Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/src/tigr/tigrinc.cc @ 69:33d812a61356

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
parents
children
rev   line source
jpayne@69 1 #include "tigrinc.hh"
jpayne@69 2
jpayne@69 3
jpayne@69 4 FILE * File_Open (const char * Filename, const char * Mode)
jpayne@69 5
jpayne@69 6 /* Open Filename in Mode and return a pointer to its control
jpayne@69 7 * block. If fail, print a message and exit. */
jpayne@69 8
jpayne@69 9 {
jpayne@69 10 FILE * fp;
jpayne@69 11
jpayne@69 12 fp = fopen (Filename, Mode);
jpayne@69 13 if (fp == NULL)
jpayne@69 14 {
jpayne@69 15 fprintf (stderr, "ERROR: Could not open file %s \n", Filename);
jpayne@69 16 exit (EXIT_FAILURE);
jpayne@69 17 }
jpayne@69 18
jpayne@69 19 return fp;
jpayne@69 20 }
jpayne@69 21
jpayne@69 22
jpayne@69 23
jpayne@69 24 void * Safe_calloc (size_t N, size_t Len)
jpayne@69 25
jpayne@69 26 /* Allocate and return a pointer to an array of N elements of
jpayne@69 27 * Len bytes each. All set to 0. Exit if fail. */
jpayne@69 28
jpayne@69 29 {
jpayne@69 30 void * P;
jpayne@69 31
jpayne@69 32 P = calloc (N, Len);
jpayne@69 33 if (P == NULL)
jpayne@69 34 {
jpayne@69 35 fprintf (stderr,
jpayne@69 36 "ERROR: calloc failed, there is not enough memory\n");
jpayne@69 37 exit (EXIT_FAILURE);
jpayne@69 38 }
jpayne@69 39
jpayne@69 40 return P;
jpayne@69 41 }
jpayne@69 42
jpayne@69 43
jpayne@69 44
jpayne@69 45 void * Safe_malloc (size_t Len)
jpayne@69 46
jpayne@69 47 /* Allocate and return a pointer to Len bytes of memory.
jpayne@69 48 * Exit if fail. */
jpayne@69 49
jpayne@69 50 {
jpayne@69 51 void * P;
jpayne@69 52
jpayne@69 53 P = malloc (Len);
jpayne@69 54 if (P == NULL)
jpayne@69 55 {
jpayne@69 56 fprintf (stderr,
jpayne@69 57 "ERROR: malloc failed, there is not enough memory\n");
jpayne@69 58 exit (EXIT_FAILURE);
jpayne@69 59 }
jpayne@69 60
jpayne@69 61 return P;
jpayne@69 62 }
jpayne@69 63
jpayne@69 64
jpayne@69 65
jpayne@69 66 void * Safe_realloc (void * Q, size_t Len)
jpayne@69 67
jpayne@69 68 /* Reallocate memory for Q to Len bytes and return a
jpayne@69 69 * pointer to the new memory. Exit if fail. */
jpayne@69 70
jpayne@69 71 {
jpayne@69 72 void * P;
jpayne@69 73
jpayne@69 74 P = realloc (Q, Len);
jpayne@69 75 if (P == NULL)
jpayne@69 76 {
jpayne@69 77 fprintf (stderr,
jpayne@69 78 "ERROR: realloc failed, there is not enough memory\n");
jpayne@69 79 exit (EXIT_FAILURE);
jpayne@69 80 }
jpayne@69 81
jpayne@69 82 return P;
jpayne@69 83 }
jpayne@69 84
jpayne@69 85
jpayne@69 86
jpayne@69 87 char Complement (char Ch)
jpayne@69 88
jpayne@69 89 /* Returns the DNA complement of Ch . */
jpayne@69 90
jpayne@69 91 {
jpayne@69 92 switch (tolower (Ch))
jpayne@69 93 {
jpayne@69 94 case 'a' :
jpayne@69 95 return 't';
jpayne@69 96 case 'c' :
jpayne@69 97 return 'g';
jpayne@69 98 case 'g' :
jpayne@69 99 return 'c';
