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::TBiomol >	TBiomolPair
typedef CStaticPairArrayMap< CSeqFeatData::ESubtype, CMolInfo::TBiomol >	TBiomolMap

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

typedef CStaticPairArrayMap<CSeqFeatData::ESubtype, CMolInfo::TBiomol> TBiomolMap

Definition at line 516 of file promote.cpp.

TBiomolPair

typedef SStaticPair<CSeqFeatData::ESubtype, CMolInfo::TBiomol> 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
	)

Definition at line 635 of file promote.cpp.

References CPromote::eFeatType_Cdregion, flags, CPromote::fPromote_IncludeStop, CPromote::fPromote_RemoveTrailingX, and CPromote::PromoteCdregion().

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
	)

Definition at line 663 of file promote.cpp.

References CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::GetCompleteness(), CMolInfo_Base::IsSetCompleteness(), and CMolInfo_Base::SetCompleteness().

Referenced by CPromote::x_MakeMolinfoDesc().

USING_SCOPE()

USING_SCOPE

(

sequence

)

Variable Documentation

kBiomolMap

const TBiomolPair kBiomolMap[]

static

Initial value:

= {
    
    { CSeqFeatData::eSubtype_cdregion, CMolInfo::eBiomol_peptide },
    
    { CSeqFeatData::eSubtype_preRNA,   CMolInfo::eBiomol_pre_RNA },
    { CSeqFeatData::eSubtype_mRNA,     CMolInfo::eBiomol_mRNA },
    { CSeqFeatData::eSubtype_tRNA,     CMolInfo::eBiomol_tRNA },
    { CSeqFeatData::eSubtype_rRNA,     CMolInfo::eBiomol_rRNA },
    { CSeqFeatData::eSubtype_snRNA,    CMolInfo::eBiomol_snRNA },
    { CSeqFeatData::eSubtype_scRNA,    CMolInfo::eBiomol_scRNA },
    { CSeqFeatData::eSubtype_snoRNA,   CMolInfo::eBiomol_mRNA },
    { CSeqFeatData::eSubtype_otherRNA, CMolInfo::eBiomol_transcribed_RNA }
}

Definition at line 517 of file promote.cpp.