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placement/function/distances.cpp File Reference

`#include "genesis/placement/function/distances.hpp"`

`#include "genesis/placement/pquery.hpp"`

`#include "genesis/placement/pquery/plain.hpp"`

`#include <algorithm>`

`#include <cassert>`

`#include <cmath>`

Go to the source code of this file.

## Namespaces | |

genesis | |

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

genesis::placement | |

## Functions | |

double | placement_distance (PqueryPlacement const &place_a, PqueryPlacement const &place_b, utils::Matrix< double > const &node_distances) |

Calculate the distance between two PqueryPlacements, using their positin on the tree::TreeEdges, measured in branch length units. More... | |

double | placement_distance (PqueryPlacement const &placement, tree::TreeNode const &node, utils::Matrix< double > const &node_distances) |

Calculate the distance in branch length units between a PqueryPlacement and a tree::TreeNode. More... | |

size_t | placement_path_length_distance (PqueryPlacement const &place_a, PqueryPlacement const &place_b, utils::Matrix< size_t > const &node_path_lengths) |

size_t | placement_path_length_distance (PqueryPlacement const &placement, tree::TreeEdge const &edge, utils::Matrix< size_t > const &edge_path_lengths) |

Calculate the discrete distance from a PqueryPlacement to an edge, measured as the number of nodes between them. More... | |

double | pquery_distance (PqueryPlain const &pquery_a, PqueryPlain const &pquery_b, utils::Matrix< double > const &node_distances, bool with_pendant_length=false) |

Calculate the weighted distance between two plain pqueries. It is mainly a helper method for distance calculations (e.g., pairwise distance, variance). More... | |

template<typename DistanceFunction > | |

double | pquery_distance (Pquery const &pquery_a, Pquery const &pquery_b, DistanceFunction distance_function) |

Local helper function to avoid code duplication. More... | |

double | pquery_distance (Pquery const &pquery_a, Pquery const &pquery_b, utils::Matrix< double > const &node_distances, bool with_pendant_length=false) |

Calculate the weighted distance between two Pqueries, in branch length units, as the pairwise distance between their PqueryPlacements, and using the `like_weight_ratio` for weighing. More... | |

template<typename DistanceFunction > | |

double | pquery_distance (Pquery const &pquery, DistanceFunction distance_function) |

Local helper function to avoid code duplication. More... | |

double | pquery_distance (Pquery const &pquery, tree::TreeNode const &node, utils::Matrix< double > const &node_distances) |

Calculate the weighted distance between the PqueryPlacements of a Pquery and a tree::TreeNode, in branch length units, using the `like_weight_ratio` of the PqueryPlacements for weighing. More... | |

double | pquery_path_length_distance (Pquery const &pquery_a, Pquery const &pquery_b, utils::Matrix< size_t > const &node_path_lengths) |

Calculate the weighted discrete distance between two Pqueries, measured as the pairwise distance in number of nodes between between their PqueryPlacements, and using the `like_weight_ratio` for weighing. More... | |

double | pquery_path_length_distance (Pquery const &pquery, tree::TreeEdge const &edge, utils::Matrix< size_t > const &edge_path_lengths) |

Calculate the weighted discrete distance between the PqueryPlacements of a Pquery and a tree::TreeNode, in number of nodes, using the `like_weight_ratio` of the PqueryPlacements for weighing. More... | |