// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
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//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
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// ==========================================================================

#ifndef SEQAN_HEADER_INDEX_ESA_ALGS_MULTI_H
#define SEQAN_HEADER_INDEX_ESA_ALGS_MULTI_H

namespace seqan
{

    //////////////////////////////////////////////////////////////////////////////
    // more sophisticated algorithms on suffix trees of
    // multiple sequences (generalized suffix tree)
    //////////////////////////////////////////////////////////////////////////////


/*!
 * @class MumsIterator Mums Iterator
 * @extends BottomUpIterator
 * @headerfile <seqan/index.h>
 *
 * @brief Iterator to search for all maximum unique matches.
 *
 * @signature Iterator<TContainer, Mums>::Type;
 * @signature template <typename TContainer>
 *            class Iter<TContainer, VSTree< BottomUp<Mums> > >;
 *
 * @tparam TContainer Type of an index that can be iterated with a bottom-up
 *                    iterator. Types: @link IndexEsa @endlink
 *
 * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
 *       Iterator&lt;TContainer, Mums>::Type (which is Iter&lt;TContainer, VSTree&lt; BottomUp&lt;Mums> > >).
 */
/*!
 * @fn MumsIterator::Iter
 *
 * @brief The constructor.
 *
 * @signature Iter::Iter(index[, minLength]);
 * @signature Iter::Iter(iterator);
 *
 * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
 * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
 * @param[in] iterator  Another MultiMems iterator. Types: @link MultiMemsIterator @endlink
 */

    //////////////////////////////////////////////////////////////////////////////
    // Mums - generalized suffix tree version
    //////////////////////////////////////////////////////////////////////////////

    template < typename TSTree >
    struct GetVSTreeIteratorTraits< Iter< TSTree, VSTree< BottomUp<Mums> > > > {
        typedef PostorderEmptyEdges    Type;
    };

    template < typename TSTree >
    class Iter< TSTree, VSTree< BottomUp<Mums> > >:
        public Iter< TSTree, VSTree< BottomUp<> > >
    {
    public:
        typedef Iter< TSTree, VSTree< BottomUp<> > >    TBase;
        typedef typename Size<TSTree>::Type                TSize;
        typedef VectorSet_<TSize, Alloc<> >                TSeqSet;
//____________________________________________________________________________

        TSize        minLength;
        TSize        seqCount;
        TSeqSet        seqSet;
//____________________________________________________________________________

        Iter() :
            TBase(),
            minLength(0),
            seqCount(0)
        {}

        Iter(TSTree &_tree):
            TBase(_tree),
            minLength(1),
            seqCount(countSequences(_tree)),
            seqSet(countSequences(_tree))
        {
            indexRequire(_tree, EsaBwt());
            goNext(*this);    // the iterator starts in a suffix, i.e. not a MUM node (length(occ)<2<=seqCount)
        }

        Iter(TSTree &_tree, MinimalCtor):
            TBase(_tree, MinimalCtor()) {}

        Iter(TSTree &_tree, TSize _minLength):
            TBase(_tree),
            minLength(_minLength),
            seqCount(countSequences(_tree)),
            seqSet(countSequences(_tree))
        {
            indexRequire(_tree, EsaBwt());
            goNext(*this);    // the iterator starts in a suffix, i.e. not a MUM node (length(occ)<2<=seqCount)
        }

        Iter(Iter const &_origin):
            TBase((TBase const &)_origin),
            minLength(_origin.minLength),
            seqCount(countSequences(container(_origin))),
            seqSet(countSequences(container(_origin))) {}
    };

    template < typename TSTree >
    inline void goNext(Iter< TSTree, VSTree< BottomUp<Mums> > > &it) {
        do {
            goNext(it, PostorderEmptyEdges());
        } while (!atEnd(it) &&
                 !(    (countOccurrences(it) == it.seqCount) &&
                    (repLength(it) >= it.minLength) &&
                    isUnique(it, it.seqSet) &&
                    isLeftMaximal(it)) );
    }




