seq_map.cpp

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/*  $Id: seq_map.cpp 102039 2024-03-21 14:36:08Z vasilche $
* ===========================================================================
*
*                            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.
*
* ===========================================================================
*
* Authors: Aleksey Grichenko, Michael Kimelman, Eugene Vasilchenko,
*          Andrei Gourianov
*
* File Description:
*   Sequence map for the Object Manager. Describes sequence as a set of
*   segments of different types (data, reference, gap or end).
*
*/
 
#include <ncbi_pch.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/impl/bioseq_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/data_source.hpp>
 
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Seg_ext.hpp>
#include <objects/seq/Ref_ext.hpp>
 
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/seqloc/Seq_loc_mix.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Packed_seqint.hpp>
#include <objects/seqloc/Packed_seqpnt.hpp>
 
#include <algorithm>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
////////////////////////////////////////////////////////////////////
//  CSeqMap::CSegment
 
inline
CSeqMap::CSegment::CSegment(ESegmentType seg_type,
                            TSeqPos      length,
                            bool         unknown_len)
    : m_Position(kInvalidSeqPos),
      m_Length(length),
      m_UnknownLength(unknown_len),
      m_SegType(seg_type),
      m_ObjType(seg_type),
      m_RefMinusStrand(false),
      m_RefPosition(0)
{
}
 
 
inline
CSeqMap::CSegment::CSegment(const CSegment& seg)
    : m_Position(seg.m_Position.load()),
      m_Length(seg.m_Length.load()),
      m_UnknownLength(seg.m_UnknownLength),
      m_SegType(seg.m_SegType),
      m_ObjType(seg.m_ObjType),
      m_RefMinusStrand(seg.m_RefMinusStrand),
      m_RefPosition(seg.m_RefPosition),
      m_RefObject(seg.m_RefObject)
{
}
 
 
inline
CSeqMap::CSegment& CSeqMap::CSegment::operator=(const CSegment& seg)
{
    m_Position = seg.m_Position.load();
    m_Length = seg.m_Length.load();
    m_UnknownLength = seg.m_UnknownLength;
    m_SegType = seg.m_SegType;
    m_ObjType = seg.m_ObjType;
    m_RefMinusStrand = seg.m_RefMinusStrand;
    m_RefPosition = seg.m_RefPosition;
    m_RefObject = seg.m_RefObject;
    return *this;
}
 
 
////////////////////////////////////////////////////////////////////
//  CSeqMap
 
 
CSeqMap::CSeqMap(void)
    : m_Bioseq(0),
      m_Resolved(0),
      m_Mol(CSeq_inst::eMol_not_set),
      m_HasSegments(0),
      m_Changed(false),
      m_SeqLength(kInvalidSeqPos)
{
}
 
 
CSeqMap::CSeqMap(CSeqMap* /*parent*/, size_t /*index*/)
    : m_Bioseq(0),
      m_Resolved(0),
      m_Mol(CSeq_inst::eMol_not_set),
      m_HasSegments(0),
      m_Changed(false),
      m_SeqLength(kInvalidSeqPos)
{
}
 
 
CSeqMap::CSeqMap(const CSeq_loc& ref)
    : m_Bioseq(0),
      m_Resolved(0),
      m_Mol(CSeq_inst::eMol_not_set),
      m_HasSegments(0),
      m_Changed(false),
      m_SeqLength(kInvalidSeqPos)
{
    x_AddEnd();
    x_Add(ref);
    x_AddEnd();
}
 
/*
CSeqMap::CSeqMap(const CSeq_data& data, TSeqPos length)
    : m_Resolved(0),
      m_Mol(CSeq_inst::eMol_not_set),
      m_HasSegments(0),
      m_Changed(false),
      m_SeqLength(kInvalidSeqPos)
{
    x_AddEnd();
    x_Add(data, length);
    x_AddEnd();
}
*/
 
CSeqMap::CSeqMap(TSeqPos length)
    : m_Bioseq(0),
      m_Resolved(0),
      m_Mol(CSeq_inst::eMol_not_set),
      m_HasSegments(0),
      m_Changed(false),
      m_SeqLength(length)
{
    x_AddEnd();
    x_AddGap(length, false);
    x_AddEnd();
}
 
 
CSeqMap::CSeqMap(const CSeqMap& sm)
    : m_Bioseq(0),
      m_Segments(sm.m_Segments),
      m_Resolved(sm.m_Resolved.load()),
      m_Delta(sm.m_Delta),
      m_Mol(sm.m_Mol),
      m_HasSegments(sm.m_HasSegments.load()),
      m_Changed(sm.m_Changed),
      m_SeqLength(sm.m_SeqLength.load())
{
    NON_CONST_ITERATE ( TSegments, it, m_Segments ) {
        if ( it->m_ObjType == eSeqChunk ) {
            it->m_SegType = eSeqGap;
            it->m_ObjType = eSeqGap;
            it->m_RefObject = null;
        }
    }
}
 
 
CSeqMap::CSeqMap(const CSeq_inst& inst)
    : m_Bioseq(0),
      m_Resolved(0),
      m_Mol(CSeq_inst::eMol_not_set),
      m_HasSegments(0),
      m_Changed(false),
      m_SeqLength(kInvalidSeqPos)
{
    x_AddEnd();
 
    if ( inst.IsSetMol() ) {
        m_Mol = inst.GetMol();
    }
    if ( inst.IsSetLength() ) {
        m_SeqLength = inst.GetLength();
    }
 
