/usr/lib/emboss/include/ajseq.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef ajseq_h
#define ajseq_h
#include "ajseqdata.h"
#include "ajax.h"
/* @data AjPSeqCvt ************************************************************
**
** Sequence conversion data. Used to convert a sequence to binary.
**
** @new ajSeqCvtNew Creates from a character string of valid bases.
** @new ajSeqCvtNewText Creates from a character string of valid bases.
** @new ajSeqCvtNewZero Creates from a character string of valid bases.
** @new ajSeqCvtNewZeroS Creates from an array of strings of valid bases.
** @new ajSeqCvtNewZeroSS Creates from an array of strings of valid bases.
** @output ajSeqCvtTrace Reports on contents for debugging
*
** @alias AjSSeqCvt
** @alias AjOSeqCvt
**
** @attr size [ajint] Number of characters in table, usually
** all possible characters.
** @attr len [ajint] Number of characters defined
** @attr missing [ajint] Index of the missing character value
** @attr nrlabels [ajint] Number of row labels
** @attr bases [AjPStr] The bases which can be converted
** @attr rlabels [AjPStr*] Row labels
** @attr clabels [AjPStr*] Column labels
** @attr table [char*] Binary character value for each character in bases
** @attr nclabels [ajint] Number of column labels
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct AjSSeqCvt {
ajint size;
ajint len;
ajint missing;
ajint nrlabels;
AjPStr bases;
AjPStr* rlabels;
AjPStr* clabels;
char *table;
ajint nclabels;
char Padding[4];
} AjOSeqCvt;
#define AjPSeqCvt AjOSeqCvt*
/*
** Prototype definitions
*/
AjBool ajSeqtestIsAccession (const AjPStr accnum);
const AjPStr ajSeqtestIsSeqversion (const AjPStr sv);
void ajSeqallDel(AjPSeqall *thys);
ajlong ajSeqallGetCount (const AjPSeqall seq);
const AjPStr ajSeqallGetFilename(const AjPSeqall thys);
const AjPStr ajSeqallGetseqName (const AjPSeqall thys);
ajint ajSeqallGetseqBegin (const AjPSeqall seq);
ajint ajSeqallGetseqEnd (const AjPSeqall seq);
ajint ajSeqallGetseqLen (const AjPSeqall seqall);
const AjPStr ajSeqallGetName(const AjPSeqall seq);
ajint ajSeqallGetseqRange (const AjPSeqall thys,
ajint* begin, ajint* end);
ajlong ajSeqallGetTotlength (const AjPSeqall seq);
const AjPStr ajSeqallGetUsa (const AjPSeqall thys);
AjPSeqall ajSeqallNew (void);
void ajSeqallClear (AjPSeqall thys);
void ajSeqallClearStats (AjPSeqall thys);
AjBool ajSeqallNext (AjPSeqall seqall, AjPSeq* retseq);
void ajSeqallSetRange (AjPSeqall seq, ajint ibegin, ajint iend);
void ajSeqallSetRangeRev (AjPSeqall seq, ajint ibegin, ajint iend);
void ajSeqAddCmt(AjPSeq thys, AjPStr str);
void ajSeqAddGene(AjPSeq thys, AjPSeqGene gene);
void ajSeqAddKey(AjPSeq thys, AjPStr str);
void ajSeqAddRef(AjPSeq thys, AjPSeqRef ref);
void ajSeqAddXref(AjPSeq thys, AjPSeqXref xref);
void ajSeqAssignAccC(AjPSeq seq, const char* text);
void ajSeqAssignAccS(AjPSeq seq, const AjPStr str);
void ajSeqAssignDescC(AjPSeq seq, const char* text);
void ajSeqAssignDescS(AjPSeq seq, const AjPStr str);
void ajSeqAssignEntryC(AjPSeq seq, const char* text);
void ajSeqAssignEntryS(AjPSeq seq, const AjPStr str);
void ajSeqAssignFileC(AjPSeq seq, const char* text);
void ajSeqAssignFileS(AjPSeq seq, const AjPStr str);
void ajSeqAssignFullC(AjPSeq seq, const char* text);
void ajSeqAssignFullS(AjPSeq seq, const AjPStr str);
