annot_type_index.cpp

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/*  $Id: annot_type_index.cpp 99883 2023-05-18 17:55:27Z 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.
*
* ===========================================================================
*
* Author: Aleksey Grichenko
*
* File Description:
*   Annotation type indexes
*
*/
 
#include <ncbi_pch.hpp>
#include <corelib/ncbimtx.hpp>
#include <objmgr/impl/annot_type_index.hpp>
#include <objmgr/annot_type_selector.hpp>
#include <objmgr/annot_types_ci.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/annot_object.hpp>
#include <objmgr/impl/annot_object_index.hpp>
#include <objmgr/impl/tse_info.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
 
// All ranges are in format [x, y)
 
DEFINE_STATIC_FAST_MUTEX(sm_TablesInitializeMutex);
atomic<bool> CAnnotType_Index::sm_TablesInitialized{false};
 
Uint1 CAnnotType_Index::sm_AnnotTypeIndexRange[CAnnotType_Index::kAnnotType_size][2];
Uint1 CAnnotType_Index::sm_FeatTypeIndexRange[CAnnotType_Index::kFeatType_size][2];
Uint1 CAnnotType_Index::sm_FeatSubtypeIndex[CAnnotType_Index::kFeatSubtype_size];
Uint1 CAnnotType_Index::sm_IndexSubtype[CAnnotType_Index::kAnnotIndex_size];
 
void CAnnotType_Index::x_InitIndexTables(void)
{
    CFastMutexGuard guard(sm_TablesInitializeMutex);
    if ( sm_TablesInitialized.load(memory_order_acquire) ) {
        return;
    }
    // Check flag, lock tables
    _ASSERT(!sm_TablesInitialized);
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set][0] = 0;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Align][0] = kAnnotIndex_Align;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Align][1] = kAnnotIndex_Align+1;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Graph][0] = kAnnotIndex_Graph;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Graph][1] = kAnnotIndex_Graph+1;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Seq_table][0] = kAnnotIndex_Seq_table;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Seq_table][1] = kAnnotIndex_Seq_table+1;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable][0] = kAnnotIndex_Ftable;
 
    _ASSERT(kFeatType_size < kMax_UI1);
    _ASSERT(kFeatSubtype_size < kMax_UI1);
    _ASSERT(kAnnotIndex_size < kMax_UI1);
    vector< vector<Uint1> > type_subtypes(kFeatType_size);
    for ( Uint1 subtype = 0; subtype < kFeatSubtype_size; ++subtype ) {
        Uint1 type =
            CSeqFeatData::GetTypeFromSubtype(CSeqFeatData::ESubtype(subtype));
        if ( type != CSeqFeatData::e_not_set ||
             subtype == CSeqFeatData::eSubtype_bad ) {
            type_subtypes[type].push_back(subtype);
        }
    }
    
    Uint1 cur_idx = kAnnotIndex_Ftable;
    fill_n(sm_IndexSubtype, cur_idx,
           CSeqFeatData::eSubtype_bad);
    for ( Uint1 type = 0; type < kFeatType_size; ++type ) {
        sm_FeatTypeIndexRange[type][0] = cur_idx;
        ITERATE ( vector<Uint1>, it, type_subtypes[type] ) {
            _ASSERT(cur_idx < kAnnotIndex_size);
            sm_FeatSubtypeIndex[*it] = cur_idx;
            sm_IndexSubtype[cur_idx] = *it;
            ++cur_idx;
        }
        sm_FeatTypeIndexRange[type][1] = cur_idx;
    }
 
    sm_FeatTypeIndexRange[CSeqFeatData::e_not_set][1] = cur_idx;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable][1] = cur_idx;
    sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set][1] = cur_idx;
    _ASSERT(cur_idx <= kAnnotIndex_size);
    fill(sm_IndexSubtype+cur_idx, sm_IndexSubtype+kAnnotIndex_size,
         CSeqFeatData::eSubtype_bad);
    
    sm_TablesInitialized.store(true, memory_order_release);
 
