static void match_naive_inexact(const Chars_holder *P, const Chars_holder *S,
int max_nmis, int min_nmis, int fixedP, int fixedS)
{
int Pshift, // position of pattern left-most char relative to the subject
n2, // 1 + position of pattern right-most char relative to the subject
min_Pshift, max_n2, nmis;
const BytewiseOpTable *bytewise_match_table;
if (P->length <= 0)
error("empty pattern");
bytewise_match_table = _select_bytewise_match_table(fixedP, fixedS);
min_Pshift = P->length <= max_nmis ? 1 - P->length : -max_nmis;
max_n2 = S->length - min_Pshift;
for (Pshift = min_Pshift, n2 = min_Pshift + P->length;
n2 <= max_n2;
Pshift++, n2++)
{
nmis = _nmismatch_at_Pshift(P, S, Pshift, max_nmis,
bytewise_match_table);
if (nmis <= max_nmis && nmis >= min_nmis)
_report_match(Pshift + 1, P->length);
}
return;
}
void _match_pattern_indels(const Chars_holder *P, const Chars_holder *S,
int max_nmis, int fixedP, int fixedS)
{
int i0, j0, max_nmis1, nedit1, width1;
char c0;
const BytewiseOpTable *bytewise_match_table;
Chars_holder P1;
if (P->length <= 0)
error("empty pattern");
bytewise_match_table = _select_bytewise_match_table(fixedP, fixedS);
_init_byte2offset_with_Chars_holder(&byte2offset, P,
bytewise_match_table);
provisory_match_nedit = -1; // means no provisory match yet
j0 = 0;
while (j0 < S->length) {
while (1) {
c0 = S->ptr[j0];
i0 = byte2offset.byte2code[(unsigned char) c0];
if (i0 != NA_INTEGER) break;
j0++;
if (j0 >= S->length) goto done;
}
P1.ptr = P->ptr + i0 + 1;
P1.length = P->length - i0 - 1;
max_nmis1 = max_nmis - i0;
/*
#ifdef DEBUG_BIOSTRINGS
if (debug) {
Rprintf("[DEBUG] _match_pattern_indels(): "
"j0=%d c0=%c i0=%d max_nmis1=%d\n", j0, c0, i0, max_nmis1);
}
#endif
*/
if (max_nmis1 >= 0) {
if (max_nmis1 == 0) {
nedit1 = _nmismatch_at_Pshift(&P1, S, j0 + 1,
max_nmis1,
bytewise_match_table);
width1 = P1.length;
} else {
nedit1 = _nedit_for_Ploffset(&P1, S, j0 + 1,
max_nmis1, 1, &width1,
bytewise_match_table);
}
if (nedit1 <= max_nmis1) {
#ifdef DEBUG_BIOSTRINGS
if (debug) {
Rprintf("[DEBUG] _match_pattern_indels(): "
"provisory match found at ");
print_match(j0 + 1, width1 + 1, P, S,
bytewise_match_table);
}
#endif
report_provisory_match(j0 + 1, width1 + 1, nedit1 + i0);
}
}
j0++;
}
done:
if (provisory_match_nedit != -1)
_report_match(provisory_match_start, provisory_match_width);
return;
}