void ajSeqAssignGiC(AjPSeq seq, const char* text);
void ajSeqAssignGiS(AjPSeq
seq, const AjPStr str);
void ajSeqAssignNameC(AjPSeq seq, const char* txt);
void ajSeqAssignNameS(AjPSeq seq, const AjPStr str);
void ajSeqAssignQualLen(AjPSeq seq, const float* qual, ajuint len);
void ajSeqAssignSeqC(AjPSeq seq, const char* text);
void ajSeqAssignSeqLenC(AjPSeq seq, const char* txt, ajuint len);
void ajSeqAssignSeqS(AjPSeq seq, const AjPStr str);
void ajSeqAssignSvC(AjPSeq seq, const char* text);
void ajSeqAssignSvS(AjPSeq seq, const AjPStr str);
void ajSeqAssignUfoC(AjPSeq seq, const char* text);
void ajSeqAssignUfoS(AjPSeq seq, const AjPStr str);
void ajSeqAssignUsaC(AjPSeq seq, const char* text);
void ajSeqAssignUsaS(AjPSeq seq, const AjPStr str);
ajuint ajSeqGetBegin (const AjPSeq seq);
const float* ajSeqGetQual(const AjPSeq seq);
const char* ajSeqGetSeqC (const AjPSeq thys);
const AjPStr ajSeqGetSeqS(const AjPSeq seq);
char* ajSeqGetSeqCopyC (const AjPSeq seq);
AjPStr ajSeqGetSeqCopyS(const AjPSeq seq);
ajint ajSeqCalcCheckgcg (const AjPSeq thys);
void ajSeqClear (AjPSeq thys);
void ajSeqComplement (AjPSeq thys);
void ajSeqstrComplement (AjPStr* thys);
AjBool ajSeqstrConvertNum(const AjPStr seq, const AjPSeqCvt cvt,
AjPStr* Pnumseq);
AjPFeattable ajSeqGetFeatCopy (const AjPSeq thys);
void ajSeqCalcCount (const AjPSeq thys, ajint *b);
ajuint ajSeqstrCountGaps(const AjPStr str);
void ajSeqcvtDel (AjPSeqCvt* thys);
ajint ajSeqcvtGetCodeK (const AjPSeqCvt thys, char ch);
ajint ajSeqcvtGetCodeS (const AjPSeqCvt thys, const AjPStr ch);
ajint ajSeqcvtGetCodeAsymS (const AjPSeqCvt cvt, const AjPStr str);
ajint ajSeqcvtGetCodeAsymrowS (const AjPSeqCvt cvt, const AjPStr str);
ajuint ajSeqcvtGetLen (const AjPSeqCvt thys);
AjPSeqCvt ajSeqcvtNewC (const char* bases);
AjPSeqCvt ajSeqcvtNewNumberC (const char* bases);
AjPSeqCvt ajSeqcvtNewEndC (const char* bases);
AjPSeqCvt ajSeqcvtNewStr (const AjPPStr bases, ajint n);
AjPSeqCvt ajSeqcvtNewStrAsym (const AjPPStr bases, ajint n,
const AjPPStr rbases, ajint rn);
void ajSeqcvtTrace (const AjPSeqCvt cvt);
AjPSeqDate ajSeqdateNew(void);
AjPSeqDate ajSeqdateNewDate(const AjPSeqDate date);
AjBool ajSeqdateSetCreateS(AjPSeqDate date, const AjPStr datestr);
AjBool ajSeqdateSetModifyS(AjPSeqDate date, const AjPStr datestr);
AjBool ajSeqdateSetModseqS(AjPSeqDate date, const AjPStr datestr);
void ajSeqdateClear(AjPSeqDate date);
void ajSeqdateDel(AjPSeqDate*);
AjPSeqDesc ajSeqdescNew(void);
AjPSeqDesc ajSeqdescNewDesc(const AjPSeqDesc);
void ajSeqdescClear(AjPSeqDesc desc);
void ajSeqdescDel(AjPSeqDesc*);
AjBool ajSeqdesclistClone(const AjPList src, AjPList dest);
AjPSeqSubdesc ajSeqsubdescNew(void);
AjPSeqSubdesc ajSeqsubdescNewSubdesc(const AjPSeqSubdesc);
void ajSeqsubdescClear(AjPSeqSubdesc desc);
void ajSeqsubdescDel(AjPSeqSubdesc*);
AjBool ajSeqsubdesclistClone(const AjPList src, AjPList dest);
AjPSeqGene ajSeqgeneNew(void);
AjPSeqGene ajSeqgeneNewGene(const AjPSeqGene gene);
AjPSeqGene ajSeqgeneNewName(const AjPStr str);
void ajSeqgeneDel(AjPSeqGene*);
AjPSeqRef ajSeqrefNew(void);
AjPSeqRef ajSeqrefNewRef(const AjPSeqRef);
void ajSeqrefDel(AjPSeqRef*);
AjPSeqXref ajSeqxrefNew(void);
AjPSeqXref ajSeqxrefNewDbC(const AjPStr id, const char* db, ajuint reftype);
AjPSeqXref ajSeqxrefNewDbS(const AjPStr id, const AjPStr db, ajuint reftype);
