matrix.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
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 */

#ifndef MATRIX_H
#define MATRIX_H

#include "swps3.h"
#include <sys/types.h>

typedef int8_t * SBMatrix;
typedef double * DMatrix;

DMatrix swps3_readDMatrix( char * filename );
SBMatrix swps3_readSBMatrix( char * filename );
SBMatrix swps3_convertMatrixD2SB( double factor );
double swps3_factorFromThreshold( double threshold, double singleGapCost );

#endif /* MATRIX_H */

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