bpp-phyl  2.2.0
Public Member Functions | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::DRASDRTreeLikelihoodData Class Reference

Likelihood data structure for rate across sites models, using a double-recursive algorithm. More...

#include <Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h>

+ Inheritance diagram for bpp::DRASDRTreeLikelihoodData:
+ Collaboration diagram for bpp::DRASDRTreeLikelihoodData:

Public Member Functions

 DRASDRTreeLikelihoodData (const TreeTemplate< Node > *tree, size_t nbClasses)
 
 DRASDRTreeLikelihoodData (const DRASDRTreeLikelihoodData &data)
 
DRASDRTreeLikelihoodData & operator= (const DRASDRTreeLikelihoodData &data)
 
virtual ~DRASDRTreeLikelihoodData ()
 
DRASDRTreeLikelihoodData * clone () const
 
void setTree (const TreeTemplate< Node > *tree)
 Set the tree associated to the data. More...
 
DRASDRTreeLikelihoodNodeData & getNodeData (int nodeId)
 
const DRASDRTreeLikelihoodNodeData & getNodeData (int nodeId) const
 
DRASDRTreeLikelihoodLeafData & getLeafData (int nodeId)
 
const DRASDRTreeLikelihoodLeafData & getLeafData (int nodeId) const
 
size_t getArrayPosition (int parentId, int sonId, size_t currentPosition) const
 
const std::map< int, VVVdouble > & getLikelihoodArrays (int nodeId) const
 
std::map< int, VVVdouble > & getLikelihoodArrays (int nodeId)
 
VVVdouble & getLikelihoodArray (int parentId, int neighborId)
 
const VVVdouble & getLikelihoodArray (int parentId, int neighborId) const
 
Vdouble & getDLikelihoodArray (int nodeId)
 
const Vdouble & getDLikelihoodArray (int nodeId) const
 
Vdouble & getD2LikelihoodArray (int nodeId)
 
const Vdouble & getD2LikelihoodArray (int nodeId) const
 
VVdouble & getLeafLikelihoods (int nodeId)
 
const VVdouble & getLeafLikelihoods (int nodeId) const
 
VVVdouble & getRootLikelihoodArray ()
 
const VVVdouble & getRootLikelihoodArray () const
 
VVdouble & getRootSiteLikelihoodArray ()
 
const VVdouble & getRootSiteLikelihoodArray () const
 
Vdouble & getRootRateSiteLikelihoodArray ()
 
const Vdouble & getRootRateSiteLikelihoodArray () const
 
size_t getNumberOfDistinctSites () const
 
size_t getNumberOfSites () const
 
size_t getNumberOfStates () const
 
size_t getNumberOfClasses () const
 
const SiteContainer * getShrunkData () const
 
void initLikelihoods (const SiteContainer &sites, const SubstitutionModel &model) throw (Exception)
 Resize and initialize all likelihood arrays according to the given data set and substitution model. More...
 
void reInit () throw (Exception)
 Rebuild likelihood arrays at inner nodes. More...
 
void reInit (const Node *node) throw (Exception)
 
std::vector< size_t > & getRootArrayPositions ()
 
const std::vector< size_t > & getRootArrayPositions () const
 
size_t getRootArrayPosition (const size_t site) const
 
unsigned int getWeight (size_t pos) const
 
const std::vector< unsigned int > & getWeights () const
 
const Alphabet * getAlphabet () const
 
const TreeTemplate< Node > * getTree () const
 

Protected Member Functions

void initLikelihoods (const Node *node, const SiteContainer &sites, const SubstitutionModel &model) throw (Exception)
 This method initializes the leaves according to a sequence container. More...
 

Protected Attributes

std::vector< size_t > rootPatternLinks_
 Links between sites and patterns. More...
 
std::vector< unsigned int > rootWeights_
 The frequency of each site. More...
 
const TreeTemplate< Node > * tree_
 
const Alphabet * alphabet_
 

Private Attributes

std::map< int, DRASDRTreeLikelihoodNodeData > nodeData_
 
std::map< int, DRASDRTreeLikelihoodLeafData > leafData_
 
VVVdouble rootLikelihoods_
 
VVdouble rootLikelihoodsS_
 
Vdouble rootLikelihoodsSR_
 
SiteContainer * shrunkData_
 
size_t nbSites_
 
size_t nbStates_
 
size_t nbClasses_
 
size_t nbDistinctSites_
 

Detailed Description

Likelihood data structure for rate across sites models, using a double-recursive algorithm.

