#include <Bpp/Seq/SequenceTools.h>

Inheritance diagram for bpp::SequenceTools:

Collaboration diagram for bpp::SequenceTools:

Public Member Functions
	SequenceTools ()

virtual	~SequenceTools ()

Static Public Member Functions
static Sequence *	subseq (const Sequence &sequence, size_t begin, size_t end) throw (IndexOutOfBoundsException, Exception)
	Get a sub-sequence. More...

static Sequence *	concatenate (const Sequence &seq1, const Sequence &seq2) throw (AlphabetMismatchException, Exception)
	Concatenate two sequences. More...

static Sequence &	complement (Sequence &seq) throw (AlphabetException)
	Complement the nucleotide sequence itself. More...

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

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

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

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

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

static Sequence &	invertComplement (Sequence &seq)
	Inverse and complement a sequence. More...

static double	getPercentIdentity (const Sequence &seq1, const Sequence &seq2, bool ignoreGaps=false) throw (AlphabetMismatchException, SequenceNotAlignedException)

static size_t	getNumberOfSites (const Sequence &seq)

static size_t	getNumberOfCompleteSites (const Sequence &seq)

static Sequence *	getSequenceWithCompleteSites (const Sequence &seq)
	keep only complete sites in a sequence. More...

static size_t	getNumberOfUnresolvedSites (const Sequence &seq)

static void	removeGaps (Sequence &seq)
	Remove gaps from a sequence. More...

static Sequence *	getSequenceWithoutGaps (const Sequence &seq)
	Get a copy of the sequence without gaps. More...

static void	removeStops (Sequence &seq, const GeneticCode &gCode) throw (Exception)
	Remove stops from a codon sequence. More...

static Sequence *	getSequenceWithoutStops (const Sequence &seq, const GeneticCode &gCode) throw (Exception)
	Get a copy of the codon sequence without stops. More...

static void	replaceStopsWithGaps (Sequence &seq, const GeneticCode &gCode) throw (Exception)
	Replace stop codons by gaps. More...

static BowkerTest *	bowkerTest (const Sequence &seq1, const Sequence &seq2) throw (SequenceNotAlignedException)
	Bowker's test for homogeneity. More...

static void	getPutativeHaplotypes (const Sequence &seq, std::vector< Sequence *> &hap, unsigned int level=2)
	Get all putatives haplotypes from an heterozygous sequence. More...

static Sequence *	combineSequences (const Sequence &s1, const Sequence &s2) throw (AlphabetMismatchException)
	Combine two sequences. More...

static Sequence *	subtractHaplotype (const Sequence &s, const Sequence &h, std::string name="", unsigned int level=1) throw (SequenceNotAlignedException)
	Subtract haplotype from an heterozygous sequence. More...

static Sequence *	RNYslice (const Sequence &sequence, int ph) throw (AlphabetException)
	Get the RNY decomposition of a DNA sequence; with a given phase between 1 and 3, it gives the decomposition in this phase; in phase 1, the first triplet is centered on the first character. Without a phase the function gives the alternative succession in phases 1, 2 and 3. More...

static Sequence *	RNYslice (const Sequence &sequence) throw (AlphabetException)

static void	getCDS (Sequence &sequence, const GeneticCode &gCode, bool checkInit, bool checkStop, bool includeInit=true, bool includeStop=true)
	Extract CDS part from a codon sequence. Optionally check for intiator and stop codons, or both. More...

static size_t	findFirstOf (const Sequence &seq, const Sequence &motif, bool strict=true)
	Find the position of a motif in a sequence. More...

static Sequence *	getRandomSequence (const Alphabet *alphabet, size_t length)
	Get a random sequence of given size and alphabet, with all state with equal probability. More...

static void	getCounts (const SymbolList &list, std::map< int, size_t > &counts)
	Count all states in the list. More...

static void	getCounts (const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, size_t > > &counts) throw (DimensionException)
	Count all pair of states for two lists of the same size. More...

