A toolkit for working with phylogenetic data.
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PlacementTreeNewickReader Class Reference

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

Inherits NewickReader, DefaultTreeNewickReaderPlugin, and PlacementTreeNewickReaderPlugin.

Detailed Description

Definition at line 142 of file placement/formats/newick_reader.hpp.

Public Member Functions

 PlacementTreeNewickReader ()
 
- Public Member Functions inherited from NewickReader
 NewickReader ()=default
 
 NewickReader (NewickReader const &)=default
 
 NewickReader (NewickReader &&)=default
 
virtual ~NewickReader ()=default
 
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...
 
Tree from_file (std::string const &filename) const
 Read a Tree from a file containing a Newick tree. More...
 
void from_file (std::string const &filename, TreeSet &tree_set, std::string const &default_name="") const
 Add Trees to a TreeSet from a file containing a list of Newick trees. More...
 
void from_files (std::vector< std::string > const &filenames, TreeSet &tree_set) const
 Fill a TreeSet from a list of files containing Newick trees. More...
 
Tree from_stream (std::istream &input_stream) const
 Read a Tree from an input stream containing a Newick tree. More...
 
void from_stream (std::istream &input_stream, TreeSet &tree_set, std::string const &default_name="") const
 Add Trees to a TreeSet from an input stream containing a list of Newick trees. More...
 
Tree from_string (std::string const &tree_string) const
 Read a Tree from a string containing a Newick tree. More...
 
void from_string (std::string const &tree_string, TreeSet &tree_set, std::string const &default_name="") const
 Add Trees to a TreeSet from a string containing a list of Newick trees. More...
 
void from_strings (std::vector< std::string > const &tree_strings, TreeSet &tree_set, std::string const &default_name="") const
 Fill a TreeSet from a list of strings containing Newick trees. 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_at_semicolon(), stop after the semicolon or continue until the end of the input, checking if there are only comments. More...
 
NewickReaderstop_at_semicolon (bool value)
 Set whether reading a single tree stops after the semicolon that finishes a Newick tree. More...
 
bool stop_at_semicolon () const
 Return whether currently reading stops after the semicolon that finishes a Newick tree. More...
 
- Public Member Functions inherited from DefaultTreeNewickReaderPlugin
 DefaultTreeNewickReaderPlugin ()=default
 
 DefaultTreeNewickReaderPlugin (DefaultTreeNewickReaderPlugin const &)=default
 
 DefaultTreeNewickReaderPlugin (DefaultTreeNewickReaderPlugin &&)=default
 
virtual ~DefaultTreeNewickReaderPlugin ()=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
 
DefaultTreeNewickReaderPluginoperator= (DefaultTreeNewickReaderPlugin const &)=default
 
DefaultTreeNewickReaderPluginoperator= (DefaultTreeNewickReaderPlugin &&)=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...
 
- Public Member Functions inherited from PlacementTreeNewickReaderPlugin
 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::NewickBroker const &broker, tree::Tree &tree) const
 
PlacementTreeNewickReaderPluginoperator= (PlacementTreeNewickReaderPlugin const &)=default
 
PlacementTreeNewickReaderPluginoperator= (PlacementTreeNewickReaderPlugin &&)=default
 
void register_with (tree::NewickReader &reader) const
 

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(NewickBroker const &broker, Tree &tree) >
 Function type that allows to do some finalizing work with the NewickBroker and 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 DefaultTreeNewickReaderPlugin
using self_type = DefaultTreeNewickReaderPlugin
 
- 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_function
element_to_edge_plugins
 
std::vector
< element_to_node_function
element_to_node_plugins
 
std::vector
< finish_reading_function
finish_reading_plugins
 
std::vector
< prepare_reading_function
prepare_reading_plugins
 

Constructor & Destructor Documentation

Definition at line 153 of file placement/formats/newick_reader.hpp.


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