bpp::AbstractTreeParsimonyScore Class Reference

Partial implementation of the TreeParsimonyScore interface. More...

#include <Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h>

Inheritance diagram for bpp::AbstractTreeParsimonyScore:

Collaboration diagram for bpp::AbstractTreeParsimonyScore:

Public Member Functions
	AbstractTreeParsimonyScore (std::shared_ptr< TreeTemplate< Node >> tree, std::shared_ptr< const SiteContainerInterface > data, bool verbose, bool includeGaps)
	AbstractTreeParsimonyScore (std::shared_ptr< TreeTemplate< Node >> tree, std::shared_ptr< const SiteContainerInterface > data, std::shared_ptr< const StateMapInterface > statesMap, bool verbose)
virtual	~AbstractTreeParsimonyScore ()
const Tree &	tree () const override
	Get the tree for which scores are computed. More...
virtual const TreeTemplate< Node > &	treeTemplate () const
virtual std::shared_ptr< const TreeTemplate< Node > >	getTreeTemplate () const
std::vector< unsigned int >	getScorePerSite () const override
	Get the score for each site for the current tree, i.e. the total minimum number of changes in the tree for each site. More...
const StateMapInterface &	stateMap () const override
	Get the state map associated to this instance. More...
std::shared_ptr< const StateMapInterface >	getStateMap () const override
	Get the state map associated to this instance. More...
TreeParsimonyScoreInterface *	clone () const =0
virtual unsigned int	getScore () const =0
	Get the score for the current tree, i.e. the total minimum number of changes in the tree. More...
virtual unsigned int	getScoreForSite (size_t site) const =0
	Get the score for a given site for the current tree, i.e. the total minimum number of changes in the tree for this site. More...

Protected Member Functions
virtual Tree &	tree_ ()
virtual TreeTemplate< Node > &	treeTemplate_ ()
virtual std::shared_ptr< TreeTemplate< Node > >	getTreeTemplate_ ()

Private Member Functions
void	init_ (std::shared_ptr< const SiteContainerInterface > data, bool verbose)

Private Attributes
std::shared_ptr< TreeTemplate< Node > >	treePtr_
std::shared_ptr< const SiteContainerInterface >	data_
std::shared_ptr< const Alphabet >	alphabet_
std::shared_ptr< const StateMapInterface >	statesMap_
size_t	nbStates_

Detailed Description

Partial implementation of the TreeParsimonyScore interface.

Definition at line 20 of file AbstractTreeParsimonyScore.h.

Constructor & Destructor Documentation

AbstractTreeParsimonyScore() [1/2]

AbstractTreeParsimonyScore::AbstractTreeParsimonyScore	(	std::shared_ptr< TreeTemplate< Node >>	tree,
		std::shared_ptr< const SiteContainerInterface >	data,
		bool	verbose,
		bool	includeGaps
	)

Definition at line 14 of file AbstractTreeParsimonyScore.cpp.

References alphabet_, init_(), nbStates_, and statesMap_.

AbstractTreeParsimonyScore() [2/2]

AbstractTreeParsimonyScore::AbstractTreeParsimonyScore	(	std::shared_ptr< TreeTemplate< Node >>	tree,
		std::shared_ptr< const SiteContainerInterface >	data,
		std::shared_ptr< const StateMapInterface >	statesMap,
		bool	verbose
	)

Definition at line 31 of file AbstractTreeParsimonyScore.cpp.

References init_().

~AbstractTreeParsimonyScore()

virtual bpp::AbstractTreeParsimonyScore::~AbstractTreeParsimonyScore ( )

inlinevirtual

Definition at line 43 of file AbstractTreeParsimonyScore.h.

Member Function Documentation

clone()

TreeParsimonyScoreInterface* bpp::TreeParsimonyScoreInterface::clone ( ) const

pure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::DRTreeParsimonyScore.

getScore()

virtual unsigned int bpp::TreeParsimonyScoreInterface::getScore ( ) const

pure virtualinherited

Get the score for the current tree, i.e. the total minimum number of changes in the tree.

Returns

The minimum total number of changes in the tree.

Implemented in bpp::DRTreeParsimonyScore.

getScoreForSite()

virtual unsigned int bpp::TreeParsimonyScoreInterface::getScoreForSite ( size_t  site ) const

pure virtualinherited

Get the score for a given site for the current tree, i.e. the total minimum number of changes in the tree for this site.

Parameters

site	The corresponding site.

Returns

The minimum total number of changes in the tree for site 'site'.

Implemented in bpp::DRTreeParsimonyScore.

Referenced by getScorePerSite().

getScorePerSite()

std::vector< unsigned int > AbstractTreeParsimonyScore::getScorePerSite ( ) const

overridevirtual

Get the score for each site for the current tree, i.e. the total minimum number of changes in the tree for each site.

