#include "divsufsort/divsufsort.h"
#include <string.h>
+#define DIVSUFSORT_TMP1_SIZE (256 * sizeof(saidx_t))
+#define DIVSUFSORT_TMP2_SIZE (256 * 256 * sizeof(saidx_t))
+
/* If ENABLE_LZ_DEBUG is defined, verify that the suffix array satisfies its
* definition.
*
*
* Note: We cap the lcpprev and lcpnext values to the maximum match length so
* that the match-finder need not worry about it later, in the inner loop.
+ *
+ * Note: the LCP array is one of the inputs to this function, but it is used as
+ * temporary space and therefore will be invalidated.
*/
static void
init_salink(struct salink link[restrict],
- const lz_sarray_pos_t LCP[restrict],
+ lz_sarray_pos_t LCP[restrict],
const lz_sarray_pos_t SA[restrict],
const u8 T[restrict],
lz_sarray_pos_t n,
+ lz_sarray_len_t min_match_len,
lz_sarray_len_t max_match_len)
{
- /* Compute salink.next and salink.lcpnext. */
- link[n - 1].next = LZ_SARRAY_POS_MAX;
- link[n - 1].lcpnext = 0;
+ /* Calculate salink.dist_to_next and salink.lcpnext.
+ *
+ * Pass 1 calculates, for each suffix rank, the corresponding
+ * "next_initial" value which is the smallest larger rank that
+ * corresponds to a suffix starting earlier in the string. It also
+ * calculates "lcpnext_initial", which is the number of bytes shared
+ * with that suffix, although to eliminate checks in
+ * lz_sarray_get_matches(), "lcpnext_initial" is set to 0 if it's less
+ * than the minimum match length or set to the maximum match length if
+ * it's greater than the maximum match length.
+ *
+ * Pass 2 translates each absolute "next_initial", a 4-byte value, into
+ * a relative "dist_to_next", a 1-byte value. This is done to save
+ * memory. In the case that the true relative distance cannot be
+ * encoded in 1 byte, it is capped to 255. This is valid as long as
+ * lz_sarray_get_matches() validates each position before using it.
+ * Note that "lcpnext" need not be updated in this case because it will
+ * not be used until the actual next rank has been found anyway.
+ */
+ link[n - 1].next_initial = LZ_SARRAY_POS_MAX;
+ link[n - 1].lcpnext_initial = 0;
for (lz_sarray_pos_t r = n - 2; r != LZ_SARRAY_POS_MAX; r--) {
lz_sarray_pos_t t = r + 1;
lz_sarray_pos_t l = LCP[t];
while (t != LZ_SARRAY_POS_MAX && SA[t] > SA[r]) {
- l = min(l, link[t].lcpnext);
- t = link[t].next;
+ l = min(l, link[t].lcpnext_initial);
+ t = link[t].next_initial;
}
- link[r].next = t;
- link[r].lcpnext = min(l, max_match_len);
+ link[r].next_initial = t;
+
+ if (l < min_match_len)
+ l = 0;
+ else if (l > max_match_len)
+ l = max_match_len;
+ link[r].lcpnext_initial = l;
+ }
+ for (lz_sarray_pos_t r = 0; r < n; r++) {
+ lz_sarray_pos_t next;
+ lz_sarray_len_t l;
+ lz_sarray_delta_t dist_to_next;
+
+ next = link[r].next_initial;
+ l = link[r].lcpnext_initial;
+
+ if (next == LZ_SARRAY_POS_MAX)
+ dist_to_next = 0;
+ else if (next - r <= LZ_SARRAY_DELTA_MAX)
+ dist_to_next = next - r;
+ else
+ dist_to_next = LZ_SARRAY_DELTA_MAX;
+
+ link[r].lcpnext = l;
+ link[r].dist_to_next = dist_to_next;
}
- /* Compute salink.prev and salink.lcpprev. */
- link[0].prev = LZ_SARRAY_POS_MAX;
+ /* Calculate salink.dist_to_prev and salink.lcpprev.
+ *
+ * This is analgous to dist_to_next and lcpnext as described above, but
+ * in the other direction. That is, here we're interested in, for each
+ * rank, the largest smaller rank that corresponds to a suffix starting
+ * earlier in the string.
+ *
+ * To save memory we don't have a "prev_initial" field, but rather store
+ * those values in the LCP array.
+ */
+ LCP[0] = LZ_SARRAY_POS_MAX;
link[0].lcpprev = 0;
for (lz_sarray_pos_t r = 1; r < n; r++) {
lz_sarray_pos_t t = r - 1;
lz_sarray_pos_t l = LCP[r];
while (t != LZ_SARRAY_POS_MAX && SA[t] > SA[r]) {
l = min(l, link[t].lcpprev);
- t = link[t].prev;
+ t = LCP[t];
}
- link[r].prev = t;
- link[r].lcpprev = min(l, max_match_len);
+ LCP[r] = t;
+
+ if (l < min_match_len)
+ l = 0;
+ else if (l > max_match_len)
+ l = max_match_len;
+
+ link[r].lcpprev = l;
+ }
+ for (lz_sarray_pos_t r = 0; r < n; r++) {
+
+ lz_sarray_pos_t prev = LCP[r];
+
+ if (prev == LZ_SARRAY_POS_MAX)
+ link[r].dist_to_prev = 0;
+ else if (r - prev <= LZ_SARRAY_DELTA_MAX)
+ link[r].dist_to_prev = r - prev;
+ else
+ link[r].dist_to_prev = LZ_SARRAY_DELTA_MAX;
}
}
const lz_sarray_pos_t SA[],
const u8 T[],
lz_sarray_pos_t n,
+ lz_sarray_len_t min_match_len,
lz_sarray_len_t max_match_len)
{
#ifdef ENABLE_LZ_DEBUG
for (lz_sarray_pos_t r = 0; r < n; r++) {
for (lz_sarray_pos_t prev = r; ; ) {
if (prev == 0) {
- LZ_ASSERT(link[r].prev == LZ_SARRAY_POS_MAX);
+ LZ_ASSERT(link[r].dist_to_prev == 0);
LZ_ASSERT(link[r].lcpprev == 0);
break;
}
prev--;
if (SA[prev] < SA[r]) {
- LZ_ASSERT(link[r].prev == prev);
- LZ_ASSERT(link[r].lcpprev <= n - SA[prev]);
- LZ_ASSERT(link[r].lcpprev <= n - SA[r]);
- LZ_ASSERT(link[r].lcpprev <= max_match_len);
- LZ_ASSERT(0 == memcmp(&T[SA[prev]],
- &T[SA[r]],
- link[r].lcpprev));
- if (link[r].lcpprev < n - SA[prev] &&
- link[r].lcpprev < n - SA[r] &&
- link[r].lcpprev < max_match_len)
- {
- LZ_ASSERT(T[SA[prev] + link[r].lcpprev] !=
- T[SA[r] + link[r].lcpprev]);
- }
+ LZ_ASSERT(link[r].dist_to_prev == min(r - prev, LZ_SARRAY_DELTA_MAX));
+
+ lz_sarray_pos_t lcpprev;
+ for (lcpprev = 0;
+ lcpprev < min(n - SA[prev], n - SA[r]) &&
+ T[SA[prev] + lcpprev] == T[SA[r] + lcpprev];
+ lcpprev++)
+ ;
+ if (lcpprev < min_match_len)
+ lcpprev = 0;
+ else if (lcpprev > max_match_len)
+ lcpprev = max_match_len;
+
+ LZ_ASSERT(lcpprev == link[r].lcpprev);
break;
}
}
for (lz_sarray_pos_t next = r; ; ) {
if (next == n - 1) {
- LZ_ASSERT(link[r].next == LZ_SARRAY_POS_MAX);
+ LZ_ASSERT(link[r].dist_to_next == 0);
LZ_ASSERT(link[r].lcpnext == 0);
break;
}
next++;
if (SA[next] < SA[r]) {
- LZ_ASSERT(link[r].next == next);
- LZ_ASSERT(link[r].lcpnext <= n - SA[next]);
- LZ_ASSERT(link[r].lcpnext <= n - SA[r]);
- LZ_ASSERT(link[r].lcpnext <= max_match_len);
- LZ_ASSERT(0 == memcmp(&T[SA[next]],
- &T[SA[r]],
- link[r].lcpnext));
- if (link[r].lcpnext < n - SA[next] &&
- link[r].lcpnext < n - SA[r] &&
- link[r].lcpnext < max_match_len)
- {
- LZ_ASSERT(T[SA[next] + link[r].lcpnext] !=
- T[SA[r] + link[r].lcpnext]);
-
- }
+ LZ_ASSERT(link[r].dist_to_next == min(next - r, LZ_SARRAY_DELTA_MAX));
+
+ lz_sarray_pos_t lcpnext;
+ for (lcpnext = 0;
+ lcpnext < min(n - SA[next], n - SA[r]) &&
+ T[SA[next] + lcpnext] == T[SA[r] + lcpnext];
+ lcpnext++)
+ ;
+ if (lcpnext < min_match_len)
+ lcpnext = 0;
+ else if (lcpnext > max_match_len)
+ lcpnext = max_match_len;
+
+ LZ_ASSERT(lcpnext == link[r].lcpnext);
break;
}
}
if ((u64)2 * max_window_size * sizeof(mf->SA[0]) !=
2 * max_window_size * sizeof(mf->SA[0]))
return false;
- mf->SA = MALLOC(2 * max_window_size * sizeof(mf->SA[0]));
+ mf->SA = MALLOC(max_window_size * sizeof(mf->SA[0]) +
+ max(DIVSUFSORT_TMP1_SIZE,
+ max_window_size * sizeof(mf->SA[0])));
if (mf->SA == NULL)
return false;
if ((u64)max_window_size * sizeof(mf->salink[0]) !=
max_window_size * sizeof(mf->salink[0]))
return false;
- mf->salink = MALLOC(max_window_size * sizeof(mf->salink[0]));
+ mf->salink = MALLOC(max(DIVSUFSORT_TMP2_SIZE,
+ max_window_size * sizeof(mf->salink[0])));
if (mf->salink == NULL)
return false;
* Return the number of bytes of memory that lz_sarray_init() would allocate for
* the specified maximum window size.
*
- * This should be (20 * @max_window_size) unless the type definitions have been
+ * This should be (14 * @max_window_size) unless the type definitions have been
* changed.
*/
u64
u64 size = 0;
/* SA and ISA: 8 bytes per position */
- size += (u64)max_window_size * 2 * sizeof(((struct lz_sarray*)0)->SA[0]);
+ size += (u64)max_window_size * sizeof(((struct lz_sarray*)0)->SA[0]) +
+ max(DIVSUFSORT_TMP1_SIZE,
+ (u64)max_window_size * sizeof(((struct lz_sarray*)0)->SA[0]));
- /* salink: 12 bytes per position */
- size += (u64)max_window_size * sizeof(((struct lz_sarray*)0)->salink[0]);
+ /* salink: 6 bytes per position */
+ size += max(DIVSUFSORT_TMP2_SIZE,
+ (u64)max_window_size * sizeof(((struct lz_sarray*)0)->salink[0]));
return size;
}
/* Compute SA (Suffix Array).
*
* divsufsort() needs temporary space --- one array with 256 spaces and
- * one array with 65536 spaces. The implementation has been modified
- * from the original to use the provided temporary space instead of
- * allocating its own.
+ * one array with 65536 spaces. The implementation of divsufsort() has
+ * been modified from the original to use the provided temporary space
+ * instead of allocating its own.
*
* We also check at build-time that divsufsort() uses the same integer
* size expected by this code. Unfortunately, divsufsort breaks if
* 'sa_idx_t' is defined to be a 16-bit integer; however, that would
* limit blocks to only 65536 bytes anyway. */
- LZ_ASSERT(mf->max_window_size * sizeof(mf->SA[0])
- >= 256 * sizeof(saidx_t));
- LZ_ASSERT(mf->max_window_size * sizeof(mf->salink[0])
- >= 256 * 256 * sizeof(saidx_t));
BUILD_BUG_ON(sizeof(lz_sarray_pos_t) != sizeof(saidx_t));
divsufsort(T, mf->SA, n, (saidx_t*)&mf->SA[n], (saidx_t*)mf->salink);
* end. This is probably worth it because computing the ISA from the SA
* is very fast, and since this match-finder is memory-hungry we'd like
* to save as much memory as possible. */
+ BUILD_BUG_ON(sizeof(mf->salink[0]) < sizeof(mf->ISA[0]));
ISA = (lz_sarray_pos_t*)mf->salink;
compute_inverse_suffix_array(ISA, mf->SA, n);
verify_lcp_array(LCP, mf->SA, T, n);
/* Initialize suffix array links. */
- init_salink(mf->salink, LCP, mf->SA, T, n, mf->max_match_len);
- verify_salink(mf->salink, mf->SA, T, n, mf->max_match_len);
+ init_salink(mf->salink, LCP, mf->SA, T, n,
+ mf->min_match_len, mf->max_match_len);
+ verify_salink(mf->salink, mf->SA, T, n,
+ mf->min_match_len, mf->max_match_len);
/* Compute ISA (Inverse Suffix Array) in its final position. */
ISA = mf->SA + n;
git://wimlib.net / wimlib / blobdiff