static void	getCounts (const SymbolList &list, std::map< int, double > &counts, bool resolveUnknowns)
	Count all states in the list, optionaly resolving unknown characters. More...

static void	getCounts (const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, double > > &counts, bool resolveUnknowns) throw (DimensionException)
	Count all pair of states for two lists of the same size, optionaly resolving unknown characters. More...

static void	getFrequencies (const SymbolList &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)
	Get all states frequencies in the list. More...

static void	getFrequencies (const SymbolList &list1, const SymbolList &list2, std::map< int, std::map< int, double > > &frequencies, bool resolveUnknowns=false) throw (DimensionException)
	Get all state pairs frequencies for two lists of the same size.. More...

static double	getGCContent (const SymbolList &list, bool ignoreUnresolved=true, bool ignoreGap=true) throw (AlphabetException)
	Get the GC content of a symbol list. More...

static size_t	getNumberOfDistinctPositions (const SymbolList &l1, const SymbolList &l2) throw (AlphabetMismatchException)
	Get the number of distinct positions. More...

static size_t	getNumberOfPositionsWithoutGap (const SymbolList &l1, const SymbolList &l2) throw (AlphabetMismatchException)
	Get the number of positions without gap. More...

static void	changeGapsToUnknownCharacters (SymbolList &l)
	Change all gap elements to unknown characters. More...

static void	changeUnresolvedCharactersToGaps (SymbolList &l)
	Change all unknown characters to gap elements. More...

Static Private Attributes
static DNA	_DNA

static RNA	_RNA

static RNY	_RNY

static NucleicAcidsReplication	_DNARep

static NucleicAcidsReplication	_RNARep

static NucleicAcidsReplication	_transc

Detailed Description

SequenceTools static class.

Implement methods to manipulate sequences

Definition at line 97 of file SequenceTools.h.

Constructor & Destructor Documentation

◆ SequenceTools()

bpp::SequenceTools::SequenceTools ( )

inline

Definition at line 109 of file SequenceTools.h.

◆ ~SequenceTools()

virtual bpp::SequenceTools::~SequenceTools ( )

inlinevirtual

Definition at line 110 of file SequenceTools.h.

Member Function Documentation

◆ bowkerTest()

BowkerTest * SequenceTools::bowkerTest	(	const Sequence &	seq1,
		const Sequence &	seq2
	)
throw	(	SequenceNotAlignedException
	)

static

Bowker's test for homogeneity.

Computes the contingency table of occurrence of all pairs of states and test its symmetry using Bowker's (1948) test.

Reference:

Ababneh F. Bioinformatics 2006 22(10) 1225-1231

Parameters

seq1	The first sequence.
seq2	The second sequence.

Returns: A BowkerTest object with the computed statistic and p-value (computed from a chi square distribution).

Exceptions

SequenceNotAlignedException If the two sequences do not have the same length.

Definition at line 412 of file SequenceTools.cpp.

References bpp::Alphabet::getSize(), bpp::Alphabet::isGap(), bpp::Alphabet::isUnresolved(), bpp::BowkerTest::setPValue(), and bpp::BowkerTest::setStatistic().

◆ changeGapsToUnknownCharacters()

void SymbolListTools::changeGapsToUnknownCharacters ( SymbolList & l )

staticinherited

Change all gap elements to unknown characters.

Parameters

l	The input list of characters.

Definition at line 180 of file SymbolListTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::Alphabet::getUnknownCharacterCode(), bpp::Alphabet::isGap(), and bpp::SymbolList::size().

◆ changeUnresolvedCharactersToGaps()

void SymbolListTools::changeUnresolvedCharactersToGaps ( SymbolList & l )

staticinherited

Change all unknown characters to gap elements.

Parameters

l	The input list of characters.

Definition at line 189 of file SymbolListTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::Alphabet::getGapCharacterCode(), bpp::Alphabet::isUnresolved(), and bpp::SymbolList::size().

