Seq_entry.cpp

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/* $Id: Seq_entry.cpp 93341 2021-04-05 12:29:47Z 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:  .......
 *
 * File Description:
 *   .......
 *
 * Remark:
 *   This code was originally generated by application DATATOOL
 *   using specifications from the ASN data definition file
 *   'seqset.asn'.
 */
 
// standard includes
 
// generated includes
#include <ncbi_pch.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqset/Bioseq_set.hpp>
 
#include <objects/seq/Bioseq.hpp>
 
#include <objects/seq/seq_id_handle.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
 
// generated classes
 
BEGIN_NCBI_SCOPE
 
BEGIN_objects_SCOPE // namespace ncbi::objects::
 
// destructor
CSeq_entry::~CSeq_entry(void)
{
}
 
void CSeq_entry::ResetParentEntry(void)
{
    m_ParentEntry = 0;
}
 
void CSeq_entry::SetParentEntry(CSeq_entry* entry)
{
    m_ParentEntry = entry;
}
 
void CSeq_entry::Parentize(void)
{
    switch ( Which() ) {
    case e_Seq:
        SetSeq().SetParentEntry(this);
        break;
    case e_Set:
        SetSet().SetParentEntry(this);
        NON_CONST_ITERATE ( CBioseq_set::TSeq_set, si, SetSet().SetSeq_set() ) {
            (*si)->SetParentEntry(this);
            (*si)->Parentize();
        }
        break;
    case e_not_set:
        break;
    }
}
 
void CSeq_entry::ParentizeOneLevel(void)
{
    switch ( Which() ) {
    case e_Seq:
        SetSeq().SetParentEntry(this);
        break;
    case e_Set:
        SetSet().SetParentEntry(this);
        NON_CONST_ITERATE ( CBioseq_set::TSeq_set, si, SetSet().SetSeq_set() ) {
            (*si)->SetParentEntry(this);
        }
        break;
    case e_not_set:
        break;
    }
}
 
bool CSeq_entry::IsSetDescr(void) const
{
    switch ( Which() ) {
    case e_Seq:
        return (GetSeq().IsSetDescr());
    case e_Set:
        return (GetSet().IsSetDescr());
    default:
        break;
    }
 
    return false;
}
 
const CSeq_descr& CSeq_entry::GetDescr(void) const
{
    switch ( Which() ) {
    case e_Seq:
        return (GetSeq().GetDescr());
    case e_Set:
        return (GetSet().GetDescr());
    default:
      NCBI_THROW(CSerialException, eNotImplemented,
                 "CSeq_entry::GetDescr: unsupported entry type "
                 + SelectionName(Which()));
    }
}
 
void CSeq_entry::SetDescr(CSeq_descr& value)
{
    switch ( Which() ) {
    case e_Seq:
        SetSeq().SetDescr(value);
        break;
    case e_Set:
        SetSet().SetDescr(value);
        break;
    default:
      NCBI_THROW(CSerialException, eNotImplemented,
                 "CSeq_entry::SetDescr: unsupported entry type "
                 + SelectionName(Which()));
    }
}
 
CSeq_descr& CSeq_entry::SetDescr(void)
{
    switch ( Which() ) {
    case e_Seq:
        return (SetSeq().SetDescr());
    case e_Set:
        return (SetSet().SetDescr());
    default:
      NCBI_THROW(CSerialException, eNotImplemented,
                 "CSeq_entry::SetDescr: unsupported entry type "
                 + SelectionName(Which()));
    }
}
 
 
bool CSeq_entry::IsSetAnnot(void) const
{
    switch ( Which() ) {
    case e_Seq:
        return (GetSeq().IsSetAnnot());
    case e_Set:
        return (GetSet().IsSetAnnot());
    default:
        break;
    }
 
    return false;
}
 
const CSeq_entry::TAnnot& CSeq_entry::GetAnnot(void) const
{
    switch ( Which() ) {
    case e_Seq:
        return (GetSeq().GetAnnot());
    case e_Set:
        return (GetSet().GetAnnot());
    default:
      NCBI_THROW(CSerialException, eNotImplemented,
                 "CSeq_entry::GetAnnot: unsupported entry type "
                 + SelectionName(Which()));
    }
}
 
 
 
CSeq_entry::TAnnot& CSeq_entry::SetAnnot(void)
{
    switch ( Which() ) {
    case e_Seq:
        return (SetSeq().SetAnnot());
    case e_Set:
        return (SetSet().SetAnnot());
    default:
      NCBI_THROW(CSerialException, eNotImplemented,
                 "CSeq_entry::SetAnnot: unsupported entry type "
                 + SelectionName(Which()));
    }
}
 
 
 
