// ==========================================================================
//                 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>
// ==========================================================================
// Iterative instead of recursive implementation of segment match refinement.
// This is required for some large inputs to circumvent stack overflows.
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
#define SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_

namespace seqan2 {

struct TagExactRefinement_;
typedef Tag<TagExactRefinement_> const ExactRefinement;

// exact method, every cut is made (unless it already exists)
template<typename TValue, typename TValue2, typename TSize>
inline bool
_cutIsValid(String<std::set<TValue> > & all_nodes,
        TValue2 seq_i_pos,
        TSize,
        typename std::set<TValue>::iterator iter,
        TSize,
        Tag<TagExactRefinement_> const)
{
    //cut already exists
    if(iter != all_nodes[seq_i_pos].end())
        return false;
    return true;
}


// necessary for reversed fragments: projected position pos_j is shifted one to the left --> ++pos_j if fragement reversed
template<typename TSize, typename TSpec,typename TPos>
inline void
_updateCutPosition(Fragment<TSize, ExactReversableFragment<TSpec> > & f, TPos & pos_j)
{
    if(f.reversed)
        ++pos_j;
}
//template<typename TSize, typename TSpec,typename TPos>
//inline void
//_updateCutPosition(Fragment<TSize, ExactReversableFragment<TSpec> > const& f, TPos & pos_j)
//{
//    if(f.reversed)
//        ++pos_j;
//}

// for all other fragment types --> no shifting necessary
template<typename TFrag,typename TPos>
inline void
_updateCutPosition(TFrag &, TPos &)
{
    return;
}

///////////////////////////////////////////////////////////////////////////////////////////////////////
//Recursive Refinement
//refine position node_i on sequence seq_i
template<typename TValue, typename TAlignmentString, typename TStringSet,typename TGraph, typename TPropertyMap,typename TSeqMap, typename TTagSpec>
inline void
_refine(TValue node_i,
     TValue seq_i_id,
     TStringSet & seqs,
     TSeqMap & seq_map,
     TAlignmentString & alis,
     String<TGraph> & gs,
     String<TPropertyMap> & pms,
     String<std::set<TValue> > & all_nodes,
     TValue min_len,
     Tag<TTagSpec> tag)
{
    typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
    typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;
    //find all segment matches that contain the current position (node_i)
    String<TAlignmentPointer> relevant_segments;
    TValue seq_i_pos = idToPosition(seqs,seq_i_id);
    findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i);


    TSegmentIterator segment_it = begin(relevant_segments);
    TSegmentIterator segment_end = end(relevant_segments);
    //foreach of those segments
    while(segment_it != segment_end)
    {
        TValue match_id = (*segment_it).i1; // segment match
        TValue seg_num = (*segment_it).i2; // first or second segment in segment match?

        //get the sequence that node_i needs to be projected onto (seq_j)
        //and get the projected position (pos_j)
        TValue seq_j_id, node_j;
        _getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
        TValue seq_j_pos = idToPosition(seqs,seq_j_id);
        _updateCutPosition(alis[match_id],node_j);

        typename std::set<TValue>::iterator iter;
        iter = all_nodes[seq_j_pos].find(node_j);

        //if node does not exist yet ---> insert and continue cutting
        if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter,min_len,tag))
        {
            all_nodes[seq_j_pos].insert(node_j);
            _refine(node_j,seq_j_id,seqs,seq_map,alis,gs,pms,all_nodes,min_len,tag);
        }
        // TODO: else //verschmelzen, abschneiden und ergehen, erst sp�ter...
        // do nothing or resolve problems

        ++segment_it;
    }
}

//template<typename TFragSize, typename TFragSpec>
//void
//printMatch(Fragment<TFragSize,TFragSpec> & f)
//{
//    std::cout << "FRAGMENT:" << " f.len = "<< f.len <<std::endl;
//    std::cout << "f.seqId1 = "<< f.seqId1 << " f.begin1 = " << f.begin1 << std::endl;
//    std::cout << "f.seqId2 = "<< f.seqId2 << " f.begin2 = " << f.begin2 << std::endl;
//}

//template<typename TAlign>
//void
//printMatch(TAlign & f)
//{
//    std::cout << f;
//}

///////////////////////////////////////////////////////////////////////////////////////////////////////
// Construct interval trees
////////////////////////////////////////////////////////////////////////////////////////////////////