◆ combineSequences()

Sequence * SequenceTools::combineSequences	(	const Sequence &	s1,
		const Sequence &	s2
	)
throw	(	AlphabetMismatchException
	)

static

Combine two sequences.

Author: Sylvain Gaillard

Definition at line 516 of file SequenceTools.cpp.

References bpp::Alphabet::getGeneric().

◆ complement()

Sequence & SequenceTools::complement	(	Sequence &	seq	)
throw	(	AlphabetException
	)

static

Complement the nucleotide sequence itself.

Parameters

seq	The sequence to be complemented.

Returns: A ref toward the complemented sequence.

Exceptions

AlphabetException if the sequence is not a nucleotide sequence.

Author: Sylvain Gaillard

Definition at line 108 of file SequenceTools.cpp.

References bpp::NucleicAcidsReplication::translate().

◆ concatenate()

Sequence * SequenceTools::concatenate	(	const Sequence &	seq1,
		const Sequence &	seq2
	)
throw	(	AlphabetMismatchException,
		Exception
	)

static

Concatenate two sequences.

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

Parameters

seq1	The first sequence.
seq2	The second sequence.

Returns: A new sequence 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 89 of file SequenceTools.cpp.

◆ findFirstOf()

size_t SequenceTools::findFirstOf	(	const Sequence &	seq,
		const Sequence &	motif,
		bool	strict = `true`
	)

static

Find the position of a motif in a sequence.

Parameters

seq	The reference sequence
motif	The motif to find
strict	If true (default) find exactly the motif If false find compatible match

Returns: The position of the first occurence of the motif or the seq length.

Definition at line 684 of file SequenceTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::SymbolList::getValue(), bpp::AlphabetTools::match(), and bpp::SymbolList::size().

◆ getCDS()

void SequenceTools::getCDS	(	Sequence &	sequence,
		const GeneticCode &	gCode,
		bool	checkInit,
		bool	checkStop,
		bool	includeInit = `true`,
		bool	includeStop = `true`
	)

static

Extract CDS part from a codon sequence. Optionally check for intiator and stop codons, or both.

Parameters

sequence	The sequence to be reduced to CDS part.
gCode	The genetic code according to which start and stop codons are specified.
checkInit	If true, then everything before the initiator codon will be removed, together with the initiator codon if includeInit is false.
checkStop	If true, then everything after the first stop codon will be removed, together with the stop codon if includeStop is false.
includeInit	Tell if initiator codon should be kept or removed. No effect if checkInit is false.
includeStop	Tell if stop codon should be kept or removed. No effect if checkStop is false.

Definition at line 655 of file SequenceTools.cpp.

References bpp::SymbolList::deleteElement(), bpp::SymbolList::getAlphabet(), bpp::GeneticCode::isStart(), bpp::GeneticCode::isStop(), and bpp::SymbolList::size().

◆ getComplement()

Sequence * SequenceTools::getComplement	(	const Sequence &	sequence	)
throw	(	AlphabetException
	)

static

Get the complementary sequence of a nucleotide sequence.

See also: DNAReplication

Returns: A new sequence object with the complementary sequence.

Parameters

sequence The sequence to complement.

Exceptions

AlphabetException If the sequence is not a nucleotide sequence.

Definition at line 133 of file SequenceTools.cpp.

References bpp::NucleicAcidsReplication::translate().

◆ getCounts() [1/4]

static void bpp::SymbolListTools::getCounts	(	const SymbolList &	list,
		std::map< int, size_t > &	counts
	)

inlinestaticinherited

Count all states in the list.

Author: J. Dutheil

Parameters

list	The list.
counts	The output map to store the counts (existing counts will be incremented).

Definition at line 70 of file SymbolListTools.h.

References bpp::SymbolList::getContent().

Referenced by bpp::SiteTools::getNumberOfDistinctCharacters(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::SiteTools::isParsimonyInformativeSite(), and bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions().