    if ( inst.IsSetSeq_data() ) {
        if ( !inst.GetSeq_data().IsGap() ) {
            x_Add(inst.GetSeq_data(), inst.GetLength());
        }
        else {
            // split Seq-data
            x_AddGap(inst.GetLength(), false, inst.GetSeq_data());
        }
    }
    else if ( inst.IsSetExt() ) {
        const CSeq_ext& ext = inst.GetExt();
        switch (ext.Which()) {
        case CSeq_ext::e_Seg:
            ITERATE ( CSeq_ext::TSeg::Tdata, iter, ext.GetSeg().Get() ) {
                x_Add(**iter);
            }
            break;
        case CSeq_ext::e_Ref:
            x_Add(ext.GetRef());
            break;
        case CSeq_ext::e_Delta:
            ITERATE ( CSeq_ext::TDelta::Tdata, iter, ext.GetDelta().Get() ) {
                x_Add(**iter);
            }
            break;
        case CSeq_ext::e_Map:
            if ( m_SeqLength == kInvalidSeqPos ) {
                NCBI_THROW(CSeqMapException, eDataError,
                       "CSeq_inst.ext.map with unset CSeq_inst.length");
            }
            x_AddGap(m_SeqLength, false);
            break;
        default:
            //### Not implemented
            NCBI_THROW(CSeqMapException, eUnimplemented,
                       "CSeq_ext::??? -- not implemented");
        }
    }
    else if ( inst.GetRepr() == CSeq_inst::eRepr_virtual ) {
        // Virtual sequence -- no data, no segments
        // The total sequence is gap
        if ( m_SeqLength == kInvalidSeqPos ) {
            m_SeqLength = 0;
        }
        x_AddGap(m_SeqLength, false);
    }
    else if ( inst.GetRepr() == CSeq_inst::eRepr_map ) {
        // Virtual map sequence -- no data, no segments
        // The total sequence is gap
        if ( m_SeqLength == kInvalidSeqPos ) {
            NCBI_THROW(CSeqMapException, eDataError,
                       "CSeq_inst.repr map with unset CSeq_inst.length");
        }
        x_AddGap(m_SeqLength, false);
    }
    else if ( inst.GetRepr() != CSeq_inst::eRepr_not_set && 
              inst.IsSetLength() && inst.GetLength() != 0 ) {
        // split seq-data
        x_AddGap(inst.GetLength(), false);
    }
    else {
        if ( inst.GetRepr() != CSeq_inst::eRepr_not_set ) {
            NCBI_THROW(CSeqMapException, eDataError,
                       "CSeq_inst.repr of sequence without data "
                       "should be not_set");
        }
        if ( inst.IsSetLength() && inst.GetLength() != 0 ) {
            NCBI_THROW(CSeqMapException, eDataError,
                       "CSeq_inst.length of sequence without data "
                       "should be 0");
        }
        x_AddGap(0, false);
    }
 
    x_AddEnd();
}
 
 
CSeqMap::~CSeqMap(void)
{
    _ASSERT(!m_Bioseq);
    m_Resolved = 0;
    m_Segments.clear();
}
 
 
void CSeqMap::x_GetSegmentException(size_t /*index*/) const
{
    NCBI_THROW(CSeqMapException, eInvalidIndex,
               "Invalid segment index");
}
 
 
CSeqMap::CSegment& CSeqMap::x_SetSegment(size_t index)
{
    _ASSERT(index < m_Segments.size());
    return m_Segments[index];
}
 
 
const CBioseq_Info& CSeqMap::x_GetBioseqInfo(const CSegment& seg,
                                             CScope* scope) const
{
    CSeq_id_Handle seq_id = CSeq_id_Handle::GetHandle(x_GetRefSeqid(seg));
    if ( !scope ) {
        if ( m_Bioseq ) {
            CConstRef<CBioseq_Info> seq =
                m_Bioseq->GetTSE_Info().FindBioseq(seq_id);
            if ( seq ) {
                return *seq;
            }
        }
        NCBI_THROW_FMT(CSeqMapException, eNullPointer,
                       "Cannot resolve "<<seq_id<<": null scope pointer");
    }
    CBioseq_Handle bh = scope->GetBioseqHandle(seq_id);
    if ( !bh ) {
        NCBI_THROW_FMT(CSeqMapException, eFail,
                       "Cannot resolve "<<seq_id<<": unknown");
    }
    return bh.x_GetInfo();
}
 
 
TSeqPos CSeqMap::x_ResolveSegmentLength(size_t index, CScope* scope) const
{
    const CSegment& seg = x_GetSegment(index);
    TSeqPos length = seg.m_Length;
    if ( length == kInvalidSeqPos ) {
        if ( seg.m_SegType == eSeqSubMap ) {
            length = x_GetSubSeqMap(seg, scope)->GetLength(scope);
        }
        else if ( seg.m_SegType == eSeqRef ) {
            if ( m_Bioseq ) {
                // first look directly into TSE
                CSeq_id_Handle id =
                    CSeq_id_Handle::GetHandle(x_GetRefSeqid(seg));
                CConstRef<CBioseq_Info> seq =
                    m_Bioseq->GetTSE_Info().FindMatchingBioseq(id);
                if ( seq ) {
                    length = seq->GetBioseqLength();
                }
            }
            if ( length == kInvalidSeqPos ) {
                length = x_GetBioseqInfo(seg, scope).GetBioseqLength();
            }
        }
        if (length == kInvalidSeqPos) {
            NCBI_THROW(CSeqMapException, eDataError,
                    "Invalid sequence length");
        }
        seg.m_Length = length;
    }
    return length;
}
 
 
TSeqPos CSeqMap::x_ResolveSegmentPosition(size_t index, CScope* scope) const
{
    if ( index > x_GetLastEndSegmentIndex() ) {
        x_GetSegmentException(index);
    }
    size_t resolved = m_Resolved;
    if ( index <= resolved )
        return x_GetSegment(index).m_Position;
    TSeqPos resolved_pos = x_GetSegment(resolved).m_Position;
    do {
        TSeqPos seg_pos = resolved_pos;
        resolved_pos += x_GetSegmentLength(resolved, scope);
        if (resolved_pos < seg_pos  ||  resolved_pos == kInvalidSeqPos) {
            NCBI_THROW(CSeqMapException, eDataError,
                    "Sequence position overflow");
        }
        m_Segments[++resolved].m_Position = resolved_pos;
    } while ( resolved < index );
    {{
        CMutexGuard guard(m_SeqMap_Mtx);
        if ( m_Resolved < resolved )
            m_Resolved = resolved;
    }}
    return resolved_pos;
}
 
 
size_t CSeqMap::x_FindSegment(TSeqPos pos, CScope* scope) const
{
    size_t resolved = m_Resolved;
    TSeqPos resolved_pos = x_GetSegment(resolved).m_Position;
    if ( resolved_pos <= pos ) {
        do {
            if ( resolved >= x_GetLastEndSegmentIndex() ) {
                // end of segments
                m_Resolved = resolved;
                return size_t(-1);
            }
            TSeqPos seg_pos = resolved_pos;
            resolved_pos += x_GetSegmentLength(resolved, scope);
            if (resolved_pos < seg_pos  ||  resolved_pos == kInvalidSeqPos) {
                NCBI_THROW(CSeqMapException, eDataError,
                        "Sequence position overflow");
            }
            m_Segments[++resolved].m_Position = resolved_pos;
        } while ( resolved_pos <= pos );
        {{
            CMutexGuard guard(m_SeqMap_Mtx);
            if ( m_Resolved < resolved )
                m_Resolved = resolved;
        }}
        return resolved - 1;
    }
    else {
        TSegments::const_iterator itend = m_Segments.begin()+resolved;
        TSegments::const_iterator it = 
            upper_bound(m_Segments.begin(), itend,
                        pos, SPosLessSegment());
        if ( it == itend ) {
            return size_t(-1);
        }
        return it - m_Segments.begin();
    }
}
 
 
void CSeqMap::x_LoadObject(const CSegment& seg) const
{
    _ASSERT(seg.m_Position != kInvalidSeqPos);
    if ( seg.m_SegType != seg.m_ObjType ) {
        CConstRef<CTSE_Chunk_Info> chunk;
        {{
            CMutexGuard guard(m_SeqMap_Mtx);
            const CObject* obj = seg.m_RefObject.GetPointer();
            if ( obj && seg.m_ObjType == eSeqChunk ) {
                chunk = dynamic_cast<const CTSE_Chunk_Info*>(obj);
            }
        }}
        if ( chunk ) {
            chunk->Load();
        }
    }
}
 
