sources/multicoil/multivariate_like2_cuts.c

   1 changed
   2 void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
   3       int number_score_dim, double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
   4       double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
   5       int number_of_classifications, char gauss_param[MAXLINE])
   6 to
   7 void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
   8       int number_score_dim, double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
   9       double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
  10      char gauss_param[MAXLINE])
  11
  12 by changing
  13
  14     for (class=0; class<number_of_classifications; class++) {
  15
  16 to
  17     for (class=0; class<NUMBER_CLASSES; class++) {
  18
  19
  20
  21
  22 changed
  23 void compute_submatrices2(
  24         double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
  25         double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
  26         double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
  27         int number_classes,
  28         double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
  29         double det[MAX_CLASS_NUMBER],
  30         char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  31         int old_num_dim_table0, int old_num_dim_table1,
  32         int new_num_dim_table0, int new_num_dim_table1, int multi_trimer_pairs
  33         )
  34 to
  35 void compute_submatrices2(
  36         double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
  37         double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
  38         double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
  39         double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
  40         double det[MAX_CLASS_NUMBER],
  41         char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  42         int old_num_dim_table0, int old_num_dim_table1,
  43         int new_num_dim_table0, int new_num_dim_table1
  44         )
  45 changed
  46   for (class=0; class<number_classes; class++)
  47 to
  48   for (class=0; class<NUMBER_CLASSES; class++)
  49
  50 everywhere changed
  51       means_submatrix[class][dim1] = means[class]
  52             [old_dimension(old_num_dim_table0, old_num_dim_table1,
  53                            new_num_dim_table0, new_num_dim_table1,
  54                            multi_lib, multi_trimer_pairs,dim1)];
  55 to
  56       means_submatrix[class][dim1] = means[class]
  57             [old_dimension(old_num_dim_table0, old_num_dim_table1,
  58                            new_num_dim_table0, new_num_dim_table1,
  59                            multi_lib, dim1)];
  60
  61
  62
  63 changed
  64 int old_dimension(int old_num_dim_table0, int old_num_dim_table1,
  65                   int new_num_dim_table0, int new_num_dim_table1,
  66                   char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  67                   int multi_trimer_pairs,
  68                   int new_dim_number)
  69 to
  70 int old_dimension(int old_num_dim_table0, int old_num_dim_table1,
  71                   int new_num_dim_table0, int new_num_dim_table1,
  72                   char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  73                   int new_dim_number)
  74
  75 changed
  76
  77 type_class_score_convert(Sequence sequence,
  78                      double all_like[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],
  79                      double bound, int new_only_coiled_classes,
  80                         int number_tables, int number_classes)
  81 to
  82 type_class_score_convert(Sequence sequence,
  83                      double all_like[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],
  84                      double bound, int new_only_coiled_classes)
  85
  86
  87  Replaced:
  88
  89 int compute_dimension(int tablenum, int number_tables, int libnumber,
  90                       int number_score_dim,
  91                       int number_multi_lib[MAX_TABLE_NUMBER],
  92                       int multi_trimer_pairs)
  93 {
  94   int prev_table;
  95   int dimension=0;
  96
  97   if (!number_score_dim)   /*  old version of numbering. */
  98     return (libnumber*number_tables + tablenum);
  99   else { /* new version, works when use single freq score instead of paircoil*/