◆ getCounts() [2/4]

static void bpp::SymbolListTools::getCounts	(	const SymbolList &	list1,
		const SymbolList &	list2,
		std::map< int, std::map< int, size_t > > &	counts
	)
throw	(	DimensionException
	)

inlinestaticinherited

Count all pair of states for two lists of the same size.

NB: The two lists do node need to share the same alphabet! The states of the first list will be used as the first index in the output, and the ones from the second list as the second index.

Author: J. Dutheil

Parameters

list1	The first list.
list2	The second list.
counts	The output map to store the counts (existing counts will be incremented).

Definition at line 90 of file SymbolListTools.h.

◆ getCounts() [3/4]

void SymbolListTools::getCounts	(	const SymbolList &	list,
		std::map< int, double > &	counts,
		bool	resolveUnknowns
	)

staticinherited

Count all states in the list, optionaly resolving unknown characters.

For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.

Author: J. Dutheil

Parameters

list	The list.
counts	The output map to store the counts (existing ocunts will be incremented).
resolveUnknowns	Tell is unknown characters must be resolved. For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.

Returns: A map with all states and corresponding counts.

Definition at line 51 of file SymbolListTools.cpp.

References bpp::Alphabet::getAlias(), bpp::SymbolList::getAlphabet(), and bpp::SymbolList::getContent().

◆ getCounts() [4/4]

void SymbolListTools::getCounts	(	const SymbolList &	list1,
		const SymbolList &	list2,
		std::map< int, std::map< int, double > > &	counts,
		bool	resolveUnknowns
	)
throw	(	DimensionException
	)

staticinherited

Count all pair of states for two lists of the same size, optionaly resolving unknown characters.

For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.

NB: The two lists do node need to share the same alphabet! The states of the first list will be used as the first index in the output, and the ones from the second list as the second index.

Author: J. Dutheil

Parameters

list1	The first list.
list2	The second list.
counts	The output map to store the counts (existing ocunts will be incremented).
resolveUnknowns	Tell is unknown characters must be resolved. For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.

Returns: A map with all states and corresponding counts.

Definition at line 73 of file SymbolListTools.cpp.

◆ getFrequencies() [1/2]

void SymbolListTools::getFrequencies	(	const SymbolList &	list,
		std::map< int, double > &	frequencies,
		bool	resolveUnknowns = `false`
	)

staticinherited

Get all states frequencies in the list.

Author: J. Dutheil

Parameters

list	The list.
resolveUnknowns	Tell is unknown characters must be resolved. For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
frequencies	The output map with all states and corresponding frequencies. Existing frequencies will be erased if any.

Definition at line 96 of file SymbolListTools.cpp.

References bpp::SymbolList::size().

Referenced by bpp::CodonSiteTools::generateCodonSiteWithoutRareVariant(), bpp::SiteContainerTools::getConsensus(), bpp::SequenceApplicationTools::getSitesToAnalyse(), bpp::CodonSiteTools::meanNumberOfSynonymousPositions(), bpp::CodonSiteTools::piNonSynonymous(), bpp::CodonSiteTools::piSynonymous(), and bpp::SiteContainerTools::removeGapSites().

◆ getFrequencies() [2/2]

void SymbolListTools::getFrequencies	(	const SymbolList &	list1,
		const SymbolList &	list2,
		std::map< int, std::map< int, double > > &	frequencies,
		bool	resolveUnknowns = `false`
	)
throw	(	DimensionException
	)

staticinherited

Get all state pairs frequencies for two lists of the same size..

Author: J. Dutheil

Parameters

list1	The first list.
list2	The second list.
resolveUnknowns	Tell is unknown characters must be resolved. For instance, in DNA, N will be counted as A=1/4,T=1/4,C=1/4,G=1/4.
frequencies	The output map with all state pairs and corresponding frequencies. Existing frequencies will be erased if any.

Definition at line 107 of file SymbolListTools.cpp.

