sources/multicoil/sc2seq_interface_cuts.c

   1 changed
   2 void PairCoilData (FILE *fgin, FILE **fpin, int *number_tables,
   3                    int ProlineFree, int table_to_remove_from,
   4                    char *input_filename, int mode,
   5                    double prior_freq_single[MAX_TABLE_NUMBER],
   6                    double prior_freq_pair[MAX_TABLE_NUMBER], int which_priors,
   7                    int which_priorp, int good_turing,
   8                    int structural_pos[POSNUM+1])
   9 to
  10 void PairCoilData (FILE *fgin, FILE **fpin, int *number_tables,
  11                    int ProlineFree, int table_to_remove_from,
  12                    char *input_filename, int mode)
  13
  14 changed
  15       if (!(mode & WEIGHTED_PROBS)) {
  16
  17         set_unimportant_pos_to_genbnk(many_pprobs[i], many_pprobp[i],
  18                                       gprobs, gprobp, structural_pos);
  19         estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
  20                                 pfreqp[i], ptotalp[i], many_pprobp,
  21                                 ProlineFree, which_priors, which_priorp,
  22                                 prior_freq_single[i],
  23                                 prior_freq_pair[i], good_turing,
  24                                 structural_pos);
  25 to
  26       if (!(mode & WEIGHTED_PROBS)) {
  27         estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
  28                                 pfreqp[i], ptotalp[i], many_pprobp,
  29                                 ProlineFree);
  30
  31
  32 changed
  33 void recalc_prob(Sequence sequence, int input_table, int mode,
  34                  int which_priors, int which_priorp,
  35                  double prior_freq_single[MAX_TABLE_NUMBER],
  36                  double prior_freq_pair[MAX_TABLE_NUMBER],
  37                  int good_turing, int structural_pos[POSNUM+1])
  38 to
  39 void recalc_prob(Sequence sequence, int input_table, int mode)
  40
  41 and
  42     estimate_database_probs(input_table, pfreqs[input_table],
  43                             ptotals[input_table], many_pprobs,
  44                             pfreqp[input_table], ptotalp[input_table],
  45                             many_pprobp, ProlineFreeWindow, which_priors,
  46                             which_priorp, prior_freq_single[input_table],
  47                             prior_freq_pair[input_table], good_turing,
  48                             structural_pos);
  49 to
  50     estimate_database_probs2(input_table, pfreqs[input_table],
  51                             ptotals[input_table], many_pprobs,
  52                             pfreqp[input_table], ptotalp[input_table],
  53                             many_pprobp, ProlineFreeWindow);
  54
  55
  56
  57
  58
  59 in PairCoilData
  60 changed
  61   for (i=0; i<*number_tables; i++)
  62
  63
  64 change
  65
  66 void average_score_over_coils3(Sequence seq,
  67                                double StructureResLike[MAXSEQLEN][POSNUM+1],
  68                                double StructureCoilLike[MAXSEQLEN][POSNUM+1],
  69                                double CoilLike[MAXSEQLEN][POSNUM+1],
  70                                int weighted_avg, int offset_to_use,
  71                                char offsets[MAXSEQLEN],
  72                                int start_at_reg_shift, double bound,
  73                                int avg_max)
  74 to
  75 void average_score_over_coils3(Sequence seq,
  76                                double StructureResLike[MAXSEQLEN][POSNUM+1],
