bpp::PhylipDistanceMatrixFormat Class Reference

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

#include <Bpp/Seq/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
std::unique_ptr< DistanceMatrix >	readDistanceMatrix (const std::string &path) const
	Read a distance matrix from a file. More...
std::unique_ptr< DistanceMatrix >	readDistanceMatrix (std::istream &in) const
	Read a distance matrix from a stream. More...
void	writeDistanceMatrix (const DistanceMatrix &dist, const std::string &path, bool overwrite=true) const
	Write a distance matrix to a file. More...
void	writeDistanceMatrix (const DistanceMatrix &dist, std::ostream &out) const
	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 therefore not contain more than one consecutive space.

Definition at line 20 of file PhylipDistanceMatrixFormat.h.

Constructor & Destructor Documentation

PhylipDistanceMatrixFormat()

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

inline

Definition at line 28 of file PhylipDistanceMatrixFormat.h.

~PhylipDistanceMatrixFormat()

virtual bpp::PhylipDistanceMatrixFormat::~PhylipDistanceMatrixFormat ( )

inlinevirtual

Definition at line 29 of file PhylipDistanceMatrixFormat.h.

Member Function Documentation

getDataType()

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

inlinevirtualinherited

Implements bpp::IOFormat.

Definition at line 28 of file IoDistanceMatrix.h.

getFormatDescription()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 34 of file PhylipDistanceMatrixFormat.h.

getFormatName()

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

inlinevirtual

Implements bpp::IOFormat.

Definition at line 32 of file PhylipDistanceMatrixFormat.h.

readDistanceMatrix() [1/2]

std::unique_ptr<DistanceMatrix> bpp::PhylipDistanceMatrixFormat::readDistanceMatrix ( const std::string &  path ) const

inlinevirtual

Read a distance matrix from a file.

Parameters

path	The file path.

Returns

A new distance matrix object.

Exceptions

Exception

If an error occurred.

Reimplemented from bpp::AbstractIDistanceMatrix.

Definition at line 36 of file PhylipDistanceMatrixFormat.h.

References bpp::AbstractIDistanceMatrix::readDistanceMatrix().

readDistanceMatrix() [2/2]

unique_ptr< DistanceMatrix > PhylipDistanceMatrixFormat::readDistanceMatrix ( std::istream &  in ) const

virtual

Read a distance matrix from a stream.

Parameters

in	The input stream.

Returns

A new distance matrix object.

Exceptions

Exception

If an error occurred.

Implements bpp::AbstractIDistanceMatrix.

Definition at line 21 of file PhylipDistanceMatrixFormat.cpp.

References bpp::FileTools::getNextLine(), bpp::StringTokenizer::hasMoreToken(), and bpp::StringTokenizer::nextToken().

writeDistanceMatrix() [1/2]

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

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 occurred.

Reimplemented from bpp::AbstractODistanceMatrix.

Definition at line 43 of file PhylipDistanceMatrixFormat.h.

References bpp::AbstractODistanceMatrix::writeDistanceMatrix().

writeDistanceMatrix() [2/2]

void PhylipDistanceMatrixFormat::writeDistanceMatrix ( const DistanceMatrix &  dist, std::ostream &  out  ) const

virtual

Write a distance matrix to a stream.

Parameters

dist	A distance matrix object.
out	The output stream.

Exceptions

Exception

If an error occurred.

Implements bpp::AbstractODistanceMatrix.

Definition at line 64 of file PhylipDistanceMatrixFormat.cpp.

References bpp::DistanceMatrix::getName(), bpp::TextTools::resizeRight(), and bpp::DistanceMatrix::size().

Member Data Documentation

extended_

bool bpp::PhylipDistanceMatrixFormat::extended_

private

Definition at line 25 of file PhylipDistanceMatrixFormat.h.

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

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