sources/multicoil/get_defaults.c

   1
   2 /* Code by anonomous and Ethan Wolf 1995. */
   3
   4 /************************************************************************/
   5 /* get_defaults() is called in main() of sc2seq.c to get the default    */
   6 /* values for parameters of the program, such as input/output files and */
   7 /* options.                                                             */
   8 /************************************************************************/
   9
  10 #include <stdio.h>
  11 #include <stdlib.h>
  12 #include <string.h>
  13 #include "scio.h"
  14 #include "switches.h"
  15 #include  "interface.h"
  16
  17
  18 /** Returns pointer to first occurance of chrs[0]. If that not present,
  19   * returns pointer to first occurance of chrs[1]... If none of
  20   * characters in chrs[] are present then it returns NULL.
  21   * This is used to remove whitspace, tabs, returns.
  22 **/
  23 static char *strchrs(char *str, char *chrs) {
  24   char *ret=NULL;
  25
  26   while(*chrs) {
  27     if(ret=strchr(str,*chrs)) return ret;
  28     chrs++;
  29   }
  30   return ret;
  31 }
  32
  33 /************************************************************************/
  34 /* Reads in .paircoil file of default values that are normally input to */
  35 /* sc2seq in the command line.                                          */
  36 /* Any required value not read in here is expected on the command line. */
  37 void get_defaults(char *command_line_config,
  38                   char *input_location, int *mode, double *bound,
  39                     FILE **fgin, FILE **fpin,
  40                     FILE **ftotal_like, FILE **fout,
  41                     FILE **flog,
  42                     FILE **fout_coils,
  43                     int *by_coil_or_seq,
  44                     char likelihoods[MAX_TABLE_NUMBER][MAXLINE],
  45                     char *pir_name, char *lib,
  46                     char multi_lib[MAX_TABLE_NUMBER][MAXFUNCTNUM],
  47                     int *functnum,
  48                     int combine_dist[MAX_TABLE_NUMBER],
  49                     char *print, int *main_method,
  50                     int *main_preprocessor_method, int *main_table,
  51                     int *offset_to_use,
  52                     int *avg_max,
  53                     int *Coil_Score,
  54                     int *ps_res_per_line,
  55                     char class_sc_filenames[2][MAX_CLASS_NUMBER][MAXLINE],
  56                     char gaussian_parameters[2][MAXLINE],
  57                     int num_dist[MAX_TABLE_NUMBER],
  58                     double init_class_prob[MAX_CLASS_NUMBER],
  59                     int *table_to_remove_from,
  60                     char *command_line,
  61                     int window_length[MAX_TABLE_NUMBER],
  62                     double scale0s[MAX_TABLE_NUMBER],
  63                     double scale0p[MAX_TABLE_NUMBER])
  64 {
  65   char buf[500], *tmp, name[500];
  66   FILE *config; FILE *printfile;
  67   int i, number_likelihoods=0;
  68   char *input_name;
  69   int lib_numb=0;
  70
  71 /******** A hack so I don't have to eliminate all the stuff using these  ****/
  72 /******** pointers, since no longer pass them into function.             ****/
  73   int num_tab=0, *number_tables, number_classes=0, number_max_classes=0;
  74
  75   number_tables= &num_tab;
  76 /****************************************************************************/
  77
  78   strcpy(gaussian_parameters[0], "~/MULTICOIL/CONVERSION_FILES/gauss_param28+");
  79
  80   if (command_line) { /* Don't use options in config file. */
  81     if (!strcmp(command_line,"dimer")) {
  82       *table_to_remove_from = 0;
  83       printf("Input data is all removed from table 1\n");
  84       *mode |= POS_MODE;
  85       printf("pos\n");
  86     }
  87     else if (!strcmp(command_line,"trimer")) {
  88       *table_to_remove_from = 1;
