swps3.h

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/*
 * Copyright (c) 2007-2008 ETH Zürich, Institute of Computational Science
 *
 * 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.
 */

#ifndef SWPS3_H
#define SWPS3_H

/* For DMA reasons this value needs to be a multiple of 16!!! */
#define MAX_SEQ_LENGTH (1024*10)
#define MAX_SEQ_NAME_LENGTH (255)
#define MATRIX_DIM ('Z'-'A'+1)
#define __ALIGNED__ __attribute__((__aligned__(16)))

#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x),1) 
#define UNLIKELY(x) __builtin_expect((x),0) 
#define EXPORT __attribute__((visibility("default"))) 
#else
#define LIKELY(x) (x) 
#define UNLIKELY(x) (x) 
#define EXPORT 
#endif

typedef enum{
        SCALAR,
        SSE2,
        PS3,
        ALTIVEC
} SWType;

typedef struct{
        double gapOpen ;
        double gapExt ;
        double threshold ;
} Options;

#endif /* SWPS3_H */

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