Definition at line 229 of file DRASDRTreeLikelihoodData.h.

Constructor & Destructor Documentation

◆ DRASDRTreeLikelihoodData() [1/2]

bpp::DRASDRTreeLikelihoodData::DRASDRTreeLikelihoodData ( const TreeTemplate< Node > *  tree,
size_t  nbClasses 
)
inline

Definition at line 247 of file DRASDRTreeLikelihoodData.h.

Referenced by clone().

◆ DRASDRTreeLikelihoodData() [2/2]

bpp::DRASDRTreeLikelihoodData::DRASDRTreeLikelihoodData ( const DRASDRTreeLikelihoodData &  data)
inline

Definition at line 253 of file DRASDRTreeLikelihoodData.h.

References shrunkData_.

◆ ~DRASDRTreeLikelihoodData()

virtual bpp::DRASDRTreeLikelihoodData::~DRASDRTreeLikelihoodData ( )
inlinevirtual

Definition at line 287 of file DRASDRTreeLikelihoodData.h.

References shrunkData_.

Member Function Documentation

◆ clone()

DRASDRTreeLikelihoodData* bpp::DRASDRTreeLikelihoodData::clone ( ) const
inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 289 of file DRASDRTreeLikelihoodData.h.

References DRASDRTreeLikelihoodData().

Referenced by bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::operator=(), and bpp::DRNonHomogeneousTreeLikelihood::operator=().

◆ getAlphabet()

const Alphabet* bpp::AbstractTreeLikelihoodData::getAlphabet ( ) const
inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Definition at line 136 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::alphabet_.

◆ getArrayPosition()

size_t bpp::DRASDRTreeLikelihoodData::getArrayPosition ( int  parentId,
int  sonId,
size_t  currentPosition 
) const
inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 336 of file DRASDRTreeLikelihoodData.h.

◆ getD2LikelihoodArray() [1/2]

Vdouble& bpp::DRASDRTreeLikelihoodData::getD2LikelihoodArray ( int  nodeId)
inline

Definition at line 371 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode().

◆ getD2LikelihoodArray() [2/2]

const Vdouble& bpp::DRASDRTreeLikelihoodData::getD2LikelihoodArray ( int  nodeId) const
inline

Definition at line 376 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

◆ getDLikelihoodArray() [1/2]

Vdouble& bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray ( int  nodeId)
inline

Definition at line 361 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), and bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode().

◆ getDLikelihoodArray() [2/2]

const Vdouble& bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray ( int  nodeId) const
inline

Definition at line 366 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

◆ getLeafData() [1/2]

DRASDRTreeLikelihoodLeafData& bpp::DRASDRTreeLikelihoodData::getLeafData ( int  nodeId)
inline

Definition at line 326 of file DRASDRTreeLikelihoodData.h.

References leafData_.

◆ getLeafData() [2/2]

const DRASDRTreeLikelihoodLeafData& bpp::DRASDRTreeLikelihoodData::getLeafData ( int  nodeId) const
inline

Definition at line 331 of file DRASDRTreeLikelihoodData.h.

References leafData_.

◆ getLeafLikelihoods() [1/2]

VVdouble& bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods ( int  nodeId)
inline

Definition at line 381 of file DRASDRTreeLikelihoodData.h.

References leafData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), and bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate().

◆ getLeafLikelihoods() [2/2]

const VVdouble& bpp::DRASDRTreeLikelihoodData::getLeafLikelihoods ( int  nodeId) const
inline

Definition at line 386 of file DRASDRTreeLikelihoodData.h.

References leafData_.

◆ getLikelihoodArray() [1/2]

VVVdouble& bpp::DRASDRTreeLikelihoodData::getLikelihoodArray ( int  parentId,
int  neighborId 
)
inline

Definition at line 351 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), and bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays().

