/usr/lib/emboss/include/ajfeat.h is in emboss-lib 6.6.0+dfsg-6build1.
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 | /* @include ajfeat ************************************************************
**
** A genome feature (in AJAX program context) is a description of a
** genomic entity which was determined by some 'source' analysis
** (which may be of 'wet lab' experimental or 'in silico'
** computational nature), has a 'primary' descriptor ('Primary_Tag'),
** may have some 'score' asserting the level of analysis confidence in
** its identity (e.g. log likelihood relative to a null hypothesis or
** other similar entity), has a 'Position' in the genome, and may have
** any arbitrary number of descriptor tags associated with it.
**
** @author Copyright (C) 1999 Richard Bruskiewich
** @version $Revision: 1.80 $
** @modified 2000 Ian Longden.
** @modified 2001 Peter Rice.
** @modified $Date: 2013/06/29 22:31:59 $ by $Author: rice $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library 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
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
******************************************************************************/
#ifndef AJFEAT_H
#define AJFEAT_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajexcept.h"
#include "ajmem.h"
#include "ajreg.h"
#include "ajstr.h"
#include "ajtagval.h"
#include "ajfile.h"
#include "ajtime.h"
#include "ajfmt.h"
#include "ajfeatdata.h"
#include "ajseqdata.h"
#include <stdlib.h>
#include <stdio.h>
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
ajint ajFeatCompByEnd(const void *a, const void *b);
ajint ajFeatCompByGroup(const void *a, const void *b);
ajint ajFeatCompByStart(const void *a, const void *b);
ajint ajFeatCompByType(const void *a, const void *b);
const AjPTable ajFeatVocabGetTags(const char* name);
const AjPTable ajFeatVocabGetTagsNuc(const char* name);
const AjPTable ajFeatVocabGetTagsProt(const char* name);
const AjPTable ajFeatVocabGetTypes(const char* name);
const AjPTable ajFeatVocabGetTypesNuc(const char* name);
const AjPTable ajFeatVocabGetTypesProt(const char* name);
const AjPTable ajFeatVocabInit(const char* name);
const AjPTable ajFeatVocabInitNuc(const char* name);
const AjPTable ajFeatVocabInitProt(const char* name);
AjPFeature ajFeatNewFeat(const AjPFeature orig);
void ajFeatDel(AjPFeature *pthis);
void ajFeatExit(void);
ajuint ajFeatGetEnd(const AjPFeature thys);
char ajFeatframeGetFrame(ajint frame);
char ajFeatframeGetFrameNuc(ajint frame);
char ajFeatstrandGetStrand(ajint strand);
AjBool ajFeatGetForward(const AjPFeature thys);
ajint ajFeatGetFrame(const AjPFeature thys);
ajuint ajFeatGetLength(const AjPFeature thys);
AjBool ajFeatGetNoteC(const AjPFeature thys, const char* name,
AjPStr* val);
AjBool ajFeatGetNoteCI(const AjPFeature thys, const char* name,
ajint count, AjPStr* val);
AjBool ajFeatGetNoteSI(const AjPFeature thys, const AjPStr name,
ajint count, AjPStr* val);
AjBool ajFeatGetNoteS(const AjPFeature thys, const AjPStr name,
AjPStr* val);
AjBool ajFeatGetRemoteseq(const AjPFeature thys, const AjPStr usa,
AjPSeq seq);
float ajFeatGetScore(const AjPFeature thys);
AjBool ajFeatGetScorerange(const AjPFeature thys,
float *minscore, float *maxscore);
const AjPStr ajFeatGetSubtype(const AjPFeature thys);
const AjPStr ajFeatGetSource(const AjPFeature thys);
AjBool ajFeatGetFlags(const AjPFeature thys, AjPStr* Pflagstr);
AjBool ajFeatGetSeq(const AjPFeature feat,
const AjPSeq seq, AjPStr* seqstr);
AjBool ajFeatGetSeqJoin(const AjPFeature thys,
const AjPSeq seq, AjPStr* Pseqstr);
