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 INIT_H 16 #define INIT_H 17 18 #include "utilities.h" 19 20 void Init_Cseq(align *this); 21 void Init_Eigen_Struct(eigen *this); 22 void Init_Scalar_Dbl(scalar_dbl *p); 23 void Init_Scalar_Int(scalar_int *p); 24 void Init_Vect_Dbl(int len,vect_dbl *p); 25 void Init_Vect_Int(int len,vect_int *p); 26 void Init_Tree(t_tree *tree,int n_otu); 27 void Init_Edge_Light(t_edge *b,int num); 28 void Init_Node_Light(t_node *n,int num); 29 void Init_NNI(t_nni *a_nni); 30 void Init_Nexus_Format(nexcom **com); 31 void Init_Mat(matrix *mat,calign *data); 32 void Set_Defaults_Input(option *io); 33 void Set_Defaults_Model(t_mod *mod); 34 void Set_Defaults_Optimiz(t_opt *s_opt); 35 void XML_Init_Node(xml_node *prev,xml_node *new_node,char *name); 36 void Init_One_Spr(t_spr *a_spr); 37 void Init_Model(calign *data,t_mod *mod,option *io); 38 int Init_Qmat_Dayhoff(phydbl *daa,phydbl *pi); 39 int Init_Qmat_DCMut(phydbl *daa,phydbl *pi); 40 int Init_Qmat_MtArt(phydbl *daa,phydbl *pi); 41 int Init_Qmat_HIVb(phydbl *daa,phydbl *pi); 42 int Init_Qmat_HIVw(phydbl *daa,phydbl *pi); 43 int Init_Qmat_JTT(phydbl *daa,phydbl *pi); 44 int Init_Qmat_MtREV(phydbl *daa,phydbl *pi); 45 int Init_Qmat_LG(phydbl *daa,phydbl *pi); 46 int Init_Qmat_WAG(phydbl *daa,phydbl *pi); 47 int Init_Qmat_RtREV(phydbl *daa,phydbl *pi); 48 int Init_Qmat_CpREV(phydbl *daa,phydbl *pi); 49 int Init_Qmat_VT(phydbl *daa,phydbl *pi); 50 int Init_Qmat_Blosum62(phydbl *daa,phydbl *pi); 51 int Init_Qmat_MtMam(phydbl *daa,phydbl *pi); 52 int Init_Qmat_AB(phydbl *daa, phydbl *pi); 53 void XML_Init_Attribute(xml_attr *attr); 54 void Init_String(t_string *ts); 55 void Init_Efrq(phydbl *b_frq, t_efrq *f); 56 void RATES_Init_Rate_Struct(t_rate *rates, t_rate *existing_rates, int n_otu); 57 void TIMES_Init_Time_Struct(t_time *times, t_time *existing_time, int n_otu); 58 void Init_Rmat(t_rmat *rmat); 59 void Init_MGF_Bl(t_tree *tree); 60 int Init_Qmat_FLU(phydbl *daa, phydbl *pi); 61 void Set_Defaults_Ras(t_ras *ras); 62 void GEO_Init_Coord(t_geo_coord *t, int n_dim); 63 void PHYREX_Init_Disk_Event(t_dsk *t, int n_dim, t_phyrex_mod *mod); 64 void PHYREX_Init_Lindisk_Node(t_ldsk *t, t_dsk *devt, int n_dim); 65 void PHYREX_Init_Migrep_Mod(t_phyrex_mod *t, int n_dim, phydbl min_lat, phydbl min_lon, phydbl max_lat, phydbl max_lon); 66 void MCMC_Init_MCMC_Struct(char *filename, option *io, t_mcmc *mcmc); 67 void Init_Calibration(t_cal *cal); 68 void Init_All_Calibration(t_tree *tree); 69 void Init_Sarea(t_sarea *s); 70 void Init_Efrqs_Using_Observed_Freqs(t_efrq *f, phydbl *o, int ns); 71 void Init_Calign(int n_otu, int crunch_len, int init_len, calign *this); 72 void Init_Linked_List(t_ll *list); 73 void Init_Target_Tip(t_clad *clade, t_tree *tree); 74 void Init_NNI_Score(phydbl val, t_edge *b, t_tree *tree); 75 void M4_Init_Model(m4 *m4mod, calign *data, t_mod *mod); 76 void RW_Init_Contrasts(int dim_idx, t_tree *tree); 77 void PHYREX_Set_Default_Migrep_Mod(int n_otu, t_phyrex_mod *t); 78 79 #endif 80