// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>
// ==========================================================================
// Tests for the blast module
// ==========================================================================

#ifndef SEQAN_TESTS_TEST_BLAST_STATISTICS_H_
#define SEQAN_TESTS_TEST_BLAST_STATISTICS_H_

using namespace seqan2;

SEQAN_DEFINE_TEST(test_blast_scoring_scheme_conversion)
{
    typedef Blosum62 TScheme;
    BlastScoringScheme<TScheme> scheme;
    setScoreGapExtend(scheme, -1);
    setScoreGapOpenBlast(scheme, -11);
    SEQAN_ASSERT(isValid(scheme));

    SEQAN_ASSERT_EQ(scoreGapExtend(scheme), -1);
    SEQAN_ASSERT_EQ(scoreGapOpenBlast(scheme), -11);
    SEQAN_ASSERT_EQ(scoreGapOpen(scheme), -12);

    SEQAN_ASSERT_EQ(scoreGapExtend(seqanScheme(scheme)), -1);
    SEQAN_ASSERT_EQ(scoreGapOpen(seqanScheme(scheme)), -12);

    setScoreGapExtend(scheme, -3);
    SEQAN_ASSERT(!isValid(scheme)); // no karlin altschul values exist for this combination
    SEQAN_ASSERT_EQ(scoreGapExtend(scheme), -3);
    SEQAN_ASSERT_EQ(scoreGapOpenBlast(scheme), -11);
    SEQAN_ASSERT_EQ(scoreGapOpen(scheme), -14); // open changed as well!

    SEQAN_ASSERT_EQ(scoreGapExtend(seqanScheme(scheme)), -3);
    SEQAN_ASSERT_EQ(scoreGapOpen(seqanScheme(scheme)), -14);

    setScoreGapExtend(scheme, -2);
    setScoreGapOpen(scheme, -9); // setScorGapOpen in seqan convention
    SEQAN_ASSERT(isValid(scheme)); // valid again
    SEQAN_ASSERT_EQ(scoreGapExtend(scheme), -2);
    SEQAN_ASSERT_EQ(scoreGapOpenBlast(scheme), -7);
    SEQAN_ASSERT_EQ(scoreGapOpen(scheme), -9); // open changed as well!

    SEQAN_ASSERT_EQ(scoreGapExtend(seqanScheme(scheme)), -2);
    SEQAN_ASSERT_EQ(scoreGapOpen(seqanScheme(scheme)), -9);
}

SEQAN_DEFINE_TEST(test_blast_scoring_scheme)
{
    // Blosum62 and some general stuff
    {
        typedef Blosum62 TScheme;
        BlastScoringScheme<TScheme> scheme;
        setScoreGapOpenBlast(scheme, -11);
        setScoreGapExtend(scheme, -1);

        // TEST isValid()
        SEQAN_ASSERT(isValid(scheme));
        // TEST get*
        SEQAN_ASSERT_EQ(getLambda(scheme), 0.267);
        SEQAN_ASSERT_EQ(getKappa(scheme),  0.041);
        SEQAN_ASSERT_EQ(getH(scheme),      0.140);
        SEQAN_ASSERT_EQ(getAlpha(scheme),  1.900);
        SEQAN_ASSERT_EQ(getBeta(scheme), -30.000);

        setScoreGapOpen(scheme, -1);
        setScoreGapExtend(scheme, -11);
        SEQAN_ASSERT(!isValid(scheme));// invalid parameters, because not the setScoreGap*Blast version

        // reset to valid
        setScoreGapOpenBlast(scheme, -11);
        setScoreGapExtend(scheme, -1);

        // now check values again
        SEQAN_ASSERT(isValid(scheme));
        // TEST get*
        SEQAN_ASSERT_EQ(getLambda(scheme), 0.267);
        SEQAN_ASSERT_EQ(getKappa(scheme),  0.041);
        SEQAN_ASSERT_EQ(getH(scheme),      0.140);
        SEQAN_ASSERT_EQ(getAlpha(scheme),  1.900);
        SEQAN_ASSERT_EQ(getBeta(scheme), -30.000);
    }

