bpp::AbstractTreeParsimonyData Class Reference

Partial implementation of the TreeParsimonyData interface. More...

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

Inheritance diagram for bpp::AbstractTreeParsimonyData:

Collaboration diagram for bpp::AbstractTreeParsimonyData:

Public Member Functions
	AbstractTreeParsimonyData (std::shared_ptr< const TreeTemplate< Node >> tree)
	AbstractTreeParsimonyData (const AbstractTreeParsimonyData &atpd)
AbstractTreeParsimonyData &	operator= (const AbstractTreeParsimonyData &atpd)
virtual	~AbstractTreeParsimonyData ()
size_t	getRootArrayPosition (size_t site) const override
unsigned int	getWeight (size_t pos) const
const TreeTemplate< Node > &	tree () const override
std::shared_ptr< const TreeTemplate< Node > >	getTree () const override
TreeParsimonyDataInterface *	clone () const override=0
virtual size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition) const =0
virtual TreeParsimonyNodeDataInterface &	nodeData (int nodeId)=0
virtual const TreeParsimonyNodeDataInterface &	nodeData (int nodeId) const =0

Protected Member Functions
void	setTree (std::shared_ptr< const TreeTemplate< Node >> tree)

Protected Attributes
std::vector< size_t >	rootPatternLinks_
std::vector< unsigned int >	rootWeights_
std::shared_ptr< const TreeTemplate< Node > >	tree_

Detailed Description

Partial implementation of the TreeParsimonyData interface.

This data structure provides a simple compression, by performing and storing computations only one time per identical sites.

The compression is achieved by the TreeParsimonyScore object. The correspondence between sites in the dataset and the arrays in the structures is given by the rootPatternLinks_ array: the array indice for site if given by:

rootPatternLinks_[i]

Finally, the rootWeights_ array gives for each array position, the number of sites with this pattern. The global parsimony score is then given by the sum of all scores for each array position, weighted by the corresponding number of sites.

Definition at line 31 of file AbstractTreeParsimonyData.h.

Constructor & Destructor Documentation

AbstractTreeParsimonyData() [1/2]

bpp::AbstractTreeParsimonyData::AbstractTreeParsimonyData ( std::shared_ptr< const TreeTemplate< Node >>  tree )

inline

Definition at line 40 of file AbstractTreeParsimonyData.h.

AbstractTreeParsimonyData() [2/2]

bpp::AbstractTreeParsimonyData::AbstractTreeParsimonyData ( const AbstractTreeParsimonyData &  atpd )

inline

Definition at line 46 of file AbstractTreeParsimonyData.h.

~AbstractTreeParsimonyData()

virtual bpp::AbstractTreeParsimonyData::~AbstractTreeParsimonyData ( )

inlinevirtual

Definition at line 61 of file AbstractTreeParsimonyData.h.

Member Function Documentation

clone()

TreeParsimonyDataInterface* bpp::TreeParsimonyDataInterface::clone ( ) const

overridepure virtualinherited

Implements bpp::Clonable.

Implemented in bpp::DRTreeParsimonyData.

getArrayPosition()

virtual size_t bpp::TreeParsimonyDataInterface::getArrayPosition ( int  parentId, int  sonId, size_t  currentPosition  ) const

pure virtualinherited

Implemented in bpp::DRTreeParsimonyData.

getRootArrayPosition()

size_t bpp::AbstractTreeParsimonyData::getRootArrayPosition ( size_t  site ) const

inlineoverridevirtual

Implements bpp::TreeParsimonyDataInterface.

Definition at line 64 of file AbstractTreeParsimonyData.h.

References rootPatternLinks_.

getTree()

std::shared_ptr<const TreeTemplate<Node> > bpp::AbstractTreeParsimonyData::getTree ( ) const

inlineoverridevirtual

Implements bpp::TreeParsimonyDataInterface.

Definition at line 76 of file AbstractTreeParsimonyData.h.

References tree_.

getWeight()

unsigned int bpp::AbstractTreeParsimonyData::getWeight ( size_t  pos ) const

inline

Definition at line 69 of file AbstractTreeParsimonyData.h.

References rootWeights_.

nodeData() [1/2]

virtual const TreeParsimonyNodeDataInterface& bpp::TreeParsimonyDataInterface::nodeData ( int  nodeId ) const

pure virtualinherited

Implemented in bpp::DRTreeParsimonyData.

nodeData() [2/2]

virtual TreeParsimonyNodeDataInterface& bpp::TreeParsimonyDataInterface::nodeData ( int  nodeId )

pure virtualinherited

Implemented in bpp::DRTreeParsimonyData.

operator=()

AbstractTreeParsimonyData& bpp::AbstractTreeParsimonyData::operator= ( const AbstractTreeParsimonyData &  atpd )

inline

Definition at line 52 of file AbstractTreeParsimonyData.h.

References rootPatternLinks_, rootWeights_, and tree_.

Referenced by bpp::DRTreeParsimonyData::operator=().

setTree()

void bpp::AbstractTreeParsimonyData::setTree ( std::shared_ptr< const TreeTemplate< Node >>  tree )

inlineprotected

Definition at line 79 of file AbstractTreeParsimonyData.h.

References tree(), and tree_.

Referenced by bpp::DRTreeParsimonyData::setTree().

tree()

const TreeTemplate<Node>& bpp::AbstractTreeParsimonyData::tree ( ) const

inlineoverridevirtual

Implements bpp::TreeParsimonyDataInterface.

Definition at line 74 of file AbstractTreeParsimonyData.h.

References tree_.

Referenced by bpp::DRTreeParsimonyData::init(), bpp::DRTreeParsimonyData::reInit(), setTree(), and bpp::DRTreeParsimonyData::setTree().

Member Data Documentation

rootPatternLinks_

std::vector<size_t> bpp::AbstractTreeParsimonyData::rootPatternLinks_

protected

Definition at line 35 of file AbstractTreeParsimonyData.h.

Referenced by getRootArrayPosition(), bpp::DRTreeParsimonyData::init(), and operator=().

rootWeights_

std::vector<unsigned int> bpp::AbstractTreeParsimonyData::rootWeights_

protected

Definition at line 36 of file AbstractTreeParsimonyData.h.

Referenced by getWeight(), bpp::DRTreeParsimonyData::init(), and operator=().

tree_

std::shared_ptr<const TreeTemplate<Node> > bpp::AbstractTreeParsimonyData::tree_

protected

Definition at line 37 of file AbstractTreeParsimonyData.h.

Referenced by getTree(), operator=(), setTree(), bpp::DRTreeParsimonyData::setTree(), and tree().

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

• Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h