bpp-phyl3  3.0.0
SubstitutionRegister.h File Reference
#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

 bpp
 Defines the basic types of data flow nodes.