// ==========================================================================
//                         test_evaluate_alignment.h
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
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// ==========================================================================
// 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_
