Utilitary functions for codon sites. More...

#include <Bpp/Seq/CodonSiteTools.h>

Inheritance diagram for bpp::CodonSiteTools:

Collaboration diagram for bpp::CodonSiteTools:

Public Member Functions
	CodonSiteTools ()

virtual	~CodonSiteTools ()

Static Public Member Functions
static bool	hasGapOrStop (const Site &site, const GeneticCode &gCode) throw (AlphabetException)
	Method to know if a codon site contains gap(s) or stop codons. More...

static bool	hasStop (const Site &site, const GeneticCode &gCode) throw (AlphabetException)
	Method to know if a codon site contains stop codon or not. More...

static bool	isMonoSitePolymorphic (const Site &site) throw (AlphabetException, EmptySiteException)
	Method to know if a polymorphic codon site is polymorphic at only one site. More...

static bool	isSynonymousPolymorphic (const Site &site, const GeneticCode &gCode) throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
	Method to know if polymorphism at a codon site is synonymous. More...

static Site *	generateCodonSiteWithoutRareVariant (const Site &site, const GeneticCode &gCode, double freqmin) throw (AlphabetException, EmptySiteException)
	generate a codon site without rare variants More...

static size_t	numberOfDifferences (int i, int j, const CodonAlphabet &ca)
	Compute the number of differences between two codons. More...

static double	numberOfSynonymousDifferences (int i, int j, const GeneticCode &gCode, bool minchange=false)
	Compute the number of synonymous differences between two codons. More...

static double	piSynonymous (const Site &site, const GeneticCode &gCode, bool minchange=false) throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
	Compute the synonymous pi per codon site. More...

static double	piNonSynonymous (const Site &site, const GeneticCode &gCode, bool minchange=false) throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
	Compute the non-synonymous pi per codon site. More...

static double	numberOfSynonymousPositions (int i, const GeneticCode &gCode, double ratio=1.0) throw (Exception)
	Return the number of synonymous positions of a codon. More...

static double	meanNumberOfSynonymousPositions (const Site &site, const GeneticCode &gCode, double ratio=1) throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
	Return the mean number of synonymous positions per codon site. More...

static size_t	numberOfSubsitutions (const Site &site, const GeneticCode &gCode, double freqmin=0.) throw (AlphabetException, EmptySiteException)
	Return the number of subsitutions per codon site. More...

static size_t	numberOfNonSynonymousSubstitutions (const Site &site, const GeneticCode &gCode, double freqmin=0.) throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
	Return the number of Non Synonymous subsitutions per codon site. More...

static std::vector< size_t >	fixedDifferences (const Site &siteIn, const Site &siteOut, int i, int j, const GeneticCode &gCode) throw (AlphabetException, AlphabetMismatchException, EmptySiteException)
	Return a vector with the number of fixed synonymous and non-synonymous differences per codon site. More...

static bool	isFourFoldDegenerated (const Site &site, const GeneticCode &gCode)

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...

Detailed Description

Utilitary functions for codon sites.

Definition at line 60 of file CodonSiteTools.h.

Constructor & Destructor Documentation

◆ CodonSiteTools()

bpp::CodonSiteTools::CodonSiteTools ( )

inline

Definition at line 64 of file CodonSiteTools.h.

◆ ~CodonSiteTools()

virtual bpp::CodonSiteTools::~CodonSiteTools ( )

inlinevirtual

Definition at line 65 of file CodonSiteTools.h.

Member Function Documentation

◆ 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().

◆ fixedDifferences()

vector< size_t > CodonSiteTools::fixedDifferences	(	const Site &	siteIn,
		const Site &	siteOut,
		int	i,
		int	j,
		const GeneticCode &	gCode
	)
throw	(	AlphabetException,
		AlphabetMismatchException,
		EmptySiteException
	)

static

Return a vector with the number of fixed synonymous and non-synonymous differences per codon site.

Compute the number of synonymous and non-synonymous differences between the concensus codon of SiteIn (i) and SiteOut (j), which are fixed within each alignement. Example:

SiteIn
 ATT
 ATT
 ATC

SiteOut
 CTA
 CTA
 CTA

Here, the first position is non-synonymous different and fixed, the third position is synonymous different but not fixed (polymorphic in SiteIn). The return vector is thus [0,1]. In case of complex codon, the path that gives the minimum number of non-synonymous changes is chosen. The argument minchange=true is sent to numberOfSynonymousDifferences used in this method. Otherwise, a non-integer number could be return.

Rare variants (<= freqmin) can be excluded.

Parameters

siteIn	a Site
siteOut	a Site
i	an integer
j	an integer
gCode	a GeneticCode

Exceptions

AlphabetException	If the alphabet associated to one of the sites is not a codon alphabet.
AlphabetMismatchException	If the codon alphabet each the site do not match the codon alphabet of the genetic code.
EmptySiteException	If one of the sites has size 0.

