1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662
|
/* BaitFisher (version 1.2.8) a program for designing DNA target enrichment baits
* BaitFilter (version 1.0.6) a program for selecting optimal bait regions
* Copyright 2013-2017 by Christoph Mayer
*
* This source file is part of the BaitFisher-package.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with BaitFisher. If not, see <http://www.gnu.org/licenses/>.
*
*
* For any enquiries send an Email to Christoph Mayer
* c.mayer.zfmk@uni-bonn.de
*
* When publishing work that is based on the results please cite:
* Mayer et al. 2016: BaitFisher: A software package for multi-species target DNA enrichment probe design
*
*/
#ifndef DNA_ROUTINES_H
#define DNA_ROUTINES_H
/* Todo: count DNA bases, guess data type, is AA, etc. */
// Changes 10/11.11.2016:
// * Removed a bug: (c == 'O' && c == 'U') should read (c == 'O' || c == 'U').
// The impact of this error is low. Basically, we overlook O or U as not allowed amino acids.
// Since they should not occur in normal amino acid sequences, it does not make much of a difference.
// * added the blosum symbols, lists and functions
// * added some upper lists and functions.
// * added a look-up table for the blosum symbols. This is much more efficient.
// * removed z from aa_symbols, aa_symbols_ext and _upper, since it as an ambiguity character.
#include <cstring>
#include <cctype>
static const char DNARNA_symbols[] = "aAcCgGtTuU";
static const char DNARNA_symbols_upper[] = "ACGTU";
static const char aa_symbols[] = "aArRnNdDcCeEqQgGhHiIlLkKmMfFpPsStTwWyYvVxX";
static const char aa_symbols_upper[] = "ARNDCEQGHILKMFPSTWYVX";
// Extended also includes: O and U:
static const char aa_symbols_ext[] = "aArRnNdDcCeEqQgGhHiIlLkKmMfFpPsStTwWyYvVxXuUoO*";
static const char aa_symbols_ext_upper [] = "ARNDCEQGHILKMFPSTWYVXUO*";
static const char non_aa_in_ABC [] = "BJOUZbjouz";
// AA ambiguity characters: J is a very rare ambiguity character also included in this set.
// J is not allowed in many programs.
static const char aa_ambig [] = "bBzZjJxX";
// Usually a safe list of allowed characters are those in the blosum matrix:
// Lists the symbols that are allowed in the blosum matrix: Contains B,Z but not J as ambiguity character.
// See also the look up tables: is_aa_blosum_code[] and is_aa_blosum_code_or_gap[]
static const char aa_symbols_blosum[] = "aArRnNdDcCeEqQzZgGhHiIlLkKmMfFpPsStTwWyYvVbBxX*";
static const char aa_symbols_blosum_upper [] = "ARNDCEQZGHILKMFPSTWYVBX*";
static const char non_aa_symbols_blosum[] = "jJoOuU";
static const char non_aa_symbols_blosum_upper [] = "JOU";
static const char DNARNA_iupac_symbols [] = "aAcCgGtTuURYSWryswKMBDkmbdHVNhvn";
static const char phylip_DNARNA_allowed_symbols [] = "?-nNaAcCgGtTuURYSWryswKMBDkmbdHVhvoOxX";
static const char phylip_neither_aa_dna_symbol [] = "jJzZ";
static const char allowed_non_ABC [] = "-?*";
// O and U are special amino acids that are usually not in the models.
