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

Labelling substitution count. More...

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

+ Inheritance diagram for bpp::LabelSubstitutionCount:
+ Collaboration diagram for bpp::LabelSubstitutionCount:

Public Member Functions

 LabelSubstitutionCount (const SubstitutionModel *model)
 
virtual ~LabelSubstitutionCount ()
 
LabelSubstitutionCount * clone () const
 
double getNumberOfSubstitutions (size_t initialState, size_t finalState, double length, size_t type=1) const
 Get the number of susbstitutions on a branch, given the initial and final states, and the branch length. More...
 
Matrix< double > * getAllNumbersOfSubstitutions (double length, size_t type=1) const
 Get the numbers of susbstitutions on a branch, for each initial and final states, and given the branch length. More...
 
std::vector< double > getNumberOfSubstitutionsForEachType (size_t initialState, size_t finalState, double length) const
 Get the numbers of susbstitutions on a branch for all types, for an initial and final states, given the branch length. More...
 
void setSubstitutionModel (const SubstitutionModel *model)
 Set the substitution model associated with this count, if relevent. More...
 
void setSubstitutionRegister (SubstitutionRegister *reg) throw (Exception)
 
bool hasSubstitutionRegister () const
 
const SubstitutionRegister * getSubstitutionRegister () const
 
SubstitutionRegister * getSubstitutionRegister ()
 
virtual size_t getNumberOfSubstitutionTypes () const
 Short cut function, equivalent to getSubstitutionRegister().getNumberOfSubstitutionTypes(). More...
 
virtual 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::auto_ptr< SubstitutionRegister > register_
 

Private Member Functions

void substitutionRegisterHasChanged ()
 

Private Attributes

LinearMatrix< double > label_
 
std::vector< int > supportedChars_
 

Detailed Description

Labelling substitution count.

This substitution count return a distinct number for each possible mutation.

  • 0 if $i = j$,
  • $a(i,j)$ if $i \neq j $, where 'a' is an index giving a unique value for each combination of i and j.

Definition at line 134 of file NaiveSubstitutionCount.h.

Constructor & Destructor Documentation

◆ LabelSubstitutionCount()

LabelSubstitutionCount::LabelSubstitutionCount ( const SubstitutionModel *  model)

Definition at line 58 of file NaiveSubstitutionCount.cpp.

References label_, and supportedChars_.

Referenced by clone().

◆ ~LabelSubstitutionCount()

virtual bpp::LabelSubstitutionCount::~LabelSubstitutionCount ( )
inlinevirtual

Definition at line 144 of file NaiveSubstitutionCount.h.

Member Function Documentation

◆ clone()

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

Implements bpp::SubstitutionCount.

Definition at line 146 of file NaiveSubstitutionCount.h.

References LabelSubstitutionCount().

◆ getAllNumbersOfSubstitutions()

Matrix<double>* bpp::LabelSubstitutionCount::getAllNumbersOfSubstitutions ( double  length,
size_t  type = 1 
) const
inlinevirtual

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::SubstitutionCount.

Definition at line 154 of file NaiveSubstitutionCount.h.

References label_.

◆ getAlphabet()

virtual const Alphabet* bpp::SubstitutionCount::getAlphabet ( ) const
inlinevirtualinherited

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

Returns
The alphabet associated to this substitution count.

Definition at line 112 of file SubstitutionCount.h.

References bpp::SubstitutionRegister::getAlphabet(), and bpp::SubstitutionCount::getSubstitutionRegister().

◆ getNumberOfStates()

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

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

Returns
The number of states in the model/alphabet.

Definition at line 119 of file SubstitutionCount.h.

References bpp::SubstitutionRegister::getAlphabet(), and bpp::SubstitutionCount::getSubstitutionRegister().

◆ getNumberOfSubstitutions()

double bpp::LabelSubstitutionCount::getNumberOfSubstitutions ( size_t  initialState,
size_t  finalState,
double  length,
size_t  type = 1 
) const
inlinevirtual

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::SubstitutionCount.

Definition at line 149 of file NaiveSubstitutionCount.h.

References label_.

◆ getNumberOfSubstitutionsForEachType()

std::vector<double> bpp::LabelSubstitutionCount::getNumberOfSubstitutionsForEachType ( size_t  initialState,
size_t  finalState,
double  length 
) const
inlinevirtual

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::SubstitutionCount.

Definition at line 159 of file NaiveSubstitutionCount.h.

References label_.

◆ getNumberOfSubstitutionTypes()

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

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

Returns
The number of substitution types supported by this instance.

Definition at line 105 of file SubstitutionCount.h.

References bpp::SubstitutionRegister::getNumberOfSubstitutionTypes(), and bpp::SubstitutionCount::getSubstitutionRegister().

Referenced by bpp::NaiveSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::UniformizationSubstitutionCount::getNumberOfSubstitutionsForEachType(), bpp::DecompositionSubstitutionCount::getNumberOfSubstitutionsForEachType(), and bpp::ProbabilisticSubstitutionMapping::getNumberOfSubstitutionTypes().

◆ getSubstitutionRegister() [1/2]

const SubstitutionRegister* 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::SubstitutionCount.

Definition at line 206 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ getSubstitutionRegister() [2/2]

SubstitutionRegister* bpp::AbstractSubstitutionCount::getSubstitutionRegister ( )
inlinevirtualinherited
Returns
The SubstitutionRegister object associated to this instance. The register contains the description of the various substitutions types that are mapped.

Implements bpp::SubstitutionCount.

Definition at line 208 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::SubstitutionCount.

Definition at line 192 of file SubstitutionCount.h.

References bpp::AbstractSubstitutionCount::register_.

◆ setSubstitutionModel()

void bpp::LabelSubstitutionCount::setSubstitutionModel ( const SubstitutionModel *  model)
inlinevirtual

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

Parameters
modelThe substitution model to use with this count.

Implements bpp::SubstitutionCount.

Definition at line 166 of file NaiveSubstitutionCount.h.

References bpp::SubstitutionModel::getAlphabetStates(), and supportedChars_.

◆ setSubstitutionRegister()

void bpp::LabelSubstitutionCount::setSubstitutionRegister ( SubstitutionRegister *  reg)
throw (Exception
)
inlinevirtual
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::SubstitutionCount.

Definition at line 171 of file NaiveSubstitutionCount.h.

◆ substitutionRegisterHasChanged()

void bpp::LabelSubstitutionCount::substitutionRegisterHasChanged ( )
inlineprivatevirtual

Implements bpp::AbstractSubstitutionCount.

Definition at line 176 of file NaiveSubstitutionCount.h.

Member Data Documentation

◆ label_

LinearMatrix<double> bpp::LabelSubstitutionCount::label_
private

Definition at line 138 of file NaiveSubstitutionCount.h.

Referenced by getAllNumbersOfSubstitutions(), getNumberOfSubstitutions(), getNumberOfSubstitutionsForEachType(), and LabelSubstitutionCount().

◆ register_

std::auto_ptr<SubstitutionRegister> bpp::AbstractSubstitutionCount::register_
protectedinherited

Definition at line 170 of file SubstitutionCount.h.

Referenced by bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeProducts_(), bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::NaiveSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::NaiveSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractSubstitutionCount::getSubstitutionRegister(), bpp::AbstractSubstitutionCount::hasSubstitutionRegister(), bpp::UniformizationSubstitutionCount::initBMatrices_(), bpp::DecompositionSubstitutionCount::initBMatrices_(), bpp::AbstractSubstitutionCount::operator=(), bpp::UniformizationSubstitutionCount::resetBMatrices_(), bpp::DecompositionSubstitutionCount::resetBMatrices_(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::DecompositionSubstitutionCount::setSubstitutionModel(), bpp::AbstractSubstitutionCount::setSubstitutionRegister(), bpp::UniformizationSubstitutionCount::substitutionRegisterHasChanged(), bpp::DecompositionSubstitutionCount::substitutionRegisterHasChanged(), bpp::UniformizationSubstitutionCount::weightsHaveChanged(), and bpp::DecompositionSubstitutionCount::weightsHaveChanged().

◆ supportedChars_

std::vector<int> bpp::LabelSubstitutionCount::supportedChars_
private

Definition at line 139 of file NaiveSubstitutionCount.h.

Referenced by LabelSubstitutionCount(), and setSubstitutionModel().

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