// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, Knut Reinert, FU Berlin
// Copyright (c) 2013 NVIDIA Corporation
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// ==========================================================================
// Author: Jochen Singer <jochen.singer@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_INDEX_TEST_INDEX_FM_ITER_H_
#define TESTS_INDEX_TEST_INDEX_FM_ITER_H_

using namespace seqan2;

template <typename TIter>
void fmIndexIteratorConstuctor(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text;
    generateText(text);

    Index<TText> esa(text);
    typename Iterator<Index<TText>, TopDown<> >::Type esaIt(esa);
    goDown(esaIt);

    TIndex fmIndex(text, 10);
    TIter it(fmIndex);

    SEQAN_ASSERT_EQ(isRoot(it), true);
    SEQAN_ASSERT_EQ(repLength(it), 0u);
    SEQAN_ASSERT_EQ(goDown(it), true);
    SEQAN_ASSERT_EQ(isRoot(it), false);
    SEQAN_ASSERT_EQ(repLength(it), 1u);
    SEQAN_ASSERT_EQ(representative(it), 'A');
    SEQAN_ASSERT_EQ(goRight(it), true);
    SEQAN_ASSERT_EQ(representative(it), 'C');
    SEQAN_ASSERT_EQ(repLength(it), 1u);
    SEQAN_ASSERT_EQ(goRight(it), true);
    SEQAN_ASSERT_EQ(representative(it), 'G');
    SEQAN_ASSERT_EQ(repLength(it), 1u);
    SEQAN_ASSERT_EQ(goRight(it), true);
    SEQAN_ASSERT_EQ(representative(it), 'T');
    SEQAN_ASSERT_EQ(repLength(it), 1u);
    SEQAN_ASSERT_EQ(goRight(it), false);
    SEQAN_ASSERT_EQ(representative(it), 'T');
    SEQAN_ASSERT_EQ(repLength(it), 1u);
    SEQAN_ASSERT_EQ(goDown(it), true);
    SEQAN_ASSERT_EQ(goDown(it), true);
}

template <typename TIter>
void fmIndexIteratorGoDown(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text;
    text = "ACGACG";
    TIndex fmIndex(text);

    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(representative(it), "ACGA");
        SEQAN_ASSERT_EQ(goDown(it), false);
        SEQAN_ASSERT_EQ(representative(it), "ACGA");
    }
    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(goDown(it, 'G'), true);
        SEQAN_ASSERT_EQ(representative(it), "G");
        SEQAN_ASSERT_EQ(goDown(it, 'G'), false);
        SEQAN_ASSERT_EQ(representative(it), "G");
    }
    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(goDown(it, 'G'), true);
        SEQAN_ASSERT_EQ(goDown(it, 'C'), true);
        SEQAN_ASSERT_EQ(goDown(it, 'A'), true);
        SEQAN_ASSERT_EQ(goDown(it, 'G'), true);
        SEQAN_ASSERT_EQ(goDown(it, 'C'), true);
        SEQAN_ASSERT_EQ(goDown(it, 'A'), true);
        SEQAN_ASSERT_EQ(representative(it), "ACGACG");
        SEQAN_ASSERT_EQ(goDown(it, 'G'), false);
        SEQAN_ASSERT_EQ(representative(it), "ACGACG");
    }
    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(goDown(it, "GCAGCA"), true);
        SEQAN_ASSERT_EQ(representative(it), "ACGACG");
        SEQAN_ASSERT_EQ(goDown(it, 'G'), false);
        SEQAN_ASSERT_EQ(representative(it), "ACGACG");
    }
}

template <typename TIter>
void fmIndexIteratorIsLeaf(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text = "ACGACG";
    TIndex fmIndex(text);

    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(isLeaf(it), false);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(isLeaf(it), false);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(isLeaf(it), false);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(isLeaf(it), false);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(isLeaf(it), true);
        SEQAN_ASSERT_EQ(representative(it), "ACGA");
        SEQAN_ASSERT_EQ(goDown(it), false);
        SEQAN_ASSERT_EQ(representative(it), "ACGA");
    }
}

template <typename TIter>
void fmIndexIteratorGoRight(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text = "ACGACG";
    TIndex fmIndex(text);

    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(goDown(it), true);
        SEQAN_ASSERT_EQ(representative(it), "A");
        SEQAN_ASSERT_EQ(goRight(it), true);
        SEQAN_ASSERT_EQ(representative(it), "C");
        SEQAN_ASSERT_EQ(goRight(it), true);
        SEQAN_ASSERT_EQ(representative(it), "G");
        SEQAN_ASSERT_EQ(goRight(it), false);
        SEQAN_ASSERT_EQ(representative(it), "G");
    }
}

template <typename TIter>
void fmIndexIteratorGoUp(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text = "ACGACG";
    TIndex fmIndex(text);

    {
        TIter it(fmIndex);
        SEQAN_ASSERT_EQ(goDown(it, "GCAGCA"), true);
        SEQAN_ASSERT_EQ(representative(it), "ACGACG");
        SEQAN_ASSERT_EQ(goUp(it), true);
        SEQAN_ASSERT_EQ(representative(it), "CGACG");
        SEQAN_ASSERT_EQ(goUp(it), true);
        SEQAN_ASSERT_EQ(representative(it), "GACG");
        SEQAN_ASSERT_EQ(goUp(it), true);
        SEQAN_ASSERT_EQ(representative(it), "ACG");
        SEQAN_ASSERT_EQ(goUp(it), true);
        SEQAN_ASSERT_EQ(representative(it), "CG");
        SEQAN_ASSERT_EQ(goUp(it), true);
        SEQAN_ASSERT_EQ(representative(it), "G");
        SEQAN_ASSERT_EQ(goUp(it), true);
        SEQAN_ASSERT_EQ(representative(it), "");
        SEQAN_ASSERT_EQ(goUp(it), false);
        SEQAN_ASSERT_EQ(representative(it), "");
    }
}

template <typename TIter>
void fmIndexIteratorIsRoot(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text = "ACGACG";
    TIndex fmIndex(text);

