/*  $Id: alnmerger.cpp 670464 2023-07-25 17:29:42Z grichenk $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
*
*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author:  Kamen Todorov, NCBI
*
* File Description:
*   Alignment merger
*
* ===========================================================================
*/


#include <ncbi_pch.hpp>
#include <objtools/alnmgr/alnmerger.hpp>
#include <objtools/alnmgr/alnseq.hpp>
#include <objtools/alnmgr/alnmatch.hpp>
#include <objtools/alnmgr/alnmap.hpp>

#include <algorithm>


BEGIN_NCBI_SCOPE
BEGIN_objects_SCOPE // namespace ncbi::objects::


CAlnMixMerger::CAlnMixMerger(CRef<CAlnMixMatches>& aln_mix_matches,
                             TCalcScoreMethod calc_score)
    : m_DsCnt(aln_mix_matches->m_DsCnt),
      m_AlnMixMatches(aln_mix_matches),
      m_Matches(aln_mix_matches->m_Matches),
      m_AlnMixSequences(aln_mix_matches->m_AlnMixSequences),
      m_Seqs(aln_mix_matches->m_Seqs),
      m_Rows(m_AlnMixSequences->m_Rows),
      m_ExtraRows(m_AlnMixSequences->m_ExtraRows),
      m_AlnMixSegments(new CAlnMixSegments(m_AlnMixSequences)),
      m_SingleRefseq(false),
      x_CalculateScore(calc_score)
{
}


void
CAlnMixMerger::Reset()
{
    m_SingleRefseq = false;
    if (m_DS) {
        m_DS.Reset();
    }
    if (m_Aln) {
        m_Aln.Reset();
    }
    m_AlnMixSegments->m_Segments.clear();
    m_Rows.clear();
    m_ExtraRows.clear();
    NON_CONST_ITERATE (TSeqs, seq_i, m_Seqs) {
        (*seq_i)->SetStarts().clear();
        (*seq_i)->m_ExtraRow = 0;
    }
}


void
CAlnMixMerger::Merge(TMergeFlags flags)
{
    if ( !m_DsCnt ) {
        NCBI_THROW(CAlnException, eMergeFailure,
                   "CAlnMixMerger::Merge(): "
                   "No alignments were added for merging.");
    }
    if ( !m_DS  ||  m_MergeFlags != flags) {
        Reset();
        m_MergeFlags = flags;
        x_Merge();
    }
}


void
CAlnMixMerger::x_Merge()
{
    bool first_refseq = true; // mark the first loop

    // Find the refseq (if such exists)
    {{
        m_SingleRefseq = false;
        m_IndependentDSs = m_DsCnt > 1;

        unsigned int ds_cnt;
        NON_CONST_ITERATE (TSeqs, it, m_Seqs){
            ds_cnt = (*it)->m_DsCnt;
            if (ds_cnt > 1) {
                m_IndependentDSs = false;
            }
            if (ds_cnt == m_DsCnt) {
                m_SingleRefseq = true;
                if ( !first_refseq ) {
                    CRef<CAlnMixSeq> refseq = *it;
                    m_Seqs.erase(it);
                    m_Seqs.insert(m_Seqs.begin(), refseq);
                }
                break;
            }
            first_refseq = false;
        }
    }}

    // Index the sequences
    {{
        int seq_idx=0;
        NON_CONST_ITERATE (TSeqs, seq_i, m_Seqs) {
            (*seq_i)->m_SeqIdx = seq_idx++;
        }
    }}


    // Set the widths if the mix contains both AA & NA
    // or in case we force translation
    if ((m_AlnMixMatches->m_ContainsNA  &&  m_AlnMixMatches->m_ContainsAA)  ||
        (m_AlnMixMatches->m_AddFlags & CAlnMixMatches::fForceTranslation)) {
        NON_CONST_ITERATE (TSeqs, seq_i, m_Seqs) {
            (*seq_i)->m_Width = (*seq_i)->m_IsAA ? 1 : 3;
        }
    }



    CAlnMixSeq * refseq = 0, * seq1 = 0, * seq2 = 0;
    TSeqPos start, start1, start2, len, curr_len;
    int width1 = 0, width2 = 0;
    CAlnMixMatch * match;
    CAlnMixSeq::TMatchList::iterator match_list_iter1, match_list_iter2;
    CAlnMixSeq::TMatchList::iterator match_list_i;
    TSecondRowFits second_row_fits;

    refseq = *(m_Seqs.begin());
    TMatches::iterator match_i = m_Matches.begin();
    m_MatchIdx = 0;
    
    CRef<CAlnMixSegment> seg;
    CAlnMixStarts::iterator start_i, lo_start_i, hi_start_i, tmp_start_i;

    first_refseq = true; // mark the first loop

    x_SetTaskTotal(int(m_Matches.size()));

    while (true) {

        // need to cancel?
        if (x_InterruptTask()) {
            Reset();
            return;
        }
        
        // reached the end?
        if (first_refseq ?
            match_i == m_Matches.end()  &&  m_Matches.size() :
            refseq->m_MatchList.empty()  ||  
            match_list_i == refseq->m_MatchList.end()) {

            // move on to the next refseq
            refseq->m_RefBy = 0;

