A toolkit for working with phylogenetic data.
v0.24.0
CommonTreeNewickReader Class Reference

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

Inherits NewickReader, and CommonTreeNewickReaderPlugin.

Detailed Description

Read default Newick trees, i.e., trees with names and branch lengths.

This class is a convenience wrapper that combines a NewickReader with a CommonTreeNewickReaderPlugin. It is intended to be used for standard use cases, and produces a Tree with CommonNodeData and CommonEdgeData at its nodes and edges.

It is also possible to register additional plugins on top of this class.

Behind the curtain, this class derives from both NewickReader and CommonTreeNewickReaderPlugin. This is a bit ugly, but we use it for simplicity. This allows to use an instance as if it was a reader (i.e., call from_... functions), but also change the plugin settings in a natural way.

Definition at line 326 of file tree/common_tree/newick_reader.hpp.

Public Member Functions

 CommonTreeNewickReader ()
 
- Public Member Functions inherited from NewickReader
 NewickReader ()=default
 
 NewickReader (NewickReader const &)=default
 
 NewickReader (NewickReader &&)=default
 
virtual ~NewickReader ()=default
 
Tree broker_to_tree (NewickBroker const &broker) const
 Build a Tree from a NewickBroker. More...
 
Tree broker_to_tree_destructive (NewickBroker &broker) const
 Build a Tree from a NewickBroker. More...
 
NewickReaderenable_tags (bool value)
 Set whether Newick tags are enabled for reading. More...
 
bool enable_tags () const
 Return whether currently Newick tags are enabled. More...
 
NewickReaderoperator= (NewickReader const &)=default
 
NewickReaderoperator= (NewickReader &&)=default
 
void parse_multiple_trees (utils::InputStream &input_stream, TreeSet &tree_set, std::string const &default_name) const
 Parse until the end of the stream and add all Trees to the TreeSet. More...
 
std::pair< std::string, Treeparse_named_tree (utils::InputStream &input_stream) const
 Parse one named tree, i.e., a tree as described here. More...
 
Tree parse_single_tree (utils::InputStream &input_stream) const
 Parse a single tree. Depending on stop_after_semicolon(), stop after the semicolon or continue until the end of the input, checking if there are only comments. More...
 
Tree read (std::shared_ptr< utils::BaseInputSource > source) const
 Read a single Tree from an input source containing a Newick tree. More...
 
void read (std::shared_ptr< utils::BaseInputSource > source, TreeSet &target, std::string const &default_name="") const
 Add Trees to a TreeSet from an input source containing a list of Newick trees. More...
 
void read (std::vector< std::shared_ptr< utils::BaseInputSource >> sources, TreeSet &target, std::string const &default_name="") const
 Fill a TreeSet from a list of input sources containing Newick trees. More...
 
TreeSet read (std::vector< std::shared_ptr< utils::BaseInputSource >> sources, std::string const &default_name="") const
 Return a TreeSet from a list of input sources containing Newick trees. More...
 
NewickReaderstop_after_semicolon (bool value)
 Set whether reading a single tree stops after the semicolon that finishes a Newick tree. More...
 
bool stop_after_semicolon () const
 Return whether currently reading stops after the semicolon that finishes a Newick tree. More...
 
- Public Member Functions inherited from CommonTreeNewickReaderPlugin
 CommonTreeNewickReaderPlugin ()=default
 
 CommonTreeNewickReaderPlugin (CommonTreeNewickReaderPlugin const &)=default
 
 CommonTreeNewickReaderPlugin (CommonTreeNewickReaderPlugin &&)=default
 
virtual ~CommonTreeNewickReaderPlugin ()=default
 
double default_branch_length () const
 Get the default branch length used when there is none given for an edge. More...
 
self_typedefault_branch_length (double value)
 Set the default branch length used when there is none given for an edge. More...
 
std::string const & default_inner_name () const
 Get the default named used when there is none given for an inner node. More...
 
self_typedefault_inner_name (std::string const &value)
 Set the default named used when there is none given for an inner node. More...
 
std::string const & default_leaf_name () const
 Get the default named used when there is none given for a leaf node. More...
 
self_typedefault_leaf_name (std::string const &value)
 Set the default named used when there is none given for a leaf node. More...
 
std::string const & default_root_name () const
 Get the default named used when there is none given for the root node. More...
 
self_typedefault_root_name (std::string const &value)
 Set the default named used when there is none given for the root node. More...
 
void element_to_edge (NewickBrokerElement const &element, TreeEdge &edge) const
 
void element_to_node (NewickBrokerElement const &element, TreeNode &node) const
 
CommonTreeNewickReaderPluginoperator= (CommonTreeNewickReaderPlugin const &)=default
 
CommonTreeNewickReaderPluginoperator= (CommonTreeNewickReaderPlugin &&)=default
 
void register_with (NewickReader &reader) const
 
bool replace_name_underscores () const
 Return whether currently this plugin replaces underscores with spaces. More...
 
self_typereplace_name_underscores (bool value)
 Set whether to replace all underscores ('_') in names with spaces (' '). 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 unnamed nodes with a default name. More...
 

Additional Inherited Members

- Public Types inherited from NewickReader
using create_edge_data_function = std::function< void(TreeEdge &edge) >
 Function type used to create the data pointer for each TreeEdge. More...
 
using create_node_data_function = std::function< void(TreeNode &node) >
 Function type used to create the data pointer for each TreeNode. More...
 
using element_to_edge_function = std::function< void(NewickBrokerElement const &element, TreeEdge &edge) >
 Function type that translates from a NewickBrokerElement to a TreeEdge. More...
 
using element_to_node_function = std::function< void(NewickBrokerElement const &element, TreeNode &node) >
 Function type that translates from a NewickBrokerElement to a TreeNode. More...
 
using finish_reading_function = std::function< void(Tree &tree) >
 Function type that allows to do some finalizing work with the Tree after the actual tree reading finished. More...
 
using prepare_reading_function = std::function< void(NewickBroker const &broker, Tree &tree) >
 Function type that allows to do some preparatory work with the NewickBroker and Tree before the actual tree reading begins. More...
 
- Public Types inherited from CommonTreeNewickReaderPlugin
using self_type = CommonTreeNewickReaderPlugin
 
- Public Attributes inherited from NewickReader
create_edge_data_function create_edge_data_plugin
 
create_node_data_function create_node_data_plugin
 
std::vector< element_to_edge_functionelement_to_edge_plugins
 
std::vector< element_to_node_functionelement_to_node_plugins
 
std::vector< finish_reading_functionfinish_reading_plugins
 
std::vector< prepare_reading_functionprepare_reading_plugins
 

Constructor & Destructor Documentation

◆ CommonTreeNewickReader()

Definition at line 336 of file tree/common_tree/newick_reader.hpp.


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