NCBI C++ ToolKit
Classes | Macros | Functions
seq_loc_mapper.cpp File Reference
#include <ncbi_pch.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/impl/synonyms.hpp>
#include <objmgr/impl/seq_align_mapper.hpp>
#include <objmgr/impl/seq_loc_cvt.hpp>
#include <objmgr/gc_assembly_parser.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqloc/Seq_loc_equiv.hpp>
#include <objects/seqloc/Seq_bond.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <objects/genomecoll/genome_collection__.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/Seq_gap.hpp>
#include <algorithm>
+ Include dependency graph for seq_loc_mapper.cpp:

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Classes

class  CScope_Mapper_Sequence_Info
 

Macros

#define STRAND_TO_INDEX(is_set, strand)    ((is_set) ? size_t((strand) + 1) : 0)
 
#define INDEX_TO_STRAND(idx)    s_IndexToStrand(idx)
 

Functions

ENa_strand s_IndexToStrand (size_t idx)
 
CSeq_loc_Mapper_OptionsSetOptionsScope (CSeq_loc_Mapper_Options &options, CScope *scope)
 
bool s_IsLocalRandomChrId (const CSeq_id &id)
 
const CSeq_ids_GetSeqIdAlias (const CGC_TypedSeqId &id, CSeq_loc_Mapper::EGCAssemblyAlias alias)
 

Macro Definition Documentation

◆ INDEX_TO_STRAND

#define INDEX_TO_STRAND (   idx)     s_IndexToStrand(idx)

Definition at line 160 of file seq_loc_mapper.cpp.

◆ STRAND_TO_INDEX

#define STRAND_TO_INDEX (   is_set,
  strand 
)     ((is_set) ? size_t((strand) + 1) : 0)

Definition at line 157 of file seq_loc_mapper.cpp.

Function Documentation

◆ s_GetSeqIdAlias()

const CSeq_id* s_GetSeqIdAlias ( const CGC_TypedSeqId id,
CSeq_loc_Mapper::EGCAssemblyAlias  alias 
)

◆ s_IndexToStrand()

ENa_strand s_IndexToStrand ( size_t  idx)
inline

Definition at line 151 of file seq_loc_mapper.cpp.

References _ASSERT.

◆ s_IsLocalRandomChrId()

bool s_IsLocalRandomChrId ( const CSeq_id id)
inline

Definition at line 803 of file seq_loc_mapper.cpp.

Referenced by CSeq_loc_Mapper::x_IsUCSCRandomChr().

◆ SetOptionsScope()

CSeq_loc_Mapper_Options& SetOptionsScope ( CSeq_loc_Mapper_Options options,
CScope scope 
)
Modified on Tue Jul 23 17:48:31 2024 by modify_doxy.py rev. 669887