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#include "libc.h"
#include "types.h"
#include "misc.h"
#include "seq.h"
#include "encoding.h"
#include "charvec.h"
#ifndef __lint
static const char rcsid[] =
"$Id: seq_read.c,v 1.2 2000/06/05 22:48:19 florea Exp $";
#endif
static SEQ *seq_mask_inplace(SEQ *seq);
static int getpair(FILE *fp, int *a, int *b);
static char *byte_fill_range(uchar *p, int l, int c, int a, int b);
static int ws(int c);
static int getnwc(FILE *fp);
static void un_getc(int c, FILE *fp);
static void char_append(charvec_t *s, int c);
static int ws(int c)
{
return (c == ' ' || c == '\t' || c == '\n' || c == '\f' || c == '\r');
}
static int getnwc(FILE *fp)
{
int c = EOF;
if (!feof(fp)) do c = getc(fp); while (c != EOF && ws(c));
return c;
}
static void un_getc(int c, FILE *fp)
{
if (c != EOF)
if (ungetc(c, fp) == EOF)
fatalf("cannot ungetc '%c'", c);
}
static void char_append(charvec_t *s, int c)
{
if (!charvec_append(s, c))
fatal("cannot append");
}
int seq_read(SEQ *seq)
{
int b, c;
charvec_t shdr = charvec_INIT(ckrealloc,free);
charvec_t sseq = charvec_INIT(ckrealloc,free);
if (feof(seq->fp))
return 0;
if (seq->count > 0) {
if (seq->flags & SEQ_IS_SUBRANGE) {
return 0;
} else {
seq->from = 1;
seq->slen = -1; /* will be computed below */
}
}
if (seq->header) ZFREE(seq->header);
if (seq->seq) ZFREE(seq->seq);
seq->offset = ftell(seq->fp);
/* --- header --- */
c = getnwc(seq->fp);
if (c == '>') {
while (c != '\n' && c != EOF) {
char_append(&shdr, c);
c = getc(seq->fp);
}
} else {
un_getc(c, seq->fp);
}
char_append(&shdr, 0);
seq->header = shdr.a;
seq->hlen = shdr.len;
/* --- seq --- */
b = '\n';
c = getnwc(seq->fp);
while ((c != EOF) && !(b == '\n' && c == '>')) {
switch (nfasta_ctype[c]) {
case Nfasta_nt:
char_append(&sseq, c);
break;
case Nfasta_ws:
/* skip space */
break;
case Nfasta_amb:
if (seq->flags & SEQ_ALLOW_AMB) {
char_append(&sseq, c);
break;
}
/* FALLTHRU */
default:
fatalf("non-DNA character '%c' in sequence '%s'", c, seq->fname);
break;
}
b = c;
c = getc(seq->fp);
}
un_getc(c, seq->fp);
/* check conformance */
if (SEQ_LEN(seq) == -1) {
char_append(&sseq, 0);
charvec_fit(&sseq);
seq->seq = (uchar*)sseq.a;
seq->slen = sseq.len;
if (seq->slen > 0) --seq->slen; /* don't include '\0' */
} else {
charvec_t ssub = charvec_INIT(ckrealloc,free);
int i;
if (SEQ_FROM(seq) < 1 ||
(int)sseq.len < SEQ_FROM(seq) ||
SEQ_TO(seq) < 1 ||
(int)sseq.len < SEQ_TO(seq) ||
SEQ_TO(seq) < SEQ_FROM(seq))
fatalf("range [%d,%d] incommensurate with sequence [%d,%d]",
SEQ_FROM(seq), SEQ_TO(seq), 1, sseq.len);
for (i = SEQ_FROM(seq); i <= SEQ_TO(seq); ++i)
char_append(&ssub, sseq.a[i-1]);
char_append(&ssub, 0);
charvec_fini(&sseq);
seq->seq = (uchar*)ssub.a;
}
seq->flags = seq->flags &~ SEQ_IS_REVCOMP;
if (seq->flags & SEQ_DO_REVCOMP) {
(void)seq_revcomp_inplace(seq);
}
if (seq->flags & SEQ_HAS_MASK) {
(void)seq_mask_inplace(seq);
}
seq->count++;
return 1;
}
static SEQ *seq_mask_inplace(SEQ *seq)
{
int a, b;
FILE *fp = fopen(seq->maskname, "r");
if (fp == 0) {
fatalfr("cannot open '%s'", seq->maskname);
return 0;
} else {
while (getpair(fp, &a, &b))
byte_fill_range(SEQ_CHARS(seq),SEQ_LEN(seq),'X',a,b);
fclose(fp);
seq->flags |= SEQ_HAS_MASK;
return seq;
}
}
#define BUF 128
static int getpair(FILE *fp, int *a, int *b)
{
char buf[BUF];
/* XXX - should handle comments, etc */
if (fgets(buf, (int)sizeof(buf), fp) == 0)
return 0;
if (sscanf(buf, "%d%d", a, b) != 2)
return 0;
return 1;
}
static char *byte_fill_range(uchar *p, int l, int c, int a, int b)
{
/* fill [a,b] (1-indexed) in p with c */
a--; b = b-a; /* make it into a 0-indexed, open interval */
return (b < 0 || l < b) ? 0 : memset(p+a, c, (size_t)b);
}
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