    // Blosum45
    {
        typedef Blosum45 TScheme;
        BlastScoringScheme<TScheme> scheme;
        setScoreGapOpenBlast(scheme, -11);
        setScoreGapExtend(scheme, -3);

        // TEST isValid()
        SEQAN_ASSERT(isValid(scheme));
        // TEST get*
        SEQAN_ASSERT_EQ(getLambda(scheme), 0.190);
        SEQAN_ASSERT_EQ(getKappa(scheme),  0.031);
        SEQAN_ASSERT_EQ(getH(scheme),      0.095);
        SEQAN_ASSERT_EQ(getAlpha(scheme),  2.000);
        SEQAN_ASSERT_EQ(getBeta(scheme), -38.000);
    }

    // Blosum80
    {
        typedef Blosum80 TScheme;
        BlastScoringScheme<TScheme> scheme;
        setScoreGapOpenBlast(scheme, -11);
        setScoreGapExtend(scheme, -1);

        // TEST isValid()
        SEQAN_ASSERT(isValid(scheme));
        // TEST get*
        SEQAN_ASSERT_EQ(getLambda(scheme), 0.314);
        SEQAN_ASSERT_EQ(getKappa(scheme),  0.095);
        SEQAN_ASSERT_EQ(getH(scheme),      0.350);
        SEQAN_ASSERT_EQ(getAlpha(scheme),  0.900);
        SEQAN_ASSERT_EQ(getBeta(scheme),  -9.000);
    }

    // Pam250
    {
        typedef Pam250 TScheme;
        BlastScoringScheme<TScheme> scheme;
        setScoreGapOpenBlast(scheme, -11);
        setScoreGapExtend(scheme, -3);

        // TEST isValid()
        SEQAN_ASSERT(isValid(scheme));
        // TEST get*
        SEQAN_ASSERT_EQ(getLambda(scheme), 0.174);
        SEQAN_ASSERT_EQ(getKappa(scheme),  0.020);
        SEQAN_ASSERT_EQ(getH(scheme),      0.070);
        SEQAN_ASSERT_EQ(getAlpha(scheme),  2.500);
        SEQAN_ASSERT_EQ(getBeta(scheme), -48.000);
    }

    // SimpleScore
    {
        typedef Score<int, Simple> TScheme;
        BlastScoringScheme<TScheme> scheme;
        setScoreMatch(scheme, 2);
        setScoreMismatch(scheme, -3);
        setScoreGapOpenBlast(scheme, -4);
        setScoreGapExtend(scheme, -2);

        // TEST isValid()
        SEQAN_ASSERT(isValid(scheme));
        // TEST get*
        SEQAN_ASSERT_EQ(getLambda(scheme), 0.610);
        SEQAN_ASSERT_EQ(getKappa(scheme),  0.350);
        SEQAN_ASSERT_EQ(getH(scheme),      0.680);
        SEQAN_ASSERT_EQ(getAlpha(scheme),  0.900);
        SEQAN_ASSERT_EQ(getBeta(scheme),  -3.000);
    }
}

SEQAN_DEFINE_TEST(test_blast_blastmatch_stats_and_score)
{
    typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps;
    typedef BlastMatch<TGaps, TGaps> TBlastMatch;

    TBlastMatch m;

    String<AminoAcid> src0 = "ARNDAYVBRNDCQFGCYVBQARNDCQEGEG";
    String<AminoAcid> src1 = "ARNAYVBRNDCCYCYVBQARNQEGEG";

    assignSource(m.alignRow0, src0);
    assignSource(m.alignRow1, src1);

    typedef Blosum62 TScheme;
    BlastScoringScheme<TScheme> scheme;
    setScoreGapOpenBlast(scheme, -11);
    setScoreGapExtend(scheme, -1);
    SEQAN_ASSERT(isValid(scheme));

    int score = globalAlignment(m.alignRow0, m.alignRow1, seqanScheme(scheme));
//     ARNDAYVBRNDCQFGCYVBQARNDCQEGEG
//     ||| ||||||||   ||||||||  |||||
//     ARN-AYVBRNDCCY-CYVBQARN--QEGEG

