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; }