A toolkit for working with phylogenetic data.
v0.24.0
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 const &)=default
 
 PlacementTreeNewickReaderPlugin (PlacementTreeNewickReaderPlugin &&)=default
 
virtual ~PlacementTreeNewickReaderPlugin ()=default
 
void element_to_edge (tree::NewickBrokerElement const &element, tree::TreeEdge &edge) const
 
void finish_reading (tree::Tree &tree) const
 
PlacementTreeNewickReaderPluginget_edge_num_from_comments (bool value)
 Set whether to use tags or comments of the Newick tree for the edge nums. More...
 
bool get_edge_num_from_comments () const
 Get whether to use tags or comments of the Newick tree for the edge nums. More...
 
PlacementTreeNewickReaderPluginoperator= (PlacementTreeNewickReaderPlugin const &)=default
 
PlacementTreeNewickReaderPluginoperator= (PlacementTreeNewickReaderPlugin &&)=default
 
void register_with (tree::NewickReader &reader) const
 

Constructor & Destructor Documentation

◆ PlacementTreeNewickReaderPlugin() [1/3]

◆ ~PlacementTreeNewickReaderPlugin()

virtual ~PlacementTreeNewickReaderPlugin ( )
virtualdefault

◆ PlacementTreeNewickReaderPlugin() [2/3]

◆ PlacementTreeNewickReaderPlugin() [3/3]

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]

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.

◆ get_edge_num_from_comments() [2/2]

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.

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ register_with()

void register_with ( tree::NewickReader reader) const
inline

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


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