    {
        TIter it(fmIndex);

        SEQAN_ASSERT_EQ(isRoot(it), true);
        SEQAN_ASSERT_EQ(goDown(it, "GCAGCA"), true);
        SEQAN_ASSERT_EQ(isRoot(it), false);
    }
}

template <typename TIter>
void fmIndexIteratorRepresentative(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;

    TText text = "ACGACG";
    TIndex fmIndex(text);

    {
        TIter it(fmIndex);

        SEQAN_ASSERT_EQ(representative(it), "");
        SEQAN_ASSERT_EQ(goDown(it, "GCAGCA"), true);
        SEQAN_ASSERT_EQ(representative(it), "ACGACG");
    }
}

template <typename TIter>
void fmIndexIteratorCountOccurrences(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;
    typedef Index<TText, IndexEsa<> > TEsaIndex;
    typedef typename Iterator<TEsaIndex, TopDown<ParentLinks<> > >::Type TEsaIter;

    TText text;
    generateText(text);

    StringSet<String<typename Value<TIndex>::Type> > pattern;
    generatePattern(pattern, text);

    TIndex fmIndex(text);
    TEsaIndex esaIndex(text);

    TIter it(fmIndex);
    TEsaIter esaIt(esaIndex);

    for (unsigned i = 0; i < length(pattern); ++i)
    {
        reverse(pattern[i]);
        bool _goDown = goDown(it, pattern[i]);
        reverse(pattern[i]);
        SEQAN_ASSERT_EQ(_goDown, goDown(esaIt, pattern[i]));
        if (_goDown)
        {
            SEQAN_ASSERT_EQ(countOccurrences(it), countOccurrences(esaIt));
        }
        goRoot(it);
        goRoot(esaIt);
    }
}

template <typename TIter>
void fmIndexIteratorRange(TIter & /*tag*/)
{
    typedef typename Container<TIter>::Type TIndex;
    typedef typename Fibre<TIndex, FibreText>::Type TText;
    typedef Index<TText, IndexEsa<> > TEsaIndex;
    typedef typename Iterator<TEsaIndex, TopDown<ParentLinks<> > >::Type TEsaIter;

    TText text;
    generateText(text);

    StringSet<String<typename Value<TIndex>::Type> > pattern;
    generatePattern(pattern, text);

    TIndex fmIndex(text);
    TEsaIndex esaIndex(text);

    TIter it(fmIndex);
    TEsaIter esaIt(esaIndex);

    for (unsigned i = 0; i < length(pattern); ++i)
    {
        reverse(pattern[i]);
        bool _goDown = goDown(it, pattern[i]);
        reverse(pattern[i]);
        SEQAN_ASSERT_EQ(_goDown, goDown(esaIt, pattern[i]));
        if (_goDown)
        {
            SEQAN_ASSERT_EQ(range(it).i1 - 1, range(esaIt).i1);
            SEQAN_ASSERT_EQ(range(it).i2 - 1, range(esaIt).i2);
        }
        goRoot(it);
        goRoot(esaIt);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_constuctor)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "AAA";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorConstuctor(dnaTag);
    }
    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorConstuctor(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_go_down)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    {
        DnaString genome;
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorGoDown(dnaTag);
    }
    {
        DnaString genome;
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorGoDown(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_is_leaf)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "A";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorIsLeaf(dnaTag);
    }
    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorIsLeaf(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_go_right)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "A";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorGoRight(dnaTag);
    }
    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorGoRight(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_go_up)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "A";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorGoUp(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_representative)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "A";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorRepresentative(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_is_root)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "A";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorIsRoot(dnaTag);
    }
    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorIsRoot(dnaTag);
    }
}

SEQAN_DEFINE_TEST(fm_index_iterator_count_occurrences)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    {
        DnaString genome;
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorCountOccurrences(dnaTag);
    }
    {
        DnaString genome;
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorCountOccurrences(dnaTag);
    }
//     {
//         StringSet<DnaString> genome;
//         Index<StringSet<DnaString>,TDefaultIndex> index(genome);
//         Iterator<Index<StringSet<DnaString>,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag;
//         fmIndexIteratorCountOccurrences(dnaTag);
//     }

}

SEQAN_DEFINE_TEST(fm_index_iterator_range)
{
    using namespace seqan2;

    typedef FMIndex<WT<>, void> TDefaultIndex;
    typedef TopDown<> TIterSpec;
    typedef TopDown<ParentLinks<> > TParentLinksIterSpec;

    DnaString genome = "A";

    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TIterSpec>::Type dnaTag(index);
        fmIndexIteratorRange(dnaTag);
    }
    {
        Index<DnaString,TDefaultIndex> index(genome);
        Iterator<Index<DnaString,TDefaultIndex>, TParentLinksIterSpec>::Type dnaTag(index);
        fmIndexIteratorRange(dnaTag);
    }
}

#endif // TESTS_INDEX_TEST_INDEX_FM_ITER_H_


