sources/multicoil/get_defaults_cuts.c

   1       else if(!strncmp(buf,"differ_lib",10)) {/* Read in a variable number  */
   2         char *end;                          /*  of distances to be used in  */
   3         int val;                            /*  PairCoilDiffer scores.      */
   4         int do_each_dist_separately =0;
   5
   6         if (!strncmp(buf,"differ_lib dim",14))
   7           do_each_dist_separately = 1;
   8
   9         if (!strncmp(buf,"differ_lib = all",16))
  10           {
  11                            /* For scscore.c will go through each dist on own*/
  12             for (i=0; i<7; i++)
  13               differ_lib[i] = i;
  14             *differ_functnum = 1;
  15             *number_differ_lib = 7;
  16             printf("differ_lib = all dimensions");
  17           }
  18
  19         else  {
  20           if (do_each_dist_separately)
  21             printf("differ_lib dimensions= ");
  22           else printf("differ_lib = ");
  23
  24           tmp = strchr(buf, '=');
  25           tmp++;
  26           /* strip leading whitespace */
  27           while(!isdigit(*tmp)&&*tmp) tmp++;
  28           while(end = strchrs(tmp, " \t\n\r")) {
  29             *end = 0;
  30             end++;
  31             /* strip leading whitespace */
  32             while(*tmp&&!isdigit(*tmp)) tmp++;
  33             if(*tmp) {
  34               val = atoi(tmp);
  35               differ_lib[(*differ_functnum)++] = val;
  36               printf("%d ", val);
  37             }
  38             tmp = end;
  39           }
  40           printf("\n");
  41
  42           if (do_each_dist_separately) {
  43             *number_differ_lib = *differ_functnum;
  44             *differ_functnum=1;
  45               /* Each distance is a library to itself. */
  46           }
  47         }
  48       }
  49
  50
  51
  52       else if (!strncmp(buf, "New coil at reg shift",21))
  53         *start_coil_at_reg_shift = 1;
  54
  55
  56       else if(!strncmp(buf,"differ class scores dimer",25)) {
  57
  58         sscanf(buf,"differ class scores dimer = %s",
  59                differ_class_sc_filenames[0]);
  60         printf("differ class scores dimers = %s\n",
  61                differ_class_sc_filenames[0]);
  62
  63       }
  64
  65       else if(!strncmp(buf,"differ gauss_param",18)) {
  66         sscanf(buf,"differ gauss_param = %s",differ_gaussian_parameters);
  67         printf("differ gauss_param = %s\n",differ_gaussian_parameters);
  68       }
  69
  70
  71       else if(!strncmp(buf,"prior freq single",17)) {
  72         int the_table;
  73         if (!strncmp(buf,"prior freq single =",19)) {
  74           sscanf(buf,"prior freq single = %lf", &prior_freq_single[0]);
  75           for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
  76             prior_freq_single[the_table] = prior_freq_single[0];
  77             printf("prior_freq_single %d = %lf\n", the_table,
  78                    prior_freq_single[the_table]);
  79           }
  80         }             /* All tables get same scale0. **/
  81         else {
  82           sscanf(buf,"prior freq single %d", &the_table);
  83           sscanf(buf,"prior freq single %d = %lf", &the_table,
  84                  &prior_freq_single[the_table-1]);
  85         printf("prior_freq_single %d = %lf\n",
  86                the_table,prior_freq_single[the_table-1]);
  87         }
  88       }
  89       else if(!strncmp(buf,"prior freq pair",15)) {
  90         int the_table;
  91         if (!strncmp(buf,"prior freq pair =",17)) {
  92           sscanf(buf,"prior freq pair = %lf", &prior_freq_pair[0]);
  93           for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
  94             prior_freq_pair[the_table] = prior_freq_pair[0];
  95             printf("prior_freq_pair %d = %lf\n", the_table,
  96                    prior_freq_pair[the_table]);
  97           }
  98         }             /* All tables get same scale0. **/
  99         else {
 100           sscanf(buf,"prior freq pair %d", &the_table);
 101           sscanf(buf,"prior freq pair %d = %lf", &the_table,
 102                  &prior_freq_pair[the_table-1]);
 103         printf("prior_freq_pair %d = %lf\n",
 104                the_table,prior_freq_pair[the_table-1]);
 105         }
 106       }
 107
 108
 109 /***********************************************************/
 110       else if(!strncmp(buf,"structurally important pos",26)) {
 111         char *end;
 112         int val;
 113
 114         i =0;
 115         printf("structurally important pos = ");
 116         tmp = strchr(buf, '=');
 117         tmp++;
 118         /* strip leading whitespace */
 119         while(!islower(*tmp)&&*tmp) tmp++;
