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ADD libapat so that everything is included when fetching the project from svn

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@411 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Frédéric Boyer
2012-04-26 16:23:35 +00:00
parent aedee0c154
commit 4315aecbf0
11 changed files with 1708 additions and 0 deletions
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14
src/libapat/CODES/dft_code.h Normal file
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/* ----------------------------------------------- */
/* dft_pat_seq_code.h */
/* default alphabet encoding for alpha */
/* ----------------------------------------------- */
0x00000001 /* A */, 0x00000002 /* B */, 0x00000004 /* C */,
0x00000008 /* D */, 0x00000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000200 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002000 /* N */, 0x00004000 /* O */,
0x00008000 /* P */, 0x00010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00100000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x00800000 /* X */,
0x01000000 /* Y */, 0x02000000 /* Z */

71
src/libapat/CODES/dna_code.h Normal file
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/* ----------------------------------------------- */
/* dna_code.h */
/* alphabet encoding for dna/rna */
/* ----------------------------------------- */
/* IUPAC encoding */
/* ----------------------------------------- */
/* G/A/T/C */
/* U=T */
/* R=AG */
/* Y=CT */
/* M=AC */
/* K=GT */
/* S=CG */
/* W=AT */
/* H=ACT */
/* B=CGT */
/* V=ACG */
/* D=AGT */
/* N=ACGT */
/* X=ACGT */
/* EFIJLOPQZ not recognized */
/* ----------------------------------------- */
/* dual encoding */
/* ----------------------------------------- */
/* A=ADHMNRVW */
/* B=BCDGHKMNRSTUVWY */
/* C=BCHMNSVY */
/* D=ABDGHKMNRSTUVWY */
/* G=BDGKNRSV */
/* H=ABCDHKMNRSTUVWY */
/* K=BDGHKNRSTUVWY */
/* M=ABCDHMNRSVWY */
/* N=ABCDGHKMNRSTUVWY */
/* R=ABDGHKMNRSVW */
/* S=BCDGHKMNRSVY */
/* T=BDHKNTUWY */
/* U=BDHKNTUWY */
/* V=ABCDGHKMNRSVWY */
/* W=ABDHKMNRTUVWY */
/* X=ABCDGHKMNRSTUVWY */
/* Y=BCDHKMNSTUVWY */
/* EFIJLOPQZ not recognized */
/* ----------------------------------------------- */
#ifndef USE_DUAL
/* IUPAC */
0x00000001 /* A */, 0x00080044 /* B */, 0x00000004 /* C */,
0x00080041 /* D */, 0x00000000 /* E */, 0x00000000 /* F */,
0x00000040 /* G */, 0x00080005 /* H */, 0x00000000 /* I */,
0x00000000 /* J */, 0x00080040 /* K */, 0x00000000 /* L */,
0x00000005 /* M */, 0x00080045 /* N */, 0x00000000 /* O */,
0x00000000 /* P */, 0x00000000 /* Q */, 0x00000041 /* R */,
0x00000044 /* S */, 0x00080000 /* T */, 0x00080000 /* U */,
0x00000045 /* V */, 0x00080001 /* W */, 0x00080045 /* X */,
0x00080004 /* Y */, 0x00000000 /* Z */
#else
/* DUAL */
0x00623089 /* A */, 0x017e34ce /* B */, 0x01243086 /* C */,
0x017e34cb /* D */, 0x00000000 /* E */, 0x00000000 /* F */,
0x0026244a /* G */, 0x017e348f /* H */, 0x00000000 /* I */,
0x00000000 /* J */, 0x017e24ca /* K */, 0x00000000 /* L */,
0x0166308f /* M */, 0x017e34cf /* N */, 0x00000000 /* O */,
0x00000000 /* P */, 0x00000000 /* Q */, 0x006634cb /* R */,
0x012634ce /* S */, 0x0158248a /* T */, 0x0158248a /* U */,
0x016634cf /* V */, 0x017a348b /* W */, 0x017e34cf /* X */,
0x017c348e /* Y */, 0x00000000 /* Z */
#endif

51
src/libapat/CODES/prot_code.h Normal file
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/* ----------------------------------------------- */
/* prot_code.h */
/* alphabet encoding for proteins */
/* ----------------------------------------- */
/* IUPAC encoding */
/* ----------------------------------------- */
/* B=DN */
/* Z=EQ */
/* X=any - {X} */
/* JOU not recognized */
/* ----------------------------------------- */
/* dual encoding */
/* ----------------------------------------- */
/* B=BDN */
/* D=BD */
/* E=EZ */
/* N=BN */
/* Q=QZ */
/* X=any - {X} */
/* Z=EQZ */
/* JOU not recognized */
/* ----------------------------------------------- */
#ifndef USE_DUAL
/* IUPAC */
