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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// 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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#ifndef TESTS_ALIGN_TEST_ALIGN_SIMD_GLOBAL_H_
#define TESTS_ALIGN_TEST_ALIGN_SIMD_GLOBAL_H_
#include "test_align_simd_base.h"
// ----------------------------------------------------------------------------
// Global Alignments.
// ----------------------------------------------------------------------------
SEQAN_TYPED_TEST(SimdAlignTestCommon, Linear_Align)
{
using TAlignConf = typename TestFixture::TAlignConfig;
using TLengthParam = typename TestFixture::TLengthParam;
using TBandSwitch = typename TestFixture::TBandSwitch;
testAlignSimd<seqan2::Dna>(impl::test_align_simd::GlobalAlignTester_(), seqan2::Score<int>(2, -1, -1),
TAlignConf(), TLengthParam(), TBandSwitch());
testAlignSimd<seqan2::AminoAcid>(impl::test_align_simd::GlobalAlignTester_(), seqan2::Blosum62(-2),
TAlignConf(), TLengthParam(), TBandSwitch());
}
SEQAN_TYPED_TEST(SimdAlignTestCommon, Linear_Score)
{
using TAlignConf = typename TestFixture::TAlignConfig;
using TLengthParam = typename TestFixture::TLengthParam;
using TBandSwitch = typename TestFixture::TBandSwitch;
testAlignSimdScore<seqan2::Dna>(impl::test_align_simd::GlobalAlignScoreTester_(), seqan2::Score<int>(2, -1, -1),
TAlignConf(), TLengthParam(), TBandSwitch());
testAlignSimdScore<seqan2::AminoAcid>(impl::test_align_simd::GlobalAlignScoreTester_(), seqan2::Blosum62(-2),
TAlignConf(), TLengthParam(), TBandSwitch());
}
SEQAN_TYPED_TEST(SimdAlignTestCommon, Affine_Align)
{
using TAlignConf = typename TestFixture::TAlignConfig;
using TLengthParam = typename TestFixture::TLengthParam;
using TBandSwitch = typename TestFixture::TBandSwitch;
testAlignSimd<seqan2::Dna>(impl::test_align_simd::GlobalAlignTester_(), seqan2::Score<int>(2, -1, -1, -3),
TAlignConf(), TLengthParam(), TBandSwitch());
testAlignSimd<seqan2::AminoAcid>(impl::test_align_simd::GlobalAlignTester_(), seqan2::Blosum62(-2, -4),
TAlignConf(), TLengthParam(), TBandSwitch());
}
SEQAN_TYPED_TEST(SimdAlignTestCommon, Dynamic_Score_Matrix_Align)
{
using namespace seqan2;
using TAlignConf = typename TestFixture::TAlignConfig;
using TLengthParam = typename TestFixture::TLengthParam;
using TBandSwitch = typename TestFixture::TBandSwitch;
Score<int, ScoreMatrix<AminoAcid, ScoreSpecSelectable> > dynScore{-2, -4};
setScoreMatrixById(dynScore, AminoAcidScoreMatrixID::PAM120);
testAlignSimd<seqan2::AminoAcid>(::impl::test_align_simd::GlobalAlignTester_(), dynScore,
TAlignConf(), TLengthParam(), TBandSwitch());
}
SEQAN_TYPED_TEST(SimdAlignTestCommon, Affine_Score)
{
using TAlignConf = typename TestFixture::TAlignConfig;
using TLengthParam = typename TestFixture::TLengthParam;
using TBandSwitch = typename TestFixture::TBandSwitch;
testAlignSimdScore<seqan2::Dna>(impl::test_align_simd::GlobalAlignScoreTester_(), seqan2::Score<int>(2, -1, -1, -3),
TAlignConf(), TLengthParam(), TBandSwitch());
testAlignSimdScore<seqan2::AminoAcid>(impl::test_align_simd::GlobalAlignScoreTester_(), seqan2::Blosum62(-2, -4),
TAlignConf(), TLengthParam(), TBandSwitch());
}
SEQAN_TYPED_TEST(SimdAlignTestCommon, Dynamic_Score_Matrix)
{
using namespace seqan2;
using TAlignConf = typename TestFixture::TAlignConfig;
using TLengthParam = typename TestFixture::TLengthParam;
using TBandSwitch = typename TestFixture::TBandSwitch;
Score<int, ScoreMatrix<AminoAcid, ScoreSpecSelectable> > dynScore{-2, -4};
setScoreMatrixById(dynScore, AminoAcidScoreMatrixID::PAM120);
testAlignSimdScore<seqan2::AminoAcid>(::impl::test_align_simd::GlobalAlignScoreTester_(), dynScore,
TAlignConf(), TLengthParam(), TBandSwitch());
}
#endif // #ifndef TESTS_ALIGN_TEST_ALIGN_SIMD_GLOBAL_H_
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