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 (std::shared_ptr< const StateMapInterface > stateMap, 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 override
	Get the substitution type far a given pair of model states. More...

size_t	getNumberOfSubstitutionTypes () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

const std::string &	getName () const override
	Get the name of the register. More...

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...

std::shared_ptr< const StateMapInterface >	stateMap_

std::string	name_

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 484 of file SubstitutionRegister.h.

Constructor & Destructor Documentation

◆ SelectedSubstitutionRegister()

bpp::SelectedSubstitutionRegister::SelectedSubstitutionRegister	(	std::shared_ptr< const StateMapInterface >	stateMap,
		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 490 of file SubstitutionRegister.h.

References bpp::StateMapInterface::alphabet(), categoryNames_, bpp::Alphabet::getStateIndex(), bpp::StringTokenizer::hasMoreToken(), bpp::GeneralSubstitutionRegister::matrix_, bpp::StringTokenizer::nextToken(), bpp::StringTokenizer::numberOfRemainingTokens(), bpp::AbstractSubstitutionRegister::stateMap(), bpp::TextTools::toString(), and bpp::GeneralSubstitutionRegister::updateTypes_().

Referenced by clone().

◆ ~SelectedSubstitutionRegister()

bpp::SelectedSubstitutionRegister::~SelectedSubstitutionRegister ( )

inline

Definition at line 540 of file SubstitutionRegister.h.

Member Function Documentation

◆ alphabet()

const Alphabet& bpp::AbstractSubstitutionRegister::alphabet ( ) const

inlineoverridevirtualinherited

Returns: The alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 133 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

◆ clone()

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

inlinevirtual

Reimplemented from bpp::GeneralSubstitutionRegister.

Definition at line 538 of file SubstitutionRegister.h.

References SelectedSubstitutionRegister().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractSubstitutionRegister::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr toward the alphabet associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 135 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

◆ getName()

const std::string& bpp::AbstractSubstitutionRegister::getName ( ) const

inlineoverridevirtualinherited

Get the name of the register.

Returns: A string describing the register.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 137 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::name_.

◆ getNumberOfSubstitutionTypes()

size_t bpp::GeneralSubstitutionRegister::getNumberOfSubstitutionTypes ( ) const

inlineoverridevirtualinherited

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

Implements bpp::SubstitutionRegisterInterface.

Definition at line 456 of file SubstitutionRegister.h.

References bpp::GeneralSubstitutionRegister::types_.

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractSubstitutionRegister::getStateMap ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr toward the state map associated to this instance.

Implements bpp::SubstitutionRegisterInterface.

Definition at line 131 of file SubstitutionRegister.h.

References bpp::AbstractSubstitutionRegister::stateMap_.

◆ getType()

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

inlineoverridevirtualinherited

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::SubstitutionRegisterInterface.

Definition at line 451 of file SubstitutionRegister.h.

References bpp::GeneralSubstitutionRegister::matrix_.