masses.cpp File Reference

Implementation of the Placement Functions.

Definition in file masses.cpp.

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

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

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

`#include "genesis/tree/common_tree/distances.hpp"`

`#include "genesis/tree/common_tree/functions.hpp"`

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

`#include "genesis/tree/function/functions.hpp"`

`#include "genesis/tree/function/operators.hpp"`

`#include "genesis/utils/core/algorithm.hpp"`

`#include "genesis/utils/core/std.hpp"`

`#include <algorithm>`

`#include <cassert>`

`#include <cmath>`

`#include <exception>`

`#include <regex>`

`#include <string>`

`#include <unordered_map>`

`#include <unordered_set>`

`#include <vector>`

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 | |

std::vector< double > | placement_mass_per_edge_without_multiplicities (Sample const &sample) |

Return a vector that contains the sum of the masses of the PqueryPlacements per edge of the tree of the Sample. More... | |

utils::Matrix< double > | placement_mass_per_edge_without_multiplicities (SampleSet const &sample_set) |

Return a Matrix that contains the placement masses per edge. More... | |

std::vector< double > | placement_mass_per_edges_with_multiplicities (Sample const &sample) |

Return a vector that contains the sum of the masses of the PqueryPlacements per edge of the tree of the Sample, using the multiplicities as factors. More... | |

utils::Matrix< double > | placement_mass_per_edges_with_multiplicities (SampleSet const &sample_set) |

Return a Matrix that contains the placement masses per edge, using the multiplicities as factors. More... | |

double | total_multiplicity (Pquery const &pqry) |

Return the sum of all multiplicities of the Pquery. More... | |

double | total_multiplicity (Sample const &sample) |

Return the sum of all multiplicities of all the Pqueries of the Sample. More... | |

double | total_placement_mass_with_multiplicities (Sample const &smp) |

Get the mass of all PqueryPlacements of the Sample, using the multiplicities as factors. More... | |

double | total_placement_mass_without_multiplicities (Sample const &smp) |

Get the summed mass of all PqueryPlacements in all Pqueries of the given Sample, where mass is measured by the like_weight_ratios of the PqueryPlacements. More... | |