121 lines
4.5 KiB
C
121 lines
4.5 KiB
C
|
/* ==================================================== */
|
||
|
|
/* Copyright (c) Atelier de BioInformatique */
|
||
|
|
/* Dec. 94 */
|
||
|
|
/* File: apat.h */
|
||
|
|
/* Purpose: pattern scan */
|
||
|
|
/* History: */
|
||
|
|
/* 28/12/94 : <Gloup> ascan first version */
|
||
|
|
/* 14/05/99 : <Gloup> last revision */
|
||
|
|
/* ==================================================== */
|
||
|
|
|
||
|
|
|
||
|
|
#ifndef H_apat
|
||
|
|
#define H_apat
|
||
|
|
|
||
|
|
|
||
|
|
#include "libstki.h"
|
||
|
|
#include "inttypes.h"
|
||
|
|
#include "../libecoPCR/ecoPCR.h"
|
||
|
|
|
||
|
|
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
/* constantes */
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
|
||
|
|
#ifndef BUFSIZ
|
||
|
|
#define BUFSIZ 1024 /* io buffer size */
|
||
|
|
#endif
|
||
|
|
|
||
|
|
#define MAX_NAME_LEN BUFSIZ /* max length of sequence name */
|
||
|
|
|
||
|
|
#define ALPHA_LEN 4 /* alphabet length */
|
||
|
|
/* *DO NOT* modify */
|
||
|
|
|
||
|
|
#define MAX_PATTERN 4 /* max # of patterns */
|
||
|
|
/* *DO NOT* modify */
|
||
|
|
|
||
|
|
#define MAX_PAT_LEN 32 /* max pattern length */
|
||
|
|
/* *DO NOT* modify */
|
||
|
|
|
||
|
|
#define MAX_PAT_ERR 32 /* max # of errors */
|
||
|
|
/* *DO NOT* modify */
|
||
|
|
|
||
|
|
#define PATMASK 0x3ffffff /* mask for 26 symbols */
|
||
|
|
/* *DO NOT* modify */
|
||
|
|
|
||
|
|
#define OBLIBIT 0x4000000 /* bit 27 to 1 -> oblig. pos */
|
||
|
|
/* *DO NOT* modify */
|
||
|
|
|
||
|
|
/* mask for position */
|
||
|
|
#define ONEMASK 0x80000000 /* mask for highest position */
|
||
|
|
|
||
|
|
/* masks for Levenhstein edit */
|
||
|
|
#define OPER_IDT 0x00000000 /* identity */
|
||
|
|
#define OPER_INS 0x40000000 /* insertion */
|
||
|
|
#define OPER_DEL 0x80000000 /* deletion */
|
||
|
|
#define OPER_SUB 0xc0000000 /* substitution */
|
||
|
|
|
||
|
|
#define OPER_SHFT 30 /* <unused> shift */
|
||
|
|
|
||
|
|
/* Levenhstein Opcodes */
|
||
|
|
#define SOPER_IDT 0x0 /* identity */
|
||
|
|
#define SOPER_INS 0x1 /* insertion */
|
||
|
|
#define SOPER_DEL 0x2 /* deletion */
|
||
|
|
#define SOPER_SUB 0x3 /* substitution */
|
||
|
|
|
||
|
|
/* Levenhstein Opcodes masks */
|
||
|
|
#define OPERMASK 0xc0000000 /* mask for Opcodes */
|
||
|
|
#define NOPERMASK 0x3fffffff /* negate of previous */
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
/* data structures */
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
|
||
|
|
|
||
|
|
typedef uint32_t pattern_t[ALPHA_LEN], *ppattern_t;
|
||
|
|
|
||
|
|
/* -------------------- */
|
||
|
|
typedef struct { /* pattern */
|
||
|
|
/* -------------------- */
|
||
|
|
int patlen; /* pattern length */
|
||
|
|
int maxerr; /* max # of errors */
|
||
|
|
uint32_t omask; /* oblig. bits mask */
|
||
|
|
bool_t circular; /* is circular sequence */
|
||
|
|
} patternParam_t, *ppatternParam_t;
|
||
|
|
|
||
|
|
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
/* macros */
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
|
||
|
|
#ifndef NEW
|
||
|
|
#define NEW(typ) (typ*)malloc(sizeof(typ))
|
||
|
|
#define NEWN(typ, dim) (typ*)malloc((unsigned long)(dim) * sizeof(typ))
|
||
|
|
#define REALLOC(typ, ptr, dim) (typ*)realloc((void *) (ptr), (unsigned long)(dim) * sizeof(typ))
|
||
|
|
#define FREE(ptr) free((void *) ptr)
|
||
|
|
#endif
|
||
|
|
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
/* prototypes */
|
||
|
|
/* ----------------------------------------------- */
|
||
|
|
|
||
|
|
/* apat_search.c */
|
||
|
|
|
||
|
|
int32_t ManberNoErr(pecoseq_t pseq,ppattern_t pat,
|
||
|
|
ppatternParam_t param,
|
||
|
|
StackiPtr stkpos);
|
||
|
|
|
||
|
|
int32_t ManberSub(pecoseq_t pseq,ppattern_t pat,
|
||
|
|
ppatternParam_t param,
|
||
|
|
StackiPtr stkpos);
|
||
|
|
|
||
|
|
int32_t ManberAll(pecoseq_t pseq,ppattern_t pat,
|
||
|
|
ppatternParam_t param,
|
||
|
|
StackiPtr stkpos);
|
||
|
|
|
||
|
|
|
||
|
|
#endif /* H_apat */
|
||
|
|
|