Parsimony data structure for double-recursive (DR) algorithm. More...

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

Inheritance diagram for bpp::DRTreeParsimonyData:

Collaboration diagram for bpp::DRTreeParsimonyData:

Public Member Functions
	DRTreeParsimonyData (const TreeTemplate< Node > *tree)
	DRTreeParsimonyData (const DRTreeParsimonyData &data)
DRTreeParsimonyData &	operator= (const DRTreeParsimonyData &data)
virtual	~DRTreeParsimonyData ()
DRTreeParsimonyData *	clone () const
void	setTree (const TreeTemplate< Node > *tree)
	Set the tree associated to the data.
DRTreeParsimonyNodeData &	getNodeData (int nodeId)
const DRTreeParsimonyNodeData &	getNodeData (int nodeId) const
DRTreeParsimonyLeafData &	getLeafData (int nodeId)
const DRTreeParsimonyLeafData &	getLeafData (int nodeId) const
std::vector< Bitset > &	getBitsetsArray (int nodeId, int neighborId)
const std::vector< Bitset > &	getBitsetsArray (int nodeId, int neighborId) const
std::vector< unsigned int > &	getScoresArray (int nodeId, int neighborId)
const std::vector< unsigned int > &	getScoresArray (int nodeId, int neighborId) const
size_t	getArrayPosition (int parentId, int sonId, size_t currentPosition) const
std::vector< Bitset > &	getRootBitsets ()
const std::vector< Bitset > &	getRootBitsets () const
const Bitset &	getRootBitset (size_t i) const
std::vector< unsigned int > &	getRootScores ()
const std::vector< unsigned int > &	getRootScores () const
unsigned int	getRootScore (size_t i) const
size_t	getNumberOfDistinctSites () const
size_t	getNumberOfSites () const
size_t	getNumberOfStates () const
void	init (const SiteContainer &sites, const StateMap &stateMap) throw (Exception)
void	reInit () throw (Exception)
size_t	getRootArrayPosition (size_t site) const
unsigned int	getWeight (size_t pos) const
const TreeTemplate< Node > *	getTree () const
Protected Member Functions
void	init (const Node *node, const SiteContainer &sites, const StateMap &stateMap) throw (Exception)
void	reInit (const Node *node) throw (Exception)
void	setTreeP_ (const TreeTemplate< Node > *tree)
const TreeTemplate< Node > *	getTreeP_ () const
Protected Attributes
std::vector< size_t >	rootPatternLinks_
std::vector< unsigned int >	rootWeights_
const TreeTemplate< Node > *	tree_
Private Attributes
std::map< int, DRTreeParsimonyNodeData >	nodeData_
std::map< int, DRTreeParsimonyLeafData >	leafData_
std::vector< Bitset >	rootBitsets_
std::vector< unsigned int >	rootScores_
SiteContainer *	shrunkData_
size_t	nbSites_
size_t	nbStates_
size_t	nbDistinctSites_

Detailed Description

Parsimony data structure for double-recursive (DR) algorithm.

States are coded using bitsets for faster computing (

See also:: AbstractTreeParsimonyData). For each inner node in the tree, we store a DRTreeParsimonyNodeData object in nodeData_. For each leaf node in the tree, we store a DRTreeParsimonyLeafData object in leafData_.

The dataset is first compressed, removing all identical sites. The resulting dataset is stored in shrunkData_. The corresponding positions are stored in rootPatternLinks_, inherited from AbstractTreeParsimonyData.

Definition at line 195 of file DRTreeParsimonyData.h.

Constructor & Destructor Documentation

bpp::DRTreeParsimonyData::DRTreeParsimonyData ( const TreeTemplate< Node > * tree ) [inline]

Definition at line 209 of file DRTreeParsimonyData.h.

Referenced by clone().

DRTreeParsimonyData::DRTreeParsimonyData ( const DRTreeParsimonyData & data )

Definition at line 52 of file DRTreeParsimonyData.cpp.

References bpp::SiteContainer::clone(), and shrunkData_.

virtual bpp::DRTreeParsimonyData::~DRTreeParsimonyData ( ) [inline, virtual]

Definition at line 225 of file DRTreeParsimonyData.h.

References shrunkData_.

Member Function Documentation

DRTreeParsimonyData* bpp::DRTreeParsimonyData::clone ( ) const [inline, virtual]

Implements bpp::TreeParsimonyData.

Definition at line 227 of file DRTreeParsimonyData.h.

References DRTreeParsimonyData().

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

size_t bpp::DRTreeParsimonyData::getArrayPosition	(	int	parentId,
		int	sonId,
		size_t	currentPosition
	)		const `[inline, virtual]`

Implements bpp::TreeParsimonyData.

Definition at line 290 of file DRTreeParsimonyData.h.

std::vector<Bitset>& bpp::DRTreeParsimonyData::getBitsetsArray	(	int	nodeId,
		int	neighborId
	)		`[inline]`

Definition at line 272 of file DRTreeParsimonyData.h.

