// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
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// modification, are permitted provided that the following conditions are met:
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//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
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// ==========================================================================
// Author: Tobias Rausch <rausch@embl.de>
// Author: Anne-Katrin Emde <anne-katrin.emde@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_

namespace seqan2 {


///////////////////////////////////////////////////////////////////////////////////////////////////////
//Functions for Fragments
//project onto other sequence for Graph<Alignment>
template<typename TFragSize, typename TFragSpec,typename TValue,typename TId1, typename TPos1, typename TId2, typename TPos2, typename TMap>
void
_getOtherSequenceAndProject(Fragment<TFragSize,TFragSpec> & 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);

    //if(seq_i_id == sequenceId(segment,0))
    //    seq_j_id = sequenceId(segment,1);
    //else
    //    seq_j_id = sequenceId(segment,0);
}


//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 TFragSize, typename TFragSpec, typename TId, typename TPosition, typename TId2>
void
_getSeqBeginAndEnd(Fragment<TFragSize,TFragSpec> & segment,
                  std::map<const void * ,int> &,
                  TId & seq_i_id,
                  TPosition & begin_i,
                  TPosition & end_i,
                  TId2 seq)
{
    seq_i_id = sequenceId(segment,seq);
    if(seq==0)
        begin_i = segment.begin1; // fragmentBegin(segment,seq_i_id);
    else
        begin_i = segment.begin2; // fragmentBegin(segment,seq_i_id);
    end_i = begin_i + segment.len; //fragmentLength(segment,seq_i_id);
}


////////////////////////////////////////////////////////////////////////////////////////
// 50000 _getRefinedMatchScore Functions
////////////////////////////////////////////////////////////////////////////////////////
//get score for alignment starting at pos_i on one sequence (first sequence if i_am_first==true)
//and pos_j on other sequence (second sequence if i_am_first==true), if len1!=len2 then the refinement
//process was stopped (the cut is not exact)
//template<typename TScore,typename TStringSet,typename TFragId,typename TFragPos,typename TFragSize, typename TFragSpec,typename TValue>
//typename Value<TScore>::Type
//_getRefinedMatchScore(TScore & score_type,
//         TStringSet & seqs,
//         Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment,
//         TValue pos_i,
//         TValue pos_j,
//         TValue len1,
//         TValue len2)
//{
//    typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
//    typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
//    int i = 0;
//    typename Value<TScore>::Type ret_score = 0;
//    TValue len = (len1 < len2) ? len1 : len2;
//    while(i < len)
//    {
//        ret_score += score(score_type,label0[i],label1[i]);
//        ++i;
//    }
//    len = (len1 > len2) ? len1 : len2;
//    ret_score += (len - i) * scoreGapExtend(score_type);
//    return ret_score;
//}
//
//
///////////////////////////////////////////////////////////////////////////////////////////////
////die n�chsten beiden funktionen: f�r Fragmente und Score vom Typ Simple
////f�r den fall dass es keine mismatches innerhalb der segmente gibt und Score vom typ Simple ist
////TODO: m�sste f�r einen bestimmten TFragSpec sein (Exact oder noMismatches)
////get score for alignment starting at pos_i on one sequence (first sequence if i_am_first==true)
////and pos_j on other sequence (second sequence if i_am_first==true), if len1!=len2 then the refinement
////process was stopped (the cut is not exact)
//template<typename TScoreValue,typename TStringSet,typename TFragId,typename TFragPos,typename TFragSize, typename TFragSpec>
//TScoreValue
//_getRefinedMatchScore(Score<TScoreValue, Simple> & score_type,
//         TStringSet & seqs,
//         Fragment<TFragId,TFragPos,TFragSize,TFragSpec> & segment,
//         TFragPos pos_i,
//         TFragPos pos_j,
//         TFragSize len1,
//         TFragSize len2)
//{
//    typename Infix<typename Value<TStringSet>::Type>::Type label0 = label(segment,seqs,sequenceId(segment,0));
//    typename Infix<typename Value<TStringSet>::Type>::Type label1 = label(segment,seqs,sequenceId(segment,1));
//    TScoreValue ret_score = 0;
//    TFragSize len;
//    if (len1 < len2) len = len1;
//    else len = len2;
//    if(len1 <= len2)
//    {
//        ret_score += len1 * scoreMatch(score_type);
//        ret_score += (len2 - len1) * scoreGapExtend(score_type);
//    }
//    else{
//        ret_score += len2 * scoreMatch(score_type);
//        ret_score += (len1 - len2) * scoreGapExtend(score_type);
//    }
//    return ret_score;
//}


//get score for alignment of length len starting at pos_i on one sequence (first sequence if i_am_first==true)
//and pos_j on other sequence (second sequence if i_am_first==true)
template<typename TScoreValue,typename TScoreSpec,typename TStringSet,typename TFragment,typename TFragPos,typename TFragSize>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue,TScoreSpec> & score_type,
         TStringSet & seqs,
         TFragment& segment,
         TFragPos pos_i,
         TFragPos pos_j,
         TFragSize len,
         TFragSize)
{
    typedef typename Infix<typename Value<TStringSet>::Type>::Type TSegmentLabel;
    TSegmentLabel label0 = label(segment,seqs, sequenceId(segment, 0));
    TSegmentLabel label1 = label(segment,seqs, sequenceId(segment, 1));
    typename Iterator<TSegmentLabel, Rooted>::Type label_it0 = begin(label0) + (pos_i - fragmentBegin(segment,sequenceId(segment,0)));
    typename Iterator<TSegmentLabel, Rooted>::Type label_it1 = begin(label1) + (pos_j - fragmentBegin(segment,sequenceId(segment,1)));
    int i = 0;
    TScoreValue ret_score = 0;
    while(i < (int) len)
    {
        ret_score += score(score_type,*label_it0,*label_it1);
        ++label_it0;
        ++label_it1;
        ++i;
    }
    return ret_score;
}


//get score for alignment of length len starting at pos_i on one sequence (first sequence if i_am_first==true)
//and pos_j on other sequence (second sequence if i_am_first==true)
template<typename TScoreValue,typename TStringSet,typename TFragPos,typename TFragSize, typename TSpec>
TScoreValue
_getRefinedMatchScore(Score<TScoreValue, Simple> & score_type,
         TStringSet &,
         Fragment<TFragSize,ExactFragment<TSpec> > &,
         TFragPos,
         TFragPos,
         TFragSize len,
         TFragSize)
{
    return len*scoreMatch(score_type);
}


}  // namespace

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_FRAGMENT_H_
