A toolkit for working with phylogenetic data.
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PlacementTreeNewickWriter Class Reference

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

Inherits NewickWriter, DefaultTreeNewickWriterPlugin, and PlacementTreeNewickWriterPlugin.

Detailed Description

Definition at line 148 of file placement/formats/newick_writer.hpp.

Public Member Functions

 PlacementTreeNewickWriter ()
 
- Public Member Functions inherited from NewickWriter
 NewickWriter ()=default
 
 NewickWriter (NewickWriter const &)=default
 
 NewickWriter (NewickWriter &&)=default
 
virtual ~NewickWriter ()=default
 
NewickWriteroperator= (NewickWriter const &)=default
 
NewickWriteroperator= (NewickWriter &&)=default
 
NewickWriterquotation_marks (char value)
 Set the type of quotation marks used for node names that contain special characters. More...
 
char quotation_marks () const
 Get the currently set type of quotation marks used for node names. More...
 
void to_file (Tree const &tree, std::string const &filename) const
 Writes the tree to a file in Newick format. More...
 
void to_string (Tree const &tree, std::string &ts) const
 Gives a Newick string representation of the tree. More...
 
std::string to_string (Tree const &tree) const
 Returns a Newick string representation of the tree. More...
 
NewickWriterwrite_comments (bool value)
 Set whether to write Newick comments (e.g., some forms of bootstrap values). More...
 
bool write_comments () const
 Get whether Newick comments (e.g., some forms of bootstrap values) are written. More...
 
NewickWriterwrite_names (bool value)
 Set whether to write Newick node names. More...
 
bool write_names () const
 Get whether Newick node names are written. More...
 
NewickWriterwrite_tags (bool value)
 Set whether to write Newick tags (e.g., for jplace files). More...
 
bool write_tags () const
 Get whether Newick tags (e.g., for jplace files) are written. More...
 
NewickWriterwrite_values (bool value)
 Set whether to write Newick values (e.g., branch lengths). More...
 
bool write_values () const
 Get whether Newick values (e.g., branch lengths) are written. More...
 
- Public Member Functions inherited from DefaultTreeNewickWriterPlugin
 DefaultTreeNewickWriterPlugin ()=default
 
 DefaultTreeNewickWriterPlugin (DefaultTreeNewickWriterPlugin const &)=default
 
 DefaultTreeNewickWriterPlugin (DefaultTreeNewickWriterPlugin &&)=default
 
virtual ~DefaultTreeNewickWriterPlugin ()=default
 
int branch_length_precision () const
 Get the currently set maximum precision (in number of digits) used for printing the branch_length floating point numbers. More...
 
self_typebranch_length_precision (int value)
 Set the maximum precision (in number of digits) used for printing the branch_length floating point numbers. More...
 
std::string const & default_inner_name () const
 Get the named used to filter out an inner node name. More...
 
self_typedefault_inner_name (std::string const &value)
 Set the named used to filter out an inner node name. More...
 
std::string const & default_leaf_name () const
 Get the named used to filter out a leaf node name. More...
 
self_typedefault_leaf_name (std::string const &value)
 Set the named used to filter out a leaf node name. More...
 
std::string const & default_root_name () const
 Get the named used to filter out the root node name. More...
 
self_typedefault_root_name (std::string const &value)
 Set the named used to filter out the root node name. More...
 
void edge_to_element (TreeEdge const &edge, NewickBrokerElement &element) const
 
self_typeenable_branch_lengths (bool value)
 Set whether to write branch lengths. More...
 
bool enable_branch_lengths () const
 Get whether currently any branch lengths are written. More...
 
self_typeenable_names (bool value)
 Set whether to write node names at all. More...
 
bool enable_names () const
 Get whether currently any node names are written at all. More...
 
void node_to_element (TreeNode const &node, NewickBrokerElement &element) const
 
DefaultTreeNewickWriterPluginoperator= (DefaultTreeNewickWriterPlugin const &)=default
 
DefaultTreeNewickWriterPluginoperator= (DefaultTreeNewickWriterPlugin &&)=default
 
void register_with (NewickWriter &writer) const
 
bool replace_name_spaces () const
 Return whether currently this plugin replaces spaces with underscores. More...
 
self_typereplace_name_spaces (bool value)
 Set whether to replace all spaces (' ') in names with underscores ('_'). More...
 
self_typeset_default_names (std::string const &value)
 Shorthand to set the default names for leaf, inner and root node at once, to one value. More...
 
bool use_default_names () const
 Return whether currently default names are activated in this plugin. More...
 
self_typeuse_default_names (bool value)
 Set whether to replace default named nodes with an empty string. More...
 
- Public Member Functions inherited from PlacementTreeNewickWriterPlugin
 PlacementTreeNewickWriterPlugin ()=default
 
 PlacementTreeNewickWriterPlugin (PlacementTreeNewickWriterPlugin const &)=default
 
 PlacementTreeNewickWriterPlugin (PlacementTreeNewickWriterPlugin &&)=default
 
virtual ~PlacementTreeNewickWriterPlugin ()=default
 
void edge_to_element (tree::TreeEdge const &edge, tree::NewickBrokerElement &element) const
 
bool enable_edge_nums () const
 
void enable_edge_nums (bool value)
 
bool enable_placement_counts () const
 
void enable_placement_counts (bool value)
 
PlacementTreeNewickWriterPluginoperator= (PlacementTreeNewickWriterPlugin const &)=default
 
PlacementTreeNewickWriterPluginoperator= (PlacementTreeNewickWriterPlugin &&)=default
 
void prepare_sample (Sample const &smp)
 
void register_with (tree::NewickWriter &writer) const
 

Additional Inherited Members

- Public Types inherited from NewickWriter
using edge_to_element_function = std::function< void(TreeEdge const &edge, NewickBrokerElement &element) >
 Function type that translates from a TreeEdge to a NewickBrokerElement. More...
 
using finish_writing_function = std::function< void(Tree const &tree, NewickBroker &broker) >
 Function type that allows to do some finalizing work with the Tree and NewickBroker after the actual tree writing finished. More...
 
using node_to_element_function = std::function< void(TreeNode const &node, NewickBrokerElement &element) >
 Function type that translates from a TreeNode to a NewickBrokerElement. More...
 
using prepare_writing_function = std::function< void(Tree const &tree, NewickBroker &broker) >
 Function type that allows to do some preparatory work with the Tree and NewickBroker before the actual tree writing begins. More...
 
- Public Types inherited from DefaultTreeNewickWriterPlugin
using self_type = DefaultTreeNewickWriterPlugin
 
- Public Attributes inherited from NewickWriter
std::vector
< edge_to_element_function
edge_to_element_plugins
 Collect all functions to be called for each TreeEdge in order to translate it to a Newick representation. More...
 
std::vector
< finish_writing_function
finish_writing_plugins
 Collect all functions to be called after finishing the actual tree writing. More...
 
std::vector
< node_to_element_function
node_to_element_plugins
 Collect all functions to be called for each TreeNode in order to translate it to a Newick representation. More...
 
std::vector
< prepare_writing_function
prepare_writing_plugins
 Collect all functions to be called before starting the actual tree writing. More...
 

Constructor & Destructor Documentation

Definition at line 159 of file placement/formats/newick_writer.hpp.


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