References nodeData_.

const std::vector<Bitset>& bpp::DRTreeParsimonyData::getBitsetsArray	(	int	nodeId,
		int	neighborId
	)		const `[inline]`

Definition at line 276 of file DRTreeParsimonyData.h.

References nodeData_.

DRTreeParsimonyLeafData& bpp::DRTreeParsimonyData::getLeafData ( int nodeId ) [inline]

Definition at line 263 of file DRTreeParsimonyData.h.

References leafData_.

Referenced by bpp::DRTreeParsimonyScore::computeScoresPostorder(), and bpp::DRTreeParsimonyScore::computeScoresPreorder().

const DRTreeParsimonyLeafData& bpp::DRTreeParsimonyData::getLeafData ( int nodeId ) const [inline]

Definition at line 267 of file DRTreeParsimonyData.h.

References leafData_.

DRTreeParsimonyNodeData& bpp::DRTreeParsimonyData::getNodeData ( int nodeId ) [inline, virtual]

Implements bpp::TreeParsimonyData.

Definition at line 254 of file DRTreeParsimonyData.h.

References nodeData_.

Referenced by bpp::DRTreeParsimonyScore::computeScores(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), and bpp::DRTreeParsimonyScore::computeScoresPreorder().

const DRTreeParsimonyNodeData& bpp::DRTreeParsimonyData::getNodeData ( int nodeId ) const [inline, virtual]

Implements bpp::TreeParsimonyData.

Definition at line 258 of file DRTreeParsimonyData.h.

References nodeData_.

size_t bpp::DRTreeParsimonyData::getNumberOfDistinctSites ( ) const [inline]

Definition at line 303 of file DRTreeParsimonyData.h.

References nbDistinctSites_.

size_t bpp::DRTreeParsimonyData::getNumberOfSites ( ) const [inline]

Definition at line 304 of file DRTreeParsimonyData.h.

References nbSites_.

size_t bpp::DRTreeParsimonyData::getNumberOfStates ( ) const [inline]

Definition at line 305 of file DRTreeParsimonyData.h.

References nbStates_.

size_t bpp::AbstractTreeParsimonyData::getRootArrayPosition ( size_t site ) const [inline, virtual, inherited]

Implements bpp::TreeParsimonyData.

Definition at line 99 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::rootPatternLinks_.

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

const Bitset& bpp::DRTreeParsimonyData::getRootBitset ( size_t i ) const [inline]

Definition at line 297 of file DRTreeParsimonyData.h.

References rootBitsets_.

std::vector<Bitset>& bpp::DRTreeParsimonyData::getRootBitsets ( ) [inline]

Definition at line 295 of file DRTreeParsimonyData.h.

References rootBitsets_.

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

const std::vector<Bitset>& bpp::DRTreeParsimonyData::getRootBitsets ( ) const [inline]

Definition at line 296 of file DRTreeParsimonyData.h.

References rootBitsets_.

unsigned int bpp::DRTreeParsimonyData::getRootScore ( size_t i ) const [inline]

Definition at line 301 of file DRTreeParsimonyData.h.

References rootScores_.

Referenced by bpp::DRTreeParsimonyScore::getScore(), and bpp::DRTreeParsimonyScore::getScoreForSite().

std::vector<unsigned int>& bpp::DRTreeParsimonyData::getRootScores ( ) [inline]

Definition at line 299 of file DRTreeParsimonyData.h.

References rootScores_.

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

const std::vector<unsigned int>& bpp::DRTreeParsimonyData::getRootScores ( ) const [inline]

Definition at line 300 of file DRTreeParsimonyData.h.

References rootScores_.

std::vector<unsigned int>& bpp::DRTreeParsimonyData::getScoresArray	(	int	nodeId,
		int	neighborId
	)		`[inline]`

Definition at line 281 of file DRTreeParsimonyData.h.

References nodeData_.

const std::vector<unsigned int>& bpp::DRTreeParsimonyData::getScoresArray	(	int	nodeId,
		int	neighborId
	)		const `[inline]`

Definition at line 285 of file DRTreeParsimonyData.h.

References nodeData_.

const TreeTemplate<Node>* bpp::AbstractTreeParsimonyData::getTree ( ) const [inline, virtual, inherited]

Implements bpp::TreeParsimonyData.

Definition at line 109 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::tree_.

const TreeTemplate<Node>* bpp::AbstractTreeParsimonyData::getTreeP_ ( ) const [inline, protected, inherited]

Definition at line 113 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::tree_.

Referenced by reInit().

unsigned int bpp::AbstractTreeParsimonyData::getWeight ( size_t pos ) const [inline, inherited]

Definition at line 104 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::rootWeights_.

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

void DRTreeParsimonyData::init	(	const SiteContainer &	sites,
		const StateMap &	stateMap
	)		throw (Exception)

Definition at line 90 of file DRTreeParsimonyData.cpp.

References bpp::SitePatterns::getIndices(), bpp::SitePatterns::getSites(), and bpp::SitePatterns::getWeights().

void DRTreeParsimonyData::init	(	const Node *	node,
		const SiteContainer &	sites,
		const StateMap &	stateMap
	)		throw (Exception) `[protected]`

Definition at line 112 of file DRTreeParsimonyData.cpp.