Returns

The minimum total number of changes in the tree for each site.

Implements bpp::TreeParsimonyScoreInterface.

Definition at line 69 of file AbstractTreeParsimonyScore.cpp.

References data_, and bpp::TreeParsimonyScoreInterface::getScoreForSite().

getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractTreeParsimonyScore::getStateMap ( ) const

inlineoverridevirtual

Get the state map associated to this instance.

Returns

A shared pointer toward the underlying state map.

Implements bpp::TreeParsimonyScoreInterface.

Definition at line 54 of file AbstractTreeParsimonyScore.h.

References statesMap_.

Referenced by bpp::DRTreeParsimonyScore::init_().

getTreeTemplate()

virtual std::shared_ptr<const TreeTemplate<Node> > bpp::AbstractTreeParsimonyScore::getTreeTemplate ( ) const

inlinevirtual

Definition at line 51 of file AbstractTreeParsimonyScore.h.

References treePtr_.

Referenced by bpp::DRTreeParsimonyScore::DRTreeParsimonyScore(), and bpp::DRTreeParsimonyScore::operator=().

getTreeTemplate_()

virtual std::shared_ptr<TreeTemplate<Node> > bpp::AbstractTreeParsimonyScore::getTreeTemplate_ ( )

inlineprotectedvirtual

Definition at line 59 of file AbstractTreeParsimonyScore.h.

References treePtr_.

init_()

void AbstractTreeParsimonyScore::init_ ( std::shared_ptr< const SiteContainerInterface >  data, bool  verbose  )

private

Definition at line 45 of file AbstractTreeParsimonyScore.cpp.

References data_, bpp::TreeTemplateTools::deleteBranchLengths(), bpp::ApplicationTools::displayWarning(), bpp::PatternTools::getSequenceSubset(), and treePtr_.

Referenced by AbstractTreeParsimonyScore().

stateMap()

const StateMapInterface& bpp::AbstractTreeParsimonyScore::stateMap ( ) const

inlineoverridevirtual

Get the state map associated to this instance.

Returns

The underlying state map.

Implements bpp::TreeParsimonyScoreInterface.

Definition at line 53 of file AbstractTreeParsimonyScore.h.

References statesMap_.

tree()

const Tree& bpp::AbstractTreeParsimonyScore::tree ( ) const

inlineoverridevirtual

Get the tree for which scores are computed.

Returns

The tree associated to this object.

Implements bpp::TreeParsimonyScoreInterface.

Definition at line 49 of file AbstractTreeParsimonyScore.h.

References treePtr_.

Referenced by bpp::DRTreeParsimonyScore::topology().

tree_()

virtual Tree& bpp::AbstractTreeParsimonyScore::tree_ ( )

inlineprotectedvirtual

Definition at line 57 of file AbstractTreeParsimonyScore.h.

References treePtr_.

treeTemplate()

virtual const TreeTemplate<Node>& bpp::AbstractTreeParsimonyScore::treeTemplate ( ) const

inlinevirtual

Definition at line 50 of file AbstractTreeParsimonyScore.h.

References treePtr_.

Referenced by bpp::DRTreeParsimonyScore::computeScores(), and bpp::DRTreeParsimonyScore::testNNI().

treeTemplate_()

virtual TreeTemplate<Node>& bpp::AbstractTreeParsimonyScore::treeTemplate_ ( )

inlineprotectedvirtual

Definition at line 58 of file AbstractTreeParsimonyScore.h.

References treePtr_.

Referenced by bpp::DRTreeParsimonyScore::doNNI().

Member Data Documentation

alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTreeParsimonyScore::alphabet_

private

Definition at line 26 of file AbstractTreeParsimonyScore.h.

Referenced by AbstractTreeParsimonyScore().

data_

std::shared_ptr<const SiteContainerInterface> bpp::AbstractTreeParsimonyScore::data_

private

Definition at line 25 of file AbstractTreeParsimonyScore.h.

Referenced by getScorePerSite(), and init_().

nbStates_

size_t bpp::AbstractTreeParsimonyScore::nbStates_

private

Definition at line 28 of file AbstractTreeParsimonyScore.h.

Referenced by AbstractTreeParsimonyScore().

statesMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractTreeParsimonyScore::statesMap_

private

Definition at line 27 of file AbstractTreeParsimonyScore.h.

Referenced by AbstractTreeParsimonyScore(), getStateMap(), and stateMap().

treePtr_

std::shared_ptr<TreeTemplate<Node> > bpp::AbstractTreeParsimonyScore::treePtr_

private

Definition at line 24 of file AbstractTreeParsimonyScore.h.

Referenced by getTreeTemplate(), getTreeTemplate_(), init_(), tree(), tree_(), treeTemplate(), and treeTemplate_().

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

• Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h
• Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp