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...

#include <Bpp/Phyl/Mapping/SubstitutionRegister.h>

Inheritance diagram for bpp::SelectedSubstitutionRegister:

Collaboration diagram for bpp::SelectedSubstitutionRegister:

Public Member Functions
	SelectedSubstitutionRegister (const SubstitutionModel *model, std::string selectedSubstitutions)

SelectedSubstitutionRegister *	clone () const

	~SelectedSubstitutionRegister ()

std::string	getTypeName (size_t type) const
	names of the types are their number. More...

size_t	getType (size_t i, size_t j) const
	Get the substitution type far a given pair of model states. More...

size_t	getNumberOfSubstitutionTypes () const

const SubstitutionModel *	getSubstitutionModel () const

const Alphabet *	getAlphabet () const

Protected Member Functions
void	updateTypes_ ()

Protected Attributes
size_t	size_
	The size of the matrix, i.e. the number of states. More...

RowMatrix< size_t >	matrix_
	The matrix of the substitution register. More...

std::map< size_t, std::map< size_t, std::vector< size_t > > >	types_
	The map from substitution types to the map of from states to the vector of target states. More...

const SubstitutionModel *	model_

Private Attributes
std::map< size_t, std::string >	categoryNames_

Detailed Description

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.

Author: Juraj Michalik

Definition at line 573 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ SelectedSubstitutionRegister()

bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister	(	const SubstitutionModel *	model,
		std::string	selectedSubstitutions
	)

inline

This constructor creates an empty square matrix (nrow = ncol = length of alphabet) and takes a string with specific syntax to mark a substitutions with a certain index depending on the string entered.

The same group of substitution is delimited by parentheses. The name, if entered, is entered at the start of a string and followed by ";". Substitutions are delimited by ",", and each substitution is defined with a "->" symbol.

Definition at line 579 of file SubstitutionRegister.h.

References categoryNames_, bpp::SubstitutionModel::getAlphabet(), bpp::GeneralSubstitutionRegister::matrix_, bpp::AbstractSubstitutionRegister::model_, and bpp::GeneralSubstitutionRegister::updateTypes_().

Referenced by clone().

◆ ~SelectedSubstitutionRegister()

bpp::SelectedSubstitutionRegister::~SelectedSubstitutionRegister ( )

inline

Definition at line 629 of file SubstitutionRegister.h.

Member Function Documentation

◆ clone()

SelectedSubstitutionRegister* bpp::SelectedSubstitutionRegister::clone ( ) const

inlinevirtual

Reimplemented from bpp::GeneralSubstitutionRegister.

Definition at line 627 of file SubstitutionRegister.h.

References SelectedSubstitutionRegister().

◆ getAlphabet()

const Alphabet* bpp::AbstractSubstitutionRegister::getAlphabet ( ) const

inlinevirtualinherited

Returns: The alphabet associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 147 of file SubstitutionRegister.h.

References bpp::SubstitutionModel::getAlphabet(), and bpp::AbstractSubstitutionRegister::model_.

◆ getNumberOfSubstitutionTypes()

size_t bpp::GeneralSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlinevirtualinherited

Returns: The number of substitution types supported by this class.

Implements bpp::SubstitutionRegister.

Definition at line 544 of file SubstitutionRegister.h.

References bpp::GeneralSubstitutionRegister::types_.

◆ getSubstitutionModel()

const SubstitutionModel* bpp::AbstractSubstitutionRegister::getSubstitutionModel ( ) const

inlinevirtualinherited

Returns: The substitution model associated to this instance.

Implements bpp::SubstitutionRegister.

Definition at line 145 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::model_.

◆ getType()

size_t bpp::GeneralSubstitutionRegister::getType	(	size_t	fromState,
		size_t	toState
	)		const

inlinevirtualinherited

Get the substitution type far a given pair of model states.

Parameters

fromState	Initial state (should be a state supported by the specified alphabet).
toState	Final state (should be a state supported by the specified alphabet).

Returns: The index of the corresponding substitution type, ranging from 0 to 'getNumberOfSubstitutionTypes' + 1, as non-substitution (that is when fromState == toState) will always return 0.

Implements bpp::SubstitutionRegister.

Definition at line 539 of file SubstitutionRegister.h.

References bpp::GeneralSubstitutionRegister::matrix_.