coissac
ebe8c0b516
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@5 60f365c0-8329-0410-b2a4-ec073aeeaa1d
173 lines
7.3 KiB
C
173 lines
7.3 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_Gtypes
|
|
#include "Gtypes.h"
|
|
#endif
|
|
|
|
#ifndef _H_libstki
|
|
#include "libstki.h"
|
|
#endif
|
|
|
|
#define H_apat
|
|
|
|
/* ----------------------------------------------- */
|
|
/* constantes */
|
|
/* ----------------------------------------------- */
|
|
|
|
#ifndef BUFSIZ
|
|
#define BUFSIZ 1024 /* io buffer size */
|
|
#endif
|
|
|
|
#define MAX_NAME_LEN BUFSIZ /* max length of sequence name */
|
|
|
|
#define ALPHA_LEN 26 /* 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 */
|
|
|
|
/* special chars in pattern */
|
|
#define PATCHARS "[]!#"
|
|
|
|
/* 26 letter alphabet */
|
|
/* in alphabetical order */
|
|
|
|
#define ORD_ALPHA "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
|
|
|
|
/* protein alphabet */
|
|
|
|
#define PROT_ALPHA "ACDEFGHIKLMNPQRSTVWY"
|
|
|
|
/* dna/rna alphabet */
|
|
|
|
#define DNA_ALPHA "ABCDGHKMNRSTUVWXY"
|
|
|
|
|
|
/* ----------------------------------------------- */
|
|
/* data structures */
|
|
/* ----------------------------------------------- */
|
|
|
|
/* -------------------- */
|
|
typedef enum { /* data encoding */
|
|
/* -------------------- */
|
|
alpha = 0, /* [A-Z] */
|
|
dna, /* IUPAC DNA */
|
|
protein /* IUPAC proteins */
|
|
} CodType;
|
|
|
|
/* -------------------- */
|
|
typedef struct { /* sequence */
|
|
/* -------------------- */
|
|
char *name; /* sequence name */
|
|
Int32 seqlen; /* sequence length */
|
|
Int32 seqsiz; /* sequence buffer size */
|
|
Int32 datsiz; /* data buffer size */
|
|
UInt8 *data; /* data buffer */
|
|
char *cseq; /* sequence buffer */
|
|
StackiPtr hitpos[MAX_PATTERN]; /* stack of hit pos. */
|
|
StackiPtr hiterr[MAX_PATTERN]; /* stack of errors */
|
|
} Seq, *SeqPtr;
|
|
|
|
/* -------------------- */
|
|
typedef struct { /* pattern */
|
|
/* -------------------- */
|
|
int patlen; /* pattern length */
|
|
int maxerr; /* max # of errors */
|
|
char *cpat; /* pattern string */
|
|
Int32 *patcode; /* encoded pattern */
|
|
UInt32 *smat; /* S matrix */
|
|
UInt32 omask; /* oblig. bits mask */
|
|
Bool hasIndel; /* are indels allowed */
|
|
Bool ok; /* is pattern ok */
|
|
} Pattern, *PatternPtr;
|
|
|
|
/* ----------------------------------------------- */
|
|
/* 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_seq.c */
|
|
|
|
SeqPtr FreeSequence (SeqPtr pseq);
|
|
SeqPtr NewSequence (void);
|
|
int ReadNextSequence (SeqPtr pseq);
|
|
int WriteSequence (FILE *filou , SeqPtr pseq);
|
|
|
|
/* apat_parse.c */
|
|
|
|
Int32 *GetCode (CodType ctype);
|
|
int CheckPattern (Pattern *ppat);
|
|
int EncodePattern (Pattern *ppat, CodType ctype);
|
|
int ReadPattern (Pattern *ppat);
|
|
void PrintDebugPattern (Pattern *ppat);
|
|
|
|
/* apat_search.c */
|
|
|
|
int CreateS (Pattern *ppat, Int32 lalpha);
|
|
Int32 ManberNoErr (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
|
|
Int32 ManberSub (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
|
|
Int32 ManberIndel (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
|
|
Int32 ManberAll (Seq *pseq , Pattern *ppat, int patnum,int begin,int length);
|
|
Int32 NwsPatAlign (Seq *pseq , Pattern *ppat, Int32 nerr ,
|
|
Int32 *reslen , Int32 *reserr);
|
|
|
|
/* apat_sys.c */
|
|
|
|
float UserCpuTime (int reset);
|
|
float SysCpuTime (int reset);
|
|
char *StrCpuTime (int reset);
|
|
void Erreur (char *msg , int stat);
|
|
int AccessFile (char *path, char *mode);
|
|
|