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// ==========================================================================
// test_evaluate_alignment.h
// ==========================================================================
// 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
#ifndef TESTS_ALIGN_TEST_EVALUATE_ALIGNMENT_H_
#define TESTS_ALIGN_TEST_EVALUATE_ALIGNMENT_H_
SEQAN_DEFINE_TEST(test_align_compute_alignment_stats)
{
seqan2::Peptide subject =
"MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE"
"DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH"
"PGDFGADAQGAMNKALELFRKDMASNYK";
seqan2::Peptide query =
"MSLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSA"
"QLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARF"
"PADFTAEAHAAWDKFLSVTEKYR";
seqan2::Align<seqan2::Peptide> align;
resize(rows(align), 2);
setSource(row(align, 0), subject);
setSource(row(align, 1), query);
// Compute the alignment.
seqan2::Blosum62 scoringScheme(-1, -12);
int score = globalAlignment(align, scoringScheme);
// std::cerr << align;
SEQAN_ASSERT_EQ(score, 159);
// Compute alignment statistics.
seqan2::AlignmentStats stats;
score = computeAlignmentStats(stats, align, scoringScheme);
SEQAN_ASSERT_EQ(score, 159);
SEQAN_ASSERT_EQ(stats.numGapOpens, 2u);
SEQAN_ASSERT_EQ(stats.numGapExtensions, 9u);
SEQAN_ASSERT_EQ(stats.numMatches, 41u);
SEQAN_ASSERT_EQ(stats.numMismatches, 96u);
SEQAN_ASSERT_EQ(stats.numPositiveScores, 69u);
SEQAN_ASSERT_EQ(stats.numNegativeScores, 68u);
SEQAN_ASSERT_EQ(stats.alignmentScore, 159);
}
#endif // #ifndef TESTS_ALIGN_TEST_EVALUATE_ALIGNMENT_H_
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