/*--------------------------------------------------
pagc_tools.c (combine_path_file)
called by util.c (open_aux_file)
calls char_append
--------------------------------------------------*/
void combine_path_file( char global_path_separator ,
char *input_head ,
char *input_tail ,
char *output_path_name ) {
char combine_buf[ 2 ] ;
combine_buf[ 0 ] = global_path_separator ;
combine_buf[ 1 ] = SENTINEL ;
if ( ( input_head != NULL ) &&
( input_head[ 0 ] != SENTINEL ) ) {
append_string_to_max( output_path_name ,
input_head ,
PATHNAME_LEN ) ;
char_append( combine_buf ,
output_path_name ,
input_tail ,
PATHNAME_LEN ) ;
return ;
}
append_string_to_max( output_path_name ,
input_tail ,
PATHNAME_LEN ) ;
}
int seq_read_fasta(SEQ *seq)
{
int b, c;
charvec_t shdr = charvec_INIT(ckrealloc,ckfree);
charvec_t sseq = charvec_INIT(ckrealloc,ckfree);
if (feof(seq->fp) || ferror(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);
}
if (ferror(seq->fp))
Fatalfr("seq_read(%s)", seq->fname);
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);
if (ferror(seq->fp))
Fatalfr("seq_read(%s)", seq->fname);
/* 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,ckfree);
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;
}
