| 1 | /* |
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| 2 | |
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| 3 | PHYML : a program that computes maximum likelihood phylogenies from |
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| 4 | DNA or AA homologous sequences |
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| 5 | |
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| 6 | Copyright (C) Stephane Guindon. Oct 2003 onward |
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| 7 | |
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| 8 | All parts of the source except where indicated are distributed under |
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| 9 | the GNU public licence. See http://www.opensource.org for details. |
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| 10 | |
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| 11 | */ |
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| 12 | |
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| 13 | #include <config.h> |
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| 14 | |
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| 15 | #ifndef CURR_H |
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| 16 | #define CURR_H |
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| 17 | |
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| 18 | #include "utilities.h" |
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| 19 | #include "lk.h" |
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| 20 | #include "optimiz.h" |
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| 21 | #include "models.h" |
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| 22 | #include "free.h" |
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| 23 | #include "spr.h" |
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| 24 | #include "pars.h" |
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| 25 | #include "alrt.h" |
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| 26 | |
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| 27 | void Simu_Loop(t_tree *tree); |
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| 28 | int Simu(t_tree *tree,int n_step_max); |
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| 29 | void Select_Edges_To_Swap(t_tree *tree,t_edge **sorted_b,int *n_neg); |
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| 30 | void Update_Bl(t_tree *tree,phydbl fact); |
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| 31 | void Make_N_Swap(t_tree *tree,t_edge **b,int beg,int end); |
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| 32 | int Make_Best_Swap(t_tree *tree); |
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| 33 | int Mov_Backward_Topo_Bl(t_tree *tree,phydbl lk_old,t_edge **tested_b,int n_tested); |
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| 34 | void Unswap_N_Branch(t_tree *tree,t_edge **b,int beg,int end); |
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| 35 | void Swap_N_Branch(t_tree *tree,t_edge **b,int beg,int end); |
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| 36 | void Check_NNI_Scores_Around(t_node *a, t_node *d, t_edge *b, phydbl *best_score, t_tree *tree); |
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| 37 | int Mov_Backward_Topo_Pars(t_tree *tree, int pars_old, t_edge **tested_b, int n_tested); |
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| 38 | void Simu_Pars(t_tree *tree, int n_step_max); |
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| 39 | |
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| 40 | #endif |
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