AjPSeqXref ajSeqxrefNewRef(const AjPSeqXref);
void ajSeqxrefDel(AjPSeqXref*);
AjBool ajSeqdescAppendName(AjPSeqDesc desc, const AjPStr str);
AjBool ajSeqdescSetName(AjPSeqDesc desc, const AjPStr str);
AjBool ajSeqsubdescAppendName(AjPSeqSubdesc desc, const AjPStr str);
AjBool ajSeqsubdescSetName(AjPSeqSubdesc desc, const AjPStr str);
AjBool ajSeqgeneAppendName(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneAppendSynonyms(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneAppendOrf(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneAppendOln(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneSetName(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneSetSynonyms(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneSetOrf(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgeneSetOln(AjPSeqGene gene, const AjPStr str);
AjBool ajSeqgenelistClone(const AjPList src, AjPList dest);
AjBool ajSeqrefAppendAuthors(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefAppendComment(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefAppendGroupname(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefAppendLocation(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefAppendPosition(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefAppendTitle(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefAppendXref(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefFmtAuthorsEmbl(const AjPSeqRef ref, AjPStr* Pdest);
AjBool ajSeqrefFmtAuthorsGb(const AjPSeqRef ref, AjPStr* Pdest);
AjBool ajSeqrefFmtLocationEmbl(const AjPSeqRef ref, AjPStr* Pdest);
AjBool ajSeqrefFmtLocationGb(const AjPSeqRef ref, AjPStr* Pdest);
AjBool ajSeqrefFmtTitleGb(const AjPSeqRef ref, AjPStr* Pdest);
AjBool ajSeqreflistClone(const AjPList src, AjPList dest);
ajuint ajSeqreflistGetXrefs(const AjPList src, AjPList *Plist);
AjBool ajSeqrefSetAuthors(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetComment(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetGroupname(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetLocation(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetLoctype(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetnumNumber(AjPSeqRef ref, ajuint num);
AjBool ajSeqrefSetPosition(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetTitle(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefSetXref(AjPSeqRef ref, const AjPStr str);
AjBool ajSeqrefStandard(AjPSeqRef ref);
AjBool ajSeqxreflistClone(const AjPList src, AjPList dest);
void ajSeqSetName(AjPSeq thys, const AjPStr setname);
void ajSeqSetNameMulti(AjPSeq thys, const AjPStr setname);
void ajSeqDel (AjPSeq* pthis);
void ajSeqDelarray(AjPSeq **PPseq);
ajuint ajSeqGetEnd (const AjPSeq seq);
void ajSeqExit(void);
void ajSeqGapFill (AjPSeq seq, ajuint len);
ajuint ajSeqCountGaps(const AjPSeq seq);
void ajSeqGapStandard (AjPSeq thys, char gapch);
const char* ajSeqGetAccC (const AjPSeq thys);
const AjPStr ajSeqGetAccS (const AjPSeq thys);
const char* ajSeqGetDbC (const AjPSeq thys);
const AjPStr ajSeqGetDbS (const AjPSeq thys);
const char* ajSeqGetDescC (const AjPSeq thys);
const AjPStr ajSeqGetDescS (const AjPSeq thys);
const char* ajSeqGetEntryC (const AjPSeq thys);
const AjPStr ajSeqGetEntryS (const AjPSeq thys);
const AjPFeattable ajSeqGetFeat (const AjPSeq thys);