 100     for (prev_table =0; prev_table<tablenum; prev_table++)
 101       dimension+= compute_num_multilib(prev_table, number_multi_lib,
 102                                        multi_trimer_pairs);
 103
 104     return (dimension + libnumber);
 105   }
 106 }
 107
 108 by
 109
 110
 111 int compute_dimension2(int tablenum, int libnumber,
 112                        int num_dist[MAX_TABLE_NUMBER],
 113                        int combine_dist[MAX_TABLE_NUMBER])
 114 {
 115   int prev_table;
 116   int dimension=0;
 117
 118   for (prev_table =0; prev_table<tablenum; prev_table++)
 119     dimension+= num_table_dimensions(num_dist[prev_table],
 120                                      combine_dist[prev_table]);
 121
 122   return (dimension + libnumber);
 123 }
 124
 125
 126
 127 added
 128
 129 int num_table_dimensions(int num_dist_table,
 130                          int combine_dist_table)
 131 {
 132
 133   return ((1-combine_dist_table)*num_dist_table +
 134           combine_dist_table);
 135 }
 136
 137
 138
 139
 140 /**********************************************************/
 141
 142
 143 Changed
 144
 145
 146
 147 void convert_raw_scores_to_gauss_prob_like2(
 148    double all_raw_scores[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],int seq_len,
 149    int number_tables, double class_means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
 150  double inverse_covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
 151    double determinants[MAX_CLASS_NUMBER],
 152    int number_classes, double init_class_prob[MAX_CLASS_NUMBER],
 153    int number_score_dim, int consider_only_positive_classes, double bound,
 154    int Offset_to_Use, int last_class_gets_sum_prev)
 155
 156 to
 157
 158 void convert_raw_scores_to_gauss_prob_like2(
 159    double all_raw_scores[MAX_NUM_SCORE_DIM][MAXSEQLEN][POSNUM+1],int seq_len,
 160    int number_tables, double class_means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
 161  double inverse_covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
 162    double determinants[MAX_CLASS_NUMBER],
 163    int number_classes, double init_class_prob[MAX_CLASS_NUMBER],
 164    int number_score_dim, int consider_only_positive_classes, double bound,
 165    int Offset_to_Use)
 166
 167 In that function:
 168
 169 Cut
 170  if (all_one || !last_class_gets_sum_prev)
 171     last_class_for_scores = number_classes;
 172   else  last_class_for_scores = number_classes-1;  /* Last class will be sum */
 173                                                    /* of prob for prev. class*/
 174
 175
 176 Cut
 177   int last_class_for_scores, number_tables_to_write;
 178
 179 cut
 180   if (number_classes > number_tables) number_tables_to_write = number_classes;
 181   else number_tables_to_write = number_tables;
 182
 183 Changed
 184         if (Offset_to_Use == -1)  /*  Want reg 7 to have max of other reg */
 185           for (tablenum =0; tablenum<last_class_for_scores; tablenum++)
 186
 187 to
 188         if (Offset_to_Use == -1)  /*  Want reg 7 to have max of other reg */
 189           for (tablenum =0; tablenum<number_classes; tablenum++)
 190
 191
 192 Changed
 193       else    /** Compute reg 7 as max of previous registers for offset -1 **/
 194         for (tablenum=0; tablenum < last_class_for_scores; tablenum++)
 195           like_in_class[tablenum] = max_class_like[tablenum];
 196
 197 to
 198
 199
 200       else    /** Compute reg 7 as max of previous registers for offset -1 **/
 201         for (tablenum=0; tablenum < number_classes; tablenum++)
 202           like_in_class[tablenum] = max_class_like[tablenum];
 203
 204
 205
 206 Changed
 207
 208     /** Temporary hack to set the class we are interested to the table. **/
 209     /** So make class 1 =cctb, class 2 = trimer-, class 3 = pdb- in .paircoil*/
 210     /** Lets ASSUME that class= number_classes-1 is always pdb- */
 211     /** so for table>=number_classes-1 output sum of other classes prob. **/
 212     /** (which is the positive prob (prob of being coiled)).             **/
 213       for (tablenum=0; tablenum < number_tables_to_write; tablenum++)  {
 214         if (tablenum < last_class_for_scores) {
 215           all_raw_scores[tablenum][i][reg] = like_in_class[tablenum];
 216         }
 217         else {