// Chars that are not an aa symbol: B, J, O, U, Z
// X is the amibuity code
// Includes the symbols which occur in the blosum matrices:
const int is_aa_blosum_code_lookup[] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,1,0,0,0,0,0,0,0, // 40-49 45: - is not included, 42: * included
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,0,0,1,1,1,1,1, // 60-69 63: ? is not included
1,1,1,1,0,1,1,1,1,0, // 70-79
1,1,1,1,1,0,1,1,1,1, // 80-89
1,0,0,0,0,0,0,1,1,1, // 90-99
1,1,1,1,1,1,0,1,1,1, //100-109
1,0,1,1,1,1,1,0,1,1, //110-119
1,1,1,0,0,0,0,0 //120-127
};
// Includes the symbols which occur in the blosum matrices and the gap character:
const int is_aa_blosum_code_or_gap_lookup[] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,1,0,0,1,0,0,0,0, // 40-49 45: - is included, 42: * included
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,0,0,1,1,1,1,1, // 60-69 63: ? is not included
1,1,1,1,0,1,1,1,1,0, // 70-79
1,1,1,1,1,0,1,1,1,1, // 80-89
1,0,0,0,0,0,0,1,1,1, // 90-99
1,1,1,1,1,1,0,1,1,1, //100-109
1,0,1,1,1,1,1,0,1,1, //110-119
1,1,1,0,0,0,0,0 //120-127
};
// Inlcudes all DNA symbols, no ambiguity characters
const char is_DNA_lookup[128] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,0,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,0,0,1,0,1,0,0, // 60-69 63:'?', 65:'A' to 69:'E'
0,1,0,0,0,0,0,0,0,0, // 70-79
0,0,0,0,1,0,0,0,0,0, // 80-89
0,0,0,0,0,0,0,1,0,1, // 90-99
0,0,0,1,0,0,0,0,0,0, //100-109
0,0,0,0,0,0,1,0,0,0, //110-119
0,0,0,0,0,0,0,0 //120-127
};
// Inlcudes all DNA symbols and gap '-', no ambiguity characters
const char is_DNA_or_GAP_lookup[128] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,1,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,0,0,1,0,1,0,0, // 60-69 63:'?', 65:'A' to 69:'E'
0,1,0,0,0,0,0,0,0,0, // 70-79
0,0,0,0,1,0,0,0,0,0, // 80-89
0,0,0,0,0,0,0,1,0,1, // 90-99
0,0,0,1,0,0,0,0,0,0, //100-109
0,0,0,0,0,0,1,0,0,0, //110-119
0,0,0,0,0,0,0,0 //120-127
};
// Inlcudes all ambiguity characters as well as ?
const char is_DNA_or_AMBIG_lookup[128] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,0,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,1,0,1,1,1,1,0, // 60-69 63:'?', 65:'A' to 69:'E'
0,1,1,0,0,1,0,1,1,0, // 70-79
0,0,1,1,1,0,1,1,0,1, // 80-89
0,0,0,0,0,0,0,1,1,1, // 90-99
1,0,0,1,1,0,0,0,0,0, //100-109
0,0,0,0,1,0,1,0,1,1, //110-119
0,1,0,0,0,0,0,0 //120-127
};
// Inlcudes all ambiguity characters as well as ? and -
const char is_DNA_or_AMBIG_or_GAP_lookup[128] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,1,0,0,0,0, // 40-49 45: - is included
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,1,0,1,1,1,1,0, // 60-69 63:'?', 65:'A' to 69:'E'
0,1,1,0,0,1,0,1,1,0, // 70-79
0,0,1,1,1,0,1,1,0,1, // 80-89
0,0,0,0,0,0,0,1,1,1, // 90-99
1,0,0,1,1,0,0,0,0,0, //100-109
0,0,0,0,1,0,1,0,1,1, //110-119
0,1,0,0,0,0,0,0 //120-127
};
/* inline bool is_DNA_base_upper(char c) */
/* { */
/* if (c == 'A' || c == 'C' || c == 'G' || c == 'T' ) */
/* return true; */
/* return false; */
/* } */
/* inline bool is_DNA_base_lower(char c) */
/* { */
/* if (c == 'a' || c == 'c' || c == 'g' || c == 't' ) */
/* return true; */
/* return false; */
/* } */
// Only defined if c <= 127
inline bool is_DNA_base(char c)
{
return is_DNA_lookup[(int)c];
}
inline bool is_DNA_base_or_GAP(char c)
{
return is_DNA_or_GAP_lookup[(int)c];
}
inline bool is_DNA_or_DNA_ambig(char c)
{
return is_DNA_or_AMBIG_lookup[(int)c];
}
inline bool is_DNA_or_DNA_ambig_or_GAP(char c)
{
return is_DNA_or_AMBIG_or_GAP_lookup[(int)c];
}
inline bool is_DNA_or_RNA_base(char c)
{
if (c == 'A' || c == 'C' || c == 'G' || c == 'T' ||
c == 'a' || c == 'c' || c == 'g' || c == 't' || c == 'U' || c == 'u')
return true;
return false;
}
inline bool is_allowed_non_ABC(char c)
{
if (c == '-' || c == '?' || c == '*')
return true;
else
return false;
}
inline bool is_phylip_aa_dna_symbol(char c) // Does not include -? or similar
{
// Only one character is not allowed:
if (c=='o' || c == 'O')
return false;
if (c >='a' && c <= 'z')
{
return true;
}
else if (c >='A' && c <= 'Z')
{
return true;
}
return false;
}
inline bool is_gap(char c)
{
return c == '-';
}
// Only defined if c <= 127
// Includes only DNA ambig symbols. Does not include DNA symbols. See also is_DNA_or_AMBIG below.