/*!
 * @class MultiMemsIterator Multi Mems Iterator
 * @extends BottomUpIterator
 * @headerfile <seqan/index.h>
 *
 * @brief Iterator to search for MultiMems.
 *
 * @signature Iterator<TContainer, MultiMems>::Type;
 * @signature template <typename TContainer>
 *            class Iter<TContainer, VSTree< BottomUp<MultiMems> > >;
 *
 * @tparam TContainer Type of an index that can be iterated with a bottom-up
 *                    iterator. Types: IndexEsa
 *
 * @note Instead of using the class Iter directly we recommend to use the result of the metafunction
 *       Iterator&lt;TContainer, MultiMems&gt;::Type (which is Iter<TContainer, VSTree< BottomUp<MultiMems&gt; &gt; &gt;).
 */
/*!
 * @fn MultiMemsIterator::Iter
 * @brief The constructor
 *
 * @signature Iter::Iter(index[, minLength]);
 * @signature Iter::Iter(iterator);
 *
 * @param[in] index     The index to be used for the iteration. Types: @link IndexEsa @endlink
 * @param[in] minLength Minimum length of the supermaximal repeats, default value is 1.
 * @param[in] iterator  Another MultiMemsIterator iterator. Types: @link MultiMemsIterator @endlink
 */

    //////////////////////////////////////////////////////////////////////////////
    // MultiMems
    //////////////////////////////////////////////////////////////////////////////

    // contains a set of fraction compounds
    // one compound for each sequence
    template <typename TValue, typename TSize>
    struct FractionMultiCompound_ {
        typedef FractionCompound_<TValue, TSize>    TCompound;
        typedef String<TCompound>                    TSet;    // seqNo..unsigned, compound: bwt character->suffixes

        TSet    set;
    };


    template < typename TSTree >
    class Iter< TSTree, VSTree< BottomUp<MultiMems> > >:
        public Iter< TSTree, VSTree< BottomUp<> > >
    {
    public:
        typedef Iter< TSTree, VSTree< BottomUp<> > >    TBase;
        typedef typename Value<TSTree>::Type            TValue;
        typedef typename Size<TSTree>::Type                TSize;

        typedef FractionMultiCompound_<TValue, TSize>    TMultiCompound;
        typedef String<TMultiCompound, Block<> >        TSetStack;
        typedef String<TSize>                            TPositionList;

        typedef typename TMultiCompound::TSet            TSet;
        typedef typename Iterator<TSet>::Type            TSetIterator;

        typedef typename HistoryStackEntry_<TBase>::Type TStackEntry;

//____________________________________________________________________________

        TSize            minLength;
        unsigned        minSupport;    // the support is the number of distinct sequences
        unsigned        maxSupport;    // a repeat/match occurs in
        TSetStack        setStack;
        TPositionList    posList;    // this list is indexed just as SA is and contains the next entry's index
        bool            canMerge;    // is false, if parent node appears after its first child on stack
//____________________________________________________________________________

        Iter() :
            TBase(),
            minLength(0),
            minSupport(0),
            maxSupport(0),
            canMerge(0)
        {}

        Iter(TSTree &_index):
            TBase(_index, MinimalCtor()),
            minSupport(countSequences(_index)),
            maxSupport(countSequences(_index)),
            canMerge(true)
        {
            indexRequire(_index, EsaSA());
            indexRequire(_index, EsaLcp());
            indexRequire(_index, EsaBwt());
            resize(posList, length(_index));

            if (!empty(indexSA(_index)))
            {
                TStackEntry e;
                e.range.i1 = 0;
                e.range.i2 = 0;
                _dfsOnPush(*this, e);
                goNext(*this);
            }
        }

        Iter(TSTree &_tree, MinimalCtor):
            TBase(_tree, MinimalCtor()) {}

        Iter(TSTree &_index, TSize _minLength):
            TBase(_index, MinimalCtor()),
            minLength(_minLength),
            minSupport(countSequences(_index)),
            maxSupport(countSequences(_index)),
            canMerge(true)
        {
            indexRequire(_index, EsaSA());
            indexRequire(_index, EsaLcp());
            indexRequire(_index, EsaBwt());
            resize(posList, length(_index));

            if (!empty(indexSA(_index)))
            {
                TStackEntry e;
                e.range.i1 = 0;
                e.range.i2 = 0;
                _dfsOnPush(*this, e);
                goNext(*this);
            }
        }

        Iter(Iter const &_origin):
            TBase((TBase const &)_origin),
            minLength(_origin.minLength),
            minSupport(_origin.minSupport),
            maxSupport(_origin.maxSupport),
            setStack(_origin.setStack),
            posList(_origin.posList),
            canMerge(_origin.canMerge) {}

//____________________________________________________________________________

        inline bool hasRepeats()
        {
            if (length(setStack) < 2) return false;

            TMultiCompound &child  = back(setStack);
            TMultiCompound &parent = backPrev(setStack);

            TValue prevKey = TValue();
            TValue equalKey = TValue();

            unsigned distinctSeqs = 0;
            bool distinctKeys = false;

