source: trunk/GDE/PHYML20130708/phyml/src/mg.h

Last change on this file was 10307, checked in by aboeckma, 11 years ago

added most recent version of phyml
File size: 3.4 KB
Line 
1#include <config.h>
2
3#ifndef PART_H
4#define PART_H
5
6#include "utilities.h"
7
8void Menu_Supertree(option *input);
9void PART_Print_Nodes(t_node *a, t_node *d, supert_tree *st);
10supert_tree *PART_Make_Supert_tree_Light(option *input);
11void PART_Make_Supert_tree_Full(supert_tree *st, option *input, calign **data);
12void PART_Get_List_Of_Reachable_Tips(t_node *a, t_node *d, calign **data, supert_tree *st);
13void PART_Get_List_Of_Reachable_Tips_Pre(t_node *a, t_node *d, supert_tree *st);
14void PART_Get_List_Of_Reachable_Tips_Post(t_node *a, t_node *d, supert_tree *st);
15void PART_Prune_St_Topo(t_tree *tree, calign *data, supert_tree *st);
16void PART_Match_St_Nodes_In_Gt_Recurr(t_node *a_gt, t_node *d_gt, t_node *a_st, t_node *d_st, t_tree *gt, supert_tree *st);
17void PART_Match_St_Nodes_In_Gt(t_tree *tree, supert_tree *st);
18void PART_Match_St_Edges_In_Gt(t_tree *gt, supert_tree *st);
19void PART_Match_St_Edges_In_Gt_Recurr(t_node *a, t_node *d, t_node *a_st, t_node *d_st, t_tree *gt, supert_tree *st);
20void PART_Simu(supert_tree *tr);
21int PART_Mov_Backward_Topo_Bl(supert_tree *st, phydbl lk_old, t_edge **tested_b, int n_tested);
22int PART_Get_Species_Found_In_St(supert_tree *st, calign *data);
23void PART_Map_St_Nodes_In_Gt_Pre(t_node *a_st, t_node *d_st, t_tree *gt, supert_tree *st);
24void PART_Map_St_Nodes_In_Gt_Post(t_node *a_st, t_node *d_st, t_tree *gt, supert_tree *st);
25void PART_Map_St_Nodes_In_Gt(t_tree *gt, supert_tree *st);
26void PART_Map_St_Nodes_In_Gt_One_Edge(t_node *a_st, t_node *d_st, t_edge *b_st, t_tree *gt, supert_tree *st);
27void PART_Map_St_Edges_In_Gt(t_tree *gt, supert_tree *st);
28phydbl PART_Lk(supert_tree *st);
29int PART_Pars(supert_tree *st);
30int PART_Spr(phydbl init_lnL, supert_tree *st);
31void PART_Speed_Spr(supert_tree *st);
32int Map_Spr_Move(t_edge *st_pruned, t_edge *st_target, t_node *st_link, t_tree *gt, supert_tree *st);
33void PART_Test_All_Spr_Targets(t_edge *pruned, t_node *n_link, supert_tree *st);
34void PART_Test_One_Spr_Target_Recur(t_node *a, t_node *d, t_edge *target, t_edge *pruned, t_node *n_link, supert_tree *st);
35void PART_Test_One_Spr_Target(t_edge *st_p, t_edge *st_t, t_node *n_link, supert_tree *st);
36int PART_Test_List_Of_Regraft_Pos(t_spr **st_spr_list, int list_size, supert_tree *st);
37int PART_Try_One_Spr_Move(t_spr *st_move, supert_tree *st);
38void PART_Map_Gt_Edges_In_St(t_tree *gt, supert_tree *st);
39void PART_NNI(t_edge *st_b, supert_tree *st);
40void PART_Swap(t_node *st_a, t_node *st_b, t_node *st_c, t_node *st_d, supert_tree *st);
41void PART_Set_Bl(phydbl **bl, supert_tree *st);
42void PART_Restore_Br_Len(supert_tree *st);
43void PART_Record_Br_Len(supert_tree *st);
44phydbl PART_Lk_At_Given_Edge(t_edge *st_b, supert_tree *st);
45phydbl PART_Update_Lk_At_Given_Edge(t_edge *st_b, supert_tree *st);
46void PART_Fill_Model_Partitions_Table(supert_tree *st);
47phydbl PART_Br_Len_Brent(t_edge *st_b, int quickdirty, supert_tree *tree);
48void PART_Initialise_Bl_Partition(supert_tree *st);
49void PART_Update_P_Lk(t_edge *st_b, t_node *st_n, supert_tree *st);
50void PART_Optimize_Br_Len_Serie(t_node *st_a, t_node *st_d, t_edge *st_b, supert_tree *st);
51void PART_Update_Bl_Swaped(t_edge **st_b, int n, supert_tree *st);
52void PART_Update_Bl(phydbl fact, supert_tree *st);
53void PART_Make_N_Swap(t_edge **st_b, int beg, int end, supert_tree *st);
54void PART_Do_Mapping(supert_tree *st);
55void PART_Update_PMat(t_edge *st_b, supert_tree *st);
56void PART_Print_Bl(supert_tree *st);
57void PART_Check_Extra_Taxa(supert_tree *st);
58int PART_main(int argc, char **argv);
59#endif
60
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