source: branches/ali/GDE/PHYML20130708/phyml/src/mixt.h

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

added most recent version of phyml
File size: 3.6 KB
Line 
1/*
2
3PHYML :  a program that  computes maximum likelihood  phylogenies from
4DNA or AA homologous sequences
5
6Copyright (C) Stephane Guindon. Oct 2003 onward
7
8All parts of  the source except where indicated  are distributed under
9the GNU public licence.  See http://www.opensource.org for details.
10
11*/
12
13#include <config.h>
14
15#ifndef MIXT_H
16#define MIXT_H
17
18#include "utilities.h"
19
20void MIXT_Connect_Edges_To_Next_Prev_Child_Parent(t_tree *tree);
21void MIXT_Connect_Nodes_To_Next_Prev_Child_Parent(t_tree *tree);
22void MIXT_Connect_Sprs_To_Next_Prev_Child_Parent(t_tree *tree);
23void MIXT_Turn_Branches_OnOff(int onoff,t_tree *tree);
24phydbl *MIXT_Get_Lengths_Of_This_Edge(t_edge *mixt_b, t_tree *tree);
25void MIXT_Set_Lengths_Of_This_Edge(phydbl *lens,t_edge *mixt_b, t_tree *tree);
26void MIXT_Post_Order_Lk(t_node *mixt_a,t_node *mixt_d,t_tree *mixt_tree);
27void MIXT_Pre_Order_Lk(t_node *mixt_a,t_node *mixt_d,t_tree *mixt_tree);
28phydbl MIXT_Lk(t_edge *mixt_b,t_tree *mixt_tree);
29void MIXT_Update_P_Lk(t_tree *mixt_tree,t_edge *mixt_b,t_node *mixt_d);
30void MIXT_Update_PMat_At_Given_Edge(t_edge *mixt_b,t_tree *mixt_tree);
31int *MIXT_Get_Number_Of_Classes_In_All_Mixtures(t_tree *mixt_tree);
32t_tree **MIXT_Record_All_Mixtures(t_tree *mixt_tree);
33void MIXT_Break_All_Mixtures(int *c_max,t_tree *mixt_tree);
34void MIXT_Reconnect_All_Mixtures(t_tree **tree_list,t_tree *mixt_tree);
35int *MIXT_Record_Has_Invariants(t_tree *mixt_tree);
36void MIXT_Reset_Has_Invariants(int *has_invariants,t_tree *mixt_tree);
37void MIXT_Check_Invar_Setup(t_tree *mixt_tree);
38void MIXT_Prune_Subtree(t_node *mixt_a,t_node *mixt_d,t_edge **mixt_target,t_edge **mixt_residual,t_tree *mixt_tree);
39void MIXT_Graft_Subtree(t_edge *mixt_target,t_node *mixt_link,t_edge *mixt_residual,t_tree *mixt_tree);
40void MIXT_Br_Len_Brent(phydbl prop_min, phydbl prop_max,t_edge *mixt_b, t_tree *mixt_tree);
41void MIXT_Check_Number_Of_Invar_Classes(t_tree *mixt_tree);
42void MIXT_Prepare_Tree_For_Lk(t_tree *tree);
43void MIXT_Check_Invar_Struct_In_Each_Partition_Elem(t_tree *mixt_tree);
44void MIXT_Check_RAS_Struct_In_Each_Partition_Elem(t_tree *mixt_tree);
45void MIXT_Br_Len_Involving_Invar(t_tree *mixt_tree);
46void MIXT_Br_Len_Not_Involving_Invar(t_tree *mixt_tree);
47phydbl MIXT_Unscale_Br_Len_Multiplier_Tree(t_tree *mixt_tree);
48phydbl MIXT_Rescale_Br_Len_Multiplier_Tree(t_tree *mixt_tree);
49void MIXT_Set_Alias_Subpatt(int onoff, t_tree *mixt_tree);
50phydbl Lk_Core(int state, int ambiguity_check, t_edge *b, t_tree *tree);
51void MIXT_Check_Single_Edge_Lens(t_tree *mixt_tree);
52void MIXT_Update_Eigen(t_mod *mixt_mod);
53int MIXT_Pars(t_edge *mixt_b, t_tree *mixt_tree);
54void MIXT_Set_Pars_Thresh(t_tree *mixt_tree);
55void MIXT_Bootstrap(char *best_tree, xml_node *root);
56void MIXT_Chain_All(t_tree *mixt_tree);
57void MIXT_Chain_String(t_string *curr, t_string *next);
58void MIXT_Chain_Scalar_Dbl(scalar_dbl *curr, scalar_dbl *next);
59void MIXT_Chain_Rmat(t_rmat *curr, t_rmat *next);
60void MIXT_Chain_Rmat(t_rmat *curr, t_rmat *next);
61void MIXT_Chain_Efrq(t_efrq *curr, t_efrq *next);
62void MIXT_Chain_RAS(t_ras *curr, t_ras *next);
63void MIXT_Chain_Eigen(eigen *curr, eigen *next);
64void MIXT_Chain_Vector_Dbl(vect_dbl *curr, vect_dbl *next);
65void MIXT_Chain_Sprs(t_tree *tree);
66void MIXT_Chain_Nodes(t_tree *tree);
67void MIXT_Chain_Edges(t_tree *tree);
68void MIXT_Chain_Triplets(t_tree *tree);
69phydbl MIXT_Get_Mean_Edge_Len(t_edge *mixt_b, t_tree *tree);
70phydbl MIXT_Get_Sum_Chained_Scalar_Dbl(scalar_dbl *s);
71phydbl MIXT_Get_Sum_Of_Probas_Across_Mixtures(phydbl r_mat_weight_sum, phydbl e_frq_weight_sum, t_tree *mixt_tree);
72phydbl MIXT_Rescale_Free_Rate_Tree(t_tree *mixt_tree);
73void MIXT_Set_Br_Len_Var(t_tree *mixt_tree);
74
75#endif
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