  77                                double StructureCoilLike[MAXSEQLEN][POSNUM+1],
  78                                double CoilLike[MAXSEQLEN][POSNUM+1],
  79                                int offset_to_use,
  80                                char offsets[MAXSEQLEN],
  81                                int start_at_reg_shift, double bound,
  82                                int avg_max)
  83
  84
  85 replaced
  86
  87 void MultiCoilDimensionScore (int mode, Sequence sequence, char lib[MAXFUNCTNUM], double *maxscore, int table, char offsets[MAXSEQLEN], double scores[MAXSEQLEN][POSNUM+1], int offset_to_use, int pairs)
  88 by
  89 void MultiCoilDimensionScore (int mode, Sequence sequence, char lib[MAXFUNCTNUM], double *maxscore, int table, char offsets[MAXSEQLEN], double scores[MAXSEQLEN][POSNUM+1], int offset_to_use)
  90
  91
  92
  93 in PairCoilData:
  94   changed
  95     else if (i > 1) {  /* If there are 2 other tables average them.  */
  96       average_many_pprob(i);
  97       combine_many_weight(i);
  98     }
  99     else {
 100       fprintf(stderr, "\nCould not make combination table number %d.",i);
 101       fprintf(stderr, "\nAll later tables will be unavailable.\n");
 102       *number_tables=i;
 103     }
 104
 105 to
 106     else {
 107       fprintf(stderr, "\nCould not make input table number %d.",i);
 108       exit(-1);
 109     }
 110
 111
 112 and
 113     if (*number_tables != i)  {      /*  Just check for above where couldn't */
 114       #ifdef AVG_WEIRD_PROBS        /* make table.     */
 115         calc_weird_pprob_avg(many_pprobp[i], many_pprobs[i]);
 116       #else
 117         calc_weird_pprob_sum(many_pprobp[i], many_pprobs[i]);
 118       #endif
 119       }
 120 to
 121 #ifdef AVG_WEIRD_PROBS        /* make table.     */
 122     calc_weird_pprob_avg(many_pprobp[i], many_pprobs[i]);
 123 #else
 124     calc_weird_pprob_sum(many_pprobp[i], many_pprobs[i]);
 125 #endif
 126
 127
 128
 129 /*******************************ROUND 2 *****************************/
 130 CUT
 131
 132 /* #define PAIR_PIR_TXT "/local/bab/pir_pair.txt"  */
 133
 134
 135 double many_weights[MAX_TABLE_NUMBER][AANUM][POSNUM],
 136              many_weightp[MAX_TABLE_NUMBER][AANUM][AANUM][POSNUM][POSNUM];
 137
 138 double dist_weight[POSNUM];
 139 double prior_probs[NUM_RES_TYPE][POSNUM],
 140         prior_probp[NUM_RES_TYPE][NUM_RES_TYPE][POSNUM][POSNUM];
 141 double (*weights)[POSNUM];
 142 double (*weightp)[AANUM][POSNUM][POSNUM];
 143
 144 typedef double real;
 145
 146
 147 in switch_tables()
 148      cut    weights= many_weights[table];
 149             weightp= many_weightp[table];
 150
 151
 152 Cut
 153 /*  NOTE THAT THE many_pprob variables are globally defined in interface.h. */
 154 /** This gives the current_table probabilities the average of tables 1 and 2 */
 155 void average_many_pprob(int current_table)
 156 {
 157   int reg1, reg2, res1, res2;
 158
 159   for (res1=0; res1<AANUM; res1++)
 160     for (reg1=0; reg1<POSNUM; reg1++) {
 161       many_pprobs[current_table][res1][reg1] =
 162           (many_pprobs[0][res1][reg1] + many_pprobs[1][res1][reg1])/2;
 163
 164       for (res2=0; res2<AANUM; res2++)
 165         for (reg2=0; reg2<POSNUM; reg2++)
 166           many_pprobp[current_table][res1][res2][reg1][reg2] =
 167             (many_pprobp[0][res1][res2][reg1][reg2] +
 168                 many_pprobp[1][res1][res2][reg1][reg2]) /2;
 169     }
 170 }
 171
 172
 173 in recalc_prob()
 174      cut
 175   else {    /* Do weighted paircoil. */