    SEQAN_ASSERT_EQ(score, 94);

    computeAlignmentStats(m.alignStats, m.alignRow0, m.alignRow1, seqanScheme(scheme));

    SEQAN_ASSERT_EQ(m.alignStats.alignmentScore, score);
    SEQAN_ASSERT_EQ(m.alignStats.alignmentLength, 30u);
    SEQAN_ASSERT_EQ(m.alignStats.numMatches, 24u);
    SEQAN_ASSERT_EQ(m.alignStats.numPositiveScores, 25u);
    SEQAN_ASSERT_EQ(m.alignStats.numMismatches, 2u);
    SEQAN_ASSERT_EQ(m.alignStats.numGapExtensions, 1u);
    SEQAN_ASSERT_EQ(m.alignStats.numGapOpens, 3u);
}

SEQAN_DEFINE_TEST(test_blast_blastmatch_bit_score_e_value)
{
    typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps;
    typedef BlastMatch<TGaps, TGaps> TBlastMatch;
    typedef Blosum62 TScheme;

    TBlastMatch m;

    String<AminoAcid> src0 =
    "SSITEEKHIPHKEQDKDAEFLSKEALKTHMTENVLQMDRRAVQDPSTSFLQLLKAKGLLG"
    "LPDYEVNLADVNSPGFRKVAYAQTKPRRLCFPNGGTRRGSFIMDTAVVVMVSLRYVNIGK"
    "VIFPGATDVSEGEDEFWAGLPQAYGCLATEFLCIHIAIYSWIHVQSSRYDDMNASVIRAK"
    "LNLPGGLTLIQARGNEKETI";
    String<AminoAcid> src1 = "VAYAQPRKLCYP";

    assignSource(m.alignRow0, src0);
    assignSource(m.alignRow1, src1);

    BlastScoringScheme<TScheme> scheme;
    setScoreGapOpenBlast(scheme, -11);
    setScoreGapExtend(scheme, -1);
    SEQAN_ASSERT(isValid(scheme));

    int score = localAlignment(m.alignRow0, m.alignRow1, seqanScheme(scheme));
//         VAYAQTKPRRLCFP
//         |||||  || || |
//         VAYAQ--PRKLCYP

    SEQAN_ASSERT_EQ(score, 48);

    computeAlignmentStats(m.alignStats, m.alignRow0, m.alignRow1, seqanScheme(scheme));

    SEQAN_ASSERT_EQ(m.alignStats.alignmentScore, score);
    SEQAN_ASSERT_EQ(m.alignStats.alignmentLength, 14u);
    SEQAN_ASSERT_EQ(m.alignStats.numMatches, 10u);
    SEQAN_ASSERT_EQ(m.alignStats.numPositiveScores, 12u);
    SEQAN_ASSERT_EQ(m.alignStats.numMismatches, 2u);
    SEQAN_ASSERT_EQ(m.alignStats.numGapExtensions, 1u);
    SEQAN_ASSERT_EQ(m.alignStats.numGapOpens, 1u);

    // same as previous test until here (just local)

    m.bitScore = computeBitScore(m.alignStats.alignmentScore, scheme);
    double epsilon = 1e-4;
    SEQAN_ASSERT_LEQ(std::abs(m.bitScore - 23.0978), epsilon);

    m.eValue = computeEValue(m.alignStats.alignmentScore, length(src1), length(src0), scheme);
    epsilon = 1e-8; // evalues are smaller
    SEQAN_ASSERT_LEQ(std::abs(m.eValue - 0.000267348), epsilon);
}

#endif  // SEQAN_TESTS_TEST_BLAST_STATISTICS_H_