0x00000001 /* A */, 0x00002008 /* B */, 0x00000004 /* C */,
0x00000008 /* D */, 0x00000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000000 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002000 /* N */, 0x00000000 /* O */,
0x00008000 /* P */, 0x00010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00000000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x037fffff /* X */,
0x01000000 /* Y */, 0x00010010 /* Z */
#else
/* DUAL */
0x00000001 /* A */, 0x0000200a /* B */, 0x00000004 /* C */,
0x0000000a /* D */, 0x02000010 /* E */, 0x00000020 /* F */,
0x00000040 /* G */, 0x00000080 /* H */, 0x00000100 /* I */,
0x00000000 /* J */, 0x00000400 /* K */, 0x00000800 /* L */,
0x00001000 /* M */, 0x00002002 /* N */, 0x00000000 /* O */,
0x00008000 /* P */, 0x02010000 /* Q */, 0x00020000 /* R */,
0x00040000 /* S */, 0x00080000 /* T */, 0x00000000 /* U */,
0x00200000 /* V */, 0x00400000 /* W */, 0x037fffff /* X */,
0x01000000 /* Y */, 0x02010010 /* Z */
#endif

97
src/libapat/Gmach.h Normal file
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/* ---------------------------------------------------------------- */
/* Copyright (c) Atelier de BioInformatique */
/* @file: Gmach.h */
/* @desc: machine dependant setup */
/* @+ *should* be included in all ABI softs */
/* */
/* @history: */
/* @+ <Gloup> : Jul 95 : MWC first draft */
/* @+ <Gloup> : Jan 96 : adapted to Pwg */
/* @+ <Gloup> : Nov 00 : adapted to Mac_OS_X */
/* ---------------------------------------------------------------- */
#ifndef _H_Gmach
/* OS names */
#define _H_Gmach
/* Macintosh Classic */
/* Think C environment */
#ifdef THINK_C
#define MACINTOSH
#define MAC_OS_C
#endif
/* Macintosh Classic */
/* Code-Warrior */
#ifdef __MWERKS__
#define MACINTOSH
#define MAC_OS_C
#endif
/* Macintosh OS-X */
#ifdef MAC_OS_X
#define MACINTOSH
#define UNIX
#define UNIX_BSD
#endif
/* LINUX */
#ifdef LINUX
#define UNIX
#define UNIX_BSD
#endif
/* other Unix Boxes */
/* SunOS / Solaris */
#ifdef SUN
#define UNIX
#ifdef SOLARIS
#define UNIX_S7
#else
#define UNIX_BSD
#endif
#endif
/* SGI Irix */
#ifdef SGI
#define UNIX
#define UNIX_S7
#endif
/* ansi setup */
/* for unix machines see makefile */
#ifndef PROTO
#define PROTO 1
#endif
#ifndef ANSI_PROTO
#define ANSI_PROTO PROTO
#endif
#ifndef ANSI_STR
#define ANSI_STR 1
#endif
/* unistd.h header file */
#ifdef UNIX
#define HAS_UNISTD_H <unistd.h>
#endif
/* getopt.h header file */
#ifdef MAC_OS_C
#define HAS_GETOPT_H "getopt.h"
#endif
#ifdef SGI
#define HAS_GETOPT_H <getopt.h>
#endif
#endif

104
src/libapat/Gtypes.h Normal file
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/* ---------------------------------------------------------------- */
/* Copyright (c) Atelier de BioInformatique */
/* @file: Gtypes.h */
/* @desc: general & machine dependant types */
/* @+ *should* be included in all ABI softs */
/* */
/* @history: */
/* @+ <Gloup> : Jan 91 : MWC first draft */
/* @+ <Gloup> : Jul 95 : Gmach addition */
/* ---------------------------------------------------------------- */
#define _H_Gtypes
#ifndef _H_Gmach
#include "Gmach.h"
#endif
#ifndef NULL
#include <stdio.h> /* is the official NULL here ? */
#endif
/* ==================================================== */
/* constantes */
/* ==================================================== */
#ifndef PROTO
#define PROTO 1 /* prototypes flag */
#endif
#ifdef MAC_OS_C
#define Vrai true /* TC boolean values */
#define Faux false /* */
#else
#define Vrai 0x1 /* bool values = TRUE */
#define Faux 0x0 /* = FALSE */
#endif
#define Nil NULL /* nil pointer */
#define kBigInt16 0x7fff /* plus grand 16 bits signe */
#define kBigInt32 0x7fffffff /* plus grand 32 bits signe */
#define kBigUInt16 0xffff /* plus grand 16 bits ~signe */
#define kBigUInt32 0xffffffff /* plus grand 32 bits ~signe */
#ifdef MAC_OS_C
/* ==================================================== */
/* Types (for Macintosh ThinK C || MWerks) */
/* ==================================================== */
/* --- specific sizes --------- */
