MafStatistics.h File Reference

#include "MafBlock.h"
#include <Bpp/Utils/MapTools.h>
#include <Bpp/Numeric/VectorTools.h>
#include <Bpp/Numeric/Number.h>
#include <map>
#include <string>

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Classes
class	bpp::MafStatisticsResult
	General interface for storing statistical results. More...
class	bpp::SimpleMafStatisticsResult
	A simple maf statistics result, with only one value. More...
class	bpp::MafStatistics
	General interface for computing statistics based on a Maf block. More...
class	bpp::AbstractMafStatistics
	Partial implementation of MafStatistics, for convenience. More...
class	bpp::AbstractMafStatisticsSimple
	Partial implementation of MafStatistics, for convenience. More...
class	bpp::PairwiseDivergenceMafStatistics
	Computes the pairwise divergence for a pair of sequences in a maf block. More...
class	bpp::BlockSizeMafStatistics
	Computes the number of sequences in a maf block. More...
class	bpp::BlockLengthMafStatistics
	Computes the number of columns in a maf block. More...
class	bpp::SequenceLengthMafStatistics
	Retrieve the sequence length (number of nucleotides) for a given species in a maf block. More...
class	bpp::AlignmentScoreMafStatistics
	Retrieves the alignment score of a maf block. More...
class	bpp::AbstractSpeciesSelectionMafStatistics
	Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner. More...
class	bpp::AbstractSpeciesMultipleSelectionMafStatistics
	Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner. More...
class	bpp::CharacterCountsMafStatistics
	Compute the base frequencies of a maf block. More...
class	bpp::SiteFrequencySpectrumMafStatistics
	Compute the Site Frequency Spectrum of a maf block. More...
class	bpp::SiteFrequencySpectrumMafStatistics::Categorizer
class	bpp::FourSpeciesPatternCountsMafStatistics
	Compute the frequency of site patterns for a quadruplet of species. More...
class	bpp::SiteMafStatistics
	Compute a few site statistics in a maf block. More...
class	bpp::PolymorphismMafStatistics
	Counts number of polymorphic / fixed sites in two populations. More...
class	bpp::SequenceDiversityMafStatistics
	Provide estimates of sequence diversity. More...

Namespaces
	bpp