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 55 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 (PqueryName &&)=default
	PqueryName (PqueryName const &)=default
	PqueryName (std::string const &name, double multiplicity=1.0)
	Constructor that takes a name and optionally a multiplicity. More...
	~PqueryName ()=default
	operator std::string & ()
	Implicit conversion to std::string that returns the name for simplicity. More...
	operator std::string const & () const
	Implicit conversion to std::string that returns the name for simplicity. More...
PqueryName &	operator= (PqueryName &&)=default
PqueryName &	operator= (PqueryName const &)=default

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

Constructor & Destructor Documentation

PqueryName() [1/4]

PqueryName ( )

default

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

PqueryName() [2/4]

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

inlineexplicit

Constructor that takes a name and optionally a multiplicity.

Definition at line 72 of file name.hpp.

~PqueryName()

~PqueryName ( )

default

PqueryName() [3/4]

PqueryName ( PqueryName const &  )

default

PqueryName() [4/4]

PqueryName ( PqueryName &&  )

default

Member Function Documentation

operator std::string &()

operator std::string & ( )

inline

Implicit conversion to std::string that returns the name for simplicity.

Definition at line 92 of file name.hpp.

operator std::string const &()

operator std::string const & ( ) const

inline

Implicit conversion to std::string that returns the name for simplicity.

Definition at line 100 of file name.hpp.

operator=() [1/2]

PqueryName& operator= ( PqueryName &&  )

default

operator=() [2/2]

PqueryName& operator= ( PqueryName const &  )

default

Member Data Documentation

multiplicity

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 131 of file name.hpp.

name

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 118 of file name.hpp.

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

• name.hpp