            // try to find the best scoring 'connected' candidate
            NON_CONST_ITERATE (TSeqs, it, m_Seqs){
                if ( !((*it)->m_MatchList.empty())  &&
                     (*it)->m_RefBy == refseq) {
                    if (refseq == *it) {
                        NCBI_THROW(CAlnException, eMergeFailure,
                                   "CAlnMixMerger::x_Merge(): "
                                   "Infinitue loop detected "
                                   "while searching for a connected candidate.");
                    }
                    refseq = *it;
                    break;
                }
            }
            if (refseq->m_RefBy == 0) {
                // no candidate was found 'connected' to the refseq
                // continue with the highest scoring candidate
                NON_CONST_ITERATE (TSeqs, it, m_Seqs){
                    if ( !((*it)->m_MatchList.empty()) ) {
                        if (refseq == *it) {
                            NCBI_THROW(CAlnException, eMergeFailure,
                                       "CAlnMixMerger::x_Merge(): "
                                       "Infinitue loop detected "
                                       "while searching for a new candidate.");
                        }
                        refseq = *it;
                        break;
                    }
                }
            }

            if (refseq->m_MatchList.empty()) {
                break; // done
            } else {
                first_refseq = false;
                match_list_i = refseq->m_MatchList.begin();
            }
            continue;
        } else {
            // iterate
            if (first_refseq) {
                match = *match_i;
                ++match_i;
            } else {
                match = *match_list_i;
                ++match_list_i;
                if (refseq == match->m_AlnSeq2  &&  refseq == match->m_AlnSeq1) {
                    // This is the rare case of a match b/n a seq and
                    // itself.  We need one more incrementation since
                    // the match would be recorded twice
                    _ASSERT(refseq->m_MatchList.size() >= 2);
                    ++match_list_i;
                }
            }
        }
        
        curr_len = len = match->m_Len;

        // is it a match with this refseq?
        if (match->m_AlnSeq1 == refseq) {
            seq1 = match->m_AlnSeq1;
            start1 = match->m_Start1;
            _ASSERT(seq1);
            match_list_iter1 = match->m_MatchIter1;
            seq2 = match->m_AlnSeq2;
            start2 = match->m_Start2;
            if ( seq2 )
                match_list_iter2 = match->m_MatchIter2;
        } else if (match->m_AlnSeq2 == refseq) {
            seq1 = match->m_AlnSeq2;
            start1 = match->m_Start2;
            _ASSERT(seq1);
            match_list_iter1 = match->m_MatchIter2;
            seq2 = match->m_AlnSeq1;
            start2 = match->m_Start1;
            if ( seq2 )
                match_list_iter2 = match->m_MatchIter1;
        } else {
            seq1 = match->m_AlnSeq1;
            seq2 = match->m_AlnSeq2;

            // mark the two refseqs, they are candidates for next refseq(s)
            _ASSERT(seq1);
            match->m_MatchIter1 =
                seq1->m_MatchList.insert(seq1->m_MatchList.end(), match);
            if (seq2) {
                match->m_MatchIter2 =
                    seq2->m_MatchList.insert(seq2->m_MatchList.end(), match);
            }
            _ASSERT(match->IsGood());

            // mark that there's no match with this refseq
            seq1 = 0;
        }

        // save the match info into the segments map
        if (seq1) {
            x_SetTaskCompleted(int(m_MatchIdx++));

            // this match is used, erase from seq1 list
            if ( !first_refseq ) {
                if ( !seq1->m_MatchList.empty() ) {
                    seq1->m_MatchList.erase(match_list_iter1);
                    match_list_iter1 = seq1->m_MatchList.end();
                }
            }

            // order the match
            match->m_AlnSeq1 = seq1;
            match->m_Start1 = start1;
            match->m_AlnSeq2 = seq2;
            match->m_Start2 = start2;
            match->m_MatchIter1 = match_list_iter1;
            if ( seq2 )
                match->m_MatchIter2 = match_list_iter2;

            if (m_MergeFlags & fTruncateOverlaps  &&  seq2) {
                CDiagRangeCollection::TAlnRng rng(match->m_Start1,
                                                  match->m_Start2,
                                                  match->m_Len,
                                                  !match->m_StrandsDiffer);
                CDiagRangeCollection::TAlnRngColl substrahend, diff;
                substrahend.insert(rng);
                CDiagRangeCollection* plane;
                TPlanes::iterator plane_it;
                if ((plane_it = m_Planes.find(make_pair(seq1, seq2))) !=
                    m_Planes.end()) {
                    plane = &(plane_it->second);
                } else {
                    CDiagRangeCollection new_plane(match->m_AlnSeq1->m_Width,
                                                   match->m_AlnSeq2->m_Width);
                    plane = &(m_Planes[make_pair(seq1, seq2)] = new_plane);
                }
                plane->Diff(substrahend, diff);

                if (diff.empty()) {
                    continue;
                }
                rng = *diff.begin();
                plane->insert(rng);

                // reset the ones below,
                // since match may have been modified
                start1 = match->m_Start1 = rng.GetFirstFrom();
                start2 = match->m_Start2 = rng.GetSecondFrom();
                curr_len = len = match->m_Len = rng.GetLength();
            }

            width1 = seq1->m_Width;
            if (seq2) {
                width2 = seq2->m_Width;
            }

            // in case of translated refseq
            if (width1 == 3) {
                x_SetSeqFrame(match, match->m_AlnSeq1);
                {{
                    // reset the ones below,
                    // since match may have been modified
                    seq1 = match->m_AlnSeq1;
                    start1 = match->m_Start1;
                    match_list_iter1 = match->m_MatchIter1;
                    seq2 = match->m_AlnSeq2;
                    start2 = match->m_Start2;
                    if ( seq2 )
                        match_list_iter2 = match->m_MatchIter2;
                    curr_len = len = match->m_Len;
                }}
            }

            // if a subject sequence place it in the proper row
            if ( !first_refseq  &&  m_MergeFlags & fQuerySeqMergeOnly) {
                bool proper_row_found = false;
                while (true) {
                    if (seq1->m_DsIdx == match->m_DsIdx) {
                        proper_row_found = true;
                        break;
                    } else {
                        if (seq1->m_ExtraRow) {
                            seq1 = match->m_AlnSeq1 = seq1->m_ExtraRow;
                        } else {
                            break;
                        }
                    }
                }
                if ( !proper_row_found   &&
                     !(m_MergeFlags & fTruncateOverlaps)) {
                    NCBI_THROW(CAlnException, eMergeFailure,
                               "CAlnMixMerger::x_Merge(): "
                               "Proper row not found for the match. "
                               "Cannot use fQuerySeqMergeOnly?");
                }
            }
            
            CAlnMixStarts& starts = seq1->SetStarts();
            if (seq2) {
                // mark it, it is linked to the refseq
                seq2->m_RefBy = refseq;

                // this match is used erase from seq2 list
                if ( !first_refseq ) {
                    if ( !seq2->m_MatchList.empty() ) {
                        seq2->m_MatchList.erase(match_list_iter2);
                        match_list_iter2 = seq2->m_MatchList.end();
                        match->m_MatchIter2 = match_list_iter2;
                    }
                }
            }

            start_i = starts.end();
            lo_start_i = starts.end();
            hi_start_i = starts.end();


            // create a copy of the match,
            // which we could work with temporarily
            // without modifying the original
            CAlnMixMatch tmp_match = *match;
            match = &tmp_match; // point to the new tmp_match


            if (seq2) {
                if (width2 == 3) {
                    // Set the frame if necessary
                    x_SetSeqFrame(match, match->m_AlnSeq2);
                }
                // check if the second row fits
                // this will truncate the match if 
                // there's an inconsistent overlap
                // and truncation was requested
                second_row_fits = x_SecondRowFits(match);
                if (second_row_fits == eIgnoreMatch) {
                    continue;
                }
                {{
                    // reset the ones below,
                    // since match may have been modified
                    seq1 = match->m_AlnSeq1;
                    start1 = match->m_Start1;
                    match_list_iter1 = match->m_MatchIter1;
                    seq2 = match->m_AlnSeq2;
                    start2 = match->m_Start2;
                    if ( seq2 )
                        match_list_iter2 = match->m_MatchIter2;
                    curr_len = len = match->m_Len;
                }}
                while (second_row_fits == eTranslocation) {
                    if (!seq2->m_ExtraRow) {
                        // create an extra row
                        CRef<CAlnMixSeq> row (new CAlnMixSeq);
                        row->m_BioseqHandle = seq2->m_BioseqHandle;
                        row->m_SeqId = seq2->m_SeqId;
                        row->m_Width = seq2->m_Width;
                        row->m_Frame = start2 % 3;
                        row->m_SeqIdx = seq2->m_SeqIdx;
                        row->m_ChildIdx = seq2->m_ChildIdx + 1;
                        if (m_MergeFlags & fQuerySeqMergeOnly) {
                            row->m_DsIdx = match->m_DsIdx;
                        }
                        m_ExtraRows.push_back(row);
                        row->m_ExtraRowIdx = seq2->m_ExtraRowIdx + 1;
                        seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow = row;
                        break;
                    }
                    seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow;

                    second_row_fits = x_SecondRowFits(match);
                    {{
                        // reset the ones below,
                        // since match may have been modified
                        seq1 = match->m_AlnSeq1;
                        start1 = match->m_Start1;
                        match_list_iter1 = match->m_MatchIter1;
                        seq2 = match->m_AlnSeq2;
                        start2 = match->m_Start2;
                        if ( seq2 )
                            match_list_iter2 = match->m_MatchIter2;
                        curr_len = len = match->m_Len;
                    }}
                }
            }


            if (!starts.size()) {
                // no starts exist yet

                if ( !m_IndependentDSs ) {
                    // Stop the algorithm after merging with respect to the first refseq.
                    // Clear all MatchLists and exit
                    if ( !(m_SingleRefseq  ||  first_refseq) ) {
                        NON_CONST_ITERATE (TSeqs, it, m_Seqs){
                            if ( !((*it)->m_MatchList.empty()) ) {
                                (*it)->m_MatchList.clear();
                            }
                        }
                        break; 
                    }
                }

                // this seq has not yet been used, set the strand
                if (m_AlnMixMatches->m_AddFlags & CAlnMixMatches::fForceTranslation) {
                    seq1->m_PositiveStrand = (seq1->m_StrandScore >= 0);
                } else {
                    seq1->m_PositiveStrand = ! (m_MergeFlags & fNegativeStrand);
                }

                //create the first one
                seg = new CAlnMixSegment();
                seg->m_Len = len;
                seg->m_DsIdx = match->m_DsIdx;
                starts[start1] = seg;
                seg->SetStartIterator
                    (seq1, lo_start_i = hi_start_i = starts.begin());

                if (m_MergeFlags & fQuerySeqMergeOnly) {
                    seq2->m_DsIdx = match->m_DsIdx;
                }
                // DONE!
            } else {
                // some starts exist already

                // look ahead
                if ((lo_start_i = start_i = starts.lower_bound(start1))
                    == starts.end()  ||
                    start1 < start_i->first) {
                    // the start position does not exist
                    if (lo_start_i != starts.begin()) {
                        --lo_start_i;
                    }
                }

                // look back
                if (hi_start_i == starts.end()  &&  start_i != lo_start_i) {
                    CAlnMixSegment * prev_seg = lo_start_i->second;
                    if (lo_start_i->first + prev_seg->m_Len * width1 >
                        start1) {
                        // x----..   becomes  x-x--..
                        //   x--..
                        