typedef long Int32; /* Int32 = 32 bits signe */
typedef unsigned long UInt32; /* UInt32 = 32 bits ~signe */
typedef short Int16; /* Int16 = 16 bits signe */
typedef unsigned short UInt16; /* UInt32 = 16 bits ~signe */
typedef char Int8; /* Int8 = 8 bits signe */
typedef unsigned char UInt8; /* UInt8 = 8 bits ~signe */
/* --- default types ---------- */
typedef Boolean Bool; /* booleen */
typedef long Int; /* 'natural' int (>= 32 bits) */
typedef void *Ptr; /* pointeur */
#elif ((defined SUN) || (defined SGI) || (defined UNIX))
/* ==================================================== */
/* Types (for Sun & Iris - 32 bits machines) */
/* ==================================================== */
/* --- specific sizes --------- */
typedef int Int32; /* Int32 = 32 bits signe */
typedef unsigned int UInt32; /* UInt32 = 32 bits ~signe */
typedef short Int16; /* Int16 = 16 bits signe */
typedef unsigned short UInt16; /* UInt32 = 16 bits ~signe */
typedef char Int8; /* Int8 = 8 bits signe */
typedef unsigned char UInt8; /* UInt8 = 8 bits ~signe */
/* --- default types ---------- */
typedef int Bool; /* booleen (int for ANSI) */
typedef int Int; /* 'natural' int (>= 32 bits) */
typedef void *Ptr; /* pointeur */
#else
/* ==================================================== */
/* Types (for undefined machines) */
/* ==================================================== */
#error undefined MACHINE <please edit Gmach.h>
#endif
/* ==================================================== */
/* special macro for prototypes */
/* ==================================================== */
#if PROTO
#define P(s) s
#else
#define P(s) ()
#endif

24
src/libapat/Makefile Normal file
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SOURCES = apat_parse.c \
apat_search.c \
libstki.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libapat.a
RANLIB=ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

173
src/libapat/apat.h Normal file
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/* ==================================================== */
/* 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 */
Int32 circular;
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);

369
src/libapat/apat_parse.c Normal file
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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Mar. 92 */
/* File: apat_parse.c */
/* Purpose: Codage du pattern */
/* History: */
/* 00/07/94 : <Gloup> first version (stanford) */
/* 00/11/94 : <Gloup> revised for DNA/PROTEIN */
/* 30/12/94 : <Gloup> modified EncodePattern */
/* for manber search */
/* 14/05/99 : <Gloup> indels added */
/* ==================================================== */
#include <ctype.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "Gtypes.h"
#include "apat.h"
/* -------------------- */
/* default char */
/* encodings */
/* -------------------- */
static Int32 sDftCode[] = {
#include "CODES/dft_code.h"
};
/* -------------------- */
/* char encodings */
/* IUPAC */
/* -------------------- */
/* IUPAC Proteins */
static Int32 sProtCode[] = {
#include "CODES/prot_code.h"
};
/* IUPAC Dna/Rna */
static Int32 sDnaCode[] = {
#include "CODES/dna_code.h"
};
/* -------------------------------------------- */
/* internal replacement of gets */
/* -------------------------------------------- */
static char *sGets(char *buffer, int size) {
char *ebuf;
if (! fgets(buffer, size-1, stdin))
return NULL;
/* remove trailing line feed */
ebuf = buffer + strlen(buffer);
while (--ebuf >= buffer) {
if ((*ebuf == '\n') || (*ebuf == '\r'))
*ebuf = '\000';
else
break;
}
return buffer;
}
/* -------------------------------------------- */
/* returns actual code associated to type */
/* -------------------------------------------- */
Int32 *GetCode(CodType ctype)
{
Int32 *code = sDftCode;
switch (ctype) {
case dna : code = sDnaCode ; break;
case protein : code = sProtCode ; break;
default : code = sDftCode ; break;
}
return code;
}
/* -------------------------------------------- */
#define BAD_IF(tst) if (tst) return 0
