/usr/lib/emboss/include/ajcod.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.
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extern "C"
{
#endif
#ifndef ajcod_h
#define ajcod_h
/* @data AjPCod ***************************************************************
**
** Ajax codon object.
**
** Holds arrays describing codon usage
** The length is known and held internally.
**
** AjPCod is implemented as a pointer to a C data structure.
**
** @alias AjSCod
** @alias AjOCod
**
** @attr Name [AjPStr] Name of codon file
** @attr Species [AjPStr] Species
** @attr Division [AjPStr] Division (gbbct etc.)
** @attr Release [AjPStr] Database name and release
** @attr Desc [AjPStr] Description
** @attr CdsCount [ajint] Number of coding sequences used
** @attr CodonCount [ajint] Number of individual codons used
** @attr aa [ajint*] Amino acid represented by codon
** @attr num [ajint*] Number of codons
** @attr tcount [double*] Codons per thousand
** @attr fraction [double*] Fraction of amino acids of this type
** @attr back [ajint*] Index of favoured amino acid for back translation
** @attr GeneticCode [ajint] Genetic code NCBI number to match
** amino acids to codons.
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/
typedef struct AjSCod
{
AjPStr Name;
AjPStr Species;
AjPStr Division;
AjPStr Release;
AjPStr Desc;
ajint CdsCount;
ajint CodonCount;
ajint *aa;
ajint *num;
double *tcount;
double *fraction;
ajint *back;
ajint GeneticCode;
char Padding[4];
} AjOCod;
#define AjPCod AjOCod*
/*
** Prototype definitions
*/
void ajCodSetCodenum(AjPCod thys, ajint geneticcode);
void ajCodSetDescC(AjPCod thys, const char* desc);
void ajCodSetDescS(AjPCod thys, const AjPStr desc);
void ajCodSetDivisionC(AjPCod thys, const char* division);
void ajCodSetDivisionS(AjPCod thys, const AjPStr division);
void ajCodSetNameC(AjPCod thys, const char* name);
void ajCodSetNameS(AjPCod thys, const AjPStr name);
void ajCodSetNumcds(AjPCod thys, ajint numcds);
void ajCodSetNumcodons(AjPCod thys, ajint numcodon);
void ajCodSetReleaseC(AjPCod thys, const char* release);
void ajCodSetReleaseS(AjPCod thys, const AjPStr release);
void ajCodSetSpeciesC(AjPCod thys, const char* species);
void ajCodSetSpeciesS(AjPCod thys, const AjPStr species);
void ajCodBacktranslate(AjPStr *b, const AjPStr a, const AjPCod thys);
void ajCodBacktranslateAmbig(AjPStr *b, const AjPStr a,
const AjPCod thys);
ajint ajCodBase(ajint c);
double ajCodCalcCaiCod(const AjPCod thys);
double ajCodCalcCaiSeq(const AjPCod cod, const AjPStr str);
void ajCodCalcGribskov(AjPCod thys, const AjPStr s);
double ajCodCalcNc(const AjPCod thys);
void ajCodCalcUsage(AjPCod thys, ajint c);
void ajCodClear(AjPCod thys);
void ajCodClearData(AjPCod thys);
void ajCodComp(ajint *NA, ajint *NC, ajint *NG, ajint *NT,
const char *str);
void ajCodSetTripletsS(AjPCod thys, const AjPStr s, ajint *c);
void ajCodDel (AjPCod *thys);
ajint ajCodGetCode(const AjPCod thys);
const AjPStr ajCodGetDesc(const AjPCod thys);
const char* ajCodGetDescC(const AjPCod thys);
const AjPStr ajCodGetDivision(const AjPCod thys);
const char* ajCodGetDivisionC(const AjPCod thys);
void ajCodExit(void);
void ajCodGetCodonlist(const AjPCod cod, AjPList list);
const AjPStr ajCodGetName(const AjPCod thys);
const char* ajCodGetNameC(const AjPCod thys);
ajint ajCodGetNumcds(const AjPCod thys);
ajint ajCodGetNumcodon(const AjPCod thys);
const AjPStr ajCodGetRelease(const AjPCod thys);
const char* ajCodGetReleaseC(const AjPCod thys);
const AjPStr ajCodGetSpecies(const AjPCod thys);
const char* ajCodGetSpeciesC(const AjPCod thys);
ajint ajCodIndex(const AjPStr s);
ajint ajCodIndexC(const char *codon);
AjPCod ajCodNew(void);
AjPCod ajCodNewCodenum(ajint code);
AjPCod ajCodNewCod (const AjPCod thys);
AjBool ajCodRead(AjPCod thys, const AjPStr fn, const AjPStr format);
void ajCodSetBacktranslate(AjPCod thys);
char* ajCodTriplet(ajint idx);
void ajCodWrite(AjPCod thys, AjPFile outf);
void ajCodWriteOut( const AjPCod thys, AjPOutfile outf);
ajint ajCodOutFormat(const AjPStr name);
void ajCodPrintFormat(AjPFile outf, AjBool full);
/*
** End of prototype definitions
*/
__deprecated AjPCod ajCodDup (const AjPCod thys);
__deprecated AjPCod ajCodNewCode(ajint code);
__deprecated void ajCodAssCode(AjPCod thys, ajint geneticcode);
__deprecated void ajCodAssDesc(AjPCod thys, const AjPStr desc);
__deprecated void ajCodAssDescC(AjPCod thys, const char* desc);
__deprecated void ajCodAssDivision(AjPCod thys, const AjPStr division);
__deprecated void ajCodAssDivisionC(AjPCod thys, const char* division);
__deprecated void ajCodAssNumcds(AjPCod thys, ajint numcds);
__deprecated void ajCodAssNumcodon(AjPCod thys, ajint numcodon);
__deprecated void ajCodAssRelease(AjPCod thys, const AjPStr release);
__deprecated void ajCodAssReleaseC(AjPCod thys, const char* release);
__deprecated void ajCodAssSpecies(AjPCod thys, const AjPStr species);
__deprecated void ajCodAssSpeciesC(AjPCod thys, const char* species);
__deprecated void ajCodAssName(AjPCod thys, const AjPStr name);
__deprecated void ajCodAssNameC(AjPCod thys, const char* name);
__deprecated void ajCodCountTriplets(AjPCod thys,
const AjPStr s, ajint *c);
__deprecated double ajCodCalcCai(const AjPCod cod, const AjPStr str);
__deprecated void ajCodCalculateUsage(AjPCod thys, ajint c);
#endif
#ifdef __cplusplus
}
#endif
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