                        TSeqPos len1 = (start1 - lo_start_i->first) / width1;
                        TSeqPos len2 = prev_seg->m_Len - len1;
                        
                        // create the second seg
                        seg = new CAlnMixSegment();
                        seg->m_Len = len2;
                        seg->m_DsIdx = match->m_DsIdx;
                        starts[start1] = seg;
                        
                        // create rows info
                        ITERATE (CAlnMixSegment::TStartIterators, it, 
                                 prev_seg->m_StartIts) {
                            CAlnMixSeq * seq = it->first;
                            tmp_start_i = it->second;
                            if (seq->m_PositiveStrand ==
                                seq1->m_PositiveStrand) {
                                seq->SetStarts()
                                    [tmp_start_i->first + len1 * seq->m_Width]
                                    = seg;
                                if (tmp_start_i != seq->SetStarts().end()) {
                                    seg->SetStartIterator(seq, ++tmp_start_i);
                                } else {
                                    NCBI_THROW(CAlnException, eMergeFailure,
                                               "CAlnMixMerger::x_Merge(): "
                                               "Internal error: tmp_start_i == seq->GetStarts().end()");
                                }
                            } else {
                                seq->SetStarts()
                                    [tmp_start_i->first + len2 * seq->m_Width]
                                    = prev_seg;
                                seq->SetStarts()[tmp_start_i->first] = seg;
                                seg->SetStartIterator(seq, tmp_start_i);
                                if (tmp_start_i != seq->SetStarts().end()) {
                                    prev_seg->SetStartIterator(seq, ++tmp_start_i);
                                } else {
                                    NCBI_THROW(CAlnException, eMergeFailure,
                                               "CAlnMixMerger::x_Merge(): "
                                               "Internal error: tmp_start_i == seq->GetStarts().end()");
                                }
                            }
                        }
                        
                        // truncate the first seg
                        prev_seg->m_Len = len1;
                        
                        if (start_i != starts.begin()) {
                            start_i--; // point to the newly created start
                        }
                    }
                    if (lo_start_i != starts.end()) {
                        lo_start_i++;
                    }
                }
            }

            // loop through overlapping segments
            start = start1;
            while (hi_start_i == starts.end()) {
                if (start_i != starts.end()  &&  start_i->first == start) {
                    CAlnMixSegment * prev_seg = start_i->second;
                    if (prev_seg->m_Len > curr_len) {
                        // x-------)  becomes  x----)x--)
                        // x----)
                        
                        // create the second seg
                        seg = new CAlnMixSegment();
                        TSeqPos len1 = 
                            seg->m_Len = prev_seg->m_Len - curr_len;
                        start += curr_len * width1;

                        // truncate the first seg
                        prev_seg->m_Len = curr_len;
                        
                        // create rows info
                        ITERATE (CAlnMixSegment::TStartIterators, it, 
                                prev_seg->m_StartIts) {
                            CAlnMixSeq * seq = it->first;
                            tmp_start_i = it->second;
                            if (seq->m_PositiveStrand ==
                                seq1->m_PositiveStrand) {
                                seq->SetStarts()[tmp_start_i->first +
                                             curr_len * seq->m_Width]
                                    = seg;
                                if (tmp_start_i != seq->SetStarts().end()) {
                                    seg->SetStartIterator(seq, ++tmp_start_i);
                                } else {
                                    NCBI_THROW(CAlnException, eMergeFailure,
                                               "CAlnMixMerger::x_Merge(): "
                                               "Internal error: tmp_start_i == seq->GetStarts().end()");
                                }
                            } else{
                                seq->SetStarts()[tmp_start_i->first +
                                             len1 * seq->m_Width]
                                    = prev_seg;
                                seq->SetStarts()[tmp_start_i->first] = seg;
                                seg->SetStartIterator(seq, tmp_start_i);
                                if (tmp_start_i != seq->SetStarts().end()) {
                                    prev_seg->SetStartIterator(seq, ++tmp_start_i);
                                } else {
                                    NCBI_THROW(CAlnException, eMergeFailure,
                                               "CAlnMixMerger::x_Merge(): "
                                               "Internal error: tmp_start_i == seq->GetStarts().end()");
                                }
                            }
                        }
#if _DEBUG && _ALNMGR_DEBUG                        
                        seg->StartItsConsistencyCheck(*seq1,
                                                      start,
                                                      m_MatchIdx);
                        prev_seg->StartItsConsistencyCheck(*seq1,
                                                           start,
                                                           m_MatchIdx);
#endif


