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DynProgr_sse_byte.h
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/*
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* Copyright (c) 2007-2008 ETH Zürich, Institute of Computational Science
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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#ifndef STRIPED_BYTE_H
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#define STRIPED_BYTE_H
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#include "
swps3.h
"
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#include "
matrix.h
"
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#include <xmmintrin.h>
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typedef
struct
{
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int
len
;
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unsigned
char
bias
;
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__m128i *
profile
;
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__m128i *
rD
;
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__m128i *
storeOpt
;
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__m128i *
loadOpt
;
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u_int8_t data[1];
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}
ProfileByte
;
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ProfileByte
*
swps3_createProfileByteSSE
(
const
char
* query,
int
queryLen,
SBMatrix
matrix );
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double
swps3_alignmentByteSSE
(
ProfileByte
* query,
const
char
* db,
int
dbLen,
Options
* options );
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void
swps3_freeProfileByteSSE
(
ProfileByte
*
profile
);
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#endif
/* STRIPED_BYTE_H */
DynProgr_sse_byte.h
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