int CheckPattern(Pattern *ppat)
{
int lev;
char *pat;
pat = ppat->cpat;
BAD_IF (*pat == '#');
for (lev = 0; *pat ; pat++)
switch (*pat) {
case '[' :
BAD_IF (lev);
BAD_IF (*(pat+1) == ']');
lev++;
break;
case ']' :
lev--;
BAD_IF (lev);
break;
case '!' :
BAD_IF (lev);
BAD_IF (! *(pat+1));
BAD_IF (*(pat+1) == ']');
break;
case '#' :
BAD_IF (lev);
BAD_IF (*(pat-1) == '[');
break;
default :
if (! isupper(*pat))
return 0;
break;
}
return (lev ? 0 : 1);
}
#undef BAD_IF
/* -------------------------------------------- */
static char *skipOblig(char *pat)
{
return (*(pat+1) == '#' ? pat+1 : pat);
}
/* -------------------------------------------- */
static char *splitPattern(char *pat)
{
switch (*pat) {
case '[' :
for (; *pat; pat++)
if (*pat == ']')
return skipOblig(pat);
return NULL;
break;
case '!' :
return splitPattern(pat+1);
break;
}
return skipOblig(pat);
}
/* -------------------------------------------- */
static Int32 valPattern(char *pat, Int32 *code)
{
Int32 val;
switch (*pat) {
case '[' :
return valPattern(pat+1, code);
break;
case '!' :
val = valPattern(pat+1, code);
return (~val & PATMASK);
break;
default :
val = 0x0;
while (isupper(*pat)) {
val |= code[*pat - 'A'];
pat++;
}
return val;
}
return 0x0;
}
/* -------------------------------------------- */
static Int32 obliBitPattern(char *pat)
{
return (*(pat + strlen(pat) - 1) == '#' ? OBLIBIT : 0x0);
}
/* -------------------------------------------- */
static int lenPattern(char *pat)
{
int lpat;
lpat = 0;
while (*pat) {
if (! (pat = splitPattern(pat)))
return 0;
pat++;
lpat++;
}
return lpat;
}
/* -------------------------------------------- */
/* Interface */
/* -------------------------------------------- */
/* -------------------------------------------- */
/* encode un pattern */
/* -------------------------------------------- */
int EncodePattern(Pattern *ppat, CodType ctype)
{
int pos, lpat;
Int32 *code;
char *pp, *pa, c;
ppat->ok = Faux;
code = GetCode(ctype);
ppat->patlen = lpat = lenPattern(ppat->cpat);
if (lpat <= 0)
return 0;
if (! (ppat->patcode = NEWN(Int32, lpat)))
return 0;
pa = pp = ppat->cpat;
pos = 0;
while (*pa) {
pp = splitPattern(pa);
c = *++pp;
*pp = '\000';
ppat->patcode[pos++] = valPattern(pa, code) | obliBitPattern(pa);
*pp = c;
pa = pp;
}
ppat->ok = Vrai;
return lpat;
}
/* -------------------------------------------- */
/* remove blanks */
/* -------------------------------------------- */
static char *RemBlanks(char *s)
{
char *sb, *sc;
for (sb = sc = s ; *sb ; sb++)
if (! isspace(*sb))
*sc++ = *sb;
return s;
}
/* -------------------------------------------- */
/* count non blanks */
/* -------------------------------------------- */
static Int32 CountAlpha(char *s)
{
Int32 n;
for (n = 0 ; *s ; s++)
if (! isspace(*s))
n++;
return n;
}
/* -------------------------------------------- */
/* lit un pattern */
/* <pattern> #mis */
/* ligne starting with '/' are comments */
/* -------------------------------------------- */
int ReadPattern(Pattern *ppat)
{
int val;
char *spac;
char buffer[BUFSIZ];
ppat->ok = Vrai;
if (! sGets(buffer, sizeof(buffer)))
return 0;
if (*buffer == '/')
return ReadPattern(ppat);
if (! CountAlpha(buffer))
return ReadPattern(ppat);
for (spac = buffer ; *spac ; spac++)
if ((*spac == ' ') || (*spac == '\t'))
break;
ppat->ok = Faux;
if (! *spac)
return 0;
if (sscanf(spac, "%d", &val) != 1)
return 0;
ppat->hasIndel = (val < 0);
ppat->maxerr = ((val >= 0) ? val : -val);
*spac = '\000';
(void) RemBlanks(buffer);
if ((ppat->cpat = NEWN(char, strlen(buffer)+1)))
strcpy(ppat->cpat, buffer);
ppat->ok = (ppat->cpat != NULL);
return (ppat->ok ? 1 : 0);
}
/* -------------------------------------------- */
/* ecrit un pattern - Debug - */
/* -------------------------------------------- */
void PrintDebugPattern(Pattern *ppat)
{
int i;
printf("Pattern : %s\n", ppat->cpat);
printf("Encoding : \n\t");
for (i = 0 ; i < ppat->patlen ; i++) {
printf("0x%8.8x ", ppat->patcode[i]);
if (i%4 == 3)
printf("\n\t");
}
printf("\n");
}