                        hi_start_i = start_i; // DONE!
                    } else if (curr_len == prev_seg->m_Len) {
                        // x----)
                        // x----)
                        hi_start_i = start_i; // DONE!
                    } else {
                        // x----)     becomes  x----)x--)
                        // x-------)
                        start += prev_seg->m_Len * width1;
                        curr_len -= prev_seg->m_Len;
                        if (start_i != starts.end()) {
                            start_i++;
                        }
                    }
                } else {
                    seg = new CAlnMixSegment();
                    starts[start] = seg;
                    tmp_start_i = start_i;
                    if (tmp_start_i != starts.begin()) {
                        tmp_start_i--;
                    }
                    seg->SetStartIterator(seq1, tmp_start_i);
                    if (start_i != starts.end()  &&
                        start + curr_len * width1 > start_i->first) {
                        //       x--..
                        // x--------..
                        seg->m_Len = (start_i->first - start) / width1;
                        seg->m_DsIdx = match->m_DsIdx;
                    } else {
                        //       x-----)
                        // x---)
                        seg->m_Len = curr_len;
                        seg->m_DsIdx = match->m_DsIdx;
                        hi_start_i = start_i;
                        if (hi_start_i != starts.begin()) {
                            hi_start_i--; // DONE!
                        }
                    }
                    start += seg->m_Len * width1;
                    curr_len -= seg->m_Len;
                    if (lo_start_i == start_i) {
                        if (lo_start_i != starts.begin()) {
                            lo_start_i--;
                        }
                    }
                }
            }
                 
            // try to resolve the second row
            if (seq2) {

                while (second_row_fits != eSecondRowFitsOk  &&
                       second_row_fits != eIgnoreMatch) {
                    if (!seq2->m_ExtraRow) {
                        // create an extra row
                        CRef<CAlnMixSeq> row (new CAlnMixSeq);
                        row->m_BioseqHandle = seq2->m_BioseqHandle;
                        row->m_SeqId = seq2->m_SeqId;
                        row->m_Width = seq2->m_Width;
                        row->m_Frame = start2 % 3;
                        row->m_SeqIdx = seq2->m_SeqIdx;
                        row->m_ChildIdx = seq2->m_ChildIdx + 1;
                        if (m_MergeFlags & fQuerySeqMergeOnly) {
                            row->m_DsIdx = match->m_DsIdx;
                        }
                        m_ExtraRows.push_back(row);
                        row->m_ExtraRowIdx = seq2->m_ExtraRowIdx + 1;
                        seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow = row;
                        break;
                    }
                    seq2 = match->m_AlnSeq2 = seq2->m_ExtraRow;

                    second_row_fits = x_SecondRowFits(match);
                    {{
                        // reset the ones below,
                        // since match may have been modified
                        seq1 = match->m_AlnSeq1;
                        start1 = match->m_Start1;
                        match_list_iter1 = match->m_MatchIter1;
                        seq2 = match->m_AlnSeq2;
                        start2 = match->m_Start2;
                        if ( seq2 )
                            match_list_iter2 = match->m_MatchIter2;
                        curr_len = len = match->m_Len;
                    }}
                }
                if (second_row_fits == eIgnoreMatch) {
                    continue;
                }

                if (m_MergeFlags & fTruncateOverlaps) {
                    // we need to reset these shtorcuts
                    // in case the match was truncated
                    start1 = match->m_Start1;
                    start2 = match->m_Start2;
                    len = match->m_Len;
                }

                // set the strand if first time
                if (seq2->GetStarts().empty()) {
                    seq2->m_PositiveStrand = 
                        (seq1->m_PositiveStrand ?
                         !match->m_StrandsDiffer :
                         match->m_StrandsDiffer);
                }

                // create row info
                CAlnMixStarts& starts2 = match->m_AlnSeq2->SetStarts();
                start = start2;
                CAlnMixStarts::iterator start2_i
                    = starts2.lower_bound(start2);
                start_i = match->m_StrandsDiffer ? hi_start_i : lo_start_i;

                while(start < start2 + len * width2) {
                    if (start2_i != starts2.end() &&
                        start2_i->first == start) {
                        // this position already exists

                        if (start2_i->second != start_i->second) {
                            // merge the two segments

                            // store the seg in a CRef to delay its deletion
                            // until after the iteration on it is finished
                            CRef<CAlnMixSegment> tmp_seg(start2_i->second);

                            ITERATE (CAlnMixSegment::TStartIterators,
                                     it, 
                                     tmp_seg->m_StartIts) {
                                CAlnMixSeq * tmp_seq = it->first;
                                tmp_start_i = it->second;
                                tmp_start_i->second = start_i->second;
                                start_i->second->SetStartIterator(tmp_seq, tmp_start_i);
                            }
#if _DEBUG && _ALNMGR_DEBUG                        
                            start_i->second->StartItsConsistencyCheck(*seq2,
                                                                      start,
                                                                      m_MatchIdx);
#endif
                        }
                    } else {
                        // this position does not exist, create it
                        seq2->SetStarts()[start] = start_i->second;

                        // start2_i != starts.begin() because we just 
                        // made an insertion, so decrement is ok
                        start2_i--;
                        
                        // point this segment's row start iterator
                        if (start_i->second->m_StartIts.find(seq2) !=
                            start_i->second->m_StartIts.end()) {
                            // consistency check fails
                            NCBI_THROW(CAlnException, eMergeFailure,
                                       "CAlnMixMerger::x_Merge(): "
                                       "Internal error: "
                                       "Start iterator already exists for seq2.");
                        }
                        start_i->second->SetStartIterator(seq2, start2_i);
#if _DEBUG && _ALNMGR_DEBUG                        
                        start_i->second->StartItsConsistencyCheck(*seq2,
                                                                  start,
                                                                  m_MatchIdx);
#endif
                    }

