bpp::PhylipDistanceMatrixFormat Class Reference

Distance matrix I/O in Phylip format. More...

#include <Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h>

Inheritance diagram for bpp::PhylipDistanceMatrixFormat:

Collaboration diagram for bpp::PhylipDistanceMatrixFormat:

Public Member Functions
	PhylipDistanceMatrixFormat (bool extended=false)
virtual	~PhylipDistanceMatrixFormat ()
const std::string	getFormatName () const
const std::string	getFormatDescription () const
DistanceMatrix *	read (const std::string &path) const throw (Exception)
	Read a distance matrix from a file. More...
DistanceMatrix *	read (std::istream &in) const throw (Exception)
	Read a distance matrix from a stream. More...
void	write (const DistanceMatrix &dist, const std::string &path, bool overwrite=true) const throw (Exception)
	Write a distance matrix to a file. More...
void	write (const DistanceMatrix &dist, std::ostream &out) const throw (Exception)
	Write a distance matrix to a stream. More...
virtual const std::string	getDataType () const

Private Attributes
bool	extended_

Detailed Description

Distance matrix I/O in Phylip format.

Entry names must be 10 characters long. If 'extended' is set to true, then entry names can be of any size, and should be separated from the data by at least two spaces. Names should therefor not contian more than one consecutive space.

Definition at line 55 of file PhylipDistanceMatrixFormat.h.

Constructor & Destructor Documentation

PhylipDistanceMatrixFormat()

bpp::PhylipDistanceMatrixFormat::PhylipDistanceMatrixFormat ( bool  extended = false )

inline

Definition at line 63 of file PhylipDistanceMatrixFormat.h.

~PhylipDistanceMatrixFormat()

virtual bpp::PhylipDistanceMatrixFormat::~PhylipDistanceMatrixFormat ( )

inlinevirtual

Definition at line 64 of file PhylipDistanceMatrixFormat.h.

Member Function Documentation

getDataType()

virtual const std::string bpp::IODistanceMatrix::getDataType ( ) const

inlinevirtualinherited

Definition at line 65 of file IoDistanceMatrix.h.

getFormatDescription()

const std::string bpp::PhylipDistanceMatrixFormat::getFormatDescription ( ) const

inline

Definition at line 69 of file PhylipDistanceMatrixFormat.h.

getFormatName()

const std::string bpp::PhylipDistanceMatrixFormat::getFormatName ( ) const

inline

Definition at line 67 of file PhylipDistanceMatrixFormat.h.

read() [1/2]

DistanceMatrix* bpp::PhylipDistanceMatrixFormat::read ( const std::string &  path ) const throw ( Exception )

inlinevirtual

Read a distance matrix from a file.

Parameters

path	The file path.

Returns

A new distance matrix object.

Exceptions

Exception

If an error occured.

Reimplemented from bpp::AbstractIDistanceMatrix.

Definition at line 70 of file PhylipDistanceMatrixFormat.h.

References bpp::AbstractIDistanceMatrix::read().

read() [2/2]

DistanceMatrix * PhylipDistanceMatrixFormat::read ( std::istream &  in ) const throw ( Exception )

virtual

Read a distance matrix from a stream.

Parameters

in	The input stream.

Returns

A new distance matrix object.

Exceptions

Exception

If an error occured.

Implements bpp::AbstractIDistanceMatrix.

Definition at line 56 of file PhylipDistanceMatrixFormat.cpp.

write() [1/2]

void bpp::PhylipDistanceMatrixFormat::write ( const DistanceMatrix &  dist, const std::string &  path, bool  overwrite = true  ) const throw ( Exception )

inlinevirtual

Write a distance matrix to a file.

Parameters

dist	A distance matrix object.
path	The file path.
overwrite	Tell if existing file must be overwritten. Otherwise append to the file.

Exceptions

Exception

If an error occured.

Reimplemented from bpp::AbstractODistanceMatrix.

Definition at line 76 of file PhylipDistanceMatrixFormat.h.

References bpp::AbstractODistanceMatrix::write().

write() [2/2]

void PhylipDistanceMatrixFormat::write ( const DistanceMatrix &  dist, std::ostream &  out  ) const throw ( Exception )

virtual

Write a distance matrix to a stream.

Parameters

dist	A distance matrix object.
out	The output stream.

Exceptions

Exception

If an error occured.

Implements bpp::AbstractODistanceMatrix.

Definition at line 96 of file PhylipDistanceMatrixFormat.cpp.

Member Data Documentation

extended_

bool bpp::PhylipDistanceMatrixFormat::extended_

private

Definition at line 60 of file PhylipDistanceMatrixFormat.h.

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

• Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h
• Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp