biomcmc-lib  0.1
low level library for phylogenetic analysis
Data Structures | Typedefs | Functions
distance_matrix.h File Reference

distance matrix, that can be used in alignments and trees, and patristic-distance based species distances More...

#include "hashtable.h"
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Data Structures

struct  distance_matrix_struct
struct  spdist_matrix_struct


typedef struct distance_matrix_structdistance_matrix
typedef struct spdist_matrix_structspdist_matrix


distance_matrix new_distance_matrix (int nseqs)
 creates new matrix of pairwise distances
void zero_lower_distance_matrix (distance_matrix dist)
 specially in gene/sptree distance methods (GLASS, STEAC, etc.) lower is used for means and upper for min. This function resets matrix elements
void transpose_distance_matrix (distance_matrix dist)
 invert lower and upper diagonals of matrix (since some functions like upgma expect upper, etc.)
void del_distance_matrix (distance_matrix dist)
 releases memory allocated to distance_matrix (this structure has no smart ref_counter)
spdist_matrix new_spdist_matrix (int n_species)
void zero_all_spdist_matrix (spdist_matrix dist)
void finalise_spdist_matrix (spdist_matrix dist)
void finalise_spdist_matrix_with_rescaling (spdist_matrix dist, double scale)
void complete_missing_spdist_from_global_spdist (spdist_matrix local, spdist_matrix global)
void copy_spdist_matrix_to_distance_matrix_upper (spdist_matrix spd, distance_matrix dist, bool use_means)
void del_spdist_matrix (spdist_matrix dist)
void fill_species_dists_from_gene_dists (distance_matrix spdist, distance_matrix gendist, int *sp_id, bool use_upper_gene)
 updates distances between species based on genes and gene-to-species mapping, with min on upper and mean on lower diagonal
void update_species_dists_from_spdist (distance_matrix global, distance_matrix local, int *spexist)
 update global (over loci) species distances besed on local (within locus) species distances
int prepare_spdistmatrix_from_gene_species_map (spdist_matrix spdist, int *sp_id, int n_sp_id)
void fill_spdistmatrix_from_gene_dists (spdist_matrix spdist, distance_matrix gendist, int *sp_id, bool use_upper_gene)
void fill_spdistmatrix_from_gene_dist_vector (spdist_matrix spdist, double *gdist, int n_gdist, int *sp_id)
 initialise spdist_matrix with patristic distances from gdist vector of size n_gdist (1D)
void update_spdistmatrix_from_spdistmatrix (spdist_matrix global, spdist_matrix local)

Detailed Description

distance matrix, that can be used in alignments and trees, and patristic-distance based species distances

These functions don't know about trees/topologies: topology_common.c creates the actual patristic distances, and downstream software or genetree.h should decide how to use this information

Function Documentation

◆ zero_all_spdist_matrix()

void zero_all_spdist_matrix ( spdist_matrix  dist)

zero both mean[] and min[] since we only look at average (never min) across loci