ajuint ajFeatGetStart(const AjPFeature thys);
char ajFeatGetStrand(const AjPFeature thys);
AjBool ajFeatGetTagC(const AjPFeature thys, const char* tname,
ajint num, AjPStr* val);
AjBool ajFeatGetTagS(const AjPFeature thys, const AjPStr name,
ajint num, AjPStr* val);
AjBool ajFeatGetTranslation(const AjPFeature feat, AjPStr* seqstr);
const AjPStr ajFeatGetType(const AjPFeature thys);
AjBool ajFeatGetXrefs(const AjPFeature thys, AjPList *Pxreflist);
AjBool ajFeatIsCompMult(const AjPFeature gf);
AjBool ajFeatIsLocal(const AjPFeature gf);
AjBool ajFeatIsLocalRange(const AjPFeature gf,
ajuint start, ajuint end);
AjBool ajFeatIsMultiple(const AjPFeature gf);
AjBool ajFeatLocMark(const AjPFeature thys, const AjPFeattable table,
AjPStr* Pseqstr);
AjPFeature ajFeatNew(AjPFeattable thys,
const AjPStr source, const AjPStr type,
ajint Start, ajint End, float score,
char strand, ajint frame);
AjPFeature ajFeatNewII(AjPFeattable thys,
ajint Start, ajint End);
AjPFeature ajFeatNewIIRev(AjPFeattable thys,
ajint Start, ajint End);
AjPFeature ajFeatNewBetween(AjPFeattable thys,
ajint Start);
AjPFeature ajFeatNewNuc(AjPFeattable thys,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score, char strand,
ajint frame, ajint exon,
ajint Start2, ajint End2,
const AjPStr entryid, const AjPStr label);
AjPFeature ajFeatNewNucFlags(AjPFeattable thys,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score, char strand,
ajint frame, ajint exon,
ajint Start2, ajint End2,
const AjPStr entryid, const AjPStr label,
ajuint flags);
AjPFeature ajFeatNewProt(AjPFeattable thys,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score);
AjPFeature ajFeatNewProtFlags(AjPFeattable thys,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score,
ajuint flags);
AjPFeature ajFeatNewSub(AjPFeattable thys, AjPFeature parent,
const AjPStr source, const AjPStr type,
ajint Start, ajint End, float score,
char strand, ajint frame);
AjPFeature ajFeatNewIISub(AjPFeattable thys, AjPFeature parent,
ajint Start, ajint End);
AjPFeature ajFeatNewIIRevSub(AjPFeattable thys, AjPFeature parent,
ajint Start, ajint End);
AjPFeature ajFeatNewNucSub(AjPFeattable thys, AjPFeature parent,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score, char strand,
ajint frame, ajint exon,
ajint Start2, ajint End2,
const AjPStr entryid, const AjPStr label);
AjPFeature ajFeatNewNucFlagsSub(AjPFeattable thys, AjPFeature parent,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score, char strand,
ajint frame, ajint exon,
ajint Start2, ajint End2,
const AjPStr entryid, const AjPStr label,
ajuint flags);
AjPFeature ajFeatNewProtSub(AjPFeattable thys, AjPFeature parent,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score);
AjPFeature ajFeatNewProtFlagsSub(AjPFeattable thys, AjPFeature parent,
const AjPStr source, const AjPStr type,
ajint Start, ajint End,
float score,
ajuint flags);
void ajFeatReverse(AjPFeature thys, ajint ilen);
void ajFeatSetDesc(AjPFeature thys, const AjPStr desc);
void ajFeatSetDescApp(AjPFeature thys, const AjPStr desc);
void ajFeatSetScore(AjPFeature thys, float score);
void ajFeatSetSource(AjPFeature thys, const AjPStr source);
void ajFeatSetStrand(AjPFeature thys, AjBool rev);
void ajFeatSortByEnd(AjPFeattable Feattab);
void ajFeatSortByStart(AjPFeattable Feattab);
void ajFeatSortByType(AjPFeattable Feattab);
void ajFeattableAdd(AjPFeattable thys, AjPFeature feature);
void ajFeattableAddNew(AjPFeattable thys, AjPFeature feature);
void ajFeattableClear(AjPFeattable thys);
void ajFeattableDel(AjPFeattable *pthis);
