bpp::CountDistanceEstimationMafIterator Class Reference

Compute A simple distance using observed counts. More...

#include <Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h>

Inheritance diagram for bpp::CountDistanceEstimationMafIterator:

Collaboration diagram for bpp::CountDistanceEstimationMafIterator:

Public Member Functions
	CountDistanceEstimationMafIterator (MafIterator *iterator, const std::string &gapOption, bool unresolvedAsGap)
	Build a new distance estimation maf iterator, based on the SiteContainerTools::computeSimilarityMatrix method. More...
std::string	getPropertyName () const
DistanceMatrix *	estimateDistanceMatrixForBlock (const MafBlock &block)

Private Attributes
std::string	gapOption_
bool	unresolvedAsGap_

Detailed Description

Compute A simple distance using observed counts.

Definition at line 50 of file CountDistanceEstimationMafIterator.h.

Constructor & Destructor Documentation

CountDistanceEstimationMafIterator()

bpp::CountDistanceEstimationMafIterator::CountDistanceEstimationMafIterator ( MafIterator *  iterator, const std::string &  gapOption, bool  unresolvedAsGap  )

inline

Build a new distance estimation maf iterator, based on the SiteContainerTools::computeSimilarityMatrix method.

See also

SiteContainerTools

Parameters

iterator	The input iterator.
gapOption	How to deal with gaps. Option forawarded to the computeSimilarityMatrix method.
unresolvedAsGap	Tell if unresolved characters should be considered as gaps. Option forawarded to the computeSimilarityMatrix method.

Definition at line 66 of file CountDistanceEstimationMafIterator.h.

Member Function Documentation

estimateDistanceMatrixForBlock()

DistanceMatrix * CountDistanceEstimationMafIterator::estimateDistanceMatrixForBlock ( const MafBlock &  block )

virtual

Implements bpp::AbstractDistanceEstimationMafIterator.

Definition at line 46 of file CountDistanceEstimationMafIterator.cpp.

References gapOption_, and unresolvedAsGap_.

getPropertyName()

std::string bpp::CountDistanceEstimationMafIterator::getPropertyName ( ) const

inlinevirtual

Implements bpp::AbstractDistanceEstimationMafIterator.

Definition at line 72 of file CountDistanceEstimationMafIterator.h.

Member Data Documentation

gapOption_

std::string bpp::CountDistanceEstimationMafIterator::gapOption_

private

Definition at line 54 of file CountDistanceEstimationMafIterator.h.

Referenced by estimateDistanceMatrixForBlock().

unresolvedAsGap_

bool bpp::CountDistanceEstimationMafIterator::unresolvedAsGap_

private

Definition at line 55 of file CountDistanceEstimationMafIterator.h.

Referenced by estimateDistanceMatrixForBlock().

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

• Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h
• Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.cpp