const char* ajSeqGetGiC (const AjPSeq thys);
const AjPStr ajSeqGetGiS (const AjPSeq thys);
const char* ajSeqGetNameC (const AjPSeq thys);
const AjPStr ajSeqGetNameS (const AjPSeq thys);
ajuint ajSeqGetOffend(const AjPSeq seq);
ajuint ajSeqGetOffset(const AjPSeq seq);
ajuint ajSeqGetRange (const AjPSeq thys, ajint* begin, ajint* end);
AjBool ajSeqGetRev (const AjPSeq thys);
const char* ajSeqGetSvC (const AjPSeq thys);
const AjPStr ajSeqGetSvS (const AjPSeq thys);
const char* ajSeqGetTaxC (const AjPSeq thys);
const AjPStr ajSeqGetTaxS (const AjPSeq thys);
ajuint ajSeqGetTaxid(const AjPSeq seq);
const char* ajSeqGetUsaC (const AjPSeq thys);
const AjPStr ajSeqGetUsaS (const AjPSeq thys);
AjBool ajSeqIsNuc (const AjPSeq thys);
AjBool ajSeqIsProt (const AjPSeq thys);
ajuint ajSeqGetLen (const AjPSeq seq);
ajuint ajSeqGetLenTrimmed (const AjPSeq seq);
ajuint ajSeqGetLenUngapped (const AjPSeq seq);
const char* ajSeqclsGetEmbl(const AjPStr cls);
AjBool ajSeqclsSetEmbl(AjPStr *cls, const AjPStr clsembl);
AjBool ajSeqclsSetGb(AjPStr *cls, const AjPStr clsembl);
const char* ajSeqdivGetEmbl(const AjPStr divi);
const char* ajSeqdivGetGb(const AjPStr divi);
AjBool ajSeqdivSetEmbl(AjPStr *Pdivi, const AjPStr divembl);
AjBool ajSeqdivSetGb(AjPStr *Pdivi, const AjPStr divembl);
const char* ajSeqmolGetEmbl(const AjPStr mol);
const char* ajSeqmolGetGb(const AjPStr mol);
AjBool ajSeqmolSetEmbl(AjPStr *mol, const AjPStr molembl);
AjBool ajSeqmolSetGb(AjPStr *mol, const AjPStr molgb);
void ajSeqSetUnique(AjPSeq seq);
float ajSeqCalcMolwt (const AjPSeq seq);
float ajSeqstrCalcMolwt (const AjPStr seq);
AjPSeq ajSeqNew (void);
AjPSeq ajSeqNewNameC(const char* txt, const char* name);
AjPSeq ajSeqNewNameS(const AjPStr str, const AjPStr name);
AjPSeq ajSeqNewRes (size_t size);
AjPSeq ajSeqNewSeq (const AjPSeq seq);
AjPSeq ajSeqNewRangeC(const char* txt,
ajint offset, ajint offend, AjBool rev);
AjPSeq ajSeqNewRangeS(const AjPStr str,
ajint offset, ajint offend, AjBool rev);
AjBool ajSeqConvertNum (const AjPSeq thys, const AjPSeqCvt cvt,
AjPStr *numseq);
AjBool ajSeqIsReversedTrue(const AjPSeq seq);
AjBool ajSeqIsReversed (const AjPSeq thys);
AjBool ajSeqIsSpeciesBsubtilis(const AjPSeq seq);
AjBool ajSeqIsSpeciesHuman(const AjPSeq seq);
AjBool ajSeqIsSpeciesMouse(const AjPSeq seq);
AjBool ajSeqIsSpeciesYeast(const AjPSeq seq);
AjBool ajSeqIsTaxon(const AjPSeq seq, ajuint taxid);
AjBool ajSeqIsTrimmed (const AjPSeq thys);
void ajSeqReverseDo (AjPSeq thys);
void ajSeqReverseForce (AjPSeq thys);
void ajSeqstrReverse (AjPStr* thys);
void ajSeqReverseOnly (AjPSeq thys);
ajuint ajSeqsetGetBegin (const AjPSeqset seq);
void ajSeqsetDel(AjPSeqset *thys);
void ajSeqsetDelarray(AjPSeqset **thys);
ajuint ajSeqsetGetEnd (const AjPSeqset seq);
ajint ajSeqsetFill (AjPSeqset seq);
const AjPStr ajSeqsetGetFormat (const AjPSeqset thys);
const char* ajSeqsetGetNameC (const AjPSeqset thys);
const AjPStr ajSeqsetGetNameS (const AjPSeqset thys);
ajint ajSeqsetGetOffend(const AjPSeqset seq);
ajint ajSeqsetGetOffset(const AjPSeqset seq);
ajint ajSeqsetGetRange (const AjPSeqset thys, ajint* begin, ajint* end);
const AjPSeq ajSeqsetGetseqSeq (const AjPSeqset thys, ajuint i);
const char* ajSeqsetGetseqSeqC (const AjPSeqset thys, ajuint i);
const AjPStr ajSeqsetGetseqSeqS (const AjPSeqset thys, ajuint i);