Definition at line 682 of file CodonSiteTools.cpp.

References bpp::CodonAlphabet::getFirstPosition(), bpp::CodonAlphabet::getNucleicAlphabet(), bpp::CodonAlphabet::getSecondPosition(), bpp::CodonAlphabet::getThirdPosition(), bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

◆ generateCodonSiteWithoutRareVariant()

Site * CodonSiteTools::generateCodonSiteWithoutRareVariant	(	const Site &	site,
		const GeneticCode &	gCode,
		double	freqmin
	)
throw	(	AlphabetException,
		EmptySiteException
	)

static

generate a codon site without rare variants

Rare variants are replaced by the most frequent allele. This method is used to exclude rare variants in some analyses as in McDonald-Kreitman Test (McDonald & Kreitman, 1991, Nature 351 pp652-654). For an application, see for example (Fay et al. 2001, Genetics 158 pp 1227-1234).

Parameters

site	a Site
gCode	The genetic code according to which stop codons are specified.
freqmin	a double, allele in frequency stricly lower than freqmin are replaced

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
EmptySiteException	If the site has size 0.

Definition at line 158 of file CodonSiteTools.cpp.

References bpp::CodonAlphabet::getFirstPosition(), bpp::SymbolListTools::getFrequencies(), bpp::CodonAlphabet::getNucleicAlphabet(), bpp::CodonAlphabet::getSecondPosition(), bpp::CodonAlphabet::getThirdPosition(), bpp::BasicSymbolList::getValue(), bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

Referenced by numberOfSubsitutions().

◆ 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 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 generateCodonSiteWithoutRareVariant(), bpp::SiteContainerTools::getConsensus(), bpp::SequenceApplicationTools::getSitesToAnalyse(), meanNumberOfSynonymousPositions(), piNonSynonymous(), 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.

◆ 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.

◆ hasGapOrStop()

bool CodonSiteTools::hasGapOrStop	(	const Site &	site,
		const GeneticCode &	gCode
	)
throw	(	AlphabetException
	)

static

Method to know if a codon site contains gap(s) or stop codons.

Parameters

site	a Site
gCode	The genetic code according to which stop codons are specified.

Exceptions

AlphabetException If the alphabet associated to the site is not a codon alphabet.

Definition at line 60 of file CodonSiteTools.cpp.

References bpp::AlphabetTools::isCodonAlphabet().

◆ hasStop()

bool CodonSiteTools::hasStop	(	const Site &	site,
		const GeneticCode &	gCode
	)
throw	(	AlphabetException
	)

static

Method to know if a codon site contains stop codon or not.

Parameters

site	a Site
gCode	The genetic code according to which stop codons are specified.

Exceptions

AlphabetException If the alphabet associated to the site is not a codon alphabet.

Definition at line 75 of file CodonSiteTools.cpp.

References bpp::AlphabetTools::isCodonAlphabet().

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

◆ isFourFoldDegenerated()

bool CodonSiteTools::isFourFoldDegenerated	(	const Site &	site,
		const GeneticCode &	gCode
	)

static

Returns: True if all sequences have a fourfold degenerated codon in the site (that is, if a mutation in the fourth position does not change the aminoacid).

Author: Benoit Nabholz, Annabelle Haudry

Parameters

site	The site to analyze.
gCode	The genetic code to use.

If non-synonymous mutation

Definition at line 807 of file CodonSiteTools.cpp.

References bpp::BasicSymbolList::getValue(), bpp::SiteTools::isConstant(), bpp::GeneticCode::isFourFoldDegenerated(), isSynonymousPolymorphic(), and bpp::BasicSymbolList::size().

◆ isMonoSitePolymorphic()

bool CodonSiteTools::isMonoSitePolymorphic	(	const Site &	site	)
throw	(	AlphabetException,
		EmptySiteException
	)

static

Method to know if a polymorphic codon site is polymorphic at only one site.

Parameters

site a Site

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
EmptySiteException	If the site has size 0.

Definition at line 90 of file CodonSiteTools.cpp.

References bpp::CodonAlphabet::getFirstPosition(), bpp::CodonAlphabet::getNucleicAlphabet(), bpp::CodonAlphabet::getSecondPosition(), bpp::CodonAlphabet::getThirdPosition(), bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

◆ isSynonymousPolymorphic()

bool CodonSiteTools::isSynonymousPolymorphic	(	const Site &	site,
		const GeneticCode &	gCode
	)
throw	(	AlphabetException,
		AlphabetMismatchException,
		EmptySiteException
	)

static

Method to know if polymorphism at a codon site is synonymous.

Parameters

site	a Site
gCode	a GeneticCode

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
AlphabetMismatchException	If the codon alphabet of the site do not match the codon alphabet of the genetic code.
EmptySiteException	If the site has size 0.