                    // increment values
                    start += start_i->second->m_Len * width2;
                    if (start2_i != starts2.end()) {
                        start2_i++;
                    }
                    if (match->m_StrandsDiffer) {
                        if (start_i != starts.begin()) {
                            start_i--;
                        }
                    } else {
                        if (start_i != starts.end()) {
                            start_i++;
                        }
                    }
                }
            }
        }
    }
    x_SetTaskCompleted(int(m_MatchIdx));
    
    m_AlnMixSequences->BuildRows();
    m_AlnMixSegments->Build(m_MergeFlags & fGapJoin,
                            m_MergeFlags & fMinGap,
                            m_MergeFlags & fRemoveLeadTrailGaps);
    if (m_MergeFlags & fFillUnalignedRegions) {
        m_AlnMixSegments->FillUnalignedRegions();
    }
    x_CreateDenseg();
}


CAlnMixMerger::TSecondRowFits
CAlnMixMerger::x_SecondRowFits(CAlnMixMatch * match) const
{
    CAlnMixSeq*&            seq1    = match->m_AlnSeq1;
    CAlnMixSeq*&            seq2    = match->m_AlnSeq2;
    TSeqPos&                start1  = match->m_Start1;
    TSeqPos&                start2  = match->m_Start2;
    TSeqPos&                len     = match->m_Len;
    const int&              width1  = seq1->m_Width;
    const int&              width2  = seq2->m_Width;
    CAlnMixStarts::const_iterator starts2_i;
    TSignedSeqPos           delta, delta1, delta2;
    TSecondRowFits          result  = eSecondRowFitsOk;

    // subject sequences go on separate rows if requested
    if (m_MergeFlags & fQuerySeqMergeOnly) {
        if (seq2->m_DsIdx) {
            if ( !(m_MergeFlags & fTruncateOverlaps) ) {
                if (seq2->m_DsIdx == match->m_DsIdx) {
                    return result;
                } else {
                    return eForceSeparateRow;
                }
            }
        } else {
            seq2->m_DsIdx = match->m_DsIdx;
            if ( !(m_MergeFlags & fTruncateOverlaps) ) {
                return result;
            }
        }
    }

    if ( !seq2->GetStarts().empty() ) {

        // check strand
        while (true) {
            if (seq2->m_PositiveStrand !=
                (seq1->m_PositiveStrand ?
                 !match->m_StrandsDiffer :
                 match->m_StrandsDiffer)) {
                if (seq2->m_ExtraRow) {
                    seq2 = seq2->m_ExtraRow;
                } else {
                    return eInconsistentStrand;
                }
            } else {
                break;
            }
        }

        // check frame
        if (seq2->m_Width == 3  &&  seq2->m_Frame != (int)(start2 % 3)) {
            return eInconsistentFrame;
        }

        starts2_i = seq2->GetStarts().lower_bound(start2);

        // check below
        if (starts2_i != seq2->GetStarts().begin()) {
            starts2_i--;
            
            // check for inconsistency on the first row
            if ( !m_IndependentDSs ) {
                CAlnMixSegment::TStartIterators::const_iterator seq1_start_it_i =
                    starts2_i->second->m_StartIts.find(seq1);
                if (seq1_start_it_i != starts2_i->second->m_StartIts.end()) {
                    const TSeqPos& existing_start1 = seq1_start_it_i->second->first;
                    if (match->m_StrandsDiffer) {
                        delta = start1 + len * width1 - existing_start1;
                        if (delta > 0) {
                            if (m_MergeFlags & fTruncateOverlaps) {
                                delta /= width1;
                                if (delta < (TSignedSeqPos)len) {
                                    // target above
                                    // x----- x-)-)
                                    // (----x (---x
                                    // target below
                                    len -= delta;
                                    start2 += delta * width2;
                                } else if (delta > (TSignedSeqPos)len  &&
                                           m_MergeFlags & fAllowTranslocation) {
                                    // Translocation
                                    // below target above
                                    // x---- x-)--- 
                                    //       (----x (------x
                                    //       target below
                                    delta = (existing_start1 + 
                                             starts2_i->second->m_Len - start1) /
                                        width1;
                                    if (delta > 0) {
                                        if (delta < (TSignedSeqPos)len) {
                                            start1 += delta * width1;
                                            len -= delta;
                                        } else {
                                            return eIgnoreMatch;
                                        }
                                    }
                                    return eTranslocation;
                                } else {
                                    return eIgnoreMatch;
                                }
                            } else {
                                return eFirstRowOverlapAbove;
                            }
                        }
                    } else {
                        delta = existing_start1
                            + starts2_i->second->m_Len * width1
                            - start1;
                        if (delta > 0) {
                            if (m_MergeFlags & fTruncateOverlaps) {
                                delta /= width1;
                                if (len > (TSeqPos)delta) {
                                    // below target
                                    // x---- x-)--)
                                    // x---) x----)
                                    // below target
                                    len -= delta;
                                    start1 += delta * width1;
                                    start2 += delta * width2;
                                } else if (delta > (TSignedSeqPos)len  &&
                                           m_MergeFlags & fAllowTranslocation) {
                                    // Translocation
                                    //       target above
                                    //       x--x-) ----)
                                    // x---) x----)
                                    // below target
                                    delta = (existing_start1 - start1) / width1;
                                    if (delta < (TSignedSeqPos)len) {
                                        len = delta;
                                        if ( !len ) {
                                            return eIgnoreMatch;
                                        }
                                    }
                                    return eTranslocation;
                                } else {
                                    return eIgnoreMatch;
                                }
                            } else {
                                return eFirstRowOverlapBelow;
                            }
                        }
                    }
                }
            }