 
CRef<CTSE_Chunk_Info> CSeqMap::x_GetChunkToLoad(const CSegment& seg) const
{
    _ASSERT(seg.m_Position != kInvalidSeqPos);
    if ( seg.m_SegType != seg.m_ObjType ) {
        CRef<CTSE_Chunk_Info> chunk;
        {{
            CMutexGuard guard(m_SeqMap_Mtx);
            const CObject* obj = seg.m_RefObject.GetPointer();
            if ( obj && seg.m_ObjType == eSeqChunk ) {
                chunk = dynamic_cast<CTSE_Chunk_Info*>(const_cast<CObject*>(obj));
            }
        }}
        if ( chunk && chunk->NotLoaded() ) {
            return chunk;
        }
    }
    return null;
}
 
 
const CObject* CSeqMap::x_GetObject(const CSegment& seg) const
{
    if ( seg.m_SegType != seg.m_ObjType ) {
        x_LoadObject(seg);
    }
    if ( !seg.m_RefObject || seg.m_SegType != seg.m_ObjType ) {
        NCBI_THROW(CSeqMapException, eNullPointer, "null object pointer");
    }
    return seg.m_RefObject.GetPointer();
}
 
 
void CSeqMap::x_SetObject(CSegment& seg, const CObject& obj)
{
    // lock for object modification
    CMutexGuard guard(m_SeqMap_Mtx);
    // check for object
    if ( seg.m_RefObject && seg.m_SegType == seg.m_ObjType ) {
        NCBI_THROW(CSeqMapException, eDataError, "object already set");
    }
    // set object
    seg.m_RefObject.Reset(&obj);
    seg.m_ObjType = seg.m_SegType;
    m_Changed = true;
}
 
 
void CSeqMap::x_SetChunk(CSegment& seg, CTSE_Chunk_Info& chunk)
{
    // lock for object modification
    //CMutexGuard guard(m_SeqMap_Mtx);
    // check for object
    if ( seg.m_ObjType == eSeqChunk ||
         (seg.m_RefObject && seg.m_SegType == seg.m_ObjType) ) {
        NCBI_THROW(CSeqMapException, eDataError, "object already set");
    }
    // set object
    seg.m_RefObject.Reset(&chunk);
    seg.m_ObjType = eSeqChunk;
}
 
 
CConstRef<CSeqMap> CSeqMap::x_GetSubSeqMap(const CSegment& seg, CScope* scope,
                                           bool resolveExternal) const
{
    CConstRef<CSeqMap> ret;
    if ( seg.m_SegType == eSeqSubMap ) {
        ret.Reset(static_cast<const CSeqMap*>(x_GetObject(seg)));
    }
    else if ( resolveExternal && seg.m_SegType == eSeqRef ) {
        ret.Reset(&x_GetBioseqInfo(seg, scope).GetSeqMap());
    }
    return ret;
}
 
 
void CSeqMap::x_SetSubSeqMap(size_t /*index*/, CSeqMap_Delta_seqs* /*subMap*/)
{
    // not valid in generic seq map -> incompatible objects
    NCBI_THROW(CSeqMapException, eDataError, "Invalid parent map");
}
 
 
const CSeq_data& CSeqMap::x_GetSeq_data(const CSegment& seg) const
{
    if ( seg.m_SegType == eSeqData ) {
        return *static_cast<const CSeq_data*>(x_GetObject(seg));
    }
    else if ( seg.m_SegType == eSeqGap && seg.m_ObjType == eSeqData ) {
        return static_cast<const CSeq_data&>(*seg.m_RefObject);
    }
    else if ( seg.m_SegType == eSeqGap && seg.m_ObjType == eSeqLiteral ) {
        const CSeq_literal& literal = static_cast<const CSeq_literal&>(*seg.m_RefObject);
        if ( literal.IsSetSeq_data() ) {
            return literal.GetSeq_data();
        }
    }
    NCBI_THROW(CSeqMapException, eSegmentTypeError,
               "Invalid segment type");
}
 
 
CConstRef<CSeq_literal> CSeqMap::x_GetSeq_literal(const CSegment& seg) const
{
    if ( seg.m_ObjType == eSeqLiteral ) {
        return ConstRef(static_cast<const CSeq_literal*>(&*seg.m_RefObject));
    }
    return null;
}
 
 
void CSeqMap::x_SetSeq_data(size_t index, CSeq_data& data)
{
    // check segment type
    CSegment& seg = x_SetSegment(index);
    if ( seg.m_SegType != eSeqData ) {
        NCBI_THROW(CSeqMapException, eSegmentTypeError,
                   "Invalid segment type");
    }
    if ( data.IsGap() ) {
        ERR_POST("CSeqMap: gap Seq-data was split as real data");
        seg.m_SegType = eSeqGap;
    }
    x_SetObject(seg, data);
}
 
 
int CSeqMap::x_GetSequenceClass(void) const
{
    if ( m_Bioseq ) {
        return m_Bioseq->GetSequenceClass();
    }
    return CBioseq_Handle::eSequenceClass_none;
}
 
 
void CSeqMap::x_SetChanged(size_t index)
{
    while ( m_Resolved > index ) {
        x_SetSegment(m_Resolved--).m_Position = kInvalidSeqPos;
    }
    m_SeqLength = kInvalidSeqPos;
    m_HasSegments = 0;
    if ( !m_Changed ) {
        m_Changed = true;
        if ( m_Bioseq ) {
            m_Bioseq->x_SetChangedSeqMap();
        }
    }
}
 
 
void CSeqMap::x_StartEditing(void)
{
    if ( !m_Bioseq ) {
        NCBI_THROW(CSeqMapException, eSegmentTypeError,
                   "Cannot edit unattached sequence map");
    }
    if ( !m_Bioseq->GetDataSource().CanBeEdited() ) {
        NCBI_THROW(CSeqMapException, eSegmentTypeError,
                   "Bioseq is not in edit state");
    }
}
 
