binaries/src/tcoffee/t_coffee_source/dp_lib/fsa_dp.h

   1 /******************************COPYRIGHT NOTICE*******************************/
   2 /*  (c) Centro de Regulacio Genomica                                                        */
   3 /*  and                                                                                     */
   4 /*  Cedric Notredame                                                                        */
   5 /*  12 Aug 2014 - 22:07.                                                                    */
   6 /*All rights reserved.                                                                      */
   7 /*This file is part of T-COFFEE.                                                            */
   8 /*                                                                                          */
   9 /*    T-COFFEE is free software; you can redistribute it and/or modify                      */
  10 /*    it under the terms of the GNU General Public License as published by                  */
  11 /*    the Free Software Foundation; either version 2 of the License, or                     */
  12 /*    (at your option) any later version.                                                   */
  13 /*                                                                                          */
  14 /*    T-COFFEE is distributed in the hope that it will be useful,                           */
  15 /*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
  16 /*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
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  22 /*...............................................                                           */
  23 /*  If you need some more information                                                       */
  24 /*  cedric.notredame@europe.com                                                             */
  25 /*...............................................                                           */
  26 /******************************COPYRIGHT NOTICE*******************************/
  27 #ifndef FSA_DP_H
  28 #define FSA_DP_H
  29
  30 /*By convention, 0: START, 1: END*/
  31
  32 struct Hmm
  33 {
  34
  35   double freeT;           /*Free transition*/
  36   double forbiden;        /*Forbiden transition*/
  37   int start;              /*start, by convention: 0*/
  38   int end;                /*end, by convention: 1*/
  39
  40   int nS;                 /*Number of states*/
  41   int order;
  42   struct HmmState  **S;   /*State List*/
  43
  44   /*Bounded HMM*/
  45   double **T;             /*Transition matrix*/
  46   int **fromM;            /*For any sate s, fromM[0]->number of states leading to s*/
  47   int **toM;              /*For any sate s, toM[0]->number of s can go to*/
  48                           /*End and Start are NOT included in toM and FromM*/
  49
  50
  51 };
  52 typedef struct Hmm Hmm;
  53
  54 struct HmmAln
  55 {
  56   Hmm *H;
  57   int *state_list;
  58 };
  59 typedef struct HmmAln HmmAln;
  60
  61 typedef double (*Generic_em_func)(struct Hmm*, struct HmmState*, int);
  62
  63 struct HmmState
  64 {
  65 char name[100];
  66 int state;
  67 int DJ;
  68 int DI;
  69
  70   /*Pair HMM*/
  71 double em;
  72 Col_cost_func em_func;
  73
  74   /*Linear HMM*/
  75 double *em2;
  76 Generic_em_func em_func2;
  77 int nT;
  78 struct StateTrans **T;
  79 };
  80 typedef struct HmmState HmmState;
  81
  82 struct StateTrans
  83 {
  84   char name[101];
  85   double tr;
  86 };
  87 typedef struct StateTrans StateTrans;
  88
  89 struct MatState
  90 {
  91   int i;
  92   int j;
  93   int st;
  94   int pst;
  95   double sc;
  96   struct MatState *n;
  97   struct MatState *p;
  98   struct MatState *m; /*memory*/
  99   struct MatState *s; /*memory of the start point*/
 100   /*Heap Mamagement: Never copy*/
 101   struct MatState *Hn;/*Heap Next*/
 102   struct MatState *Hp;/*Heap Previous*/
 103
 104   struct MatState *Mn;/*Marked Heap section*/
 105   struct MatState *Mp;/*Marked Heap Section*/
 106   int free;
 107 };
 108 typedef struct MatState MatState;
 109
 110
 111 /*********************************************************************************/
 112 /*                                                                               */
 113 /*                                                                               */
 114 /*                     simple HMM: Viterbi                                       */
 115 /*                                                                               */
 116 /*                                                                               */
 117 /*********************************************************************************/
 118 int seq_viterbi_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
 119
 120 /*********************************************************************************/
 121 /*                                                                               */
 122 /*                                                                               */
 123 /*                     HMM: Viterbi                                              */
 124 /*                                                                               */
 125 /*                                                                               */
 126 /*********************************************************************************/
 127
 128 int viterbi_pair_wise_OLD (Alignment *A,int*ns, int **ls,Constraint_list *CL);
 129 Alignment * viterbipath2aln (Alignment *A, int *ns,int **ls,int *tb, Hmm *H);
 130 double*** viterbi_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL);
 131 int * viterbi2path (int l1,int l2, Hmm *H, double ***M);
 132 /*********************************************************************************/
 133 /*                                                                               */
 134 /*                                                                               */
 135 /*                      HMM modeling                                             */
 136 /*                                                                               */
 137 /*                                                                               */
 138 /*********************************************************************************/
 139 int viterbiL_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
 140 MatState* RviterbiL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E);
 141 MatState* viterbiL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL, MatState *S, MatState *E);
 142
 143 int viterbiD_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
 144 double lu_RviterbiD_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
 145 MatState* RviterbiD_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
 146 MatState* viterbiD_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL, MatState *S, MatState *E, int **seg_list);
 147 int **seglist2table ( int **seglist,int l1, int l2);
 148 int *seglist2line ( int **seglist, int line, int start, int end);
 149 int * traceback (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
 150
 151 int viterbiDGL_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
 152 double lu_RviterbiDGL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
 153 MatState* RviterbiDGL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
 154 MatState* viterbiDGL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
 155
 156
 157 /*********************************************************************************/
 158 /*                                                                               */
 159 /*                                                                               */
 160 /*                      HMM modeling                                             */
 161 /*                                                                               */
 162 /*                                                                               */
 163 /*********************************************************************************/
 164 int MatStateAreIdentical (MatState*I, MatState*O);
 165 int MaxDeltaMatState (MatState*I, MatState*O);
 166 int MinDeltaMatState (MatState*I, MatState*O);
 167
 168 MatState * ManageMatState(int Mode, MatState *C);
 169 MatState* CopyMatState ( MatState*I, MatState*O);
 170
 171 Hmm* read_hmm(char *file);
 172 Hmm* declare_hmm(int n);
 173 Hmm* free_Hmm(Hmm*H);
 174 void DisplayHmm ( Hmm *H);
 175
 176 /*********************************************************************************/
 177 /*                                                                               */
 178 /*                                                                               */
 179 /*                      HMM Models                                               */
 180 /*                                                                               */
 181 /*                                                                               */
 182 /*********************************************************************************/
 183 Hmm* define_two_mat_model(Constraint_list *CL);
 184 Hmm* define_probcons_model(Constraint_list *CL);
 185 Hmm* define_simple_model(Constraint_list *CL);
 186
 187 Hmm * bound_hmm ( Hmm *H);
 188
 189 #endif // FSA_DP_H