1 /* 2 3 PHYML : a program that computes maximum likelihood phylogenies from 4 DNA or AA homologous sequences 5 6 Copyright (C) Stephane Guindon. Oct 2003 onward 7 8 All parts of the source except where indicated are distributed under 9 the GNU public licence. See http://www.opensource.org for details. 10 11 */ 12 13 #include <config.h> 14 15 #ifndef CURR_H 16 #define CURR_H 17 18 #include "utilities.h" 19 20 int Simu(t_tree *tree, int n_step_max, phydbl delta_lnL, phydbl init_T, phydbl delta_T, int min_n_edges_traversed); 21 void Simu_Loop(t_tree *tree); 22 void Select_Edges_To_Swap(t_tree *tree,t_edge **sorted_b,int *n_neg); 23 void Update_Bl(t_tree *tree,phydbl fact); 24 void Make_N_Swap(t_tree *tree,t_edge **b,int beg,int end); 25 int Make_Best_Swap(t_tree *tree); 26 int Mov_Backward_Topo_Bl(t_tree *tree,phydbl lk_old,t_edge **tested_b,int n_tested); 27 void Unswap_N_Branch(t_tree *tree,t_edge **b,int beg,int end); 28 void Swap_N_Branch(t_tree *tree,t_edge **b,int beg,int end); 29 void Check_NNI_Scores_Around(t_node *a, t_node *d, t_edge *b, phydbl *best_score, t_tree *tree); 30 int Mov_Backward_Topo_Pars(t_tree *tree, int pars_old, t_edge **tested_b, int n_tested); 31 void Simu_Pars(t_tree *tree, int n_step_max); 32 void NNI_Traversal(t_node *a, t_node *d, t_node *v, t_edge *b, int opt_edges, t_tree *tree); 33 void NNI_Core(t_node *a, t_node *d, t_node *v, t_edge *b, int opt_edges, t_tree *tree); 34 35 #endif 36