  89       printf("Input data is all removed from table 2\n");
  90       *mode |= POS_MODE;
  91       printf("pos\n");
  92     }
  93     else if (!strcmp(command_line, "dimer-1")) {
  94         *mode |= TST_MODE0;
  95         printf("Input is data from table 1\n");
  96         *mode |= POS_MODE;
  97         printf("pos\n");
  98       }
  99     else if (!strcmp(command_line, "trimer-1")) {
 100       *mode |= TST_MODE1;
 101       printf("Input is data from table 2\n");
 102       *mode |= POS_MODE;
 103       printf("pos\n");
 104     }
 105     else if (!strcmp(command_line, "negatives")) {
 106       printf("Not doing pos mode");
 107     }
 108     else if (!strcmp(command_line, "config_file")) {
 109       printf("Doing pos options as in config file\n");
 110       command_line =NULL;
 111     }
 112     else { /*  Bad command line input.  **/
 113       usage("paircoil");
 114       exit(-1);
 115     }
 116
 117   }
 118
 119 /************************** For Automating output file name. ****/
 120   /** Strip off directories to get just the program name.  **/
 121   i=strlen(input_location);
 122   while ((i>=0) && (input_location[i] != '/') )
 123     i--;
 124   input_name= &input_location[i+1];
 125 /***************************/
 126
 127
 128   /*  What directory to look for paircoil defauts in.  Set environment  */
 129   /*  variable MULTICOIL_CONFIG to be a path to this file.               */
 130
 131   if (command_line_config) {  /** Read config location at command line.  **/
 132     strcpy(buf, command_line_config);
 133     fprintf(stderr,"config = %c",buf);
 134   }
 135   else
 136     if (tmp=getenv("MULTICOIL_CONFIG")) {
 137       strcpy(buf,tmp);
 138     }
 139     else {
 140       strcpy(buf,getenv("HOME"));
 141       strcat(buf,"/MULTICOIL/multicoil_config");
 142     }
 143
 144   if (config=fopen(buf,"r")) {
 145     printf("Config file %s\n", buf);
 146     while (fgets(buf,500,config)) {
 147
 148       if (!command_line)  { /** Read from file since it wasn't **/
 149                             /** a command line param. **/
 150         if(!strncmp(buf,"pos",3)) {        /* If "pos" is in the .paircoil  */
 151           *mode |= POS_MODE;               /* default file, then the test   */
 152           printf("pos\n");                 /* file is assumed to be a .pos  */
 153         }                                  /* file, where each seq has its  */
 154
 155         else if(!strncmp(buf,"remove all input from table",27)) {
 156           sscanf(buf,"remove all input from table %d",table_to_remove_from);
 157           (*table_to_remove_from)--;
 158           printf("Input is data is all removed from table %d\n",
 159                  (*table_to_remove_from) +1);
 160         }
 161
 162         else if(!strncmp(buf,"input pos1",10)) {
 163           *mode |= TST_MODE0;
 164           printf("Input is data from table 1\n");
 165         }
 166         else if(!strncmp(buf,"input pos2",10)) {
 167           *mode |= TST_MODE1;
 168           printf("Input is data from table 2\n");
 169         }
 170       }
 171
 172
 173
 174    /**** Now do the rest of the possible non-command line options. *****/
 175
 176       if(!strncmp(buf,"genbnk",6)) {      /* Get location of genbnk file  */
 177         sscanf(buf,"genbnk = %s",name);    /* and open it.                 */
 178         *fgin = sopen(name,"r");
 179 /***
 180         printf("genbnk = %s\n",name);
 181 ***/
 182       }
 183       else if(!strncmp(buf,"table",5)) {   /* Get location of postable file */
 184         sscanf(buf,"table %d = %s",&i, name);
 185         fpin[i-1] = sopen(name,"r");
 186 /***
 187         printf("table %d = %s\n",i,name);
 188 ***/
 189         (*number_tables)++;
 190       }
 191
 192       else if(!strncmp(buf,"pir",3)) {   /* Get location of pir file */
 193         sscanf(buf,"pir = %s",pir_name);
 194 /****
 195         printf("pir = %s\n",pir_name);
 196 ***/
 197       }