            TSetIterator parentCompound    = begin(parent.set);
            TSetIterator parentEnd        = end(parent.set);
            TSetIterator childCompound    = begin(child.set);
            TSetIterator childEnd        = end(child.set);

            while (childCompound != childEnd && parentCompound != parentEnd)
            {
                int result = _haveMaximalRepeats(*childCompound, *parentCompound, equalKey);
                if (result > 0) {
                    if (!distinctKeys && result == 1) {
                        if (distinctSeqs > 0 && prevKey != equalKey)
                            distinctKeys = true;                        // there is a left maximal repeat
                        prevKey = equalKey;
                    } else
                        distinctKeys = true;

                    if (++distinctSeqs > minSupport && distinctKeys)    // if it is also a  repeat in at least
                        return true;                                    // minSequences distinct sequences then
                }                                                        // we have at least one repeat
                ++childCompound;
                ++parentCompound;
            }
            return false;
        }
/*
        inline TSize countRepeats()
        {
            if (length(setStack) < 2) return 0;

            TFractionCompound &child  = back(setStack);
            TFractionCompound &parent = backPrev(setStack);

            TSetIterator childFraction    = begin(child.set);
            TSetIterator childEnd        = end(child.set);
            TSetIterator parentFraction    = begin(parent.set);
            TSetIterator parentEnd        = end(parent.set);

            TSize sum = 0;
            for(; childFraction != childEnd; ++childFraction) {
                for(; parentFraction != parentEnd; ++parentFraction) {
                    if (keyOf(childFraction) != keyOf(parentFraction))
                        sum += (*childFraction).size * (*parentFraction).size;

                    sum += child.leftmost.size * (*parentFraction).size;
                }
                sum += (*childFraction).size * parent.leftmost.size;
            }
            sum += child.leftmost.size * parent.leftmost.size;
            return sum;
        }
*/
//____________________________________________________________________________
/*
        inline void _dump() const {
            std::cerr << "SETSTACK of " << representative(*this) << ":" << std::endl;
            typename Iterator<TSetStack const>::Type it = begin(setStack), itEnd = end(setStack);
            while (it != itEnd) {
                TSet const &set = (*it).set;
                typename Iterator<TSet const>::Type sit = begin(set), sitEnd = end(set);

                while (sit != sitEnd) {
                    std::cerr << keyOf(sit) << "::";
                    typename TFractionCompound::TFractionHeader head = objectOf(sit);
                    TSize i = head.begin;
                    while (!_isSizeInval(i)) {
                        std::cerr << i << "  ";
                        i = posList[i];
                    }
                    std::cerr << std::endl;
                    ++sit;
                }

                std::cerr << "_________________________" << std::endl;
                ++it;
            }
        }
*/
    };

    // add bwt partitions of child to parent node
    template < typename TSTree, typename TSpec, typename TValue, typename TSize >
    inline void _fractionMerge(
        Iter<TSTree, VSTree< BottomUp<TSpec> > > &it,
        FractionMultiCompound_<TValue, TSize> &parent,
        FractionMultiCompound_<TValue, TSize> &child)
    {
        typedef FractionMultiCompound_<TValue, TSize>    TCompound;
        typedef typename TCompound::TSet                TSet;
        typedef typename Iterator<TSet, Standard>::Type    TSetIterator;

        TSetIterator parentCompound    = begin(parent.set, Standard());
        TSetIterator parentEnd        = end(parent.set, Standard());
        TSetIterator childCompound    = begin(child.set, Standard());
        TSetIterator childEnd        = end(child.set, Standard());

        while (childCompound != childEnd && parentCompound != parentEnd)
        {
            // append child compound to parent compound
            _fractionMerge(it, *parentCompound, *childCompound);
            ++childCompound;
            ++parentCompound;
        }
    }

    template < typename TSTree >
    inline void _dfsOnLeaf(Iter<TSTree, VSTree< BottomUp<MultiMems> > > &it)
    {
        typedef Iter<TSTree, VSTree< BottomUp<> > > TBase;
        _dfsOnLeaf((TBase&)it);

        typedef typename Value<TSTree>::Type        TValue;
        typedef typename Size<TSTree>::Type            TSize;
        typedef typename SAValue<TSTree>::Type        TSAValue;
        typedef FractionHeader_<TSize>                TFractionHeader;
        typedef Pair<TValue, TFractionHeader>        TFraction;
        //typedef typename Set<TFraction>::Type        TFractionSet;

        typedef FractionCompound_<TValue, TSize>    TCompound;
        //typedef Pair<unsigned, TCompound>            TCompoundPair;
        //typedef typename Set<TCompoundPair>::Type    TSet;

        push(it.setStack);

