// ==========================================================================
//                 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_ALGORITHM_REFINE_ALIGN_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_

namespace seqan2 {


///////////////////////////////////////////////////////////////////////////////////////////////////////
//Functions for Align<TSource,TSpec>
//project onto other sequence
template<typename TSource,typename TSpec,typename TValue, typename TId1, typename TPos1, typename TId2, typename TPos2,typename TMap>
void
_getOtherSequenceAndProject(Align<TSource,TSpec> & segment,
                TValue seg_num,
                            TMap & seq_map,
                           TId1 ,
                           TPos1 node_i,
                           TId2 & seq_j_id,
                           TPos2 & node_j)
{

    if(seg_num == 0)
    {
        seq_j_id = seq_map[getObjectId(source(row(segment, 1)))];
        TPos1 view_clipped_end_pos = clippedEndPosition(row(segment,0)) - clippedBeginPosition(row(segment, 0));
        if(node_i >= (TPos1)toSourcePosition(row(segment, 0), view_clipped_end_pos))
            node_j = static_cast<TPos2>(-1);
        else
            node_j = toSourcePosition(row(segment, 1), toViewPosition(row(segment, 0), node_i));
    }
    else
    {
        seq_j_id  = seq_map[getObjectId(source(row(segment, 0)))];
        TPos1 view_clipped_end_pos = clippedEndPosition(row(segment, 1)) - clippedBeginPosition(row(segment, 1));
        if(node_i >= (TPos1)toSourcePosition(row(segment, 1), view_clipped_end_pos))
            node_j = static_cast<TPos2>(-1);
        else
            node_j = toSourcePosition(row(segment, 0), toViewPosition(row(segment, 1), node_i));
    }
}


//unspektakul�re funktion, die die int ID zur�ckgibt (braucht man damit es f�r alle alignment typen geht)
//template<typename TSource,typename TSpec, typename TValue, typename TSeqMap>
//int
//_getSeqMapId(TSeqMap & seq_map,
//            Align<TSource,TSpec> & segment,
//            TValue seq_i)
//{
//    return seq_map[getObjectId(source(row(segment,seq_i)))];
//}
//
//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 TAliSource,typename TAliSpec, typename TId, typename TPosition, typename TId2>
void
_getSeqBeginAndEnd(Align<TAliSource,TAliSpec> & segment,
                  std::map<const void * ,int> & seq_map,
                  TId & seq_i_id,
                  TPosition & begin_i,
                  TPosition & end_i,
                  TId2 seq)
{
    seq_i_id = seq_map[getObjectId(source(row(segment,seq)))];
    begin_i = clippedBeginPosition(row(segment, seq));
    end_i = toSourcePosition(row(segment, seq), clippedEndPosition(row(segment, seq)) - begin_i);
}



////////////////////////////////////////////////////////////////////////////////////////
// 50000 _getRefinedMatchScore Functions
////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////

//TODO(singer): Remove this forward
template <typename T>
struct Row;

//for Align<TAliSource,TAliSpec>
//get score for alignment of length len starting at pos_i on first sequence
//and pos_j on second sequence
template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TAliSource,typename TAliSpec,typename TValue>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
         TStringSet &,
         Align<TAliSource,TAliSpec> & segment,
         TValue pos_i,
         TValue pos_j,
         TValue len,
         TValue)
{
    typedef Align<TAliSource,TAliSpec> TAlign;
    typedef typename Row<TAlign>::Type TRow;
//    typedef typename Iterator<TRow,GapsIterator<ArrayGaps> >::Type TIterator;
    typedef typename Iterator<TRow, Rooted>::Type TIterator;
    TIterator row0_it, row1_it;
    row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
    row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
    len = toViewPosition(row(segment,0),pos_i + len) - toViewPosition(row(segment,0),pos_i);
    TValue i = 0;
    TScoreValue ret_score = 0;
    while(i < len)
    {
        if(isGap(row1_it)||isGap(row0_it))
            ret_score += scoreGapExtend(score_type);
        else
            ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
        ++i;
        ++row0_it;
        ++row1_it;
    }
    return ret_score;
}


//get score for alignment starting at pos_i on first sequence
//and pos_j on second sequence, if len1!=len2 then the refinement
//process was stopped (the cut is not exact)
//template<typename TScore,typename TStringSet, typename TAliSource,typename TAliSpec,typename TValue>
//typename Value<TScore>::Type
//_getRefinedMatchScore(TScore & score_type,
//         TStringSet &,
//         Align<TAliSource,TAliSpec> & segment,
//         TValue pos_i,
//         TValue pos_j,
//         TValue len1,
//         TValue len2)
//{
//    typedef Align<TAliSource,TAliSpec> TAlign;
//    typedef typename Row<TAlign>::Type TRow;
//    typedef typename Iterator<TRow>::Type TIterator;
//    TIterator row0_it, row1_it;
//    TValue len;
//    row0_it = iter(row(segment,0),toViewPosition(row(segment,0),pos_i));
//    row1_it = iter(row(segment,1),toViewPosition(row(segment,1),pos_j));
//    len1 = toViewPosition(row(segment,0),pos_i + len1) - toViewPosition(row(segment,0),pos_i);
//    len2 = toViewPosition(row(segment,1),pos_j + len2) - toViewPosition(row(segment,1),pos_j);
//    len = (len1 < len2) ? len1 : len2;
//    int i = 0;
//    typename Value<TScore>::Type ret_score = 0;
//
//    //calculate score for aligned region
//    while(i < len)
//    {
//        ret_score += score(score_type,getValue(row0_it),getValue(row1_it));
//        ++i;
//        ++row0_it;
//        ++row1_it;
//    }
//    //fill up with gaps if one sequence is longer than the other
//    len = (len1 > len2) ? len1 : len2;
//    ret_score += (len - i) * scoreGapExtend(score_type);
//
//    return ret_score;
//}

}  // namespace seqan2

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_ALIGN_H_
