# Uploaded samtools version 0.1.14-1.

[samtools.git] / kstring.c

diff --git a/kstring.c b/kstring.c
index e0203fa3e877604f53291b39ff6a2f273e6dff8f..b2a0dab03c36f616c50aa6e5b79709134855db8e 100644 (file)
--- a/kstring.c
+++ b/kstring.c
@@ -24,6 +24,32 @@ int ksprintf(kstring_t *s, const char *fmt, ...)
        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)
 {
@@ -66,11 +92,13 @@ int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
  * Boyer-Moore search *
  **********************/
 
+typedef unsigned char ubyte_t;
+
 // reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
-int *ksBM_prep(const uint8_t *pat, int m)
+static int *ksBM_prep(const ubyte_t *pat, int m)
 {
        int i, *suff, *prep, *bmGs, *bmBc;
-       prep = calloc(m + 256, 1);
+       prep = calloc(m + 256, sizeof(int));
        bmGs = prep; bmBc = prep + m;
        { // preBmBc()
                for (i = 0; i < 256; ++i) bmBc[i] = m;
@@ -107,39 +135,49 @@ int *ksBM_prep(const uint8_t *pat, int m)
        return prep;
 }
 
-int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
+void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
 {
-       int i, j, *prep, *bmGs, *bmBc;
-       int *matches = 0, mm = 0, nm = 0;
-       prep = _prep? _prep : ksBM_prep(pat, m);
+       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) {
-                       if (nm == mm) {
-                               mm = mm? mm<<1 : 1;
-                               matches = realloc(matches, mm * sizeof(int));
-                       }
-                       matches[nm++] = j;
-                       j += bmGs[0];
-               } else {
+               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);
        }
-       *n_matches = nm;
        if (_prep == 0) free(prep);
-       return matches;
+       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);
@@ -148,17 +186,26 @@ int main()
        fields = ksplit(s, 0, &n);
        for (i = 0; i < n; ++i)
                printf("field[%d] = '%s'\n", i, s->s + fields[i]);
-       free(s);
+       // 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 = "abcdefgcdg";
+               static char *str = "abcdefgcdgcagtcakcdcd";
                static char *pat = "cd";
-               int n, *matches;
-               matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n);
-               printf("%d: \n", n);
-               for (i = 0; i < n; ++i)
-                       printf("- %d\n", matches[i]);
-               free(matches);
+               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;
 }