inline bool is_DNA_ambig(char c)
{
return is_DNA_or_AMBIG_lookup[(int)c] && !is_DNA_lookup[(int)c];
/* if (c == 'N' || c == '?' || c == 'n' || */
/* c == 'R' || c == 'Y' || c == 'S' || c == 'W' || */
/* c == 'r' || c == 'y' || c == 's' || c == 'w' || */
/* c == 'K' || c == 'M' || c == 'B' || c == 'D' || */
/* c == 'k' || c == 'm' || c == 'b' || c == 'd' || */
/* c == 'H' || c == 'V' || */
/* c == 'h' || c == 'v') */
/* return true; */
/* else */
/* return false; */
}
/* inline bool is_DNA_iupac_ambig_upper(char c) */
/* { */
/* if (c == 'N' || c == '?' || */
/* c == 'R' || c == 'Y' || c == 'S' || c == 'W' || */
/* c == 'K' || c == 'M' || c == 'B' || c == 'D' || */
/* c == 'H' || c == 'V') */
/* return true; */
/* else */
/* return false; */
/* } */
// A list can be found here: https://en.wikipedia.org/wiki/Amino_acid
// The acceptance of J as an ambiguous amino acid symbol is low.
// J does not occur in the blosm matrix and is not allowed in some programs.
inline bool is_aa_ambig(char c)
{
if (c == 'b' || c == 'B' || c == '?' || c == 'x' || c == 'X' ||
c == 'j' || c == 'J' || c == 'z' || c == 'Z')
return true;
else
return false;
}
inline bool is_aa_blosum_code(unsigned char c)
{
return (is_aa_blosum_code_lookup[c] != 0);
}
inline bool is_aa_blosum_code_or_gap(unsigned char c)
{
return (is_aa_blosum_code_or_gap_lookup[c] != 0);
}
inline int is_aa_upper(char c)
{
if (c >='A' && c <= 'Z')
{
// AA ambigs:
if (c == 'B' || c == 'X' || c == 'J' || c == 'Z')
return false;
// The few symbols that represent nothing.
// Indeed they are listed as the 21st and 22nd amino acid in https://en.wikipedia.org/wiki/Amino_acid
// But they are usually not handled by programs, so we return false.
