static void print_match(int start, int width, const cachedCharSeq *P,
const cachedCharSeq *S)
{
int end, j0, nedit0, width0;
char mbuf[1001];
if (width >= sizeof(mbuf))
error("sizeof(mbuf) too small");
j0 = start - 1;
end = j0 + width;
snprintf(mbuf, width + 1, "%s", S->seq + j0);
nedit0 = _nedit_for_Ploffset(P, S, j0, P->length, 1, &width0);
Rprintf("start=%d end=%d (%s) nedit0=%d\n", start, end, mbuf, nedit0);
return;
}
static void print_match(int start, int width,
const Chars_holder *P, const Chars_holder *S,
const BytewiseOpTable *bytewise_match_table)
{
int end, j0, nedit0, width0;
char mbuf[1001];
if (width >= sizeof(mbuf))
error("sizeof(mbuf) too small");
j0 = start - 1;
end = j0 + width;
snprintf(mbuf, width + 1, "%s", S->ptr + j0);
nedit0 = _nedit_for_Ploffset(P, S, j0, P->length, 1, &width0,
bytewise_match_table);
Rprintf("start=%d end=%d (%s) nedit0=%d\n", start, end, mbuf, nedit0);
return;
}
void _match_pattern_indels(const cachedCharSeq *P, const cachedCharSeq *S,
int max_nmis, int fixedP, int fixedS)
{
int i0, j0, max_nmis1, nedit1, width1;
char c0;
cachedCharSeq P1;
if (P->length <= 0)
error("empty pattern");
_select_nmismatch_at_Pshift_fun(fixedP, fixedS);
if (!fixedP || !fixedS)
error("'fixed' must be TRUE when 'algorithm=\"indels\"' (for now)");
// Before we can support fixedP=FALSE or fixedS=FALSE in
// _match_pattern_indels(), we need to support them in
// _init_byte2offset_with_cachedCharSeq() and _nedit_for_Ploffset().
_init_byte2offset_with_cachedCharSeq(byte2offset, P, 0);
provisory_match_nedit = -1; // means no provisory match yet
j0 = 0;
while (j0 < S->length) {
while (1) {
c0 = S->seq[j0];
i0 = byte2offset[(unsigned char) c0];
if (i0 != NA_INTEGER) break;
j0++;
if (j0 >= S->length) goto done;
}
P1.seq = P->seq + 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 = _selected_nmismatch_at_Pshift_fun(&P1, S, j0 + 1, max_nmis1);
width1 = P1.length;
} else {
nedit1 = _nedit_for_Ploffset(&P1, S, j0 + 1, max_nmis1, 1, &width1);
}
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);
}
#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;
}
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;
}