 
void CSeqMap::x_SetSegmentGap(size_t index,
                              TSeqPos length,
                              CSeq_data* gap_data)
{
    if ( gap_data && !gap_data->IsGap() ) {
        NCBI_THROW(CSeqMapException, eSegmentTypeError,
                   "SetSegmentGap: Seq-data is not gap");
    }
    CMutexGuard guard(m_SeqMap_Mtx);
    x_StartEditing();
    CSegment& seg = x_SetSegment(index);
    seg.m_SegType = seg.m_ObjType = eSeqGap;
    if ( gap_data ) {
        seg.m_ObjType = eSeqData;
        seg.m_RefObject = gap_data;
    }
    seg.m_Length = length;
    x_SetChanged(index);
}
 
 
void CSeqMap::x_SetSegmentData(size_t index,
                               TSeqPos length,
                               CSeq_data& data)
{
    CMutexGuard guard(m_SeqMap_Mtx);
    x_StartEditing();
    CSegment& seg = x_SetSegment(index);
    seg.m_SegType = data.IsGap()? eSeqGap: eSeqData;
    seg.m_ObjType = eSeqData;
    seg.m_RefObject = &data;
    seg.m_Length = length;
    x_SetChanged(index);
}
 
 
void CSeqMap::x_SetSegmentRef(size_t index,
                              TSeqPos length,
                              const CSeq_id& ref_id,
                              TSeqPos ref_pos,
                              bool ref_minus_strand)
{
    CMutexGuard guard(m_SeqMap_Mtx);
    x_StartEditing();
    CSegment& seg = x_SetSegment(index);
    seg.m_SegType = seg.m_ObjType = eSeqRef;
    CRef<CSeq_id> id(new CSeq_id);
    id->Assign(ref_id);
    seg.m_RefObject = id.GetPointer();
    seg.m_RefPosition = ref_pos;
    seg.m_RefMinusStrand = ref_minus_strand;
    seg.m_Length = length;
    x_SetChanged(index);
}
 
 
void CSeqMap::SetSegmentRef(const CSeqMap_CI& seg,
                            TSeqPos length,
                            const CSeq_id_Handle& ref_id,
                            TSeqPos ref_pos,
                            bool ref_minus)
{
    _ASSERT(&seg.x_GetSegmentInfo().x_GetSeqMap() == this);
    size_t index = seg.x_GetSegmentInfo().x_GetIndex();
    x_SetSegmentRef(index, length, *ref_id.GetSeqId(), ref_pos, ref_minus);
}
 
 
void CSeqMap::SetSegmentGap(const CSeqMap_CI& seg,
                            TSeqPos length)
{
    _ASSERT(&seg.x_GetSegmentInfo().x_GetSeqMap() == this);
    size_t index = seg.x_GetSegmentInfo().x_GetIndex();
    x_SetSegmentGap(index, length);
}
 
 
void CSeqMap::SetSegmentGap(const CSeqMap_CI& seg,
                            TSeqPos length,
                            CSeq_data& gap_data)
{
    _ASSERT(&seg.x_GetSegmentInfo().x_GetSeqMap() == this);
    size_t index = seg.x_GetSegmentInfo().x_GetIndex();
    x_SetSegmentGap(index, length, &gap_data);
}
 
 
void CSeqMap::SetSegmentData(const CSeqMap_CI& seg,
                             TSeqPos length,
                             CSeq_data& data)
{
    _ASSERT(&seg.x_GetSegmentInfo().x_GetSeqMap() == this);
    size_t index = seg.x_GetSegmentInfo().x_GetIndex();
    x_SetSegmentData(index, length, data);
}
 
 
CSeqMap_CI CSeqMap::InsertSegmentGap(const CSeqMap_CI& seg0,
                                     TSeqPos length)
{
    _ASSERT(&seg0.x_GetSegmentInfo().x_GetSeqMap() == this);
    size_t index = seg0.x_GetSegmentInfo().x_GetIndex();
    TSeqPos pos = x_GetSegmentPosition(index, 0);
    CMutexGuard guard(m_SeqMap_Mtx);
    x_StartEditing();
    _ASSERT(m_Resolved >= index);
    m_Segments.insert(m_Segments.begin() + index, CSegment(eSeqGap, length));
    ++m_Resolved;
    x_SetSegment(index).m_Position = pos;
    x_SetChanged(index);
    return CSeqMap_CI(seg0, *this, index, pos);
}
 
 
CSeqMap_CI CSeqMap::RemoveSegment(const CSeqMap_CI& seg0)
{
    _ASSERT(&seg0.x_GetSegmentInfo().x_GetSeqMap() == this);
    size_t index = seg0.x_GetSegmentInfo().x_GetIndex();
    TSeqPos pos = x_GetSegmentPosition(index, 0);
    CMutexGuard guard(m_SeqMap_Mtx);
    x_StartEditing();
    CSegment& seg = x_SetSegment(index);
    if ( seg.m_SegType == eSeqEnd ) {
        NCBI_THROW(CSeqMapException, eSegmentTypeError,
                   "cannot remove end segment");
    }
    _ASSERT(m_Resolved >= index);
    m_Segments.erase(m_Segments.begin() + index);
    if ( m_Resolved > index ) {
        --m_Resolved;
    }
    x_SetSegment(index).m_Position = pos;
    x_SetChanged(index);
    _ASSERT(m_Resolved == index);
    return CSeqMap_CI(seg0, *this, index, pos);
}
 
 
void CSeqMap::LoadSeq_data(TSeqPos pos, TSeqPos len,
                           const CSeq_data& data)
{
    size_t index = x_FindSegment(pos, 0);
    const CSegment& seg = x_GetSegment(index);
    if ( seg.m_Position != pos || seg.m_Length != len ) {
        NCBI_THROW(CSeqMapException, eDataError,
                   "Invalid segment size");
    }
    x_SetSeq_data(index, const_cast<CSeq_data&>(data));
}
 
 
const CSeq_id& CSeqMap::x_GetRefSeqid(const CSegment& seg) const
{
    if ( seg.m_SegType == eSeqRef ) {
        return static_cast<const CSeq_id&>(*x_GetObject(seg));
    }
    NCBI_THROW(CSeqMapException, eSegmentTypeError,
               "Invalid segment type");
}
 
 
TSeqPos CSeqMap::x_GetRefPosition(const CSegment& seg) const
{
    return seg.m_RefPosition;
}
 
 
bool CSeqMap::x_GetRefMinusStrand(const CSegment& seg) const
{
    return seg.m_RefMinusStrand;
}
 
 
CSeqMap_CI CSeqMap::Begin(CScope* scope) const
{
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, SSeqMapSelector());
}
 
 
CSeqMap_CI CSeqMap::End(CScope* scope) const
{
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, SSeqMapSelector(),
                      kMax_UInt);
}
 
 
CSeqMap_CI CSeqMap::FindSegment(TSeqPos pos, CScope* scope) const
{
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, SSeqMapSelector(), pos);
}
 
 
CSeqMap::const_iterator CSeqMap::begin(CScope* scope) const
{
    return Begin(scope);
}
 