Definition at line 128 of file CodonSiteTools.cpp.

References bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

Referenced by isFourFoldDegenerated().

◆ meanNumberOfSynonymousPositions()

double CodonSiteTools::meanNumberOfSynonymousPositions	(	const Site &	site,
		const GeneticCode &	gCode,
		double	ratio = `1`
	)
throw	(	AlphabetException,
		AlphabetMismatchException,
		EmptySiteException
	)

static

Return the mean number of synonymous positions per codon site.

A site is consider as x% synonymous if x% of the possible mutations are synonymous Transition/transversion ratio can be taken into account (use the variable ratio) The mean is computed over the VectorSite.

Unresolved and stop codons are counted as 0.

Parameters

site	a Site
gCode	a GeneticCode
ratio	a double Set by default to 1

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
AlphabetMismatchException	If the codon alphabet of the site do not match the codon alphabet of the genetic code.
EmptySiteException	If the site has size 0.

Definition at line 563 of file CodonSiteTools.cpp.

References bpp::SymbolListTools::getFrequencies(), and bpp::AlphabetTools::isCodonAlphabet().

◆ numberOfDifferences()

size_t CodonSiteTools::numberOfDifferences	(	int	i,
		int	j,
		const CodonAlphabet &	ca
	)

static

Compute the number of differences between two codons.

Parameters

i	a int
j	a int
ca	a CodonAlphabet

Definition at line 220 of file CodonSiteTools.cpp.

References bpp::CodonAlphabet::getFirstPosition(), bpp::CodonAlphabet::getSecondPosition(), and bpp::CodonAlphabet::getThirdPosition().

◆ numberOfNonSynonymousSubstitutions()

size_t CodonSiteTools::numberOfNonSynonymousSubstitutions	(	const Site &	site,
		const GeneticCode &	gCode,
		double	freqmin = `0.`
	)
throw	(	AlphabetException,
		AlphabetMismatchException,
		EmptySiteException
	)

static

Return the number of Non Synonymous subsitutions per codon site.

It is assumed that the path linking amino acids only involved one substitution by step.

Rare variants (<= freqmin) can be excluded. In case of complex codon, the path that gives the minimum number of non-synonymous changes is chosen. The argument minchange=true is sent to numberOfSynonymousDifferences used in this method. Otherwise, a non-integer number could be return.

Parameters

site	a Site
gCode	a GeneticCode
freqmin	a double To exclude snp in frequency strictly lower than freqmin (by default freqmin = 0).

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
AlphabetMismatchException	If the codon alphabet of the site do not match the codon alphabet of the genetic code.
EmptySiteException	If the site has size 0.

Definition at line 633 of file CodonSiteTools.cpp.

References bpp::SymbolListTools::getCounts(), bpp::SiteTools::hasGap(), bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

◆ numberOfSubsitutions()

size_t CodonSiteTools::numberOfSubsitutions	(	const Site &	site,
		const GeneticCode &	gCode,
		double	freqmin = `0.`
	)
throw	(	AlphabetException,
		EmptySiteException
	)

static

Return the number of subsitutions per codon site.

No recombination is assumed, that is in complex codon homoplasy is assumed. Example:

ATT
ATT
ATT
ATC
ATC
AGT
AGT
AGC

Here, 3 substitutions are counted. Assuming that the last codon (AGC) is a recombinant between ATC and AGT would have lead to counting only 2 subsitutions.

Rare variants (<= freqmin) can be excluded.

Parameters

site	a Site
gCode	a GeneticCode
freqmin	a double To exclude snp in frequency strictly lower than freqmin (by default freqmin = 0)

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
EmptySiteException	If the site has size 0.

Definition at line 588 of file CodonSiteTools.cpp.

References generateCodonSiteWithoutRareVariant(), bpp::CodonAlphabet::getFirstPosition(), bpp::CodonAlphabet::getNucleicAlphabet(), bpp::SiteTools::getNumberOfDistinctCharacters(), bpp::CodonAlphabet::getSecondPosition(), bpp::CodonAlphabet::getThirdPosition(), bpp::BasicSymbolList::getValue(), bpp::SiteTools::hasGap(), bpp::AlphabetTools::isCodonAlphabet(), bpp::SiteTools::isConstant(), and bpp::BasicSymbolList::size().

◆ numberOfSynonymousDifferences()

double CodonSiteTools::numberOfSynonymousDifferences	(	int	i,
		int	j,
		const GeneticCode &	gCode,
		bool	minchange = `false`
	)

static

Compute the number of synonymous differences between two codons.

For complex codon: If minchange = false (default option) the different paths are equally weighted. If minchange = true the path with the minimum number of non-synonymous change is chosen. Paths included stop codons are excluded.