◆ getGCContent()

double SymbolListTools::getGCContent	(	const SymbolList &	list,
		bool	ignoreUnresolved = `true`,
		bool	ignoreGap = `true`
	)
throw	(	AlphabetException
	)

staticinherited

Get the GC content of a symbol list.

Parameters

list The list.

Returns: The proportion of G and C states in the list.

Parameters

ignoreUnresolved	Do not count unresolved states. Otherwise, weight by each state probability in case of ambiguity (e.g. the R state counts for 0.5).
ignoreGap	Do not count gaps in total.

Exceptions

AlphabetException If the list is not made of nucleotide states.

Definition at line 119 of file SymbolListTools.cpp.

◆ getInvert()

Sequence * SequenceTools::getInvert ( const Sequence & 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).

Parameters

sequence The sequence to inverse.

Returns: A new sequence object containing the inverted sequence.

Author: Sylvain Gaillard

Definition at line 198 of file SequenceTools.cpp.

References bpp::Sequence::clone().

◆ getNumberOfCompleteSites()

size_t SequenceTools::getNumberOfCompleteSites ( const Sequence & seq )

static

Returns: The number of complete sites in the sequences, i.e. all positions without gaps and unresolved states (generic characters).

Parameters

seq	The sequence to analyse.

Definition at line 293 of file SequenceTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::Alphabet::isGap(), bpp::Alphabet::isUnresolved(), and bpp::SymbolList::size().

◆ getNumberOfDistinctPositions()

size_t SymbolListTools::getNumberOfDistinctPositions	(	const SymbolList &	l1,
		const SymbolList &	l2
	)
throw	(	AlphabetMismatchException
	)

staticinherited

Get the number of distinct positions.

The comparison in achieved from position 0 to the minimum size of the two vectors.

Parameters

l1	SymbolList 1.
l2	SymbolList 2.

Returns: The number of distinct positions.

Exceptions

AlphabetMismatchException if the two lists have not the same alphabet type.

Definition at line 158 of file SymbolListTools.cpp.

◆ getNumberOfPositionsWithoutGap()

size_t SymbolListTools::getNumberOfPositionsWithoutGap	(	const SymbolList &	l1,
		const SymbolList &	l2
	)
throw	(	AlphabetMismatchException
	)

staticinherited

Get the number of positions without gap.

The comparison in achieved from position 0 to the minimum size of the two vectors.

Parameters

l1	SymbolList 1.
l2	SymbolList 2.

Returns: The number of positions without gap.

Exceptions

AlphabetMismatchException if the two lists have not the same alphabet type.

Definition at line 169 of file SymbolListTools.cpp.

◆ getNumberOfSites()

size_t SequenceTools::getNumberOfSites ( const Sequence & seq )

static

Returns: The number of sites in the sequences, i.e. all positions without gaps.

Parameters

seq	The sequence to analyse.

Definition at line 279 of file SequenceTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::Alphabet::isGap(), and bpp::SymbolList::size().

◆ getNumberOfUnresolvedSites()

size_t SequenceTools::getNumberOfUnresolvedSites ( const Sequence & seq )

static

Returns: The number of unresolved sites in the sequence.

Parameters

seq	The sequence to analyse.

Author: Sylvain Gaillard

Definition at line 323 of file SequenceTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::Alphabet::isUnresolved(), and bpp::SymbolList::size().

◆ getPercentIdentity()

double SequenceTools::getPercentIdentity	(	const Sequence &	seq1,
		const Sequence &	seq2,
		bool	ignoreGaps = `false`
	)
throw	(	AlphabetMismatchException,
		SequenceNotAlignedException
	)

static

Returns: The identity percent of 2 sequence. One match is counted if the two sequences have identical states.

Parameters

seq1	The first sequence.
seq2	The second sequence.
ignoreGaps	If true, only positions without gaps will be used for the counting.

Exceptions

AlphabetMismatchException	If the two sequences do not have the same alphabet.
SequenceNotAlignedException	If the two sequences do not have the same length.

