Utilitary functions dealing with both sites and sequences. More...

#include <Bpp/Seq/SymbolListTools.h>

Inheritance diagram for bpp::SymbolListTools:

Public Member Functions
	SymbolListTools ()

virtual	~SymbolListTools ()

Static Public Member Functions
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 dealing with both sites and sequences.

Definition at line 56 of file SymbolListTools.h.

Constructor & Destructor Documentation

◆ SymbolListTools()

bpp::SymbolListTools::SymbolListTools ( )

inline

Definition at line 59 of file SymbolListTools.h.

◆ ~SymbolListTools()

virtual bpp::SymbolListTools::~SymbolListTools ( )

inlinevirtual

Definition at line 60 of file SymbolListTools.h.

Member Function Documentation

◆ changeGapsToUnknownCharacters()

void SymbolListTools::changeGapsToUnknownCharacters ( SymbolList & l )

static

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 )

static

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().

◆ getCounts() [1/4]

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

inlinestatic

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
	)

inlinestatic

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
	)

static

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
	)

static

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`
	)

static

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
	)

static

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
	)

static

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
	)

static

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
	)

static

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.

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

Bpp/Seq/SymbolListTools.h
Bpp/Seq/SymbolListTools.cpp

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ SymbolListTools()

◆ ~SymbolListTools()

Member Function Documentation

◆ changeGapsToUnknownCharacters()

◆ changeUnresolvedCharactersToGaps()

◆ getCounts() [1/4]

◆ getCounts() [2/4]

◆ getCounts() [3/4]

◆ getCounts() [4/4]

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getGCContent()

◆ getNumberOfDistinctPositions()

◆ getNumberOfPositionsWithoutGap()