if (c == 'O' || c == 'U') // OU
return false;
return true;
}
return false;
}
inline int is_aa_or_aa_ambig(char c) // includes '?' and B, Z, J, X
{
if (c >='a' && c <= 'z')
{
if (c != 'o' && c != 'u') // Only not allowed characters in a..z are: ou
return true;
}
else if (c >='A' && c <= 'Z')
{
if (c != 'O' && c != 'U') // Only not allowed characters in a..z are: OU
return true;
}
if (c == '?' || c == '*')
return true;
return false;
// return (strchr(aa_symbols, c) != NULL);
}
inline int is_aa_or_aa_ambig_extended(char c) // O and U are allowed // includes '?' and B, Z, J, X
{
if (c >='a' && c <= 'z')
{
return true;
}
else if (c >='A' && c <= 'Z')
{
return true;
}
if (c == '?' || c == '*')
return true;
return false;
// return (strchr(aa_symbols, c) != NULL);
}
inline char complementBase_of_upper(char c)
{
switch (c) {
case 'A': c = 'T'; break;
case 'T': c = 'A'; break;
case 'G': c = 'C'; break;
case 'C': c = 'G'; break;
case 'R': c = 'Y'; break;
case 'Y': c = 'R'; break;
case 'M': c = 'K'; break;
case 'K': c = 'M'; break;
case 'B': c = 'V'; break;
case 'V': c = 'B'; break;
case 'D': c = 'H'; break;
case 'H': c = 'D'; break;
case 'N': c = 'N'; break;
case '?': c = '?'; break;
case '-': c = '-'; break;
default:
c = '*';
break;
}
return c;
}
inline char complementBase_of_lower(char c)
{
switch (c) {
case 'a': c = 't'; break;
case 't': c = 'a'; break;
case 'g': c = 'c'; break;
case 'c': c = 'g'; break;
case 'r': c = 'y'; break;
case 'y': c = 'r'; break;
case 'm': c = 'k'; break;
case 'k': c = 'm'; break;
case 'b': c = 'v'; break;
case 'v': c = 'b'; break;
case 'd': c = 'h'; break;
case 'h': c = 'd'; break;
case 'n': c = 'n'; break;
case '?': c = '?'; break;
case '-': c = '-'; break;
default:
c = '*';
break;
}
return c;
}
inline char complementBase(char c)
{
if ( isupper(c) )
return complementBase_of_upper(c);
else
return complementBase_of_lower(c);
}
inline void CG_AT_content_in_region(const char *beg, const char *end, unsigned &AT, unsigned &CG)
{
AT = 0;
CG = 0;
char c;
while (beg != end)
{
c = *beg;
if (c == 'C' || c == 'c' || c == 'G' || c == 'g')
++CG;
else if (c == 'A' || c == 'a' || c == 'T' || c == 't')
++AT;
++beg;
}
}
inline void content_in_region_DNA(const char *beg, const char *end, unsigned &AT, unsigned &CG, unsigned &gap, unsigned &ambig, unsigned &unknown)
{
AT = 0;
CG = 0;
gap = 0;
ambig = 0;
unknown = 0;
char c;
while (beg != end)
{
c = *beg;
if (c == 'C' || c == 'c' || c == 'G' || c == 'g')
++CG;
else if (c == 'A' || c == 'a' || c == 'T' || c == 't')
++AT;
else if (c == '-')
++gap;
else if (is_DNA_ambig(c) )
++ambig;
else
++unknown;
++beg;
}
}
inline bool is_aa_blosum_code_or_gap_sequence(const char *p1, const char *p2, unsigned *offending_pos)
{
const char *startp = p1;
while (p1 != p2)
{
if (!is_aa_blosum_code_or_gap(*p1) )
{
*offending_pos = p1 - startp;
return false;
}
++p1;
}
return true;
}
// Recoding symbols:
// A char can hold 8 bits, enough for 8 characters to be "in or out",
// to be switched on or off. Thus a char can be used to hold
// all bases including ambiguities as follows:
// Say A, C, G, T are the bits 1,2,3,4,