        TSTree &index = container(it);

        TSize        gPos = posGlobalize(_dfsRange(it).i1, stringSetLimits(index));
        TSAValue    lPos;
        posLocalize(lPos, _dfsRange(it).i1, stringSetLimits(index));

        TCompound &compound = back(it.setStack).set[getValueI1(lPos)];
        if (!posAtFirstLocal(lPos))
            insert(
                TFraction(
                    bwtAt(gPos, container(it)),
                    TFractionHeader(gPos, gPos, 1)),
                compound.set);
        else
            compound.leftmost = TFractionHeader(gPos, gPos, 1);

        _setSizeInval(it.posList[gPos]);
/*
        std::cerr << "LEAF ";
        _dumpHistoryStack(it);
        it._dump();
*/    }



    //////////////////////////////////////////////////////////////////////////////
    // maximal repeat representation
    //////////////////////////////////////////////////////////////////////////////

    template <typename TSTree>
    struct MultiMem {
//        Iter< TSTree, VSTree<BottomUp<MultiMems> > > &it;
    };

    template <typename TSTree>
    struct Value< MultiMem<TSTree> > {
        typedef Pair< typename SAValue<TSTree>::Type > Type;
    };

    template <typename TSTree>
    struct Size< MultiMem<TSTree> > {
        typedef typename Size<TSTree>::Type Type;
    };


    template <typename TSTree>
    inline typename Size< MultiMem<TSTree> >::Type
    length(MultiMem<TSTree> const &repeat) {
        return repeat.it.countRepeats();
    }

/*
    template <typename TSTree>
    inline typename Iterator< MultiMem<TSTree> >::Type
    begin(MultiMem<TSTree> &repeat) {
        return Iterator< MultiMem<TSTree> >::Type(repeat.it);
    }

    template <typename TSTree>
    inline typename Iterator< MultiMem<TSTree> const >::Type
    begin(MultiMem<TSTree> const &repeat) {
        return Iterator< MultiMem<TSTree> >::Type(repeat.it);
    }
*/


    template <typename TSTree>
    class Iter< MultiMem<TSTree>, MultiMemOccurrences > {
    public:

        typedef typename Value<TSTree>::Type    TValue;
        typedef typename Size<TSTree>::Type        TSize;
        typedef typename SAValue<TSTree>::Type    TSAValue;
        typedef    Pair<TSAValue>                    TPair;

        typedef FractionCompound_<TValue, TSize> const    TFractionCompound;
        typedef typename TFractionCompound::TSet const    TSet;
        typedef typename Iterator<TSet>::Type            TSetIterator;

        typedef Iter<TSTree, VSTree<BottomUp<MultiMems> > >    const    TIterator;
        typedef typename TIterator::TPositionList const                TPositionList;

        TIterator    *mmemIt;
        bool        _atEnd;
        unsigned    seqCount;
        TPair        tmp;


        // for every sequence there is a SubState stucture
        // storing the current enumeration state
        // that is necessary to enumerate every combination
        // of left maximal multi match

        struct SubState
        {
            SubState            *prevState;
            TPositionList        *posList;
            TFractionCompound    *child, *parent;
            TSize                childPtr, parentPtr;            // per seq. suffix iterators
            TSetIterator        childFraction,  childBegin,  childEnd;
            TSetIterator        parentFraction, parentBegin, parentEnd;
            bool                leftmostChild, leftmostParent;    // use undef. bwt (leftmost) set
            TValue                leftChar;                        // are the keys of seq[1..i] equal?
            bool                charsEqual;

            inline void _updateLeftMaximality() {
                if (prevState)
                    charsEqual = prevState->charsEqual && (leftChar == keyOf(childFraction));
            }

            inline bool _innerStep()
            {
                if (_isSizeInval(childPtr = ((*posList)[childPtr]))) {
                    if (_isSizeInval(parentPtr = (*posList)[parentPtr])) {
                        parentPtr = objectOf(parentFraction).begin;
                        return false;
                    }
                    childPtr = objectOf(childFraction).begin;
                }
                return true;
            }

            inline void _firstParentFraction()
            {
                parentBegin        = parentFraction    = begin(parent->set);
                parentEnd        = end(parent->set);

                if (parentFraction != parentEnd) {
                    leftmostParent = false;
                    parentPtr = objectOf(parentFraction).begin;
                } else {
                    leftmostParent = true;
                    parentPtr = parent->leftmost.begin;
                }

                leftChar = keyOf(parentFraction);
            }

            inline void _firstChildFraction()
            {
                childBegin        = childFraction        = begin(child->set);
                childEnd        = end(child->set);

                if (childFraction != childEnd) {
                    leftmostChild = false;
                    childPtr = objectOf(childFraction).begin;
                } else {
                    leftmostChild = true;
                    childPtr = child->leftmost.begin;
                }
            }

            inline bool _nextParentFraction()
            {
                if (leftmostParent) return false;

                if (++parentFraction == parentEnd) {
                    if (parent->leftmost.size > 0) {
                        leftmostParent = true;
                        parentPtr = parent->leftmost.begin;
                    } else
                        return false;
                } else
                    parentPtr = objectOf(parentFraction).begin;

                return true;
            }

            inline bool _nextChildFraction()
            {
                if (leftmostChild) return false;

                if (++childFraction == childEnd) {
                    if (child->leftmost.size > 0) {
                        leftmostChild = true;
                        childPtr = child->leftmost.begin;
                    } else
                        return false;
                } else
                    childPtr = objectOf(childFraction).begin;

                return true;
            }

            // single per-sequence enumeration step
            inline bool _outerStep()
            {
                if (!_nextChildFraction()) {
                    _firstChildFraction();
                    if (!_nextParentFraction()) {
                        _firstParentFraction();
                        return false;
                    }
                }
                return true;
            }

        };

        String<SubState>    subState;

        Iter() :
            mmemIt(),
            _atEnd(true),
            seqCount(0)
        {}

        inline Iter(Iter<TSTree, VSTree<BottomUp<MultiMems> > > const &_maxIt):
            mmemIt(&_maxIt),
            seqCount(countSequences(container(_maxIt)))
        {
            _init();
        }

        inline bool _isLeftMaximal() {
            return !subState[seqCount - 1].charsEqual;
        }

        // inner enumeration
        inline bool _innerStep() {
            for(unsigned seq = 0; seq < seqCount; ++seq)
                if (subState[seq]._innerStep()) return true;
            return false;
        }

        inline bool _outerStepNoCheck() {
            for(unsigned seq = 0; seq < seqCount; ++seq)
                if (subState[seq]._outerStep()) return true;
            return false;
        }

        // outer enumeration
        inline bool _outerStep() {
            while (!((_atEnd = !_outerStepNoCheck()) || _isLeftMaximal())) ;
            return !_atEnd;
        }

        inline void _init()
        {
            if (length(mmemIt->setStack) < 2) {
                _atEnd = true;
                return;
            }

            resize(subState, seqCount);
            SubState *prev = NULL;
            for(unsigned seq = 0; seq < seqCount; ++seq)
            {
                SubState &state = subState[seq];

                state.prevState = prev;
                state.posList = &(mmemIt->posList);
                state.parent = &(backPrev(mmemIt->setStack).set[seq]);
                state.child = &(back(mmemIt->setStack).set[seq]);

                state._firstChildFraction();
                state._firstParentFraction();

                prev = &state;
            }

            _atEnd = false;
            while (!(_isLeftMaximal() || (_atEnd = !_outerStep()))) ;
        }
    };


    template < typename TRepeat >
    inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type &
    value(Iter<TRepeat, MultiMemOccurrences> const &it)  {
        return it.tmp;
    }

    template < typename TRepeat >
    inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type &
    value(Iter<TRepeat, MultiMemOccurrences> &it)  {
        return it.tmp;
    }

//TODO:fix me
    template < typename TRepeat >
    inline Iter<TRepeat, MultiMemOccurrences> &
    goNext(Iter<TRepeat, MultiMemOccurrences> &it)  {
        if (it._innerStep()) {
//            it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
//            it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
            return it;
        }
        if (it._outerStep()) {
//            it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
//            it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
        }
        return it;
    }

    template < typename TRepeat >
    inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> const &it) {
        return it._atEnd;
    }

    template < typename TRepeat >
    inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> &it) {
        return it._atEnd;
    }


    template <typename TSTree>
    struct Iterator< MultiMem<TSTree> > {
        typedef Iter<MultiMem<TSTree>, MultiMemOccurrences> Type;
    };

    template <typename TSTree>
    struct Size< Iter<MultiMem<TSTree>, MultiMemOccurrences> > {
        typedef typename Size<TSTree>::Type Type;
    };


    //////////////////////////////////////////////////////////////////////////////
    // Iterator wrappers
    //////////////////////////////////////////////////////////////////////////////

    template <typename TObject>
    struct Iterator< TObject, Mums > {
        typedef Iter< TObject, VSTree< BottomUp<Mums> > > Type;
    };

//}

}

#endif
