// ==========================================================================
//                 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
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Tobias Rausch <rausch@embl.de>
// Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_

//SEQAN_NO_DDDOC: do not generate documentation for this file

namespace seqan2 {


///////////////////////////////////////////////////////////////////////////////////////////////////////
//Functios for Align Graphs
//project onto other sequence for Graph<Alignment>
template<typename TAlignment,typename TId1, typename TPos1, typename TId2, typename TPos2, typename TValue,typename TMap>
void
_getOtherSequenceAndProject(Graph<TAlignment> & segment,
                TValue seg_num,
                            TMap &,
                             TId1 seq_i_id,
                            TPos1 pos_i,
                            TId2 & seq_j_id,
                            TPos2 & pos_j)
{
    getProjectedPosition(segment,seg_num,seq_i_id, pos_i,seq_j_id,pos_j);

}




//given seq and segment, get the sequenceId (seq_i) and its begin and end
//if seq = 0 get first sequence (that takes part in the segment match)
//if seq = 1 get second sequence
template<typename TAlign, typename TId, typename TPosition, typename TId2>
void
_getSeqBeginAndEnd(Graph<TAlign> & segment,
                  std::map<const void * ,int> &,
                  TId & seq_i_id,
                  TPosition & begin_i,
                  TPosition & end_i,
                  TId2 seq)
{
    //walk through edges, take first edge, target, source,
    //define: seq == 0   ==> seq_i_id = id of source of first edge
    //        seq == 1   ==> seq_i_id = id of target of first edge
    typedef Graph<TAlign> TGraph;
    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;

    TEdgeIterator ed_it(segment);
    //goBegin(ed_it);
    if(seq==0)
    {
        TVertexDescriptor src = sourceVertex(ed_it);
        seq_i_id = sequenceId(segment,src);
    }
    else
    {
        TVertexDescriptor trg = targetVertex(ed_it);
        seq_i_id = sequenceId(segment,trg);
    }
    begin_i = getFirstCoveredPosition(segment,seq_i_id);
    end_i = getLastCoveredPosition(segment,seq_i_id);


}




//////////////////////////
//for Graph<TAlign>
//vorsichtig! noch nicht richtig, bis jetzt nur ungapped exact matches...
//template<typename TScore,typename TStringSet,typename TAlignment,typename TValue>
//typename Value<TScore>::Type
//_getRefinedMatchScore(TScore & score_type,
//         TStringSet & seqs,
//         Graph<TAlignment> & segment,
//         TValue pos_i,
//         TValue pos_j,
//         TValue len)
//{
//    int pseudo_map = 0;
//    TValue pos_j_check,seq_j_id;
//    _getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,pos_i,seq_j_id,pos_j_check);
//    SEQAN_ASSERT(pos_j_check==pos_j);
//    TValue last_pos_i = pos_i + len;
//    TValue last_pos_j;
//    _getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,last_pos_i,seq_j_id,last_pos_j);
//
////    typename Infix<typename Value<TStringSet>::Type>::Type label0 = infix(getValueById(seqs,seq_i_id),pos_i,last_pos_i);
////    typename Infix<typename Value<TStringSet>::Type>::Type label1 = infix(getValueById(seqs,seq_j_id),pos_j,last_pos_j);
//
//    typename Value<TScore>::Type score = 0;
//    TValue i = 0;
//    while (i < len)
//    {
//        next_pos_j = getProjectedPosition(segment,seq_i_id,pos_i);
//        //gaps
//        if(pos_j+1 != next_pos_j)
//        {
//            if(pos_j == next_pos_j)
//            {
//                score += scoreGapExtend(score_type);
//                ++pos_i;
//                ++i;
//                continue;
//            }
//        }
//        pos_j = next_pos_j;
//        score += score(score_type,getValueById(seqs,seq_i_id)[pos_i],getValueById(seqs,seq_j_id)[pos_j]);
//        ++i;
//        ++pos_i;
//    }
//
//
//
//
//
//
//
//
//    typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,stringSet(segment)[0]);
//    typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,stringSet(segment)[1]);
//
//
//    //typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,0);
//    //typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,1);
//    int i = 0;
//    typename Value<TScore>::Type ret_score = 0;
//    while(i < len)
//    {
//        ret_score += score(score_type,label0[i],label1[i]);
//        ++i;
//    }
//    //ret_score = scoreMatch(score_type);
//    //ret_score *= len;
//    return ret_score;
//}


//////////////////////////
// get score for part of pairwise alignment graph starting in pos_i in first sequence and in
// pos_j in second sequence, and with length len and len_j respectively
// only for exact refinement
template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TAlignment,typename TValue>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
         TStringSet & seqs,
         Graph<TAlignment> & segment,
         TValue pos_i,
         TValue pos_j,
         TValue len,
         TValue len_j)
{

    typedef Graph<TAlignment> TGraph;
    typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;
    typedef typename Iterator<TGraph, EdgeIterator>::Type TEdgeIterator;
    typedef typename Iterator<TGraph, OutEdgeIterator>::Type TOutEdgeIterator;
    typedef typename TGraph::TPosToVertexMap TPosToVertexMap;
    typedef typename TPosToVertexMap::const_iterator TVertexMapIter;
    TVertexDescriptor nilVertex = getNil<TVertexDescriptor>();

    TValue seq_i_id;
    TEdgeIterator ed(segment);
    //goBegin(ed);
    seq_i_id = sequenceId(segment,sourceVertex(ed));

    int pseudo_map = 0;
    TValue pos_j_check,seq_j_id;
    _getOtherSequenceAndProject(segment,pseudo_map,seq_i_id,pos_i,seq_j_id,pos_j_check);
    SEQAN_ASSERT(pos_j_check==pos_j);
    TValue last_pos_j = pos_j + len_j;

    TScoreValue ret_score = 0;
    bool last_one_was_aligned = false;

    while(len != 0)
    {
        TValue rest = 0;
        TVertexMapIter it = segment.data_pvMap.upper_bound(std::make_pair(seq_i_id, pos_i));
        // it->second is nilVertex if pos_i lies within gap
        if(it->second == nilVertex)
        {
            ++it;
            if(it != segment.data_pvMap.end() && it->first.first == seq_i_id)
            {
                rest = fragmentBegin(segment,it->second)-pos_i;
                last_one_was_aligned = false;
                if(rest < len)//add rest many gaps
                        ret_score += rest * scoreGapExtend(score_type);
                else
                {//add len many gaps
                    ret_score += len * scoreGapExtend(score_type);
                    return ret_score;    //and done!
                }
            }
            else
            {//add len many gaps
                ret_score += len * scoreGapExtend(score_type);
                return ret_score;    //and done!
            }
        }
        else{
            TVertexDescriptor vd = it->second;
            rest = fragmentBegin(segment,vd)+fragmentLength(segment,vd)-pos_i;
            TOutEdgeIterator ed_it(segment,vd);
            if(!atEnd(ed_it)) //aligned stretch
            {
                if(last_one_was_aligned)
                {
                    TValue next_pos_j,temp;
                    getProjectedPosition(segment,seq_i_id,pos_i,temp,next_pos_j);
                    ret_score += (next_pos_j-pos_j) * scoreGapExtend(score_type);
                    pos_j = next_pos_j;
                }
                last_one_was_aligned = true;
                TValue i = 0;
                while(i < rest && i < len)
                {
                    ret_score += score(score_type,getValueById(seqs,seq_i_id)[pos_i++],getValueById(seqs,seq_j_id)[pos_j++]);
                    ++i;
                }
                if(rest>len) return ret_score; //done (last_pos_i is somewhere inside the current node)
                else
                {//last_pos_i is the first position of the next node
                    if(rest == len) //check if there is an unalgined stretch on seq_j_id that needs to be included
                    {
                        if(pos_j != last_pos_j)
                            ret_score += (last_pos_j-pos_j) * scoreGapExtend(score_type);
                    }
                }
            }
            else //gap
            {
                last_one_was_aligned = false;
                if(rest < len)//add rest many gaps
                        ret_score += rest * scoreGapExtend(score_type);
                else
                {//add len many gaps
                    ret_score += len * scoreGapExtend(score_type);
                    return ret_score;    //and done!
                }
            }
        }
        len -= rest;
    }


    return ret_score;
}

}  // namespace seqan2

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALIGN_GRAPH_ALGORITHM_REFINE_ALIGNGRAPH_H_