jpayne@69 100 case 't' :
jpayne@69 101 return 'a';
jpayne@69 102 case 'r' : // a or g
jpayne@69 103 return 'y';
jpayne@69 104 case 'y' : // c or t
jpayne@69 105 return 'r';
jpayne@69 106 case 's' : // c or g
jpayne@69 107 return 's';
jpayne@69 108 case 'w' : // a or t
jpayne@69 109 return 'w';
jpayne@69 110 case 'm' : // a or c
jpayne@69 111 return 'k';
jpayne@69 112 case 'k' : // g or t
jpayne@69 113 return 'm';
jpayne@69 114 case 'b' : // c, g or t
jpayne@69 115 return 'v';
jpayne@69 116 case 'd' : // a, g or t
jpayne@69 117 return 'h';
jpayne@69 118 case 'h' : // a, c or t
jpayne@69 119 return 'd';
jpayne@69 120 case 'v' : // a, c or g
jpayne@69 121 return 'b';
jpayne@69 122 default : // anything
jpayne@69 123 return tolower (Ch);
jpayne@69 124 }
jpayne@69 125 }
jpayne@69 126
jpayne@69 127
jpayne@69 128 bool CompareIUPAC (char x, char y)
jpayne@69 129 {
jpayne@69 130 x = tolower(x);
jpayne@69 131 y = tolower(y);
jpayne@69 132
jpayne@69 133 if ( x == 'n' || x == 'x' || y == 'n' || y == 'x' )
jpayne@69 134 return true;
jpayne@69 135
jpayne@69 136 switch ( x )
jpayne@69 137 {
jpayne@69 138 case 'a' :
jpayne@69 139 switch ( y )
jpayne@69 140 {
jpayne@69 141 case 'a':
jpayne@69 142 case 'r':
jpayne@69 143 case 'w':
jpayne@69 144 case 'm':
jpayne@69 145 case 'd':
jpayne@69 146 case 'h':
jpayne@69 147 case 'v':
jpayne@69 148 return true;
jpayne@69 149 }
jpayne@69 150 return false;
jpayne@69 151
jpayne@69 152 case 'c' :
jpayne@69 153 switch ( y )
jpayne@69 154 {
jpayne@69 155 case 'c':
jpayne@69 156 case 'y':
jpayne@69 157 case 's':
jpayne@69 158 case 'm':
jpayne@69 159 case 'b':
jpayne@69 160 case 'h':
jpayne@69 161 case 'v':
jpayne@69 162 return true;
jpayne@69 163 }
jpayne@69 164 return false;
jpayne@69 165
jpayne@69 166 case 'g' :
jpayne@69 167 switch ( y )
jpayne@69 168 {
jpayne@69 169 case 'g':
jpayne@69 170 case 'r':
jpayne@69 171 case 's':
jpayne@69 172 case 'k':
jpayne@69 173 case 'b':
jpayne@69 174 case 'd':
jpayne@69 175 case 'v':
jpayne@69 176 return true;
jpayne@69 177 }
jpayne@69 178 return false;
jpayne@69 179
jpayne@69 180 case 't' :
jpayne@69 181 switch ( y )
jpayne@69 182 {
jpayne@69 183 case 't':
jpayne@69 184 case 'y':
jpayne@69 185 case 'w':
jpayne@69 186 case 'k':
jpayne@69 187 case 'b':
jpayne@69 188 case 'd':
jpayne@69 189 case 'h':
jpayne@69 190 return true;
jpayne@69 191 }
jpayne@69 192 return false;
jpayne@69 193
jpayne@69 194 case 'r' : // a or g
jpayne@69 195 switch ( y )
jpayne@69 196 {
jpayne@69 197 case 'r':
jpayne@69 198 case 'a':
jpayne@69 199 case 'g':
jpayne@69 200 case 'd':
jpayne@69 201 case 'v':
jpayne@69 202 return true;
jpayne@69 203 }
jpayne@69 204 return false;
jpayne@69 205
jpayne@69 206 case 'y' : // c or t
jpayne@69 207 switch ( y )
jpayne@69 208 {
jpayne@69 209 case 'y':
jpayne@69 210 case 'c':
jpayne@69 211 case 't':
jpayne@69 212 case 'b':
jpayne@69 213 case 'h':
