NCBI C++ ToolKit
Macros | Typedefs | Functions | Variables
promote.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <util/static_map.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/annot_selector.hpp>
#include <objmgr/annot_ci.hpp>
#include <objmgr/seq_feat_handle.hpp>
#include <objmgr/seq_annot_handle.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/edit/edit_exception.hpp>
#include <objtools/edit/seq_entry_edit.hpp>
#include <objtools/edit/promote.hpp>
#include <objtools/error_codes.hpp>
+ Include dependency graph for promote.cpp:

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Macros

#define NCBI_USE_ERRCODE_X   Objtools_Edit
 

Typedefs

typedef SStaticPair< CSeqFeatData::ESubtype, CMolInfo::TBiomolTBiomolPair
 
typedef CStaticPairArrayMap< CSeqFeatData::ESubtype, CMolInfo::TBiomolTBiomolMap
 

Functions

 USING_SCOPE (sequence)
 
 DEFINE_STATIC_ARRAY_MAP (TBiomolMap, sc_BiomolMap, kBiomolMap)
 
void PromoteFeatures (CBioseq_Handle &seq, CPromote::TFlags flags, CPromote::TFeatTypes types)
 
void PromoteFeatures (CBioseq_Handle &seq, CSeq_annot_Handle &annot, CPromote::TFlags flags, CPromote::TFeatTypes types)
 
void PromoteCdregion (CBioseq_Handle &seq, CSeq_feat_Handle &feat, bool include_stop, bool remove_trailingX)
 
void PromoteRna (CBioseq_Handle &seq, CSeq_feat_Handle &feat)
 
void PromotePub (CBioseq_Handle &seq, CSeq_feat_Handle &feat)
 
bool SetMolInfoCompleteness (CMolInfo &mi, bool partial5, bool partial3)
 

Variables

static const TBiomolPair kBiomolMap []
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Edit

Definition at line 59 of file promote.cpp.

Typedef Documentation

◆ TBiomolMap

Definition at line 516 of file promote.cpp.

◆ TBiomolPair

Definition at line 515 of file promote.cpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP ( TBiomolMap  ,
sc_BiomolMap  ,
kBiomolMap   
)

◆ PromoteCdregion()

void PromoteCdregion ( CBioseq_Handle seq,
CSeq_feat_Handle feat,
bool  include_stop,
bool  remove_trailingX 
)

◆ PromoteFeatures() [1/2]

void PromoteFeatures ( CBioseq_Handle seq,
CPromote::TFlags  flags,
CPromote::TFeatTypes  types 
)

Definition at line 614 of file promote.cpp.

References flags, CPromote::PromoteFeatures(), and types.

◆ PromoteFeatures() [2/2]

void PromoteFeatures ( CBioseq_Handle seq,
CSeq_annot_Handle annot,
CPromote::TFlags  flags,
CPromote::TFeatTypes  types 
)

Definition at line 624 of file promote.cpp.

References flags, CPromote::PromoteFeatures(), and types.

◆ PromotePub()

void PromotePub ( CBioseq_Handle seq,
CSeq_feat_Handle feat 
)

Definition at line 657 of file promote.cpp.

References CPromote::eFeatType_Pub, and CPromote::PromotePub().

◆ PromoteRna()

void PromoteRna ( CBioseq_Handle seq,
CSeq_feat_Handle feat 
)

Definition at line 650 of file promote.cpp.

References CPromote::eFeatType_Rna, and CPromote::PromoteRna().

◆ SetMolInfoCompleteness()

bool SetMolInfoCompleteness ( CMolInfo mi,
bool  partial5,
bool  partial3 
)

◆ USING_SCOPE()

USING_SCOPE ( sequence  )

Variable Documentation

◆ kBiomolMap

const TBiomolPair kBiomolMap[]
static
Initial value:
= {
}
@ eBiomol_pre_RNA
precursor RNA of any sort really
Definition: MolInfo_.hpp:102
@ eBiomol_transcribed_RNA
transcribed RNA other than existing classes
Definition: MolInfo_.hpp:113

Definition at line 517 of file promote.cpp.

Modified on Thu Feb 29 12:22:50 2024 by modify_doxy.py rev. 669887