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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>
// ==========================================================================
// Unit tests for the global interfaces to test dynamic gap costs.
// ==========================================================================
#ifndef TESTS_ALIGN_TEST_ALIGNMENT_ALGORITHMS_DYNAMIC_GAP_H_
#define TESTS_ALIGN_TEST_ALIGNMENT_ALGORITHMS_DYNAMIC_GAP_H_
#include <seqan/basic.h>
#include <seqan/align.h>
template <typename TAlignment, bool FreeTop, bool FreeLeft, bool FreeRight, bool FreeBottom, typename TACSpec,
typename TScore>
bool _validateAlignment(TAlignment const & align,
seqan2::AlignConfig<FreeTop, FreeLeft, FreeRight, FreeBottom, TACSpec> const & /*conf*/,
TScore const & score,
seqan2::Score<TScore, seqan2::Simple> const & scoreScheme)
{
using namespace seqan2;
typedef typename Row<TAlignment const>::Type TRow;
typedef typename Iterator<TRow, Standard>::Type TRowIterator;
SEQAN_ASSERT_EQ(length(row(align,0)), length(row(align, 1)));
if (length(row(align, 0)) == 0u && length(row(align, 1)) == 0u)
return true;
TRowIterator itH = begin(row(align, 0), Standard());
TRowIterator itV = begin(row(align, 1), Standard());
bool inGapH = false;
bool inGapV = false;
int eScore = 0;
while (itH != end(row(align, 0), Standard()) && itV != end(row(align, 1), Standard()))
{
if (isGap(itH))
{
inGapV = false;
if (!inGapH)
{
eScore += scoreGapOpen(scoreScheme);
inGapH = true;
}
else
{
eScore += scoreGapExtend(scoreScheme);
}
}
else if (isGap(itV))
{
inGapH = false;
if (!inGapV)
{
eScore += scoreGapOpen(scoreScheme);
inGapV = true;
}
else
{
eScore += scoreGapExtend(scoreScheme);
}
}
else
{
inGapH = false;
inGapV = false;
if (*itH == *itV)
eScore += scoreMatch(scoreScheme);
else
eScore += scoreMismatch(scoreScheme);
}
++itH; ++itV;
}
// Resolve the begin gaps.
if (FreeLeft)
{
itH = begin(row(align, 0), Standard());
inGapH = false;
while (isGap(itH))
{
if (inGapH)
eScore -= scoreGapExtend(scoreScheme);
else
{
inGapH = true;
eScore -= scoreGapOpen(scoreScheme);
}
++itH;
}
}
if (FreeTop)
{
itV = begin(row(align, 1), Standard());
inGapV = false;
while (isGap(itV))
{
if (inGapV)
eScore -= scoreGapExtend(scoreScheme);
else
{
inGapV = true;
eScore -= scoreGapOpen(scoreScheme);
}
++itV;
}
}
if (FreeRight)
{
itH = end(row(align, 0), Standard()) - 1;
inGapH = false;
while (isGap(itH))
{
if (inGapH)
eScore -= scoreGapExtend(scoreScheme);
else
{
inGapH = true;
eScore -= scoreGapOpen(scoreScheme);
}
--itH;
}
}
if (FreeBottom)
{
itV = end(row(align, 1), Standard()) - 1;
inGapV = false;
while (isGap(itV))
{
if (inGapV)
eScore -= scoreGapExtend(scoreScheme);
else
{
inGapV = true;
eScore -= scoreGapOpen(scoreScheme);
}
--itV;
}
}
return eScore == score;
}
template <typename TAlign, typename TAlgorithm, typename TAlignConfig>
void testDynamicGapInterfaces(TAlign & alignObj,
TAlgorithm const & /*algorithm*/,
TAlignConfig const & alignConfig,
int lDiag = 0,
int uDiag = 0)
{
using namespace seqan2;
Score<int, Simple> scoreScheme(2, -2, -1, -4);
if (IsSameType<TAlgorithm, SmithWaterman>::VALUE)
{
ignoreUnusedVariableWarning(alignConfig);
int score;
if (lDiag == 0 && uDiag == 0)
score = localAlignment(alignObj, scoreScheme, DynamicGaps());
else
score = localAlignment(alignObj, scoreScheme, lDiag, uDiag, DynamicGaps());
SEQAN_ASSERT(_validateAlignment(alignObj, alignConfig, score, scoreScheme));
}
else
{
// search global alignment
int score;
if (lDiag == 0 && uDiag == 0)
score = globalAlignment(alignObj, scoreScheme, alignConfig, DynamicGaps());
