// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
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// ==========================================================================
// Author: Birte Kehr <birte.kehr@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_TESTS_ALIGN_TEST_ALIGN_ALIGMENT_OPERATIONS_H_
#define SEQAN_TESTS_ALIGN_TEST_ALIGN_ALIGMENT_OPERATIONS_H_

SEQAN_DEFINE_TEST(test_align_integrate_align)
{
    using namespace seqan2;

    // We do not test the first interface since the second one calls the first
    // one implicitely.

    // Case: Integration left of existing with leading gaps. Test second
    // specialization: One Align of Sequence, one Align of Infix of Sequence.
    {
        Dna5String seqH = "AAAACGATAAAACGAT";
        Dna5String seqV =     "CGAT"  "CGAT";

        // Alignment align:
        //
        // AAAACGATAAAACGAT
        //     CGAT----CGAT

        Align<Dna5String> align;
        resize(rows(align), 2);
        assignSource(row(align, 0), seqH);
        assignSource(row(align, 1), seqV);
        insertGaps(row(align, 1), 4, 4);

        // Alignment alignInf
        //
        // AAAACGAT
        // ----CGAT

        Align<typename Infix<Dna5String>::Type> alignInf;
        resize(rows(alignInf), 2);
        assignSource(row(alignInf, 0), infix(seqH, 0, 8));
        assignSource(row(alignInf, 1), infix(seqV, 0, 4));
        insertGaps(row(alignInf, 1), 0, 4);

        integrateAlign(align, alignInf);

        std::stringstream ssH, ssV;
        ssH << row(align, 0);
        ssV << row(align, 1);

        SEQAN_ASSERT_EQ(ssH.str(), "AAAACGATAAAACGAT");
        SEQAN_ASSERT_EQ(ssV.str(), "----CGAT----CGAT");
    }

    // Case: Integration left of existing with trailing gaps. Test second
    // specialization: One Align of Sequence, one Align of Infix of Sequence.
    {
        Dna5String seqH = "CGATATAAAAAACGAT";
        Dna5String seqV = "CGATT"     "CGAT";

        // Alignment align:
        //
        // CGATATAAAAAACGAT
        //    CGATT----CGAT

        Align<Dna5String> align;
        resize(rows(align), 2);
        assignSource(row(align, 0), seqH);
        assignSource(row(align, 1), seqV);
        insertGaps(row(align, 1), 5, 4);

        // Alignment alignInf
        //
        // CGATATAA
        // CGAT-T--

        Align<typename Infix<Dna5String>::Type> alignInf;
        resize(rows(alignInf), 2);
        assignSource(row(alignInf, 0), infix(seqH, 0, 8));
        assignSource(row(alignInf, 1), infix(seqV, 0, 5));
        insertGaps(row(alignInf, 1), 5, 2);
        insertGaps(row(alignInf, 1), 4, 1);

        integrateAlign(align, alignInf);

        std::stringstream ssH, ssV;
        ssH << row(align, 0);
        ssV << row(align, 1);

        SEQAN_ASSERT_EQ(ssH.str(), "CGATATAAAAAACGAT");
        SEQAN_ASSERT_EQ(ssV.str(), "CGAT-T------CGAT");
    }

    // Case: Integration right of existing with leading gaps. Test second
    // specialization: One Align of Sequence, one Align of Infix of Sequence.
    {
        Dna5String seqH = "AAAACGATAAAACGAT";
        Dna5String seqV =     "CGAT"  "CGAT";

        // Alignment align:
        //
        // AAAACGATAAAACGAT
        // ----CGATCGAT

        Align<Dna5String> align;
        resize(rows(align), 2);
        assignSource(row(align, 0), seqH);
        assignSource(row(align, 1), seqV);
        insertGaps(row(align, 1), 0, 4);

        // Alignment alignInf
        //
        // AAAACGAT
        // ----CGAT

        Align<typename Infix<Dna5String>::Type> alignInf;
        resize(rows(alignInf), 2);
        assignSource(row(alignInf, 0), infix(seqH, 8, 16));
        assignSource(row(alignInf, 1), infix(seqV, 4, 8));
        insertGaps(row(alignInf, 1), 0, 4);

        integrateAlign(align, alignInf);

        std::stringstream ssH, ssV;
        ssH << row(align, 0);
        ssV << row(align, 1);

