Copied from SVN revision 4710 and adapted to Git.

[samtools.git] / kstring.c

diff --git a/kstring.c b/kstring.c
index dc20faeac9fef21c88813c34f9f42ac6c69d449d..e0203fa3e877604f53291b39ff6a2f273e6dff8f 100644 (file)
--- a/kstring.c
+++ b/kstring.c
@@ -2,6 +2,7 @@
 #include <stdio.h>
 #include <ctype.h>
 #include <string.h>
+#include <stdint.h>
 #include "kstring.h"
 
 int ksprintf(kstring_t *s, const char *fmt, ...)
@@ -61,6 +62,78 @@ int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
        return n;
 }
 
+/**********************
+ * Boyer-Moore search *
+ **********************/
+
+// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
+int *ksBM_prep(const uint8_t *pat, int m)
+{
+       int i, *suff, *prep, *bmGs, *bmBc;
+       prep = calloc(m + 256, 1);
+       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;
+}
+
+int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
+{
+       int i, j, *prep, *bmGs, *bmBc;
+       int *matches = 0, mm = 0, nm = 0;
+       prep = _prep? _prep : ksBM_prep(pat, m);
+       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 {
+                       int max = bmBc[str[i+j]] - m + 1 + i;
+                       if (max < bmGs[i]) max = bmGs[i];
+                       j += max;
+               }
+       }
+       *n_matches = nm;
+       if (_prep == 0) free(prep);
+       return matches;
+}
+
 #ifdef KSTRING_MAIN
 #include <stdio.h>
 int main()
@@ -76,6 +149,17 @@ int main()
        for (i = 0; i < n; ++i)
                printf("field[%d] = '%s'\n", i, s->s + fields[i]);
        free(s);
+
+       {
+               static char *str = "abcdefgcdg";
+               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);
+       }
        return 0;
 }
 #endif