// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Helper functions for testing banded edit distance aproximate
// string search algorithms.
// ==========================================================================

using namespace std;
using namespace seqan2;

//////////////////////////////////////////////////////////////////////////////

String<int> mat;

template <typename TMatrix, typename TSeq1, typename TSeq2>
void dumpMat(TMatrix &mat, TSeq1 &seq1, TSeq2 &seq2)
{
    // diagonal DP
    for(unsigned j=0;j<=length(seq2);++j) {
        std::cerr << "mat  ";
        for(int i=length(seq1);i>=0;--i) {
            int val = mat[   j  * (length(seq1)+1) +   i];
            if (val != -9)
                std::cerr << std::setw(5) << val;
            else
                std::cerr << std::setw(5) << ' ';
        }
        if (j > 0)
            std::cerr << std::setw(5) << seq2[j-1];
        std::cerr << std::endl;
    }
}

// seq1 .. Pattern
// seq2 .. Text
template <typename TFindSpec, typename TString>
bool testMyersUkkonen(TString seq1, TString seq2, int leftClip = 0, bool dump = true)
{
    Finder<TString> finder(seq2);
//    Pattern<TString, MyersUkkonenBanded> pattern(seq1);
    PatternState_<TString, Myers<AlignTextBanded<TFindSpec, NMatchesN_, NMatchesN_>, True, void> > state;

    state.leftClip = leftClip;

    bool equal = true;
    int delta = length(seq2) - length(seq1);

    clear(mat);
    resize(mat, (length(seq1)+1) * (length(seq2)+1), -9, Exact());

    // initialize first DP column
    for (unsigned i = 0; i <= length(seq1); ++i)
        mat[i] = i;

    if (IsSameType<TFindSpec, FindInfix>::VALUE)
    {
        for (unsigned i = 0; i <= length(seq2); ++i)
            mat[i * (length(seq1) + 1)] = (i < length(seq1))? 0 : i - length(seq1) + 1;
    }
    else
    {
        for (unsigned i = 0; i <= length(seq2); ++i)
            mat[i * (length(seq1) + 1)] = i;
    }

    while (!atEnd(finder))
        find(finder, seq1, state, -1000);


#ifndef SEQAN_TEST_MYERS_STRICTBANDED

    delta = 7;

    // banded DP alignment
    for(unsigned j = 1; j <= length(seq2); ++j)
        for(unsigned i = 1; i <= length(seq1); ++i)
        {
            int diag = j+leftClip - i;
            if (0 <= diag && (diag <= delta || i+delta >= length(seq1)))
            {
                int d = mat[(j-1) * (length(seq1)+1) + i-1];
                if (seq1[i-1] != seq2[j-1]) ++d;
                int h = mat[(j-1) * (length(seq1)+1) +   i] + 1;
                int v = mat[   j  * (length(seq1)+1) + i-1] + 1;
                int min = 99;
                if (0 < diag)
                    if (min > h) min = h;
                if (diag < delta || i+delta > length(seq1))
                    if (min > v) min = v;
                if (diag <= delta || i+delta > length(seq1))
                    if (min > d) min = d;
                mat[j * (length(seq1)+1) + i] = min;
            }
        }

#else

    if (delta >= length(seq1)) return true;

    // real banded DP alignment
    for(int j = 1; j <= length(seq2); ++j)
        for(int i = 1; i <= length(seq1); ++i) {
            int diag = j+leftClip - i;
            if (0 <= diag && diag <= delta)
            {
                int d = mat[(j-1) * (length(seq1)+1) + i-1];
                if (seq1[i-1] != seq2[j-1]) ++d;
                int h = mat[(j-1) * (length(seq1)+1) +   i] + 1;
                int v = mat[   j  * (length(seq1)+1) + i-1] + 1;
                int min = 99;
                if (0 < diag) if (min > h) min = h;
                if (diag < delta) if (min > v) min = v;
                if (min > d) min = d;
                mat[j * (length(seq1)+1) + i] = min;
            }
        }