 176     calcweight(pfreqs[input_table], pfreqp[input_table],gprobs, gprobp,
 177                many_weights[input_table], many_weightp[input_table],
 178                ptotals[input_table], ptotalp[input_table],NULL);
 179
 180     calc_weighted_pprobs(pfreqs[input_table], ptotals[input_table],
 181                          many_pprobs[input_table],
 182                          ProlineFreeWindow, many_weights[input_table],
 183                          gprobs, NULL);
 184     calc_weighted_pprobp(pfreqp[input_table], ptotalp[input_table],
 185                          many_pprobs[input_table],
 186                          many_pprobp[input_table], ProlineFreeWindow,
 187                          many_weightp[input_table],
 188                          gprobp, NULL);
 189   }
 190
 191 and
 192   average_many_pprob(2);
 193   combine_many_weight(2);     /*** Recompute the combination table probs. **/
 194
 195
 196 From PairCoilData, cut:
 197   FILE *weight_file=NULL;
 198   extern char weightfile_outname[MAXLINE];
 199
 200   if ((strcmp(weightfile_outname, "/dev/null")) || (mode & WEIGHTED_PROBS))
 201     weight_file = sopen(weightfile_outname,"w");
 202     if (weight_file) fprintf(weight_file,"\nTable number %d\n",i);
 203
 204 and changed:
 205
 206       if (!(mode & WEIGHTED_PROBS)) {
 207         estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
 208                                 pfreqp[i], ptotalp[i], many_pprobp,
 209                                 ProlineFree);
 210 /******************
 211         calcpprobs(pfreqs[i], ptotals[i], many_pprobs[i], ProlineFree);
 212         calcpprobp(pfreqp[i], ptotalp[i], many_pprobs[i], many_pprobp[i],
 213                  ProlineFree);
 214 ********************/
 215
 216         if (weight_file) printfreq_prob(pfreqs[i],pfreqp[i],
 217                weight_file,many_pprobs[i], many_pprobp[i]);
 218       }
 219       else {    /* Do weighted paircoil. */
 220         double bonnies_pprobs[NUM_RES_TYPE][POSNUM];
 221         double bonnies_pprobp[NUM_RES_TYPE][NUM_RES_TYPE][POSNUM][POSNUM];
 222
 223         calcweight(pfreqs[i], pfreqp[i],gprobs, gprobp,
 224                   many_weights[i], many_weightp[i],
 225                   ptotals[i], ptotalp[i],weight_file);
 226
 227         calcpprobs(pfreqs[i], ptotals[i], bonnies_pprobs, ProlineFree);
 228         calcpprobp(pfreqp[i], ptotalp[i], bonnies_pprobs, bonnies_pprobp,
 229                  ProlineFree);
 230
 231         calc_weighted_pprobs(pfreqs[i], ptotals[i], many_pprobs[i],
 232                              ProlineFree, many_weights[i], gprobs, NULL);
 233         calc_weighted_pprobp(pfreqp[i], ptotalp[i], many_pprobs[i],
 234                              many_pprobp[i], ProlineFree, many_weightp[i],
 235                              gprobp, NULL);
 236
 237         printweight(pfreqs[i],pfreqp[i],gprobs,gprobp,many_weights[i], many_weightp[i], ptotals[i],ptotalp[i],weight_file, many_pprobs[i], many_pprobp[i],bonnies_pprobs,bonnies_pprobp);
 238       }
 239
 240
 241
 242 to
 243
 244
 245       estimate_database_probs(i, pfreqs[i], ptotals[i], many_pprobs,
 246                                 pfreqp[i], ptotalp[i], many_pprobp,
 247
 248
 249 cut
 250
 251   if (mode & WEIGHTED_PROBS) fclose(weight_file);
 252   calc_distance_weights(dist,weight);
 253
 254
 255 Moved functions:
 256   PairCoilDiffer and average_scores_over_coil2 into file
 257 PairCoilDiffer_cuts.c
 258 and PairCoilDifferDimension()  and zero_out_non_coils() and
 259  zero_out_bad_windows( into PairCoilDiffer.c
 260
 261
 262
 263