//construct intervals from allignments for each sequence (other Alignment types)
template<typename TInterval, typename TStringSet, typename TAlignmentString, typename TSeqMap>
void
_buildIntervalsForAllSequences(TAlignmentString & alis,
                               String<String<TInterval> > & intervals,
                                  TStringSet & seqs,
                               TSeqMap & seq_map)
{

    typedef typename Value<TInterval>::Type TValue;
    typedef typename Cargo<TInterval>::Type TCargo;
    typedef typename Iterator<TAlignmentString,Standard>::Type TAliIterator;
    TAliIterator ali_it = begin(alis,Standard());
    TAliIterator ali_end = end(alis,Standard());
    TValue ali_counter = 0;
    //foreach alignment
    while(ali_it != ali_end)
    {
        TValue seq_i_id,begin_,end_;
        //printMatch(*ali_it);
        //get the first sequence (and its begin and end) that takes part in the alignment (seq_i)
        _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,0);
        TValue seq_i_pos = idToPosition(seqs, seq_i_id);
        //and append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
        appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,0)));

        //get the second sequence (and its begin and end) that takes part in the alignment (seq_i)
        _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_,end_,1);
        seq_i_pos = idToPosition(seqs, seq_i_id);
        //and again append the interval (ali_begin, ali_end) with cargo ali* to the list of intervals of seq_i
        appendValue(intervals[seq_i_pos],IntervalAndCargo<TValue,TCargo>(begin_,end_,TCargo(ali_counter,1)));

        ++ali_counter;
        ++ali_it;
    }

}


//get all intervals from the alignments and construct an interval tree for each sequence
template<typename TGraph, typename TPropertyMap, typename TAlignmentString, typename TSequence, typename TSetSpec, typename TValue, typename TSeqMap>
void
_createTreesForAllSequences(String<TGraph> & gs,
                           String<TPropertyMap> & pms,
                           TAlignmentString & alis,
                           StringSet<TSequence,TSetSpec> & seqs,
                           TSeqMap & seq_map,
                           TValue numSequences)
{
    //typedef typename Value<TAlignmentString>::Type TAlignment;
//    typedef TAlignment* TCargo;
    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
    typedef IntervalAndCargo<int,TCargo> TInterval;
    //typedef typename VertexDescriptor<TGraph>::Type TVertexDescriptor;

    //std::cout <<"create interval trees...";
    // clock_t start, finish1;
    // double duration;
    // start = clock();
    //one tree for each sequence
    resize(gs,numSequences);
    resize(pms,numSequences);

    // and one string of intervals for each sequence
    String<String<TInterval> > intervals;
    resize(intervals,numSequences);
    // fill intervals
    _buildIntervalsForAllSequences(alis,intervals,seqs,seq_map);

    TValue i = 0;

    while(i < numSequences)
    {
        //std::cout << (numSequences-i) <<" more ("<<length(intervals[i])<<" intervals)... "<<std::flush;
        TValue center = length(seqs[i])/2; // center raus, hat hier nix zu suchen
        //create interval tree!
        createIntervalTree(gs[i], pms[i], intervals[i], center);

        //intervals for sequence i are not needed anymore
        clear(intervals[i]);
        ++i;
    }
    // finish1 = clock();
    // duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
    // std::cout << "\ntook " << duration << " seconds.\n";
}


///////////////////////////////////////////////////////////////////////////////////////////////////////
// Construct refined alignment graph
////////////////////////////////////////////////////////////////////////////////////////////////////

// step 1 of constructing the refined alignment graph: create all nodes
template<typename TStringSet,typename TValue,typename TAliGraph>
void
_makeRefinedGraphNodes(String<std::set<TValue> > & all_nodes,
                      TStringSet & seqs,
                      TAliGraph & ali_g)
{
    typedef typename std::set<TValue>::iterator TSetIterator;
    //for each sequence look at all cut positions and create nodes between them
    for(unsigned int seq_i_pos = 0; seq_i_pos < length(seqs); ++seq_i_pos)
    {
        TValue seq_i_id = positionToId(stringSet(ali_g), seq_i_pos);
        TSetIterator it = all_nodes[seq_i_pos].begin();
        TSetIterator end_it = all_nodes[seq_i_pos].end();
        TSetIterator next_it = it;
        if(next_it != end_it)
            ++next_it;
        else
            addVertex(ali_g, seq_i_id, 0, length(seqs[seq_i_pos]));

