bpp::SequenceWithQualityTools:

Static Public Member Functions
static void	subseq (const SequenceWithQuality &sequence, size_t begin, size_t end, SequenceWithQuality &output)
	Get a sub-sequence. More...

static std::unique_ptr< SequenceWithQuality >	subseq (const SequenceWithQuality &sequence, size_t begin, size_t end)
	Get a sub-sequence. More...

static std::unique_ptr< SequenceWithQuality >	concatenate (const SequenceWithQuality &seqwq1, const SequenceWithQuality &seqwq2)
	Concatenate two sequences. More...

static std::unique_ptr< SequenceWithQuality >	complement (const SequenceWithQuality &sequence)
	Get the complementary sequence of a nucleotide sequence. More...

static std::unique_ptr< SequenceWithQuality >	transcript (const SequenceWithQuality &sequence)
	Get the transcription sequence of a DNA sequence. More...

static std::unique_ptr< SequenceWithQuality >	reverseTranscript (const SequenceWithQuality &sequence)
	Get the reverse-transcription sequence of a RNA sequence. More...

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

static std::unique_ptr< SequenceWithQuality >	removeGaps (const SequenceWithQuality &seq)
	Remove gaps from a SequenceWithQuality. 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 26 of file SequenceWithQualityTools.h.

Member Function Documentation

◆ complement()

unique_ptr< SequenceWithQuality > SequenceWithQualityTools::complement ( const SequenceWithQuality & sequence )

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 42 of file SequenceWithQualityTools.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), bpp::SequenceWithQuality::getQualities(), and bpp::NucleicAcidsReplication::translate().

◆ concatenate()

unique_ptr< SequenceWithQuality > SequenceWithQualityTools::concatenate	(	const SequenceWithQuality &	seqwq1,
		const SequenceWithQuality &	seqwq2
	)

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 16 of file SequenceWithQualityTools.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), bpp::SimpleCommentable::getComments(), bpp::TemplateCoreSymbolListInterface< T >::getContent(), bpp::AbstractCoreSequence::getName(), and bpp::SequenceWithQuality::getQualities().

◆ invert()

unique_ptr< 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 99 of file SequenceWithQualityTools.cpp.

References bpp::SequenceWithQuality::clone(), bpp::TemplateCoreSymbolListInterface< T >::getContent(), and bpp::SequenceWithQuality::getQualities().

◆ removeGaps()

unique_ptr< 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 113 of file SequenceWithQualityTools.cpp.

References bpp::SequenceWithQuality::clone(), bpp::CruxSymbolListInterface::getAlphabet(), bpp::SequenceWithQuality::getQualities(), and bpp::CruxSymbolListInterface::size().

◆ reverseTranscript()

unique_ptr< SequenceWithQuality > SequenceWithQualityTools::reverseTranscript ( const SequenceWithQuality & sequence )

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 81 of file SequenceWithQualityTools.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), and bpp::SequenceWithQuality::getQualities().

◆ subseq() [1/2]

static std::unique_ptr<SequenceWithQuality> bpp::SequenceWithQualityTools::subseq	(	const SequenceWithQuality &	sequence,
		size_t	begin,
		size_t	end
	)

inlinestatic

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 sequence object with the given subsequence.

Definition at line 66 of file SequenceWithQualityTools.h.

References bpp::CruxSymbolListInterface::getAlphabet(), bpp::SimpleCommentable::getComments(), bpp::AbstractCoreSequence::getName(), and subseq().

◆ subseq() [2/2]

static void bpp::SequenceWithQualityTools::subseq	(	const SequenceWithQuality &	sequence,
		size_t	begin,
		size_t	end,
		SequenceWithQuality &	output
	)

inlinestatic

Get a sub-sequence.

Parameters

sequence	The sequence to trunc.
begin	The first position of the subsequence.
end	The last position of the subsequence (included).
output	A sequence object to be appended with the given subsequence.

Definition at line 44 of file SequenceWithQualityTools.h.

References bpp::SequenceWithQuality::append(), bpp::SequenceWithQuality::getQuality(), bpp::CruxSymbolListInterface::size(), and bpp::TextTools::toString().

Referenced by subseq().

◆ transcript()

unique_ptr< SequenceWithQuality > SequenceWithQualityTools::transcript ( const SequenceWithQuality & sequence )

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 66 of file SequenceWithQualityTools.cpp.

References bpp::CruxSymbolListInterface::getAlphabet(), and bpp::SequenceWithQuality::getQualities().

Member Data Documentation

◆ DNA_

DNA bpp::SequenceWithQualityTools::DNA_

staticprivate

Definition at line 29 of file SequenceWithQualityTools.h.

◆ DNARep_

NucleicAcidsReplication SequenceWithQualityTools::DNARep_

staticprivate

Definition at line 31 of file SequenceWithQualityTools.h.

◆ RNA_

RNA bpp::SequenceWithQualityTools::RNA_

staticprivate

Definition at line 30 of file SequenceWithQualityTools.h.

◆ RNARep_

NucleicAcidsReplication SequenceWithQualityTools::RNARep_

staticprivate

Definition at line 32 of file SequenceWithQualityTools.h.

◆ transc_

NucleicAcidsReplication SequenceWithQualityTools::transc_

staticprivate

Definition at line 33 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() [1/2]

◆ subseq() [2/2]

◆ transcript()

Member Data Documentation

◆ DNA_

◆ DNARep_

◆ RNA_

◆ RNARep_

◆ transc_