jpayne@69 214 return true;
jpayne@69 215 }
jpayne@69 216 return false;
jpayne@69 217
jpayne@69 218 case 's' : // c or g
jpayne@69 219 switch ( y )
jpayne@69 220 {
jpayne@69 221 case 's':
jpayne@69 222 case 'c':
jpayne@69 223 case 'g':
jpayne@69 224 case 'b':
jpayne@69 225 case 'v':
jpayne@69 226 return true;
jpayne@69 227 }
jpayne@69 228 return false;
jpayne@69 229
jpayne@69 230 case 'w' : // a or t
jpayne@69 231 switch ( y )
jpayne@69 232 {
jpayne@69 233 case 'w':
jpayne@69 234 case 'a':
jpayne@69 235 case 't':
jpayne@69 236 case 'd':
jpayne@69 237 case 'h':
jpayne@69 238 return true;
jpayne@69 239 }
jpayne@69 240 return false;
jpayne@69 241
jpayne@69 242 case 'm' : // a or c
jpayne@69 243 switch ( y )
jpayne@69 244 {
jpayne@69 245 case 'm':
jpayne@69 246 case 'a':
jpayne@69 247 case 'c':
jpayne@69 248 case 'h':
jpayne@69 249 case 'v':
jpayne@69 250 return true;
jpayne@69 251 }
jpayne@69 252 return false;
jpayne@69 253
jpayne@69 254 case 'k' : // g or t
jpayne@69 255 switch ( y )
jpayne@69 256 {
jpayne@69 257 case 'k':
jpayne@69 258 case 'g':
jpayne@69 259 case 't':
jpayne@69 260 case 'b':
jpayne@69 261 case 'd':
jpayne@69 262 return true;
jpayne@69 263 }
jpayne@69 264 return false;
jpayne@69 265
jpayne@69 266 case 'b' : // c, g or t
jpayne@69 267 switch ( y )
jpayne@69 268 {
jpayne@69 269 case 'b':
jpayne@69 270 case 'c':
jpayne@69 271 case 'g':
jpayne@69 272 case 't':
jpayne@69 273 return true;
jpayne@69 274 }
jpayne@69 275 return false;
jpayne@69 276
jpayne@69 277 case 'd' : // a, g or t
jpayne@69 278 switch ( y )
jpayne@69 279 {
jpayne@69 280 case 'd':
jpayne@69 281 case 'a':
jpayne@69 282 case 'g':
jpayne@69 283 case 't':
jpayne@69 284 return true;
jpayne@69 285 }
jpayne@69 286 return false;
jpayne@69 287
jpayne@69 288 case 'h' : // a, c or t
jpayne@69 289 switch ( y )
jpayne@69 290 {
jpayne@69 291 case 'h':
jpayne@69 292 case 'a':
jpayne@69 293 case 'c':
jpayne@69 294 case 't':
jpayne@69 295 return true;
jpayne@69 296 }
jpayne@69 297 return false;
jpayne@69 298
jpayne@69 299 case 'v' : // a, c or g
jpayne@69 300 switch ( y )
jpayne@69 301 {
jpayne@69 302 case 'v':
jpayne@69 303 case 'a':
jpayne@69 304 case 'c':
jpayne@69 305 case 'g':
jpayne@69 306 return true;
jpayne@69 307 }
jpayne@69 308 return false;
jpayne@69 309 }
jpayne@69 310 return false;
jpayne@69 311 }
jpayne@69 312
jpayne@69 313
jpayne@69 314 int Read_String (FILE * fp, char * & T, long int & Size, char Name [],
jpayne@69 315 int Partial)
jpayne@69 316
jpayne@69 317 /* Read next string from fp (assuming FASTA format) into T [1 ..]
jpayne@69 318 * which has Size characters. Allocate extra memory if needed
jpayne@69 319 * and adjust Size accordingly. Return TRUE if successful, FALSE
jpayne@69 320 * otherwise (e.g., EOF). Partial indicates if first line has
jpayne@69 321 * numbers indicating a subrange of characters to read.
