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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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A library for working with phylogenetic and population genetic data.
v0.27.0 |
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#include <genesis/tree/attribute_tree/keyed_newick_reader.hpp>
Inherits NewickReader, CommonTreeNewickReaderPlugin, and KeyedAttributeTreeNewickReaderPlugin.
Read default Newick trees, i.e., trees with names and branch lengths.
This class is a convenience wrapper that combines a NewickReader with a KeyedAttributeTreeNewickReaderPlugin. It is intended to be used for standard use cases, and produces a Tree with AttributeTreeNodeData and AttributeTreeEdgeData at its nodes and edges.
It is also possible to register additional plugins on top of this class.
Definition at line 469 of file keyed_newick_reader.hpp.
Public Member Functions | |
| KeyedAttributeTreeNewickReader () | |
 Public Member Functions inherited from NewickReader | |
| NewickReader ()=default | |
| NewickReader (NewickReader &&)=default | |
| NewickReader (NewickReader const &)=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... | |
| bool | enable_tags () const |
| Return whether currently Newick tags are enabled. More... | |
| NewickReader & | enable_tags (bool value) |
| Set whether Newick tags are enabled for reading. More... | |
| NewickReader & | operator= (NewickReader &&)=default |
| NewickReader & | operator= (NewickReader const &)=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, Tree > | parse_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... | |
| 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... | |
| 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... | |
| bool | stop_after_semicolon () const |
| Return whether currently reading stops after the semicolon that finishes a Newick tree. More... | |
| NewickReader & | stop_after_semicolon (bool value) |
| Set whether reading a single tree stops after the semicolon that finishes a Newick tree. More... | |
| Public Member Functions inherited from CommonTreeNewickReaderPlugin | |
| CommonTreeNewickReaderPlugin ()=default | |
| CommonTreeNewickReaderPlugin (CommonTreeNewickReaderPlugin &&)=default | |
| CommonTreeNewickReaderPlugin (CommonTreeNewickReaderPlugin const &)=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_type & | default_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_type & | default_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_type & | default_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_type & | default_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 |
| CommonTreeNewickReaderPlugin & | operator= (CommonTreeNewickReaderPlugin &&)=default |
| CommonTreeNewickReaderPlugin & | operator= (CommonTreeNewickReaderPlugin const &)=default |
| void | register_with (NewickReader &reader) const |
| bool | replace_name_underscores () const |
| Return whether currently this plugin replaces underscores with spaces. More... | |
| self_type & | replace_name_underscores (bool value) |
| Set whether to replace all underscores ('_') in names with spaces (' '). 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 unnamed nodes with a default name. More... | |
| Public Member Functions inherited from KeyedAttributeTreeNewickReaderPlugin | |
| KeyedAttributeTreeNewickReaderPlugin ()=default | |
| KeyedAttributeTreeNewickReaderPlugin (KeyedAttributeTreeNewickReaderPlugin &&)=default | |
| KeyedAttributeTreeNewickReaderPlugin (KeyedAttributeTreeNewickReaderPlugin const &)=default | |
| virtual | ~KeyedAttributeTreeNewickReaderPlugin ()=default |
| self_type & | add_attribute (std::string const &key, Target target) |
Store values of a key at a target (i.e., Node or Edge). More... | |
| self_type & | add_attribute (std::string const &source_key, Target target, std::string const &target_key) |
Store values of a source_key at a target (i.e., Node or Edge), using the target_key. More... | |
| self_type & | add_attribute (std::string const &source_key, Target target, std::string const &target_key, std::string const &default_value) |
Store values of a source_key at a target (i.e., Node or Edge), using the target_key, and a default_value, if the key is not found in the source. More... | |
| self_type & | add_catch_all (Target target=Target::kNode) |
| Store all key-value-pairs of the Newick data in an AttributeTree. More... | |
| self_type & | add_nhx_attributes () |
| Add typical attributes of the NHX format, and set the appropriate delimiters. More... | |
| std::string | assigner () const |
| Get the currently set assign symbol between a key and its value. More... | |
| self_type & | assigner (std::string const &value) |
| Set the assign symbol between a key and its value. More... | |
| void | clear () |
| Reset all settings to the default and delete all attribute settings. More... | |
| void | element_to_edge (NewickBrokerElement const &element, TreeEdge &edge) const |
| void | element_to_node (NewickBrokerElement const &element, TreeNode &node) const |
| self_type & | operator= (KeyedAttributeTreeNewickReaderPlugin &&)=default |
| self_type & | operator= (KeyedAttributeTreeNewickReaderPlugin const &)=default |
| std::string | prefix () const |
| Get the currently set prefix to look for in Newick comments. More... | |
| self_type & | prefix (std::string const &value) |
| Set the prefix to look for in Newick comments. More... | |
| void | register_with (NewickReader &reader) const |
| std::string | separator () const |
| Get the currently set separator between key-value-pairs. More... | |
| self_type & | separator (std::string const &value) |
| Set the separator between key-value-pairs. More... | |
| self_type & | set_delimiters (std::string const &prefix, std::string const &separator, std::string const &assigner="=") |
| Set the delimiters for key-value-pairs. More... | |
| self_type & | set_nhx_delimiters () |
| Set the delimiters to the format used by NHX. More... | |
| bool | trim () const |
| Get whether to trim keys and values before storing them in the Tree. More... | |
| self_type & | trim (bool value) |
| Set whether to trim keys and values before storing them in the Tree. 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 Types inherited from KeyedAttributeTreeNewickReaderPlugin | |
| using | self_type = KeyedAttributeTreeNewickReaderPlugin |
| enum | Target { kNode, kEdge } |
| Select where to store the data, i.e., at Nodes or Edges of the Tree. More... | |
| 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 |
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inline |
Definition at line 480 of file keyed_newick_reader.hpp.
1.8.17