AjPSeq* ajSeqsetGetSeqarray(const AjPSeqset thys);
ajint ajSeqsetGetTotlength(const AjPSeqset seq);
const AjPStr ajSeqsetGetUsa (const AjPSeqset thys);
const AjPStr ajSeqsetGetFilename(const AjPSeqset thys);
AjBool ajSeqsetIsDna (const AjPSeqset thys);
AjBool ajSeqsetIsNuc (const AjPSeqset thys);
AjBool ajSeqsetIsProt (const AjPSeqset thys);
AjBool ajSeqsetIsRna (const AjPSeqset thys);
ajuint ajSeqsetGetLen (const AjPSeqset seq);
const char* ajSeqsetGetseqAccC (const AjPSeqset seq, ajuint i);
const AjPStr ajSeqsetGetseqAccS (const AjPSeqset seq, ajuint i);
const char* ajSeqsetGetseqNameC (const AjPSeqset seq, ajuint i);
const AjPStr ajSeqsetGetseqNameS (const AjPSeqset seq, ajuint i);
AjPSeqset ajSeqsetNew (void);
void ajSeqSetOffsets(AjPSeq seq, ajint ioff, ajint ioriglen);
void ajSeqSetRange (AjPSeq seq, ajint ibegin, ajint iend);
void ajSeqSetRangeRev (AjPSeq seq, ajint ibegin, ajint iend);
void ajSeqsetReverse (AjPSeqset thys);
void ajSeqsetSetRange (AjPSeqset seq, ajint ibegin, ajint iend);
ajuint ajSeqsetGetSize (const AjPSeqset seq);
void ajSeqsetFmtLower (AjPSeqset seq);
void ajSeqsetFmtUpper (AjPSeqset seq);
float ajSeqsetGetTotweight (const AjPSeqset seq);
void ajSeqsetSortLen(AjPSeqset seq);
void ajSeqsetTrim(AjPSeqset thys);
float ajSeqsetGetseqWeight (const AjPSeqset seq, ajuint i) ;
void ajSeqFmtLower (AjPSeq thys);
void ajSeqFmtUpper (AjPSeq thys);
void ajSeqTagRev(AjPSeq seq);
void ajSeqTrace (const AjPSeq seq);
void ajSeqTraceTitle (const AjPSeq seq, const char* title);
void ajSeqTrim(AjPSeq thys);
ajuint ajSeqGetBeginTrue (const AjPSeq seq);
ajuint ajSeqGetEndTrue (const AjPSeq seq);
ajuint ajSeqGetLenTrue (const AjPSeq seq);
ajint ajSeqCalcTruepos (const AjPSeq thys, ajint ipos);
ajint ajSeqCalcTrueposMin (const AjPSeq thys, ajint imin, ajint ipos);
/*
** End of prototype definitions
*/
/*
** These prototypes do not have any corresponding .c code so cannot
** go into the block above, otherwise the VC compilation will fail
*/
const char* ajSeqdivGetDdbj(const AjPStr divi);
AjBool ajSeqdivSetDdbj(AjPStr *Pdivi, const AjPStr divembl);
const char* ajSeqmolGetDdbj(const AjPStr mol);
AjBool ajSeqmolSetDdbj(AjPStr *mol, const AjPStr molddbj);
/* End of prototypes without C code */
__deprecated ajint ajSeqallBegin(const AjPSeqall seq);
__deprecated ajint ajSeqallEnd(const AjPSeqall seq);
__deprecated ajint ajSeqallGetRange(const AjPSeqall seq,
ajint* begin, ajint* end);
__deprecated void ajSeqsetToLower(AjPSeqset seqset);
__deprecated void ajSeqsetToUpper(AjPSeqset seqset);
__deprecated AjPSeq ajSeqNewC (const char* seq, const char* name);
__deprecated AjPSeq ajSeqNewStr (const AjPStr str);
__deprecated AjPSeq ajSeqNewRange(const AjPStr seq,
ajint offset, ajint offend,
AjBool rev);
__deprecated AjPSeq ajSeqNewRangeCI(const char* seq, ajint len,
ajint offset, ajint offend,
AjBool rev);