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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Dec. 94 */
/* File: apat_search.c */
/* Purpose: recherche du pattern */
/* algorithme de Baeza-Yates/Gonnet */
/* Manber (agrep) */
/* History: */
/* 07/12/94 : <MFS> first version */
/* 28/12/94 : <Gloup> revised version */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#if 0
#ifndef THINK_C
#include <sys/types.h>
#endif
#endif
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "Gtypes.h"
#include "libstki.h"
#include "apat.h"
#define POP PopiOut
#define PUSH PushiIn
#define TOPCURS CursiToTop
#define DOWNREAD ReadiDown
#define KRONECK(x, msk) ((~x & msk) ? 0 : 1)
#define MIN(x, y) ((x) < (y) ? (x) : (y))
/* -------------------------------------------- */
/* Construction de la matrice S */
/* -------------------------------------------- */
int CreateS(Pattern *ppat, Int32 lalpha)
{
Int32 i, j, indx;
UInt32 pindx, amask, omask, *smat;
ppat->ok = Faux;
omask = 0x0L;
if (! (smat = NEWN(UInt32, lalpha)))
return 0;
for (i = 0 ; i < lalpha ; i++)
smat[i] = 0x0;
for (i = ppat->patlen - 1, amask = 0x1L ; i >= 0 ; i--, amask <<= 1) {
indx = ppat->patcode[i];
if (ppat->patcode[i] & OBLIBIT)
omask |= amask;
for (j = 0, pindx = 0x1L ; j < lalpha ; j++, pindx <<= 1)
if (indx & pindx)
smat[j] |= amask;
}
ppat->smat = smat;
ppat->omask = omask;
ppat->ok = Vrai;
return 1;
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* NoError */
/* -------------------------------------------- */
Int32 ManberNoErr(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
UInt32 pos;
UInt32 smask, r;
UInt8 *data;
StackiPtr *stkpos, *stkerr;
UInt32 end;
end = begin + length;
end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */
smask = r = 0x1L << ppat->patlen;
/* init. scan */
data = pseq->data + begin;
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
r = (r >> 1) & ppat->smat[*data++];
if (r & 0x1L) {
PUSH(stkpos, pos - ppat->patlen + 1);
PUSH(stkerr, 0);
}
r |= smask;
}
return (*stkpos)->top; /* aka # of hits */
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* Substitution only */
/* */
/* Note : r array is stored as : */
/* 0 0 r(0,j) r(0,j+1) r(1,j) r(1,j+1) ... */
/* */
/* -------------------------------------------- */
Int32 ManberSub(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
int e, emax, found;
UInt32 pos;
UInt32 smask, cmask, sindx;
UInt32 *pr, r[2 * MAX_PAT_ERR + 2];
UInt8 *data;
StackiPtr *stkpos, *stkerr;
UInt32 end;
end = begin + length;
end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */
emax = ppat->maxerr;
r[0] = r[1] = 0x0;
cmask = smask = 0x1L << ppat->patlen;
for (e = 0, pr = r + 3 ; e <= emax ; e++, pr += 2)
*pr = cmask;
cmask = ~ ppat->omask;
/* init. scan */
data = pseq->data + begin;
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
sindx = ppat->smat[*data++];
for (e = found = 0, pr = r ; e <= emax ; e++, pr += 2) {
pr[2] = pr[3] | smask;
pr[3] = ((pr[0] >> 1) & cmask) /* sub */
| ((pr[2] >> 1) & sindx); /* ident */
if (pr[3] & 0x1L) { /* found */
if (! found) {
PUSH(stkpos, pos - ppat->patlen + 1);
PUSH(stkerr, e);
}
found++;
}
}
}
return (*stkpos)->top; /* aka # of hits */
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* Substitution + Indels */
/* */
/* Note : r array is stored as : */
/* 0 0 r(0,j) r(0,j+1) r(1,j) r(1,j+1) ... */
/* */
/* Warning: may return shifted pos. */
/* */
/* -------------------------------------------- */
Int32 ManberIndel(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
int e, emax, found;
UInt32 pos;
UInt32 smask, cmask, sindx;
UInt32 *pr, r[2 * MAX_PAT_ERR + 2];
UInt8 *data;
StackiPtr *stkpos, *stkerr;
UInt32 end;
end = begin + length;
end = (end <= (size_t)(pseq->seqlen+pseq->circular)) ? end:(size_t)(pseq->seqlen+pseq->circular);
/* create local masks */
emax = ppat->maxerr;
r[0] = r[1] = 0x0;
cmask = smask = 0x1L << ppat->patlen;
for (e = 0, pr = r + 3 ; e <= emax ; e++, pr += 2) {
*pr = cmask;
cmask = (cmask >> 1) | smask;
}
cmask = ~ ppat->omask;
/* init. scan */