        SEQAN_ASSERT_EQ(ssH.str(), "AAAACGATAAAACGAT");
        SEQAN_ASSERT_EQ(ssV.str(), "----CGAT----CGAT");
    }

    // Case: Integration right of existing with trailing gaps. Test second
    // specialization: One Align of Sequence, one Align of Infix of Sequence.
    {
        Dna5String seqH = "AAAACGATCGATATAA";
        Dna5String seqV =     "CGATCGATT";

        // Alignment align:
        //
        // AAAACGATCGATATAA
        // ----CGATCGATT

        Align<Dna5String> align;
        resize(rows(align), 2);
        assignSource(row(align, 0), seqH);
        assignSource(row(align, 1), seqV);
        insertGaps(row(align, 1), 0, 4);

        // Alignment alignInf
        //
        // CGATATAA
        // CGAT-T--

        Align<typename Infix<Dna5String>::Type> alignInf;
        resize(rows(alignInf), 2);
        assignSource(row(alignInf, 0), infix(seqH, 8, 16));
        assignSource(row(alignInf, 1), infix(seqV, 4, 9));
        insertGaps(row(alignInf, 1), 5, 2);
        insertGaps(row(alignInf, 1), 4, 1);

        integrateAlign(align, alignInf);

        std::stringstream ssH, ssV;
        ssH << row(align, 0);
        ssV << row(align, 1);

        SEQAN_ASSERT_EQ(ssH.str(), "AAAACGATCGATATAA");
        SEQAN_ASSERT_EQ(ssV.str(), "----CGATCGAT-T--");
    }
}

SEQAN_DEFINE_TEST(test_align_integrate_align_infix_of_infix)
{
    using namespace seqan2;
    // Case: both align objects are infixes
    {
        Dna5String seqH = "NNNANANANANAAAAACGATCGATATAA";
        Dna5String seqV =        "NNNGGNNAACGATCGATT";

        Infix<Dna5String>::Type seqHInf1 = infix(seqH, 3, length(seqH)-1);
        Infix<Dna5String>::Type seqVInf1 = infix(seqV, 1, length(seqV));

        // ANANANANAAAAACGATCGATATA
        //      NNGGNNAACGATCGATT

        Infix<Dna5String>::Type seqHInf2 = infix(seqHInf1, 3, length(seqHInf1)-1);
        Infix<Dna5String>::Type seqVInf2 = infix(seqVInf1, 1, length(seqVInf1));

        //    NANANAAAAACGATCGATAT
        //       NGGNNAACGATCGATT

        Align<typename Infix<Dna5String>::Type> alignInf1;
        resize(rows(alignInf1), 2);
        assignSource(row(alignInf1, 0), seqHInf1);
        assignSource(row(alignInf1, 1), seqVInf1);
        insertGaps(row(alignInf1, 1), 0, 5);
        insertGaps(row(alignInf1, 1), length(row(alignInf1, 1)), 2);

        // ANANANANAAAAACGATCGATATA
        // -----NNGGNNAACGATCGATT--

        SEQAN_ASSERT_EQ(row(alignInf1, 0),
                        CharString("ANANANANAAAAACGATCGATATA"));
        SEQAN_ASSERT_EQ(row(alignInf1, 1),
                        CharString("-----NNGGNNAACGATCGATT--"));

        Align<typename Infix<Dna5String>::Type> alignInf2;
        resize(rows(alignInf2), 2);
        assignSource(row(alignInf2, 0), seqHInf2);
        assignSource(row(alignInf2, 1), seqVInf2);

        //    NANANAAAAACGATCGATAT
        //       NGGNNAACGATCGATT

        insertGaps(row(alignInf2, 0), 5, 2);
        insertGaps(row(alignInf2, 1), 7, 2);

        //    NANAN--AAAAACGATCGATAT
        //       NGGNNAA--CGATCGATT

        SEQAN_ASSERT_EQ(row(alignInf2, 0),
                        CharString("NANAN--AAAAACGATCGATAT"));
        SEQAN_ASSERT_EQ(row(alignInf2, 1),
                        CharString("NGGNNAA--CGATCGATT"));


        integrateAlign(alignInf1, alignInf2);

        SEQAN_ASSERT_EQ(row(alignInf1, 0),
                        CharString("ANANANAN--AAAAACGATCGATATA"));
        SEQAN_ASSERT_EQ(row(alignInf1, 1),
                        CharString("-----NNGGNNAA--CGATCGATT--"));
    }
}
#endif  // #ifndef SEQAN_TESTS_ALIGN_TEST_ALIGN_ALIGMENT_OPERATIONS_H_
