bpp-phyl3 3.0.0
Public Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
bpp::OneJumpSubstitutionCount Class Reference

Computes the probability that at least one jump occurred on a branch, given the initial and final state. More...

#include <Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h>

+ Inheritance diagram for bpp::OneJumpSubstitutionCount:
+ Collaboration diagram for bpp::OneJumpSubstitutionCount:

Public Member Functions

 OneJumpSubstitutionCount (std::shared_ptr< const SubstitutionModelInterface > model)
 
 OneJumpSubstitutionCount (std::shared_ptr< const StateMapInterface > statemap)
 
 OneJumpSubstitutionCount (const OneJumpSubstitutionCount &ojsc)
 
OneJumpSubstitutionCount & operator= (const OneJumpSubstitutionCount &ojsc)
 
virtual ~OneJumpSubstitutionCount ()
 
virtual OneJumpSubstitutionCount * clone () const override
 
double getNumberOfSubstitutions (size_t initialState, size_t finalState, double length, size_t type=1) const override
 Get the number of susbstitutions on a branch, given the initial and final states, and the branch length. More...
 
std::unique_ptr< Matrix< double > > getAllNumbersOfSubstitutions (double length, size_t type=1) const override
 Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...
 
void storeAllNumbersOfSubstitutions (double length, size_t type, Eigen::MatrixXd &mat) const override
 Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...
 
std::vector< double > getNumberOfSubstitutionsPerType (size_t initialState, size_t finalState, double length) const override
 Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length. More...
 
void setSubstitutionModel (std::shared_ptr< const SubstitutionModelInterface > model) override
 Set the substitution model associated with this count, if relevant. More...
 
void setSubstitutionRegister (std::shared_ptr< const SubstitutionRegisterInterface > reg) override
 
bool hasSubstitutionRegister () const
 
std::shared_ptr< const SubstitutionRegisterInterface > getSubstitutionRegister () const
 
virtual size_t getNumberOfSubstitutionTypes () const
 Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes(). More...
 
virtual std::shared_ptr< const Alphabet > getAlphabet () const
 Short cut function, equivalent to getSubstitutionRegister()->getAlphabet(). More...
 
virtual size_t getNumberOfStates () const
 Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize(). More...
 

Protected Attributes

std::shared_ptr< const SubstitutionRegisterInterface > register_
 

Private Member Functions

void substitutionRegisterHasChanged () override
 

Private Attributes

std::shared_ptr< const SubstitutionModelInterface > model_
 
RowMatrix< double > tmp_
 

Detailed Description

Computes the probability that at least one jump occurred on a branch, given the initial and final state.

This probability is defined as

\[ p_{x,y}(l) = \left\{\begin{array}{ll}1 & \mathrm{if} x \neq y \\ 1 - \exp{\left(Q \cdot t\right)}_{x,y} & \mathrm{otherwise.}\end{array}\right. \]

Author
Julien Dutheil

Definition at line 24 of file OneJumpSubstitutionCount.h.

Constructor & Destructor Documentation

◆ OneJumpSubstitutionCount() [1/3]

bpp::OneJumpSubstitutionCount::OneJumpSubstitutionCount ( std::shared_ptr< const SubstitutionModelInterface >  model)
inline

Definition at line 32 of file OneJumpSubstitutionCount.h.

Referenced by clone().

◆ OneJumpSubstitutionCount() [2/3]

bpp::OneJumpSubstitutionCount::OneJumpSubstitutionCount ( std::shared_ptr< const StateMapInterface >  statemap)
inline

Definition at line 36 of file OneJumpSubstitutionCount.h.

◆ OneJumpSubstitutionCount() [3/3]

bpp::OneJumpSubstitutionCount::OneJumpSubstitutionCount ( const OneJumpSubstitutionCount &  ojsc)
inline

Definition at line 40 of file OneJumpSubstitutionCount.h.

◆ ~OneJumpSubstitutionCount()

virtual bpp::OneJumpSubstitutionCount::~OneJumpSubstitutionCount ( )
inlinevirtual

Definition at line 52 of file OneJumpSubstitutionCount.h.

Member Function Documentation

◆ clone()

virtual OneJumpSubstitutionCount * bpp::OneJumpSubstitutionCount::clone ( ) const
inlineoverridevirtual

Implements bpp::SubstitutionCountInterface.

Definition at line 54 of file OneJumpSubstitutionCount.h.

References OneJumpSubstitutionCount().

◆ getAllNumbersOfSubstitutions()

unique_ptr< Matrix< double > > OneJumpSubstitutionCount::getAllNumbersOfSubstitutions ( double  length,
size_t  type = 1 
) const
overridevirtual

Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.

Parameters
lengthThe length of the branch.
typeThe type of susbstitution to count.
Returns
A matrix with all numbers of substitutions for each initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 10 of file OneJumpSubstitutionCount.cpp.

References model_, and tmp_.

◆ getAlphabet()

virtual std::shared_ptr< const Alphabet > bpp::SubstitutionCountInterface::getAlphabet ( ) const
inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet().

Returns
The alphabet associated to this substitution count.

Definition at line 78 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

◆ getNumberOfStates()

virtual size_t bpp::SubstitutionCountInterface::getNumberOfStates ( ) const
inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister()->getAlphabet()->getSize().

Returns
The number of states in the model/alphabet.

Definition at line 85 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

◆ getNumberOfSubstitutions()

double bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions ( size_t  initialState,
size_t  finalState,
double  length,
size_t  type = 1 
) const
inlineoverridevirtual

Get the number of susbstitutions on a branch, given the initial and final states, and the branch length.