data = pseq->data + begin;
stkpos = pseq->hitpos + patnum;
stkerr = pseq->hiterr + patnum;
/* loop on text data */
for (pos = begin ; pos < end ; pos++) {
sindx = ppat->smat[*data++];
for (e = found = 0, pr = r ; e <= emax ; e++, pr += 2) {
pr[2] = pr[3] | smask;
pr[3] = (( pr[0] /* ins */
| (pr[0] >> 1) /* sub */
| (pr[1] >> 1)) /* del */
& cmask)
| ((pr[2] >> 1) & sindx); /* ident */
if (pr[3] & 0x1L) { /* found */
if (! found) {
PUSH(stkpos, pos - ppat->patlen + 1);
PUSH(stkerr, e);
}
found++;
}
}
}
return (*stkpos)->top; /* aka # of hits */
}
/* -------------------------------------------- */
/* Baeza-Yates/Manber algorithm */
/* API call to previous functions */
/* -------------------------------------------- */
Int32 ManberAll(Seq *pseq, Pattern *ppat, int patnum,int begin,int length)
{
if (ppat->maxerr == 0)
return ManberNoErr(pseq, ppat, patnum, begin, length);
else if (ppat->hasIndel)
return ManberIndel(pseq, ppat, patnum, begin, length);
else
return ManberSub(pseq, ppat, patnum, begin, length);
}
/* -------------------------------------------- */
/* Alignement NWS */
/* pour edition des hits */
/* (avec substitution obligatoire aux bords) */
/* -------------------------------------------- */
Int32 NwsPatAlign(pseq, ppat, nerr, reslen, reserr)
Seq *pseq;
Pattern *ppat;
Int32 nerr, *reslen, *reserr;
{
UInt8 *sseq, *px;
Int32 i, j, lseq, lpat, npos, dindel, dsub,
*pc, *pi, *pd, *ps;
UInt32 amask;
static Int32 sTab[(MAX_PAT_LEN+MAX_PAT_ERR+1) * (MAX_PAT_LEN+1)];
lseq = pseq->seqlen;
pc = sTab; /* |----|----| --> i */
pi = pc - 1; /* | ps | pd | | */
pd = pi - lseq; /* |----|----| | */
ps = pd - 1; /* | pi | pc | v j */
/* |---------| */
lseq = pseq->seqlen;
lpat = ppat->patlen;
sseq = pseq->data - 1;
amask = ONEMASK >> lpat;
for (j = 0 ; j <= lpat ; j++) {
for (i = 0 , px = sseq ; i <= lseq ; i++, px++) {
if (i && j) {
dindel = MIN(*pi, *pd) + 1;
dsub = *ps + KRONECK(ppat->smat[*px], amask);
*pc = MIN(dindel, dsub);
}
else if (i) /* j == 0 */
*pc = *pi + 1;
else if (j) /* i == 0 */
*pc = *pd + 1;
else /* root */
*pc = 0;
pc++;
pi++;
pd++;
ps++;
}
amask <<= 1;
}
pc--;
for (i = lseq, npos = 0 ; i >= 0 ; i--, pc--) {
if (*pc <= nerr) {
*reslen++ = i;
*reserr++ = *pc;
npos++;
}
}
return npos;
}

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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Mar. 92 */
/* File: libstki.c */
/* Purpose: A library to deal with 'stacks' of */
/* integers */
/* Note: 'stacks' are dynamic (i.e. size is */
/* automatically readjusted when needed) */
/* History: */
/* 00/03/92 : <Gloup> first draft */
/* 15/08/93 : <Gloup> revised version */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "Gtypes.h"
#include "libstki.h"
/* ============================ */
/* Constantes et Macros locales */
/* ============================ */
#define ExpandStack(stkh) ResizeStacki((stkh), (*stkh)->size << 1)
#define ShrinkStack(stkh) ResizeStacki((stkh), (*stkh)->size >> 1)
static Int16 sStkiLastError = kStkiNoErr;
/* -------------------------------------------- */
/* gestion des erreurs */
/* get/reset erreur flag */
/* */
/* @function: StkiError */
/* -------------------------------------------- */
Int16 StkiError(Bool reset)
{
Int16 err;
err = sStkiLastError;
if (reset)
sStkiLastError = kStkiNoErr;
return err;
} /* end of StkiError */
/* -------------------------------------------- */
/* creation d'un stack */
/* */
/* @function: NewStacki */
/* -------------------------------------------- */
StackiPtr NewStacki(Int32 size)
{
StackiPtr stki;
if (! (stki = NEW(Stacki)))
return NULL;
stki->size = size;
stki->top = 0;
stki->cursor = 0;
if ( ! (stki->val = NEWN(Int32, size))) {
sStkiLastError = kStkiMemErr;
return FreeStacki(stki);
}
return stki;
} /* end of NewStacki */
/* -------------------------------------------- */
/* liberation d'un stack */
/* */
/* @function: FreeStacki */
/* -------------------------------------------- */
StackiPtr FreeStacki(StackiPtr stki)
{
if (stki) {
if (stki->val)
FREE(stki->val);
FREE(stki);
}
