bpp::TreeParsimonyScoreInterface Class Reference

Compute a parsimony score. More...

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

Inheritance diagram for bpp::TreeParsimonyScoreInterface:

Collaboration diagram for bpp::TreeParsimonyScoreInterface:

Public Member Functions
	TreeParsimonyScoreInterface ()
virtual	~TreeParsimonyScoreInterface ()
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...
virtual std::vector< unsigned int >	getScorePerSite () const =0
	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...
virtual const Tree &	tree () const =0
	Get the tree for which scores are computed. More...
virtual const StateMapInterface &	stateMap () const =0
	Get the state map associated to this instance. More...
virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0
	Get the state map associated to this instance. More...

Detailed Description

Compute a parsimony score.

Definition at line 20 of file TreeParsimonyScore.h.

Constructor & Destructor Documentation

TreeParsimonyScoreInterface()

bpp::TreeParsimonyScoreInterface::TreeParsimonyScoreInterface ( )

inline

Definition at line 24 of file TreeParsimonyScore.h.

~TreeParsimonyScoreInterface()

virtual bpp::TreeParsimonyScoreInterface::~TreeParsimonyScoreInterface ( )

inlinevirtual

Definition at line 25 of file TreeParsimonyScore.h.

Member Function Documentation

clone()

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

pure virtual

Implements bpp::Clonable.

Implemented in bpp::DRTreeParsimonyScore.

getScore()

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

pure virtual

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 virtual

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 bpp::AbstractTreeParsimonyScore::getScorePerSite().

getScorePerSite()

virtual std::vector<unsigned int> bpp::TreeParsimonyScoreInterface::getScorePerSite ( ) const

pure virtual

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.

Implemented in bpp::AbstractTreeParsimonyScore.

getStateMap()

virtual std::shared_ptr<const StateMapInterface> bpp::TreeParsimonyScoreInterface::getStateMap ( ) const

pure virtual

Get the state map associated to this instance.

Returns

A shared pointer toward the underlying state map.

Implemented in bpp::AbstractTreeParsimonyScore.

stateMap()

virtual const StateMapInterface& bpp::TreeParsimonyScoreInterface::stateMap ( ) const

pure virtual

Get the state map associated to this instance.

Returns

The underlying state map.

Implemented in bpp::AbstractTreeParsimonyScore.

tree()

virtual const Tree& bpp::TreeParsimonyScoreInterface::tree ( ) const

pure virtual

Get the tree for which scores are computed.

Returns

The tree associated to this object.

Implemented in bpp::AbstractTreeParsimonyScore.

---

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

• Bpp/Phyl/Parsimony/TreeParsimonyScore.h