 218           all_raw_scores[tablenum][i][reg]=
 219             calc_total_coil_likelihood(like_in_class, number_classes,reg,
 220                                        Offset_to_Use,
 221                                        &max_class_like[tablenum],
 222                                        init_class_prob);
 223         }
 224
 225 to
 226
 227       for (tablenum=0; tablenum < number_classes; tablenum++)  {
 228         all_raw_scores[tablenum][i][reg] = like_in_class[tablenum];
 229         }
 230
 231
 232
 233 /********************************************************************/
 234
 235
 236 Cut
 237
 238
 239
 240 int compute_num_multilib(int tablenum, int number_multi_lib[MAX_TABLE_NUMBER],
 241                          int multi_trimer_pairs)
 242 {
 243   int use_pairs;
 244
 245   if (tablenum <0) return 0;
 246   else if (tablenum ==0) use_pairs =1;  /*  Use pairs for cctb */
 247   else if (tablenum ==1) use_pairs = multi_trimer_pairs;
 248
 249   if (!use_pairs)  return 1;
 250   else return number_multi_lib[tablenum];
 251 }
 252
 253
 254
 255 changed
 256
 257 void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
 258       int number_score_dim, double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
 259       double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
 260       char gauss_param[MAXLINE])
 261 to
 262
 263 void get_gauss_param_all_classes2(char sc_filenames[MAX_CLASS_NUMBER][MAXLINE],
 264       int number_score_dim,
 265       double means[MAX_CLASS_NUMBER][NUM_DIM_IN_ORIG_MATRIX],
 266       double covars[MAX_CLASS_NUMBER]
 267                         [NUM_DIM_IN_ORIG_MATRIX][NUM_DIM_IN_ORIG_MATRIX],
 268       char gauss_param[MAXLINE])
 269
 270
 271
 272 Changed
 273
 274 void compute_submatrices2(
 275         double means[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
 276         double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
 277         double covars[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
 278         double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
 279         double det[MAX_CLASS_NUMBER],
 280         char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
 281         int old_num_dim_table0, int old_num_dim_table1,
 282         int new_num_dim_table0, int new_num_dim_table1
 283         )
 284
 285 to
 286 void compute_submatrices2(
 287         double means[MAX_CLASS_NUMBER][NUM_DIM_IN_ORIG_MATRIX],
 288         double means_submatrix[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM],
 289         double covars[MAX_CLASS_NUMBER]
 290                           [NUM_DIM_IN_ORIG_MATRIX][NUM_DIM_IN_ORIG_MATRIX],
 291         double inv[MAX_CLASS_NUMBER][MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM],
 292         double det[MAX_CLASS_NUMBER],
 293         char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
 294         int old_num_dim_table0, int old_num_dim_table1,
 295         int new_num_dim_table0, int new_num_dim_table1
 296         )
 297
 298 Changed
 299
 300 void multivariate_gauss_from_scfile2(char *sc_filename, int number_score_dim,
 301                   double  mean[MAX_NUM_SCORE_DIM],
 302                   double  covar[MAX_NUM_SCORE_DIM][MAX_NUM_SCORE_DIM])
 303
 304 to
 305 void multivariate_gauss_from_scfile2(char *sc_filename, int number_score_dim,
 306                   double  mean[NUM_DIM_IN_ORIG_MATRIX],
 307                   double covar[NUM_DIM_IN_ORIG_MATRIX][NUM_DIM_IN_ORIG_MATRIX])
 308 and in that function changed
 309
 310   long  n_below_mean[MAX_NUM_SCORE_DIM];
 311   long _counts[MAX_NUM_SCORE_DIM][-4*MINSCORE +1];
 312   long *counts[MAX_NUM_SCORE_DIM];
 313   int table,table2;
 314   int all_places_good,  place[MAX_NUM_SCORE_DIM];
 315   int number_high=0, number_low=0;
 316   int maxplaces[MAX_NUM_SCORE_DIM], minplaces[MAX_NUM_SCORE_DIM];
 317
 318   double score[MAX_NUM_SCORE_DIM];
 319
 320 to
 321   long  n_below_mean[NUM_DIM_IN_ORIG_MATRIX];
 322   long _counts[NUM_DIM_IN_ORIG_MATRIX][-4*MINSCORE +1];
 323   long *counts[NUM_DIM_IN_ORIG_MATRIX];
 324   int table,table2;
 325   int all_places_good,  place[NUM_DIM_IN_ORIG_MATRIX];
 326   int number_high=0, number_low=0;
 327   int maxplaces[NUM_DIM_IN_ORIG_MATRIX], minplaces[NUM_DIM_IN_ORIG_MATRIX];
 328
 329   double score[NUM_DIM_IN_ORIG_MATRIX];