__deprecated AjPSeq ajSeqNewL (size_t size);
__deprecated AjPSeq ajSeqNewS (const AjPSeq seq);
__deprecated void ajSeqAssAcc (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssAccC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssDesc (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssDescC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssEntry (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssEntryC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssFile (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssFileC(AjPSeq thys, const char* text);
__deprecated void ajSeqAssFull (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssFullC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssGi (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssGiC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssName (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssNameC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssSeq(AjPSeq seq, const AjPStr str);
__deprecated void ajSeqAssSeqC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssSeqCI (AjPSeq thys, const char* text,
ajint ilen);
__deprecated void ajSeqAssSvC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssSv (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssUfo (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssUfoC (AjPSeq thys, const char* text);
__deprecated void ajSeqAssUsa (AjPSeq thys, const AjPStr str);
__deprecated void ajSeqAssUsaC (AjPSeq thys, const char* text);
__deprecated void ajSeqSetRangeDir (AjPSeq seq,
ajint ibegin, ajint iend,
AjBool rev);
__deprecated void ajSeqReplace (AjPSeq thys, const AjPStr seq);
__deprecated void ajSeqReplaceC (AjPSeq thys, const char* seq);
__deprecated void ajSeqMakeUsa (AjPSeq thys, const AjPSeqin seqin);
__deprecated void ajSeqMakeUsaS(const AjPSeq thys,
const AjPSeqin seqin, AjPStr* usa);
__deprecated void ajSeqCompOnly (AjPSeq thys);
__deprecated void ajSeqToLower (AjPSeq thys);
__deprecated void ajSeqToUpper (AjPSeq thys);
__deprecated void ajSeqRevOnly (AjPSeq thys);
__deprecated AjBool ajSeqReverse (AjPSeq thys);
__deprecated const AjPStr ajSeqGetAcc (const AjPSeq thys);
__deprecated ajint ajSeqBegin (const AjPSeq seq);
__deprecated ajint ajSeqTrueBegin (const AjPSeq seq);
__deprecated const AjPStr ajSeqGetDesc (const AjPSeq thys);
__deprecated ajint ajSeqEnd (const AjPSeq seq);
__deprecated ajint ajSeqTrueEnd (const AjPSeq seq);
__deprecated const AjPStr ajSeqGetEntry (const AjPSeq thys);
__deprecated AjPFeattable ajSeqCopyFeat (const AjPSeq thys);
__deprecated const AjPStr ajSeqGetGi (const AjPSeq thys);
__deprecated ajint ajSeqLen (const AjPSeq seq);
__deprecated ajint ajSeqTrueLen (const AjPSeq seq);
__deprecated const char* ajSeqName (const AjPSeq seq);
__deprecated const AjPStr ajSeqGetName (const AjPSeq thys);
__deprecated ajint ajSeqOffend (const AjPSeq seq);
__deprecated ajint ajSeqOffset (const AjPSeq seq);
__deprecated AjBool ajSeqGetReverse (const AjPSeq thys);
__deprecated AjBool ajSeqGetReversed (const AjPSeq thys);
__deprecated const AjPStr ajSeqStr (const AjPSeq thys);
__deprecated const char* ajSeqChar (const AjPSeq thys);
__deprecated AjPStr ajSeqStrCopy (const AjPSeq thys);
__deprecated char* ajSeqCharCopy (const AjPSeq seq);
__deprecated char* ajSeqCharCopyL (const AjPSeq seq, size_t size);
__deprecated const AjPStr ajSeqGetSv (const AjPSeq thys);
__deprecated const AjPStr ajSeqGetTax (const AjPSeq thys);
__deprecated const AjPStr ajSeqGetUsa (const AjPSeq thys);
__deprecated AjBool ajSeqRev (const AjPSeq thys);
__deprecated ajint ajSeqCheckGcg (const AjPSeq thys);
__deprecated void ajSeqCount (const AjPSeq thys, ajint *b);
__deprecated ajint ajSeqPos (const AjPSeq thys, ajint ipos);
__deprecated ajint ajSeqPosI (const AjPSeq thys,
ajint imin, ajint ipos);
