#include <genesis/placement/pquery.hpp>

Detailed Description

A pquery holds a set of PqueryPlacements and a set of PqueryNames.

According to the jplace standard, a pquery is a container object that represents the possible phylogenetic placement positions of a sequence (or set of sequences). Each such position is stored as a PqueryPlacement and can be accessed via the functions of this class.

Furthermore, it might be useful to combine the placement positions of several sequences into one object. This is for example the case if there are replicate sequences. Thus, a Pquery supports to store multiple PqueryNames, each of them containing an identifying name string and a so called multiplicity, which can be used as e.g., an abundance count for the associated name, and is used as a factor for the weights of the placements in some calculations.

Definition at line 82 of file pquery.hpp.

Public Member Functions
	Pquery ()=default

	Pquery (Pquery &&)=default

	Pquery (Pquery const &)=default

	~Pquery ()=default

PqueryName &	add_name (PqueryName const &other)
	Create a new PqueryName as a copy of the provided one, add it to the Pquery and return it. More...

PqueryName &	add_name (std::string name="", double multiplicity=1.0)
	Create a new PqueryName using the provided parameters, add it to the Pquery and return it. More...

PqueryPlacement &	add_placement (PlacementTreeEdge &edge)
	Create a new PqueryPlacement at a given PlacementTreeEdge, add it to the Pquery and return it. More...

PqueryPlacement &	add_placement (PlacementTreeEdge &edge, PqueryPlacement const &val)
	Create a new PqueryPlacement at a given PlacementTreeEdge, add it to the Pquery and return it. The property values of the provided PqueryPlacement are copied. More...

PqueryPlacement &	add_placement (PqueryPlacement const &val)
	Create a new PqueryPlacement as a copy of the provided one, add it to the Pquery and return it. More...

iterator_names	begin_names ()

const_iterator_names	begin_names () const

iterator_placements	begin_placements ()

const_iterator_placements	begin_placements () const

void	clear ()
	Clear all data stored in this Pquery, i.e., clear all PqueryNames and all PqueryPlacements. More...

void	clear_names ()
	Delete all PqueryNames of this Pquery. More...

void	clear_placements ()
	Delete all PqueryPlacements of this Pquery. More...

iterator_names	end_names ()

const_iterator_names	end_names () const

iterator_placements	end_placements ()

const_iterator_placements	end_placements () const

std::vector< PqueryName > &	expose_names ()

std::vector< PqueryPlacement > &	expose_placements ()

PqueryName &	name_at (size_t index)
	Return the PqueryName at a certain index. More...

PqueryName const &	name_at (size_t index) const
	Return the PqueryName at a certain index. More...

size_t	name_size () const
	Return the number of PqueryNames stored in this Pquery. More...

utils::Range< iterator_names >	names ()
	Return a Range iterator to the PqueryNames. More...

utils::Range< const_iterator_names >	names () const
	Return a const Range iterator to the PqueryNames. More...

Pquery &	operator= (Pquery &&)=default

Pquery &	operator= (Pquery const &)=default

PqueryPlacement &	placement_at (size_t index)
	Return the PqueryPlacement at a certain index. More...

PqueryPlacement const &	placement_at (size_t index) const
	Return the PqueryPlacement at a certain index. More...

size_t	placement_size () const
	Return the number of PqueryPlacements stored in this Pquery. More...

utils::Range< iterator_placements >	placements ()
	Return a Range iterator to the PqueryPlacements. More...

utils::Range< const_iterator_placements >	placements () const
	Return a const Range iterator to the PqueryPlacements. More...

void	remove_name_at (size_t index)
	Remove the PqueryName at a certain index position within this Pquery. More...

void	remove_placement_at (size_t index)
	Remove the PqueryPlacement at a certain index position within this Pquery. More...

Public Types
typedef std::vector< PqueryName >::const_iterator	const_iterator_names

typedef std::vector< PqueryPlacement >::const_iterator	const_iterator_placements

typedef std::vector< PqueryName >::iterator	iterator_names

typedef std::vector< PqueryPlacement >::iterator	iterator_placements

typedef std::vector< PqueryName >	PqueryNames

typedef std::vector< PqueryPlacement >	PqueryPlacements

Constructor & Destructor Documentation

◆ Pquery() [1/3]

Pquery ( )

default

◆ ~Pquery()

~Pquery ( )

default

◆ Pquery() [2/3]

Pquery ( Pquery const & )

default

◆ Pquery() [3/3]

Pquery ( Pquery && )

default

Member Function Documentation

◆ add_name() [1/2]

PqueryName & add_name ( PqueryName const & other )

Create a new PqueryName as a copy of the provided one, add it to the Pquery and return it.

As this function might reallocate the memory where names are stored, all iterators and pointer to PqueryNamess are considered to be invalidated.

Definition at line 187 of file pquery.cpp.

◆ add_name() [2/2]

PqueryName & add_name	(	std::string	name = `""`,
		double	multiplicity = `1.0`
	)

Create a new PqueryName using the provided parameters, add it to the Pquery and return it.

As this function might reallocate the memory where names are stored, all iterators and pointer to PqueryNamess are considered to be invalidated.

Definition at line 181 of file pquery.cpp.

◆ add_placement() [1/3]

PqueryPlacement & add_placement ( PlacementTreeEdge & edge )

Create a new PqueryPlacement at a given PlacementTreeEdge, add it to the Pquery and return it.

The values of the placement can then be adjusted using the returned object reference.

It is important that the provided edge belongs to the same PlacementTree as the Pquery and its containing Sample do. This is up to the user and not checked.

As this function might reallocate the memory where placements are stored, all iterators and pointer to PqueryPlacements are invalidated.

Definition at line 92 of file pquery.cpp.

◆ add_placement() [2/3]

PqueryPlacement & add_placement	(	PlacementTreeEdge &	edge,
		PqueryPlacement const &	val
	)

Create a new PqueryPlacement at a given PlacementTreeEdge, add it to the Pquery and return it. The property values of the provided PqueryPlacement are copied.

It is important that the provided edge belongs to the same PlacementTree as the Pquery and its containing Sample do. This is up to the user and not checked.

As this function might reallocate the memory where placements are stored, all iterators and pointer to PqueryPlacements are considered to be invalidated.

Definition at line 104 of file pquery.cpp.

◆ add_placement() [3/3]

PqueryPlacement & add_placement ( PqueryPlacement const & val )

Create a new PqueryPlacement as a copy of the provided one, add it to the Pquery and return it.

As this function might reallocate the memory where placements are stored, all iterators and pointer to PqueryPlacements are considered to be invalidated.

Definition at line 98 of file pquery.cpp.

◆ begin_names() [1/2]

Pquery::const_iterator_names begin_names ( )

Definition at line 142 of file pquery.cpp.

◆ begin_names() [2/2]

const_iterator_names begin_names ( ) const

◆ begin_placements() [1/2]

Pquery::const_iterator_placements begin_placements ( )

Definition at line 53 of file pquery.cpp.

◆ begin_placements() [2/2]

const_iterator_placements begin_placements ( ) const

◆ clear()

void clear ( )

Clear all data stored in this Pquery, i.e., clear all PqueryNames and all PqueryPlacements.

Definition at line 43 of file pquery.cpp.

◆ clear_names()

void clear_names ( )

Delete all PqueryNames of this Pquery.

Definition at line 213 of file pquery.cpp.

◆ clear_placements()

void clear_placements ( )

Delete all PqueryPlacements of this Pquery.

Definition at line 133 of file pquery.cpp.

◆ end_names() [1/2]

Pquery::const_iterator_names end_names ( )

Definition at line 147 of file pquery.cpp.

◆ end_names() [2/2]

const_iterator_names end_names ( ) const

◆ end_placements() [1/2]

Pquery::const_iterator_placements end_placements ( )

Definition at line 58 of file pquery.cpp.

◆ end_placements() [2/2]

const_iterator_placements end_placements ( ) const

◆ expose_names()

std::vector< PqueryName > & expose_names ( )

Definition at line 172 of file pquery.cpp.

◆ expose_placements()

std::vector< PqueryPlacement > & expose_placements ( )

Definition at line 83 of file pquery.cpp.

◆ name_at() [1/2]

PqueryName & name_at ( size_t index )

Return the PqueryName at a certain index.

The index must be smaller than name_size(), otherwise this functions throws an exception.

Definition at line 198 of file pquery.cpp.

◆ name_at() [2/2]

PqueryName const & name_at ( size_t index ) const

Return the PqueryName at a certain index.

The index must be smaller than name_size(), otherwise this functions throws an exception.

Definition at line 203 of file pquery.cpp.

◆ name_size()

size_t name_size ( ) const

Return the number of PqueryNames stored in this Pquery.

Definition at line 193 of file pquery.cpp.

