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code cleanup; added a missing file

This commit is contained in:
Heng Li 2013-02-01 14:38:44 -05:00
parent 620ad6e5b9
commit f8f3b7577a
4 changed files with 421 additions and 31 deletions
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50
bwamem.c
View File

@ -19,6 +19,15 @@ memopt_t *mem_opt_init()
* SMEM iterator interface * * SMEM iterator interface *
***************************/ ***************************/
struct __smem_i {
const bwt_t *bwt;
const uint8_t *query;
int start, len;
bwtintv_v *matches; // matches; to be returned by smem_next()
bwtintv_v *sub; // sub-matches inside the longest match; temporary
bwtintv_v *tmpvec[2]; // temporary arrays
};
smem_i *smem_itr_init(const bwt_t *bwt) smem_i *smem_itr_init(const bwt_t *bwt)
{ {
smem_i *itr; smem_i *itr;
@ -47,25 +56,25 @@ void smem_set_query(smem_i *itr, int len, const uint8_t *query)
itr->len = len; itr->len = len;
} }
int smem_next(smem_i *itr, int split_len) const bwtintv_v *smem_next(smem_i *itr, int split_len)
{ {
int i, max, max_i; int i, max, max_i;
itr->tmpvec[0]->n = itr->tmpvec[1]->n = itr->matches->n = 0; itr->tmpvec[0]->n = itr->tmpvec[1]->n = itr->matches->n = itr->sub->n = 0;
if (itr->start >= itr->len || itr->start < 0) return -1; if (itr->start >= itr->len || itr->start < 0) return 0;
while (itr->start < itr->len && itr->query[itr->start] > 3) ++itr->start; // skip ambiguous bases while (itr->start < itr->len && itr->query[itr->start] > 3) ++itr->start; // skip ambiguous bases
if (itr->start == itr->len) return -1; if (itr->start == itr->len) return 0;
itr->start = bwt_smem1(itr->bwt, itr->len, itr->query, itr->start, 1, itr->matches, itr->tmpvec); itr->start = bwt_smem1(itr->bwt, itr->len, itr->query, itr->start, 1, itr->matches, itr->tmpvec); // search for SMEM
if (itr->matches->n == 0) return itr->start; if (itr->matches->n == 0) return itr->matches; // well, in theory, we should never come here
for (i = max = 0, max_i = 0; i < itr->matches->n; ++i) { for (i = max = 0, max_i = 0; i < itr->matches->n; ++i) { // look for the longest match
bwtintv_t *p = &itr->matches->a[i]; bwtintv_t *p = &itr->matches->a[i];
int len = (uint32_t)p->info - (p->info>>32); int len = (uint32_t)p->info - (p->info>>32);
if (max < len) max = len, max_i = i; if (max < len) max = len, max_i = i;
} }
if (split_len > 0 && max >= split_len && itr->matches->a[max_i].x[2] == 1) { if (split_len > 0 && max >= split_len && itr->matches->a[max_i].x[2] == 1) { // if the longest SMEM is unique and long
int j; int j;
bwtintv_v *a = itr->tmpvec[0]; bwtintv_v *a = itr->tmpvec[0]; // reuse tmpvec[0] for merging
bwtintv_t *p = &itr->matches->a[max_i]; bwtintv_t *p = &itr->matches->a[max_i];
bwt_smem1(itr->bwt, itr->len, itr->query, ((uint32_t)p->info + (p->info>>32))>>1, 2, itr->sub, itr->tmpvec); // starting from the middle of the longest match bwt_smem1(itr->bwt, itr->len, itr->query, ((uint32_t)p->info + (p->info>>32))>>1, 2, itr->sub, itr->tmpvec); // starting from the middle of the longest MEM