// Implemented here to prevent CBioseq dependency on CSeq_entry
CConstRef<CSeqdesc> CBioseq::GetClosestDescriptor (CSeqdesc::E_Choice choice, int* level) const
{
    CSeq_entry* se;
    int lvl = 0;
  
    for (se = GetParentEntry(); se; se = se->GetParentEntry(), lvl++) {
        if (se->IsSetDescr()) {
            ITERATE (CSeq_descr::Tdata, sd_itr, se->GetDescr().Get()) {
                const CSeqdesc& desc = **sd_itr;
                if ( desc.Which() == choice ) {
                    if (level != NULL) {
                        *level = lvl;
                    }
                    return *sd_itr;
                }
            }
        }
    }
  
    if (level != NULL) {
        *level = lvl;
    }
    return CConstRef<CSeqdesc> ();
}
 
 
void CSeq_entry::UserOp_Assign(const CSerialUserOp& /* source */)
{
    m_ParentEntry = 0;
    ParentizeOneLevel();
}
 
bool CSeq_entry::UserOp_Equals(const CSerialUserOp& /*object*/) const
{
    return true;
}
 
 
static CBioseq::ELabelType s_GetBioseqLabelType(CSeq_entry::ELabelType lt)
{
    switch (lt) {
        case CSeq_entry::eType:    return CBioseq::eType;
        case CSeq_entry::eContent: return CBioseq::eContent;
        default:
            _ASSERT(lt==CSeq_entry::eBoth);
            return CBioseq::eBoth;
    }
}
 
 
static CBioseq_set::ELabelType s_GetBioseqSetLabelType(CSeq_entry::ELabelType lt)
{
    switch (lt) {
        case CSeq_entry::eType:    return CBioseq_set::eType;
        case CSeq_entry::eContent: return CBioseq_set::eContent;
        default:
            _ASSERT(lt==CSeq_entry::eBoth);
            return CBioseq_set::eBoth;
    }
}
 
 
void CSeq_entry::GetLabel(string* label, ELabelType type) const
{
    switch ( Which() ) {
    case e_Seq:
        GetSeq().GetLabel(label, s_GetBioseqLabelType(type));
        break;
    case e_Set:
        GetSet().GetLabel(label, s_GetBioseqSetLabelType(type));
        break;
    case e_not_set:
    default:
        *label += "???";
    }
}
 
 
BEGIN_LOCAL_NAMESPACE;
 
// mapping entries:
// [Seq-id, null] == null - no replacement for the Seq-id.
// [Seq-id, null] == gi - needs replacement, gi is the next suffix number.
// [Seq-id, Bioseq] == null - needs replacement id, not yet assigned.
// [Seq-id, Bioseq] == gi - no need for replacement.
// [Seq-id, Bioseq] == new Seq-id - replacement id.
typedef pair<CSeq_id_Handle, CConstRef<CBioseq> > TIdKey;
typedef map<TIdKey, CSeq_id_Handle> TIdMap;
typedef pair<TIdMap::iterator, bool> TIdInsert;
 
 
inline bool sx_CanReassign(CSeq_id::E_Choice type)
{
    return type == CSeq_id::e_Local || type == CSeq_id::e_General ||
        type == CSeq_id::e_Ddbj || type == CSeq_id::e_Genbank ||
        type == CSeq_id::e_Embl || type == CSeq_id::e_Other;
}
 
 
TIdInsert
sx_AddId(TIdMap& id_map, const CSeq_id_Handle& id, const CBioseq* seq = 0)
{
    return id_map.insert(TIdMap::value_type(TIdKey(id, ConstRef(seq)), null));
}
 
 
CSeq_id_Handle sx_MakeUniqueId(const CSeq_id_Handle& idh, TIdMap& id_map)
{
    CRef<CSeq_id> new_id(SerialClone(*idh.GetSeqId()));
    CObject_id* obj_id = 0;
    switch ( new_id->Which() ) {
    case CSeq_id::e_Local: obj_id = &new_id->SetLocal(); break;
    case CSeq_id::e_General: obj_id = &new_id->SetGeneral().SetTag(); break;
    case CSeq_id::e_Ddbj:
    case CSeq_id::e_Genbank:
    case CSeq_id::e_Embl:
    case CSeq_id::e_Other:
    {
        string lcl = new_id->AsFastaString();
        NStr::ReplaceInPlace(lcl, "|", "_");
        new_id->SetLocal().SetStr(lcl);
        obj_id = &new_id->SetLocal();
        break;
    }
    default:
        NCBI_THROW(CException, eUnknown,
                   "CSeq_entry::ReassignConflictingIds: "
                   "bad type of conflicting id: "+new_id->AsFastaString());
    }
    string base;
    if ( obj_id->IsStr() ) {
        base = obj_id->GetStr();
    }
    else {
        base = NStr::NumericToString(obj_id->GetId());
    }
    base += "_";
    CSeq_id_Handle& suffix_id = id_map[TIdKey(idh, null)];
    for ( TGi k = suffix_id.GetGi(); ; ++k ) {
        obj_id->SetStr(base+NStr::NumericToString(k));
        CSeq_id_Handle new_idh = CSeq_id_Handle::GetHandle(*new_id);
        if ( sx_AddId(id_map, new_idh).second ) {
            suffix_id = CSeq_id_Handle::GetGiHandle(k+GI_CONST(1));
            return new_idh;
        }
    }
}
 
