A Matrix class to store phylogenetic distances. More...

#include <Bpp/Seq/DistanceMatrix.h>

Inheritance diagram for bpp::DistanceMatrix:

Collaboration diagram for bpp::DistanceMatrix:

Public Member Functions
	DistanceMatrix (const std::vector< std::string > &names)
	Build a new distance matrix with specified names. More...

	DistanceMatrix (size_t n)
	Build a new distance matrix with specified size. More...

virtual	~DistanceMatrix ()

	DistanceMatrix (const DistanceMatrix &dist)

DistanceMatrix &	operator= (const DistanceMatrix &dist)

void	reset ()
	Reset the distance matrix: all distances are set to 0. More...

size_t	size () const

const std::vector< std::string > &	getNames () const

const std::string &	getName (size_t i) const throw (IndexOutOfBoundsException)

void	setName (size_t i, const std::string &name) throw (IndexOutOfBoundsException)
	Set the ith name. More...

void	setNames (const std::vector< std::string > &names) throw (DimensionException)
	Set the names associated to the matrix. More...

size_t	getNameIndex (const std::string &name) const throw (Exception)
	Get the index of a given name. More...

void	resize (size_t n)
	Change the dimension of the matrix. More...

virtual const double &	operator() (const std::string &iName, const std::string &jName) const throw (Exception)
	Access by name. More...

virtual double &	operator() (const std::string &iName, const std::string &jName) throw (Exception)
	Access by name. More...

virtual const double &	operator() (size_t i, size_t j) const

virtual double &	operator() (size_t i, size_t j)

RowMatrix *	clone () const

size_t	getNumberOfRows () const

size_t	getNumberOfColumns () const

std::vector< double >	row (size_t i) const

std::vector< double >	col (size_t j) const

void	resize (size_t nRows, size_t nCols)

void	addRow (const std::vector< double > &newRow)

virtual bool	equals (const Matrix &m, double threshold=NumConstants::TINY())

Private Attributes
std::vector< std::string >	names_

Detailed Description

A Matrix class to store phylogenetic distances.

Definition at line 55 of file DistanceMatrix.h.

Constructor & Destructor Documentation

bpp::DistanceMatrix::DistanceMatrix ( const std::vector< std::string > & names )

inline

Build a new distance matrix with specified names.

The dimension of the matrix will be equal to the number of names

Parameters

names The names to use.

Definition at line 71 of file DistanceMatrix.h.

References reset().

bpp::DistanceMatrix::DistanceMatrix ( size_t n )

inline

Build a new distance matrix with specified size.

Row names will be named 'Taxon 0', 'Taxon 1', and so on.

Parameters

n	The size of the matrix.

Definition at line 84 of file DistanceMatrix.h.

References resize().

virtual bpp::DistanceMatrix::~DistanceMatrix ( )

inlinevirtual

Definition at line 90 of file DistanceMatrix.h.

bpp::DistanceMatrix::DistanceMatrix ( const DistanceMatrix & dist )

inline

Definition at line 92 of file DistanceMatrix.h.

Member Function Documentation

void bpp::RowMatrix< double >::addRow ( const std::vector< double > & newRow )

inherited

RowMatrix * bpp::RowMatrix< double >::clone ( ) const

virtualinherited

Implements bpp::Clonable.

std::vector< double > bpp::RowMatrix< double >::col ( size_t j ) const

virtualinherited

Implements bpp::Matrix< Scalar >.

const std::string& bpp::DistanceMatrix::getName ( size_t i ) const throw (IndexOutOfBoundsException)

inline

Returns: The ith name.

Parameters

i	Name index.

Exceptions

IndexOutOfBoundsException If i is not a valid index.

Definition at line 141 of file DistanceMatrix.h.

References names_, size(), and size().

size_t DistanceMatrix::getNameIndex ( const std::string & name ) const throw (Exception)

Get the index of a given name.

Parameters

name	The name to look for.

Returns: The position of the name.

Exceptions

Exception If no names are attached to this matrix, or if the name was not found.

Definition at line 45 of file DistanceMatrix.cpp.

Referenced by operator()(), operator()(), operator()(), and operator()().

const std::vector<std::string>& bpp::DistanceMatrix::getNames ( ) const

inline

Returns: The names associated to the matrix.

Definition at line 134 of file DistanceMatrix.h.