Definition at line 245 of file SequenceTools.cpp.

◆ getPutativeHaplotypes()

void SequenceTools::getPutativeHaplotypes	(	const Sequence &	seq,
		std::vector< Sequence *> &	hap,
		unsigned int	level = `2`
	)

static

Get all putatives haplotypes from an heterozygous sequence.

Parameters

seq	The sequence to resolve
hap	The vector to fill with the new sequences
level	The maximum number of states that a generic char must code (if this number is higher than level, the state will not be resolved). For instance if level = 3 and Alphabet is DNA, all generic char will be resolved but N.

Author: Sylvain Gaillard

Definition at line 463 of file SequenceTools.cpp.

References bpp::SymbolList::addElement(), bpp::Alphabet::getAlias(), bpp::SymbolList::getAlphabet(), bpp::Alphabet::getGapCharacterCode(), bpp::Sequence::getName(), bpp::Sequence::setName(), and bpp::SymbolList::size().

◆ getRandomSequence()

Sequence * SequenceTools::getRandomSequence	(	const Alphabet *	alphabet,
		size_t	length
	)

static

Get a random sequence of given size and alphabet, with all state with equal probability.

Parameters

alphabet	The alphabet to use.
length	The length of the sequence to generate.

Returns: A pointer toward a new Sequence object.

Definition at line 716 of file SequenceTools.cpp.

References bpp::Alphabet::getSize().

◆ getSequenceWithCompleteSites()

Sequence * SequenceTools::getSequenceWithCompleteSites ( const Sequence & seq )

static

keep only complete sites in a sequence.

The deleteElement method of the Sequence object will be used where appropriate.

Parameters

seq	The sequence to analyse.

Definition at line 307 of file SequenceTools.cpp.

References bpp::Sequence::clone(), bpp::SymbolList::getAlphabet(), bpp::Alphabet::isGap(), bpp::Alphabet::isUnresolved(), bpp::Sequence::setContent(), and bpp::SymbolList::size().

◆ getSequenceWithoutGaps()

Sequence * SequenceTools::getSequenceWithoutGaps ( const Sequence & seq )

static

Get a copy of the sequence without gaps.

A whole new sequence will be created by adding all non-gap positions. The original sequence will be cloned to serve as a template.

Parameters

seq	The sequence to analyse.

Returns: A new sequence object without gaps.

Definition at line 337 of file SequenceTools.cpp.

References bpp::Sequence::clone(), bpp::SymbolList::getAlphabet(), bpp::Alphabet::isGap(), bpp::Sequence::setContent(), and bpp::SymbolList::size().

◆ getSequenceWithoutStops()

Sequence * SequenceTools::getSequenceWithoutStops	(	const Sequence &	seq,
		const GeneticCode &	gCode
	)
throw	(	Exception
	)

static

Get a copy of the codon sequence without stops.

A whole new sequence will be created by adding all non-stop positions. The original sequence will be cloned to serve as a template.

Parameters

seq	The sequence to analyse.
gCode	The genetic code according to which stop codons are specified.

Returns: A new sequence object without stops.

Exceptions

Exception if the input sequence does not have a codon alphabet.

Definition at line 365 of file SequenceTools.cpp.

References bpp::Sequence::setContent().

◆ invert()

Sequence & SequenceTools::invert ( Sequence & seq )

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).

Parameters

seq	The sequence to inverse.

Returns: A ref toward the sequence.

Author: Sylvain Gaillard

Definition at line 181 of file SequenceTools.cpp.

References bpp::SymbolList::getValue(), bpp::SymbolList::setElement(), and bpp::SymbolList::size().

◆ invertComplement()

Sequence & SequenceTools::invertComplement ( Sequence & seq )

static

Inverse and complement a sequence.

This methode is more accurate than calling invert and complement separatly.

Parameters

seq	The sequence to inverse and complement.

Returns: A ref toward the sequence.