 
CSeqMap::const_iterator CSeqMap::end(CScope* scope) const
{
    return End(scope);
}
 
 
CSeqMap_CI CSeqMap::BeginResolved(CScope*                scope,
                                  const SSeqMapSelector& sel) const
{
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, sel);
}
 
 
CSeqMap_CI CSeqMap::BeginResolved(CScope* scope) const
{
    SSeqMapSelector sel;
    sel.SetResolveCount(kMax_UInt);
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, sel);
}
 
 
CSeqMap_CI CSeqMap::EndResolved(CScope* scope) const
{
    SSeqMapSelector sel;
    sel.SetResolveCount(kMax_UInt);
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, sel, kMax_UInt);
}
 
 
CSeqMap_CI CSeqMap::EndResolved(CScope*                scope,
                                const SSeqMapSelector& sel) const
{
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, sel, kMax_UInt);
}
 
 
CSeqMap_CI CSeqMap::FindResolved(CScope*                scope,
                                 TSeqPos                pos,
                                 const SSeqMapSelector& selector) const
{
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, selector, pos);
}
 
 
CSeqMap_CI CSeqMap::ResolvedRangeIterator(CScope* scope,
                                          TSeqPos from,
                                          TSeqPos length,
                                          ENa_strand strand,
                                          size_t maxResolveCount,
                                          TFlags flags) const
{
    SSeqMapSelector sel;
    sel.SetFlags(flags).SetResolveCount(maxResolveCount);
    sel.SetRange(from, length).SetStrand(strand);
    return CSeqMap_CI(CConstRef<CSeqMap>(this), scope, sel);
}
 
 
bool CSeqMap::HasSegmentOfType(ESegmentType type) const
{
    if ( m_HasSegments == 0 ) {
        THasSegments flags = 0;
        ITERATE ( TSegments, it, m_Segments ) {
            flags = flags | THasSegments(1 << it->m_SegType);
        }
        m_HasSegments = flags;
    }
    return bool((m_HasSegments >> type) & 1);
}
 
 
size_t CSeqMap::CountSegmentsOfType(ESegmentType type) const
{
    size_t count = 0;
    ITERATE ( TSegments, it, m_Segments ) {
        if ( it->m_SegType == type ) {
            ++count;
        }
    }
    return count;
}
 
 
bool CSeqMap::HasZeroGapAt(TSeqPos pos, CScope* scope) const
{
    size_t index = x_FindSegment(pos, scope);
    if ( index == size_t(-1) && pos == GetLength(scope) ) {
        index = x_GetLastEndSegmentIndex();
    }
    const CSegment& seg = x_GetSegment(index);
    TSeqPos pos_in_seg = pos - seg.m_Position;
    _ASSERT(index == x_GetLastEndSegmentIndex() || pos_in_seg < seg.m_Length);
    if ( pos_in_seg > 0 ) {
        if ( seg.m_SegType != eSeqRef ) {
            // not zero length segment
            return false;
        }
        CConstRef<CSeqMap> sub_map = x_GetSubSeqMap(seg, scope, true);
        TSeqPos sub_pos;
        if ( !seg.m_RefMinusStrand ) {
            sub_pos = seg.m_RefPosition + pos_in_seg;
        }
        else {
            sub_pos = seg.m_RefPosition + (seg.m_Length-pos_in_seg);
        }
        return sub_map->HasZeroGapAt(sub_pos, scope);
    }
    else {
        // pos_in_seg == 0, check previous segments
        while ( index > x_GetFirstEndSegmentIndex() ) {
            const CSegment& pseg = x_GetSegment(--index);
            if ( pseg.m_Position < pos ) {
                // no more zero length segments
                return false;
            }
            if ( pseg.m_SegType == eSeqGap ) {
                // found zero gap segment
                return true;
            }
        }
    }
    return false;
}
 
 
bool CSeqMap::CanResolveRange(CScope* scope,
                              TSeqPos from,
                              TSeqPos length,
                              ENa_strand strand,
                              size_t depth,
                              TFlags flags) const
{
    SSeqMapSelector sel;
    sel.SetFlags(flags).SetResolveCount(depth);
    sel.SetRange(from, length).SetStrand(strand);
    return CanResolveRange(scope, sel);
}
 
 
namespace {
    struct PByLoader {
        static CDataLoader* Get(const CRef<CTSE_Chunk_Info>& c) {
            return &c->GetSplitInfo().GetDataLoader();
        }
        bool operator()(const CRef<CTSE_Chunk_Info>& c1,
                        const CRef<CTSE_Chunk_Info>& c2) const {
            const CTSE_Split_Info* s1 = &c1->GetSplitInfo();
            const CTSE_Split_Info* s2 = &c2->GetSplitInfo();
            CDataLoader* l1 = &s1->GetDataLoader();
            CDataLoader* l2 = &s2->GetDataLoader();
            if ( l1 != l2 ) {
                return l1 < l2;
            }
            if ( s1 != s2 ) {
                return s1 < s2;
            }
            return c1->GetChunkId() < c2->GetChunkId();
        }
    };
}
 
 
bool CSeqMap::CanResolveRange(CScope* scope, const SSeqMapSelector& sel) const
{
    try {
        TSeqPos length = kInvalidSeqPos;
        if ( scope ) {
            length = GetLength(scope);
        }
        TSeqPos start = sel.m_Position;
        if ( start >= length ) {
            return false;
        }
        TSeqPos stop = length;
        if ( sel.m_Length != kInvalidSeqPos ) {
            stop = start + sel.m_Length;
            if ( stop < start || stop > length ) {
                return false;
            }
        }
        TSeqPos found_length = 0;
        
        if ( scope && sel.m_LinkUsedTSE && sel.m_TopTSE &&
             !sel.x_HasLimitTSE() ) {
            // Faster BFS search with batch load requests.
            // We will do it only if loaded data will be locked in scope.
            // That's why we verify that scope exists, and start TSE is set.
            bool deeper = true;
            size_t next_depth = 0;
            vector<CTSE_Handle> all_tse;
            vector<CTSE_Handle> parent_tse;
            vector<CSeq_id_Handle> next_ids;
            CDataLoader::TChunkSet load_chunks, chunks;
            vector< AutoPtr<CInitGuard> > guards;
 