 198       else if(!strncmp(buf,"printfile",9)) {   /* File to output printouts to*/
 199         sscanf(buf,"printfile = %s",print);
 200         printf("printfile = %s\n",print);
 201         printfile=sopen(print,"w");  /* We are going to append to this, */
 202         sclose(printfile);           /*  So first make it empty.   */
 203       }
 204       else if(!strncmp(buf,"likelihoods",11)) {
 205         sscanf(buf,"likelihoods %d = %s",&i, likelihoods[number_likelihoods]);
 206 /****
 207         printf("likelihoods %d = %s\n",number_likelihoods,
 208                likelihoods[number_likelihoods]); ***/  /* likelihood lines.  */
 209         number_likelihoods++;
 210         likelihoods[number_likelihoods][0]= ',';
 211       }
 212
 213
 214       else if(!strncmp(buf,"class scores combo",18)) {
 215         sscanf(buf,"class scores combo %d with init prob %lf = %s",&i,
 216                &init_class_prob[number_classes],
 217                class_sc_filenames[0][number_classes]);
 218         printf("combo class scores %d = %s with init prob %lf\n",
 219                i,class_sc_filenames[0][number_classes],
 220                init_class_prob[number_classes]);  /* likelihood lines.  */
 221         number_classes++;
 222       }
 223
 224
 225       else if(!strncmp(buf,"class scores max",16)) {
 226         sscanf(buf,"class scores max %d with init prob %lf = %s",&i,
 227                &init_class_prob[number_max_classes],
 228                class_sc_filenames[1][number_max_classes]);
 229         printf("max class scores %d = %s with init prob %lf\n",
 230                i,class_sc_filenames[1][number_max_classes],
 231                init_class_prob[number_max_classes]);  /* likelihood lines.  */
 232         number_max_classes++;
 233       }
 234
 235       else if(!strncmp(buf,"gauss_param =",13))
 236         sscanf(buf,"gauss_param = %s",gaussian_parameters[0]);
 237
 238       else if(!strncmp(buf,"gauss_param combo",17)) {
 239         sscanf(buf,"gauss_param combo = %s",gaussian_parameters[0]);
 240 /****
 241        printf("gauss_param combo = %s\n",gaussian_parameters[0]);
 242 ****/
 243       }
 244
 245       else if(!strncmp(buf,"gauss_param max",15)) {
 246         sscanf(buf,"gauss_param max = %s",gaussian_parameters[1]);
 247 /***
 248         printf("gauss_param max = %s\n",gaussian_parameters[1]);
 249 ***/
 250       }
 251
 252       else if(!strncmp(buf,"no GUI",6)) {
 253         *mode |= NO_GUI;
 254         printf("NO GUI\n");
 255       }
 256
 257
 258       else if(!strncmp(buf,"pair_lib",8)) { /*  Read in a variable number   */
 259         char *end;                          /*  of distances to be used in  */
 260         int val;                            /*  pair scores.  The number    */
 261                                             /*  of variables is stored in   */
 262         printf("pair_lib = ");              /*  in the global variable      */
 263         tmp = strchr(buf, '=');             /*  functnum.  The distances    */
 264         tmp++;                              /*  are stored in               */
 265         /* strip leading whitespace */      /*  lib[0],...,lib[functnum-1]. */
 266         while(!isdigit(*tmp)&&*tmp) tmp++;
 267         while(end = strchrs(tmp, " \t\n\r")) {
 268           *end = 0;
 269           end++;
 270           /* strip leading whitespace */
 271           while(*tmp&&!isdigit(*tmp)) tmp++;
 272           if(*tmp) {
 273             val = atoi(tmp);
 274             lib[(*functnum)++] = val-1;  /** scscore.c needs takes residues **/
 275                                          /** at dist lib +1 apart.          **/
 276             printf("%d ", val);
 277           }
 278           tmp = end;
 279         }
 280         printf("\n");
 281       }
 282
 283
 284
 285       else if(!strncmp(buf,"multi_lib",9)) { /*  Read in a variable number   */
 286         if (! (*mode & LIB_AT_COMMAND_LINE)) { /* This flags that **/
