added license and a couple of comments

diff --git a/ksw.c b/ksw.c
index a39385276bef4a91f74106a42af4e63bf71ce1fb..09b7fb090ec343447aac3e2910ab31966944b1c8 100644 (file)
--- a/ksw.c
+++ b/ksw.c
@@ -1,3 +1,28 @@
+/* The MIT License
+
+   Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
 #include <stdlib.h>
 #include <stdint.h>
 #include <emmintrin.h>
@@ -17,7 +42,7 @@ struct _ksw_query_t {
        __m128i *qp, *H0, *H1, *E;
 };
 
-ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat)
+ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_t *mat)
 {
        ksw_query_t *q;
        int8_t *t;
@@ -89,7 +114,6 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
                __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
                h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
                h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x86 is little-endian
-//             for (score=0;score<16;++score)printf("%d ", ((int8_t*)&S[0])[score]);printf("\n");
                for (j = 0; LIKELY(j < slen); ++j) {
                        // at the beginning, h=H'(i-1,j-1)
                        h = _mm_adds_epu8(h, S[j]);
@@ -111,9 +135,9 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
                        h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
                }
                gmax = _mm_max_epu8(gmax, max); // NB: H(i,j) updated in the lazy-F loop cannot exceed max
-//             for (score=0;score<16;++score)printf("%d ", ((int8_t*)&gmax)[score]);printf("\n");
+               //for (score=0;score<16;++score)printf("%d ", ((int8_t*)&gmax)[score]);printf("\n");
                // NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
-               for (k = 0; LIKELY(k < 16); ++k) {
+               for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3
                        f = _mm_slli_si128(f, 1);
                        for (j = 0; LIKELY(j < slen); ++j) {
                                h = _mm_load_si128(H1 + j);
@@ -196,7 +220,7 @@ int main(int argc, char *argv[])
        while (kseq_read(ksq) > 0) {
                ksw_query_t *q;
                for (i = 0; i < ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
-               q = ksw_qinit(ksq->seq.l, (uint8_t*)ksq->seq.s, 16, 5, mat);
+               q = ksw_qinit(16, ksq->seq.l, (uint8_t*)ksq->seq.s, 5, mat);
                gzrewind(fpt); kseq_rewind(kst);
                while (kseq_read(kst) > 0) {
                        int s;

diff --git a/ksw.h b/ksw.h
index 2f0176aa5b1e9e39b5270aa0a42196321e684cdd..83fe224a6e5e9c5f95942e0cb4f1822974d59919 100644 (file)
--- a/ksw.h
+++ b/ksw.h
@@ -8,7 +8,7 @@ typedef struct _ksw_query_t ksw_query_t;
 extern "C" {
 #endif
 
-ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat); // to free, simply call free()
+ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_t *mat); // to free, simply call free()
 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