ajint ajFeattableGetBegin(const AjPFeattable thys);
ajint ajFeattableGetEnd(const AjPFeattable thys);
const AjPStr ajFeattableGetEntry(const AjPFeattable thys);
ajint ajFeattableGetLen(const AjPFeattable thys);
const AjPStr ajFeattableGetName(const AjPFeattable thys);
const char* ajFeattableGetQryC(const AjPFeattable ftable);
const AjPStr ajFeattableGetQryS(const AjPFeattable ftable);
AjBool ajFeattableGetScorerange(const AjPFeattable thys,
float *minscore, float *maxscore);
ajuint ajFeattableGetSize(const AjPFeattable thys);
const char* ajFeattableGetTypeC(const AjPFeattable thys);
const AjPStr ajFeattableGetTypeS(const AjPFeattable thys);
AjBool ajFeattableGetXrefs(const AjPFeattable thys, AjPList *Pxreflist,
ajuint *Ptaxid);
AjBool ajFeattableIsCircular(const AjPFeattable thys);
AjBool ajFeattableIsNuc(const AjPFeattable thys);
AjBool ajFeattableIsProt(const AjPFeattable thys);
ajuint ajFeattableMerge(AjPFeattable thys, const AjPFeattable srctable);
AjPFeattable ajFeattableNew(const AjPStr name);
AjPFeattable ajFeattableNewDna(const AjPStr name);
AjPFeattable ajFeattableNewFtable(const AjPFeattable orig);
AjPFeattable ajFeattableNewFtableLimit(const AjPFeattable orig, ajint limit);
AjPFeattable ajFeattableNewProt(const AjPStr name);
AjPFeattable ajFeattableNewSeq(const AjPSeq seq);
ajuint ajFeattablePos(const AjPFeattable thys, ajint ipos);
ajuint ajFeattablePosI(const AjPFeattable thys,
ajuint imin, ajint ipos);
ajuint ajFeattablePosII(ajuint ilen, ajuint imin, ajint ipos);
void ajFeattableReset(AjPFeattable thys, const AjPStr name);
void ajFeattableReverse(AjPFeattable thys);
void ajFeattableSetCircular(AjPFeattable thys);
void ajFeattableSetDefname(AjPFeattable thys, const AjPStr setname);
void ajFeattableSetLength(AjPFeattable thys, ajuint len);
void ajFeattableSetLinear(AjPFeattable thys);
void ajFeattableSetNuc(AjPFeattable thys);
void ajFeattableSetProt(AjPFeattable thys);
void ajFeattableSetRange(AjPFeattable thys,
ajint fbegin, ajint fend);
void ajFeattableSetReverse(AjPFeattable thys);
void ajFeattableTrace(const AjPFeattable thys);
AjBool ajFeattableTrim(AjPFeattable thys);
AjBool ajFeattableTrimOff(AjPFeattable thys,
ajuint ioffset, ajuint ilen);
AjPFeatGfftags ajFeatGfftagsNew(void);
void ajFeatGfftagsDel(AjPFeatGfftags*Pthys);
AjPFeatGfftags ajFeatGetGfftags(const AjPFeature thys);
void ajFeatGfftagTrace(const AjPFeature thys);
const AjPStr ajFeatGetId(const AjPFeature thys);
const AjPStr ajFeatGetParent(const AjPFeature thys);
ajuint ajFeatGfftagAddSS(AjPFeature thys,
const AjPStr tag, const AjPStr value);
ajuint ajFeatGfftagAddCS(AjPFeature thys,
const char* tag, const AjPStr value);
AjBool ajFeatGfftagAddTag(AjPFeature thys, const AjPTagval tagval);
AjBool ajFeatTagAddSS(AjPFeature thys,
const AjPStr tag, const AjPStr value);
AjBool ajFeatTagAddCS(AjPFeature thys,
const char* tag, const AjPStr value);
AjBool ajFeatTagAddCC(AjPFeature thys,
const char* tag, const char* value);
AjBool ajFeatTagAddTag(AjPFeature thys, const AjPTagval tagval);
AjIList ajFeatSubIter(const AjPFeature thys);
AjIList ajFeatTagIter(const AjPFeature thys);
AjBool ajFeatTagSet(AjPFeature thys,
const AjPStr tag, const AjPStr value);
AjBool ajFeatTagSetC(AjPFeature thys,
const char* tag, const AjPStr value);
void ajFeatTagTrace(const AjPFeature thys);
AjBool ajFeatTagval(AjIList iter, AjPStr* tagnam,
AjPStr* tagval);
void ajFeatTest(void);
void ajFeatTrace(const AjPFeature thys);
AjBool ajFeatTrimOffRange(AjPFeature ft, ajuint ioffset,
ajuint begin, ajuint end,
AjBool dobegin, AjBool doend);
