swps3
matrix.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
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28  */
29 
30 #ifndef MATRIX_H
31 #define MATRIX_H
32 
33 #include "swps3.h"
34 #include <sys/types.h>
35 
36 typedef int8_t * SBMatrix;
37 typedef double * DMatrix;
38 
39 DMatrix swps3_readDMatrix( char * filename );
40 SBMatrix swps3_readSBMatrix( char * filename );
41 SBMatrix swps3_convertMatrixD2SB( double factor );
42 double swps3_factorFromThreshold( double threshold, double singleGapCost );
43 
44 #endif /* MATRIX_H */