Utilitary methods dealing with sites. More...

#include <Bpp/Seq/SiteTools.h>

Inheritance diagram for bpp::SiteTools:

Collaboration diagram for bpp::SiteTools:

Public Member Functions
	SiteTools ()
virtual	~SiteTools ()
Static Public Member Functions
static bool	hasGap (const Site &site)
static bool	isGapOnly (const Site &site)
static bool	isGapOrUnresolvedOnly (const Site &site)
static bool	hasUnknown (const Site &site)
static bool	hasStopCodon (const Site &site)
static bool	isComplete (const Site &site)
static bool	isConstant (const Site &site, bool ignoreUnknown=false, bool unresolvedRaisesException=true) throw (EmptySiteException)
	Tell if a site is constant, that is displaying the same state in all sequences that do not present a gap.
static bool	areSitesIdentical (const Site &site1, const Site &site2)
static double	variabilityShannon (const Site &site, bool resolveUnknowns) throw (EmptySiteException)
	Compute the Shannon entropy index of a site.
static double	variabilityFactorial (const Site &site) throw (EmptySiteException)
	Compute the factorial diversity index of a site.
static double	mutualInformation (const Site &site1, const Site &site2, bool resolveUnknowns) throw (DimensionException,EmptySiteException)
	Compute the mutual information between two sites.
static double	entropy (const Site &site, bool resolveUnknowns) throw (EmptySiteException)
	Compute the entropy of a site. This is an alias of method variabilityShannon.
static double	jointEntropy (const Site &site1, const Site &site2, bool resolveUnknowns) throw (DimensionException,EmptySiteException)
	Compute the joint entropy between two sites.
static double	heterozygosity (const Site &site) throw (EmptySiteException)
	Compute the heterozygosity index of a site.
static size_t	getNumberOfDistinctCharacters (const Site &site) throw (EmptySiteException)
	Give the number of distinct characters at a site.
static bool	hasSingleton (const Site &site) throw (EmptySiteException)
	Tell if a site has singletons.
static bool	isParsimonyInformativeSite (const Site &site) throw (EmptySiteException)
	Tell if a site is a parsimony informative site.
static bool	isTriplet (const Site &site) throw (EmptySiteException)
	Tell if a site has more than 2 distinct characters.
static void	getCounts (const SymbolList &list, std::map< int, size_t > &counts)
	Count all states in the list.
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.
static void	getCounts (const SymbolList &list, std::map< int, double > &counts, bool resolveUnknowns)
	Count all states in the list, optionaly resolving unknown characters.
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.
static void	getFrequencies (const SymbolList &list, std::map< int, double > &frequencies, bool resolveUnknowns=false)
	Get all states frequencies in the list.
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..
static double	getGCContent (const SymbolList &list, bool ignoreUnresolved=true, bool ignoreGap=true) throw (AlphabetException)
	Get the GC content of a symbol list.
static size_t	getNumberOfDistinctPositions (const SymbolList &l1, const SymbolList &l2) throw (AlphabetMismatchException)
	Get the number of distinct positions.
static size_t	getNumberOfPositionsWithoutGap (const SymbolList &l1, const SymbolList &l2) throw (AlphabetMismatchException)
	Get the number of positions without gap.
static void	changeGapsToUnknownCharacters (SymbolList &l)
	Change all gap elements to unknown characters.
static void	changeUnresolvedCharactersToGaps (SymbolList &l)
	Change all unknown characters to gap elements.

Detailed Description

Utilitary methods dealing with sites.

Definition at line 57 of file SiteTools.h.

Constructor & Destructor Documentation

bpp::SiteTools::SiteTools ( ) [inline]

Definition at line 61 of file SiteTools.h.

virtual bpp::SiteTools::~SiteTools ( ) [inline, virtual]

Definition at line 62 of file SiteTools.h.

Member Function Documentation

bool SiteTools::areSitesIdentical	(	const Site &	site1,
		const Site &	site2
	)		`[static]`

Parameters:

site1	The first site.
site2	The second site.

Returns:: True if the two states have the same content (and, of course, alphabet).

Definition at line 137 of file SiteTools.cpp.

References bpp::BasicSymbolList::getAlphabet(), bpp::Alphabet::getAlphabetType(), and bpp::BasicSymbolList::size().

void SymbolListTools::changeGapsToUnknownCharacters ( SymbolList & l ) [static, inherited]

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().

void SymbolListTools::changeUnresolvedCharactersToGaps ( SymbolList & l ) [static, inherited]

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().

static double bpp::SiteTools::entropy	(	const Site &	site,
		bool	resolveUnknowns
	)		throw (EmptySiteException) `[inline, static]`

Compute the entropy of a site. This is an alias of method variabilityShannon.

$I = - \sum_x f_x\cdot \ln(f_x)$

where $f_x$ is the frequency of state $x$ .

Author:: J. Dutheil

Parameters:

site	A site.
resolveUnknowns	Tell is unknown characters must be resolved.

Returns:: The Shannon entropy index of this site.

Exceptions:

EmptySiteException If the site has size 0.

Definition at line 183 of file SiteTools.h.

References variabilityShannon().

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

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

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

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.

References bpp::SymbolList::size().

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

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().

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

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.

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

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().

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

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.

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

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.

size_t SiteTools::getNumberOfDistinctCharacters ( const Site & site ) throw (EmptySiteException) [static]

Give the number of distinct characters at a site.

Parameters:

site a Site

Returns:: The number of distinct characters in the given site.

Definition at line 349 of file SiteTools.cpp.

References bpp::SymbolListTools::getCounts(), and isConstant().