 120         while(end = strchrs(tmp, " \t\n\r")) {
 121           *end = 0;
 122           end++;
 123           /* strip leading whitespace */
 124           while(*tmp&&!islower(*tmp)) tmp++;
 125           if(*tmp) {
 126             val = (*tmp)- 'a';
 127             if ((val>=7) || (val<0))
 128               printf(" **ILLEGAL position %c ignored** ", 'a' + val);
 129             else {
 130               printf("%c ", 'a' + val);
 131               structural_pos[i]= val;
 132               i++;
 133             }
 134           }
 135           tmp = end;
 136         }
 137         printf("\n");
 138         structural_pos[i] = -1;  /*  Flag that at end. */
 139       }
 140
 141       else if(!strncmp(buf,"good_turing",11)) {
 142         *good_turing_fixed_disc = 1;
 143         printf("Estimating prob using good_turing method.\n");
 144       }
 145       else if(!strncmp(buf,"modified_good_turing",20)) {
 146         *good_turing_fixed_disc = 3;
 147         printf("Estimating prob using modified good_turing method.\n");
 148       }
 149       else if(!strncmp(buf,"fixed_disc",10)) {
 150         *good_turing_fixed_disc = 2;
 151         printf("Estimating prob using fixed_discount method with discount determined by SCALE0.\n");
 152       }
 153 /**********************************************************/
 154       else if(!strncmp(buf,"zero freqs from dimers",22)) {
 155         *priors =-1;
 156         printf("zero freqs for trimers from dimers.\n");
 157       }
 158
 159       else if(!strncmp(buf,"add priors if less than dimer expectation",41)) {
 160         *priors =-2;
 161         printf("Add priors only if freq is less than dimer expectation.\n");
 162       }
 163
 164       else if(!strncmp(buf,"prior singles from",18)) {
 165                                             /* Reads in what to use as   */
 166         tmp = &buf[19]; /* One past space */
 167         if (!strncmp(tmp,"dimers",6 )) {     /* prior prob in estimating   */
 168           *priors = 1;
 169           printf("priors from dimers\n");    /* trimer table probs.  */
 170         }
 171         else if (!strncmp(tmp,"genbnk",6 )) {
 172           *priors = 2;
 173           printf("priors from genbnk\n");
 174         }
 175         else if (!strncmp(tmp,"average",7 )) {
 176           *priors = 3;
 177           printf("priors from average of dimers and genbnk\n");
 178         }
 179       }
 180
 181       else if(!strncmp(buf,"zero freqp from dimers",22)) {
 182         *priorp =-1;
 183         printf("zero freqp for trimers from dimers.\n");
 184       }
 185       else if(!strncmp(buf,"add priorp if less than dimer expectation",41)) {
 186         *priorp =-2;
 187         printf("Add priorp only if freq is less than dimer expectation.\n");
 188       }
 189
 190        else if(!strncmp(buf,"prior pairs from",16)) {
 191                                             /* Reads in what to use as   */
 192         tmp = &buf[17]; /* One past space */
 193         if (!strncmp(tmp,"dimers",6 )) {     /* prior prob in estimating   */
 194           *priorp = 1;
 195           printf("priorp from dimers\n");    /* trimer table probs.  */
 196         }
 197         else if (!strncmp(tmp,"genbnk",6 )) {
 198           *priorp = 2;
 199           printf("priorp from genbnk\n");
 200         }
 201         else if (!strncmp(tmp,"average",7 )) {
 202           *priorp = 3;
 203           printf("priorp from average of dimers and genbnk\n");
 204         }
 205
 206         else if (!strncmp(tmp,"product of singles",18 )) {
 207           *priorp = 4;
 208           printf("priorp from product of singles\n");
 209         }
 210       }
 211 /**************************************************************/
 212       else if(!strncmp(buf,"differentiator window length",28)) {
 213           sscanf(buf,"differentiator window length = %d",
 214                  differ_window_length);
 215           printf("differentiator window length = %d\n",
 216                  *differ_window_length);
 217         }
 218
 219
 220
 221
 222 /**************************************************************/
 223 /************************Round 2 of cuts **********************/
 224 /**************************************************************/
 225
 226       else if(!strncmp(buf,"coil conflicts",14)) {
 227         if (!strncmp(buf,"coil conflicts dir",19)){ /* automate the name **/
 228          sscanf(buf,"coil conflicts dir = %s",name);
 229          strcat(name,input_name);
 230          strcat(name,".coil_conflicts");
 231
 232           /**** Apend on the library distances.  ***/
 233           if (multi_functnum[0] == 1) { /* make sure do dimension scores */