return NULL;
} /* end of FreeStacki */
/* -------------------------------------------- */
/* creation d'un vecteur de stacks */
/* */
/* @function: NewStackiVector */
/* -------------------------------------------- */
StackiHdle NewStackiVector(Int32 vectSize, Int32 stackSize)
{
Int32 i;
StackiHdle stkh;
if (! (stkh = NEWN(StackiPtr, vectSize))) {
sStkiLastError = kStkiMemErr;
return NULL;
}
for (i = 0 ; i < vectSize ; i++)
if (! (stkh[i] = NewStacki(stackSize)))
return FreeStackiVector(stkh, i);
return stkh;
} /* end of NewStackiVector */
/* -------------------------------------------- */
/* liberation d'un vecteur de stacks */
/* */
/* @function: FreeStackiVector */
/* -------------------------------------------- */
StackiHdle FreeStackiVector(StackiHdle stkh, Int32 vectSize)
{
Int32 i;
if (stkh) {
for (i = 0 ; i < vectSize ; i++)
(void) FreeStacki(stkh[i]);
FREE(stkh);
}
return NULL;
} /* end of FreeStackiVector */
/* -------------------------------------------- */
/* resize d'un stack */
/* */
/* @function: ResizeStacki */
/* -------------------------------------------- */
Int32 ResizeStacki(StackiHdle stkh, Int32 size)
{
Int32 resize = 0; /* assume error */
Int32 *val;
if ((val = REALLOC(Int32, (*stkh)->val, size))) {
(*stkh)->size = resize = size;
(*stkh)->val = val;
}
if (! resize)
sStkiLastError = kStkiMemErr;
return resize;
} /* end of ResizeStacki */
/* -------------------------------------------- */
/* empilage(/lement) */
/* */
/* @function: PushiIn */
/* -------------------------------------------- */
Bool PushiIn(StackiHdle stkh, Int32 val)
{
if (((*stkh)->top >= (*stkh)->size) && (! ExpandStack(stkh)))
return Faux;
(*stkh)->val[((*stkh)->top)++] = val;
return Vrai;
} /* end of PushiIn */
/* -------------------------------------------- */
/* depilage(/lement) */
/* */
/* @function: PopiOut */
/* -------------------------------------------- */
Bool PopiOut(StackiHdle stkh, Int32 *val)
{
if ((*stkh)->top <= 0)
return Faux;
*val = (*stkh)->val[--((*stkh)->top)];
if ( ((*stkh)->top < ((*stkh)->size >> 1))
&& ((*stkh)->top > kMinStackiSize))
(void) ShrinkStack(stkh);
return Vrai;
} /* end of PopiOut */
/* -------------------------------------------- */
/* lecture descendante */
/* */
/* @function: ReadiDown */
/* -------------------------------------------- */
Bool ReadiDown(StackiPtr stki, Int32 *val)
{
if (stki->cursor <= 0)
return Faux;
*val = stki->val[--(stki->cursor)];
return Vrai;
} /* end of ReadiDown */
/* -------------------------------------------- */
/* lecture ascendante */
/* */
/* @function: ReadiUp */
/* -------------------------------------------- */
Bool ReadiUp(StackiPtr stki, Int32 *val)
{
if (stki->cursor >= stki->top)
return Faux;
*val = stki->val[(stki->cursor)++];
return Vrai;
} /* end of ReadiUp */
/* -------------------------------------------- */
/* remontee/descente du curseur */
/* */
/* @function: CursiToTop */
/* @function: CursiToBottom */
/* -------------------------------------------- */
void CursiToTop(StackiPtr stki)
{
stki->cursor = stki->top;
} /* end of CursiToTop */
void CursiToBottom(stki)
StackiPtr stki;
{
stki->cursor = 0;
} /* end of CursiToBottom */
/* -------------------------------------------- */
/* echange des valeurs cursor <-> (top - 1) */
/* */
/* @function: CursiSwap */
/* -------------------------------------------- */
void CursiSwap(StackiPtr stki)
{
Int32 tmp;
if ((stki->top <= 0) || (stki->cursor < 0))
return;
tmp = stki->val[stki->cursor];
stki->val[stki->cursor] = stki->val[stki->top - 1];
stki->val[stki->top - 1] = tmp;
} /* end of CursiSwap */
/* -------------------------------------------- */
/* Recherche d'une valeur en stack a partir du */
/* curseur courant en descendant. */
/* on laisse le curseur a l'endroit trouve */
/* */
/* @function: SearchDownStacki */
/* -------------------------------------------- */
Bool SearchDownStacki(StackiPtr stki, Int32 sval)
{
Int32 val;
Bool more;
while ((more = ReadiDown(stki, &val)))
if (val == sval)
break;
return more;
