bpp-phyl
2.2.0
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Partial implementation of the TreeLikelihood interface. More...
#include <Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h>
Classes | |
class | ConstNoPartitionBranchModelDescription |
class | ConstNoPartitionBranchModelIterator |
class | ConstNoPartitionSiteModelDescription |
class | SimpleBranchIterator |
A very simple branch iterator. More... | |
class | SimpleSiteIterator |
A very simple site iterator. More... | |
Public Member Functions | |
AbstractTreeLikelihood () | |
AbstractTreeLikelihood (const AbstractTreeLikelihood &lik) | |
AbstractTreeLikelihood & | operator= (const AbstractTreeLikelihood &lik) |
virtual | ~AbstractTreeLikelihood () |
Abstract class destructor. More... | |
TreeLikelihood * | clone () const =0 |
virtual void | setData (const SiteContainer &sites)=0 |
Set the dataset for which the likelihood must be evaluated. More... | |
virtual TreeLikelihoodData * | getLikelihoodData ()=0 |
virtual const TreeLikelihoodData * | getLikelihoodData () const =0 |
virtual double | getLikelihoodForASite (size_t site) const =0 |
Get the likelihood for a site. More... | |
virtual double | getLogLikelihoodForASite (size_t site) const =0 |
Get the logarithm of the likelihood for a site. More... | |
virtual double | getLikelihoodForASiteForAState (size_t site, int state) const =0 |
Get the likelihood for a site and for a state. More... | |
virtual double | getLogLikelihoodForASiteForAState (size_t site, int state) const =0 |
Get the logarithm of the likelihood for a site and for a state. More... | |
virtual double | getLikelihood () const =0 |
Get the likelihood for the whole dataset. More... | |
virtual double | getLogLikelihood () const =0 |
Get the logarithm of the likelihood for the whole dataset. More... | |
virtual size_t | getNumberOfStates () const =0 |
virtual int | getAlphabetStateAsInt (size_t i) const =0 |
virtual std::string | getAlphabetStateAsChar (size_t i) const =0 |
virtual const std::vector< int > & | getAlphabetStates () const =0 |
virtual ParameterList | getDerivableParameters () const =0 |
All derivable parameters. More... | |
virtual ParameterList | getNonDerivableParameters () const =0 |
All non derivable parameters. More... | |
The TreeLikelihood interface. | |
const SiteContainer * | getData () const |
Get the dataset for which the likelihood must be evaluated. More... | |
const Alphabet * | getAlphabet () const |
Get the alphabet associated to the dataset. More... | |
Vdouble | getLikelihoodForEachSite () const |
Get the likelihood for each site. More... | |
Vdouble | getLogLikelihoodForEachSite () const |
Get the logarithm of the likelihood for each site. More... | |
VVdouble | getLikelihoodForEachSiteForEachState () const |
Get the likelihood for each site and for each state. More... | |
VVdouble | getLogLikelihoodForEachSiteForEachState () const |
Get the logarithm of the likelihood for each site and for each state. More... | |
size_t | getNumberOfSites () const |
Get the number of sites in the dataset. More... | |
const Tree & | getTree () const |
Get the tree (topology and branch lengths). More... | |
void | enableDerivatives (bool yn) |
Tell if derivatives must be computed. More... | |
void | enableFirstOrderDerivatives (bool yn) |
void | enableSecondOrderDerivatives (bool yn) |
bool | enableFirstOrderDerivatives () const |
bool | enableSecondOrderDerivatives () const |
bool | isInitialized () const |
void | initialize () throw (Exception) |
Init the likelihood object. More... | |
Retrieve some particular parameters subsets. | |
virtual ParameterList | getBranchLengthsParameters () const =0 |
Get the branch lengths parameters. More... | |
virtual ParameterList | getSubstitutionModelParameters () const =0 |
Get the parameters associated to substitution model(s). More... | |
virtual const SubstitutionModel * | getSubstitutionModel (int nodeId, size_t siteIndex) const =0 throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
virtual SubstitutionModel * | getSubstitutionModel (int nodeId, size_t siteIndex)=0 throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
virtual VVdouble | getTransitionProbabilities (int nodeId, size_t siteIndex) const =0 |
Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More... | |
virtual ConstBranchModelIterator * | getNewBranchModelIterator (int nodeId) const =0 |
virtual ConstSiteModelIterator * | getNewSiteModelIterator (size_t siteIndex) const =0 |
virtual size_t | getSiteIndex (size_t site) const =0 throw (IndexOutOfBoundsException) |
Get the index (used for inner computations) of a given site (original alignment column). More... | |
virtual const std::vector< double > & | getRootFrequencies (size_t siteIndex) const =0 |
Get the values of the frequencies for each state in the alphabet at the root node. More... | |
Protected Attributes | |
const SiteContainer * | data_ |
TreeTemplate< Node > * | tree_ |
bool | computeFirstOrderDerivatives_ |
bool | computeSecondOrderDerivatives_ |
bool | initialized_ |
Partial implementation of the TreeLikelihood interface.