jpayne@69 322 */
jpayne@69 323
jpayne@69 324 {
jpayne@69 325 char * P, Line [MAX_LINE];
jpayne@69 326 long int Len, Lo, Hi;
jpayne@69 327 int Ch, Ct;
jpayne@69 328
jpayne@69 329 while ((Ch = fgetc (fp)) != EOF && Ch != '>')
jpayne@69 330 ;
jpayne@69 331
jpayne@69 332 if (Ch == EOF)
jpayne@69 333 return FALSE;
jpayne@69 334
jpayne@69 335 fgets (Line, MAX_LINE, fp);
jpayne@69 336 Len = strlen (Line);
jpayne@69 337 assert (Len > 0 && Line [Len - 1] == '\n');
jpayne@69 338 P = strtok (Line, " \t\n");
jpayne@69 339 if (P != NULL)
jpayne@69 340 strcpy (Name, P);
jpayne@69 341 else
jpayne@69 342 Name [0] = '\0';
jpayne@69 343 Lo = 0; Hi = LONG_MAX;
jpayne@69 344 if (Partial)
jpayne@69 345 {
jpayne@69 346 P = strtok (NULL, " \t\n");
jpayne@69 347 if (P != NULL)
jpayne@69 348 {
jpayne@69 349 Lo = strtol (P, NULL, 10);
jpayne@69 350 P = strtok (NULL, " \t\n");
jpayne@69 351 if (P != NULL)
jpayne@69 352 Hi = strtol (P, NULL, 10);
jpayne@69 353 }
jpayne@69 354 assert (Lo <= Hi);
jpayne@69 355 }
jpayne@69 356
jpayne@69 357 Ct = 0;
jpayne@69 358 T [0] = '\0';
jpayne@69 359 Len = 1;
jpayne@69 360 while ((Ch = fgetc (fp)) != EOF && Ch != '>')
jpayne@69 361 {
jpayne@69 362 if (isspace (Ch))
jpayne@69 363 continue;
jpayne@69 364
jpayne@69 365 Ct ++;
jpayne@69 366 if (Ct < Lo || Ct > Hi)
jpayne@69 367 continue;
jpayne@69 368
jpayne@69 369 if (Len >= Size)
jpayne@69 370 {
jpayne@69 371 Size += INCR_SIZE;
jpayne@69 372 T = (char *) Safe_realloc (T, Size);
jpayne@69 373 }
jpayne@69 374 Ch = tolower (Ch);
jpayne@69 375
jpayne@69 376 if (! isalpha (Ch) && Ch != '*')
jpayne@69 377 {
jpayne@69 378 fprintf (stderr, "Unexpected character `%c\' in string %s\n",
jpayne@69 379 Ch, Name);
jpayne@69 380 Ch = 'x';
jpayne@69 381 }
jpayne@69 382
jpayne@69 383 T [Len ++] = Ch;
jpayne@69 384 }
jpayne@69 385
jpayne@69 386 T [Len] = '\0';
jpayne@69 387 if (Ch == '>')
jpayne@69 388 ungetc (Ch, fp);
jpayne@69 389
jpayne@69 390 return TRUE;
jpayne@69 391 }
jpayne@69 392
jpayne@69 393
jpayne@69 394
jpayne@69 395 void Reverse_Complement
jpayne@69 396 (char S [], long int Lo, long int Hi)
jpayne@69 397
jpayne@69 398 // Convert substring S [Lo .. Hi] to its Watson-Crick reverse
jpayne@69 399 // complement
jpayne@69 400
jpayne@69 401 {
jpayne@69 402 char Ch;
jpayne@69 403
jpayne@69 404 while (Lo <= Hi)
jpayne@69 405 {
jpayne@69 406 Ch = S [Hi];
jpayne@69 407 S [Hi] = Complement (S [Lo]);
jpayne@69 408 S [Lo] = Complement (Ch);
jpayne@69 409 Lo ++;
jpayne@69 410 Hi --;
jpayne@69 411 }
jpayne@69 412
jpayne@69 413 return;
jpayne@69 414 }
jpayne@69 415