bpp-phyl
2.2.0
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Likelihood data structure for a node. More...
#include <Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h>
Public Member Functions | |
DRASDRTreeLikelihoodNodeData () | |
DRASDRTreeLikelihoodNodeData (const DRASDRTreeLikelihoodNodeData &data) | |
DRASDRTreeLikelihoodNodeData & | operator= (const DRASDRTreeLikelihoodNodeData &data) |
virtual | ~DRASDRTreeLikelihoodNodeData () |
DRASDRTreeLikelihoodNodeData * | clone () const |
const Node * | getNode () const |
Get the node associated to this data structure. More... | |
void | setNode (const Node *node) |
Set the node associated to this data. More... | |
const std::map< int, VVVdouble > & | getLikelihoodArrays () const |
std::map< int, VVVdouble > & | getLikelihoodArrays () |
VVVdouble & | getLikelihoodArrayForNeighbor (int neighborId) |
const VVVdouble & | getLikelihoodArrayForNeighbor (int neighborId) const |
Vdouble & | getDLikelihoodArray () |
const Vdouble & | getDLikelihoodArray () const |
Vdouble & | getD2LikelihoodArray () |
const Vdouble & | getD2LikelihoodArrayForNeighbor () const |
bool | isNeighbor (int neighborId) const |
void | eraseNeighborArrays () |
Private Attributes | |
std::map< int, VVVdouble > | nodeLikelihoods_ |
This contains all likelihood values used for computation. More... | |
Vdouble | nodeDLikelihoods_ |
This contains all likelihood first order derivatives values used for computation. More... | |
Vdouble | nodeD2Likelihoods_ |
This contains all likelihood second order derivatives values used for computation. More... | |
const Node * | node_ |
Likelihood data structure for a node.
This class is for use with the DRASDRTreeLikelihoodData class.
Store for each neighbor node an array with conditionnal likelihoods.
Definition at line 113 of file DRASDRTreeLikelihoodData.h.
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inline |
Definition at line 156 of file DRASDRTreeLikelihoodData.h.
Referenced by clone().
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inline |
Definition at line 158 of file DRASDRTreeLikelihoodData.h.
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inlinevirtual |
Definition at line 174 of file DRASDRTreeLikelihoodData.h.
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inlinevirtual |
Implements bpp::TreeLikelihoodNodeData.
Definition at line 181 of file DRASDRTreeLikelihoodData.h.
References DRASDRTreeLikelihoodNodeData().
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inline |
Definition at line 218 of file DRASDRTreeLikelihoodData.h.
References nodeD2Likelihoods_, nodeDLikelihoods_, and nodeLikelihoods_.
Referenced by bpp::DRASDRTreeLikelihoodData::reInit().
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inline |
Definition at line 209 of file DRASDRTreeLikelihoodData.h.
References nodeD2Likelihoods_.
Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASDRTreeLikelihoodData::reInit().
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Definition at line 211 of file DRASDRTreeLikelihoodData.h.
References nodeD2Likelihoods_.
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Definition at line 205 of file DRASDRTreeLikelihoodData.h.
References nodeDLikelihoods_.
Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASDRTreeLikelihoodData::reInit().
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Definition at line 207 of file DRASDRTreeLikelihoodData.h.
References nodeDLikelihoods_.
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inline |
Definition at line 195 of file DRASDRTreeLikelihoodData.h.
References nodeLikelihoods_.
Referenced by bpp::DRASDRTreeLikelihoodData::reInit(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().
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inline |
Definition at line 200 of file DRASDRTreeLikelihoodData.h.
References nodeLikelihoods_.
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inline |
Definition at line 191 of file DRASDRTreeLikelihoodData.h.
References nodeLikelihoods_.
Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods().
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Definition at line 193 of file DRASDRTreeLikelihoodData.h.
References nodeLikelihoods_.
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inlinevirtual |
Get the node associated to this data structure.
Implements bpp::TreeLikelihoodNodeData.
Definition at line 187 of file DRASDRTreeLikelihoodData.h.
References node_.
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inline |
Definition at line 213 of file DRASDRTreeLikelihoodData.h.
References nodeLikelihoods_.
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inline |
Definition at line 165 of file DRASDRTreeLikelihoodData.h.
References node_, nodeD2Likelihoods_, nodeDLikelihoods_, and nodeLikelihoods_.
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inlinevirtual |
Set the node associated to this data.
A pointer toward this node will be created and associated to this data.
node | The node to be associated to this data. |
Implements bpp::TreeLikelihoodNodeData.
Definition at line 189 of file DRASDRTreeLikelihoodData.h.
References node_.
Referenced by bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASDRTreeLikelihoodData::reInit().
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private |
Definition at line 153 of file DRASDRTreeLikelihoodData.h.
Referenced by getNode(), operator=(), and setNode().
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mutableprivate |
This contains all likelihood second order derivatives values used for computation.
x[i] |---------> Site i
We call this the d2Likelihood array for each node.
Definition at line 151 of file DRASDRTreeLikelihoodData.h.
Referenced by eraseNeighborArrays(), getD2LikelihoodArray(), getD2LikelihoodArrayForNeighbor(), and operator=().
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mutableprivate |
This contains all likelihood first order derivatives values used for computation.
x[i] |---------> Site i
We call this the dLikelihood array for each node.
Definition at line 140 of file DRASDRTreeLikelihoodData.h.
Referenced by eraseNeighborArrays(), getDLikelihoodArray(), and operator=().
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mutableprivate |
This contains all likelihood values used for computation.
x[b][i][c][s] |------------> Neighbor node of n (id) |---------> Site i |------> Rate class c |---> Ancestral state s
We call this the likelihood array for each node.
Definition at line 130 of file DRASDRTreeLikelihoodData.h.
Referenced by eraseNeighborArrays(), getLikelihoodArrayForNeighbor(), getLikelihoodArrays(), isNeighbor(), and operator=().