static void get_find_palindromes_at(const char *x, int x_len,
int i1, int i2, int max_loop_len1, int min_arm_len, int max_nmis,
const int *lkup, int lkup_len)
{
int arm_len, valid_indices;
char c1, c2;
arm_len = 0;
while (((valid_indices = i1 >= 0 && i2 < x_len) &&
i2 - i1 <= max_loop_len1) || arm_len != 0)
{
if (valid_indices) {
c1 = x[i1];
c2 = x[i2];
if (is_match(c1, c2, lkup, lkup_len) ||
max_nmis-- > 0) {
arm_len++;
goto next;
}
}
if (arm_len >= min_arm_len)
_report_match(i1 + 2, i2 - i1 - 1);
arm_len = 0;
next:
i1--;
i2++;
}
return;
}
static void match_naive_exact(const Chars_holder *P, const Chars_holder *S)
{
const char *p, *s;
int plen, slen, start, n2;
if (P->length <= 0)
error("empty pattern");
p = P->ptr;
plen = P->length;
s = S->ptr;
slen = S->length;
for (start = 1, n2 = plen; n2 <= slen; start++, n2++, s++) {
if (memcmp(p, s, plen) == 0)
_report_match(start, P->length);
}
return;
}
static void report_provisory_match(int start, int width, int nedit)
{
int end;
end = start + width - 1;
if (provisory_match_nedit != -1) {
// Given how we walk on S, 'start' is always guaranteed to be >
// 'provisory_match_start'.
if (end > provisory_match_end)
_report_match(provisory_match_start, provisory_match_width);
else if (nedit > provisory_match_nedit)
return;
}
provisory_match_start = start;
provisory_match_end = end;
provisory_match_width = width;
provisory_match_nedit = nedit;
return;
}
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 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;
}
static void BOC2_exact_search(const char *P, int nP, const char *S, int nS,
char c1, char c2, char c3, char c4,
const int *buf, const double *means,
const int *table1, const int *table2, const int *table3, const int *table4)
{
int n1, n1max, n2, c1_oc, c2_oc, c3_oc, Psignature,
nPsuf4, *Psuf4_offsets[4], Psuf4_noffsets[4], i, j, *offsets, noffsets;
char c, Ppre4, codes[4];
const char *Psuf4, *Ssuf4;
#ifdef DEBUG_BIOSTRINGS
int count_preapprovals = 0;
#endif
c1_oc = c2_oc = c3_oc = 0;
for (n2 = 0; n2 < nP; n2++) {
c = P[n2];
if (c == c1) c1_oc++;
else if (c == c2) c2_oc++;
else if (c == c3) c3_oc++;
else if (c != c4)
error("'pattern' contains non-base DNA letters");
}
Ppre4 = make_pre4(P, c1, c2, c3, c4);
Psignature = make_32bit_signature(c1_oc, c2_oc, c3_oc, Ppre4);
#ifdef DEBUG_BIOSTRINGS
if (debug)
Rprintf("[DEBUG] pattern: c1_oc=%d c2_oc=%d c3_oc=%d Ppre4=%d\n",
c1_oc, c2_oc, c3_oc, Ppre4);
#endif
Psuf4 = P + 4;
nPsuf4 = nP - 4;
codes[0] = c1;
codes[1] = c2;
codes[2] = c3;
codes[3] = c4;
for (i = 0; i < 4; i++)
Psuf4_offsets[i] = Salloc((long) nP, int);
split4_offsets(codes, Psuf4_offsets, Psuf4_noffsets, Psuf4, nPsuf4);
n1max = nS - nP;
for (n1 = 0, Ssuf4 = S + 4; n1 <= n1max; n1++, Ssuf4++, buf++) {
if (Psignature != *buf)
continue;
#ifdef DEBUG_BIOSTRINGS
count_preapprovals++;
#endif
if (memcmp(Psuf4, Ssuf4, nPsuf4) != 0)
continue; // same as goto continue0;
/*
// Uncomment the 2 lines above if you want to use the fancy
// comparison method below.
for (i = 0; i < 3; i++) {
c = codes[i];
offsets = Psuf4_offsets[i];
noffsets = Psuf4_noffsets[i];
for (j = 0; j < noffsets; j++)
if (c != Ssuf4[offsets[j]])
goto continue0;
}
*/
_report_match(n1 + 1, nP);
continue0: ;
}
#ifdef DEBUG_BIOSTRINGS
if (debug)
Rprintf("[DEBUG] count_preapprovals=%d\n", count_preapprovals);
#endif
return;
}