References bpp::DRTreeParsimonyNodeData::eraseNeighborArrays(), bpp::Alphabet::getAlias(), bpp::DRTreeParsimonyLeafData::getBitsetsArray(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), bpp::Sequence::getValue(), bpp::DRTreeParsimonyNodeData::setNode(), and bpp::DRTreeParsimonyLeafData::setNode().

DRTreeParsimonyData & DRTreeParsimonyData::operator= ( const DRTreeParsimonyData & data )

Definition at line 71 of file DRTreeParsimonyData.cpp.

References bpp::SiteContainer::clone(), leafData_, nbDistinctSites_, nbSites_, nbStates_, nodeData_, rootBitsets_, rootScores_, and shrunkData_.

void DRTreeParsimonyData::reInit ( ) throw (Exception)

Definition at line 178 of file DRTreeParsimonyData.cpp.

References bpp::AbstractTreeParsimonyData::getTreeP_().

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

void DRTreeParsimonyData::reInit ( const Node * node ) throw (Exception) [protected]

Definition at line 184 of file DRTreeParsimonyData.cpp.

References bpp::DRTreeParsimonyNodeData::eraseNeighborArrays(), bpp::DRTreeParsimonyNodeData::getBitsetsArrayForNeighbor(), bpp::Node::getId(), bpp::DRTreeParsimonyNodeData::getScoresArrayForNeighbor(), and bpp::DRTreeParsimonyNodeData::setNode().

void bpp::DRTreeParsimonyData::setTree ( const TreeTemplate< Node > * tree ) [inline]

Set the tree associated to the data.

All node data will be actualized accordingly by calling the setNode() method on the corresponding nodes.

Warning:: : the old tree and the new tree must be two clones! And particularly, they have to share the same topology and nodes id.

Parameters:

tree	The tree to be associated to this data.

Definition at line 239 of file DRTreeParsimonyData.h.

References bpp::TreeTemplate< N >::getNode(), leafData_, nodeData_, bpp::AbstractTreeParsimonyData::setTreeP_(), and bpp::AbstractTreeParsimonyData::tree_.

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

void bpp::AbstractTreeParsimonyData::setTreeP_ ( const TreeTemplate< Node > * tree ) [inline, protected, inherited]

Definition at line 112 of file AbstractTreeParsimonyData.h.

References bpp::AbstractTreeParsimonyData::tree_.

Referenced by setTree().

Member Data Documentation

std::map<int, DRTreeParsimonyLeafData> bpp::DRTreeParsimonyData::leafData_ [mutable, private]

Definition at line 200 of file DRTreeParsimonyData.h.

Referenced by getLeafData(), operator=(), and setTree().

size_t bpp::DRTreeParsimonyData::nbDistinctSites_ [private]

Definition at line 206 of file DRTreeParsimonyData.h.

Referenced by getNumberOfDistinctSites(), and operator=().

size_t bpp::DRTreeParsimonyData::nbSites_ [private]

Definition at line 204 of file DRTreeParsimonyData.h.

Referenced by getNumberOfSites(), and operator=().

size_t bpp::DRTreeParsimonyData::nbStates_ [private]

Definition at line 205 of file DRTreeParsimonyData.h.

Referenced by getNumberOfStates(), and operator=().

std::map<int, DRTreeParsimonyNodeData> bpp::DRTreeParsimonyData::nodeData_ [mutable, private]

Definition at line 199 of file DRTreeParsimonyData.h.

Referenced by getBitsetsArray(), getNodeData(), getScoresArray(), operator=(), and setTree().

std::vector<Bitset> bpp::DRTreeParsimonyData::rootBitsets_ [mutable, private]

Definition at line 201 of file DRTreeParsimonyData.h.

Referenced by getRootBitset(), getRootBitsets(), and operator=().

std::vector<size_t> bpp::AbstractTreeParsimonyData::rootPatternLinks_ [protected, inherited]

Definition at line 70 of file AbstractTreeParsimonyData.h.

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

std::vector<unsigned int> bpp::DRTreeParsimonyData::rootScores_ [mutable, private]

Definition at line 202 of file DRTreeParsimonyData.h.

Referenced by getRootScore(), getRootScores(), and operator=().

std::vector<unsigned int> bpp::AbstractTreeParsimonyData::rootWeights_ [protected, inherited]

Definition at line 71 of file AbstractTreeParsimonyData.h.

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

SiteContainer* bpp::DRTreeParsimonyData::shrunkData_ [private]

Definition at line 203 of file DRTreeParsimonyData.h.

Referenced by DRTreeParsimonyData(), operator=(), and ~DRTreeParsimonyData().

const TreeTemplate<Node>* bpp::AbstractTreeParsimonyData::tree_ [protected, inherited]

Definition at line 72 of file AbstractTreeParsimonyData.h.

Referenced by bpp::AbstractTreeParsimonyData::getTree(), bpp::AbstractTreeParsimonyData::getTreeP_(), bpp::AbstractTreeParsimonyData::operator=(), setTree(), and bpp::AbstractTreeParsimonyData::setTreeP_().

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

Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation