PlacementTreeNewickReaderPlugin Class Reference

#include <genesis/placement/formats/newick_reader.hpp>

Inherited by PlacementTreeNewickReader.

Detailed Description

Definition at line 56 of file placement/formats/newick_reader.hpp.

Public Member Functions
	PlacementTreeNewickReaderPlugin ()=default
	PlacementTreeNewickReaderPlugin (PlacementTreeNewickReaderPlugin &&)=default
	PlacementTreeNewickReaderPlugin (PlacementTreeNewickReaderPlugin const &)=default
virtual	~PlacementTreeNewickReaderPlugin ()=default
void	element_to_edge (tree::NewickBrokerElement const &element, tree::TreeEdge &edge) const
void	finish_reading (tree::Tree &tree) const
bool	get_edge_num_from_comments () const
	Get whether to use tags or comments of the Newick tree for the edge nums. More...
PlacementTreeNewickReaderPlugin &	get_edge_num_from_comments (bool value)
	Set whether to use tags or comments of the Newick tree for the edge nums. More...
PlacementTreeNewickReaderPlugin &	operator= (PlacementTreeNewickReaderPlugin &&)=default
PlacementTreeNewickReaderPlugin &	operator= (PlacementTreeNewickReaderPlugin const &)=default
void	register_with (tree::NewickReader &reader) const

Constructor & Destructor Documentation

PlacementTreeNewickReaderPlugin() [1/3]

PlacementTreeNewickReaderPlugin ( )

default

~PlacementTreeNewickReaderPlugin()

virtual ~PlacementTreeNewickReaderPlugin ( )

virtualdefault

PlacementTreeNewickReaderPlugin() [2/3]

PlacementTreeNewickReaderPlugin ( PlacementTreeNewickReaderPlugin const &  )

default

PlacementTreeNewickReaderPlugin() [3/3]

PlacementTreeNewickReaderPlugin ( PlacementTreeNewickReaderPlugin &&  )

default

Member Function Documentation

element_to_edge()

void element_to_edge ( tree::NewickBrokerElement const &  element, tree::TreeEdge &  edge  ) const

inline

Definition at line 77 of file placement/formats/newick_reader.hpp.

finish_reading()

void finish_reading ( tree::Tree &  tree ) const

inline

Definition at line 133 of file placement/formats/newick_reader.hpp.

get_edge_num_from_comments() [1/2]

bool get_edge_num_from_comments ( ) const

inline

Get whether to use tags or comments of the Newick tree for the edge nums.

See the setter function for details.

Definition at line 266 of file placement/formats/newick_reader.hpp.

get_edge_num_from_comments() [2/2]

PlacementTreeNewickReaderPlugin& get_edge_num_from_comments ( bool  value )

inline

Set whether to use tags or comments of the Newick tree for the edge nums.

In version 1 of the jplace standard, the edge num properties of the reference tree were noted down as Newick comments in brackets (e.g., [42]) instead of the curly braces used in later versions of the standard (e.g., {42}). By default, we use the newer tags. Set this to true in order to fall back to the old version using comments instead.

Definition at line 255 of file placement/formats/newick_reader.hpp.

operator=() [1/2]

PlacementTreeNewickReaderPlugin& operator= ( PlacementTreeNewickReaderPlugin &&  )

default

operator=() [2/2]

PlacementTreeNewickReaderPlugin& operator= ( PlacementTreeNewickReaderPlugin const &  )

default

register_with()

void register_with ( tree::NewickReader &  reader ) const

inline

Definition at line 216 of file placement/formats/newick_reader.hpp.

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

• placement/formats/newick_reader.hpp