#if defined(_DEBUG)
    _TRACE("Index size: "<<cur_idx<<" of "<<kAnnotIndex_size);
    _ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_not_set) == TIndexRange(0, cur_idx));
    _ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_Locs) == TIndexRange(0, 0));
    _ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_Ids) == TIndexRange(0, 0));
    //_ASSERT(GetAnnotTypeRange(CSeq_annot::C_Data::e_MaxChoice) == TIndexRange(0, 0));
    _ASSERT(GetFeatTypeRange(CSeqFeatData::e_not_set) == TIndexRange(kAnnotIndex_Ftable, cur_idx));
    //_ASSERT(GetFeatTypeRange(CSeqFeatData::e_MaxChoice) == TIndexRange(0, 0));
    _ASSERT(GetSubtypeIndex(CSeqFeatData::eSubtype_bad) == kAnnotIndex_Ftable);
    _ASSERT(GetSubtypeIndex(CSeqFeatData::eSubtype_max) == 0);
    _ASSERT(GetSubtypeIndex(CSeqFeatData::eSubtype_any) == 0);
    for ( size_t type = 0; type < kFeatType_size; ++type ) {
        CSeqFeatData::E_Choice feat_type = CSeqFeatData::E_Choice(type);
        TIndexRange range = GetFeatTypeRange(feat_type);
        _TRACE("type: "<<feat_type
               << " range: "<<range.first<<"-"<<range.second);
        if ( type == 0 ) {
            continue;
        }
        for ( size_t ind = range.first; ind < range.second; ++ind ) {
            SAnnotTypeSelector sel = GetTypeSelector(ind);
            _TRACE("index: "<<ind
                   << " type: "<<sel.GetFeatType()
                   << " subtype: "<<sel.GetFeatSubtype());
            _ASSERT(sel.GetAnnotType() == CSeq_annot::C_Data::e_Ftable);
            _ASSERT(sel.GetFeatType() == feat_type);
            _ASSERT(GetSubtypeIndex(sel.GetFeatSubtype()) == ind);
        }
    }
    for ( size_t st = 0; st <= CSeqFeatData::eSubtype_max; ++st ) {
        CSeqFeatData::ESubtype subtype = CSeqFeatData::ESubtype(st);
        CSeqFeatData::E_Choice type =
            CSeqFeatData::GetTypeFromSubtype(subtype);
        if ( type != CSeqFeatData::e_not_set ||
             subtype == CSeqFeatData::eSubtype_bad ) {
            size_t ind = GetSubtypeIndex(subtype);
            _ASSERT(GetSubtypeForIndex(ind) == subtype);
        }
    }
#endif
}
 
 
CAnnotType_Index::TIndexRange
CAnnotType_Index::GetTypeIndex(const CAnnotObject_Info& info)
{
    Initialize();
    if ( info.GetFeatSubtype() != CSeqFeatData::eSubtype_any ) {
        size_t index = GetSubtypeIndex(info.GetFeatSubtype());
        if ( index ) {
            return TIndexRange(index, index+1);
        }
    }
    else if ( info.GetFeatType() != CSeqFeatData::e_not_set ) {
        return GetFeatTypeRange(info.GetFeatType());
    }
    return GetAnnotTypeRange(info.GetAnnotType());
}
 
 
CAnnotType_Index::TIndexRange
CAnnotType_Index::GetIndexRange(const SAnnotTypeSelector& sel)
{
    Initialize();
    TIndexRange r;
    if ( sel.GetFeatSubtype() != CSeqFeatData::eSubtype_any ) {
        r.first = GetSubtypeIndex(sel.GetFeatSubtype());
        r.second = r.first? r.first + 1: 0;
    }
    else if ( sel.GetFeatType() != CSeqFeatData::e_not_set ) {
        r = GetFeatTypeRange(sel.GetFeatType());
    }
    else {
        r = GetAnnotTypeRange(sel.GetAnnotType());
    }
    return r;
}
 
 
CAnnotType_Index::TIndexRange
CAnnotType_Index::GetIndexRange(const SAnnotTypeSelector& sel,
                                const SIdAnnotObjs& objs)
{
    TIndexRange range;
    range = GetIndexRange(sel);
    range.second = min(range.second, objs.m_AnnotSet.size());
    return range;
}
 
 
SAnnotTypeSelector CAnnotType_Index::GetTypeSelector(size_t index)
{
    SAnnotTypeSelector sel;
    switch (index) {
    case kAnnotIndex_Align:
        sel.SetAnnotType(CSeq_annot::C_Data::e_Align);
        break;
    case kAnnotIndex_Graph:
        sel.SetAnnotType(CSeq_annot::C_Data::e_Graph);
        break;
    case kAnnotIndex_Seq_table:
        sel.SetAnnotType(CSeq_annot::C_Data::e_Seq_table);
        break;
    default:
        sel.SetFeatSubtype(GetSubtypeForIndex(index));
        break;
    }
    return sel;
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE