annot_type_index.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: annot_type_index.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:22:45 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: annot_type_index.cpp,v 1000.1 2004/06/01 19:22:45 gouriano Exp $
- * ===========================================================================
- *
- * 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 <objmgr/impl/annot_type_index.hpp>
- #include <objmgr/annot_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)
- const size_t kAnnotTypeMax = CSeq_annot::C_Data::e_MaxChoice - 1;
- const size_t kFeatTypeMax = CSeqFeatData::e_MaxChoice - 1;
- const size_t kFeatSubtypeMax = CSeqFeatData::eSubtype_max;
- CAnnotType_Index::TIndexRangeTable CAnnotType_Index::sm_AnnotTypeIndexRange;
- CAnnotType_Index::TIndexRangeTable CAnnotType_Index::sm_FeatTypeIndexRange;
- CAnnotType_Index::TIndexTable CAnnotType_Index::sm_FeatSubtypeIndex;
- bool CAnnotType_Index::sm_TablesInitialized = false;
- void CAnnotType_Index::x_InitIndexTables(void)
- {
- // Check flag, lock tables
- _ASSERT(!sm_TablesInitialized);
- sm_AnnotTypeIndexRange.resize(kAnnotTypeMax + 1);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set].first = 0;
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Align] = TIndexRange(0,1);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Graph] = TIndexRange(1,2);
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable].first = 2;
- vector< vector<size_t> > type_subtypes(kFeatTypeMax+1);
- for ( size_t subtype = 0; subtype <= kFeatSubtypeMax; ++subtype ) {
- size_t type = CSeqFeatData::
- GetTypeFromSubtype(CSeqFeatData::ESubtype(subtype));
- if ( type != CSeqFeatData::e_not_set ||
- subtype == CSeqFeatData::eSubtype_bad ) {
- type_subtypes[type].push_back(subtype);
- }
- }
- sm_FeatTypeIndexRange.resize(kFeatTypeMax + 1);
- sm_FeatSubtypeIndex.resize(kFeatSubtypeMax + 1);
- size_t cur_idx =
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable].first;
- for ( size_t type = 0; type <= kFeatTypeMax; ++type ) {
- sm_FeatTypeIndexRange[type].first = cur_idx;
- if ( type != CSeqFeatData::e_not_set ) {
- sm_FeatTypeIndexRange[type].second =
- cur_idx + type_subtypes[type].size();
- }
- ITERATE ( vector<size_t>, it, type_subtypes[type] ) {
- sm_FeatSubtypeIndex[*it] = cur_idx++;
- }
- }
- sm_FeatTypeIndexRange[CSeqFeatData::e_not_set].second = cur_idx;
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_Ftable].second = cur_idx;
- sm_AnnotTypeIndexRange[CSeq_annot::C_Data::e_not_set].second = cur_idx;
-
- sm_TablesInitialized = true;
- }
- size_t CAnnotType_Index::GetTypeIndex(const CAnnotObject_Info& info)
- {
- Initialize();
- if ( info.GetFeatSubtype() != CSeqFeatData::eSubtype_any ) {
- size_t index = GetSubtypeIndex(info.GetFeatSubtype());
- if ( index ) {
- return index;
- }
- }
- else if ( info.GetFeatType() != CSeqFeatData::e_not_set ) {
- const TIndexRange r = GetFeatTypeRange(info.GetFeatType());
- if ( r.second == r.first + 1 ) {
- return r.first;
- }
- }
- else {
- const TIndexRange r = GetAnnotTypeRange(info.GetAnnotType());
- if ( r.second == r.first + 1 ) {
- return r.first;
- }
- }
- NCBI_THROW(CObjMgrException, eOtherError,
- "CAnnotObject_Info is incompatible with CAnnotType_Index indexes");
- }
- size_t CAnnotType_Index::GetTypeIndex(const SAnnotObject_Key& key)
- {
- Initialize();
- return GetTypeIndex(*key.m_AnnotObject_Info);
- }
- 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;
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ---------------------------------------------------------------------------
- * $Log: annot_type_index.cpp,v $
- * Revision 1000.1 2004/06/01 19:22:45 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
- *
- * Revision 1.3 2004/05/21 21:42:12 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.2 2004/03/16 15:47:27 vasilche
- * Added CBioseq_set_Handle and set of EditHandles
- *
- * Revision 1.1 2004/02/04 18:03:21 grichenk
- * Initial revision
- *
- *
- * ===========================================================================
- */