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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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#include <genesis/placement/formats/newick_writer.hpp>
Inherits NewickWriter, CommonTreeNewickWriterPlugin, and PlacementTreeNewickWriterPlugin.
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 &&)=default | |
| NewickWriter (NewickWriter const &)=default | |
| virtual | ~NewickWriter ()=default |
| bool | force_quotation_marks () const |
| Get whether all names are wrapped in quotation marks. More... | |
| NewickWriter & | force_quotation_marks (bool value) |
If set to true, all names are wrapped in quotation marks, regardless of whether the name contains any characters that need to be wrapped. More... | |
| size_t | line_length () const |
| Get the currently set approximate maximal line length. More... | |
| NewickWriter & | line_length (size_t value) |
| Set the approximate maximal line length to use when writing Newick trees. More... | |
| NewickWriter & | operator= (NewickWriter &&)=default |
| NewickWriter & | operator= (NewickWriter const &)=default |
| char | quotation_mark () const |
| Get the currently set type of quotation marks used for node names. More... | |
| NewickWriter & | quotation_mark (char value) |
| Set the type of quotation marks used for node names that contain special characters. More... | |
| std::string | to_string (Tree const &tree) const |
| Shorthand to write a Tree to Newick format and return it is a string. More... | |
| bool | trailing_new_line () const |
Get the current setting for whether a new line char \n is written to the end of each tree. More... | |
| NewickWriter & | trailing_new_line (bool value) |
Set whether to write a new line char \n at the end of each tree. More... | |
| NewickBroker | tree_to_broker (Tree const &tree) const |
| Transform the information of the tree into a NewickBroker object. More... | |
| void | write (NewickBroker const &broker, std::shared_ptr< utils::BaseOutputTarget > target) const |
| Write a NewickBroker to an output target, in Newick format. More... | |
| void | write (Tree const &tree, std::shared_ptr< utils::BaseOutputTarget > target) const |
| Write a Tree to an output target, using the Newick format. More... | |
| void | write (TreeSet const &tree_set, std::shared_ptr< utils::BaseOutputTarget > target, bool with_names=false) const |
| Write all Trees in a TreeSet to an output target, using the Newick format. More... | |
| bool | write_comments () const |
| Get whether Newick comments (e.g., some forms of bootstrap values) are written. More... | |
| NewickWriter & | write_comments (bool value) |
| Set whether to write Newick comments (e.g., some forms of bootstrap values). More... | |
| bool | write_names () const |
| Get whether Newick node names are written. More... | |
| NewickWriter & | write_names (bool value) |
| Set whether to write Newick node names. More... | |
| bool | write_tags () const |
Get whether Newick tags (e.g., for jplace files) are written. More... | |
| NewickWriter & | write_tags (bool value) |
Set whether to write Newick tags (e.g., for jplace files). More... | |
| bool | write_values () const |
| Get whether Newick values (e.g., branch lengths) are written. More... | |
| NewickWriter & | write_values (bool value) |
| Set whether to write Newick values (e.g., branch lengths). More... | |
| Public Member Functions inherited from CommonTreeNewickWriterPlugin | |
| 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 Member Functions inherited from PlacementTreeNewickWriterPlugin | |
| PlacementTreeNewickWriterPlugin ()=default | |
| PlacementTreeNewickWriterPlugin (PlacementTreeNewickWriterPlugin &&)=default | |
| PlacementTreeNewickWriterPlugin (PlacementTreeNewickWriterPlugin const &)=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) |
| PlacementTreeNewickWriterPlugin & | operator= (PlacementTreeNewickWriterPlugin &&)=default |
| PlacementTreeNewickWriterPlugin & | operator= (PlacementTreeNewickWriterPlugin const &)=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 CommonTreeNewickWriterPlugin | |
| using | self_type = CommonTreeNewickWriterPlugin |
| 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... | |
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inline |
Definition at line 159 of file placement/formats/newick_writer.hpp.
1.8.17