◆ getLikelihoodArray() [2/2]

const VVVdouble& bpp::DRASDRTreeLikelihoodData::getLikelihoodArray ( int  parentId,
int  neighborId 
) const
inline

Definition at line 356 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

◆ getLikelihoodArrays() [1/2]

const std::map<int, VVVdouble>& bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays ( int  nodeId) const
inline

Definition at line 341 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), and bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix().

◆ getLikelihoodArrays() [2/2]

std::map<int, VVVdouble>& bpp::DRASDRTreeLikelihoodData::getLikelihoodArrays ( int  nodeId)
inline

Definition at line 346 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

◆ getNodeData() [1/2]

DRASDRTreeLikelihoodNodeData& bpp::DRASDRTreeLikelihoodData::getNodeData ( int  nodeId)
inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 316 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

◆ getNodeData() [2/2]

const DRASDRTreeLikelihoodNodeData& bpp::DRASDRTreeLikelihoodData::getNodeData ( int  nodeId) const
inlinevirtual

Implements bpp::TreeLikelihoodData.

Definition at line 321 of file DRASDRTreeLikelihoodData.h.

References nodeData_.

◆ getNumberOfClasses()

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfClasses ( ) const
inline

Definition at line 406 of file DRASDRTreeLikelihoodData.h.

References nbClasses_.

◆ getNumberOfDistinctSites()

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfDistinctSites ( ) const
inlinevirtual
Returns
The number of non redundant patterns.

Implements bpp::TreeLikelihoodData.

Definition at line 400 of file DRASDRTreeLikelihoodData.h.

References nbDistinctSites_.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate().

◆ getNumberOfSites()

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfSites ( ) const
inlinevirtual
Returns
The total number of sites.

Implements bpp::TreeLikelihoodData.

Definition at line 402 of file DRASDRTreeLikelihoodData.h.

References nbSites_.

◆ getNumberOfStates()

size_t bpp::DRASDRTreeLikelihoodData::getNumberOfStates ( ) const
inlinevirtual
Returns
Get the number of states used in the model.

Implements bpp::TreeLikelihoodData.

Definition at line 404 of file DRASDRTreeLikelihoodData.h.

References nbStates_.

◆ getRootArrayPosition()

size_t bpp::AbstractTreeLikelihoodData::getRootArrayPosition ( const size_t  site) const
inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Reimplemented in bpp::DRASRTreeLikelihoodData.

Definition at line 123 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

Referenced by bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousTreeLikelihood::getSiteIndex(), and bpp::DRNonHomogeneousTreeLikelihood::getSiteIndex().

◆ getRootArrayPositions() [1/2]

std::vector<size_t>& bpp::AbstractTreeLikelihoodData::getRootArrayPositions ( )
inlineinherited

Definition at line 121 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

◆ getRootArrayPositions() [2/2]

const std::vector<size_t>& bpp::AbstractTreeLikelihoodData::getRootArrayPositions ( ) const
inlineinherited

Definition at line 122 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootPatternLinks_.

◆ getRootLikelihoodArray() [1/2]

VVVdouble& bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray ( )
inline

Definition at line 391 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoods_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState().

◆ getRootLikelihoodArray() [2/2]

const VVVdouble& bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray ( ) const
inline

Definition at line 392 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoods_.

◆ getRootRateSiteLikelihoodArray() [1/2]

Vdouble& bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray ( )
inline

Definition at line 397 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsSR_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASite().

◆ getRootRateSiteLikelihoodArray() [2/2]

const Vdouble& bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray ( ) const
inline

Definition at line 398 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsSR_.

◆ getRootSiteLikelihoodArray() [1/2]

VVdouble& bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray ( )
inline

Definition at line 394 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsS_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass().

◆ getRootSiteLikelihoodArray() [2/2]

const VVdouble& bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray ( ) const
inline

Definition at line 395 of file DRASDRTreeLikelihoodData.h.

References rootLikelihoodsS_.

◆ getShrunkData()

const SiteContainer* bpp::DRASDRTreeLikelihoodData::getShrunkData ( ) const
inline

Definition at line 408 of file DRASDRTreeLikelihoodData.h.

References shrunkData_.

