#include <genesis/tree/common_tree/newick_writer.hpp>

Inherited by PlacementTreeNewickWriter, CommonTreeNewickWriter, and SimpleNewickTreeNewickWriter.

Detailed Description

Provide a set of plugin functions for NewickWriter to write a CommonTree.

Definition at line 51 of file tree/common_tree/newick_writer.hpp.

Public Member Functions
	CommonTreeNewickWriterPlugin ()=default

	CommonTreeNewickWriterPlugin (CommonTreeNewickWriterPlugin &&)=default

	CommonTreeNewickWriterPlugin (CommonTreeNewickWriterPlugin const &)=default

virtual	~CommonTreeNewickWriterPlugin ()=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_type &	branch_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_type &	default_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_type &	default_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_type &	default_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

bool	enable_branch_lengths () const
	Get whether currently any branch lengths are written. More...

self_type &	enable_branch_lengths (bool value)
	Set whether to write branch lengths. More...

bool	enable_names () const
	Get whether currently any node names are written at all. More...

self_type &	enable_names (bool value)
	Set whether to write node names at all. More...

void	node_to_element (TreeNode const &node, NewickBrokerElement &element) const

CommonTreeNewickWriterPlugin &	operator= (CommonTreeNewickWriterPlugin &&)=default

CommonTreeNewickWriterPlugin &	operator= (CommonTreeNewickWriterPlugin const &)=default

void	register_with (NewickWriter &writer) const

bool	replace_invalid_chars () const
	Return whether currently this plugin replaces characters that are invalid in the Newick file format with underscores. More...

self_type &	replace_invalid_chars (bool value)
	Set whether to replace all characters that are invalid in the Newick file format in names with underscores ('_'). More...

self_type &	set_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_type &	use_default_names (bool value)
	Set whether to replace default named nodes with an empty string. More...

Public Types
using	self_type = CommonTreeNewickWriterPlugin

Constructor & Destructor Documentation

◆ CommonTreeNewickWriterPlugin() [1/3]

CommonTreeNewickWriterPlugin ( )

default

◆ ~CommonTreeNewickWriterPlugin()

virtual ~CommonTreeNewickWriterPlugin ( )

virtualdefault

◆ CommonTreeNewickWriterPlugin() [2/3]

CommonTreeNewickWriterPlugin ( CommonTreeNewickWriterPlugin const & )

default

◆ CommonTreeNewickWriterPlugin() [3/3]

CommonTreeNewickWriterPlugin ( CommonTreeNewickWriterPlugin && )

default

Member Function Documentation

◆ branch_length_precision() [1/2]

int branch_length_precision ( ) const

inline

Get the currently set maximum precision (in number of digits) used for printing the branch_length floating point numbers.

Definition at line 253 of file tree/common_tree/newick_writer.hpp.

◆ branch_length_precision() [2/2]

self_type& branch_length_precision ( int value )

inline

Set the maximum precision (in number of digits) used for printing the branch_length floating point numbers.

Common is 6.

Definition at line 264 of file tree/common_tree/newick_writer.hpp.

◆ default_inner_name() [1/2]

std::string const& default_inner_name ( ) const

inline

Get the named used to filter out an inner node name.

Definition at line 98 of file tree/common_tree/newick_writer.hpp.

◆ default_inner_name() [2/2]

self_type& default_inner_name ( std::string const & value )

inline

Set the named used to filter out an inner node name.

Definition at line 106 of file tree/common_tree/newick_writer.hpp.

◆ default_leaf_name() [1/2]

std::string const& default_leaf_name ( ) const

inline

Get the named used to filter out a leaf node name.

Definition at line 81 of file tree/common_tree/newick_writer.hpp.

◆ default_leaf_name() [2/2]

self_type& default_leaf_name ( std::string const & value )

inline

Set the named used to filter out a leaf node name.

Definition at line 89 of file tree/common_tree/newick_writer.hpp.

◆ default_root_name() [1/2]

std::string const& default_root_name ( ) const

inline

Get the named used to filter out the root node name.

Definition at line 115 of file tree/common_tree/newick_writer.hpp.

◆ default_root_name() [2/2]

self_type& default_root_name ( std::string const & value )

inline

Set the named used to filter out the root node name.

Definition at line 123 of file tree/common_tree/newick_writer.hpp.

◆ edge_to_element()

void edge_to_element	(	TreeEdge const &	edge,
		NewickBrokerElement &	element
	)		const

inline

Definition at line 303 of file tree/common_tree/newick_writer.hpp.

◆ enable_branch_lengths() [1/2]

bool enable_branch_lengths ( ) const

inline

Get whether currently any branch lengths are written.

Definition at line 244 of file tree/common_tree/newick_writer.hpp.

◆ enable_branch_lengths() [2/2]

self_type& enable_branch_lengths ( bool value )

inline

Set whether to write branch lengths.

Definition at line 235 of file tree/common_tree/newick_writer.hpp.

◆ enable_names() [1/2]

bool enable_names ( ) const

inline

Get whether currently any node names are written at all.