 234             lib_numb=0;
 235             while (lib_numb < number_multi_lib[0]) {
 236               sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
 237               lib_numb++; }
 238             sprintf(&buf[lib_numb],"_");
 239             strncat(name,buf,number_multi_lib[0]+1);
 240
 241
 242             lib_numb=0;
 243             while (lib_numb < number_multi_lib[1]) {
 244               sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
 245               lib_numb++; }
 246             strncat(name,buf,number_multi_lib[1]);
 247           }
 248
 249         }
 250         else sscanf(buf,"coil conflicts = %s",name);
 251         *flog_coil_conflicts = sopen(name,"w");
 252         printf("coil conflicts = %s\n",name);
 253       }
 254
 255 changed
 256       else if(!strncmp(buf,"table",5)) {   /* Get location of postable file */
 257         sscanf(buf,"table %d = %s",&i, name);
 258         if (strcmp("combination",name)) {  /* If it is combination, just  */
 259           fpin[*number_tables] = sopen(name,"r");  /* increment number tables*/
 260         }                                    /* Otherwise open file.       */
 261         printf("table %d = %s\n",*number_tables,name);
 262         (*number_tables)++;
 263         fpin[*number_tables]= NULL;
 264       }
 265
 266 to
 267
 268       else if(!strncmp(buf,"table",5)) {   /* Get location of postable file */
 269         sscanf(buf,"table %d = %s",&i, name);
 270         fpin[i-1] = sopen(name,"r");
 271         printf("table %d = %s\n",i,name);
 272         (*number_tables)++;
 273         fpin[i]= NULL;
 274       }
 275
 276
 277 changed
 278             if (!strncmp(buf,"multi_lib dim =",15)) {
 279               first_table=0; last_table=*number_tables;
 280             }             /* All tables get same lib. **/
 281             else {
 282               sscanf(buf,"multi_lib dim %d", &last_table);
 283               first_table = last_table-1;
 284             }
 285           }
 286           else if (!strncmp(buf,"multi_lib =",11)) {
 287             first_table=0; last_table=*number_tables;
 288           }             /* All tables get same lib. **/
 289
 290 to
 291
 292             if (!strncmp(buf,"multi_lib dim =",15)) {
 293               first_table=0; last_table=NUMBER_TABLES;
 294             }             /* All tables get same lib. **/
 295
 296             else {
 297               sscanf(buf,"multi_lib dim %d", &last_table);
 298               first_table = last_table-1;
 299             }
 300           }
 301           else if (!strncmp(buf,"multi_lib =",11)) {
 302             first_table=0; last_table= NUMBER_TABLES;
 303           }             /* All tables get same lib. **/
 304
 305
 306
 307
 308 cut
 309          if (*weighted_avg)
 310            strcat(name,"_WtdAvg");
 311
 312
 313       else if (!strncmp(buf,"weighted_avg", 12)) {
 314         sscanf(buf, "weighted_avg = %d", weighted_avg);
 315                    /* 0 means just avg. res score over coil.  */
 316                    /* 1 means do weighted avg. by likelihoods */
 317         if ( (*weighted_avg !=0)  &&(*weighted_avg !=1)) {
 318           fprintf(stderr,"\n Illegal weighted_avg method.  Defaults to 0.\n");
 319           *weighted_avg = 0;
 320         }
 321         else fprintf(stderr,"weighted_avg = %d\n", *weighted_avg);
 322       }
 323     }
 324
 325
 326
 327
 328 cut
 329
 330       else if(!strncmp(buf,"tab diff stats",14)) {
 331         sscanf(buf,"tab diff stats = %s",table_diff_stats_filename);
 332         printf("tablediff stats = %s\n",table_diff_stats_filename);
 333       }
 334       else if(!strncmp(buf,"weightfile outname",18)) {
 335         sscanf(buf,"weightfile outname = %s",weightfile_outname);
 336         printf("weightfile outname = %s\n",weightfile_outname);
 337       }
 338
 339
 340 changed
 341
 342       else if(!strncmp(buf,"class scores combo",18)) {
 343         sscanf(buf,"class scores combo %d with init prob %lf = %s",&i,
 344                &init_class_prob[*number_classes],
 345                class_sc_filenames[0][*number_classes]);
 346         printf("combo class scores %d = %s with init prob %lf\n",
 347                *number_classes,class_sc_filenames[0][*number_classes],
 348                init_class_prob[*number_classes]);  /* likelihood lines.  */
 349         (*number_classes)++;
 350         class_sc_filenames[0][*number_classes][0]= ',';
 351       }
 352
 353
 354       else if(!strncmp(buf,"class scores max",16)) {
 355         sscanf(buf,"class scores max %d with init prob %lf = %s",&i,
 356                &init_class_prob[number_max_classes],
 357                class_sc_filenames[1][number_max_classes]);
