A toolkit for working with phylogenetic data.
v0.24.0
taxonomy/functions/tree.cpp File Reference

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Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::taxonomy
 

Functions

static void add_subtaxonomy_ (Taxonomy const &taxonomy, bool keep_singleton_inner_nodes, bool keep_inner_node_names, int max_level, int parent_level, tree::NewickBroker &broker)
 Recursive local helper function to add taxa to the tree broker. More...
 
tree::Tree taxonomy_to_tree (Taxonomy const &taxonomy, bool keep_singleton_inner_nodes=false, bool keep_inner_node_names=false, int max_level=-1)
 Turn a Taxonomy into a (possibly multifurcating) Tree. More...
 
tree::Tree taxonomy_to_tree (Taxonomy const &taxonomy, std::unordered_map< std::string, Taxopath > const &extra_taxa, bool keep_singleton_inner_nodes=false, bool keep_inner_node_names=false, int max_level=-1, bool add_extra_taxa_parents=true)
 Turn a Taxonomy into a (possibly multifurcating) Tree, and allow to add extra tips to it. More...
 
tree::Tree taxonomy_to_tree (std::unordered_map< std::string, Taxopath > const &taxon_map, bool keep_singleton_inner_nodes=false, bool keep_inner_node_names=false, int max_level=-1)
 Turn a list of Taxa into a (possibly multifurcating) Tree. More...