◆ getTree()

const TreeTemplate<Node>* bpp::AbstractTreeLikelihoodData::getTree ( ) const
inlinevirtualinherited

Implements bpp::TreeLikelihoodData.

Definition at line 138 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::tree_.

◆ getWeight()

unsigned int bpp::AbstractTreeLikelihoodData::getWeight ( size_t  pos) const
inlinevirtualinherited
Returns
The frequency of a given pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 127 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootWeights_.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

◆ getWeights()

const std::vector<unsigned int>& bpp::AbstractTreeLikelihoodData::getWeights ( ) const
inlinevirtualinherited
Returns
Frequencies for each pattern.

Implements bpp::TreeLikelihoodData.

Definition at line 131 of file AbstractTreeLikelihoodData.h.

References bpp::AbstractTreeLikelihoodData::rootWeights_.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), and bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood().

◆ initLikelihoods() [1/2]

void DRASDRTreeLikelihoodData::initLikelihoods ( const SiteContainer &  sites,
const SubstitutionModel &  model 
)
throw (Exception
)

Resize and initialize all likelihood arrays according to the given data set and substitution model.

Parameters
sitesThe sequences to use as data.
modelThe substitution model to use.
Exceptions
Exceptionif an error occures.

Definition at line 51 of file DRASDRTreeLikelihoodData.cpp.

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

◆ initLikelihoods() [2/2]

void DRASDRTreeLikelihoodData::initLikelihoods ( const Node *  node,
const SiteContainer &  sites,
const SubstitutionModel &  model 
)
throw (Exception
)
protected

This method initializes the leaves according to a sequence container.

Here the container shrunkData_ is used. Likelihood is set to 1 for the state corresponding to the sequence site, otherwise it is set to 0.

All likelihood arrays at each nodes are initialized according to alphabet size and sequences length, and filled with 1.

NB: This method is recursive.

Parameters
nodeThe node defining the subtree to analyse.
sitesThe sequence container to use.
modelThe model, used for initializing leaves' likelihoods.

Definition at line 104 of file DRASDRTreeLikelihoodData.cpp.

References bpp::DRASDRTreeLikelihoodNodeData::getD2LikelihoodArray(), bpp::DRASDRTreeLikelihoodNodeData::getDLikelihoodArray(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodLeafData::getLikelihoodArray(), bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrays(), bpp::Node::isLeaf(), bpp::DRASDRTreeLikelihoodLeafData::setNode(), and bpp::DRASDRTreeLikelihoodNodeData::setNode().

◆ operator=()

DRASDRTreeLikelihoodData& bpp::DRASDRTreeLikelihoodData::operator= ( const DRASDRTreeLikelihoodData &  data)
inline

Definition at line 267 of file DRASDRTreeLikelihoodData.h.

References leafData_, nbClasses_, nbDistinctSites_, nbSites_, nbStates_, nodeData_, bpp::AbstractTreeLikelihoodData::operator=(), rootLikelihoods_, rootLikelihoodsS_, rootLikelihoodsSR_, and shrunkData_.

◆ reInit() [1/2]

void DRASDRTreeLikelihoodData::reInit ( )
throw (Exception
)

Rebuild likelihood arrays at inner nodes.

This method is to be called when the topology of the tree has changed. Node arrays relationship are rebuilt according to the new topology of the tree. The leaves likelihood remain unchanged, so as for the first and second order derivatives.

Definition at line 209 of file DRASDRTreeLikelihoodData.cpp.

References bpp::AbstractTreeLikelihoodData::tree_.

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

◆ reInit() [2/2]

void DRASDRTreeLikelihoodData::reInit ( const Node *  node)
throw (Exception
)

Definition at line 214 of file DRASDRTreeLikelihoodData.cpp.

References bpp::DRASDRTreeLikelihoodNodeData::eraseNeighborArrays(), bpp::DRASDRTreeLikelihoodNodeData::getD2LikelihoodArray(), bpp::DRASDRTreeLikelihoodNodeData::getDLikelihoodArray(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrayForNeighbor(), bpp::DRASDRTreeLikelihoodLeafData::setNode(), and bpp::DRASDRTreeLikelihoodNodeData::setNode().