 287                                         /** got it at command line.         **/
 288           int first_table, last_table;
 289           int the_table;
 290           int combine_distances =1;
 291
 292           if (!strncmp(buf,"multi_lib dim",13)) {
 293             combine_distances = 0;
 294
 295             if (!strncmp(buf,"multi_lib dim =",15)) {
 296               first_table=0; last_table=NUMBER_TABLES;
 297             }             /* All tables get same lib. **/
 298             else {
 299               sscanf(buf,"multi_lib dim %d", &last_table);
 300               first_table = last_table-1;
 301             }
 302           }
 303           else if (!strncmp(buf,"multi_lib =",11)) {
 304             combine_distances = 0;
 305             first_table=0; last_table= NUMBER_TABLES;
 306           }             /* All tables get same lib. **/
 307           else {
 308             sscanf(buf,"multi_lib %d", &last_table);
 309             first_table = last_table-1;
 310           }
 311
 312           for (the_table=first_table; the_table<last_table; the_table++) {
 313             combine_dist[the_table]= combine_distances;
 314             num_dist[the_table]=0;
 315           }
 316
 317           if (!strncmp(buf,"multi_lib = all",15))
 318             {
 319                            /* For scscore.c will go through each dist on own*/
 320               for (the_table=first_table; the_table<last_table; the_table++)
 321                 for (i=0; i<7; i++) {
 322                   multi_lib[the_table][i] = i;
 323                   num_dist[the_table] = 7;
 324                   combine_dist[the_table] = 0;
 325                 }
 326             }
 327
 328           else {
 329             char *end;                      /*  of distances to be used in  */
 330             int val;                        /*  pair scores.  The number    */
 331                                             /*  of variables is stored in   */
 332             printf("multi_lib = ");         /*  in the global variable      */
 333             tmp = strchr(buf, '=');         /*  functnum.  The distances    */
 334             tmp++;                          /*  are stored in               */
 335             /* strip leading whitespace */  /*  lib[0],...,lib[functnum-1]. */
 336             while(!isdigit(*tmp)&&*tmp) tmp++;
 337             while(end = strchrs(tmp, " \t\n\r")) {
 338               *end = 0;
 339               end++;
 340               /* strip leading whitespace */
 341               while(*tmp&&!isdigit(*tmp)) tmp++;
 342               if(*tmp) {
 343                 val = atoi(tmp);
 344                 for (the_table=first_table; the_table<last_table; the_table++){
 345                   multi_lib[the_table][num_dist[the_table]] = val-1;
 346                   /** scscore.c needs takes residues at dist lib +1 apart.  **/
 347                   num_dist[the_table]+= 1;
 348 /**               combine_dist[the_table] = combine_distances;  **/
 349                 }
 350                 printf("%d ", val);
 351               }
 352               tmp = end;
 353             }
 354             for (the_table=first_table; the_table<last_table; the_table++)
 355               if (num_dist[the_table] ==1) combine_dist[the_table] =0;
 356
 357             printf("\n");
 358           }
 359         }
 360       }
 361
 362
 363
 364       else if(!strncmp(buf,"Maximize total like",4)) {
 365         sscanf(buf,"Maximize total like = %s",name); /* Compute the sum */
 366         *ftotal_like = sopen(name,"w");              /* over classes of */
 367         printf("ftotal_like = %s\n",name);           /* the gauss value */
 368                                        /* for the score for various settings */
 369                                        /* of the initial class parameters, so*/
 370                                        /* we can choose values max total like*/
 371       }
