NCBI C++ ToolKit
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#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>
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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_Options & | SetOptionsScope (CSeq_loc_Mapper_Options &options, CScope *scope) |
bool | s_IsLocalRandomChrId (const CSeq_id &id) |
const CSeq_id * | s_GetSeqIdAlias (const CGC_TypedSeqId &id, CSeq_loc_Mapper::EGCAssemblyAlias alias) |
#define INDEX_TO_STRAND | ( | idx | ) | s_IndexToStrand(idx) |
Definition at line 160 of file seq_loc_mapper.cpp.
#define STRAND_TO_INDEX | ( | is_set, | |
strand | |||
) | ((is_set) ? size_t((strand) + 1) : 0) |
Definition at line 157 of file seq_loc_mapper.cpp.
const CSeq_id* s_GetSeqIdAlias | ( | const CGC_TypedSeqId & | id, |
CSeq_loc_Mapper::EGCAssemblyAlias | alias | ||
) |
Definition at line 868 of file seq_loc_mapper.cpp.
References CGC_TypedSeqId_Base::e_External, CGC_TypedSeqId_Base::e_Genbank, CGC_TypedSeqId_Base::e_Private, CGC_TypedSeqId_Base::e_Refseq, CSeq_loc_Mapper::eGCA_Genbank, CSeq_loc_Mapper::eGCA_GenbankAcc, CSeq_loc_Mapper::eGCA_Other, CSeq_loc_Mapper::eGCA_Refseq, CSeq_loc_Mapper::eGCA_RefseqAcc, and CSeq_loc_Mapper::eGCA_UCSC.
Referenced by CSeq_loc_Mapper::x_InitGCSequence().
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inline |
Definition at line 151 of file seq_loc_mapper.cpp.
References _ASSERT.
Definition at line 803 of file seq_loc_mapper.cpp.
Referenced by CSeq_loc_Mapper::x_IsUCSCRandomChr().
CSeq_loc_Mapper_Options& SetOptionsScope | ( | CSeq_loc_Mapper_Options & | options, |
CScope * | scope | ||
) |
Definition at line 164 of file seq_loc_mapper.cpp.
References CSeq_loc_Mapper_Options::GetMapperSequenceInfo(), and CSeq_loc_Mapper_Options::SetMapperSequenceInfo().