            // check for overlap with the segment below on second row
            delta = starts2_i->first + starts2_i->second->m_Len * width2
                - start2;
            if (delta > 0) {
                //       target
                // ----- ------
                // x---- x-)--)
                // below target
                if (m_MergeFlags & fTruncateOverlaps) {
                    delta /= width2;
                    if (len > (TSeqPos)delta) {
                        len -= delta;
                        start2 += delta * width2;
                        if ( !match->m_StrandsDiffer ) {
                            start1 += delta * width1;
                        }
                    } else {
                        return eIgnoreMatch;
                    }
                } else {
                    return eSecondRowOverlap;
                }
            }
            if (starts2_i != seq2->GetStarts().end()) {
                starts2_i++;
            }
        }

        // check the overlapping area for consistency
        while (starts2_i != seq2->GetStarts().end()  &&  
               starts2_i->first < start2 + len * width2) {
            if ( !m_IndependentDSs ) {
                CAlnMixSegment::TStartIterators::const_iterator seq1_start_it_i =
                    starts2_i->second->m_StartIts.find(seq1);
                if (seq1_start_it_i != starts2_i->second->m_StartIts.end()) {
                    const TSeqPos& existing_start1 = seq1_start_it_i->second->first;
                    if (match->m_StrandsDiffer) {
                        // x---..- x---..--)
                        // (---..- (--x..--x
                        delta1 = (start1 - existing_start1) / width1 +
                            len - starts2_i->second->m_Len;
                    } else {
                        // x--..- x---...-)
                        // x--..- x---...-)
                        delta1 = (existing_start1 - start1) / width1;
                    }
                    delta2 = (starts2_i->first - start2) / width2;
                    if (delta1 != delta2) {
                        if (m_MergeFlags & fTruncateOverlaps) {
                            delta = (delta1 < delta2 ? delta1 : delta2);
                            if (delta > 0) {
                                if (match->m_StrandsDiffer) {
                                    start1 += (len - delta) * width1;
                                }
                                len = delta;
                            } else if (m_MergeFlags & fAllowTranslocation) {
                                return eTranslocation;
                            } else {
                                return eInconsistentOverlap;
                            }
                        } else {
                            return eInconsistentOverlap;
                        }
                    }
                }
            }
            starts2_i++;
        }

        // check above for consistency
        if (starts2_i != seq2->GetStarts().end()) {
            if ( !m_IndependentDSs ) {
                CAlnMixSegment::TStartIterators::const_iterator seq1_start_it_i =
                    starts2_i->second->m_StartIts.find(seq1);
                if (seq1_start_it_i != starts2_i->second->m_StartIts.end()) {
                    const TSeqPos& existing_start1 = seq1_start_it_i->second->first;
                    if (match->m_StrandsDiffer) {
                        delta = existing_start1 + 
                            starts2_i->second->m_Len * width1 - start1;
                        if (delta > 0) {
                            // below target
                            // x---- x-)--)
                            // (---x (----x
                            // above target
                            if (m_MergeFlags & fTruncateOverlaps) {
                                if (len > (TSeqPos)(delta / width1)) {
                                    len -= delta / width1;
                                    start1 += delta;
                                } else {
                                    if (m_MergeFlags & fAllowTranslocation) {
                                        return eFirstRowOverlapBelow;
                                    } else {
                                        return eIgnoreMatch;
                                    }
                                }
                            } else {
                                return eFirstRowOverlapBelow;
                            }
                        }
                    } else {
                        delta = start1 + len * width1 - existing_start1;
                        if (delta > 0) {
                            // target above
                            // x--x-) ----)
                            // x----) x---)
                            // target above
                            if (m_MergeFlags & fTruncateOverlaps) {
                                if (len <= (TSeqPos)delta / width1) {
                                    if (m_MergeFlags & fAllowTranslocation) {
                                        return eFirstRowOverlapAbove;
                                    } else {
                                        return eIgnoreMatch;
                                    }
                                } else {
                                    len -= delta / width1;
                                }
                            } else {
                                return eFirstRowOverlapAbove;
                            }
                        }
                    }
                }
            }
        }

        // check for inconsistent matches
        CAlnMixStarts::const_iterator starts1_i = seq1->GetStarts().find(start1);
        if (starts1_i == seq1->GetStarts().end() ||
            starts1_i->first != start1) {
            // commenting out for now, since moved the function call ahead            
//             NCBI_THROW(CAlnException, eMergeFailure,
//                        "CAlnMixMerger::x_SecondRowFits(): "
//                        "Internal error: seq1->m_Starts do not match");
        } else {
            CAlnMixSegment::TStartIterators::const_iterator seq2_start_it_i;
            TSeqPos tmp_start =
                match->m_StrandsDiffer ? start2 + len * width2 : start2;
            while (starts1_i != seq1->GetStarts().end()  &&
                   starts1_i->first < start1 + len * width1) {

                const CAlnMixSegment::TStartIterators& seg_start_its = 
                    starts1_i->second->m_StartIts;

                if (match->m_StrandsDiffer) {
                    tmp_start -= starts1_i->second->m_Len * width2;
                }

                if ((seq2_start_it_i = seg_start_its.find(seq2)) !=
                    seg_start_its.end()) {
                    if (seq2_start_it_i->second->first != tmp_start) {
                        // found an inconsistent prev match
                        return eSecondRowInconsistency;
                    }
                }