 372       else if(!strncmp(buf,"out",3)) {
 373         if (!strncmp(buf,"out dir",7)) { /** automate the name **/
 374           sscanf(buf,"out dir = %s",name);
 375           strcat(name,input_name);
 376           strcat(name,".out");
 377         }
 378         else sscanf(buf,"out = %s",name);  /* Read in the filename in which */
 379                                            /* to output the residue scores  */
 380         *fout = sopen(name,"w");            /* and open it.                  */
 381         printf("out = %s\n",name);
 382       }
 383
 384       else if(!strncmp(buf,"sparse_out",10)) {
 385         if (!strncmp(buf,"sparse_out dir",14)) { /** automate the name **/
 386           sscanf(buf,"sparse_out dir = %s",name);
 387           strcat(name,input_name);
 388           strcat(name,".out");
 389         }
 390         else sscanf(buf,"sparse_out = %s",name); /*Read in filename in which */
 391                                            /* to output the residue scores  */
 392         *fout = sopen(name,"w");            /* and open it.                  */
 393         printf("sparse_out = %s\n",name);
 394         *mode ^= WEB_OUT_MODE;        /* Don't want web output mode.  */
 395       }
 396
 397
 398       else if(!strncmp(buf,"raw_out",7)) {
 399         *mode |= RAW_OUT;
 400         if (!strncmp(buf,"raw_out dir",11)) { /** automate the name **/
 401           sscanf(buf,"raw_out dir = %s",name);
 402           strcat(name,input_name);
 403           strcat(name,".raw_out");
 404         }
 405         else sscanf(buf,"raw_out = %s",name);
 406
 407         *fout= sopen(name,"w");
 408         printf("Opened %s for output of raw scores\n",name);
 409       }
 410
 411       else if(!strncmp(buf,"log",3)) {
 412         if (!strncmp(buf,"log dir",7)){ /* automate the name **/
 413           sscanf(buf,"log dir = %s",name);
 414           strcat(name,input_name);
 415           strcat(name,".log");
 416
 417           /**** Apend on the library distances.  ***/
 418           if (combine_dist[0] == 0) { /* make sure do dimension scores */
 419             lib_numb=0;
 420             while (lib_numb < num_dist[0]) {
 421               sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
 422               lib_numb++; }
 423             sprintf(&buf[lib_numb],"_");
 424             strncat(name,buf,num_dist[0]+1);
 425
 426             lib_numb=0;
 427             while (lib_numb < num_dist[1]) {
 428               sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
 429               lib_numb++; }
 430             strncat(name,buf,num_dist[1]);
 431           }
 432
 433         }                                   /* Read in the filename in which */
 434         else sscanf(buf,"log = %s",name);   /* to output the sequences which */
 435         *flog = sopen(name,"w");            /* score above the PRN_MODE      */
 436         printf("log = %s\n",name);      /* threshhold.  This file will   */
 437                                             /* get human readable output.    */
 438       }
 439
 440       else if (!strncmp(buf,"Log Like Pos",12))
 441         *mode |= POS_STYLE_LOG;
 442
 443
 444
 445       else if (!strncmp(buf,"By seq pos regions",18))
 446         *by_coil_or_seq =1;
 447
 448 /*************************************************************************/
 449 /*******Two Ways of doing same command:  "coil scores" and "seq scores" **/
 450 /*** Although slightly diff't since they modify "by_coil_or_seq"  diff'tly**/
 451
 452       else if(!strncmp(buf,"coil scores",11)) {
 453         *by_coil_or_seq =0;   /** Do coil scores. **/
 454         if (!strncmp(buf,"coil scores dir",15)) { /* automate the name **/
 455           sscanf(buf,"coil scores dir = %s",name);
 456           strcat(name,input_name);
 457           strcat(name,".coil_scores");
 458           if (*mode & VER_MODE)
 459             strcat(name,"_NoTxt");
 460
 461           /**** Apend on the library distances.  ***/