This class implements a few methods useful for most of likelihood computation methods.
It includes a tree_ and a data_ pointers. This objects are owned by the class, and hence hard copied when cloning, and destroyed by the destructor.
It also adds an abstract method for recursive computations.
Definition at line 69 of file AbstractTreeLikelihood.h.
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inline |
Definition at line 232 of file AbstractTreeLikelihood.h.
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inline |
Definition at line 240 of file AbstractTreeLikelihood.h.
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inlinevirtual |
Abstract class destructor.
This destructor is empty.
Definition at line 272 of file AbstractTreeLikelihood.h.
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pure virtualinherited |
Implemented in bpp::NNIHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousClockTreeLikelihood, bpp::DRTreeLikelihood, bpp::DiscreteRatesAcrossSitesClockTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::ClockTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.
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inlinevirtual |
Tell if derivatives must be computed.
This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.
yn | Yes or no. |
Implements bpp::TreeLikelihood.
Definition at line 292 of file AbstractTreeLikelihood.h.
References computeFirstOrderDerivatives_, and computeSecondOrderDerivatives_.
Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood(), and bpp::DistanceEstimation::computeMatrix().
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inline |
Definition at line 293 of file AbstractTreeLikelihood.h.
References computeFirstOrderDerivatives_.
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inline |
Definition at line 295 of file AbstractTreeLikelihood.h.
References computeFirstOrderDerivatives_.
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inline |
Definition at line 294 of file AbstractTreeLikelihood.h.
References computeFirstOrderDerivatives_, and computeSecondOrderDerivatives_.
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inline |
Definition at line 296 of file AbstractTreeLikelihood.h.
References computeSecondOrderDerivatives_.
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inlinevirtual |
Get the alphabet associated to the dataset.
Implements bpp::TreeLikelihood.
Definition at line 285 of file AbstractTreeLikelihood.h.
References data_.
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pure virtualinherited |
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
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pure virtualinherited |
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
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pure virtualinherited |
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
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pure virtualinherited |
Get the branch lengths parameters.
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
Referenced by bpp::OptimizationTools::ScaleFunction::ScaleFunction().
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inlinevirtual |
Get the dataset for which the likelihood must be evaluated.
Implements bpp::TreeLikelihood.
Definition at line 284 of file AbstractTreeLikelihood.h.
References data_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().
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pure virtualinherited |
All derivable parameters.
Usually, this contains all branch lengths parameters.
Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
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pure virtualinherited |
Get the likelihood for the whole dataset.
Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.
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pure virtualinherited |
Implemented in bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::DRTreeLikelihood.
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pure virtualinherited |
Implemented in bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::DRTreeLikelihood.
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pure virtualinherited |
Get the likelihood for a site.
site | The site index to analyse. |
Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.
Referenced by getLikelihoodForEachSite().
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pure virtualinherited |
Get the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Referenced by getLikelihoodForEachSiteForEachState().
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virtual |
Get the likelihood for each site.
Implements bpp::TreeLikelihood.
Definition at line 46 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLikelihoodForASite(), and getNumberOfSites().
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virtual |
Get the likelihood for each site and for each state.
Implements bpp::TreeLikelihood.
Definition at line 64 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLikelihoodForASiteForAState(), getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().
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pure virtualinherited |
Get the logarithm of the likelihood for the whole dataset.
Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.
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pure virtualinherited |
Get the logarithm of the likelihood for a site.
site | The site index to analyse. |
Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.
Referenced by getLogLikelihoodForEachSite().