// the ambiguity {A,C} is 1+2 = 3
// A: 65, 97 -> 1
// C: 67, 99 -> 2
// G: 71,103 -> 4
// T: 84,116 -> 8
// R(AG): 82,114 -> 5
// Y(CT): 89,121 -> 10
// S(CG): 83,115 -> 6
// W(TA): 87,119 -> 9
// K(TG): 75,107 -> 12
// M(CA): 77,109 -> 3
// B(CTG): 66,98 -> 14
// D(ATG): 68,100 -> 13
// H(ATC): 72,104 -> 11
// V(ACG): 86,118 -> 7
// N(ACGT): 78,110 -> 15
// - 45 -> 0
// ? 63 -> 15
const char ascii2recode_DNA[128] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,0,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,15,0,1,14,2,13,0, // 60-69
0,4,11,0,0,12,0,3,15,0, // 70-79
0,0,5,6,8,0,7,9,0,10, // 80-89
0,0,0,0,0,0,0,1,14,2, // 90-99
13,0,0,4,11,0,0,0,0,0, //100-109
0,0,0,0,5,0,8,0,7,9, //110-119
0,10,0,0,0,0,0,0 //120-127
};
const char recode2ascii_DNA[128] = {
45,65,67,77,71,82,83,86,84,87, // 0- 9
89,72,75,68,66,78,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,0,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,0,0,0,0,0,0,0, // 60-69
0,0,0,0,0,0,0,0,0,0, // 70-79
0,0,0,0,0,0,0,0,0,0, // 80-89
0,0,0,0,0,0,0,0,0,0, // 90-99
0,0,0,0,0,0,0,0,0,0, //100-109
0,0,0,0,0,0,0,0,0,0, //110-119
0,0,0,0,0,0,0,0 //120-127
};
const char recodeISDNAamig[128] = {
0,0,0,1,0,1,1,1,0,1, // 0- 9
1,1,1,1,1,1,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,0,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,0,0,0,0,0,0,0, // 60-69
0,0,0,0,0,0,0,0,0,0, // 70-79
0,0,0,0,0,0,0,0,0,0, // 80-89
0,0,0,0,0,0,0,0,0,0, // 90-99
0,0,0,0,0,0,0,0,0,0, //100-109
0,0,0,0,0,0,0,0,0,0, //110-119
0,0,0,0,0,0,0,0 //120-127
};
inline unsigned char recode_DNA(unsigned char c)
{
return ascii2recode_DNA[c];
}
inline unsigned char backrecode_DNA(unsigned char c)
{
return recode2ascii_DNA[c];
}
inline unsigned char recode_is_DNA_ambig(unsigned char c)
{
return recodeISDNAamig[c];
}
inline bool is_base_in_recode(unsigned char recode, unsigned char base)
{
return recode & recode_DNA(base);
}
inline bool is_valid_recode_DNA(unsigned char c)
{
if (c > 15)
return false;
else
return true;
}
inline bool is_recode_gap(unsigned char c)
{
return (c == 0);
}
// A Ala Alanine 01 65
// R Arg Arginine 02 82
// N Asn Asparagine 03 78
// D Asp Aspartic acid 08 68
// C Cys Cysteine 16 67
// Q Gln Glutamine 32 81
// E Glu Glutamic acid 64 69
// G Gly Glycine 128 71
// H His Histidine 256 72
// I Ile Isoleucine 512 73
// L Leu Leucine 1024 76
// K Lys Lysine 2048 75
// M Met Methionine 4096 77
// F Phe Phenylalanine 8192 70
// P Pro Proline 16384 80
// S Ser Serine 32768 83
// T Thr Threonine 65536 84
// W Trp Tryptophan 131072 87
// Y Tyr Tyrosine 262144 89
// V Val Valine 524288 86
// - 45 -> 0
// ? 63 -> 1048575
// X 88 -> 1048575
const int ascii2recode_aa[128] = {
0,0,0,0,0,0,0,0,0,0, // 0- 9
0,0,0,0,0,0,0,0,0,0, // 10-19
0,0,0,0,0,0,0,0,0,0, // 20-29
0,0,0,0,0,0,0,0,0,0, // 30-39
0,0,0,0,0,64,0,0,0,0, // 40-49
0,0,0,0,0,0,0,0,0,0, // 50-59
0,0,0,15,0,1,14,2,13,0, // 60-69
0,4,11,0,0,12,0,3,15,0, // 70-79
0,0,5,6,8,0,7,9,0,10, // 80-89
0,0,0,0,0,0,0,1,14,2, // 90-99
13,0,0,4,11,0,0,0,0,0, //100-109
0,0,0,0,5,0,8,0,7,9, //110-119
0,10,0,0,0,0,0,0 //120-127
};
#endif
|