            SSeqMapSelector next_sel(sel);
            while ( deeper ) {
                deeper = false;
                if ( next_depth > sel.m_MaxResolveCount ) {
                    break;
                }
                next_sel.SetResolveCount(next_depth);
                next_sel.SetFlags(fFindAnyLeaf);
                parent_tse.clear();
                next_ids.clear();
                chunks.clear();
                {{
                    CSeqMap_CI it(ConstRef(this), scope, next_sel);
                    for(; it; ++it) {
                        if ( it.m_Selector.m_MaxResolveCount != 0 ) {
                            continue;
                        }
                        if ( it.GetType() == eSeqRef ) {
                            parent_tse.push_back(it.x_GetSegmentInfo().m_TSE);
                            _ASSERT(parent_tse.back());
                            next_ids.push_back(it.GetRefSeqid());
                            _ASSERT(next_ids.back());
                        }
                        else {
                            found_length += it.GetLength();
                            CRef<CTSE_Chunk_Info> chunk = it.x_GetSeqMap()
                                .x_GetChunkToLoad(it.x_GetSegment());
                            if ( chunk ) {
                                chunks.push_back(chunk);
                            }
                        }
                    }
                    if ( it.GetPosition() < stop ) {
                        return false;
                    }
                }}
                sort(chunks.begin(), chunks.end(), PByLoader());
                chunks.erase(unique(chunks.begin(), chunks.end()), chunks.end());
                while ( !chunks.empty() ) {
                    // Collect and lock chunks from one loader to be loaded
                    CDataLoader* loader = PByLoader::Get(chunks.back());
                    load_chunks.clear();
                    guards.clear();
                    // find start index of chunks from this loader
                    size_t s = chunks.size();
                    while ( s > 0 && PByLoader::Get(chunks[s-1]) == loader ) {
                        --s;
                    }
                    // lock chunks to be loaded
                    for ( size_t i = s; i < chunks.size(); ++i ) {
                        AutoPtr<CInitGuard> guard = chunks[i]->GetLoadInitGuard();
                        if ( guard.get() && *guard.get() ) {
                            load_chunks.push_back(chunks[i]);
                            guards.push_back(guard);
                        }
                    }
                    // load the chunks
                    if ( !load_chunks.empty() ) {
                        loader->GetChunks(load_chunks);
                        guards.clear();
                    }
                    // done with this loader
                    chunks.resize(s);
                }
                if ( !next_ids.empty() ) {
                    deeper = true;
                    vector<CBioseq_Handle> seqs =
                        scope->GetBioseqHandles(next_ids);
                    _ASSERT(seqs.size() == parent_tse.size());
                    for ( size_t i = 0; i < seqs.size(); ++i ) {
                        if ( !seqs[i] ) {
                            return false;
                        }
                        const CTSE_Handle& tse = seqs[i].GetTSE_Handle();
                        all_tse.push_back(tse);
                        if ( !parent_tse[i].AddUsedTSE(tse) ) {
                            sel.AddUsedTSE(tse);
                        }
                    }
                }
                ++next_depth;
            }
        }
        else {
            CSeqMap_CI it(ConstRef(this), scope, sel);
            for(; it; ++it) {
                found_length += it.GetLength();
            }
            if ( it.GetPosition() < stop ) {
                return false;
            }
        }
        if ( stop != kInvalidSeqPos && stop-start != found_length ) {
            return false;
        }
        return true;
    }
    catch (exception&) {
        return false;
    }
}
 
 
CRef<CSeqMap> CSeqMap::CreateSeqMapForBioseq(const CBioseq& seq)
{
    return Ref(new CSeqMap(seq.GetInst()));
}
 
 
CRef<CSeqMap> CSeqMap::CloneFor(const CBioseq& seq) const
{
    return CreateSeqMapForBioseq(seq);
}
 
 
CRef<CSeqMap> CSeqMap::CreateSeqMapForSeq_loc(const CSeq_loc& loc,
                                              CScope* scope)
{
    TMol mol = CSeq_inst::eMol_not_set;
    CRef<CSeqMap> ret(new CSeqMap(loc));
    if ( scope && ret->m_Mol == CSeq_inst::eMol_not_set ) {
        if ( mol == CSeq_inst::eMol_not_set ) {
            for ( size_t i = 1; ; ++i ) {
                const CSegment& seg = ret->x_GetSegment(i);
                if ( seg.m_SegType == eSeqEnd ) {
                    break;
                }
                else if ( seg.m_SegType == eSeqRef ) {
                    CBioseq_Handle bh =
                        scope->GetBioseqHandle(ret->x_GetRefSeqid(seg));
                    if ( bh ) {
                        mol = bh.GetSequenceType();
                        break;
                    }
                }
            }
        }
        ret->m_Mol = mol;
    }
    return ret;
}
 
 
CConstRef<CSeqMap> CSeqMap::GetSeqMapForSeq_loc(const CSeq_loc& loc,
                                                CScope* scope)
{
    TMol mol = CSeq_inst::eMol_not_set;
    if ( scope ) {
        if ( loc.IsInt() ) {
            const CSeq_interval& locint = loc.GetInt();
            if ( locint.GetFrom() == 0 &&
                 (!locint.IsSetStrand() || !IsReverse(locint.GetStrand())) ) {
                CBioseq_Handle bh = scope->GetBioseqHandle(locint.GetId());
                if ( bh ) {
                    if ( bh.GetBioseqLength() == locint.GetTo()+1 ) {
                        return ConstRef(&bh.GetSeqMap());
                    }
                    mol = bh.GetSequenceType();
                }
            }
        }
        else if ( loc.IsWhole() ) {
            CBioseq_Handle bh = scope->GetBioseqHandle(loc.GetWhole());
            if ( bh ) {
                return ConstRef(&bh.GetSeqMap());
            }
        }
    }
    CRef<CSeqMap> ret(new CSeqMap(loc));
    if ( scope && ret->m_Mol == CSeq_inst::eMol_not_set ) {
        if ( mol == CSeq_inst::eMol_not_set ) {
            for ( size_t i = 1; ; ++i ) {
                const CSegment& seg = ret->x_GetSegment(i);
                if ( seg.m_SegType == eSeqEnd ) {
                    break;
                }
                else if ( seg.m_SegType == eSeqRef ) {
                    CBioseq_Handle bh =
                        scope->GetBioseqHandle(ret->x_GetRefSeqid(seg));
                    if ( bh ) {
                        mol = bh.GetSequenceType();
                        break;
                    }
                }
            }
        }
        ret->m_Mol = mol;
    }
    return ret;
}
 
 
inline
void CSeqMap::x_AddSegment(ESegmentType type,
                           TSeqPos len,
                           bool unknown_len)
{
    m_Segments.push_back(CSegment(type, len, unknown_len));
}
 
 
void CSeqMap::x_AddSegment(ESegmentType type, TSeqPos len,
                           const CObject* object)
{
    x_AddSegment(type, len);
    CSegment& ret = m_Segments.back();
    ret.m_RefObject.Reset(object);
}
 
 
void CSeqMap::x_AddSegment(ESegmentType type,
                           const CObject* object,
                           TSeqPos refPos,
                           TSeqPos len,
                           ENa_strand strand)
{
    x_AddSegment(type, len, object);
    CSegment& ret = m_Segments.back();
    ret.m_RefPosition = refPos;
    ret.m_RefMinusStrand = IsReverse(strand);
}
 
