SubstitutionRegister.h File Reference

#include "../Model/SubstitutionModel.h"
#include "../Model/Nucleotide/NucleotideSubstitutionModel.h"
#include "../Model/Codon/CodonSubstitutionModel.h"
#include <Bpp/Clonable.h>
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/Text/StringTokenizer.h>
#include <Bpp/Seq/Alphabet/NucleicAlphabet.h>
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
#include <vector>
#include <string>
#include <algorithm>

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Classes
class	bpp::SubstitutionRegister
	The SubstitutionRegister interface. More...
class	bpp::AbstractSubstitutionRegister
class	bpp::CategorySubstitutionRegister
	Gather states into defined categories, and count the changes between categories. More...
class	bpp::TotalSubstitutionRegister
	Count all substitutions. More...
class	bpp::CompleteSubstitutionRegister
	Completion of a given substitution register to consider all substitutions. The new substitutions are considered in an additional type. More...
class	bpp::ComprehensiveSubstitutionRegister
	Distinguishes all types of substitutions. More...
class	bpp::GeneralSubstitutionRegister
	Sets a Register based on a matrix of integers. If M is the matrix, M[i,j] is the number of the substitution type from i to j, or 0 if there is no substitution type from i to j. More...
class	bpp::SelectedSubstitutionRegister
	Class inheriting from GeneralSubstitutionRegister, this one uses a special constructor which allows it to build a substitution matrix from string input specifying a desired substitutions. More...
class	bpp::AAInteriorSubstitutionRegister
	Indexes only intra amino-acid substitutions. Every group represents a substitutions for the same amino acid. Met and Trp are not taken into account due their non-degenerescence. More...
class	bpp::AAExteriorSubstitutionRegister
	Indexes only substitutions between amino-acids. Groups are distinguished by their direction. More...
class	bpp::GCSubstitutionRegister
	Distinguishes AT<->GC from GC<->AT. More...
class	bpp::TsTvSubstitutionRegister
	Distinguishes transitions from transversions. More...
class	bpp::DnDsSubstitutionRegister
	Distinguishes synonymous from non-synonymous substitutions. More...
class	bpp::GCSynonymousSubstitutionRegister
	Distinguishes AT->GC vs GC->AT inside synonymous substitutions on third codon position. More...

Namespaces
	bpp