 
inline
size_t sx_Level(const CSeq_entry* entry)
{
    size_t level = 0;
    while ( entry ) {
        ++level;
        entry = entry->GetParentEntry();
    }
    return level;
}
 
 
inline
size_t sx_GetParentLevel(const CSeq_entry* entry1, size_t level1,
                         const CSeq_entry* entry2, size_t level2)
{
    if ( level2 > level1 ) {
        return sx_GetParentLevel(entry2, level2, entry1, level1);
    }
    // go to the same level
    while ( level1 > level2 ) {
        entry1 = entry1->GetParentEntry();
        --level1;
    }
    // find common parent
    while ( entry1 != entry2 ) {
        entry1 = entry1->GetParentEntry();
        entry2 = entry2->GetParentEntry();
        --level1;
    }
    return level1;
}
 
 
inline
bool sx_ComesBefore(const CSeq_entry* entry1, size_t level1,
                    const CSeq_entry* entry2, size_t level2)
{
    if ( level2 > level1 ) {
        return !sx_ComesBefore(entry2, level2, entry1, level1);
    }
    // go to the same level
    while ( level1 > level2 ) {
        entry1 = entry1->GetParentEntry();
        --level1;
    }
    // find common parent
    const CSeq_entry* parent = 0;
    for ( ;; ) {
        parent = entry1->GetParentEntry();
        const CSeq_entry* parent2 = entry2->GetParentEntry();
        if ( parent == parent2 ) {
            break;
        }
        entry1 = parent;
        entry2 = parent2;
    }
    // look which entry comes first in the common parent
    const CBioseq_set& set = parent->GetSet();
    ITERATE ( CBioseq_set::TSeq_set, it, set.GetSeq_set() ) {
        if ( *it == entry1 ) {
            return true;
        }
        if ( *it == entry2 ) {
            return false;
        }
    }
    // should not come here, but we'll return false anyway
    return false;
}
 
 
typedef map<CSeq_id_Handle, CSeq_id_Handle> TIdMapCache;
 
const CSeq_id_Handle& sx_FindBestId(const TIdMap& id_map,
                                    TIdMapCache& cache,
                                    const CSeq_entry& annot_entry,
                                    const CSeq_id_Handle& id)
{
    CSeq_id_Handle& cached = cache[id];
    if ( cached ) {
        // use cached value
        return cached;
    }
    // find correct replacement
    // first scan for closest inner sequence, it's easier and usually succeeds
    const CSeq_entry* closest_entry = 0;
    size_t closest_level = kMax_Int;
    for ( TIdMap::const_iterator it = id_map.lower_bound(TIdKey(id, null));
          it != id_map.end() && it->first.first == id; ++it ) {
        if ( !it->first.second ) { // skip non-bioseq entry
            continue;
        }
        const CBioseq& seq = *it->first.second;
        const CSeq_entry* seq_entry = seq.GetParentEntry();
        size_t seq_level = 0;
        for ( const CSeq_entry* entry = seq_entry;
              entry; entry = entry->GetParentEntry(), ++seq_level ) {
            if ( entry == &annot_entry ) {
                // inner
                if ( seq_level < closest_level ) {
                    closest_level = seq_level;
                    closest_entry = seq_entry;
                    cached = it->second;
                }
                else if ( seq_level == closest_level &&
                          sx_ComesBefore(seq_entry, seq_level,
                                         closest_entry, closest_level) ) {
                    // same level, use the one that comes first
                    closest_entry = seq_entry;
                    cached = it->second;
                }
                break;
            }
        }
    }
    if ( cached ) {
        // found inner sequence
        return cached;
    }
    // now scan for closest outer sequence in order:
    // 1. closest commont parent
    // 2. closest distance (through the commont parent)
    // 3. comes first at fork
    size_t annot_level = sx_Level(&annot_entry);
    size_t closest_seq_level = kMax_Int;
    // full scan for best candidate
    for ( TIdMap::const_iterator it = id_map.lower_bound(TIdKey(id, null));
          it != id_map.end() && it->first.first == id; ++it ) {
        if ( !it->first.second ) {
            continue;
        }
        const CBioseq& seq = *it->first.second;
        const CSeq_entry* seq_entry = seq.GetParentEntry();
        size_t seq_level = sx_Level(seq_entry);
        size_t parent_level = sx_GetParentLevel(&annot_entry, annot_level,
                                                seq_entry, seq_level);
        size_t level = annot_level - parent_level;
        if ( level < closest_level ) {
            closest_level = level;
            closest_seq_level = seq_level;
            closest_entry = seq_entry;
            cached = it->second;
        }
        else if ( level == closest_level &&
                  seq_level < closest_seq_level ) {
            closest_seq_level = seq_level;
            closest_entry = seq_entry;
            cached = it->second;
        }
        else if ( level == closest_level &&
                  seq_level == closest_seq_level &&
                  sx_ComesBefore(seq_entry, seq_level,
                                 closest_entry, closest_seq_level) ) {
            closest_entry = seq_entry;
            cached = it->second;
        }
    }
    return cached;
}
 