 358         printf("max class scores %d = %s with init prob %lf\n",
 359                number_max_classes,class_sc_filenames[1][number_max_classes],
 360                init_class_prob[number_max_classes]);  /* likelihood lines.  */
 361         number_max_classes++;
 362         class_sc_filenames[1][number_max_classes][0]= ',';
 363       }
 364
 365 to
 366       else if(!strncmp(buf,"class scores combo",18)) {
 367         sscanf(buf,"class scores combo %d with init prob %lf = %s",&i,
 368                &init_class_prob[i-1],
 369                class_sc_filenames[0][i-1]);
 370         printf("combo class scores %d = %s with init prob %lf\n",
 371                i,class_sc_filenames[0][i-1],
 372                init_class_prob[*number_classes]);  /* likelihood lines.  */
 373         class_sc_filenames[0][i][0]= ',';
 374       }
 375
 376
 377       else if(!strncmp(buf,"class scores max",16)) {
 378         sscanf(buf,"class scores max %d with init prob %lf = %s",&i,
 379                &init_class_prob[i-1],
 380                class_sc_filenames[1][i-1]);
 381         printf("max class scores %d = %s with init prob %lf\n",
 382                i,class_sc_filenames[1][i-1],
 383                init_class_prob[i-1]);  /* likelihood lines.  */
 384         class_sc_filenames[1][i][0]= ',';
 385
 386
 387
 388 CUT
 389       else if(!strncmp(buf,"average differentiator by coil window",37)) {
 390         *which_differentiator = 4;
 391         printf("The differentiator score is over the entire coiled region\n");
 392       }
 393
 394
 395       else if(!strncmp(buf,"differentiator by coil window",29)) {
 396         *which_differentiator = 3;
 397         printf("The differentiator score is over the entire coiled region\n");
 398       }
 399       else if(!strncmp(buf,"differentiator by window score",30)) {
 400         *which_differentiator = 1;
 401         printf("The differentiator residue score is the score of the window starting at that residue\n");
 402       }
 403       else if(!strncmp(buf,"differentiator by max-min window score",38)) {
 404         *which_differentiator = 2;
 405         printf("The differentiator residue score is the scores for the max and min window containing that residue\n");
 406       }
 407
 408
 409
 410
 411 Completely rewrote stuff to read in multi_lib to deal with variables
 412 num_dist and combined_dist.
 413
 414
 415 Cut
 416
 417       else if(!strncmp(buf,"differ class scores trimer",26)) {
 418
 419         sscanf(buf,"differ class scores trimer = %s",
 420                differ_class_sc_filenames[1]);
 421         printf("differ class scores trimers = %s\n",
 422                differ_class_sc_filenames[1]);
 423
 424       }
 425
 426
 427 Changed
 428
 429             lib_numb=0;
 430             while (lib_numb < number_multi_lib[0]) {
 431               sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
 432               lib_numb++; }
 433             sprintf(&buf[lib_numb],"_");
 434             strncat(name,buf,number_multi_lib[0]+1);
 435
 436             lib_numb=0;
 437             while (lib_numb < number_multi_lib[1]) {
 438               sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
 439               lib_numb++; }
 440             strncat(name,buf,number_multi_lib[1]);
 441
 442 to
 443
 444             while (lib_numb < num_dist[0]) {
 445               sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
 446               lib_numb++; }
 447             sprintf(&buf[lib_numb],"_");
 448             strncat(name,buf,num_dist[0]+1);
 449
 450             lib_numb=0;
 451             while (lib_numb < num_dist[1]) {
 452               sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
 453               lib_numb++; }
 454             strncat(name,buf,num_dist[1]);
 455
 456
 457
 458 Changed
 459           /**** Apend on the library distances.  ***/
 460           if (multi_functnum[0] == 1) { /* make sure do dimension scores */
 461             lib_numb=0;
 462 to
 463           if (combine_dist[0] == 0)
 464
 465
 466
 467 Cut
 468         class_sc_filenames[0][number_classes][0]= ',';
 469 and
 470         class_sc_filenames[1][number_max_classes][0]= ',';
 471       }
 472
 473 from when reading in class filenames.
 474
 475
 476
 477 Modified stuff that reads in "coil scores = ...."
 478 so can also read it in as "seq scores = ...."
 479 and seq by_coil_or_seq based on if used "coil" or "seq".
 480 Therefore, could eliminate
 481       else if (!strncmp(buf,"By coil",7))
 482         *by_coil_or_seq = 0;
 483       else if (!strncmp(buf,"By seq",6))
 484         *by_coil_or_seq =2;
 485 but kept
 486       else if (!strncmp(buf,"By seq pos regions",18))
 487         *by_coil_or_seq =1;
 488