Parameters
initialStateThe initial state.
finalStateThe final state.
lengthThe length of the branch.
typeThe type of substitution to count.
Returns
The number of substitutions on a branch of specified length and according to initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 57 of file OneJumpSubstitutionCount.h.

References model_.

Referenced by getNumberOfSubstitutionsPerType().

◆ getNumberOfSubstitutionsPerType()

std::vector< double > bpp::OneJumpSubstitutionCount::getNumberOfSubstitutionsPerType ( size_t  initialState,
size_t  finalState,
double  length 
) const
inlineoverridevirtual

Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length.

Parameters
initialStateThe initial state.
finalStateThe final state.
lengthThe length of the branch.
Returns
A matrix with all numbers of substitutions for each initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 70 of file OneJumpSubstitutionCount.h.

References getNumberOfSubstitutions().

◆ getNumberOfSubstitutionTypes()

virtual size_t bpp::SubstitutionCountInterface::getNumberOfSubstitutionTypes ( ) const
inlinevirtualinherited

Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes().

Returns
The number of substitution types supported by this instance.

Definition at line 71 of file SubstitutionCount.h.

References bpp::SubstitutionCountInterface::getSubstitutionRegister().

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsPerType(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsPerType(), and bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsPerType().

◆ getSubstitutionRegister()

std::shared_ptr< const SubstitutionRegisterInterface > bpp::AbstractSubstitutionCount::getSubstitutionRegister ( ) const
inlinevirtualinherited
Returns
The SubstitutionRegister object associated to this instance. The register contains the description of the various substitutions types that are mapped.

Implements bpp::SubstitutionCountInterface.

Definition at line 170 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ hasSubstitutionRegister()

bool bpp::AbstractSubstitutionCount::hasSubstitutionRegister ( ) const
inlinevirtualinherited
Returns
Tell if a substitution register has been attached to this class.

Implements bpp::SubstitutionCountInterface.

Definition at line 156 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ operator=()

OneJumpSubstitutionCount & bpp::OneJumpSubstitutionCount::operator= ( const OneJumpSubstitutionCount &  ojsc)
inline

Definition at line 44 of file OneJumpSubstitutionCount.h.

References model_, and tmp_.

◆ setSubstitutionModel()

void bpp::OneJumpSubstitutionCount::setSubstitutionModel ( std::shared_ptr< const SubstitutionModelInterface >  model)
inlineoverridevirtual

Set the substitution model associated with this count, if relevant.

Parameters
modelThe substitution model to use with this count.

Implements bpp::SubstitutionCountInterface.

Definition at line 77 of file OneJumpSubstitutionCount.h.

References model_.

◆ setSubstitutionRegister()

void bpp::OneJumpSubstitutionCount::setSubstitutionRegister ( std::shared_ptr< const SubstitutionRegisterInterface >  reg)
inlineoverridevirtual
Parameters
regThe new SubstitutionRegister object to be associated to this instance. The register contains the description of the various substitutions types that are mapped.

Implements bpp::SubstitutionCountInterface.

Definition at line 83 of file OneJumpSubstitutionCount.h.

◆ storeAllNumbersOfSubstitutions()

void OneJumpSubstitutionCount::storeAllNumbersOfSubstitutions ( double  length,
size_t  type,
Eigen::MatrixXd &  mat 
) const
overridevirtual

Stores the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length.

Parameters
lengthThe length of the branch.
typeThe type of susbstitution to count.
matThe matrix filled with all numbers of substitutions for each initial and final states.

Implements bpp::SubstitutionCountInterface.

Definition at line 28 of file OneJumpSubstitutionCount.cpp.

References model_, and tmp_.

◆ substitutionRegisterHasChanged()

void bpp::OneJumpSubstitutionCount::substitutionRegisterHasChanged ( )
inlineoverrideprivatevirtual

Implements bpp::AbstractSubstitutionCount.

Definition at line 89 of file OneJumpSubstitutionCount.h.

Member Data Documentation

◆ model_

std::shared_ptr<const SubstitutionModelInterface> bpp::OneJumpSubstitutionCount::model_
private

Definition at line 28 of file OneJumpSubstitutionCount.h.

Referenced by getAllNumbersOfSubstitutions(), getNumberOfSubstitutions(), operator=(), setSubstitutionModel(), and storeAllNumbersOfSubstitutions().

◆ register_

std::shared_ptr<const SubstitutionRegisterInterface> bpp::AbstractSubstitutionCount::register_
protectedinherited

Definition at line 146 of file SubstitutionCount.h.

Referenced by bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::distancesHaveChanged(), bpp::UniformizationSubstitutionCount::distancesHaveChanged(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::NaiveSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractSubstitutionCount::getSubstitutionRegister(), bpp::AbstractSubstitutionCount::hasSubstitutionRegister(), bpp::UniformizationSubstitutionCount::initBMatrices_(), bpp::DecompositionSubstitutionCount::initCounts_(), bpp::UniformizationSubstitutionCount::resetBMatrices_(), bpp::DecompositionSubstitutionCount::setDistanceBMatrices_(), bpp::UniformizationSubstitutionCount::setDistanceBMatrices_(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::AbstractSubstitutionCount::setSubstitutionRegister(), bpp::NaiveSubstitutionCount::storeAllNumbersOfSubstitutions(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::weightsHaveChanged(), and bpp::UniformizationSubstitutionCount::weightsHaveChanged().

◆ tmp_

RowMatrix<double> bpp::OneJumpSubstitutionCount::tmp_
mutableprivate

Definition at line 29 of file OneJumpSubstitutionCount.h.

Referenced by getAllNumbersOfSubstitutions(), operator=(), and storeAllNumbersOfSubstitutions().

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