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

Data structure to store the result of a DetailedSiteSimulator. More...

#include <Bpp/Phyl/Simulation/DetailedSiteSimulator.h>

+ Inheritance diagram for bpp::RASiteSimulationResult:
+ Collaboration diagram for bpp::RASiteSimulationResult:

Public Member Functions

 RASiteSimulationResult (const Tree *tree, const Alphabet *alphabet, size_t ancestralStateIndex, double rate)
 
virtual ~RASiteSimulationResult ()
 
virtual double getRate () const
 
virtual const Alphabet * getAlphabet () const
 
virtual void addNode (int nodeId, MutationPath path)
 
virtual size_t getAncestralState (size_t i) const
 
virtual size_t getAncestralState (int nodeId) const
 
virtual const MutationPath & getMutationPath (size_t i) const
 
virtual const MutationPath & getMutationPath (int nodeId) const
 
virtual size_t getSubstitutionCount (size_t i) const
 
virtual void getSubstitutionCount (size_t i, const SubstitutionRegister &reg, std::vector< double > &counts) const
 
virtual size_t getSubstitutionCount (int nodeId) const
 
virtual void getSubstitutionCount (int nodeId, const SubstitutionRegister &reg, std::vector< double > &counts) const
 
virtual VVdouble getSubstitutionVector (const SubstitutionRegister &reg) const
 
virtual std::vector< size_t > getFinalStates () const
 
virtual Site * getSite (const SubstitutionModel &model) const
 
virtual std::vector< std::string > getLeaveNames () const
 

Protected Attributes

double rate_
 

Detailed Description

Data structure to store the result of a DetailedSiteSimulator.

This sructure inherits from the SequenceSimulationResult class, and add support for rate variation across sites.

Definition at line 206 of file DetailedSiteSimulator.h.

Constructor & Destructor Documentation

◆ RASiteSimulationResult()

bpp::RASiteSimulationResult::RASiteSimulationResult ( const Tree *  tree,
const Alphabet *  alphabet,
size_t  ancestralStateIndex,
double  rate 
)
inline

Definition at line 213 of file DetailedSiteSimulator.h.

◆ ~RASiteSimulationResult()

virtual bpp::RASiteSimulationResult::~RASiteSimulationResult ( )
inlinevirtual

Definition at line 217 of file DetailedSiteSimulator.h.

Member Function Documentation

◆ addNode()

virtual void bpp::SiteSimulationResult::addNode ( int  nodeId,
MutationPath  path 
)
inlinevirtualinherited

Definition at line 117 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_, bpp::SiteSimulationResult::currentIndex_, bpp::MutationPath::getFinalState(), bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

Referenced by bpp::NonHomogeneousSequenceSimulator::dEvolveInternal().

◆ getAlphabet()

virtual const Alphabet* bpp::SiteSimulationResult::getAlphabet ( ) const
inlinevirtualinherited
Returns
The alphabet associated to this simulation.

Definition at line 115 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::alphabet_.

◆ getAncestralState() [1/2]

virtual size_t bpp::SiteSimulationResult::getAncestralState ( size_t  i) const
inlinevirtualinherited

Definition at line 125 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_.

◆ getAncestralState() [2/2]

virtual size_t bpp::SiteSimulationResult::getAncestralState ( int  nodeId) const
inlinevirtualinherited

Definition at line 127 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_, and bpp::SiteSimulationResult::indexes_.

◆ getFinalStates()

virtual std::vector<size_t> bpp::SiteSimulationResult::getFinalStates ( ) const
inlinevirtualinherited
Returns
The states at the leaves.

Definition at line 159 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::ancestralStates_, bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::leavesId_.

Referenced by bpp::SiteSimulationResult::getSite().

◆ getLeaveNames()

virtual std::vector<std::string> bpp::SiteSimulationResult::getLeaveNames ( ) const
inlinevirtualinherited
Returns
A vector with the leaves names.

Definition at line 185 of file DetailedSiteSimulator.h.

References bpp::Tree::getNodeName(), bpp::SiteSimulationResult::leavesId_, and bpp::SiteSimulationResult::tree_.

◆ getMutationPath() [1/2]

virtual const MutationPath& bpp::SiteSimulationResult::getMutationPath ( size_t  i) const
inlinevirtualinherited

Definition at line 129 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::paths_.

◆ getMutationPath() [2/2]

virtual const MutationPath& bpp::SiteSimulationResult::getMutationPath ( int  nodeId) const
inlinevirtualinherited

Definition at line 131 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

◆ getRate()

virtual double bpp::RASiteSimulationResult::getRate ( ) const
inlinevirtual
Returns
The rate of this simulation.

Definition at line 223 of file DetailedSiteSimulator.h.

References rate_.

◆ getSite()

virtual Site* bpp::SiteSimulationResult::getSite ( const SubstitutionModel &  model) const
inlinevirtualinherited
Returns
The site corresponding to this simulation.

Definition at line 173 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::alphabet_, bpp::SubstitutionModel::getAlphabetStateAsInt(), and bpp::SiteSimulationResult::getFinalStates().

◆ getSubstitutionCount() [1/4]

virtual size_t bpp::SiteSimulationResult::getSubstitutionCount ( size_t  i) const
inlinevirtualinherited

Definition at line 133 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::paths_.

◆ getSubstitutionCount() [2/4]

virtual void bpp::SiteSimulationResult::getSubstitutionCount ( size_t  i,
const SubstitutionRegister &  reg,
std::vector< double > &  counts 
) const
inlinevirtualinherited

Definition at line 135 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::paths_.

◆ getSubstitutionCount() [3/4]

virtual size_t bpp::SiteSimulationResult::getSubstitutionCount ( int  nodeId) const
inlinevirtualinherited

Definition at line 139 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

◆ getSubstitutionCount() [4/4]

virtual void bpp::SiteSimulationResult::getSubstitutionCount ( int  nodeId,
const SubstitutionRegister &  reg,
std::vector< double > &  counts 
) const
inlinevirtualinherited

Definition at line 141 of file DetailedSiteSimulator.h.

References bpp::SiteSimulationResult::indexes_, and bpp::SiteSimulationResult::paths_.

◆ getSubstitutionVector()

virtual VVdouble bpp::SiteSimulationResult::getSubstitutionVector ( const SubstitutionRegister &  reg) const
inlinevirtualinherited

Definition at line 145 of file DetailedSiteSimulator.h.

References bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), and bpp::SiteSimulationResult::paths_.

Member Data Documentation

◆ rate_

double bpp::RASiteSimulationResult::rate_
protected

Definition at line 210 of file DetailedSiteSimulator.h.

Referenced by getRate().

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