◆ setTree()

void bpp::DRASDRTreeLikelihoodData::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
treeThe tree to be associated to this data.

Definition at line 301 of file DRASDRTreeLikelihoodData.h.

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

Referenced by bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::operator=(), and bpp::DRNonHomogeneousTreeLikelihood::operator=().

Member Data Documentation

◆ alphabet_

const Alphabet* bpp::AbstractTreeLikelihoodData::alphabet_
protectedinherited

Definition at line 95 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getAlphabet(), and bpp::AbstractTreeLikelihoodData::operator=().

◆ leafData_

std::map<int, DRASDRTreeLikelihoodLeafData> bpp::DRASDRTreeLikelihoodData::leafData_
mutableprivate

Definition at line 235 of file DRASDRTreeLikelihoodData.h.

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

◆ nbClasses_

size_t bpp::DRASDRTreeLikelihoodData::nbClasses_
private

Definition at line 243 of file DRASDRTreeLikelihoodData.h.

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

◆ nbDistinctSites_

size_t bpp::DRASDRTreeLikelihoodData::nbDistinctSites_
private

Definition at line 244 of file DRASDRTreeLikelihoodData.h.

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

◆ nbSites_

size_t bpp::DRASDRTreeLikelihoodData::nbSites_
private

Definition at line 241 of file DRASDRTreeLikelihoodData.h.

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

◆ nbStates_

size_t bpp::DRASDRTreeLikelihoodData::nbStates_
private

Definition at line 242 of file DRASDRTreeLikelihoodData.h.

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

◆ nodeData_

std::map<int, DRASDRTreeLikelihoodNodeData> bpp::DRASDRTreeLikelihoodData::nodeData_
mutableprivate

Definition at line 234 of file DRASDRTreeLikelihoodData.h.

Referenced by getD2LikelihoodArray(), getDLikelihoodArray(), getLikelihoodArray(), getLikelihoodArrays(), getNodeData(), operator=(), and setTree().

◆ rootLikelihoods_

VVVdouble bpp::DRASDRTreeLikelihoodData::rootLikelihoods_
mutableprivate

Definition at line 236 of file DRASDRTreeLikelihoodData.h.

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

◆ rootLikelihoodsS_

VVdouble bpp::DRASDRTreeLikelihoodData::rootLikelihoodsS_
mutableprivate

Definition at line 237 of file DRASDRTreeLikelihoodData.h.

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

◆ rootLikelihoodsSR_

Vdouble bpp::DRASDRTreeLikelihoodData::rootLikelihoodsSR_
mutableprivate

Definition at line 238 of file DRASDRTreeLikelihoodData.h.

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

◆ rootPatternLinks_

std::vector<size_t> bpp::AbstractTreeLikelihoodData::rootPatternLinks_
protectedinherited

Links between sites and patterns.

The size of this vector is equal to the number of sites in the container, each element corresponds to a site in the container and points to the corresponding column in the likelihood array of the root node. If the container contains no repeated site, there will be a strict equivalence between each site and the likelihood array of the root node. However, if this is not the case, some pointers may point toward the same element in the likelihood array.

Definition at line 86 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::AbstractTreeLikelihoodData::getRootArrayPositions(), and bpp::AbstractTreeLikelihoodData::operator=().

◆ rootWeights_

std::vector<unsigned int> bpp::AbstractTreeLikelihoodData::rootWeights_
protectedinherited

The frequency of each site.

Definition at line 91 of file AbstractTreeLikelihoodData.h.

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

◆ shrunkData_

SiteContainer* bpp::DRASDRTreeLikelihoodData::shrunkData_
private

Definition at line 240 of file DRASDRTreeLikelihoodData.h.

Referenced by DRASDRTreeLikelihoodData(), getShrunkData(), operator=(), and ~DRASDRTreeLikelihoodData().

◆ tree_

const TreeTemplate<Node>* bpp::AbstractTreeLikelihoodData::tree_
protectedinherited

Definition at line 93 of file AbstractTreeLikelihoodData.h.

Referenced by bpp::AbstractTreeLikelihoodData::getTree(), bpp::AbstractTreeLikelihoodData::operator=(), reInit(), bpp::DRASRTreeLikelihoodData::setTree(), and setTree().

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