A toolkit for working with phylogenetic data.
v0.19.0
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sample_set.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::placement
 

Functions

void adjust_branch_lengths (SampleSet &sample_set, tree::Tree const &source)
 Take the branch lengths of the source Tree and use them as the new branch lengths of the Samples in the sample_set. More...
 
void adjust_to_average_branch_lengths (SampleSet &sample_set)
 Set the branch lengths of all Samples in the sample_set to the respecitve average branch length of the Samples. More...
 
bool all_identical_trees (SampleSet const &sample_set)
 Returns true iff all Trees of the Samples in the set are identical. More...
 
tree::Tree average_branch_length_tree (SampleSet const &sample_set)
 Return the Tree that has edges with the average branch length of the respective edges of the Trees in the Samples of the given SampleSet. More...
 
Sample * find_sample (SampleSet &sample_set, std::string const &name)
 Get the first Sample in a SampleSet that has a given name, or nullptr if not found. More...
 
Sample const * find_sample (SampleSet const &sample_set, std::string const &name)
 Get the first Sample in a SampleSet that has a given name, or nullptr if not found. More...
 
Sample merge_all (SampleSet const &sample_set)
 Returns a Sample where all Samples of a SampleSet have been merged into. More...
 
std::ostream & operator<< (std::ostream &out, SampleSet const &sample_set)
 
size_t total_pquery_count (SampleSet const &sample_set)
 Return the total number of Pqueries in the Samples of the SampleSet. More...
 
tree::TreeSet tree_set (SampleSet const &sample_set)
 Return a TreeSet containing all the trees of the SampleSet. More...