 
inline
void sx_ProcessId(const TIdMap& id_map,
                  TIdMapCache& cache,
                  const CSeq_entry& entry,
                  CSeq_id& id)
{
    if ( !sx_CanReassign(id.Which()) ) {
        return;
    }
    CSeq_id_Handle idh = CSeq_id_Handle::GetHandle(id);
    auto id_it = id_map.find(TIdKey(idh, null));
    if ( id_it == id_map.end() || !id_it->second ) {
        // no mapping is necessary
        return;
    }
    const CSeq_id_Handle& new_id = sx_FindBestId(id_map, cache, entry, idh);
    if ( !new_id.IsGi() ) {
        id.Assign(*new_id.GetSeqId());
    }
}
 
 
END_LOCAL_NAMESPACE;
 
 
void CSeq_entry::ReassignConflictingIds(void)
{
    TIdMap id_map;
    // id_map states:
    // [{id, null}] -> null : unique/first id - no change
    // [{id, null}] -> gi : next replacement suffix to try for the id
    // [{id, seq}] -> new_id : replace 'id' of 'seq' with 'new_id'
    // [{id, seq}] -> null : slot for replacement
 
    // gather conflicting ids
    bool has_conflict = false;
    CSeq_id_Handle gi1 = CSeq_id_Handle::GetGiHandle(GI_CONST(1));
    for ( CTypeConstIterator<CBioseq> it(ConstBegin(*this)); it; ++it ) {
        ITERATE ( CBioseq::TId, idit, it->GetId() ) {
            if ( !sx_CanReassign((**idit).Which()) ) {
                // only local ids can be reassigned
                continue;
                NCBI_THROW_FMT(CException, eUnknown,
                               "CSeq_entry::ReassignConflictingIds: "
                               "conflicting id is not a Seq-id.local: "<<
                               (*idit)->AsFastaString());
            }
            CSeq_id_Handle id = CSeq_id_Handle::GetHandle(**idit);
            TIdInsert ins = sx_AddId(id_map, id);
            if ( ins.second ) {
                // first time occurence - keep it as it is
                // make slot marking no replacement
                sx_AddId(id_map, id, &*it).first->second = gi1;
            }
            else {
                has_conflict = true;
                // duplicate id, start replacement search with suffix 1
                if ( !ins.first->second ) {
                    ins.first->second = gi1;
                }
                // make mapping slot
                sx_AddId(id_map, id, &*it);
            }
        }
    }
    if ( !has_conflict ) {
        // no conflicts
        return;
    }
    Parentize();
    // assign new ids to Bioseqs
    for ( CTypeIterator<CBioseq> it(*this); it; ++it ) {
        NON_CONST_ITERATE ( CBioseq::TId, idit, it->SetId() ) {
            if ( !sx_CanReassign((**idit).Which()) ) {
                continue;
            }
            CSeq_id_Handle id = CSeq_id_Handle::GetHandle(**idit);
            TIdMap::iterator map_it = id_map.find(TIdKey(id, ConstRef(&*it)));
            if ( map_it != id_map.end() && !map_it->second ) {
                // make replacement id
                map_it->second = sx_MakeUniqueId(id, id_map);
                // change it in the Bioseq
                *idit = SerialClone(*map_it->second.GetSeqId());
            }
        }
    }
    // replace annotation ids
    for ( CTypeIterator<CSeq_entry> it(*this); it; ++it ) {
        if ( it->IsSetAnnot() ) {
            TIdMapCache cache;
            NON_CONST_ITERATE ( CSeq_entry::TAnnot, ait, it->SetAnnot() ) {
                for ( CTypeIterator<CSeq_id> idit(**ait); idit; ++idit ) {
                    sx_ProcessId(id_map, cache, *it, *idit);
                }
            }
        }
    }
}
 
 
END_objects_SCOPE // namespace ncbi::objects::
 
END_NCBI_SCOPE