Author: Sylvain Gaillard

Definition at line 207 of file SequenceTools.cpp.

References bpp::SymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), bpp::SymbolList::getValue(), bpp::SymbolList::setElement(), bpp::SymbolList::size(), and bpp::NucleicAcidsReplication::translate().

◆ removeGaps()

void SequenceTools::removeGaps ( Sequence & seq )

static

Remove gaps from a sequence.

The deleteElement method of the Sequence object will be used where appropriate.

Parameters

seq	The sequence to analyse.

Definition at line 353 of file SequenceTools.cpp.

References bpp::SymbolList::deleteElement(), bpp::SymbolList::getAlphabet(), bpp::Alphabet::isGap(), and bpp::SymbolList::size().

Referenced by bpp::SiteContainerTools::alignNW().

◆ removeStops()

void SequenceTools::removeStops	(	Sequence &	seq,
		const GeneticCode &	gCode
	)
throw	(	Exception
	)

static

Remove stops from a codon sequence.

The deleteElement method of the Sequence object will be used where appropriate.

Parameters

seq	The sequence to analyse.
gCode	The genetic code according to which stop codons are specified.

Exceptions

Exception if the input sequence does not have a codon alphabet.

Definition at line 383 of file SequenceTools.cpp.

◆ replaceStopsWithGaps()

void SequenceTools::replaceStopsWithGaps	(	Sequence &	seq,
		const GeneticCode &	gCode
	)
throw	(	Exception
	)

static

Replace stop codons by gaps.

The setElement method of the Sequence object will be used where appropriate.

Parameters

seq	The sequence to analyse.
gCode	The genetic code according to which stop codons are specified.

Exceptions

Exception if the input sequence does not have a codon alphabet.

Definition at line 397 of file SequenceTools.cpp.

References bpp::AbstractAlphabet::getGapCharacterCode().

◆ reverseTranscript()

Sequence * SequenceTools::reverseTranscript	(	const Sequence &	sequence	)
throw	(	AlphabetException
	)

static

Get the reverse-transcription sequence of a RNA sequence.

Translate RNA sequence into DNA sequence.

See also: DNAReplication

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

Parameters

sequence The sequence to reverse-transcript.

Exceptions

AlphabetException If the sequence is not a RNA sequence.

Definition at line 168 of file SequenceTools.cpp.

◆ RNYslice() [1/2]

Sequence * SequenceTools::RNYslice	(	const Sequence &	sequence,
		int	ph
	)
throw	(	AlphabetException
	)

static

Get the RNY decomposition of a DNA sequence; with a given phase between 1 and 3, it gives the decomposition in this phase; in phase 1, the first triplet is centered on the first character. Without a phase the function gives the alternative succession in phases 1, 2 and 3.

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

Parameters

sequence	The sequence to transcript.
ph	The phase to use (1,2 or 3).

Exceptions

AlphabetException If the sequence is not a DNA sequence.

Author: Laurent Guéguen

Definition at line 575 of file SequenceTools.cpp.

Referenced by bpp::SequenceApplicationTools::getSiteContainer().

◆ RNYslice() [2/2]

Sequence * SequenceTools::RNYslice	(	const Sequence &	sequence	)
throw	(	AlphabetException
	)

static

Definition at line 617 of file SequenceTools.cpp.

◆ subseq()

Sequence * SequenceTools::subseq	(	const Sequence &	sequence,
		size_t	begin,
		size_t	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 sequence object with the given subsequence.

Exceptions

IndexOutOfBoundsException,Exception In case of bad indices.

Definition at line 68 of file SequenceTools.cpp.

Referenced by bpp::GeneticCode::getCodingSequence().

◆ subtractHaplotype()

Sequence * SequenceTools::subtractHaplotype	(	const Sequence &	s,
		const Sequence &	h,
		std::string	name = `""`,
		unsigned int	level = `1`
	)
throw	(	SequenceNotAlignedException
	)

static

Subtract haplotype from an heterozygous sequence.

Subtract an haplotype (i.e. a fully resolved sequence) from an heterozygous sequence to get the other haplotype. The new haplotype could be an unresolved sequence if unresolved characters in the sequence code for more than 2 states.

For example:

>heterozygous sequence
ATTCGGGKWTATRYRM
>haplotype
ATTCGGGTATATGCAA
>subtracted haplotype
ATTCGGGGTTATATGC

Parameters

s	The heterozygous sequence.
h	The haplotype to subtract.
name	The name of the new computed haplotype.
level	The number of states from which the site is set to fully unresolved.

Exceptions

SequenceNotAlignedException if s and h don't have the same size.

Author: Sylvain Gaillard

Definition at line 541 of file SequenceTools.cpp.

References bpp::Alphabet::getAlias(), bpp::Alphabet::getGeneric(), bpp::Alphabet::getName(), bpp::Alphabet::getUnknownCharacterCode(), bpp::Alphabet::intToChar(), and bpp::Alphabet::isUnresolved().

◆ transcript()

Sequence * SequenceTools::transcript	(	const Sequence &	sequence	)
throw	(	AlphabetException
	)

static

Get the transcription sequence of a DNA sequence.

Translate DNA sequence into RNA sequence.

See also: DNAReplication

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

Parameters

sequence The sequence to transcript.

Exceptions

AlphabetException If the sequence is not a DNA sequence.

Definition at line 155 of file SequenceTools.cpp.

Member Data Documentation

◆ _DNA

DNA SequenceTools::_DNA

staticprivate

Definition at line 101 of file SequenceTools.h.

◆ _DNARep

NucleicAcidsReplication bpp::SequenceTools::_DNARep

staticprivate

Definition at line 104 of file SequenceTools.h.

◆ _RNA

RNA SequenceTools::_RNA

staticprivate

Definition at line 102 of file SequenceTools.h.

◆ _RNARep

NucleicAcidsReplication bpp::SequenceTools::_RNARep

staticprivate

Definition at line 105 of file SequenceTools.h.

◆ _RNY

RNY SequenceTools::_RNY

staticprivate

Definition at line 103 of file SequenceTools.h.

◆ _transc

NucleicAcidsReplication bpp::SequenceTools::_transc

staticprivate

Definition at line 106 of file SequenceTools.h.

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

Bpp/Seq/SequenceTools.h
Bpp/Seq/SequenceTools.cpp

Public Member Functions

Static Public Member Functions

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SequenceTools()

◆ ~SequenceTools()

Member Function Documentation

◆ bowkerTest()

◆ changeGapsToUnknownCharacters()

◆ changeUnresolvedCharactersToGaps()

◆ combineSequences()

◆ complement()

◆ concatenate()

◆ findFirstOf()

◆ getCDS()

◆ getComplement()

◆ getCounts() [1/4]

◆ getCounts() [2/4]

◆ getCounts() [3/4]

◆ getCounts() [4/4]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getGCContent()

◆ getInvert()

◆ getNumberOfCompleteSites()

◆ getNumberOfDistinctPositions()

◆ getNumberOfPositionsWithoutGap()

◆ getNumberOfSites()

◆ getNumberOfUnresolvedSites()

◆ getPercentIdentity()

◆ getPutativeHaplotypes()

◆ getRandomSequence()

◆ getSequenceWithCompleteSites()

◆ getSequenceWithoutGaps()

◆ getSequenceWithoutStops()

◆ invert()

◆ invertComplement()

◆ removeGaps()

◆ removeStops()

◆ replaceStopsWithGaps()

◆ reverseTranscript()

◆ RNYslice() [1/2]

◆ RNYslice() [2/2]

◆ subseq()

◆ subtractHaplotype()

◆ transcript()

Member Data Documentation

◆ _DNA

◆ _DNARep

◆ _RNA

◆ _RNARep

◆ _RNY

◆ _transc