swps3
swps3.h
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1 /*
2  * Copyright (c) 2007-2008 ETH Zürich, Institute of Computational Science
3  *
4  * Permission is hereby granted, free of charge, to any person
5  * obtaining a copy of this software and associated documentation
6  * files (the "Software"), to deal in the Software without
7  * restriction, including without limitation the rights to use,
8  * copy, modify, merge, publish, distribute, sublicense, and/or sell
9  * copies of the Software, and to permit persons to whom the
10  * Software is furnished to do so, subject to the following
11  * conditions:
12  *
13  * The above copyright notice and this permission notice shall be
14  * included in all copies or substantial portions of the Software.
15  *
16  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17  * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
18  * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19  * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
20  * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
21  * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
23  * OTHER DEALINGS IN THE SOFTWARE.
24  */
25 
26 #ifndef SWPS3_H
27 #define SWPS3_H
28 
29 /* For DMA reasons this value needs to be a multiple of 16!!! */
30 #define MAX_SEQ_LENGTH (1024*10)
31 #define MAX_SEQ_NAME_LENGTH (255)
32 #define MATRIX_DIM ('Z'-'A'+1)
33 #define __ALIGNED__ __attribute__((__aligned__(16)))
34 
35 #ifdef __GNUC__
36 #define LIKELY(x) __builtin_expect((x),1)
37 #define UNLIKELY(x) __builtin_expect((x),0)
38 #define EXPORT __attribute__((visibility("default")))
39 #else
40 #define LIKELY(x) (x)
41 #define UNLIKELY(x) (x)
42 #define EXPORT
43 #endif
44 
45 typedef enum{
48  PS3,
50 } SWType;
51 
52 typedef struct{
53  double gapOpen ;
54  double gapExt ;
55  double threshold ;
56 } Options;
57 
58 #endif /* SWPS3_H */