bpp::RewardMappingTools Class Reference

Provide methods to compute reward mappings. More...

#include <Bpp/Phyl/Mapping/RewardMappingTools.h>

Public Member Functions
	RewardMappingTools ()
virtual	~RewardMappingTools ()

Static Public Member Functions
static ProbabilisticRewardMapping *	computeRewardVectors (const DRTreeLikelihood &drtl, const std::vector< int > &nodeIds, Reward &reward, bool verbose=true) throw (Exception)
	Compute the reward vectors for a particular dataset using the double-recursive likelihood computation. More...
static void	writeToStream (const ProbabilisticRewardMapping &rewards, const SiteContainer &sites, std::ostream &out) throw (IOException)
	Write the reward vectors to a stream. More...
static void	readFromStream (std::istream &in, ProbabilisticRewardMapping &rewards) throw (IOException)
	Read the reward vectors from a stream. More...
static double	computeSumForBranch (const RewardMapping &smap, size_t branchIndex)
	Sum all rewards of a given branch (specified by its index). More...
static double	computeSumForSite (const RewardMapping &smap, size_t siteIndex)
	Sum all substitutions for each type of a given site (specified by its index). More...

Detailed Description

Provide methods to compute reward mappings.

For now, 4 methods are implemented, and provide reward mappings.

See: Minin, V.N. and Suchard, M.A., Fast, accurate and simulation-free stochastic mapping Philosophical Transactions of the Royal Society B 2008 363:3985-95.

Author

Laurent Guéguen

Definition at line 62 of file RewardMappingTools.h.

Constructor & Destructor Documentation

RewardMappingTools()

bpp::RewardMappingTools::RewardMappingTools ( )

inline

Definition at line 65 of file RewardMappingTools.h.

~RewardMappingTools()

virtual bpp::RewardMappingTools::~RewardMappingTools ( )

inlinevirtual

Definition at line 66 of file RewardMappingTools.h.

Member Function Documentation

computeRewardVectors()

ProbabilisticRewardMapping * RewardMappingTools::computeRewardVectors ( const DRTreeLikelihood &  drtl, const std::vector< int > &  nodeIds, Reward &  reward, bool  verbose = true  ) throw ( Exception )

static

Compute the reward vectors for a particular dataset using the double-recursive likelihood computation.

Parameters

drtl	A DRTreeLikelihood object.
nodeIds	The Ids of the nodes the reward vectors are computed on.
reward	The Reward to use.
verbose	Print info to screen.

Returns

A vector of reward vectors (one for each site).

Exceptions

Exception

If the likelihood object is not initialized.

Definition at line 58 of file RewardMappingTools.cpp.

References bpp::Node::getDistanceToFather(), bpp::Node::getFather(), bpp::Node::getId(), bpp::TreeLikelihood::ConstBranchModelDescription::getModel(), bpp::TreeLikelihood::ConstBranchModelDescription::getNewSiteIterator(), bpp::TreeTemplate< N >::getNodes(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::TreeLikelihood::ConstBranchModelIterator::hasNext(), and bpp::TreeLikelihood::ConstBranchModelIterator::next().

Referenced by bpp::SubstitutionMappingTools::getNormalizationsPerBranch().

computeSumForBranch()

double RewardMappingTools::computeSumForBranch ( const RewardMapping &  smap, size_t  branchIndex  )

static

Sum all rewards of a given branch (specified by its index).

Parameters

smap	The reward map to use.
branchIndex	The index of the reward vector for which the counts should be computed.

Returns

A vector will all rewards summed.

Definition at line 423 of file RewardMappingTools.cpp.

References bpp::Mapping::getNumberOfSites().

computeSumForSite()

double RewardMappingTools::computeSumForSite ( const RewardMapping &  smap, size_t  siteIndex  )

static

Sum all substitutions for each type of a given site (specified by its index).

Parameters

smap	The substitution map to use.
siteIndex	The index of the substitution vector for which the counts should be computed.

Returns

A vector will all counts summed for each types of substitutions.

Definition at line 436 of file RewardMappingTools.cpp.

References bpp::Mapping::getNumberOfBranches().

readFromStream()

void RewardMappingTools::readFromStream ( std::istream &  in, ProbabilisticRewardMapping &  rewards  ) throw ( IOException )

static

Read the reward vectors from a stream.

Parameters

in	The input stream where to read the vectors.
rewards	The mapping object to fill.

Exceptions

IOException

If an input error happens.

Definition at line 379 of file RewardMappingTools.cpp.

writeToStream()

void RewardMappingTools::writeToStream ( const ProbabilisticRewardMapping &  rewards, const SiteContainer &  sites, std::ostream &  out  ) throw ( IOException )

static

Write the reward vectors to a stream.

Parameters

rewards	The reward vectors to write.
sites	The dataset associated to the vectors (needed to know the position of each site in the dataset).
out	The output stream where to write the vectors.

Exceptions

IOException

If an output error happens.

Definition at line 350 of file RewardMappingTools.cpp.

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

• Bpp/Phyl/Mapping/RewardMappingTools.h
• Bpp/Phyl/Mapping/RewardMappingTools.cpp