i = j = 0; a->n = 0; i = j = 0; a->n = 0;
while (i < itr->matches->n && j < itr->sub->n) { // ordered merge while (i < itr->matches->n && j < itr->sub->n) { // ordered merge
if (itr->matches->a[i].info < itr->sub->a[j].info) { if (itr->matches->a[i].info < itr->sub->a[j].info) {
@ -80,7 +89,7 @@ int smem_next(smem_i *itr, int split_len)
for (; j < itr->sub->n; ++j) kv_push(bwtintv_t, *a, itr->sub->a[j]); for (; j < itr->sub->n; ++j) kv_push(bwtintv_t, *a, itr->sub->a[j]);
kv_copy(bwtintv_t, *itr->matches, *a); kv_copy(bwtintv_t, *itr->matches, *a);
} }
return itr->start; return itr->matches;
} }
#include "kbtree.h" #include "kbtree.h"
@ -98,7 +107,7 @@ static int test_and_merge(const memopt_t *opt, memchain1_t *c, const memseed_t *
return 1; // contained seed; do nothing return 1; // contained seed; do nothing
x = p->qbeg - last->qbeg; // always positive x = p->qbeg - last->qbeg; // always positive
y = p->rbeg - last->rbeg; y = p->rbeg - last->rbeg;
if (y > 0 && x - y <= opt->w && y - x <= opt->w && x - last->len < opt->max_chain_gap && y - last->len < opt->max_chain_gap) { if (y > 0 && x - y <= opt->w && y - x <= opt->w && x - last->len < opt->max_chain_gap && y - last->len < opt->max_chain_gap) { // grow the chain
if (c->n == c->m) { if (c->n == c->m) {
c->m <<= 1; c->m <<= 1;
c->seeds = realloc(c->seeds, c->m * sizeof(memseed_t)); c->seeds = realloc(c->seeds, c->m * sizeof(memseed_t));
@ -106,30 +115,31 @@ static int test_and_merge(const memopt_t *opt, memchain1_t *c, const memseed_t *
c->seeds[c->n++] = *p; c->seeds[c->n++] = *p;
return 1; return 1;
} }
return 0; return 0; // request to add a new chain
} }
static void mem_insert_seed(const memopt_t *opt, kbtree_t(chn) *tree, smem_i *itr) static void mem_insert_seed(const memopt_t *opt, kbtree_t(chn) *tree, smem_i *itr)
{ {
while (smem_next(itr, opt->min_seed_len<<1) > 0) { const bwtintv_v *a;
while ((a = smem_next(itr, opt->min_seed_len<<1)) != 0) { // to find all SMEM and some internal MEM
int i; int i;
for (i = 0; i < itr->matches->n; ++i) { for (i = 0; i < a->n; ++i) { // go through each SMEM/MEM up to itr->start
bwtintv_t *p = &itr->matches->a[i]; bwtintv_t *p = &a->a[i];
int slen = (uint32_t)p->info - (p->info>>32); // seed length int slen = (uint32_t)p->info - (p->info>>32); // seed length
int64_t k; int64_t k;
if (slen < opt->min_seed_len || p->x[2] > opt->max_occ) continue; if (slen < opt->min_seed_len || p->x[2] > opt->max_occ) continue; // ignore if too short or too repetitive
for (k = 0; k < p->x[2]; ++k) { for (k = 0; k < p->x[2]; ++k) {
memchain1_t tmp, *lower, *upper; memchain1_t tmp, *lower, *upper;
memseed_t s; memseed_t s;
int to_add = 0; int to_add = 0;
s.rbeg = tmp.pos = bwt_sa(itr->bwt, p->x[0] + k); s.rbeg = tmp.pos = bwt_sa(itr->bwt, p->x[0] + k); // this is the base coordinate in the forward-reverse reference
s.qbeg = p->info>>32; s.qbeg = p->info>>32;
s.len = slen; s.len = slen;
if (kb_size(tree)) { if (kb_size(tree)) {
kb_intervalp(chn, tree, &tmp, &lower, &upper); kb_intervalp(chn, tree, &tmp, &lower, &upper); // find the closest chain
if (!lower || !test_and_merge(opt, lower, &s)) to_add = 1; if (!lower || !test_and_merge(opt, lower, &s)) to_add = 1;
} else to_add = 1; } else to_add = 1;
if (to_add) { if (to_add) { // add the seed as a new chain
tmp.n = 1; tmp.m = 4; tmp.n = 1; tmp.m = 4;
tmp.seeds = calloc(tmp.m, sizeof(memseed_t)); tmp.seeds = calloc(tmp.m, sizeof(memseed_t));
tmp.seeds[0] = s; tmp.seeds[0] = s;

11
bwamem.h
View File

@ -3,13 +3,8 @@
#include "bwt.h" #include "bwt.h"
typedef struct { struct __smem_i;
const bwt_t *bwt; typedef struct __smem_i smem_i;
const uint8_t *query;
int start, len;
bwtintv_v *matches; // matches
bwtintv_v *tmpvec[2], *sub; // these are temporary arrays
} smem_i;
typedef struct { typedef struct {
int64_t rbeg; int64_t rbeg;
@ -39,7 +34,7 @@ extern "C" {
smem_i *smem_itr_init(const bwt_t *bwt); smem_i *smem_itr_init(const bwt_t *bwt);
void smem_itr_destroy(smem_i *itr); void smem_itr_destroy(smem_i *itr);
void smem_set_query(smem_i *itr, int len, const uint8_t *query); void smem_set_query(smem_i *itr, int len, const uint8_t *query);
int smem_next(smem_i *itr, int split_len); const bwtintv_v *smem_next(smem_i *itr, int split_len);
memopt_t *mem_opt_init(void); memopt_t *mem_opt_init(void);

7
fastmap.c
View File

@ -76,6 +76,7 @@ int main_fastmap(int argc, char *argv[])
bwt_t *bwt; bwt_t *bwt;
bntseq_t *bns; bntseq_t *bns;
smem_i *itr; smem_i *itr;
const bwtintv_v *a;
while ((c = getopt(argc, argv, "w:l:ps")) >= 0) { while ((c = getopt(argc, argv, "w:l:ps")) >= 0) {
switch (c) { switch (c) {
@ -111,9 +112,9 @@ int main_fastmap(int argc, char *argv[])
for (i = 0; i < seq->seq.l; ++i) for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]]; seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
smem_set_query(itr, seq->seq.l, (uint8_t*)seq->seq.s); smem_set_query(itr, seq->seq.l, (uint8_t*)seq->seq.s);
while (smem_next(itr, split_long? min_len<<1 : 0) > 0) { while ((a = smem_next(itr, split_long? min_len<<1 : 0)) != 0) {
for (i = 0; i < itr->matches->n; ++i) { for (i = 0; i < a->n; ++i) {
bwtintv_t *p = &itr->matches->a[i]; bwtintv_t *p = &a->a[i];
if ((uint32_t)p->info - (p->info>>32) < min_len) continue; if ((uint32_t)p->info - (p->info>>32) < min_len) continue;
printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]); printf("EM\t%d\t%d\t%ld", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
if (p->x[2] <= min_iwidth) { if (p->x[2] <= min_iwidth) {

384
kbtree.h 100644
View File

@ -0,0 +1,384 @@
/*-
* Copyright 1997-1999, 2001, John-Mark Gurney.
* 2008-2009, Attractive Chaos <attractor@live.co.uk>
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
*
* 1. Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
* OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
* SUCH DAMAGE.