else
score = globalAlignment(alignObj, scoreScheme, alignConfig, lDiag, uDiag, DynamicGaps());
SEQAN_ASSERT(_validateAlignment(alignObj, alignConfig, score, scoreScheme));
}
}
template <typename TAlgorithm, typename TAlignConfig>
void testDynamicGapInterfaces(TAlgorithm const & algo,
TAlignConfig const & alignConfig,
int lDiag = 0,
int uDiag = 0)
{
using namespace seqan2;
{
DnaString str1 = "AAAAACTACGTACGTTTCTGGCCCCC"; // A G T A G C T A C G T A C G T T T C T G G A T G A C
DnaString str2 = "CCCCCCACGTGTTACGTACGTAAAAA"; // G G T G A C A C G T G T T A C G T A C G T A A
Align<DnaString> alignObj;
resize(rows(alignObj), 2);
assignSource(row(alignObj, 0), str1);
assignSource(row(alignObj, 1), str2);
testDynamicGapInterfaces(alignObj, algo, alignConfig, lDiag, uDiag);
}
{
DnaString str1 = "AAAAACTACGTACGTTTCTGGCCCCC";
DnaString str2 = "CCCCCCACGTGTTACGTACGTAAAAA";
Align<DnaString> alignObj;
resize(rows(alignObj), 2);
assignSource(row(alignObj, 0), str1);
assignSource(row(alignObj, 1), str2);
testDynamicGapInterfaces(alignObj, algo, alignConfig, lDiag, uDiag);
}
{
DnaString str1 = "AAAAAGGGGTTTT";
DnaString str2 = "AAAGTT";
Align<DnaString> alignObj;
resize(rows(alignObj), 2);
assignSource(row(alignObj, 0), str1);
assignSource(row(alignObj, 1), str2);
testDynamicGapInterfaces(alignObj, algo, alignConfig, lDiag, uDiag);
}
{
DnaString str1 = "AAAAAATTTTTGGG";
DnaString str2 = "TTTTTTTTGGGGGGGG";
Align<DnaString> alignObj;
resize(rows(alignObj), 2);
assignSource(row(alignObj, 0), str1);
assignSource(row(alignObj, 1), str2);
testDynamicGapInterfaces(alignObj, algo, alignConfig, lDiag, uDiag);
}
{
DnaString str1 = "GGGGCTTTTTTAAAGAGCGCCCTTTTTTGGGG";
DnaString str2 = "AAAACTTTTTTGGTTTTTTAAAA";
Align<DnaString> alignObj;
resize(rows(alignObj), 2);
assignSource(row(alignObj, 0), str1);
assignSource(row(alignObj, 1), str2);
testDynamicGapInterfaces(alignObj, algo, alignConfig, lDiag, uDiag);
}
}
SEQAN_DEFINE_TEST(test_alignment_algorithms_global_dynamic_cost)
{
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<>());
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<false, true, true, false>());
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<true, false, false, true>());
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<true, true, true, true>());
}
SEQAN_DEFINE_TEST(test_alignment_algorithms_global_dynamic_cost_banded)
{
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<>(), -3, 3);
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<false, true, true, false>(), -3, 3);
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<true, false, false, true>(), -3, 3);
testDynamicGapInterfaces(seqan2::NeedlemanWunsch(), seqan2::AlignConfig<true, true, true, true>(), -3, 3);
}
SEQAN_DEFINE_TEST(test_alignment_algorithms_local_dynamic_cost)
{
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>());
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>());
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>());
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>());
}
SEQAN_DEFINE_TEST(test_alignment_algorithms_local_dynamic_cost_banded)
{
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>(), -3, 3);
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>(), -3, 3);
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>(), -3, 3);
testDynamicGapInterfaces(seqan2::SmithWaterman(), seqan2::AlignConfig<>(), -3, 3);
}
#endif // TESTS_ALIGN_TEST_ALIGNMENT_ALGORITHMS_DYNAMIC_GAP_H_
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