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view pyPRADA_1.2/tools/samtools-0.1.16/kstring.c @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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#include <stdarg.h> #include <stdio.h> #include <ctype.h> #include <string.h> #include <stdint.h> #include "kstring.h" int ksprintf(kstring_t *s, const char *fmt, ...) { va_list ap; int l; va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'. va_end(ap); if (l + 1 > s->m - s->l) { s->m = s->l + l + 2; kroundup32(s->m); s->s = (char*)realloc(s->s, s->m); va_start(ap, fmt); l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); } va_end(ap); s->l += l; return l; } char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux) { const char *p, *start; if (sep) { // set up the table if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished aux->finished = 0; if (sep[1]) { aux->sep = -1; aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0; for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f); } else aux->sep = sep[0]; } if (aux->finished) return 0; else if (str) aux->p = str - 1, aux->finished = 0; if (aux->sep < 0) { for (p = start = aux->p + 1; *p; ++p) if (aux->tab[*p>>6]>>(*p&0x3f)&1) break; } else { for (p = start = aux->p + 1; *p; ++p) if (*p == aux->sep) break; } aux->p = p; // end of token if (*p == 0) aux->finished = 1; // no more tokens return (char*)start; } // s MUST BE a null terminated string; l = strlen(s) int ksplit_core(char *s, int delimiter, int *_max, int **_offsets) { int i, n, max, last_char, last_start, *offsets, l; n = 0; max = *_max; offsets = *_offsets; l = strlen(s); #define __ksplit_aux do { \ if (_offsets) { \ s[i] = 0; \ if (n == max) { \ max = max? max<<1 : 2; \ offsets = (int*)realloc(offsets, sizeof(int) * max); \ } \ offsets[n++] = last_start; \ } else ++n; \ } while (0) for (i = 0, last_char = last_start = 0; i <= l; ++i) { if (delimiter == 0) { if (isspace(s[i]) || s[i] == 0) { if (isgraph(last_char)) __ksplit_aux; // the end of a field } else { if (isspace(last_char) || last_char == 0) last_start = i; } } else { if (s[i] == delimiter || s[i] == 0) { if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field } else { if (last_char == delimiter || last_char == 0) last_start = i; } } last_char = s[i]; } *_max = max; *_offsets = offsets; return n; } /********************** * Boyer-Moore search * **********************/ typedef unsigned char ubyte_t; // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html static int *ksBM_prep(const ubyte_t *pat, int m) { int i, *suff, *prep, *bmGs, *bmBc; prep = calloc(m + 256, sizeof(int)); bmGs = prep; bmBc = prep + m; { // preBmBc() for (i = 0; i < 256; ++i) bmBc[i] = m; for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1; } suff = calloc(m, sizeof(int)); { // suffixes() int f = 0, g; suff[m - 1] = m; g = m - 1; for (i = m - 2; i >= 0; --i) { if (i > g && suff[i + m - 1 - f] < i - g) suff[i] = suff[i + m - 1 - f]; else { if (i < g) g = i; f = i; while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g; suff[i] = f - g; } } } { // preBmGs() int j = 0; for (i = 0; i < m; ++i) bmGs[i] = m; for (i = m - 1; i >= 0; --i) if (suff[i] == i + 1) for (; j < m - 1 - i; ++j) if (bmGs[j] == m) bmGs[j] = m - 1 - i; for (i = 0; i <= m - 2; ++i) bmGs[m - 1 - suff[i]] = m - 1 - i; } free(suff); return prep; } void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep) { int i, j, *prep = 0, *bmGs, *bmBc; const ubyte_t *str, *pat; str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat; prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep; if (_prep && *_prep == 0) *_prep = prep; bmGs = prep; bmBc = prep + m; j = 0; while (j <= n - m) { for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i); if (i >= 0) { int max = bmBc[str[i+j]] - m + 1 + i; if (max < bmGs[i]) max = bmGs[i]; j += max; } else return (void*)(str + j); } if (_prep == 0) free(prep); return 0; } char *kstrstr(const char *str, const char *pat, int **_prep) { return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep); } char *kstrnstr(const char *str, const char *pat, int n, int **_prep) { return (char*)kmemmem(str, n, pat, strlen(pat), _prep); } /*********************** * The main() function * ***********************/ #ifdef KSTRING_MAIN #include <stdio.h> int main() { kstring_t *s; int *fields, n, i; ks_tokaux_t aux; char *p; s = (kstring_t*)calloc(1, sizeof(kstring_t)); // test ksprintf() ksprintf(s, " abcdefg: %d ", 100); printf("'%s'\n", s->s); // test ksplit() fields = ksplit(s, 0, &n); for (i = 0; i < n; ++i) printf("field[%d] = '%s'\n", i, s->s + fields[i]); // test kstrtok() s->l = 0; for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) { kputsn(p, aux.p - p, s); kputc('\n', s); } printf("%s", s->s); // free free(s->s); free(s); free(fields); { static char *str = "abcdefgcdgcagtcakcdcd"; static char *pat = "cd"; char *ret, *s = str; int *prep = 0; while ((ret = kstrstr(s, pat, &prep)) != 0) { printf("match: %s\n", ret); s = ret + prep[0]; } free(prep); } return 0; } #endif