 462           if (combine_dist[0] == 0) { /* make sure do dimension scores */
 463             lib_numb=0;
 464             while (lib_numb < num_dist[0]) {
 465               sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
 466               lib_numb++; }
 467             sprintf(&buf[lib_numb],"_");
 468             strncat(name,buf,num_dist[0]+1);
 469
 470             lib_numb=0;
 471             while (lib_numb < num_dist[1]) {
 472               sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
 473               lib_numb++; }
 474             strncat(name,buf,num_dist[1]);
 475           }
 476         }
 477         else sscanf(buf,"coil scores = %s",name);
 478         *fout_coils = sopen(name,"w");         /* For just choosing 1 score */
 479         printf("coil scores = %s\n",name);   /* per pos file coil,  or seq   */
 480       }
 481
 482       else if(!strncmp(buf,"seq scores",10)) {
 483         *by_coil_or_seq =2;   /** Do seq scores. **/
 484         if (!strncmp(buf,"seq scores dir",14)) { /* automate the name **/
 485           sscanf(buf,"seq scores dir = %s",name);
 486           strcat(name,input_name);
 487           strcat(name,".seq_scores");
 488           if (*mode & VER_MODE)
 489             strcat(name,"_NoTxt");
 490
 491           /**** Apend on the library distances.  ***/
 492           if (combine_dist[0] == 0) { /* make sure do dimension scores */
 493             lib_numb=0;
 494             while (lib_numb < num_dist[0]) {
 495               sprintf(&buf[lib_numb],"%d",multi_lib[0][lib_numb]);
 496               lib_numb++; }
 497             sprintf(&buf[lib_numb],"_");
 498             strncat(name,buf,num_dist[0]+1);
 499
 500             lib_numb=0;
 501             while (lib_numb < num_dist[1]) {
 502               sprintf(&buf[lib_numb],"%d",multi_lib[1][lib_numb]);
 503               lib_numb++; }
 504             strncat(name,buf,num_dist[1]);
 505           }
 506         }
 507         else sscanf(buf,"seq scores = %s",name);
 508         *fout_coils = sopen(name,"w");         /* For just choosing 1 score */
 509         printf("seq scores = %s\n",name);   /* per pos file coil,  or seq   */
 510       }
 511
 512 /*************************/
 513
 514       else if(!strncmp(buf,"ps res per line",15)) {/* Reads in the length of */
 515         sscanf(buf,"ps res per line = %d", ps_res_per_line); /* print line */
 516         fprintf(stderr,"res per line = %d\n", *ps_res_per_line);
 517       }
 518       else if(!strncmp(buf,"one print line",14)) {
 519         *ps_res_per_line = -1;  /* Flag to print on just one line. */
 520         fprintf(stderr,"Sequences will be printed on one line in ps file.\n");
 521       }
 522
 523       else if(!strncmp(buf,"max window then combine dist",28)) {
 524         *mode |= MAX_WINDOW_BEFORE_COMBINE_MODE;        /* In scseqadj in */
 525         printf("max window before combine distances\n"); /* scscore.c, this */                                       /* defines how to compute score. */
 526       }
 527
 528       else if(!strncmp(buf,"only coiled classes",19)) {
 529         *mode |= ONLY_COILED_CLASSES;
 530         printf("The paircoil like will be fraction of all positive classes likelihoods (no pdb- class.\n");
 531       }
 532
 533       else if(!strncmp(buf,"ScoresAboveBound",16)) {  /** Only output scores */
 534         *mode |= ABOVE_BOUND_MODE;            /* to score/out/txt files      */
 535         printf("Above Bound Mode\n");         /* that are above bound.       */
 536       }
 537
 538 #ifdef TEST_VERSION       /** Only for testing..... ***/
 539       else if(!strncmp(buf,"Prolines",8)) {
 540         *mode ^= PROLINE_FREE_MODE;                  /* Score Prolines   */
 541         printf("Score Prolines\n");
 542       }
 543 #endif
 544
 545       else if(!strncmp(buf,"Show Seq",8)) {
 546         *mode |= DEBUG_MODE;                /* Option to get seq printed in  */
