bpp::UserAlphabetIndex2 Class Reference

Alphabet index given by user. More...

#include <Bpp/Seq/AlphabetIndex/UserAlphabetIndex2.h>

Inheritance diagram for bpp::UserAlphabetIndex2:

Collaboration diagram for bpp::UserAlphabetIndex2:

Public Member Functions
	UserAlphabetIndex2 (std::shared_ptr< const Alphabet > alph, const Matrix< double > &mat)
	UserAlphabetIndex2 (const UserAlphabetIndex2 &uAlph)
UserAlphabetIndex2 &	operator= (const UserAlphabetIndex2 &uAlph)
virtual	~UserAlphabetIndex2 ()
UserAlphabetIndex2 *	clone () const
double	getIndex (int state1, int state2) const
	Get the index associated to a pair of states. More...
double	getIndex (const std::string &state1, const std::string &state2) const
	Get the index associated to a pair of states. More...
void	setIndexMatrix (const Matrix< double > &mat)
LinearMatrix< double > *	getIndexMatrix () const
std::shared_ptr< const Alphabet >	getAlphabet () const
	Get the alphabet associated to this index. More...
const Alphabet &	alphabet () const
	Get the alphabet associated to this index. More...
virtual bool	isSymmetric () const

Private Attributes
std::shared_ptr< const Alphabet >	alph_
LinearMatrix< double >	index_
bool	sym_

Detailed Description

Alphabet index given by user.

Definition at line 21 of file UserAlphabetIndex2.h.

Constructor & Destructor Documentation

UserAlphabetIndex2() [1/2]

bpp::UserAlphabetIndex2::UserAlphabetIndex2 ( std::shared_ptr< const Alphabet >  alph, const Matrix< double > &  mat  )

inline

Definition at line 30 of file UserAlphabetIndex2.h.

References index_, bpp::MatrixTools::isSymmetric(), and sym_.

Referenced by clone().

UserAlphabetIndex2() [2/2]

bpp::UserAlphabetIndex2::UserAlphabetIndex2 ( const UserAlphabetIndex2 &  uAlph )

inline

Definition at line 38 of file UserAlphabetIndex2.h.

~UserAlphabetIndex2()

virtual bpp::UserAlphabetIndex2::~UserAlphabetIndex2 ( )

inlinevirtual

Definition at line 53 of file UserAlphabetIndex2.h.

Member Function Documentation

alphabet()

const Alphabet& bpp::UserAlphabetIndex2::alphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 78 of file UserAlphabetIndex2.h.

References alph_.

clone()

UserAlphabetIndex2* bpp::UserAlphabetIndex2::clone ( ) const

inlinevirtual

Implements bpp::AlphabetIndex2.

Definition at line 55 of file UserAlphabetIndex2.h.

References UserAlphabetIndex2().

getAlphabet()

std::shared_ptr<const Alphabet> bpp::UserAlphabetIndex2::getAlphabet ( ) const

inlinevirtual

Get the alphabet associated to this index.

Returns

Alphabet The alphabet associated to this index.

Implements bpp::AlphabetIndex2.

Definition at line 76 of file UserAlphabetIndex2.h.

References alph_.

getIndex() [1/2]

double bpp::UserAlphabetIndex2::getIndex ( const std::string &  state1, const std::string &  state2  ) const

inlinevirtual

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 63 of file UserAlphabetIndex2.h.

References alph_, and index_.

getIndex() [2/2]

double bpp::UserAlphabetIndex2::getIndex ( int  state1, int  state2  ) const

inlinevirtual

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 58 of file UserAlphabetIndex2.h.

References alph_, and index_.

getIndexMatrix()

LinearMatrix<double>* bpp::UserAlphabetIndex2::getIndexMatrix ( ) const

inlinevirtual

Returns

A matrix object with all indices.

Implements bpp::AlphabetIndex2.

Definition at line 74 of file UserAlphabetIndex2.h.

References index_.

isSymmetric()

virtual bool bpp::UserAlphabetIndex2::isSymmetric ( ) const

inlinevirtual

Returns

True if the index is symatric (that is, index(i,j) == index(j, i)).

Implements bpp::AlphabetIndex2.

Definition at line 83 of file UserAlphabetIndex2.h.

References sym_.

operator=()

UserAlphabetIndex2& bpp::UserAlphabetIndex2::operator= ( const UserAlphabetIndex2 &  uAlph )

inline

Definition at line 44 of file UserAlphabetIndex2.h.

References alph_, index_, and sym_.

setIndexMatrix()

void bpp::UserAlphabetIndex2::setIndexMatrix ( const Matrix< double > &  mat )

inline

Definition at line 68 of file UserAlphabetIndex2.h.

References index_, bpp::MatrixTools::isSymmetric(), and sym_.

Member Data Documentation

alph_

std::shared_ptr<const Alphabet> bpp::UserAlphabetIndex2::alph_

private

Definition at line 25 of file UserAlphabetIndex2.h.

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

index_

LinearMatrix<double> bpp::UserAlphabetIndex2::index_

private

Definition at line 26 of file UserAlphabetIndex2.h.

Referenced by getIndex(), getIndexMatrix(), operator=(), setIndexMatrix(), and UserAlphabetIndex2().

sym_

bool bpp::UserAlphabetIndex2::sym_

private

Definition at line 27 of file UserAlphabetIndex2.h.

Referenced by isSymmetric(), operator=(), setIndexMatrix(), and UserAlphabetIndex2().

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

• Bpp/Seq/AlphabetIndex/UserAlphabetIndex2.h