bpp::IOTreepuzzlePairedSiteLikelihoods Class Reference

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

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

Inheritance diagram for bpp::IOTreepuzzlePairedSiteLikelihoods:

Collaboration diagram for bpp::IOTreepuzzlePairedSiteLikelihoods:

Static Public Member Functions
static PairedSiteLikelihoods	read (std::istream &is) throw (Exception)
	Read paired-site likelihoods from a Treepuzzle/RAxML-formatted stream. More...
static PairedSiteLikelihoods	read (const std::string &path) throw (Exception)
	Read paired-site likelihoods from a Treepuzzle/RAxML-formatted file. More...
static void	write (const PairedSiteLikelihoods &psl, std::ostream &os, const std::string &delim="\)
	Write paired-site likelihoods to a stream. More...
static void	write (const PairedSiteLikelihoods &psl, const std::string &path, const std::string &delim="\)
	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 68 of file IoPairedSiteLikelihoods.h.

Member Function Documentation

read() [1/2]

PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::read ( std::istream &  is ) throw ( Exception )

static

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

Exceptions

Exception

If the format is not recognized.

Definition at line 56 of file IoPairedSiteLikelihoods.cpp.

read() [2/2]

PairedSiteLikelihoods IOTreepuzzlePairedSiteLikelihoods::read ( const std::string &  path ) throw ( Exception )

static

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

Exceptions

Exception

If the format is not recognized.

Definition at line 131 of file IoPairedSiteLikelihoods.cpp.

write() [1/2]

void IOTreepuzzlePairedSiteLikelihoods::write ( 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 defaut is a tab but two spaces might be used.

Definition at line 141 of file IoPairedSiteLikelihoods.cpp.

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

write() [2/2]

void IOTreepuzzlePairedSiteLikelihoods::write ( 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 defaut is a tab but two spaces might be used.)

Definition at line 220 of file IoPairedSiteLikelihoods.cpp.

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

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