const AjPStr ajFeatTypeGetCategory(const AjPStr type);
AjBool ajFeatTypeIsCds(const AjPFeature gf);
AjBool ajFeatTypeMatchC(const AjPFeature gf, const char* txt);
AjBool ajFeatTypeMatchS(const AjPFeature gf, const AjPStr str);
AjBool ajFeatTypeMatchWildS(const AjPFeature gf, const AjPStr str);
const AjPStr ajFeatTypeNuc(const AjPStr type);
const AjPStr ajFeatTypeProt(const AjPStr type);
AjBool ajFeattagIsNote(const AjPStr tag);
void ajFeatUnused(void);
void ajFeatWarn(const char* fmt, ...);
const AjPStr ajFeattypeGetExternal(const AjPStr type, const AjPTable table);
const AjPStr ajFeattypeGetInternal(const AjPStr type);
const AjPStr ajFeattypeGetInternalEmbl(const AjPStr type);
const AjPStr ajFeattypeGetInternalNuc(const AjPStr type);
const AjPStr ajFeattypeGetInternalPir(const AjPStr type);
const AjPStr ajFeattypeGetInternalProt(const AjPStr type);
const AjPStr ajFeattypeGetInternalRefseqp(const AjPStr type);
AjBool ajFeattagSpecial(const AjPStr tag, AjPStr* pval);
AjBool ajFeattagSpecialGff2(const AjPStr tag, AjPStr* pval);
AjBool ajFeattagSpecialGff3(const AjPStr tag, AjPStr* pval);
void ajFeattagFormat(const AjPStr name, const AjPTable table,
AjPStr* retstr);
const AjPStr ajFeattagGetNameC(const char *tag, const AjPTable table,
AjBool* known);
const AjPStr ajFeattagGetNameS(const AjPStr name, const AjPTable table,
AjBool* known);
void ajFeattagGetLimit(const AjPStr name, const AjPTable table,
AjPStr* retstr);
/*
** End of prototype definitions
*/
/*
//#define MAJFEATOBJVERIFY(p,c) ajFeatObjAssert((p), (c), \
// __FILE__, __LINE__)
//#define MAJFEATSETSCORE(p,s) (((AjPFeature)(p))->Score=(s))
//#define MAJFEATSCORE(p) ((p)->Score)
//#define MAJFEATSOURCE(p) ((p)->Source)
//#define MAJFEATTYPE(p) ((p)->Type)
//#define MAJFEATTABSETVERSION(p,v) ((p)->Version=(v))
//#define MAJFEATTABSETDATE(p,d) ((p)->Date=(d))
//#define MAJFEATTABDEFFORMAT(p,f) ((p)->DefFormat=(f))
//#define MAJFEATTABFORMAT(p) ((p)->Format)
//#define MAJFEATTABVERSION(p) ((p)->Version)
//#define MAJFEATTABDATE(p) ((p)->Date)
//#define MAJFEATTABDICTIONARY(p) ((p)->Dictionary)
//#define MAJFEATVOCABREADONLY(p,f) ((p)?(p)->ReadOnly=(f):AjTrue)
*/
#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */
#ifdef AJ_COMPILE_DEPRECATED
__deprecated AjBool ajFeatGetNoteI(const AjPFeature thys,
const AjPStr name,
ajint count, AjPStr* val);
__deprecated AjPFeature ajFeatCopy(const AjPFeature orig);
__deprecated AjPFeattable ajFeattableCopy(const AjPFeattable orig);
__deprecated AjPFeattable ajFeattableCopyLimit(const AjPFeattable orig,
ajint limit);
__deprecated AjPFeattable ajFeatUfoRead(AjPFeattabIn tabin, const AjPStr Ufo);
__deprecated AjPFeattable ajFeatRead(AjPFeattabIn ftin);
__deprecated ajint ajFeattableBegin(const AjPFeattable thys);
__deprecated ajint ajFeattableEnd(const AjPFeattable thys);
__deprecated ajint ajFeattableLen(const AjPFeattable thys);
__deprecated ajint ajFeattableSize(const AjPFeattable thys);
__deprecated void ajFeatDefName(AjPFeattable thys,
const AjPStr setname);
__deprecated AjBool ajFeatGetNote(const AjPFeature thys,
const AjPStr name, AjPStr* val);
__deprecated ajuint ajFeatGfftagAdd(AjPFeature thys,
const AjPStr tag,
const AjPStr value);
__deprecated ajuint ajFeatGfftagAddC(AjPFeature thys,
const char* tag,
const AjPStr value);
__deprecated AjBool ajFeatTagAdd(AjPFeature thys,
const AjPStr tag, const AjPStr value);
__deprecated AjBool ajFeatTagAddC(AjPFeature thys,
const char* tag, const AjPStr value);
__deprecated AjBool ajFeatIsChild(const AjPFeature gf);
#endif /* AJ_COMPILE_DEPRECATED */
AJ_END_DECLS
#endif /* AJFEAT_H */
|