Referenced by isTriplet(), and bpp::CodonSiteTools::numberOfSubsitutions().

size_t SymbolListTools::getNumberOfDistinctPositions	(	const SymbolList &	l1,
		const SymbolList &	l2
	)		throw (AlphabetMismatchException) `[static, inherited]`

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.

size_t SymbolListTools::getNumberOfPositionsWithoutGap	(	const SymbolList &	l1,
		const SymbolList &	l2
	)		throw (AlphabetMismatchException) `[static, inherited]`

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.

bool SiteTools::hasGap ( const Site & site ) [static]

Parameters:

site A site.

Returns:: True if the site contains one or several gap(s).

Definition at line 56 of file SiteTools.cpp.

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

Referenced by bpp::NoGapSiteContainerIterator::nextSiteWithoutGapPosition(), bpp::CodonSiteTools::numberOfNonSynonymousSubstitutions(), bpp::CodonSiteTools::numberOfSubsitutions(), and bpp::NoGapSiteContainerIterator::previousSiteWithoutGapPosition().

bool SiteTools::hasSingleton ( const Site & site ) throw (EmptySiteException) [static]

Tell if a site has singletons.

Parameters:

site a Site.

Returns:: True if the site has singletons.

Definition at line 370 of file SiteTools.cpp.

References isConstant().

bool SiteTools::hasStopCodon ( const Site & site ) [static]

Parameters:

site A site.

Returns:: True if the site contains a Stop Codon, when the alphabet is a CodonAlphabet.

Definition at line 108 of file SiteTools.cpp.

References bpp::BasicSymbolList::getAlphabet(), bpp::CodonAlphabet::isStop(), and bpp::BasicSymbolList::size().

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

bool SiteTools::hasUnknown ( const Site & site ) [static]

Parameters:

site A site.

Returns:: True if the site contains one or several unknwn characters.

Definition at line 95 of file SiteTools.cpp.

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

double SiteTools::heterozygosity ( const Site & site ) throw (EmptySiteException) [static]

Compute the heterozygosity index of a site.

$H = 1 - \sum_x f_x^2$

where $f_x$ is the frequency of state $x$ .

Parameters:

site A site.

Returns:: The heterozygosity index of this site.

Exceptions:

EmptySiteException If the site has size 0.

Definition at line 335 of file SiteTools.cpp.

References bpp::MapTools::getValues().

bool SiteTools::isComplete ( const Site & site ) [static]

Parameters:

site A site.

Returns:: True if the site contains no gap and no unknown characters.

Definition at line 124 of file SiteTools.cpp.

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

Referenced by bpp::CompleteSiteContainerIterator::nextCompleteSitePosition(), and bpp::CompleteSiteContainerIterator::previousCompleteSitePosition().

bool SiteTools::isConstant	(	const Site &	site,
		bool	ignoreUnknown = `false`,
		bool	unresolvedRaisesException = `true`
	)		throw (EmptySiteException) `[static]`

Tell if a site is constant, that is displaying the same state in all sequences that do not present a gap.

Parameters:

site	A site.
ignoreUnknown	If true, positions with unknown positions will be ignored. Otherwise, a site with one single state + any uncertain state will not be considered as constant.
unresolvedRaisesException	In case of ambiguous case (gap only site for instance), throw an exception. Otherwise returns false.

Returns:: True if the site is made of only one state.

Exceptions:

EmptySiteException If the site has size 0 or if the site cannot be resolved (for instance is made of gaps only) and unresolvedRaisesException is set to true.

Definition at line 157 of file SiteTools.cpp.

bool SiteTools::isGapOnly ( const Site & site ) [static]

Parameters:

site A site.

Returns:: True if the site contains only gaps.

Definition at line 69 of file SiteTools.cpp.

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

Referenced by bpp::SiteContainerTools::removeGapOnlySites(), and bpp::SiteContainerTools::removeGapOrUnresolvedOnlySites().

bool SiteTools::isGapOrUnresolvedOnly ( const Site & site ) [static]

Parameters:

site A site.

Returns:: True if the site contains only gaps.

Definition at line 82 of file SiteTools.cpp.

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

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

bool SiteTools::isParsimonyInformativeSite ( const Site & site ) throw (EmptySiteException) [static]

Tell if a site is a parsimony informative site.

At least two distinct characters must be present.

Parameters:

site a Site.

Returns:: True if the site is parsimony informative.

Definition at line 390 of file SiteTools.cpp.

References bpp::SymbolListTools::getCounts(), and isConstant().

bool SiteTools::isTriplet ( const Site & site ) throw (EmptySiteException) [static]

Tell if a site has more than 2 distinct characters.

Parameters:

site a Site.

Returns:: True if the site has more than 2 distinct characters

Definition at line 413 of file SiteTools.cpp.

References getNumberOfDistinctCharacters().

double SiteTools::jointEntropy	(	const Site &	site1,
		const Site &	site2,
		bool	resolveUnknowns
	)		throw (DimensionException,EmptySiteException) `[static]`

Compute the joint entropy between two sites.

$H_{i,j} = - \sum_x \sum_y p_{x,y}\ln\left(p_{x,y}\right)$

where $p_{x,y}$ is the frequency of the pair $(x,y)$ .

Author:: J. Dutheil

Parameters:

site1	First site
site2	Second site
resolveUnknowns	Tell is unknown characters must be resolved.

Returns:: The mutual information for the pair of sites.

Exceptions:

DimensionException	If the sites do not have the same length.
EmptySiteException	If the sites have size 0.

Definition at line 285 of file SiteTools.cpp.

double SiteTools::mutualInformation	(	const Site &	site1,
		const Site &	site2,
		bool	resolveUnknowns
	)		throw (DimensionException,EmptySiteException) `[static]`