        //first unaligned node
        if(it != end_it && *it != 0)
            addVertex(ali_g, seq_i_id, 0, *it);
        //a new node for each interval
        while(next_it != end_it)
        {
            TValue pos_i = *it;
            addVertex(ali_g, seq_i_id, pos_i, *next_it - pos_i);
            ++it;
            ++next_it;
        }
        //last unaligned node
        if(it !=end_it && *it<length(seqs[seq_i_pos]))
            addVertex(ali_g, seq_i_id, *it, (length(seqs[seq_i_pos])) - *it);
        all_nodes[seq_i_pos].clear();
    }
}


// step 2 of constructing the refined alignment graph: add all edges
// version for exact refinement
template<typename TAlignmentString,typename TStringSet,typename TSeqMap, typename TPropertyMap,typename TScore,typename TAliGraph >
void
_makeRefinedGraphEdges(TAlignmentString & alis,
                       TPropertyMap & pm,
                      TStringSet & seqs,
                      TSeqMap & seq_map,
                      TScore & score_type,
                      TAliGraph & ali_g,
                      Tag<TagExactRefinement_> const)
{
    typedef typename Value<TAlignmentString>::Type TAlign;
    typedef typename Size<TAlign>::Type TValue;
    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
    typedef typename VertexDescriptor<TAliGraph>::Type TVertexDescriptor;
    typedef typename EdgeDescriptor<TAliGraph>::Type TEdgeDescriptor;
    typedef typename Cargo<TAliGraph>::Type TCargo;
    //make edges
    TAliIterator ali_it = begin(alis);
    TAliIterator ali_end = end(alis);
    //for each segment/fragment/alignment
    while(ali_it != ali_end)
    {
        //get sequence, begin position and end position
        TValue seq_id,begin_pos,end_pos;
        _getSeqBeginAndEnd(*ali_it,seq_map,seq_id,begin_pos,end_pos,(TValue)0);
        SEQAN_ASSERT_LEQ(end_pos, length(seqs[idToPosition(seqs, seq_id)]));
        SEQAN_ASSERT(ali_it.data_container == ali_end.data_container);
        SEQAN_ASSERT(ali_it.data_iterator != ali_end.data_iterator);

        //get the node represents the current interval (begin_pos until next_cut_pos or end_pos)
        TVertexDescriptor act_knot = findVertex(ali_g,seq_id,begin_pos);
        TValue act_pos = begin_pos;
        TValue seq_j_id_temp,pos_j_begin;
        _getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id_temp,pos_j_begin);

        //for each interval that lies within the current segment/fragement/alignment
        while(act_pos < end_pos)
        {
            //get other sequence and projected position
            TValue seq_j_id,pos_j;
            _getOtherSequenceAndProject(*ali_it,(TValue)0,seq_map,seq_id,act_pos,seq_j_id,pos_j);
            SEQAN_ASSERT_NEQ(pos_j, static_cast<TValue>(-1));
            //find node that contains the projected position (pos_j)
            TVertexDescriptor vd = findVertex(ali_g, seq_j_id, pos_j);
            bool doAddEdge = true;