__deprecated ajint ajSeqPosII (ajint ilen, ajint imin, ajint ipos);
__deprecated ajint ajSeqTruePos (const AjPSeq thys, ajint ipos);
__deprecated ajint ajSeqTruePosI (const AjPSeq thys, ajint imin,
ajint ipos);
__deprecated ajint ajSeqTruePosII (ajint ilen, ajint imin, ajint ipos);
__deprecated void ajSeqallReverse (AjPSeqall thys);
__deprecated void ajSeqallToLower (AjPSeqall seqall);
__deprecated void ajSeqallToUpper (AjPSeqall seqall);
__deprecated void ajSeqReverseStr (AjPStr* thys);
__deprecated void ajSeqCompOnlyStr (AjPStr* thys);
__deprecated float ajSeqMW (const AjPStr seq);
__deprecated ajuint ajSeqCrc(const AjPStr seq );
__deprecated void ajSeqCvtDel (AjPSeqCvt* thys);
__deprecated ajint ajSeqCvtK (const AjPSeqCvt thys, char ch);
__deprecated ajint ajSeqCvtKS (const AjPSeqCvt thys, const AjPStr ch);
__deprecated ajint ajSeqCvtKSRow (const AjPSeqCvt thys,
const AjPStr ch);
__deprecated ajint ajSeqCvtKSColumn (const AjPSeqCvt thys,
const AjPStr ch);
__deprecated ajint ajSeqCvtLen (const AjPSeqCvt thys);
__deprecated AjPSeqCvt ajSeqCvtNew (const char* bases);
__deprecated AjPSeqCvt ajSeqCvtNewText (const char* bases);
__deprecated AjPSeqCvt ajSeqCvtNewZero (const char* bases);
__deprecated AjPSeqCvt ajSeqCvtNewZeroS (const AjPPStr bases, ajint n);
__deprecated AjPSeqCvt ajSeqCvtNewZeroSS (const AjPPStr bases, ajint n,
const AjPPStr rbases, ajint rn);
__deprecated void ajSeqCvtTrace (const AjPSeqCvt cvt);
__deprecated AjBool ajIsAccession (const AjPStr accnum);
__deprecated const AjPStr ajIsSeqversion (const AjPStr sv);
__deprecated ajint ajSeqallLen (const AjPSeqall seqall);
__deprecated const AjPStr ajSeqallGetNameSeq (const AjPSeqall thys);
__deprecated void ajSeqComplementOnly(AjPSeq pthis);
__deprecated void ajSeqstrComplementOnly (AjPStr* thys);
__deprecated ajuint ajSeqCalcCrc(const AjPSeq seq );
__deprecated void ajSeqDefName(AjPSeq thys, const AjPStr setname,
AjBool multi);
__deprecated ajint ajSeqFill (AjPSeq seq, ajint len);
__deprecated ajint ajSeqGapCount (const AjPSeq thys);
__deprecated ajint ajSeqGapCountS (const AjPStr str);
__deprecated void ajSeqGapStandardS(AjPStr thys, char gapch);
__deprecated void ajSeqMod (AjPSeq thys);
__deprecated AjBool ajSeqNum (const AjPSeq thys, const AjPSeqCvt cvt,
AjPStr *numseq);
__deprecated AjBool ajSeqNumS (const AjPStr thys, const AjPSeqCvt cvt,
AjPStr *numseq);
__deprecated ajint ajSeqsetBegin (const AjPSeqset seq);
__deprecated ajint ajSeqsetEnd (const AjPSeqset seq);
__deprecated const AjPStr ajSeqsetGetName (const AjPSeqset thys);
__deprecated const AjPSeq ajSeqsetGetSeq (const AjPSeqset thys, ajint i);
__deprecated AjPSeq* ajSeqsetGetSeqArray(const AjPSeqset thys);
__deprecated ajint ajSeqsetLen (const AjPSeqset seq);
__deprecated const AjPStr ajSeqsetName (const AjPSeqset seq, ajint i);
__deprecated const AjPStr ajSeqsetAcc (const AjPSeqset seq, ajint i);
__deprecated const char* ajSeqsetSeq (const AjPSeqset seq, ajint i);
__deprecated ajint ajSeqsetSize (const AjPSeqset seq);
__deprecated float ajSeqsetTotweight (const AjPSeqset seq);
__deprecated float ajSeqsetWeight (const AjPSeqset seq, ajint i) ;
__deprecated void ajSeqTraceT (const AjPSeq seq, const char* title);
#endif
#ifdef __cplusplus
}
#endif
|