 
void CSeqMap::x_AddEnd(void)
{
    TSeqPos pos = kInvalidSeqPos;
    if ( m_Segments.empty() ) {
        m_Segments.reserve(3);
        pos = 0;
    }
    x_AddSegment(eSeqEnd, 0);
    CSegment& ret = m_Segments.back();
    ret.m_Position = pos;
}
 
 
void CSeqMap::x_AddGap(TSeqPos len, bool unknown_len)
{
    x_AddSegment(eSeqGap, len, unknown_len);
}
 
 
void CSeqMap::x_AddGap(TSeqPos len, bool unknown_len,
                       const CSeq_data& gap_data)
{
    x_AddSegment(eSeqGap, len, unknown_len);
    CSegment& ret = m_Segments.back();
    ret.m_ObjType = eSeqData;
    ret.m_RefObject = &gap_data;
}
 
 
void CSeqMap::x_AddGap(TSeqPos len, bool unknown_len,
                       const CSeq_literal& gap_data)
{
    x_AddSegment(eSeqGap, len, unknown_len);
    CSegment& ret = m_Segments.back();
    ret.m_ObjType = eSeqLiteral;
    ret.m_RefObject = &gap_data;
}
 
 
void CSeqMap::x_AddUnloadedSeq_data(TSeqPos len)
{
    x_AddSegment(eSeqData, len);
}
 
 
void CSeqMap::x_Add(const CSeq_data& data, TSeqPos len)
{
    x_AddSegment(eSeqData, len, &data);
}
 
 
void CSeqMap::x_Add(const CSeq_point& ref)
{
    x_AddSegment(eSeqRef, &ref.GetId(),
                 ref.GetPoint(), 1,
                 ref.IsSetStrand()? ref.GetStrand(): eNa_strand_unknown);
}
 
 
void CSeqMap::x_Add(const CSeq_interval& ref)
{
    x_AddSegment(eSeqRef, &ref.GetId(),
                 ref.GetFrom(), ref.GetLength(),
                 ref.IsSetStrand()? ref.GetStrand(): eNa_strand_unknown);
}
 
 
void CSeqMap::x_Add(const CSeq_id& ref)
{
    x_AddSegment(eSeqRef, &ref, 0, kInvalidSeqPos);
}
 
/*
CSeqMap::CSegment& CSeqMap::x_Add(CSeqMap* submap)
{
    return x_AddSegment(eSeqSubMap, kInvalidSeqPos, submap);
}
*/
 
void CSeqMap::x_Add(const CPacked_seqint& seq)
{
    ITERATE ( CPacked_seqint::Tdata, it, seq.Get() ) {
        x_Add(**it);
    }
    //return x_Add(new CSeqMap_Seq_intervals(seq));
}
 
 
void CSeqMap::x_Add(const CPacked_seqpnt& seq)
{
    const CSeq_id& id = seq.GetId();
    ENa_strand strand = seq.IsSetStrand()? seq.GetStrand(): eNa_strand_unknown;
    ITERATE ( CPacked_seqpnt::TPoints, it, seq.GetPoints() ) {
        x_AddSegment(eSeqRef, &id, *it, 1, strand);
    }
    //return x_Add(new CSeqMap_SeqPoss(seq));
}
 
 
void CSeqMap::x_Add(const CSeq_loc_mix& seq)
{
    ITERATE ( CSeq_loc_mix::Tdata, it, seq.Get() ) {
        x_Add(**it);
    }
    //return x_Add(new CSeqMap_Seq_locs(seq, seq.Get()));
}
 
 
void CSeqMap::x_Add(const CSeq_loc_equiv& seq)
{
    ITERATE ( CSeq_loc_equiv::Tdata, it, seq.Get() ) {
        x_Add(**it);
    }
    //return x_Add(new CSeqMap_Seq_locs(seq, seq.Get()));
}
 
 
void CSeqMap::x_Add(const CSeq_literal& seq)
{
    const bool is_unknown_len = ( 
        seq.CanGetFuzz() && 
        seq.GetFuzz().IsLim() && 
        seq.GetFuzz().GetLim() == CInt_fuzz::eLim_unk );
 
    if ( !seq.IsSetSeq_data() ) {
        // No data exist - treat it like a gap
        x_AddGap(seq.GetLength(), is_unknown_len, seq); //???
    }
    else if ( seq.GetSeq_data().IsGap() ) {
        // Seq-data.gap
        x_AddGap(seq.GetLength(), is_unknown_len, seq);
    }
    else {
        x_Add(seq.GetSeq_data(), seq.GetLength());
    }
}
 
 
void CSeqMap::x_Add(const CSeq_loc& loc)
{
    switch ( loc.Which() ) {
    case CSeq_loc::e_not_set:
    case CSeq_loc::e_Null:
    case CSeq_loc::e_Empty:
        x_AddGap(0, false); // Add gap ???
        break;
    case CSeq_loc::e_Whole:
        x_Add(loc.GetWhole());
        break;
    case CSeq_loc::e_Int:
        x_Add(loc.GetInt());
        break;
    case CSeq_loc::e_Pnt:
        x_Add(loc.GetPnt());
        break;
    case CSeq_loc::e_Packed_int:
        x_Add(loc.GetPacked_int());
        break;
    case CSeq_loc::e_Packed_pnt:
        x_Add(loc.GetPacked_pnt());
        break;
    case CSeq_loc::e_Mix:
        x_Add(loc.GetMix());
        break;
    case CSeq_loc::e_Equiv:
        x_Add(loc.GetEquiv());
        break;
    case CSeq_loc::e_Bond:
        NCBI_THROW(CSeqMapException, eDataError,
                   "e_Bond is not allowed as a reference type");
    case CSeq_loc::e_Feat:
        NCBI_THROW(CSeqMapException, eDataError,
                   "e_Feat is not allowed as a reference type");
    default:
        NCBI_THROW(CSeqMapException, eDataError,
                   "invalid reference type");
    }
}
 
 
void CSeqMap::x_Add(const CDelta_seq& seq)
{
    switch ( seq.Which() ) {
    case CDelta_seq::e_Loc:
        x_Add(seq.GetLoc());
        break;
    case CDelta_seq::e_Literal:
        x_Add(seq.GetLiteral());
        break;
    default:
        NCBI_THROW(CSeqMapException, eDataError,
                   "Can not add empty Delta-seq");
    }
}
 
 
void CSeqMap::SetRegionInChunk(CTSE_Chunk_Info& chunk,
                               TSeqPos pos, TSeqPos length)
{
    if ( length == kInvalidSeqPos ) {
        _ASSERT(pos == 0);
        _ASSERT(m_SeqLength != kInvalidSeqPos);
        length = m_SeqLength;
    }
    size_t index = x_FindSegment(pos, 0);
    CMutexGuard guard(m_SeqMap_Mtx);
    while ( length ) {
        // get segment
        if ( index > x_GetLastEndSegmentIndex() ) {
            x_GetSegmentException(index);
        }
        CSegment& seg = x_SetSegment(index);
 
