bpp-phyl3 3.0.0
Public Member Functions | List of all members
bpp::PhyloSubstitutionMapping Class Referenceabstract

#include <Bpp/Phyl/Mapping/PhyloMappings/PhyloSubstitutionMapping.h>

+ Inheritance diagram for bpp::PhyloSubstitutionMapping:
+ Collaboration diagram for bpp::PhyloSubstitutionMapping:

Public Member Functions

 PhyloSubstitutionMapping ()
 
virtual ~PhyloSubstitutionMapping ()
 
PhyloSubstitutionMapping * clone () const =0
 
virtual std::shared_ptr< const TransitionModelInterface > getModel (unsigned int branchId, size_t classIndex) const =0
 Get the substitution model corresponding to a certain branch and model class. More...
 
virtual bool matchParametersValues (const ParameterList &nullParams)=0
 Checks and sets the models with given parameters. More...
 
virtual const ParameterList & getParameters () const =0
 Gets the parameters. More...
 
virtual void computeNormalizations (const ParameterList &nullParams, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, bool verbose=true)=0
 compute Normalizations More...
 
virtual bool normalizationsPerformed () const =0
 return if normalizations have been performed. More...
 
virtual bool countsPerformed () const =0
 return if counts have been performed. More...
 
virtual void computeCounts (short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)=0
 ComputeCounts. More...
 
virtual ProbabilisticSubstitutionMapping & counts ()=0
 Return the tree of counts. More...
 
virtual const ProbabilisticSubstitutionMapping & counts () const =0
 
virtual ProbabilisticSubstitutionMapping & normalizations ()=0
 Return the tree of factors. More...
 
virtual const ProbabilisticSubstitutionMapping & normalizations () const =0
 
virtual void setDistances (const AlphabetIndex2 &ndist)=0
 change Distances More...
 

Detailed Description

Definition at line 20 of file PhyloSubstitutionMapping.h.

Constructor & Destructor Documentation

◆ PhyloSubstitutionMapping()

bpp::PhyloSubstitutionMapping::PhyloSubstitutionMapping ( )
inline

Definition at line 24 of file PhyloSubstitutionMapping.h.

◆ ~PhyloSubstitutionMapping()

virtual bpp::PhyloSubstitutionMapping::~PhyloSubstitutionMapping ( )
inlinevirtual

Definition at line 25 of file PhyloSubstitutionMapping.h.

Member Function Documentation

◆ clone()

PhyloSubstitutionMapping * bpp::PhyloSubstitutionMapping::clone ( ) const
pure virtual

Implements bpp::Clonable.

Implemented in bpp::SingleProcessSubstitutionMapping, and bpp::OneProcessSequenceSubstitutionMapping.

◆ computeCounts()

virtual void bpp::PhyloSubstitutionMapping::computeCounts ( short  unresolvedOption = SubstitutionMappingTools::UNRESOLVED_ZERO,
double  threshold = -1,
bool  verbose = true 
)
pure virtual

ComputeCounts.

Parameters
unresolvedOptionmgmt of gaps in the counts (default: counted as zeros)
threshold
verbose

Implemented in bpp::SingleProcessSubstitutionMapping, and bpp::OneProcessSequenceSubstitutionMapping.

◆ computeNormalizations()

virtual void bpp::PhyloSubstitutionMapping::computeNormalizations ( const ParameterList &  nullParams,
short  unresolvedOption = SubstitutionMappingTools::UNRESOLVED_ZERO,
bool  verbose = true 
)
pure virtual

compute Normalizations

Parameters
nullParamsa list of null parameters
unresolvedOptionmgmt of gaps in the counts (default: counted as zeros)
verbose

Implemented in bpp::SingleProcessSubstitutionMapping, and bpp::OneProcessSequenceSubstitutionMapping.

◆ counts() [1/2]

virtual const ProbabilisticSubstitutionMapping & bpp::PhyloSubstitutionMapping::counts ( ) const
pure virtual

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ counts() [2/2]

virtual ProbabilisticSubstitutionMapping & bpp::PhyloSubstitutionMapping::counts ( )
pure virtual

Return the tree of counts.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ countsPerformed()

virtual bool bpp::PhyloSubstitutionMapping::countsPerformed ( ) const
pure virtual

return if counts have been performed.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ getModel()

virtual std::shared_ptr< const TransitionModelInterface > bpp::PhyloSubstitutionMapping::getModel ( unsigned int  branchId,
size_t  classIndex 
) const
pure virtual

Get the substitution model corresponding to a certain branch and model class.

Parameters
branchIdThe id of the branch.
classIndexThe model class index.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ getParameters()

virtual const ParameterList & bpp::PhyloSubstitutionMapping::getParameters ( ) const
pure virtual

Gets the parameters.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ matchParametersValues()

virtual bool bpp::PhyloSubstitutionMapping::matchParametersValues ( const ParameterList &  nullParams)
pure virtual

Checks and sets the models with given parameters.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ normalizations() [1/2]

virtual const ProbabilisticSubstitutionMapping & bpp::PhyloSubstitutionMapping::normalizations ( ) const
pure virtual

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ normalizations() [2/2]

virtual ProbabilisticSubstitutionMapping & bpp::PhyloSubstitutionMapping::normalizations ( )
pure virtual

Return the tree of factors.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ normalizationsPerformed()

virtual bool bpp::PhyloSubstitutionMapping::normalizationsPerformed ( ) const
pure virtual

return if normalizations have been performed.

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

◆ setDistances()

virtual void bpp::PhyloSubstitutionMapping::setDistances ( const AlphabetIndex2 &  ndist)
pure virtual

change Distances

Implemented in bpp::AbstractSinglePhyloSubstitutionMapping.

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