 547      /** printf("Show Sequences in log file\n"); **/ /* log file.            */
 548         *mode |= PRN_MODE;                  /* Print scores above bound    */
 549       }
 550       else if(!strncmp(buf,"view",4)) {
 551         *mode |= VIEW_MODE;                 /* Option to get a picture of    */
 552         printf("view\n");                   /* STOCKS and PairCoils predicted*/
 553       }                                     /* coil regions in the seq.      */
 554       else if(!strncmp(buf,"ver",3)) {
 555         *mode |= VER_MODE;                  /* Outputs 2 columns of maxseq   */
 556         printf("ver\n");                    /* scores, first STOCK, then us  */
 557         *main_method = STOCK_PAIR;
 558       }                                     /* in log file.                  */
 559
 560       else if(!strncmp(buf,"Just Scores",11)) {
 561         *mode |= VER_MODE;
 562         printf ("The coil scores output will contain just scores, no text.");
 563       }
 564
 565 #ifdef TEST_VERSION       /** Only want release to do pairs.  */
 566       else if (!strncmp(buf,"singles",7))
 567         *mode ^= PAIRCOIL_PAIRS;  /* Since default is 1, just XOR it.  */
 568 #endif
 569       else if (!strncmp(buf,"pairs",5))
 570         *mode |= PAIRCOIL_PAIRS;
 571
 572
 573       else if(!strncmp(buf,"prn",3)) {
 574         *mode |= PRN_MODE;                  /* Print region scores above     */
 575         sscanf(buf,"prn = %lf", bound);     /* threshhold prn to logfile.    */
 576 /***
 577         printf("prn\n");
 578 ***/
 579       }
 580
 581       else if(!strncmp(buf,"bound",5)) {
 582         *mode |= PRN_MODE;                  /* Print region scores above     */
 583         sscanf(buf,"bound = %lf", bound);     /* threshhold prn to logfile.    */
 584 /***
 585         printf("bound\n");
 586 ***/
 587       }
 588
 589
 590       else if(!strncmp(buf,"window length",13)) {
 591         int the_table;
 592         if (!strncmp(buf,"window length =",15)) {
 593           sscanf(buf,"window length = %d", &window_length[0]);
 594           for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
 595             window_length[the_table] =window_length[0];
 596             printf("window length %d = %d\n", the_table,
 597                    window_length[the_table]);
 598           }
 599         }             /* All tables get same windowlength. **/
 600         else {
 601           sscanf(buf,"window length %d", &the_table);
 602           sscanf(buf,"window length %d = %d", &the_table,
 603                  &window_length[the_table-1]);
 604           printf("window length %d = %d\n",the_table,window_length[the_table-1]);
 605         }
 606       }
 607
 608       else if(!strncmp(buf,"scale0s",7)) {
 609         int the_table;
 610         if (!strncmp(buf,"scale0s =",9)) {
 611           sscanf(buf,"scale0s = %lf", &scale0s[0]);
 612           for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
 613             scale0s[the_table] =scale0s[0];
 614             printf("scale0s %d = %lf\n", the_table,
 615                    scale0s[the_table]);
 616           }
 617         }             /* All tables get same scale0. **/
 618         else {
 619           sscanf(buf,"scale0s %d", &the_table);
 620           sscanf(buf,"scale0s %d = %lf", &the_table,
 621                  &scale0s[the_table-1]);
 622           printf("scale0s %d = %lf\n",the_table,scale0s[the_table-1]);
 623         }
 624       }
 625
 626
 627       else if(!strncmp(buf,"scale0p",7)) {
 628         int the_table;
 629         if (!strncmp(buf,"scale0p =",9)) {
 630           sscanf(buf,"scale0p = %lf", &scale0p[0]);
 631           for (the_table =0; the_table < MAX_TABLE_NUMBER; the_table++) {
 632             scale0p[the_table] =scale0s[0];
 633             printf("scale0p %d = %lf\n", the_table,
 634                    scale0p[the_table]);
 635           }
 636         }             /* All tables get same scale0. **/
