forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
kstring.c
212 lines (198 loc) · 5.26 KB
/
kstring.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
#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 = (int*)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 = (int*)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