*/
#ifndef __AC_KBTREE_H
#define __AC_KBTREE_H
#include <stdlib.h>
#include <string.h>
#include <stdint.h>
typedef struct {
int32_t is_internal:1, n:31;
} kbnode_t;
#define __KB_KEY(type, x) ((type*)((char*)x + 4))
#define __KB_PTR(btr, x) ((kbnode_t**)((char*)x + btr->off_ptr))
#define __KB_TREE_T(name) \
typedef struct { \
kbnode_t *root; \
int off_key, off_ptr, ilen, elen; \
int n, t; \
int n_keys, n_nodes; \
} kbtree_##name##_t;
#define __KB_INIT(name, key_t) \
kbtree_##name##_t *kb_init_##name(int size) \
{ \
kbtree_##name##_t *b; \
b = (kbtree_##name##_t*)calloc(1, sizeof(kbtree_##name##_t)); \
b->t = ((size - 4 - sizeof(void*)) / (sizeof(void*) + sizeof(key_t)) + 1) >> 1; \
if (b->t < 2) { \
free(b); return 0; \
} \
b->n = 2 * b->t - 1; \
b->off_ptr = 4 + b->n * sizeof(key_t); \
b->ilen = (4 + sizeof(void*) + b->n * (sizeof(void*) + sizeof(key_t)) + 3) >> 2 << 2; \
b->elen = (b->off_ptr + 3) >> 2 << 2; \
b->root = (kbnode_t*)calloc(1, b->ilen); \
++b->n_nodes; \
return b; \
}
#define __kb_destroy(b) do { \
int i, max = 8; \
kbnode_t *x, **top, **stack = 0; \
if (b) { \
top = stack = (kbnode_t**)calloc(max, sizeof(kbnode_t*)); \
*top++ = (b)->root; \
while (top != stack) { \
x = *--top; \
if (x->is_internal == 0) { free(x); continue; } \
for (i = 0; i <= x->n; ++i) \
if (__KB_PTR(b, x)[i]) { \
if (top - stack == max) { \
max <<= 1; \
stack = (kbnode_t**)realloc(stack, max * sizeof(kbnode_t*)); \
top = stack + (max>>1); \
} \
*top++ = __KB_PTR(b, x)[i]; \
} \
free(x); \
} \
} \
free(b); free(stack); \
} while (0)
#define __kb_get_first(key_t, b, ret) do { \
kbnode_t *__x = (b)->root; \
while (__KB_PTR(b, __x)[0] != 0) \
__x = __KB_PTR(b, __x)[0]; \
(ret) = __KB_KEY(key_t, __x)[0]; \
} while (0)
#define __KB_GET_AUX0(name, key_t, __cmp) \
static inline int __kb_get_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
{ \
int tr, *rr, begin, end, n = x->n >> 1; \
if (x->n == 0) return -1; \
if (__cmp(*k, __KB_KEY(key_t, x)[n]) < 0) { \
begin = 0; end = n; \
} else { begin = n; end = x->n - 1; } \
rr = r? r : &tr; \
n = end; \
while (n >= begin && (*rr = __cmp(*k, __KB_KEY(key_t, x)[n])) < 0) --n; \
return n; \
}
#define __KB_GET_AUX1(name, key_t, __cmp) \
static inline int __kb_getp_aux_##name(const kbnode_t * __restrict x, const key_t * __restrict k, int *r) \
{ \
int tr, *rr, begin = 0, end = x->n; \
if (x->n == 0) return -1; \
rr = r? r : &tr; \
while (begin < end) { \
int mid = (begin + end) >> 1; \
if (__cmp(__KB_KEY(key_t, x)[mid], *k) < 0) begin = mid + 1; \
else end = mid; \
} \
if (begin == x->n) { *rr = 1; return x->n - 1; } \
if ((*rr = __cmp(*k, __KB_KEY(key_t, x)[begin])) < 0) --begin; \
return begin; \
}
#define __KB_GET(name, key_t) \
static key_t *kb_getp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
{ \
int i, r = 0; \
kbnode_t *x = b->root; \
while (x) { \
i = __kb_getp_aux_##name(x, k, &r); \
if (i >= 0 && r == 0) return &__KB_KEY(key_t, x)[i]; \
if (x->is_internal == 0) return 0; \
x = __KB_PTR(b, x)[i + 1]; \
} \
return 0; \
} \
static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \
{ \
return kb_getp_##name(b, &k); \
}
#define __KB_INTERVAL(name, key_t) \
static void kb_intervalp_##name(kbtree_##name##_t *b, const key_t * __restrict k, key_t **lower, key_t **upper) \
{ \
int i, r = 0; \
kbnode_t *x = b->root; \
*lower = *upper = 0; \
while (x) { \
i = __kb_getp_aux_##name(x, k, &r); \
if (i >= 0 && r == 0) { \
*lower = *upper = &__KB_KEY(key_t, x)[i]; \
return; \
} \
if (i >= 0) *lower = &__KB_KEY(key_t, x)[i]; \
if (i < x->n - 1) *upper = &__KB_KEY(key_t, x)[i + 1]; \
if (x->is_internal == 0) return; \
x = __KB_PTR(b, x)[i + 1]; \
} \
} \
static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \
{ \
kb_intervalp_##name(b, &k, lower, upper); \
}
#define __KB_PUT(name, key_t, __cmp) \
/* x must be an internal node */ \
static void __kb_split_##name(kbtree_##name##_t *b, kbnode_t *x, int i, kbnode_t *y) \
{ \
kbnode_t *z; \
z = (kbnode_t*)calloc(1, y->is_internal? b->ilen : b->elen); \
++b->n_nodes; \
z->is_internal = y->is_internal; \
z->n = b->t - 1; \
memcpy(__KB_KEY(key_t, z), __KB_KEY(key_t, y) + b->t, sizeof(key_t) * (b->t - 1)); \
if (y->is_internal) memcpy(__KB_PTR(b, z), __KB_PTR(b, y) + b->t, sizeof(void*) * b->t); \
y->n = b->t - 1; \
memmove(__KB_PTR(b, x) + i + 2, __KB_PTR(b, x) + i + 1, sizeof(void*) * (x->n - i)); \
__KB_PTR(b, x)[i + 1] = z; \
memmove(__KB_KEY(key_t, x) + i + 1, __KB_KEY(key_t, x) + i, sizeof(key_t) * (x->n - i)); \
__KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[b->t - 1]; \
++x->n; \
} \
static void __kb_putp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k) \
{ \
int i = x->n - 1; \
if (x->is_internal == 0) { \
i = __kb_getp_aux_##name(x, k, 0); \
if (i != x->n - 1) \
memmove(__KB_KEY(key_t, x) + i + 2, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
__KB_KEY(key_t, x)[i + 1] = *k; \
++x->n; \
} else { \
i = __kb_getp_aux_##name(x, k, 0) + 1; \
if (__KB_PTR(b, x)[i]->n == 2 * b->t - 1) { \
__kb_split_##name(b, x, i, __KB_PTR(b, x)[i]); \
if (__cmp(*k, __KB_KEY(key_t, x)[i]) > 0) ++i; \
} \
__kb_putp_aux_##name(b, __KB_PTR(b, x)[i], k); \
} \
} \
static void kb_putp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
{ \
kbnode_t *r, *s; \
++b->n_keys; \
r = b->root; \
if (r->n == 2 * b->t - 1) { \
++b->n_nodes; \
s = (kbnode_t*)calloc(1, b->ilen); \
b->root = s; s->is_internal = 1; s->n = 0; \
__KB_PTR(b, s)[0] = r; \
__kb_split_##name(b, s, 0, r); \
r = s; \
} \
__kb_putp_aux_##name(b, r, k); \
} \
static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \
{ \
kb_putp_##name(b, &k); \
}
#define __KB_DEL(name, key_t) \
static key_t __kb_delp_aux_##name(kbtree_##name##_t *b, kbnode_t *x, const key_t * __restrict k, int s) \
{ \
int yn, zn, i, r = 0; \
kbnode_t *xp, *y, *z; \
key_t kp; \
if (x == 0) return *k; \
if (s) { /* s can only be 0, 1 or 2 */ \
r = x->is_internal == 0? 0 : s == 1? 1 : -1; \
i = s == 1? x->n - 1 : -1; \
} else i = __kb_getp_aux_##name(x, k, &r); \
if (x->is_internal == 0) { \
if (s == 2) ++i; \
kp = __KB_KEY(key_t, x)[i]; \
memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
--x->n; \
return kp; \
} \
if (r == 0) { \
if ((yn = __KB_PTR(b, x)[i]->n) >= b->t) { \
xp = __KB_PTR(b, x)[i]; \
kp = __KB_KEY(key_t, x)[i]; \
__KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 1); \
return kp; \
} else if ((zn = __KB_PTR(b, x)[i + 1]->n) >= b->t) { \
xp = __KB_PTR(b, x)[i + 1]; \
kp = __KB_KEY(key_t, x)[i]; \
__KB_KEY(key_t, x)[i] = __kb_delp_aux_##name(b, xp, 0, 2); \
return kp; \
} else if (yn == b->t - 1 && zn == b->t - 1) { \
y = __KB_PTR(b, x)[i]; z = __KB_PTR(b, x)[i + 1]; \
__KB_KEY(key_t, y)[y->n++] = *k; \
memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, z), z->n * sizeof(key_t)); \
if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, z), (z->n + 1) * sizeof(void*)); \
y->n += z->n; \
memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
--x->n; \
free(z); \
return __kb_delp_aux_##name(b, y, k, s); \
} \
} \
++i; \
if ((xp = __KB_PTR(b, x)[i])->n == b->t - 1) { \
if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n >= b->t) { \
memmove(__KB_KEY(key_t, xp) + 1, __KB_KEY(key_t, xp), xp->n * sizeof(key_t)); \
if (xp->is_internal) memmove(__KB_PTR(b, xp) + 1, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
__KB_KEY(key_t, xp)[0] = __KB_KEY(key_t, x)[i - 1]; \
__KB_KEY(key_t, x)[i - 1] = __KB_KEY(key_t, y)[y->n - 1]; \
if (xp->is_internal) __KB_PTR(b, xp)[0] = __KB_PTR(b, y)[y->n]; \
--y->n; ++xp->n; \
} else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n >= b->t) { \
__KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i]; \
__KB_KEY(key_t, x)[i] = __KB_KEY(key_t, y)[0]; \
if (xp->is_internal) __KB_PTR(b, xp)[xp->n] = __KB_PTR(b, y)[0]; \
--y->n; \
memmove(__KB_KEY(key_t, y), __KB_KEY(key_t, y) + 1, y->n * sizeof(key_t)); \
if (y->is_internal) memmove(__KB_PTR(b, y), __KB_PTR(b, y) + 1, (y->n + 1) * sizeof(void*)); \
} else if (i > 0 && (y = __KB_PTR(b, x)[i - 1])->n == b->t - 1) { \
__KB_KEY(key_t, y)[y->n++] = __KB_KEY(key_t, x)[i - 1]; \
memmove(__KB_KEY(key_t, y) + y->n, __KB_KEY(key_t, xp), xp->n * sizeof(key_t)); \
if (y->is_internal) memmove(__KB_PTR(b, y) + y->n, __KB_PTR(b, xp), (xp->n + 1) * sizeof(void*)); \
y->n += xp->n; \
memmove(__KB_KEY(key_t, x) + i - 1, __KB_KEY(key_t, x) + i, (x->n - i) * sizeof(key_t)); \
memmove(__KB_PTR(b, x) + i, __KB_PTR(b, x) + i + 1, (x->n - i) * sizeof(void*)); \
--x->n; \
free(xp); \
xp = y; \
} else if (i < x->n && (y = __KB_PTR(b, x)[i + 1])->n == b->t - 1) { \
__KB_KEY(key_t, xp)[xp->n++] = __KB_KEY(key_t, x)[i]; \
memmove(__KB_KEY(key_t, xp) + xp->n, __KB_KEY(key_t, y), y->n * sizeof(key_t)); \
if (xp->is_internal) memmove(__KB_PTR(b, xp) + xp->n, __KB_PTR(b, y), (y->n + 1) * sizeof(void*)); \
xp->n += y->n; \
memmove(__KB_KEY(key_t, x) + i, __KB_KEY(key_t, x) + i + 1, (x->n - i - 1) * sizeof(key_t)); \
memmove(__KB_PTR(b, x) + i + 1, __KB_PTR(b, x) + i + 2, (x->n - i - 1) * sizeof(void*)); \
--x->n; \
free(y); \
} \
} \
return __kb_delp_aux_##name(b, xp, k, s); \
} \
static key_t kb_delp_##name(kbtree_##name##_t *b, const key_t * __restrict k) \
{ \
kbnode_t *x; \
key_t ret; \
ret = __kb_delp_aux_##name(b, b->root, k, 0); \
--b->n_keys; \
if (b->root->n == 0 && b->root->is_internal) { \
--b->n_nodes; \
x = b->root; \
b->root = __KB_PTR(b, x)[0]; \
free(x); \
} \
return ret; \
} \
static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \
{ \
return kb_delp_##name(b, &k); \
}
typedef struct {
kbnode_t *x;
int i;
} __kbstack_t;
#define __kb_traverse(key_t, b, __func) do { \
int __kmax = 8; \
__kbstack_t *__kstack, *__kp; \
__kp = __kstack = (__kbstack_t*)calloc(__kmax, sizeof(__kbstack_t)); \
__kp->x = (b)->root; __kp->i = 0; \
for (;;) { \
while (__kp->x && __kp->i <= __kp->x->n) { \
if (__kp - __kstack == __kmax - 1) { \
__kmax <<= 1; \
__kstack = (__kbstack_t*)realloc(__kstack, __kmax * sizeof(__kbstack_t)); \
__kp = __kstack + (__kmax>>1) - 1; \
} \
(__kp+1)->i = 0; (__kp+1)->x = __kp->x->is_internal? __KB_PTR(b, __kp->x)[__kp->i] : 0; \
++__kp; \
} \
--__kp; \
if (__kp >= __kstack) { \
if (__kp->x && __kp->i < __kp->x->n) __func(&__KB_KEY(key_t, __kp->x)[__kp->i]); \
++__kp->i; \
} else break; \
} \
free(__kstack); \
} while (0)
#define KBTREE_INIT(name, key_t, __cmp) \
__KB_TREE_T(name) \
__KB_INIT(name, key_t) \
__KB_GET_AUX1(name, key_t, __cmp) \
__KB_GET(name, key_t) \
__KB_INTERVAL(name, key_t) \
__KB_PUT(name, key_t, __cmp) \
__KB_DEL(name, key_t)
#define KB_DEFAULT_SIZE 512
#define kbtree_t(name) kbtree_##name##_t
#define kb_init(name, s) kb_init_##name(s)
#define kb_destroy(name, b) __kb_destroy(b)
#define kb_get(name, b, k) kb_get_##name(b, k)
#define kb_put(name, b, k) kb_put_##name(b, k)
#define kb_del(name, b, k) kb_del_##name(b, k)
#define kb_interval(name, b, k, l, u) kb_interval_##name(b, k, l, u)
#define kb_getp(name, b, k) kb_getp_##name(b, k)
#define kb_putp(name, b, k) kb_putp_##name(b, k)
#define kb_delp(name, b, k) kb_delp_##name(b, k)
#define kb_intervalp(name, b, k, l, u) kb_intervalp_##name(b, k, l, u)
#define kb_size(b) ((b)->n_keys)
#define kb_generic_cmp(a, b) (((b) < (a)) - ((a) < (b)))
#define kb_str_cmp(a, b) strcmp(a, b)
#endif