References names_.

size_t bpp::RowMatrix< double >::getNumberOfColumns ( ) const

virtualinherited

Implements bpp::Matrix< Scalar >.

size_t bpp::RowMatrix< double >::getNumberOfRows ( ) const

virtualinherited

Implements bpp::Matrix< Scalar >.

virtual const double& bpp::DistanceMatrix::operator()	(	const std::string &	iName,
		const std::string &	jName
	)		const throw (Exception)

inlinevirtual

Access by name.

Parameters

iName	Name 1 (row)
jName	Name 2 (column)

Returns: A reference toward the specified distance.

Exceptions

Exception if the matrix has no name of if one of the name do not match existing names.

Definition at line 202 of file DistanceMatrix.h.

References getNameIndex(), and getNameIndex().

Referenced by operator()(), operator=(), and reset().

virtual double& bpp::DistanceMatrix::operator()	(	const std::string &	iName,
		const std::string &	jName
	)		throw (Exception)

inlinevirtual

Access by name.

Parameters

iName	Name 1 (row)
jName	Name 2 (column)

Returns: A reference toward the specified distance.

Exceptions

Exception if the matrix has no name of if one of the name do not match existing names.

Definition at line 217 of file DistanceMatrix.h.

References getNameIndex(), getNameIndex(), and operator()().

virtual const double& bpp::DistanceMatrix::operator()	(	size_t	i,
		size_t	j
	)		const

inlinevirtual

Implements bpp::Matrix< Scalar >.

Definition at line 224 of file DistanceMatrix.h.

References bpp::RowMatrix< Scalar >::operator()().

virtual double& bpp::DistanceMatrix::operator()	(	size_t	i,
		size_t	j
	)

inlinevirtual

Implements bpp::Matrix< Scalar >.

Definition at line 228 of file DistanceMatrix.h.

References bpp::RowMatrix< Scalar >::operator()().

DistanceMatrix& bpp::DistanceMatrix::operator= ( const DistanceMatrix & dist )

inline

Definition at line 94 of file DistanceMatrix.h.

References names_, names_, operator()(), resize(), and size().

void bpp::DistanceMatrix::reset ( )

inline

Reset the distance matrix: all distances are set to 0.

Definition at line 114 of file DistanceMatrix.h.

References operator()(), and size().

Referenced by DistanceMatrix(), and resize().

void bpp::RowMatrix< double >::resize	(	size_t	nRows,
		size_t	nCols
	)

virtualinherited

Implements bpp::Matrix< Scalar >.

void bpp::DistanceMatrix::resize ( size_t n )

inline

Change the dimension of the matrix.

Parameters

n	the new dimension of the matrix.

Definition at line 186 of file DistanceMatrix.h.

References names_, names_, reset(), bpp::RowMatrix< Scalar >::resize(), and bpp::TextTools::toString().

Referenced by DistanceMatrix(), and operator=().

std::vector< double > bpp::RowMatrix< double >::row ( size_t i ) const

virtualinherited

Implements bpp::Matrix< Scalar >.

void bpp::DistanceMatrix::setName	(	size_t	i,
		const std::string &	name
	)		throw (IndexOutOfBoundsException)

inline

Set the ith name.

Parameters

i	Name index.
name	The new name.

Exceptions

IndexOutOfBoundsException If i is not a valid index.

Definition at line 154 of file DistanceMatrix.h.

References names_, size(), and size().

void bpp::DistanceMatrix::setNames ( const std::vector< std::string > & names ) throw (DimensionException)

inline

Set the names associated to the matrix.

Parameters

names Matrix names.

Exceptions

DimensionException If 'names' have not the same size as the matrix.

Definition at line 166 of file DistanceMatrix.h.

References names_, names_, and names_.

size_t bpp::DistanceMatrix::size ( ) const

inline

Returns: The dimension of the matrix.

Definition at line 129 of file DistanceMatrix.h.

References names_.

Referenced by getName(), getName(), operator=(), reset(), setName(), and setName().

Member Data Documentation

std::vector<std::string> bpp::DistanceMatrix::names_

private

Definition at line 60 of file DistanceMatrix.h.

Referenced by getName(), getNames(), operator=(), operator=(), resize(), resize(), setName(), setNames(), setNames(), setNames(), and size().

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

Bpp/Seq/DistanceMatrix.h
Bpp/Seq/DistanceMatrix.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation