From: Heng Li <lh3@live.co.uk>
Date: Thu, 5 May 2011 17:38:26 +0000 (-0400)
Subject: allocate query profile in one memory block
X-Git-Tag: ksprintf-final~43
X-Git-Url: http://www.kaiwu.me/postgresql/commit/?a=commitdiff_plain;h=502b7bb063df94a4be24a1ff1785a1900ec41c8e;p=klib.git

allocate query profile in one memory block
---

diff --git a/ksw.c b/ksw.c
index c49b2df..ff59a0d 100644
--- a/ksw.c
+++ b/ksw.c
@@ -17,7 +17,6 @@ struct _ksw_query_t {
 	int slen;
 	uint8_t shift;
 	__m128i *qp, *H0, *H1, *E;
-	uint8_t *mem;
 };
 
 ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat)
@@ -25,17 +24,16 @@ ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_
 	ksw_query_t *q;
 	uint8_t *aligned;
 	int8_t *t;
-	int qlenp, slen, a, tmp;
+	int qlen16, slen, a, tmp;
 
-	q = calloc(1, sizeof(ksw_query_t));
-	q->slen = slen = (qlen + p - 1) / p; // length of segment
-	qlenp = slen * p; // qlenp can be divided by p
-	q->mem = malloc(64 + qlenp * (m + 2));
-	aligned = (uint8_t*)(((size_t)q->mem + 15) & ~0xful); // align memory
-	q->qp = (__m128i*)aligned;
-	q->H0 = q->qp + qlenp * m;
-	q->H1 = q->H0 + qlenp;
-	q->E  = q->H1 + qlenp;
+	slen = (qlen + p - 1) / p;
+	qlen16 = (qlen + 15) >> 4 << 4;
+	q = malloc(sizeof(ksw_query_t) + 256 + qlen16 * (m + 2)); // a single block of memory
+	q->slen = slen;
+	q->qp = (__m128i*)(((size_t)q + sizeof(ksw_query_t) + 15) >> 4 << 4);
+	q->H0 = q->qp + qlen16 * m;
+	q->H1 = q->H0 + qlen16;
+	q->E  = q->H1 + qlen16;
 	// compute shift
 	tmp = m * m;
 	for (a = 0, q->shift = 127; a < tmp; ++a) // find the minimum score (should be negative)
@@ -48,7 +46,7 @@ ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_
 		int i, k;
 		const int8_t *ma = mat + a * m;
 		for (i = 0; i < slen; ++i)
-			for (k = i; k < qlenp; k += slen) { // p iterations
+			for (k = i; k < qlen16; k += slen) { // p iterations
 				*t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;
 				//printf("%d,%d,%d,%d\n", a, i, k, *(t-1));
 			}
@@ -56,12 +54,6 @@ ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_
 	return q;
 }
 
-void ksw_qdestroy(ksw_query_t *q)
-{
-	if (!q) return;
-	free(q->mem); free(q);
-}
-
 int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, unsigned _e) // the first gap costs -(_o+_e)
 {
 	int slen, i, score;
@@ -151,7 +143,7 @@ int main()
 	uint8_t *q = (uint8_t*)"\1\1";
 	ksw_query_t *qq = ksw_qinit(2, q, 16, 2, mat);
 	int s = ksw_sse2_16(qq, 6, t, 5, 2);
-	ksw_qdestroy(qq);
+	free(qq);
 	printf("%d\n", s);
 	return 0;
 }
diff --git a/ksw.h b/ksw.h
index a3e8580..9525491 100644
--- a/ksw.h
+++ b/ksw.h
@@ -9,7 +9,6 @@ extern "C" {
 #endif
 
 ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat);
-void ksw_qdestroy(ksw_query_t *q);
 int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned o, unsigned e); // first gap costs -(o+e)
 
 #ifdef __cplusplus