Simple Substitution Matrix, with match and mismatch penalties. More...

#include <Bpp/Seq/AlphabetIndex/SimpleScore.h>

Inheritance diagram for bpp::SimpleScore:

Collaboration diagram for bpp::SimpleScore:

Public Member Functions
	SimpleScore (const Alphabet *alphabet, double match, double mismatch)
	Build a new simpleScore object. More...

	SimpleScore (const SimpleScore &sc)

SimpleScore &	operator= (const SimpleScore &sc)

virtual	~SimpleScore ()

SimpleScore *	clone () const override

Methods from the AlphabetIndex2 interface.
double	getIndex (int state1, int state2) const override
	Get the index associated to a pair of states. More...

double	getIndex (const std::string &state1, const std::string &state2) const override
	Get the index associated to a pair of states. More...

std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to this index. More...

const Alphabet &	alphabet () const override
	Get the alphabet associated to this index. More...

const Matrix< double > &	getIndexMatrix () const override

bool	isSymmetric () const override

Private Attributes
LinearMatrix< double >	distanceMatrix_

std::shared_ptr< const Alphabet >	alphabet_

Detailed Description

Simple Substitution Matrix, with match and mismatch penalties.

Definition at line 23 of file SimpleScore.h.

Constructor & Destructor Documentation

◆ SimpleScore() [1/2]

SimpleScore::SimpleScore	(	const Alphabet *	alphabet,
		double	match,
		double	mismatch
	)

Build a new simpleScore object.

Parameters

alphabet	The alphabet to use.
match	Matching score.
mismatch	Mismatching penalty.

Definition at line 14 of file SimpleScore.cpp.

References alphabet_, and distanceMatrix_.

Referenced by clone().

◆ SimpleScore() [2/2]

bpp::SimpleScore::SimpleScore ( const SimpleScore & sc )

inline

Definition at line 40 of file SimpleScore.h.

◆ ~SimpleScore()

virtual bpp::SimpleScore::~SimpleScore ( )

inlinevirtual

Definition at line 52 of file SimpleScore.h.

Member Function Documentation

◆ alphabet()

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

inlineoverridevirtual

Get the alphabet associated to this index.

Returns: Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 65 of file SimpleScore.h.

References alphabet_.

◆ clone()

SimpleScore* bpp::SimpleScore::clone ( ) const

inlineoverridevirtual

Implements bpp::AlphabetIndex2.

Definition at line 54 of file SimpleScore.h.

References SimpleScore().

◆ getAlphabet()

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

inlineoverridevirtual

Get the alphabet associated to this index.

Returns: Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 64 of file SimpleScore.h.

References alphabet_.

◆ getIndex() [1/2]

double SimpleScore::getIndex	(	const std::string &	state1,
		const std::string &	state2
	)		const

overridevirtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a string value.
state2	Second state to consider, as a string value.

Returns: The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 36 of file SimpleScore.cpp.

References alphabet_, and distanceMatrix_.

◆ getIndex() [2/2]

double SimpleScore::getIndex	(	int	state1,
		int	state2
	)		const

overridevirtual

Get the index associated to a pair of states.

Parameters

state1	First state to consider, as a int value in the Alphabet
state2	Second state to consider, as a int value in the Alphabet

Returns: The index associated to the pair of states.

Implements bpp::AlphabetIndex2.

Definition at line 29 of file SimpleScore.cpp.

References alphabet_, and distanceMatrix_.

◆ getIndexMatrix()

const Matrix<double>& bpp::SimpleScore::getIndexMatrix ( ) const

inlineoverridevirtual

Returns: A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 66 of file SimpleScore.h.

References distanceMatrix_.

◆ isSymmetric()

bool bpp::SimpleScore::isSymmetric ( ) const

inlineoverridevirtual

Returns: True if the index is symetric (that is, index(i,j) == index(j, i)).

Implements bpp::AlphabetIndex2.

Definition at line 67 of file SimpleScore.h.

◆ operator=()

SimpleScore& bpp::SimpleScore::operator= ( const SimpleScore & sc )

inline

Definition at line 45 of file SimpleScore.h.

References alphabet_, and distanceMatrix_.

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::SimpleScore::alphabet_

private

Definition at line 28 of file SimpleScore.h.

Referenced by alphabet(), getAlphabet(), getIndex(), operator=(), and SimpleScore().

◆ distanceMatrix_

LinearMatrix<double> bpp::SimpleScore::distanceMatrix_

private

Definition at line 27 of file SimpleScore.h.

Referenced by getIndex(), getIndexMatrix(), operator=(), and SimpleScore().

The documentation for this class was generated from the following files:

Bpp/Seq/AlphabetIndex/SimpleScore.h
Bpp/Seq/AlphabetIndex/SimpleScore.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SimpleScore() [1/2]

◆ SimpleScore() [2/2]

◆ ~SimpleScore()

Member Function Documentation

◆ alphabet()

◆ clone()

◆ getAlphabet()

◆ getIndex() [1/2]

◆ getIndex() [2/2]

◆ getIndexMatrix()

◆ isSymmetric()

◆ operator=()

Member Data Documentation

◆ alphabet_

◆ distanceMatrix_