◆ names() [1/2]

utils::Range< Pquery::const_iterator_names > names ( )

Return a Range iterator to the PqueryNames.

This makes iterating placements via a range based for loop easy.

Definition at line 162 of file pquery.cpp.

◆ names() [2/2]

utils::Range<const_iterator_names> names ( ) const

Return a const Range iterator to the PqueryNames.

This makes iterating placements via a range based for loop easy.

◆ operator=() [1/2]

Pquery& operator= ( Pquery && )

default

◆ operator=() [2/2]

Pquery& operator= ( Pquery const & )

default

◆ placement_at() [1/2]

PqueryPlacement & placement_at ( size_t index )

Return the PqueryPlacement at a certain index.

The index must be smaller than placement_size(), otherwise this functions throws an exception.

Definition at line 118 of file pquery.cpp.

◆ placement_at() [2/2]

PqueryPlacement const & placement_at ( size_t index ) const

Return the PqueryPlacement at a certain index.

The index must be smaller than placement_size(), otherwise this functions throws an exception.

Definition at line 123 of file pquery.cpp.

◆ placement_size()

size_t placement_size ( ) const

Return the number of PqueryPlacements stored in this Pquery.

Definition at line 113 of file pquery.cpp.

◆ placements() [1/2]

utils::Range< Pquery::const_iterator_placements > placements ( )

Return a Range iterator to the PqueryPlacements.

This makes iterating placements via a range based for loop easy.

Definition at line 73 of file pquery.cpp.

◆ placements() [2/2]

utils::Range<const_iterator_placements> placements ( ) const

Return a const Range iterator to the PqueryPlacements.

This makes iterating placements via a range based for loop easy.

◆ remove_name_at()

void remove_name_at ( size_t index )

Remove the PqueryName at a certain index position within this Pquery.

As this function moves names in the container, all iterators and pointer to PqueryNamess are considered to be invalidated.

Definition at line 208 of file pquery.cpp.

◆ remove_placement_at()

void remove_placement_at ( size_t index )

Remove the PqueryPlacement at a certain index position within this Pquery.

As this function moves placements in the container, all iterators and pointer to PqueryPlacements are considered to be invalidated.

Definition at line 128 of file pquery.cpp.

Member Typedef Documentation

◆ const_iterator_names

typedef std::vector<PqueryName>::const_iterator const_iterator_names

Definition at line 97 of file pquery.hpp.

◆ const_iterator_placements

typedef std::vector<PqueryPlacement>::const_iterator const_iterator_placements

Definition at line 94 of file pquery.hpp.

◆ iterator_names

typedef std::vector<PqueryName>::iterator iterator_names

Definition at line 96 of file pquery.hpp.

◆ iterator_placements

typedef std::vector<PqueryPlacement>::iterator iterator_placements

Definition at line 93 of file pquery.hpp.

◆ PqueryNames

typedef std::vector<PqueryName> PqueryNames

Definition at line 91 of file pquery.hpp.

◆ PqueryPlacements

typedef std::vector<PqueryPlacement> PqueryPlacements

Definition at line 90 of file pquery.hpp.

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

Detailed Description

Public Member Functions

Public Types

Constructor & Destructor Documentation

◆ Pquery() [1/3]

◆ ~Pquery()

◆ Pquery() [2/3]

◆ Pquery() [3/3]

Member Function Documentation

◆ add_name() [1/2]

◆ add_name() [2/2]

◆ add_placement() [1/3]

◆ add_placement() [2/3]

◆ add_placement() [3/3]

◆ begin_names() [1/2]

◆ begin_names() [2/2]

◆ begin_placements() [1/2]

◆ begin_placements() [2/2]

◆ clear()

◆ clear_names()

◆ clear_placements()

◆ end_names() [1/2]

◆ end_names() [2/2]

◆ end_placements() [1/2]

◆ end_placements() [2/2]

◆ expose_names()

◆ expose_placements()

◆ name_at() [1/2]

◆ name_at() [2/2]

◆ name_size()

◆ names() [1/2]

◆ names() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ placement_at() [1/2]

◆ placement_at() [2/2]

◆ placement_size()

◆ placements() [1/2]

◆ placements() [2/2]

◆ remove_name_at()

◆ remove_placement_at()

Member Typedef Documentation

◆ const_iterator_names

◆ const_iterator_placements

◆ iterator_names

◆ iterator_placements

◆ PqueryNames

◆ PqueryPlacements