Definition at line 227 of file tree/common_tree/newick_writer.hpp.

◆ enable_names() [2/2]

self_type& enable_names ( bool value )

inline

Set whether to write node names at all.

If disabled, no names are written for any node.

Definition at line 218 of file tree/common_tree/newick_writer.hpp.

◆ node_to_element()

void node_to_element	(	TreeNode const &	node,
		NewickBrokerElement &	element
	)		const

inline

Definition at line 274 of file tree/common_tree/newick_writer.hpp.

◆ operator=() [1/2]

CommonTreeNewickWriterPlugin& operator= ( CommonTreeNewickWriterPlugin && )

default

◆ operator=() [2/2]

CommonTreeNewickWriterPlugin& operator= ( CommonTreeNewickWriterPlugin const & )

default

◆ register_with()

void register_with ( NewickWriter & writer ) const

inline

Definition at line 312 of file tree/common_tree/newick_writer.hpp.

◆ replace_invalid_chars() [1/2]

bool replace_invalid_chars ( ) const

inline

Return whether currently this plugin replaces characters that are invalid in the Newick file format with underscores.

See the setter replace_invalid_chars( bool ) for details.

Definition at line 185 of file tree/common_tree/newick_writer.hpp.

◆ replace_invalid_chars() [2/2]

self_type& replace_invalid_chars ( bool value )

inline

Set whether to replace all characters that are invalid in the Newick file format in names with underscores ('_').

This is the reverse of CommonTreeNewickReaderPlugin::replace_name_underscores(), in that it replaces spaces with underscores, but also handles other invalid characters :;()[],={}" that cannot be used in Newick labels, see http://evolution.genetics.washington.edu/phylip/newicktree.html. See also NewickWriter for similar options.

It is activated by default, as this makes sure that other software can handle the names. However, as these characters cannot be part of names in Newick, if it is deactivated (set to false), all names that contain any of these characters are instead wrapped in quotation marks by the NewickWriter, see NewickWriter::quotation_marks( std::string const& ) for details. This does not work well with many other tools which cannot read these quoted names; we hence recommend to keept it at default, and replace all invalid characters.

Definition at line 207 of file tree/common_tree/newick_writer.hpp.

◆ set_default_names()

self_type& set_default_names ( std::string const & value )

inline

Shorthand to set the default names for leaf, inner and root node at once, to one value.

Definition at line 133 of file tree/common_tree/newick_writer.hpp.

◆ use_default_names() [1/2]

bool use_default_names ( ) const

inline

Return whether currently default names are activated in this plugin.

See the setter use_default_names( bool ) for details.

Definition at line 146 of file tree/common_tree/newick_writer.hpp.

◆ use_default_names() [2/2]

self_type& use_default_names ( bool value )

inline

Set whether to replace default named nodes with an empty string.

This setting activates the "reverse" operation of CommonTreeNewickReaderPlugin::use_default_names( bool ). Thus, when the default names are set to the same values as in the reader plugin, reading a Newick tree and then writing it again should yield the same names in the Newick tree again.

Common is false. In this case, all node names are written to the Newick tree, indepentenly of whether they match the default names.

If set to true, a node that has one of the default names will result in an empty node name in the Newick tree:

Leaf nodes with a name equal to default_leaf_name().
Inner nodes with a name equal to default_inner_name().
The root node with a name equal to default_root_name().

These default names can be changed by using default_leaf_name( std::string const& ), default_inner_name( std::string const& ) and default_root_name( std::string const& ), or by using set_default_names( std::string const& ) to set all three at once.

Definition at line 173 of file tree/common_tree/newick_writer.hpp.

Member Typedef Documentation

◆ self_type

using self_type = CommonTreeNewickWriterPlugin

Definition at line 59 of file tree/common_tree/newick_writer.hpp.

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

tree/common_tree/newick_writer.hpp

Detailed Description

Public Member Functions

Public Types

Constructor & Destructor Documentation

◆ CommonTreeNewickWriterPlugin() [1/3]

◆ ~CommonTreeNewickWriterPlugin()

◆ CommonTreeNewickWriterPlugin() [2/3]

◆ CommonTreeNewickWriterPlugin() [3/3]

Member Function Documentation

◆ branch_length_precision() [1/2]

◆ branch_length_precision() [2/2]

◆ default_inner_name() [1/2]

◆ default_inner_name() [2/2]

◆ default_leaf_name() [1/2]

◆ default_leaf_name() [2/2]

◆ default_root_name() [1/2]

◆ default_root_name() [2/2]

◆ edge_to_element()

◆ enable_branch_lengths() [1/2]

◆ enable_branch_lengths() [2/2]

◆ enable_names() [1/2]

◆ enable_names() [2/2]

◆ node_to_element()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ register_with()

◆ replace_invalid_chars() [1/2]

◆ replace_invalid_chars() [2/2]

◆ set_default_names()

◆ use_default_names() [1/2]

◆ use_default_names() [2/2]

Member Typedef Documentation

◆ self_type