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// ==========================================================================
// pair_align_global.cpp
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: René Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Source file for pairwise global alignment.
// ==========================================================================
#include "pair_align_lib.h"
// Set default values if preprocessor symbols are not set.
#ifndef SUFFIX_GAP_TOP
#define SUFFIX_GAP_TOP 0
#endif // SUFFIX_GAP_TOP
#ifndef SUFFIX_GAP_LEFT
#define SUFFIX_GAP_LEFT 0
#endif // SUFFIX_GAP_LEFT
#ifndef SUFFIX_GAP_RIGHT
#define SUFFIX_GAP_RIGHT 0
#endif // SUFFIX_GAP_RIGHT
#ifndef SUFFIX_GAP_BOTTOM
#define SUFFIX_GAP_BOTTOM 0
#endif // SUFFIX_GAP_BOTTOM
// Defines the suffix for every generated object file.
#define PAIR_ALIGN_GLOBAL_FUNC_SUFFIX SEQAN_JOIN(SEQAN_JOIN(SUFFIX_GAP_TOP, SUFFIX_GAP_LEFT), \
SEQAN_JOIN(SUFFIX_GAP_RIGHT, SUFFIX_GAP_BOTTOM))
// This macro expands to the function resulting from the set preprocessor values SUFFIX_GAP_*.
// Note that the cmake script generates for every AlignConfig combination
// a new object file where the preprocessor definitions are set accordingly.
#define PAIR_ALIGN_DEFINE_GLOBAL_FUNC(name) \
void name(Options const & options) \
{ \
AlignConfig<SUFFIX_GAP_TOP, SUFFIX_GAP_LEFT, SUFFIX_GAP_RIGHT, SUFFIX_GAP_BOTTOM> config; \
if (options.method == "nw") \
pairAlignConfig(options, NeedlemanWunsch(), config); \
else \
pairAlignConfig(options, Gotoh(), config); \
}
PAIR_ALIGN_DEFINE_GLOBAL_FUNC(SEQAN_JOIN(pairAlignGlobal_, PAIR_ALIGN_GLOBAL_FUNC_SUFFIX))
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