                if ( !match->m_StrandsDiffer ) {
                    tmp_start += starts1_i->second->m_Len * width2;
                }

                starts1_i++;
            }
        }
    }
    if (m_MergeFlags & fQuerySeqMergeOnly) {
        _ASSERT(m_MergeFlags & fTruncateOverlaps);
        if (seq2->m_DsIdx == match->m_DsIdx) {
            return result;
        } else {
            return eForceSeparateRow;
        }
    }
    return result;
}


void
CAlnMixMerger::x_CreateDenseg()
{
    int numrow  = 0,
        numrows = int(m_Rows.size());
    int numseg  = 0,
        numsegs = int(m_AlnMixSegments->m_Segments.size());
    int num     = numrows * numsegs;

    m_DS = new CDense_seg();
    m_DS->SetDim(numrows);
    m_DS->SetNumseg(numsegs);

    m_Aln = new CSeq_align();
    m_Aln->SetType(CSeq_align::eType_not_set);
    m_Aln->SetSegs().SetDenseg(*m_DS);
    m_Aln->SetDim(numrows);

    CDense_seg::TIds&     ids     = m_DS->SetIds();
    CDense_seg::TStarts&  starts  = m_DS->SetStarts();
    CDense_seg::TStrands& strands = m_DS->SetStrands();
    CDense_seg::TLens&    lens    = m_DS->SetLens();

    x_SetTaskName("Building");
    x_SetTaskTotal(numsegs);

    ids.resize(numrows);
    lens.resize(numsegs);
    starts.resize(num, -1);
    strands.resize(num, eNa_strand_minus);

    vector<bool> row_empty(numrows, true);

    // ids
    numrow = 0;
    ITERATE(TSeqs, row_i, m_Rows) {
        ids[numrow++] = (*row_i)->m_SeqId;
    }

    int offset = 0;
    numseg = 0;

    ITERATE(CAlnMixSegments::TSegments,
            seg_i,
            m_AlnMixSegments->m_Segments) {

        // lens
        lens[numseg] = (*seg_i)->m_Len;

        // starts
        ITERATE (CAlnMixSegment::TStartIterators, start_its_i,
                (*seg_i)->m_StartIts) {
            starts[offset + start_its_i->first->m_RowIdx] =
                start_its_i->second->first;

            if (start_its_i->second->first != kInvalidSeqPos) {
                row_empty[start_its_i->first->m_RowIdx] = false;
            }
        }

        // strands
        numrow = 0;
        ITERATE(TSeqs, row_i, m_Rows) {
            if ((*row_i)->m_PositiveStrand) {
                strands[offset + numrow] = eNa_strand_plus;
            }
            numrow++;
        }

        // next segment
        numseg++; offset += numrows;
        x_SetTaskCompleted(numseg);
    }


    // widths
    CDense_seg::TWidths*  widths = NULL;
    if ((m_AlnMixMatches->m_ContainsNA  &&  m_AlnMixMatches->m_ContainsAA)  || 
        (m_AlnMixMatches->m_AddFlags & CAlnMixMatches::fForceTranslation)) {
        widths = &m_DS->SetWidths();
        widths->resize(numrows);
        numrow = 0;
        ITERATE (TSeqs, row_i, m_Rows) {
            (*widths)[numrow++] = (*row_i)->m_Width;
        }
    }

    //remove empty rows
    for(int row = numrows-1; row >=0; --row) {
        if (row_empty[row]) {
            ids.erase(ids.begin()+row);
            if (widths) {
                widths->erase(widths->begin()+row);
            }
            for (int i = (numsegs-1)*numrows + row; i > 0; i -= numrows) {
                starts.erase(starts.begin()+i);
                strands.erase(strands.begin()+i);
            }
            --numrows;
        }
    }
    m_DS->SetDim(numrows);

#if _DEBUG
    try {
        m_DS->Validate(true);
    } catch (...) {
        _ASSERT(false);
    }
#endif    
}


void
CAlnMixMerger::x_SetSeqFrame(CAlnMixMatch* match, CAlnMixSeq*& seq)
{
    unsigned frame;
    if (seq == match->m_AlnSeq1) {
        frame = match->m_Start1 % 3;
    } else {
        frame = match->m_Start2 % 3;
    }
    if (seq->GetStarts().empty()) {
        seq->m_Frame = frame;
    } else {
        while ((unsigned)seq->m_Frame != frame) {
            if (!seq->m_ExtraRow) {
                // create an extra frame
                CRef<CAlnMixSeq> new_seq (new CAlnMixSeq);
                new_seq->m_BioseqHandle = seq->m_BioseqHandle;
                new_seq->m_SeqId = seq->m_SeqId;
                new_seq->m_PositiveStrand = seq->m_PositiveStrand;
                new_seq->m_Width = seq->m_Width;
                new_seq->m_Frame = frame;
                new_seq->m_SeqIdx = seq->m_SeqIdx;
                new_seq->m_ChildIdx = seq->m_ChildIdx + 1;
                if (m_MergeFlags & fQuerySeqMergeOnly) {
                    new_seq->m_DsIdx = match->m_DsIdx;
                }
                m_ExtraRows.push_back(new_seq);
                new_seq->m_ExtraRowIdx = seq->m_ExtraRowIdx + 1;
                seq = seq->m_ExtraRow = new_seq;
                break;
            }
            seq = seq->m_ExtraRow;
        }
    }
}


END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE
