#include "../Model/StateMap.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/ProteicAlphabet.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::SubstitutionRegisterInterface
	The SubstitutionRegister interface. More...

class	bpp::AbstractSubstitutionRegister

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::VectorOfSubstitutionRegisters
	Sets a Register based on a vector of Registers. The categories are intersection of categories of those Registers. 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::TsTvSubstitutionRegister
	Distinguishes transitions from transversions. More...

class	bpp::SWSubstitutionRegister
	Distinguishes substitutions given the link between the changed nucleotides : S for strong (GC) and W for weak (AT). More...

class	bpp::DnDsSubstitutionRegister
	Distinguishes synonymous from non-synonymous substitutions. More...

class	bpp::KrKcSubstitutionRegister
	Count conservative and radical amino-acid substitutions. More...

Namespaces
namespace	bpp
	Defines the basic types of data flow nodes.

Classes

Namespaces