Parameters

i	a int
j	a int
gCode	a GeneticCode
minchange	a boolean set by default to false

Definition at line 234 of file CodonSiteTools.cpp.

References bpp::GeneticCode::areSynonymous(), bpp::CodonAlphabet::getCodon(), bpp::WordAlphabet::getPositions(), bpp::GeneticCode::getSourceAlphabet(), and bpp::GeneticCode::isStop().

◆ numberOfSynonymousPositions()

double CodonSiteTools::numberOfSynonymousPositions	(	int	i,
		const GeneticCode &	gCode,
		double	ratio = `1.0`
	)
throw	(	Exception
	)

static

Return the number of synonymous positions of a codon.

A site is consider as x% synonymous if x% of the possible mutations are synonymous Transition/transversion ratio can be taken into account (use the variable ratio)

Unresolved codons and stop codon will return a value of 0.

Parameters

i	a int
gCode	a GeneticCode
ratio	a double set by default to 1

Definition at line 522 of file CodonSiteTools.cpp.

References bpp::CodonAlphabet::getCodon(), bpp::WordAlphabet::getPositions(), and bpp::WordAlphabet::isUnresolved().

◆ piNonSynonymous()

double CodonSiteTools::piNonSynonymous	(	const Site &	site,
		const GeneticCode &	gCode,
		bool	minchange = `false`
	)
throw	(	AlphabetException,
		AlphabetMismatchException,
		EmptySiteException
	)

static

Compute the non-synonymous pi per codon site.

The following formula is used:

$pi = frac{n}{n-1}\sum_{i,j}x_{i}x_{j}P_{ij}$

where n is the number of sequence, $x_i$ and $x_j$ the frequencies of each codon type occuring at the site $P_{i,j}$ the number of nonsynonymous difference between these codons. Be careful: here, pi is not normalized by the number of non-synonymous sites. If minchange = false (default option) the different paths are equally weighted. If minchange = true the path with the minimum number of non-synonymous change is chosen.

Parameters

site	a Site
gCode	a GeneticCode
minchange	a boolean set by default to false

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
AlphabetMismatchException	If the codon alphabet of the site do not match the codon alphabet of the genetic code.
EmptySiteException	If the site has size 0.

Definition at line 485 of file CodonSiteTools.cpp.

References bpp::SymbolListTools::getFrequencies(), bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

◆ piSynonymous()

double CodonSiteTools::piSynonymous	(	const Site &	site,
		const GeneticCode &	gCode,
		bool	minchange = `false`
	)
throw	(	AlphabetException,
		AlphabetMismatchException,
		EmptySiteException
	)

static

Compute the synonymous pi per codon site.

The following formula is used:

$pi = frac{n}{n-1}\sum_{i,j}x_{i}x_{j}P_{ij}$

where n is the number of sequence, $x_i$ and $x_j$ the frequencies of each codon type occuring at the site $P_{i,j}$ the number of synonymous difference between these codons. Be careful: here, pi is not normalized by the number of synonymous sites.

If minchange = false (default option) the different paths are equally weighted. If minchange = true the path with the minimum number of non-synonymous change is chosen.

Parameters

site	a Site
gCode	a GeneticCode
minchange	a boolean set by default to false

Exceptions

AlphabetException	If the alphabet associated to the site is not a codon alphabet.
AlphabetMismatchException	If the codon alphabet of the site do not match the codon alphabet of the genetic code.
EmptySiteException	If the site has size 0.

Definition at line 453 of file CodonSiteTools.cpp.

References bpp::SymbolListTools::getFrequencies(), bpp::AlphabetTools::isCodonAlphabet(), and bpp::SiteTools::isConstant().

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

Bpp/Seq/CodonSiteTools.h
Bpp/Seq/CodonSiteTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ CodonSiteTools()

◆ ~CodonSiteTools()

Member Function Documentation

◆ changeGapsToUnknownCharacters()

◆ changeUnresolvedCharactersToGaps()

◆ fixedDifferences()

◆ generateCodonSiteWithoutRareVariant()

◆ getCounts() [1/4]

◆ getCounts() [2/4]

◆ getCounts() [3/4]

◆ getCounts() [4/4]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getGCContent()

◆ getNumberOfDistinctPositions()

◆ getNumberOfPositionsWithoutGap()

◆ hasGapOrStop()

◆ hasStop()

◆ isFourFoldDegenerated()

◆ isMonoSitePolymorphic()

◆ isSynonymousPolymorphic()

◆ meanNumberOfSynonymousPositions()

◆ numberOfDifferences()

◆ numberOfNonSynonymousSubstitutions()

◆ numberOfSubsitutions()

◆ numberOfSynonymousDifferences()

◆ numberOfSynonymousPositions()

◆ piNonSynonymous()

◆ piSynonymous()