A toolkit for working with phylogenetic data.
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PqueryName Class Reference

#include <genesis/placement/pquery/name.hpp>

Detailed Description

A name of a Pquery and its multiplicity.

This class is modeled after the jplace standard, which allows for multiple names for a Pquery. This is useful if there are identical sequences in the original data for which the phylogenetic placement was carried out. The placements of those sequences can then be treated as one entity, i.e., one Pquery, while still maintaining all their identifiers (names).

Furthermore, each such name can have a multiplicity, which can be used to store e.g., the number of replicates of the original sequence. It is used as a factor for the weights of PqueryPlacements in some calculations.

Definition at line 61 of file name.hpp.

Public Member Functions

 PqueryName ()=default
 Default constructor. Initializes the name to an empty string and the multiplicity to 1.0. More...
 
 PqueryName (std::string name, double multiplicity=1.0)
 Constructor that takes a name and optionally a multiplicity. More...
 
 PqueryName (PqueryName const &)=default
 
 PqueryName (PqueryName &&)=default
 
 ~PqueryName ()=default
 
PqueryNameoperator= (PqueryName const &)=default
 
PqueryNameoperator= (PqueryName &&)=default
 

Public Attributes

double multiplicity = 1.0
 Multiplicity of the name. More...
 
std::string name
 Name for a Pquery. More...
 

Constructor & Destructor Documentation

PqueryName ( )
default

Default constructor. Initializes the name to an empty string and the multiplicity to 1.0.

PqueryName ( std::string  name,
double  multiplicity = 1.0 
)
inline

Constructor that takes a name and optionally a multiplicity.

Definition at line 78 of file name.hpp.

~PqueryName ( )
default
PqueryName ( PqueryName const &  )
default
PqueryName ( PqueryName &&  )
default

Member Function Documentation

PqueryName& operator= ( PqueryName const &  )
default
PqueryName& operator= ( PqueryName &&  )
default

Member Data Documentation

double multiplicity = 1.0

Multiplicity of the name.

This property is defined by the jplace standard. It is used as a count for e.g., the abundance of this Pquery (respectively this name). For some calculations, this value is used as a factor for the placment weights (see PqueryPlacement::like_weight_ratio). Thus, by default, the value is initialized to 1.0.

If a Pquery has multiple names, all their multiplicities are added when being used as a weight factor.

Definition at line 117 of file name.hpp.

std::string name

Name for a Pquery.

This property is defined by the jplace standard. It does not need to be unique. However, using unique names certainly makes iditifying Pqueries easier.

Definition at line 104 of file name.hpp.


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