NCBI C++ ToolKit
Functions | Variables
editing_action_features.cpp File Reference
#include <ncbi_pch.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <util/sequtil/sequtil_convert.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_annot_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/object_manager.hpp>
#include <gui/widgets/edit/bioseq_editor.hpp>
#include <objtools/edit/string_constraint.hpp>
#include <gui/objutils/cmd_create_feat.hpp>
#include <gui/objutils/cmd_change_seq_feat.hpp>
#include <objects/seqfeat/seqfeat_macros.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/impl/synonyms.hpp>
#include <gui/packages/pkg_sequence_edit/editing_actions.hpp>
#include <gui/packages/pkg_sequence_edit/editing_action_features.hpp>
#include <gui/packages/pkg_sequence_edit/editing_action_constraint.hpp>
+ Include dependency graph for editing_action_features.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (objects)
 
static bool s_IsATGC (char ch)
 
static const string s_GetExpansion (const string &ch)
 
static vector< stringParseDegenerateCodons (string codon)
 
IEditingActionFeatCreateActionFeat (CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)
 
IEditingActionFeatCreateActionRna (CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
 
IEditingActionFeatCreateActionCdsGeneProt (CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)
 

Variables

static const string kAmbiguities = "MRSVWYHKDBN"
 
static const string kReplacements []
 

Function Documentation

◆ CreateActionCdsGeneProt()

IEditingActionFeat* CreateActionCdsGeneProt ( CSeq_entry_Handle  seh,
string  field,
const CSeqFeatData::ESubtype  subtype,
const string ncRNA_class 
)

Definition at line 4074 of file editing_action_features.cpp.

References CSeqFeatData::GetTypeFromSubtype(), NULL, and NStr::ToLower().

Referenced by CreateAction().

◆ CreateActionFeat()

IEditingActionFeat* CreateActionFeat ( CSeq_entry_Handle  seh,
string  field,
const CSeqFeatData::ESubtype  subtype,
const CSeqFeatData::E_Choice  feat_type,
const string ncRNA_class 
)

Definition at line 3907 of file editing_action_features.cpp.

References NULL, and NStr::ToLower().

Referenced by CreateAction(), and CreateActionRna().

◆ CreateActionRna()

IEditingActionFeat* CreateActionRna ( CSeq_entry_Handle  seh,
string  field,
const CSeqFeatData::ESubtype  subtype,
const string ncRNA_class 
)

Definition at line 4053 of file editing_action_features.cpp.

References CreateActionFeat(), CSeqFeatData_Base::e_Rna, and NStr::ToLower().

Referenced by CreateAction().

◆ ParseDegenerateCodons()

static vector<string> ParseDegenerateCodons ( string  codon)
static

◆ s_GetExpansion()

static const string s_GetExpansion ( const string ch)
static

Definition at line 1695 of file editing_action_features.cpp.

References NStr::Find(), kAmbiguities, and kReplacements.

Referenced by ParseDegenerateCodons().

◆ s_IsATGC()

static bool s_IsATGC ( char  ch)
static

Definition at line 1681 of file editing_action_features.cpp.

Referenced by ParseDegenerateCodons().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ kAmbiguities

const string kAmbiguities = "MRSVWYHKDBN"
static

Definition at line 1691 of file editing_action_features.cpp.

Referenced by s_GetExpansion().

◆ kReplacements

const string kReplacements[]
static
Initial value:
= {
"AC", "AG", "CG", "ACG", "AT", "CT", "ACT", "GT", "AGT", "CGT", "ACGT" }

Definition at line 1692 of file editing_action_features.cpp.

Referenced by s_GetExpansion().

Modified on Fri Apr 12 17:20:52 2024 by modify_doxy.py rev. 669887