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pure virtualinherited |
Get the logarithm of the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Referenced by getLogLikelihoodForEachSiteForEachState().
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virtual |
Get the logarithm of the likelihood for each site.
Implements bpp::TreeLikelihood.
Definition at line 55 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLogLikelihoodForASite(), and getNumberOfSites().
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virtual |
Get the logarithm of the likelihood for each site and for each state.
Implements bpp::TreeLikelihood.
Definition at line 81 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLogLikelihoodForASiteForAState(), getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().
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pure virtualinherited |
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pure virtualinherited |
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pure virtualinherited |
All non derivable parameters.
Usually, this contains all substitution model parameters and rate distribution.
Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
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inlinevirtual |
Get the number of sites in the dataset.
Implements bpp::TreeLikelihood.
Definition at line 290 of file AbstractTreeLikelihood.h.
References data_.
Referenced by getLikelihoodForEachSite(), getLikelihoodForEachSiteForEachState(), getLogLikelihoodForEachSite(), and getLogLikelihoodForEachSiteForEachState().
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pure virtualinherited |
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
Referenced by getLikelihoodForEachSiteForEachState(), getLogLikelihoodForEachSiteForEachState(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().
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pure virtualinherited |
Get the values of the frequencies for each state in the alphabet at the root node.
For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.
For models without site partitioning, the set of frequencies is the same for all positions. For partition models, the frequencies may differ from one site to another.
siteIndex | The index of the alignment position. |
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
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pure virtualinherited |
Get the index (used for inner computations) of a given site (original alignment column).
site | An alignment position. |
Implemented in bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousTreeLikelihood.
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pure virtualinherited |
Get the substitution model associated to a given node and alignment column.
nodeId | The id of the request node. |
siteIndex | The index of the alignment position. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implemented in bpp::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.
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pure virtualinherited |
Get the substitution model associated to a given node and alignment column.
nodeId | The id of the request node. |
siteIndex | The index of the alignment position. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implemented in bpp::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.
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pure virtualinherited |
Get the parameters associated to substitution model(s).
Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.
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pure virtualinherited |
Retrieves all Pij(t) for a particular branch, defined by the upper node and site.
These intermediate results may be used by other methods.
nodeId | The node defining the branch of interest. |
siteIndex | The index of the alignment position. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
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inlinevirtual |
Get the tree (topology and branch lengths).
Implements bpp::TreeLikelihood.
Definition at line 291 of file AbstractTreeLikelihood.h.
References tree_.
Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopology(), and bpp::RNonHomogeneousMixedTreeLikelihood::init().
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inlinevirtual |
Init the likelihood object.
This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.
Exception | if something bad happened, for instance if no data are associated to the likelihood function. |
Implements bpp::TreeLikelihood.
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.
Definition at line 298 of file AbstractTreeLikelihood.h.
References initialized_.
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inlinevirtual |
Implements bpp::TreeLikelihood.
Definition at line 297 of file AbstractTreeLikelihood.h.
References initialized_.
Referenced by bpp::DRHomogeneousTreeLikelihood::getValue(), bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), and bpp::RNonHomogeneousTreeLikelihood::getValue().
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inline |
Definition at line 252 of file AbstractTreeLikelihood.h.
References computeFirstOrderDerivatives_, computeSecondOrderDerivatives_, data_, initialized_, and tree_.
Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=().
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pure virtualinherited |
Set the dataset for which the likelihood must be evaluated.
sites | The data set to use. |
Implemented in bpp::RNonHomogeneousMixedTreeLikelihood, bpp::NNIHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.
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Definition at line 227 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), enableDerivatives(), enableFirstOrderDerivatives(), enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and operator=().
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Definition at line 228 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), enableDerivatives(), enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and operator=().
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Definition at line 225 of file AbstractTreeLikelihood.h.
Referenced by AbstractTreeLikelihood(), getAlphabet(), getData(), getNumberOfSites(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), operator=(), and ~AbstractTreeLikelihood().
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Definition at line 229 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::TwoTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::TwoTreeLikelihood::initialize(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), initialize(), isInitialized(), and operator=().
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mutableprotected |
Definition at line 226 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), AbstractTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), getTree(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), bpp::RNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), and ~AbstractTreeLikelihood().