        // update segment position if not set yet
        if ( index > m_Resolved ) {
            _ASSERT(index == m_Resolved + 1);
            _ASSERT(seg.m_Position == kInvalidSeqPos || seg.m_Position == pos);
            seg.m_Position = pos;
            m_Resolved = index;
        }
        // check segment
        if ( seg.m_Position != pos || seg.m_Length > length ) {
            NCBI_THROW(CSeqMapException, eDataError,
                       "SeqMap segment crosses split chunk boundary");
        }
        if ( seg.m_SegType != eSeqGap ) {
            NCBI_THROW(CSeqMapException, eDataError,
                       "split chunk covers bad SeqMap segment");
        }
        if ( auto literal = x_GetSeq_literal(seg) ) {
            // reset temporary literal segment
            if ( !literal->IsSetFuzz() && !literal->IsSetSeq_data() ) {
                seg.m_ObjType = eSeqGap;
                seg.m_RefObject = null;
            }
        }
        _ASSERT(!seg.m_RefObject);
 
        if ( seg.m_Length > 0 ) {
            // update segment
            seg.m_SegType = eSeqData;
            x_SetChunk(seg, chunk);
            
            // next
            pos += seg.m_Length;
            length -= seg.m_Length;
        }
        ++index;
    }
}
 
 
bool CSeqMap::x_DoUpdateSeq_inst(CSeq_inst& inst)
{
    inst.SetLength(GetLength(0));
    bool single_segment = GetSegmentsCount() == 1;
    if ( HasSegmentOfType(eSeqData) ) {
        if ( single_segment && !inst.IsSetExt() ) {
            // seq-data
            CSegment& seg = x_SetSegment(x_GetFirstEndSegmentIndex() + 1);
            _ASSERT(seg.m_SegType == eSeqData);
            inst.SetSeq_data(const_cast<CSeq_data&>(x_GetSeq_data(seg)));
            inst.ResetExt();
            return true;
        }
    }
    else if ( HasSegmentOfType(eSeqGap) ) {
        if ( single_segment && !inst.IsSetExt() ) {
            inst.SetRepr(CSeq_inst::eRepr_virtual);
            inst.ResetSeq_data();
            inst.ResetExt();
            return true;
        }
    }
    else {
        if ( !inst.IsSetExt() || inst.GetExt().IsSeg() ) {
            // ref only -> CSeg_ext
            CSeg_ext::Tdata& data = inst.SetExt().SetSeg().Set();
            CSeg_ext::Tdata::iterator iter = data.begin();
            for ( size_t index = x_GetFirstEndSegmentIndex() + 1;
                  index < x_GetLastEndSegmentIndex(); ++index ) {
                CSegment& seg = x_SetSegment(index);
                _ASSERT(seg.m_SegType == eSeqRef);
                if ( iter == data.end() ) {
                    iter = data.insert(iter, CSeg_ext::Tdata::value_type());
                }
                if ( !*iter ) {
                    iter->Reset(new CSeq_loc);
                }
                CSeq_loc& loc = **iter;
                ++iter;
                CSeq_interval& interval = loc.SetInt();
                interval.SetId(const_cast<CSeq_id&>(x_GetRefSeqid(seg)));
                TSeqPos pos = seg.m_RefPosition;
                interval.SetFrom(pos);
                interval.SetTo(pos+x_GetSegmentLength(index, 0)-1);
                if ( seg.m_RefMinusStrand ) {
                    interval.SetStrand(eNa_strand_minus);
                }
                else {
                    interval.ResetStrand();
                }
                interval.ResetFuzz_from();
                interval.ResetFuzz_to();
            }
            data.erase(iter, data.end());
            return true;
        }
    }
 
    // delta
    CDelta_ext::Tdata& delta = inst.SetExt().SetDelta().Set();
    inst.SetRepr(CSeq_inst::eRepr_delta);
    CDelta_ext::Tdata::iterator iter = delta.begin();
    for ( size_t index = x_GetFirstEndSegmentIndex() + 1;
          index < x_GetLastEndSegmentIndex(); ++index ) {
        CSegment& seg = x_SetSegment(index);
        if ( iter == delta.end() ) {
            iter = delta.insert(iter, CDelta_ext::Tdata::value_type());
        }
        iter->Reset(new CDelta_seq);
        CDelta_seq& dseq = **iter;
        ++iter;
        if ( seg.m_SegType == eSeqData ) {
            CSeq_literal& lit = dseq.SetLiteral();
            lit.SetLength(x_GetSegmentLength(index, 0));
            lit.SetSeq_data(const_cast<CSeq_data&>(x_GetSeq_data(seg)));
            lit.ResetFuzz();
        }
        else if ( seg.m_SegType == eSeqGap && seg.m_ObjType == eSeqLiteral ) {
            dseq.SetLiteral(const_cast<CSeq_literal&>(*x_GetSeq_literal(seg)));
        }
        else if ( seg.m_SegType == eSeqGap ) {
            CSeq_literal& lit = dseq.SetLiteral();
            lit.SetLength(x_GetSegmentLength(index, 0));
            lit.ResetSeq_data();
            if ( seg.m_UnknownLength ) {
                lit.SetFuzz().SetLim(CInt_fuzz::eLim_unk);
            }
            else {
                lit.ResetFuzz();
            }
        }
        else {
            _ASSERT(seg.m_SegType == eSeqRef);
            CSeq_loc& loc = dseq.SetLoc();
            CSeq_interval& interval = loc.SetInt();
            interval.SetId(const_cast<CSeq_id&>(x_GetRefSeqid(seg)));
            TSeqPos pos = seg.m_RefPosition;
            interval.SetFrom(pos);
            interval.SetTo(pos+x_GetSegmentLength(index, 0)-1);
            if ( seg.m_RefMinusStrand ) {
                interval.SetStrand(eNa_strand_minus);
            }
            else {
                interval.ResetStrand();
            }
            interval.ResetFuzz_from();
            interval.ResetFuzz_to();
        }
    }
    delta.erase(iter, delta.end());
    inst.ResetSeq_data();
    return true;
}
 
 
void CSeqMap::SetRepr(CSeq_inst::TRepr /*repr*/)
{
}
 
 
void CSeqMap::ResetRepr(void)
{
}
 
 
void CSeqMap::SetMol(CSeq_inst::TMol mol)
{
    m_Mol = mol;
}
 
 
void CSeqMap::ResetMol(void)
{
    m_Mol = CSeq_inst::eMol_not_set;
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE