bpp::IOTreepuzzlePairedSiteLikelihoods Class Reference

This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format. More...

#include <Bpp/Phyl/Legacy/Io/IoPairedSiteLikelihoods.h>

Inheritance diagram for bpp::IOTreepuzzlePairedSiteLikelihoods:

Collaboration diagram for bpp::IOTreepuzzlePairedSiteLikelihoods:

Public Member Functions
virtual const std::string	getDataType () const=0
virtual const std::string	getFormatName () const=0
virtual const std::string	getFormatDescription () const=0

Static Public Member Functions
static PairedSiteLikelihoods	readPairedSiteLikelihoods (std::istream &is)
	Read paired-site likelihoods from a Treepuzzle/RAxML-formatted stream. More...
static PairedSiteLikelihoods	readPairedSiteLikelihoods (const std::string &path)
	Read paired-site likelihoods from a Treepuzzle/RAxML-formatted file. More...
static void	writePairedSiteLikelihoods (const PairedSiteLikelihoods &psl, std::ostream &os, const std::string &delim="\t")
	Write paired-site likelihoods to a stream. More...
static void	writePairedSiteLikelihoods (const PairedSiteLikelihoods &psl, const std::string &path, const std::string &delim="\t")
	Write paired-site likelihoods to a file. More...

Detailed Description

This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format.

Author

Nicolas Rochette

Definition at line 34 of file IoPairedSiteLikelihoods.h.

Member Function Documentation

readPairedSiteLikelihoods() [1/2]

PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::readPairedSiteLikelihoods ( const std::string &  path )

static

Read paired-site likelihoods from a Treepuzzle/RAxML-formatted file.

Exceptions

Exception

If the format is not recognized.

Definition at line 96 of file IoPairedSiteLikelihoods.cpp.

References readPairedSiteLikelihoods().

readPairedSiteLikelihoods() [2/2]

PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::readPairedSiteLikelihoods ( std::istream &  is )

static

Read paired-site likelihoods from a Treepuzzle/RAxML-formatted stream.

Exceptions

Exception

If the format is not recognized.

Definition at line 21 of file IoPairedSiteLikelihoods.cpp.

References bpp::TextTools::removeSurroundingWhiteSpaces().

Referenced by readPairedSiteLikelihoods().

writePairedSiteLikelihoods() [1/2]

void IOTreepuzzlePairedSiteLikelihoods::writePairedSiteLikelihoods ( const PairedSiteLikelihoods &  psl, const std::string &  path, const std::string &  delim = "\t"  )

static

Write paired-site likelihoods to a file.

Parameters

psl	The PairedSiteLikelihoods object to write.
path	The path of the output file.
delim	The delimiter between model names and likelihoods. (The default is a tab but two spaces might be used.)

Definition at line 185 of file IoPairedSiteLikelihoods.cpp.

References writePairedSiteLikelihoods().

writePairedSiteLikelihoods() [2/2]

void IOTreepuzzlePairedSiteLikelihoods::writePairedSiteLikelihoods ( const PairedSiteLikelihoods &  psl, std::ostream &  os, const std::string &  delim = "\t"  )

static

Write paired-site likelihoods to a stream.

Parameters

psl	The PairedSiteLikelihoods object to write.
os	The output stream.
delim	The delimiter between model names and likelihoods. The default is a tab but two spaces might be used.

Definition at line 106 of file IoPairedSiteLikelihoods.cpp.

References bpp::PairedSiteLikelihoods::getLikelihoods(), bpp::PairedSiteLikelihoods::getModelNames(), bpp::PairedSiteLikelihoods::getNumberOfModels(), and bpp::PairedSiteLikelihoods::getNumberOfSites().

Referenced by writePairedSiteLikelihoods().

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

• Bpp/Phyl/Legacy/Io/IoPairedSiteLikelihoods.h
• Bpp/Phyl/Legacy/Io/IoPairedSiteLikelihoods.cpp