/usr/lib/emboss/include/ajfeat.h is in emboss-lib 6.3.1-6ubuntu3.
This file is owned by root:root, with mode 0o644.
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extern "C"
{
#endif
/*
**
** ajfeat.h - AJAX Sequence Feature include file
** Version 2.0 - June 2001
**
*/
#ifndef ajfeat_h
#define ajfeat_h
#include <stdlib.h>
#include <stdio.h>
#include "ajdefine.h"
#include "ajexcept.h"
#include "ajmem.h"
#include "ajreg.h"
#include "ajstr.h"
#include "ajfile.h"
#include "ajtime.h"
#include "ajfmt.h"
#include "ajfeatdata.h"
#include "ajseqdata.h"
/* ========================================================================= */
/* ========== All functions in (more or less) alphabetical order =========== */
/* ========================================================================= */
/*
** Prototype definitions
*/
AjBool ajFeatIsChild (const AjPFeature gf);
AjPFeature ajFeatNewFeat (const AjPFeature orig);
void ajFeatDel(AjPFeature *pthis) ;
void ajFeatExit (void);
ajuint ajFeatGetEnd (const AjPFeature thys);
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);
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 AjPFeattable table,
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 ajFeatNewProt (AjPFeattable thys,
const AjPStr source, const AjPStr type,
ajint Start, ajint End, float score);
AjBool ajFeatOutFormatDefault (AjPStr* pformat);
void ajFeatPrintFormat(AjPFile outf, AjBool full);
void ajFeatPrintbookFormat(AjPFile outf);
void ajFeatoutPrintbookFormat(AjPFile outf);
void ajFeatPrintwikiFormat(AjPFile outf);
void ajFeatoutPrintwikiFormat(AjPFile outf);
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 ajFeatSetStrand (AjPFeature thys, AjBool rev);
void ajFeatSortByEnd (AjPFeattable Feattab);
void ajFeatSortByStart (AjPFeattable Feattab);
void ajFeatSortByType (AjPFeattable Feattab);
void ajFeattableAdd (AjPFeattable thys, AjPFeature feature) ;
void ajFeattableClear (AjPFeattable thys);
void ajFeattableDel (AjPFeattable *pthis) ;
ajint ajFeattableGetBegin (const AjPFeattable thys);
ajint ajFeattableGetEnd (const AjPFeattable thys);
ajint ajFeattableGetLen (const AjPFeattable thys);
const AjPStr ajFeattableGetName (const AjPFeattable thys);
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 ajFeattableIsNuc (const AjPFeattable thys);
AjBool ajFeattableIsProt (const AjPFeattable thys);
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 ajFeattableNewRead (AjPFeattabIn ftin);
AjPFeattable ajFeattableNewReadUfo (AjPFeattabIn tabin, const AjPStr Ufo);
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);
AjBool ajFeattableWriteDebug(AjPFeattabOut ftout,
const AjPFeattable ftable);
AjBool ajFeattablePrint(const AjPFeattable ftable,
AjPFile file);
void ajFeattableReverse (AjPFeattable thys) ;
void ajFeattableSetDefname(AjPFeattable thys, const AjPStr setname);
void ajFeattableSetLength(AjPFeattable thys, ajuint len);
void ajFeattableSetNuc (AjPFeattable thys);
void ajFeattableSetProt (AjPFeattable thys);
void ajFeattableSetRange (AjPFeattable thys,
ajint fbegin, ajint fend) ;
void ajFeattableTrace (const AjPFeattable thys);
AjBool ajFeattableTrim (AjPFeattable thys);
AjBool ajFeattableTrimOff (AjPFeattable thys,
ajuint ioffset, ajuint ilen);
AjBool ajFeattableWriteDasgff(AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteDdbj (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteEmbl (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteGenbank (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteRefseq (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteRefseqp (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteGff2 (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteGff3 (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWritePir (AjPFeattabOut ftout,
const AjPFeattable features);
AjBool ajFeattableWriteSwiss (AjPFeattabOut ftout,
const AjPFeattable features);
void ajFeattabInClear (AjPFeattabIn thys);
void ajFeattabInDel (AjPFeattabIn* pthis);
AjPFeattabIn ajFeattabInNew (void);
AjPFeattabIn ajFeattabInNewCSF (const char* fmt, const AjPStr name,
const char* type, AjPFilebuff buff);
AjPFeattabIn ajFeattabInNewSS (const AjPStr fmt, const AjPStr name,
const char* type);
AjPFeattabIn ajFeattabInNewSSF (const AjPStr fmt, const AjPStr name,
const char* type, AjPFilebuff buff);
AjBool ajFeattabInSetType(AjPFeattabIn thys, const AjPStr type);
AjBool ajFeattabInSetTypeC(AjPFeattabIn thys, const char* type);
void ajFeattabOutClear(AjPFeattabOut *thys);
void ajFeattabOutDel (AjPFeattabOut* pthis);
AjPFile ajFeattabOutFile (const AjPFeattabOut thys);
AjPStr ajFeattabOutFilename (const AjPFeattabOut thys);
AjBool ajFeattabOutIsLocal(const AjPFeattabOut thys);
AjBool ajFeattabOutIsOpen (const AjPFeattabOut thys);
AjPFeattabOut ajFeattabOutNew (void);
AjPFeattabOut ajFeattabOutNewCSF (const char* fmt, const AjPStr name,
const char* type, AjPFile buff);
AjPFeattabOut ajFeattabOutNewSSF (const AjPStr fmt, const AjPStr name,
const char* type, AjPFile buff);
AjBool ajFeattabOutOpen (AjPFeattabOut thys, const AjPStr ufo);
AjBool ajFeattabOutSet (AjPFeattabOut thys, const AjPStr ufo);
void ajFeattabOutSetBasename (AjPFeattabOut thys,
const AjPStr basename);
AjBool ajFeattabOutSetSeqname(AjPFeattabOut thys, const AjPStr name);
AjBool ajFeattabOutSetType(AjPFeattabOut thys, const AjPStr type);
AjBool ajFeattabOutSetTypeC(AjPFeattabOut thys, const char* type);
AjBool ajFeatTagAdd (AjPFeature thys,
const AjPStr tag, const AjPStr value);
AjBool ajFeatTagAddC (AjPFeature thys,
const char* tag, const AjPStr value);
AjBool ajFeatTagAddCC (AjPFeature thys,
const char* tag, const char* value);
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 ajFeattableWriteUfo (AjPFeattabOut ftout, const AjPFeattable ft,
const AjPStr Ufo);
AjBool ajFeattableWrite (AjPFeattabOut ftout, const AjPFeattable ft) ;
AjBool ajFeattagIsNote(const AjPStr tag);
void ajFeatUnused(void);
/*
** End of prototype definitions
*/
__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 AjBool ajFeatUfoWrite (const AjPFeattable thys,
AjPFeattabOut tabout,
const AjPStr Ufo);
__deprecated AjBool ajFeatWrite (AjPFeattabOut ftout,
const AjPFeattable ft) ;
__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);
/*
//#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)
*/
#endif /* ajfeat_h */
#ifdef __cplusplus
}
#endif
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