#endif

    for(unsigned j = 1; j <= length(seq2); ++j)
        for(unsigned i = 1; i <= length(seq1); ++i)
        {
            unsigned pos = j * (length(seq1)+1) + i;
            if (mat[pos] != state.DPMat[pos])
                equal = false;
        }

    if (equal) return true;

    if (dump)
    {
        dumpMat(state.DPMat, seq1, seq2);
        dumpMat(mat, seq1, seq2);

        for(unsigned j = 1; j <= length(seq2); ++j)
            for(unsigned i = 1; i <= length(seq1); ++i)
            {
                unsigned pos = j * (length(seq1)+1) + i;
                SEQAN_ASSERT_EQ(mat[pos], state.DPMat[pos]);
            }
    }

    return equal;
}

template <typename TFinderCSP, typename TPatternCSP, typename TText, typename TNeedle>
void testCSPImpl(TText &text, TNeedle &needle, int errors)
{
    PatternState_<TNeedle, Myers<AlignTextBanded<FindInfix, TFinderCSP,TPatternCSP>, True, void> > state;
    Finder<TText> finder(text);
    SEQAN_ASSERT(find(finder, needle, state, -1000));
    SEQAN_ASSERT_EQ(position(finder), length(text) - 1) ;
    SEQAN_ASSERT_EQ(getScore(state), -errors);
}

SEQAN_DEFINE_TEST(test_myers_find_banded_csp)
{
    {
        Dna5String text   = "ACAGTNNTAAGNNNNA";
        Dna5String needle = "ACNGTACTAAGNNNNG";
        testCSPImpl<NMatchesAll_,  NMatchesAll_>  (text, needle, 1);
        testCSPImpl<NMatchesAll_,  NMatchesN_>    (text, needle, 2);
        testCSPImpl<NMatchesN_,    NMatchesAll_>  (text, needle, 3);
        testCSPImpl<NMatchesN_,    NMatchesN_>    (text, needle, 4);
        testCSPImpl<NMatchesNone_, NMatchesNone_> (text, needle, 8);
    }
    {
        CharString text   = "ACAGTNNTAAGNNNNA";
        CharString needle = "ACNGTACTAAGNNNNG";
        testCSPImpl<NMatchesAll_,  NMatchesAll_>  (text, needle, 1);
        testCSPImpl<NMatchesAll_,  NMatchesN_>    (text, needle, 2);
        testCSPImpl<NMatchesN_,    NMatchesAll_>  (text, needle, 3);
        testCSPImpl<NMatchesN_,    NMatchesN_>    (text, needle, 4);
        testCSPImpl<NMatchesNone_, NMatchesNone_> (text, needle, 8);
    }
}

//////////////////////////////////////////////////////////////////////////////

template <typename TFindSpec>
void testMyersFindBanded()
{
    typedef Dna TValue;
    String<Dna> seq1 = "tgtaaaggagt";
    String<Dna> seq2 = "tgtgtaaaggagttgtggagttgtaaaaaggagt";

    for (unsigned li=2; li<=length(seq1); ++li)
    {
        //std::cout<<'.'<<std::flush;
        for (unsigned lj=li; lj<=length(seq2) && lj-li<8; ++lj)
            for (unsigned i=0; i+li<=length(seq1); ++i)
                for (unsigned leftClip = 0; leftClip < lj; ++leftClip)
                if (li > 8)
                {
                    String<TValue> s1 = infix(seq1, i, i+li);
                    for(unsigned j=0; j+lj<=length(seq2); ++j)
                    {
                        String<TValue> s2 = infix(seq2, j, j+lj);
                        if (!testMyersUkkonen<TFindSpec>(s1, s2, leftClip, false)) {
                            std::cerr << "DIFFERENCE("<<right<<") for " << s1 << "," << s2 << std::endl;
                            testMyersUkkonen<TFindSpec>(s1, s2, leftClip, true);
                        }
                    }
                }
    }
}

SEQAN_DEFINE_TEST(test_myers_find_banded)
{
    testMyersFindBanded<FindInfix>();
    testMyersFindBanded<FindPrefix>();
}
