1 /* 2 ** spr.h: Header file for the SPR routines. 3 ** 4 ** Wim Hordijk Last modified: 28 August 2006 5 */ 6 7 #include <config.h> 8 9 #ifndef _SPR_H_ 10 #define _SPR_H_ 11 12 #include "utilities.h" 13 14 #define ALL 1 15 #define BEST 2 16 #define ONE 3 17 18 /* 19 ** _move_: Structure for holding the relevant information for candidate SPR moves. 20 */ 21 22 typedef struct 23 { 24 t_node *v_prune, *u_prune, *v_n, *v_nx1, *u_n, **path; 25 t_edge *e_prune, *e_regraft; 26 phydbl l_connect, l_est[3], delta_lk, d_L, d_up_v, d_un_v; 27 int dist, rgrft_rank, optim_rank, globl_rank; 28 } _move_; 29 30 31 32 void Init_SPR (t_tree *tree); 33 void Clean_SPR (t_tree *tree); 34 void Optim_SPR (t_tree *tree, int max_size, int method); 35 int Perform_SPR_Moves (t_tree *tree, int max_size); 36 int Perform_Best_SPR (t_tree *tree, int max_size); 37 int Perform_One_SPR (t_tree *tree, int max_size); 38 39 void Prune (t_edge *e, t_node *v, t_edge **e_connect, t_edge **e_avail, 40 t_tree *tree); 41 void Regraft (t_edge *e, t_node *v, t_edge *avail, t_tree *tree); 42 void PostOrder_v (t_tree *tree, t_node *v, t_edge *e); 43 void PostOrder_w (t_tree *tree, t_node *v, t_edge *v_e, t_node *w, t_edge *e); 44 45 46 47 48 49 void Speed_Spr(t_tree *tree, phydbl prop_spr, int max_cycles, phydbl delta_lnL); 50 void Global_Spr_Search(t_tree *tree); 51 void Make_Spr_List(t_tree *tree); 52 void Init_One_Spr(t_spr *a_spr); 53 t_spr *Make_One_Spr(t_tree *tree); 54 int Spr(phydbl init_lnL, phydbl prop_spr, t_tree *tree); 55 int Spr_Recur(t_node *a, t_node *d, t_tree *tree); 56 int Test_All_Spr_Targets(t_edge *pulled, t_node *link, t_tree *tree); 57 void Randomize_Spr_List(t_tree *tree); 58 void Test_One_Spr_Target_Recur(t_node *a, t_node *d, t_edge *pulled, t_node *link, t_edge *residual, t_edge *init_target, int *best_found, t_spr *prev_move, t_tree *tree); 59 t_spr *Test_One_Spr_Target(t_edge *b_target, t_edge *b_arrow, t_node *n_link, t_edge *b_residual, t_edge *init_target, t_node *polarity, t_tree *tree); 60 void Apply_Spr_Moves_One_By_One(t_tree *tree); 61 int Try_One_Spr_Move_Triple(t_spr *move, t_tree *tree); 62 int Try_One_Spr_Move_Full(t_spr *move, short int apply_move, t_tree *tree); 63 void Make_Best_Spr(t_tree *tree); 64 void Random_Spr(int n_moves, t_tree *tree); 65 unsigned int Include_One_Spr_To_List_Of_Spr(t_spr **list, int list_size, t_spr *move, t_tree *tree); 66 void Reset_Spr_List(t_spr **list, int size); 67 int Evaluate_List_Of_Regraft_Pos_Triple(t_spr **spr_list, int list_size, t_tree *tree); 68 void Best_Spr(t_tree *tree); 69 int Check_Spr_Move_Validity(t_spr *this_spr_move, t_tree *tree); 70 void Spr_Subtree(t_edge *b, t_node *link, t_tree *tree); 71 void Spr_Pars(int threshold, int n_round_max, t_tree *tree); 72 void Spr_Shuffle(t_tree *tree); 73 void Sort_Spr_List_Depth(t_tree *tree); 74 void Sort_Spr_List_LnL(t_spr **list, int list_size, t_tree *tree); 75 void Spr_Random_Explore(t_tree *tree, phydbl anneal_temp, phydbl prop_spr, int do_rnd, int max_cycles); 76 void Sort_Spr_List_Pars(t_tree *tree); 77 void Spr_List_Of_Trees(t_tree *tree); 78 void Prune_Regraft_Time_Tree(t_tree *tree); 79 void Spr_Pre_Order(t_node *a, t_node *d, t_edge *b, t_tree *tree); 80 81 82 83 #endif /* _SPR_H_ */ 84 85 86 /* 87 ** EOF: spr.h 88 */ 89