} /* end of SearchDownStacki */
/* -------------------------------------------- */
/* Recherche dichotomique d'une valeur en stack */
/* le stack est suppose trie par valeurs */
/* croissantes. */
/* on place le curseur a l'endroit trouve */
/* */
/* @function: BinSearchStacki */
/* -------------------------------------------- */
Bool BinSearchStacki(StackiPtr stki, Int32 sval)
{
Int32 midd, low, high, span;
low = 0;
high = stki->top - 1;
while (high >= low) {
midd = (high + low) / 2;
span = stki->val[midd] - sval;
if (span == 0) {
stki->cursor = midd;
return Vrai;
}
if (span > 0)
high = midd - 1;
else
low = midd + 1;
}
return Faux;
} /* end of BinSearchStacki */
/* -------------------------------------------- */
/* teste l'egalite *physique* de deux stacks */
/* */
/* @function: SameStacki */
/* -------------------------------------------- */
Bool SameStacki(StackiPtr stki1, StackiPtr stki2)
{
if (stki1->top != stki2->top)
return Faux;
return ((memcmp(stki1->val, stki2->val,
stki1->top * sizeof(Int32)) == 0) ? Vrai : Faux);
} /* end of SameStacki */
/* -------------------------------------------- */
/* inverse l'ordre des elements dans un stack */
/* */
/* @function: ReverseStacki */
/* -------------------------------------------- */
Bool ReverseStacki(StackiPtr stki)
{
Int32 *t, *b, swp;
if (stki->top <= 0)
return Faux;
b = stki->val;
t = b + stki->top - 1;
while (t > b) {
swp = *t;
*t-- = *b;
*b++ = swp;
}
return Vrai;
} /* end of ReverseStacki */

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/* ==================================================== */
/* Copyright (c) Atelier de BioInformatique */
/* Mar. 92 */
/* File: libstki.h */
/* Purpose: library of dynamic stacks holding */
/* integer values */
/* History: */
/* 00/03/92 : <Gloup> first draft */
/* 07/07/93 : <Gloup> complete revision */
/* 10/03/94 : <Gloup> added xxxVector funcs */
/* 14/05/99 : <Gloup> last revision */
/* ==================================================== */
#ifndef _H_Gtypes
#include "Gtypes.h"
#endif
#define _H_libstki
/* ==================================================== */
/* Constantes de dimensionnement */
/* ==================================================== */
#ifndef kMinStackiSize
#define kMinStackiSize 2 /* taille mini stack */
#endif
#define kStkiNoErr 0 /* ok */
#define kStkiMemErr 1 /* not enough memory */
#define kStkiReset Vrai
#define kStkiGet Faux
/* ==================================================== */
/* Macros standards */
/* ==================================================== */
#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((Ptr) ptr)
#endif
/* ==================================================== */
/* Types & Structures de donnees */
/* ==================================================== */
/* -------------------- */
/* structure : pile */
/* -------------------- */
typedef struct Stacki {
/* ---------------------*/
Int32 size; /* stack size */
Int32 top; /* current free pos. */
Int32 cursor; /* current cursor */
Int32 *val; /* values */
/* ---------------------*/
} Stacki, *StackiPtr, **StackiHdle;
/* ==================================================== */
/* Prototypes (generated by mproto) */
/* ==================================================== */
/* libstki.c */
Int16 StkiError (Bool reset );
StackiPtr NewStacki (Int32 size );
StackiPtr FreeStacki (StackiPtr stki );
StackiHdle NewStackiVector (Int32 vectSize, Int32 stackSize );
StackiHdle FreeStackiVector (StackiHdle stkh, Int32 vectSize );
Int32 ResizeStacki (StackiHdle stkh , Int32 size );
Bool PushiIn (StackiHdle stkh , Int32 val );
Bool PopiOut (StackiHdle stkh , Int32 *val );
Bool ReadiDown (StackiPtr stki , Int32 *val );
Bool ReadiUp (StackiPtr stki , Int32 *val );
void CursiToTop (StackiPtr stki );
void CursiToBottom (StackiPtr stki );
void CursiSwap (StackiPtr stki );
Bool SearchDownStacki (StackiPtr stki , Int32 sval );
Bool BinSearchStacki (StackiPtr stki , Int32 sval );
Bool SameStacki (StackiPtr stki1 , StackiPtr stki2 );
Bool ReverseStacki (StackiPtr stki );