// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
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//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// ==========================================================================

// TODO(holtgrew): Move this away?

#ifndef SEQAN_HEADER_GRAPH_ALGORITHM_LIS_HIS_H
#define SEQAN_HEADER_GRAPH_ALGORITHM_LIS_HIS_H

namespace seqan2
{

struct Lcs_;
typedef Tag<Lcs_> Lcs;

//////////////////////////////////////////////////////////////////////////////
// LIS: Longest Increasing Subsequence
//////////////////////////////////////////////////////////////////////////////

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

template<typename TSortedSequence, typename TKey>
inline typename TSortedSequence::const_iterator
_previousInSortedSequence(TSortedSequence const& list, TKey const key) {
    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;

    TSortedSequenceIter a_k_it = list.lower_bound(key);
    // Now we need to move one to the front

    if (a_k_it != list.end()) {
        // If we are at the beginning, no predecessor
        if (a_k_it == list.begin()) a_k_it = list.end();
        else --a_k_it;
    } else {
        // If we are at the end, the predecessor is the last element of the list
        TSortedSequenceIter tmp = list.begin();
        if (tmp != list.end()) {
            do {
                a_k_it = tmp;
            } while(++tmp != list.end());
        }
    }
    return a_k_it;
}


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


template<typename TSortedSequence, typename TIterator>
inline typename TSortedSequence::const_iterator
_nextInSortedSequence(TSortedSequence const& list, TIterator const& prev) {
    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;

    TSortedSequenceIter b_l_it;
    if (prev == list.end()) b_l_it = list.begin();
    else b_l_it = list.upper_bound(*prev);

    return b_l_it;
}


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

/*!
 * @fn longestIncreasingSubsequence
 * @headerfile <seqan/graph_algorithms.h>
 * @brief Computes the longest increasing subsequence.
 *
 * @signature void longestIncreasingSubsequence(str, pos);
 *
 * @param[in]  str An arbitrary @link ContainerConcept @endlink object.
 * @param[out] pos A String with the positions that belong to the longest increasing subsequence.
 *
 * @section Remarks
 *
 * The last position in <tt>pos</tt> indicates the first element in the longets increasing subsequence.
 *
 * @section Example
 *
 * @include demos/dox/graph_algorithms/longest_increasing_subsequence.cpp
 *
 * @code{.console}
 * 5,3,4,9,6,2,1,8,7,10,
 * Lis:
 * 3,4,6,7,10,
 * @endcode
 *
 * @see heaviestIncreasingSubsequence
 * @see longestCommonSubsequence
 */

template<typename TString, typename TPositions>
inline void
longestIncreasingSubsequence(TString const& str, TPositions& pos) {

    // The list of decreasing covers, only the smallest number must be remembered
    // See Gusfield
    typedef std::pair<typename Value<TString>::Type, typename Position<TPositions>::Type> TKey;
    typedef std::set<TKey, std::less<TKey> > TSortedSequence;
    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
    TSortedSequence list;

    // The trace-back graph
    typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    TGraph g;

    // Walk through the sequence and build the decreasing covers
    typedef typename Iterator<TString const, Rooted>::Type TStringIter;
    TStringIter endIt = end(str);
    for(TStringIter it = begin(str); it != endIt; ++it) {
        // Get previous element
        TSortedSequenceIter a_k_it = _previousInSortedSequence(list, std::make_pair(*it, 0));

        // Get next element
        TSortedSequenceIter b_l_it = _nextInSortedSequence(list, a_k_it);

        // Delete from list
        if (b_l_it != list.end()) list.erase(*b_l_it);

        // Insert new list element
        list.insert(std::make_pair(*it, position(it)));

        // Create the corresponding node
        // Note: The VertexDescriptor == position(it)
        addVertex(g);


        // Connect to predecessor
        if (a_k_it != list.end()) addEdge(g, (TVertexDescriptor) position(it), (TVertexDescriptor) a_k_it->second);
    }

    // Trace-back
    if (list.rbegin() == list.rend()) return;
    else {
        // Start with the maximal position in the list == Vertex Descriptor
        TVertexDescriptor v = list.rbegin()->second;
        while (true) {
            appendValue(pos, v, Generous());
            if (g.data_vertex[v]) v = (*g.data_vertex[v]).data_target;
            else break;
        }
    }
}


//////////////////////////////////////////////////////////////////////////////
// LCS: Longest Common Subsequence
//////////////////////////////////////////////////////////////////////////////

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

/*!
 * @fn longestCommonSubsequence
 * @headerfile <seqan/graph_algorithms.h>
 * @brief Computes the longest common subsequence.
 *
 * @signature void longestCommonSubsequence(str1, str2, nSize, pos);
 *
 * @param[in]  str1  An arbitrary @link ContainerConcept @endlink object.
 * @param[in]  str2  A second arbitrary @link ContainerConcept @endlink object.
 * @param[in]  nSize The neighbourhood size to use.
 * @param[out] pos   A String with pairs of positions that indicate the longest common subsequence.
 *
 * @section Example
 *
 * @include demos/dox/graph_algorithms/longest_common_subsequence.cpp
 *
 * @code{.console}
 * Score = 3
 * Alignment matrix:
 *       0     .
 *         aba--cx-
 *          ||  |
 *         -baabc-a
 * @endcode
 *
 * @see heaviestIncreasingSubsequence
 * @see longestIncreasingSubsequence
 */

template<typename TString1, typename TString2, typename TNeighborhoodSize, typename TFinalPos>
inline void
longestCommonSubsequence(TString1 const& str1,
                         TString2 const& str2,
                         TNeighborhoodSize nSize,
                         TFinalPos& pos)
{
    typedef typename Value<TString1>::Type TValue;
    typedef typename Size<TString1>::Type TSize;
    typedef typename Position<TString1>::Type TPos;
    TSize alphabet_size = ValueSize<TValue>::VALUE;

    // The occurrences of each letter in the second string
    typedef String<TPos> TPositions;
    String<TPositions> occ;
    resize(occ, alphabet_size, TPositions());
    typedef typename Iterator<TString2 const, Standard>::Type TStringIter;
    TStringIter itStr2 = begin(str2, Standard());
    TStringIter endItStr2 = end(str2, Standard());
    TPos current_pos = 0;
    for(; itStr2 != endItStr2; ++itStr2, ++current_pos) appendValue(occ[ordValue(*itStr2)], current_pos, Generous());

    // Build the combined string
    String<TPos> finalSeq;
    String<TPos> mapping;
    TStringIter itStr1 = begin(str1, Standard());
    TStringIter endItStr1 = end(str1, Standard());
    current_pos = 0;
    TPos diff = 0;
    for(; itStr1 != endItStr1; ++itStr1, ++current_pos) {
        TPositions& current_occ = occ[ordValue(*itStr1)];
        for(int i = length(current_occ)-1; i>=0; --i) {
            // Do we have a neighborhood
            diff = (current_pos < current_occ[i]) ? current_occ[i] - current_pos : current_pos - current_occ[i];
            if (diff > (TPos) nSize) continue;
            appendValue(finalSeq, current_occ[i], Generous());
            appendValue(mapping, current_pos, Generous());
        }
    }

    // Call longest increasing subsequence
    typedef String<TSize> TResult;
    TResult result;
    longestIncreasingSubsequence(finalSeq, result);

    // Insert the common pairs
    typedef typename Iterator<TResult, Standard>::Type TResultIter;
    TResultIter itResult = begin(result, Standard());
    TResultIter endResult = end(result, Standard());
    for(; itResult != endResult; ++itResult)
        appendValue(pos, std::make_pair(mapping[*itResult], finalSeq[*itResult]), Generous());
}

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

template<typename TAlign, typename TStringSet>
inline int
globalAlignment(TAlign& align,
                TStringSet const& str,
                Lcs)
{
    typedef typename Id<TStringSet>::Type TId;
    typedef typename Size<TStringSet>::Type TSize;
    TId id1 = positionToId(str, 0);
    TId id2 = positionToId(str, 1);

    // Lcs between first and second string
    String<std::pair<TSize, TSize> > pos1;
    longestCommonSubsequence(str[0], str[1], 100, pos1);
    //longestCommonSubsequence(str[0], str[1], 800, pos1);

    // Extend the matches as long as possible
    TSize oldI = 0;
    TSize oldJ = 0;
    TSize totalLen = 0;
    if (length(pos1)) {
        TSize lenMatch = 1;
        int last = length(pos1)-1;
        TSize iBegin = pos1[last].first;
        TSize jBegin = pos1[last].second;
        for(int z = last - 1; z>=0; --z) {
            if ((pos1[z].first == pos1[z+1].first + 1) &&
                (pos1[z].second == pos1[z+1].second + 1))
            {
                ++lenMatch;
            } else {
                if (oldI < iBegin) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) iBegin - oldI, 1);
                if (oldJ < jBegin) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) jBegin - oldJ, 2);
                oldI = iBegin + lenMatch;
                oldJ = jBegin + lenMatch;

                _alignTracePrint(align, str[0], str[1], id1, iBegin, id2, jBegin, lenMatch, 0);
                totalLen += lenMatch;
                lenMatch = 1;
                iBegin = pos1[z].first;
                jBegin = pos1[z].second;
            }
        }
        // Process last match
        if (oldI < iBegin) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) iBegin - oldI, 1);
        if (oldJ < jBegin) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) jBegin - oldJ, 2);
        oldI = iBegin + lenMatch;
        oldJ = jBegin + lenMatch;
        _alignTracePrint(align, str[0], str[1], id1, iBegin, id2, jBegin, lenMatch, 0);
        totalLen += lenMatch;
    }
    // Process left overs
    if (oldI < length(str[0])) _alignTracePrint(align, str[0], str[1], id1, oldI, id2, (TSize) 0, (TSize) length(str[0]) - oldI,  1);
    if (oldJ < length(str[1])) _alignTracePrint(align, str[0], str[1], id1, (TSize) 0, id2, oldJ, (TSize) length(str[1]) - oldJ, 2);

    return (int) totalLen;
}


//////////////////////////////////////////////////////////////////////////////
// HIS: Heaviest Increasing Subsequence
//////////////////////////////////////////////////////////////////////////////

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

/*!
 * @fn heaviestIncreasingSubsequence
 * @headerfile <seqan/graph_algorithms.h>
 * @brief Computes the heaviest increasing subseqnece.
 *
 * @signature void heaviestIncreasingSubsequence(str, weights, pos);
 *
 * @param[in]  str     An arbitrary @link ContainerConcept @endlink object.
 * @param[in]  weights A String with a weight for each position in the string.
 * @param[out] pos     A String with positions that indicate the members of the heaviest increasing subsequence.
 *
 * @section Remarks
 *
 * The last position in pos indicates the first member of the heviest increasing subsequence.  Note that only members
 * that contribute a weight are selected, that is, positions with associated 0 weights are ignored.
 *
 * @section Example
 *
 * @include demos/dox/graph_algorithms/heaviest_increasing_subsequence.cpp
 *
 * @code{.console}
 * z(Weight=1),e(Weight=1),i(Weight=10),t(Weight=1),g(Weight=1),e(Weight=1),i(Weight=1),s(Weight=1),t(Weight=1),
 * His:
 * e,i,s,t,(Weight=13)
 * @endcode
 *
 * @see longestCommonSubsequence
 * @see longestIncreasingSubsequence
 */

template<typename TString, typename TWeightMap, typename TPositions>
inline typename Value<TWeightMap>::Type
heaviestIncreasingSubsequence(TString const& str,
                              TWeightMap const& weights,
                              TPositions& pos)
{
    typedef typename Size<TString>::Type TSize;
    typedef typename Value<TString>::Type TValue;
    typedef typename Value<TPositions>::Type TPos;
    typedef typename Value<TWeightMap>::Type TWeight;

    // The list of decreasing covers, only the smallest element of each member must be remembered
    typedef std::pair<TValue, std::pair<TWeight, TPos> > TKey;
    typedef std::set<TKey, std::less<TKey> > TSortedSequence;
    typedef typename TSortedSequence::const_iterator TSortedSequenceIter;
    TSortedSequence list;

    // The trace-back graph
    typedef Graph<Directed<void, WithoutEdgeId> > TGraph;
    typedef VertexDescriptor<TGraph>::Type TVertexDescriptor;
    TGraph g;

    // Walk through the sequence and build the decreasing covers
    typedef typename Iterator<TString const, Standard>::Type TStringIter;
    TStringIter it = begin(str, Standard());
    TStringIter endIt = end(str, Standard());
    TSize pos_of_iterator = 0;
    TWeight w = 0;
    for(; it != endIt; ++it, ++pos_of_iterator) {
        w = weights[pos_of_iterator];
        // Letters that do not contribute a weight (e.g., w = 0) are excluded!
        // Weights must increase!
        if (w == 0) {
            addVertex(g);  // Note: The vertex id corresponds to the position
            continue;
        }


        // Get previous element
        TSortedSequenceIter a_k_it = _previousInSortedSequence(list, std::make_pair(*it, std::make_pair(0, 0)));

        // Get next element
        TSortedSequenceIter b_l_it = _nextInSortedSequence(list, a_k_it);

        // Determine new weight
        if (a_k_it != list.end()) w += a_k_it->second.first;

        // Delete from list
        while ((b_l_it != list.end()) &&
                (w >= b_l_it->second.first)) {
                    TSortedSequenceIter tmp = b_l_it;
                    b_l_it = _nextInSortedSequence(list, b_l_it);
                    list.erase(*tmp);
        }

        // Insert new list element
        if ((b_l_it == list.end()) ||
            (*it < b_l_it->first)) {
                list.insert(std::make_pair(*it, std::make_pair(w, pos_of_iterator)));
        }

        // Create the corresponding node, pos_of_iterator == Vertex Descriptor
        addVertex(g);

        // Connect to predecessor
        if (a_k_it != list.end()) addEdge(g, (TVertexDescriptor) pos_of_iterator, (TVertexDescriptor) a_k_it->second.second);
    }

    // Trace-back
    w = 0;
    if (list.rbegin() == list.rend()) return 0;
    else {
        // Last vertex is end of heaviest increasing subsequence
        TVertexDescriptor v = list.rbegin()->second.second;
        while (true) {
            appendValue(pos, v, Generous());
            w+=weights[v];
            if (g.data_vertex[v]) v = (*g.data_vertex[v]).data_target;
            else break;
        }
    }
    return w;
}



}// namespace seqan2

#endif //#ifndef SEQAN_HEADER_...
