annot_collector.cpp File Reference

#include <ncbi_pch.hpp>
#include <objmgr/impl/annot_collector.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/seq_annot_handle.hpp>
#include <objmgr/seq_feat_handle.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/impl/annot_object.hpp>
#include <objmgr/impl/tse_info.hpp>
#include <objmgr/impl/annot_type_index.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/seq_annot_info.hpp>
#include <objmgr/impl/bioseq_set_info.hpp>
#include <objmgr/impl/handle_range_map.hpp>
#include <objmgr/impl/synonyms.hpp>
#include <objmgr/impl/seq_loc_cvt.hpp>
#include <objmgr/impl/seq_align_mapper.hpp>
#include <objmgr/impl/snp_annot_info.hpp>
#include <objmgr/impl/seq_table_info.hpp>
#include <objmgr/impl/bioseq_info.hpp>
#include <objmgr/impl/scope_impl.hpp>
#include <objmgr/mapped_feat.hpp>
#include <objmgr/graph_ci.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/error_codes.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqres/Seq_graph.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objects/seqloc/Seq_bond.hpp>
#include <objects/seqfeat/seqfeat__.hpp>
#include <objects/general/User_object.hpp>
#include <serial/typeinfo.hpp>
#include <serial/objostr.hpp>
#include <serial/objostrasn.hpp>
#include <serial/serial.hpp>
#include <serial/serialutil.hpp>
#include <util/timsort.hpp>
#include <algorithm>
#include <typeinfo>

Include dependency graph for annot_collector.cpp:

Go to the source code of this file.

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Classes
class	CIdRangeMap
struct	CIdRangeMap::SExtremes
struct	CAnnotObjectType_Less
class	CAnnotObjectType_Less::CNearnessTester
class	CCreateFeat
struct	CAnnotObject_Less
struct	CAnnotObject_LessReverse
class	CAnnotMappingCollector
struct	SLessByInfo

Macros
#define	NCBI_USE_ERRCODE_X   ObjMgr_AnnotCollect

Functions
	NCBI_DEFINE_ERR_SUBCODE_X (2)
static CScope::EGetBioseqFlag	sx_GetFlag (const SAnnotSelector &selector)
static bool	sx_IsEmpty (const SAnnotSelector &sel)
static bool	sx_GeneIsSuppressed (const CSeq_feat &feat)

Variables
	BEGIN_LOCAL_NAMESPACE
	END_LOCAL_NAMESPACE
static CSeqFeatData::ESubtype	s_DefaultAdaptiveTriggers []
static const bool	kTraceFullCvt = false

Macro Definition Documentation

NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   ObjMgr_AnnotCollect

Definition at line 84 of file annot_collector.cpp.

Function Documentation

NCBI_DEFINE_ERR_SUBCODE_X()

NCBI_DEFINE_ERR_SUBCODE_X

(

2

)

sx_GeneIsSuppressed()

static bool sx_GeneIsSuppressed ( const CSeq_feat &  feat )

inlinestatic

Definition at line 3034 of file annot_collector.cpp.

References data, CSeqFeatXref_Base::GetData(), CSeq_feat_Base::GetXref(), CSeqFeatXref_Base::IsSetData(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), and CSeq_feat_Base::IsSetXref().

Referenced by CAnnot_Collector::x_SearchRange().

sx_GetFlag()

static CScope::EGetBioseqFlag sx_GetFlag ( const SAnnotSelector &  selector )

static

Definition at line 2291 of file annot_collector.cpp.

References CScope::eGetBioseq_All, CScope::eGetBioseq_Loaded, SAnnotSelector::eResolve_All, and SAnnotSelector::GetResolveMethod().

Referenced by CAnnot_Collector::x_GetBioseqHandle(), and CAnnot_Collector::x_SearchLoc().

sx_IsEmpty()

static bool sx_IsEmpty ( const SAnnotSelector &  sel )

static

Definition at line 2937 of file annot_collector.cpp.

References CSeq_annot_Base::C_Data::e_not_set, and SAnnotTypeSelector::GetAnnotType().

Referenced by CAnnot_Collector::x_SearchObjects().

Variable Documentation

BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 674 of file annot_collector.cpp.

END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 1458 of file annot_collector.cpp.

kTraceFullCvt

const bool kTraceFullCvt = false

static

Definition at line 1865 of file annot_collector.cpp.

Referenced by CAnnot_Collector::x_AddPostMappingsCvt(), and CAnnot_Collector::x_Initialize().

s_DefaultAdaptiveTriggers

CSeqFeatData::ESubtype s_DefaultAdaptiveTriggers[]

static

Initial value:

= {
    CSeqFeatData::eSubtype_gene,
    CSeqFeatData::eSubtype_cdregion,
    CSeqFeatData::eSubtype_mRNA
}

Definition at line 1762 of file annot_collector.cpp.

Referenced by CAnnot_Collector::x_Initialize0().