//            if(doAddEdge && fragmentBegin(ali_g,vd)!=pos_j) // check if edge makes sense
            if (vd == getNil<TVertexDescriptor>())
                doAddEdge = false;
            else
            {
                TValue temp_seq_i_id,temp_act_pos;
                _getOtherSequenceAndProject(*ali_it,(TValue)1,seq_map,seq_j_id,static_cast<TValue>(fragmentBegin(ali_g,vd)),temp_seq_i_id,temp_act_pos);
                if(temp_act_pos == static_cast<TValue>(-1))
                    doAddEdge = false;
                else
                {
                    TVertexDescriptor temp_act_knot = findVertex(ali_g, temp_seq_i_id, temp_act_pos);
                    if(act_knot!=temp_act_knot)
                        doAddEdge = false;
                }
            }
            if(doAddEdge)
            {
                typename Value<TScore>::Type score = _getRefinedMatchScore(score_type,seqs,*ali_it,act_pos,pos_j,fragmentLength(ali_g,act_knot),fragmentLength(ali_g,vd));//,fragmentLength(ali_g,vd));
        //        typename Value<TScore>::Type score = fragmentLength(ali_g,vd);
                score *= _getRefinedAnnoScore(ali_g,pm,vd,act_knot,score_type);
            //this needs to be generalized (makes sense for positive scores only)
                if(score <= 0) score = 1;
                if(score > 0)
                {
                    if (findEdge(ali_g, act_knot, vd) == 0) {
                        //if(abs((double)fragmentLength(ali_g, act_knot) - (double)fragmentLength(ali_g, vd)) > 20) {
                        //    std::cerr << "added edge: " << fragmentLength(ali_g, act_knot) << "  " <<  fragmentLength(ali_g, vd) << std::endl;
                        //    std::cerr << *ali_it;
                        //    std::cerr << "act_pos=" << act_pos-begin_pos << " pos_j=" << pos_j-pos_j_begin << std::endl;
                        //} else {
                            addEdge(ali_g,act_knot,vd,(TCargo)score);
                        //}
                    }
                    else {
                        TEdgeDescriptor ed = findEdge(ali_g, act_knot, vd);
                        //if((TCargo)score > getCargo(ed))
                            //assignCargo(ed, score);
                        assignCargo(ed, getCargo(ed)+score);
                    }
                }
            }
            //prepare for next interval
            act_pos += fragmentLength(ali_g,act_knot);
            act_knot = findVertex(ali_g,seq_id,act_pos);
        }
        ++ali_it;
    }
}





//build refined alignment graph, nodes are numbered ascendingly:
//seq1   0  1  2  3  4
//seq2   5  6  7  8  9 10
//seq3  11 12 13 14 15
template<typename TValue,typename TAlignmentString,typename TScore,typename TSequence, typename TSetSpec,typename TAliGraph,typename TSeqMap,typename TTagSpec>
void
_makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
                   TAlignmentString & alis,
                   TScore & score_type,
                   StringSet<TSequence, TSetSpec> & seqs,
                   TSeqMap & seq_map,
                   TAliGraph & ali_g,
                      Tag<TTagSpec> const tag,
                   bool)
{
    //std::cout << "making refined alignment graph...";
    //clock_t start, finish1;
    //double duration;
    //start = clock();

    //make nodes (same function for inexact and exact refinement)
    _makeRefinedGraphNodes(all_nodes,seqs,ali_g);

    bool pm = false;
    //add edges (different functions depending on exact/inexact refinement)
    _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);

    //std::cout << "check\n";
    //finish1 = clock();
    //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
    //std::cout << "\ntook " << duration << " seconds.\n";
}


//build refined alignment graph as above, but with additional annotation information
template<typename TValue,typename TAlignmentString,typename TScore,typename TSequence, typename TSetSpec,typename TAliGraph,typename TSeqMap,typename TAnnoString,typename TTagSpec>
void
_makeAlignmentGraphFromRefinedSegments(String<std::set<TValue> > & all_nodes,
                   TAlignmentString & alis,
                   TScore & score_type,
                   StringSet<TSequence, TSetSpec> & seqs,
                   TSeqMap & seq_map,
                   TAliGraph & ali_g,
                      Tag<TTagSpec> const tag,
                   TAnnoString & annotation)
{
    //std::cout << "making refined alignment graph...";
    //clock_t start, finish1;
    //double duration;
    //start = clock();

    //make nodes (same function for inexact and exact refinement)
    _makeRefinedGraphNodes(all_nodes,seqs,ali_g);

    //add annotation to nodes
    //typedef typename Value<TAnnoString>::Type TAnnotation;
    //typedef typename Value<TAnnotation>::Type TLabel;
    typedef char TLabel;
    String<String<TLabel> > pm;
    _addNodeAnnotation(seqs,seq_map,annotation,pm,ali_g,tag);

    //add edges (different functions depending on exact/inexact refinement)
    _makeRefinedGraphEdges(alis,pm,seqs,seq_map,score_type,ali_g,tag);

    //std::cout << "check\n";
    //finish1 = clock();
    //duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
    //std::cout << "\ntook " << duration << " seconds.\n";
}





////////////////////////////////////////////////////////////////////////////////////////
//The big matchRefinement function that does everything: build interval trees, do the
//refinement and construct a refined alignment graph
////////////////////////////////////////////////////////////////////////////////////////
template<typename TAlignmentString, typename TAnnotation, typename TOutGraph, typename TSequence, typename TSetSpec, typename TScore,typename TTagSpec>
void
matchRefinement(TAlignmentString & alis,
                StringSet<TSequence, TSetSpec> & seq,
                TScore & score_type,
                TOutGraph & ali_graph,
                typename Size<typename Value<TAlignmentString>::Type>::Type min_fragment_len,
                TAnnotation & annotation,
                Tag<TTagSpec> const tag)
{
    ////////////////////////////////////////////////////////////////
    //typedefs
    typedef typename Value<TAlignmentString>::Type TAlign;
    typedef typename Iterator<TAlignmentString, Rooted>::Type TAliIterator;
    typedef typename Size<TAlign>::Type TValue;
//    typedef TValue TCargo;
//    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
    typedef Pair<unsigned,unsigned,BitPacked<31,1> > TCargo;
    typedef IntervalAndCargo<int,TCargo> TInterval;
    typedef Graph<Directed<void,WithoutEdgeId> > TGraph;
    typedef IntervalTreeNode<TInterval> TNode;
    typedef String<TNode> TPropertyMap;
    typedef typename std::set<TValue>::iterator TSetIterator;
    typedef typename Cargo<typename Value<TPropertyMap>::Type>::Type TAlignmentPointer;
    typedef typename Iterator<String<TAlignmentPointer>, Rooted>::Type TSegmentIterator;

#ifdef SEQAN_TCOFFEE_DEBUG
    double refinementTime = sysTime();
#endif

    ////////////////////////////////////////////////////////////////
    TValue numSequences = length(seq);
    //weird ID --> good ID map
    std::map<const void * ,int> seq_map;
    for(int i = 0; i < (int) numSequences; ++i)
        seq_map[getObjectId(seq[i])] = i;
    ////////////////////////////////////////////////////////////////
    //build interval trees
    String<TGraph> gs;
    String<TPropertyMap> pms;
    _createTreesForAllSequences(gs, pms, alis, seq, seq_map, numSequences);

    ////////////////////////////////////////////////////////////////
    //do refinement
    //std::cout <<"refining..."<<std::flush;
    // clock_t start, finish1;
    // double duration;
    // start = clock();

    //all_nodes = set of all cut positions
    String<std::set<TValue> > all_nodes;
    resize(all_nodes,numSequences);

    //all_nodes that need to be processed set of all cut positions
    String<std::set<TValue> > all_node_queues;
    resize(all_node_queues,numSequences);

    //call function _refine for each startknoten
    TAliIterator ali_it = begin(alis);
    TAliIterator ali_end = end(alis);
    //for each segment/fragement/alignment
    while(ali_it != ali_end)
    {
        //for each of the two sequences
        for(TValue i = 0; i < 2; ++i)
        {
            TValue seq_i_id,begin_i,end_i;
            _getSeqBeginAndEnd(*ali_it,seq_map,seq_i_id,begin_i,end_i,i);
            TValue seq_i_pos = idToPosition(seq,seq_i_id);

            all_node_queues[seq_i_pos].insert(begin_i);
            all_node_queues[seq_i_pos].insert(end_i);
        }
        ++ali_it;
    }


    TSetIterator queueIt;
    bool done = false;
    while(!done)
    {
        for(unsigned seq_i_pos = 0; seq_i_pos < numSequences; ++seq_i_pos)
        {
            queueIt = all_node_queues[seq_i_pos].begin();
            while (queueIt != all_node_queues[seq_i_pos].end())
            {
                TValue node_i = *queueIt;
                TSetIterator iter = all_nodes[seq_i_pos].find(node_i);
        //        TSetIterator qiter = all_node_queues[seq_i_pos].find(node_i);
                if(_cutIsValid(all_nodes,seq_i_pos,node_i,iter,min_fragment_len,tag))
                   //&& _cutIsValid(all_node_queues,seq_i_pos,node_i,qiter,min_fragment_len,tag))
//                if(iter == all_nodes[seq_i_pos].end())
                {
                    TValue seq_i_id = positionToId(seq, seq_i_pos);
                    all_nodes[seq_i_pos].insert(node_i);
                    String<TAlignmentPointer> relevant_segments;
                    findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i);

                    TSegmentIterator segment_it = begin(relevant_segments);
                    TSegmentIterator segment_end = end(relevant_segments);
                    //foreach of those segments
                    while(segment_it != segment_end)
                    {
                        TValue match_id = (*segment_it).i1;
                        TValue seg_num = (*segment_it).i2;                        //get the sequence that node_i needs to be projected onto (seq_j)
                        //and get the projected position (pos_j)
                        TValue seq_j_id, node_j;
                        _getOtherSequenceAndProject(alis[match_id],seg_num,seq_map,seq_i_id,node_i,seq_j_id,node_j);
                        TValue seq_j_pos = idToPosition(seq,seq_j_id);
                        _updateCutPosition(alis[match_id],node_j);

                        typename std::set<TValue>::iterator iter_j, qiter_j;
                        iter_j = all_nodes[seq_j_pos].find(node_j);
                        qiter_j = all_node_queues[seq_j_pos].find(node_j);

                        //if node does not exist yet ---> insert and continue cutting
                        if(_cutIsValid(all_nodes,seq_j_pos,node_j,iter_j,min_fragment_len,tag)
                            && _cutIsValid(all_node_queues,seq_j_pos,node_j,qiter_j,min_fragment_len,tag))
                        //if(iter_j == all_nodes[seq_j_pos].end())
                        {
                            all_node_queues[seq_j_pos].insert(node_j);
                        }

                        ++segment_it;
                    }

                }
                ++queueIt;
            }
            all_node_queues[seq_i_pos].clear();
        }
        unsigned i;
        for(i = 0; i < numSequences; ++i)
        {
            queueIt = all_node_queues[i].begin();
            if (queueIt != all_node_queues[i].end())
                break;
        }
        if(i==numSequences)
            done=true;
    }
    _addAnnotationCuts(all_nodes,alis,gs,pms,seq,seq_map,annotation,min_fragment_len,tag);

    // finish1 = clock();
    // duration = (double)(finish1 - start) / CLOCKS_PER_SEC;
    //std::cout << "\ntook " << duration << " seconds.\n";
    //for(int seq_i = 0; seq_i < length(seq); ++seq_i)
    //{
    //    typename std::set<TValue>::iterator it = all_nodes[seq_i].begin();
    //    typename std::set<TValue>::iterator end_it = all_nodes[seq_i].end();
    //
    //    while(it != end_it)
    //    {
    //        std::cout << *it << ",";
    //        ++it;
    //    }
    //    std::cout << "\n";
    //}
    //std::cout <<"building tree..."<<std::flush;

#ifdef SEQAN_TCOFFEE_DEBUG
    std::cout << std::setw(30) << std::left << "Segment-match refinement:" << std::setw(10) << std::right << sysTime() - refinementTime << "  s" << std::endl;

    double buildGraphTime = sysTime();
#endif

    ////////////////////////////////////////////////////////////////
    //build refined alignment graph
    _makeAlignmentGraphFromRefinedSegments(all_nodes,alis,score_type,seq,seq_map,ali_graph,tag,annotation);

#ifdef SEQAN_TCOFFEE_DEBUG
    std::cout << std::setw(30) << std::left << "Build alignment graph:" << std::setw(10) << std::right << sysTime() - buildGraphTime << "  s" << std::endl;
#endif

}


///////WRAPPERS

//exact refinement, score type given
template<typename TAlignmentString, typename TScoreValue,typename TScoreSpec,typename TOutGraph, typename TSequence, typename TSetSpec>
void
matchRefinement(TAlignmentString & alis,
                StringSet<TSequence, TSetSpec> & seq,
                Score<TScoreValue,TScoreSpec> & score_type,
                TOutGraph & ali_graph)
{
    //min_fragment_len = 1   ==> Exact cutting
    bool anno = false;
    matchRefinement(alis,seq,score_type,ali_graph,1,anno,ExactRefinement());
}



//exact refinement, score type not given
template<typename TFragmentString, typename TOutGraph, typename TSequence, typename TSetSpec>
void
matchRefinement(TFragmentString & matches,
                StringSet<TSequence, TSetSpec> & strSet,
                TOutGraph & ali_graph)
{
    typename Cargo<TOutGraph>::Type fake_score = 1;
    bool anno = false;
    matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement());
}

}  // namespace seqan2

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_GRAPH_ALGORITHM_REFINE_EXACT_ITERATIVE_H_
