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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/formats/phyloxml/writer.hpp>
Inherited by CommonTreePhyloxmlWriter.
Write a Tree to Phyloxml format.
This class supports to write a Tree into a Phyloxml format representation, using
PhyloxmlWriter().write( tree, utils::to_file( "path/to/tree.phyloxml" ));
It understands the Phyloxml format, but is agnostic of the actual data representation of TreeNode and TreeEdge data. This approach allows to store data in any wanted format.
In order to translate data from the Tree into a Phyloxml format representation, a set of plugin functions is used, that need to be set before writing a Tree. Those functions are a form of intermediaries, which take tree data and turn them into the wanted Phyloxml representation. It is possible to use lambdas for this, or any other function that can be stored in a std::function.
The following plugin points are provided:
For example, the CommonTreePhyloxmlWriterPlugin is a convenience class that provides such plugin functions. It translates from a CommonTree with TreeNodes that contain names and TreeEdges that contain branch lengths into the standard Phyloxml format. Using plugin classes like this additionally allows to use state for the plugin functions - that is, to use some settings for how to write data.
Furthermore, as we use vectors of plugin functions, it is possible (and often necessary) to register multiple such functions, which are then called one after another. This allows to e.g., first translate a branch length for an edge in one plugin function, and then translating a bootstrap value or edge color in another plugin function.
This whole approach is a bit tedious, but unfortunately the price for the flexibility of this class. In order to keep the standard use cases simple, we also provide classes like CommonTreePhyloxmlWriter, which hides the whole plugin system and allows simple writing of default trees to standard Phyloxml.
Definition at line 101 of file tree/formats/phyloxml/writer.hpp.
Public Member Functions | |
| PhyloxmlWriter ()=default | |
| PhyloxmlWriter (PhyloxmlWriter &&)=default | |
| PhyloxmlWriter (PhyloxmlWriter const &)=default | |
| virtual | ~PhyloxmlWriter ()=default |
| PhyloxmlWriter & | operator= (PhyloxmlWriter &&)=default |
| PhyloxmlWriter & | operator= (PhyloxmlWriter const &)=default |
| void | to_document (Tree const &tree, utils::XmlDocument &xml) const |
| Store the information of the tree into an Phyloxml-formatted XmlDocument. More... | |
| void | write (Tree const &tree, std::shared_ptr< utils::BaseOutputTarget > target) const |
| Write a Tree to an output target, using the Phyloxml format. More... | |
Public Types | |
| using | edge_to_element_function = std::function< void(TreeEdge const &edge, utils::XmlElement &element) > |
| Function type that translates from a TreeEdge to an XmlElement. More... | |
| using | finish_writing_function = std::function< void(Tree const &tree, utils::XmlDocument &xml) > |
| Function type that allows to do some finalizing work with the Tree and XmlDocument after the actual tree writing finished. More... | |
| using | node_to_element_function = std::function< void(TreeNode const &node, utils::XmlElement &element) > |
| Function type that translates from a TreeNode to an XmlElement. More... | |
| using | prepare_writing_function = std::function< void(Tree const &tree, utils::XmlDocument &xml) > |
| Function type that allows to do some preparatory work with the Tree and XmlDocument before the actual tree writing begins. More... | |
Public Attributes | |
| 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 Phyloxml 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 Phyloxml 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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| void to_document | ( | Tree const & | tree, |
| utils::XmlDocument & | xml | ||
| ) | const |
Store the information of the tree into an Phyloxml-formatted XmlDocument.
Definition at line 63 of file tree/formats/phyloxml/writer.cpp.
| void write | ( | Tree const & | tree, |
| std::shared_ptr< utils::BaseOutputTarget > | target | ||
| ) | const |
Write a Tree to an output target, using the Phyloxml format.
See the output target convenience functions utils::to_file(), utils::to_stream(), and utils::to_string() for examples of how to obtain a suitable output target.
Definition at line 56 of file tree/formats/phyloxml/writer.cpp.
| using edge_to_element_function = std::function< void( TreeEdge const& edge, utils::XmlElement& element ) > |
Function type that translates from a TreeEdge to an XmlElement.
This is called for each TreeEdge while writing the Tree to Phyloxml and is used to transfer data from the edge into a suitable representation in the Phyloxml format.
Definition at line 150 of file tree/formats/phyloxml/writer.hpp.
| using finish_writing_function = std::function< void( Tree const& tree, utils::XmlDocument& xml ) > |
Function type that allows to do some finalizing work with the Tree and XmlDocument after the actual tree writing finished.
This can for example be used for some cleanup.
Definition at line 128 of file tree/formats/phyloxml/writer.hpp.
| using node_to_element_function = std::function< void( TreeNode const& node, utils::XmlElement& element ) > |
Function type that translates from a TreeNode to an XmlElement.
This is called for each TreeNode while writing the Tree to Phyloxml and is used to transfer data from the node into a suitable representation in the Phyloxml format.
Definition at line 139 of file tree/formats/phyloxml/writer.hpp.
| using prepare_writing_function = std::function< void( Tree const& tree, utils::XmlDocument& xml ) > |
Function type that allows to do some preparatory work with the Tree and XmlDocument before the actual tree writing begins.
This is for example useful if a certain kind of value for the nodes depends on other nodes. Using this function, such data can be collected and then used when writing the nodes.
Definition at line 118 of file tree/formats/phyloxml/writer.hpp.
| 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 Phyloxml representation.
Definition at line 206 of file tree/formats/phyloxml/writer.hpp.
| std::vector<finish_writing_function> finish_writing_plugins |
Collect all functions to be called after finishing the actual tree writing.
Definition at line 194 of file tree/formats/phyloxml/writer.hpp.
| 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 Phyloxml representation.
Definition at line 200 of file tree/formats/phyloxml/writer.hpp.
| std::vector<prepare_writing_function> prepare_writing_plugins |
Collect all functions to be called before starting the actual tree writing.
Definition at line 189 of file tree/formats/phyloxml/writer.hpp.
1.8.17