swps3
DynProgr_sse_byte.h
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1 
5 /*
6  * Copyright (c) 2007-2008 ETH Zürich, Institute of Computational Science
7  *
8  * Permission is hereby granted, free of charge, to any person
9  * obtaining a copy of this software and associated documentation
10  * files (the "Software"), to deal in the Software without
11  * restriction, including without limitation the rights to use,
12  * copy, modify, merge, publish, distribute, sublicense, and/or sell
13  * copies of the Software, and to permit persons to whom the
14  * Software is furnished to do so, subject to the following
15  * conditions:
16  *
17  * The above copyright notice and this permission notice shall be
18  * included in all copies or substantial portions of the Software.
19  *
20  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
21  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
22  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
23  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
24  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
25  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
26  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
27  * OTHER DEALINGS IN THE SOFTWARE.
28  */
29 
30 #ifndef STRIPED_BYTE_H
31 #define STRIPED_BYTE_H
32 
33 #include "swps3.h"
34 #include "matrix.h"
35 #include <xmmintrin.h>
36 
37 typedef struct{
38  int len;
39  unsigned char bias;
40  __m128i * profile;
41  __m128i * rD;
42  __m128i * storeOpt;
43  __m128i * loadOpt;
44  u_int8_t data[1];
45 } ProfileByte;
46 
47 ProfileByte * swps3_createProfileByteSSE( const char * query, int queryLen, SBMatrix matrix );
48 double swps3_alignmentByteSSE( ProfileByte * query, const char * db, int dbLen, Options * options );
50 
51 #endif /* STRIPED_BYTE_H */