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esl_alphabet.h
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/
esl_alphabet.h
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/* Digital representation of biosequence symbols in Easel.
*/
#ifndef eslALPHABET_INCLUDED
#define eslALPHABET_INCLUDED
#include "esl_config.h"
#include <ctype.h> /* isascii() */
#include "easel.h"
#ifdef __cplusplus // magic to make C++ compilers happy
extern "C" {
#endif
/* Flags for alphabet types.
* Do not change, only add, because these codes are used in file formats.
*/
#define eslUNKNOWN 0 /* 0=unknown is easel-wide convention; don't change */
#define eslRNA 1
#define eslDNA 2
#define eslAMINO 3
#define eslCOINS 4 /* for toy examples */
#define eslDICE 5 /* also for toy examples */
#define eslNONSTANDARD 6
/* ... if you add here, change esl_abc_ValidateType() too. */
/* Structure: ESL_ALPHABET
*/
typedef struct {
int type; /* eslDNA, eslRNA, eslAMINO, eslNONSTANDARD, etc. */
int K; /* uniq alphabet size: 4 or 20 */
int Kp; /* total size: alphabet + degen + gap + missing */
char *sym; /* "ACGT-RYMKSWHBVDN*~", for instance [0..Kp-1] */
ESL_DSQ inmap[128]; /* inmap['A'] = 0, etc: dsq[] index for a symbol */
char **degen; /* 1/0, which syms inc which res [0..Kp-1][0..K-1] */
int *ndegen; /* # of degenerate residues per code [0..Kp-1] */
ESL_DSQ *complement; /* maps sym to complements, [0..Kp-1]; NULL if <type> not DNA/RNA */
} ESL_ALPHABET;
/* 1. An ESL_ALPHABET object.
*/
extern ESL_ALPHABET *esl_alphabet_Create(int type);
extern ESL_ALPHABET *esl_alphabet_CreateCustom(const char *alphabet, int K, int Kp);
extern int esl_alphabet_SetEquiv(ESL_ALPHABET *a, char sym, char c);
extern int esl_alphabet_SetCaseInsensitive(ESL_ALPHABET *a);
extern int esl_alphabet_SetDegeneracy(ESL_ALPHABET *a, char c, char *ds);
extern int esl_alphabet_SetIgnored(ESL_ALPHABET *a, const char *ignoredchars);
extern size_t esl_alphabet_Sizeof(ESL_ALPHABET *a);
extern void esl_alphabet_Destroy(ESL_ALPHABET *a);
/* 2. Digitized sequences.
*/
extern int esl_abc_CreateDsq(const ESL_ALPHABET *a, const char *seq, ESL_DSQ **ret_dsq);
extern int esl_abc_Digitize (const ESL_ALPHABET *a, const char *seq, ESL_DSQ *dsq);
extern int esl_abc_Textize (const ESL_ALPHABET *a, const ESL_DSQ *dsq, int64_t L, char *seq);
extern int esl_abc_TextizeN (const ESL_ALPHABET *a, const ESL_DSQ *dptr, int64_t L, char *buf);
extern int esl_abc_dsqcpy(const ESL_DSQ *dsq, int64_t L, ESL_DSQ *dcopy);
extern int esl_abc_dsqdup(const ESL_DSQ *dsq, int64_t L, ESL_DSQ **ret_dup);
extern int esl_abc_dsqcat (const ESL_DSQ *inmap, ESL_DSQ **dsq, int64_t *L, const char *s, esl_pos_t n);
extern int esl_abc_dsqcat_noalloc(const ESL_DSQ *inmap, ESL_DSQ *dsq, int64_t *L, const char *s, esl_pos_t n);
extern int64_t esl_abc_dsqlen(const ESL_DSQ *dsq);
extern int64_t esl_abc_dsqrlen(const ESL_ALPHABET *a, const ESL_DSQ *dsq);
extern int esl_abc_CDealign(const ESL_ALPHABET *abc, char *s, const ESL_DSQ *ref_ax, int64_t *opt_rlen);
extern int esl_abc_XDealign(const ESL_ALPHABET *abc, ESL_DSQ *x, const ESL_DSQ *ref_ax, int64_t *opt_rlen);
extern int esl_abc_ConvertDegen2X(const ESL_ALPHABET *abc, ESL_DSQ *dsq);
extern int esl_abc_revcomp(const ESL_ALPHABET *abc, ESL_DSQ *dsq, int n);
/* 3. Other routines in the API.