 637         else {
 638           sscanf(buf,"scale0p %d", &the_table);
 639           sscanf(buf,"scale0p %d = %lf", &the_table,
 640                  &scale0p[the_table-1]);
 641           printf("scale0p %d = %lf\n",the_table,scale0p[the_table-1]);
 642         }
 643       }
 644 /***************************************************************/
 645 /***********************************************************/
 646
 647
 648
 649       else if(!strncmp(buf,"method",6)) {     /* Reads in the method that   */
 650         sscanf(buf,"method = %s", name);     /* should output to fout.     */
 651 /*****
 652         printf("method = %s\n",name);
 653 *****/
 654         if (!strcmp(name,"PairCoil")) sprintf(name,"Coil");
 655         for (i=0; i<NUMBER_METHODS;i++)
 656           if (!strcmp(name,methodname[i]))
 657             *main_method = i;
 658       }
 659       else if(!strncmp(buf,"preprocessor",12)) {/* Reads in the method that  */
 660         sscanf(buf,"preprocessor = %s", name); /* should output to fout.   */
 661 /*****
 662         printf("preprocessor = %s\n",name);
 663 ******/
 664         if (!strcmp(name,"PairCoil")) sprintf(name,"Coil");
 665         for (i=0; i<NUMBER_PREPROCESSORS;i++)
 666           if (!strcmp(name,methodname[i]))
 667             *main_preprocessor_method = i;
 668       }
 669
 670
 671       else if(!strncmp(buf,"default table",13)) {
 672         sscanf(buf,"default table = %s", name);
 673         printf ("default table = %s",name);
 674         if (!strcmp(name, "dimer"))
 675           *main_table =0;   /* Table 0 should be dimer.  */
 676         else if (!strcmp(name, "trimer"))
 677           *main_table =1;   /* Table 1 should be trimer.  */
 678         else if (!strcmp(name, "combination"))
 679           *main_table =2;   /* Table 2 should be combination of table 0+1. */
 680         else {  /*  Just get a table number.  */
 681           sscanf(name,"%d", main_table);
 682           (*main_table)--; /* Human table number starts at 1, computer at 0 */
 683         }
 684       }
 685
 686
 687
 688 /***************The following options are for dimer-trimer likelihoods******/
 689       else if(!strncmp(buf,"avg_max", 7)) {
 690         sscanf(buf,"avg_max = %s", name);
 691         if (!strcmp(name,"avg")) *avg_max=0;
 692         else if (!strcmp(name,"max")) *avg_max=1;
 693         else if (!strcmp(name,"both")) *avg_max=2;
 694
 695         fprintf(stderr, "avg_max = %d\n", *avg_max);
 696       }
 697       else if(!strncmp(buf,"offset", 6)) {  /* -1 means every offset.  */
 698         sscanf(buf,"offset = %d", offset_to_use); /* 7 means max like offset */
 699         fprintf(stderr, "offset for TableDiff = %d\n", *offset_to_use);
 700       }
 701       else if (!strncmp(buf,"use like line",  13)) {
 702         *mode |= USE_LIKE_LINE;
 703         fprintf(stderr,"Using  likelihood line in Pair/SingleCoil computations, not the actual prob. formula.");
 704       }
 705       else if (!strncmp(buf,"weighted paircoil",  17)) {
 706         *mode |= WEIGHTED_PROBS;
 707         fprintf(stderr,"Using weights in paircoil computation.");
 708       }
 709
 710       else if (!strncmp(buf,"do coil avg score", 17)) {
 711         *Coil_Score = 1;
 712         fprintf(stderr,"\nDoing Coil avg score\n");
 713       }
 714
 715       else if (!strncmp(buf,"do coil max score", 17)) {
 716         *Coil_Score = 2;
 717         fprintf(stderr,"\nDoing Coil max score\n");
 718       }
 719     }
 720
 721   }
 722   else {
 723     fprintf(stderr,"\nCouldn't find paircoil_config file.");
 724     fprintf(stderr,"\n   Assumed it would be located in %s.",buf);
 725     fprintf(stderr,"\n   You should either place it there, or set the environment");
 726     fprintf(stderr,"\n   variable PAIRCOIL_CONFIG to its location.\n");
 727     exit(-1);
 728   }
 729 }
 730
 731
 732
 733
 734
 735
 736
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 738