*/
extern int esl_abc_ValidateType(int type);
extern int esl_abc_GuessAlphabet(const int64_t *ct, int *ret_type);
extern double esl_abc_Match (const ESL_ALPHABET *a, ESL_DSQ x, ESL_DSQ y, double *p);
extern int esl_abc_IAvgScore (const ESL_ALPHABET *a, ESL_DSQ x, const int *sc);
extern float esl_abc_FAvgScore (const ESL_ALPHABET *a, ESL_DSQ x, const float *sc);
extern double esl_abc_DAvgScore (const ESL_ALPHABET *a, ESL_DSQ x, const double *sc);
extern int esl_abc_IExpectScore(const ESL_ALPHABET *a, ESL_DSQ x, const int *sc, const float *p);
extern float esl_abc_FExpectScore(const ESL_ALPHABET *a, ESL_DSQ x, const float *sc, const float *p);
extern double esl_abc_DExpectScore(const ESL_ALPHABET *a, ESL_DSQ x, const double *sc, const double *p);
extern int esl_abc_IAvgScVec (const ESL_ALPHABET *a, int *sc);
extern int esl_abc_FAvgScVec (const ESL_ALPHABET *a, float *sc);
extern int esl_abc_DAvgScVec (const ESL_ALPHABET *a, double *sc);
extern int esl_abc_IExpectScVec(const ESL_ALPHABET *a, int *sc, const float *p);
extern int esl_abc_FExpectScVec(const ESL_ALPHABET *a, float *sc, const float *p);
extern int esl_abc_DExpectScVec(const ESL_ALPHABET *a, double *sc, const double *p);
extern int esl_abc_FCount (const ESL_ALPHABET *a, float *ct, ESL_DSQ x, float wt);
extern int esl_abc_DCount (const ESL_ALPHABET *a, double *ct, ESL_DSQ x, double wt);
extern int esl_abc_EncodeType (char *typestring);
extern int esl_abc_EncodeTypeMem(char *type, int n);
extern char *esl_abc_DecodeType (int type);
extern int esl_abc_ValidateSeq(const ESL_ALPHABET *a, const char *seq, int64_t L, char *errbuf);
/* In the tests below, remember the rules of order in internal alphabets:
* Canonical alphabet Gap Degeneracies Any None Missing
* 0..K-1 K K+1..Kp-4 (Kp-3) (Kp-2) (Kp-1)
* ACGT - RYMKSWHBVD N * ~ DNA: K=4 Kp=18
* ACDEFGHIKLMNPQRSTVWY - BJZOU X * ~ protein: K=20 Kp=29
*
* ESL_DSQ is an unsigned 8-bit type, so don't test for >= 0 or compilers will complain.
*/
#define esl_abc_DigitizeSymbol(a, c) ((a)->inmap[(int)c])
#define esl_abc_XIsValid(a, x) ((x) < (a)->Kp)
#define esl_abc_XIsResidue(a, x) ((x) < (a)->K || ((x) > (a)->K && (x) < (a)->Kp-2))
#define esl_abc_XIsCanonical(a, x) ((x) < (a)->K)
#define esl_abc_XIsGap(a, x) ((x) == (a)->K)
#define esl_abc_XIsDegenerate(a, x) ((x) > (a)->K && (x) < (a)->Kp-2)
#define esl_abc_XIsUnknown(a, x) ((x) == (a)->Kp-3)
#define esl_abc_XIsNonresidue(a, x) ((x) == (a)->Kp-2)
#define esl_abc_XIsMissing(a, x) ((x) == (a)->Kp-1)
#define esl_abc_XGetGap(a) ((a)->K)
#define esl_abc_XGetUnknown(a) ((a)->Kp-3)
#define esl_abc_XGetNonresidue(a) ((a)->Kp-2)
#define esl_abc_XGetMissing(a) ((a)->Kp-1)
#define esl_abc_CIsValid(a, c) (isascii(c) && (a)->inmap[(int)c] < (a)->Kp)
#define esl_abc_CIsResidue(a, c) ((a)->inmap[(int)c] < (a)->K || ((a)->inmap[(int)c] > (a)->K && (a)->inmap[(int)c] < (a)->Kp-2))
#define esl_abc_CIsCanonical(a, c) ((a)->inmap[(int)c] < (a)->K)
#define esl_abc_CIsGap(a, c) ((a)->inmap[(int)c] == (a)->K)
#define esl_abc_CIsDegenerate(a, c) ((a)->inmap[(int)c] > (a)->K && (a)->inmap[(int)c] < (a)->Kp-2)
#define esl_abc_CIsUnknown(a, c) ((a)->inmap[(int)c] == (a)->Kp-3)
#define esl_abc_CIsNonresidue(a, c) ((a)->inmap[(int)c] == (a)->Kp-2)
#define esl_abc_CIsMissing(a, c) ((a)->inmap[(int)c] == (a)->Kp-1)
#define esl_abc_CGetGap(a) ((a)->sym[(a)->K])
#define esl_abc_CGetUnknown(a) ((a)->sym[(a)->Kp-3])
#define esl_abc_CGetNonresidue(a) ((a)->sym[(a)->Kp-2])
#define esl_abc_CGetMissing(a) ((a)->sym[(a)->Kp-1])
#ifdef __cplusplus // magic to make C++ compilers happy
}
#endif
#endif /*eslALPHABET_INCLUDED*/