NCBI C++ ToolKit
feattable_edit.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objtools/edit/loc_edit.hpp>
#include <objtools/edit/feattable_edit.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <corelib/ncbi_message.hpp>
#include <objtools/edit/edit_error.hpp>
#include <objtools/logging/listener.hpp>
#include <objects/general/Dbtag.hpp>
#include <unordered_set>
#include <sstream>
+ Include dependency graph for feattable_edit.cpp:

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CRef< CSeq_locsProductFromString (const string str)
string sGetCdsProductName (const CSeq_feat &cds, CScope &scope)
static bool s_ShouldConvertToGeneral (const string &id)
static string s_GetTranscriptIdFromMrna (const CMappedFeat &mrna)
static bool s_IsGenbankId (const string &id)
static bool s_IsGeneralId (const string &id)
bool idAlpha (const CSeq_id_Handle &idh1, const CSeq_id_Handle idh2)
static void s_AppendProtRefInfo (CProt_ref &current_ref, const CProt_ref &other_ref)
static void s_SetProtRef (const CSeq_feat &cds, CConstRef< CSeq_feat > pMrna, CProt_ref &prot_ref)
static bool AssignLocalIdIfEmpty (CSeq_feat &feature, unsigned &id)
string sGetFeatMapKey (const CObject_id &objectId)
bool OjectIdsAreEqual (const CObject_id &lhs, const CObject_id &rhs)

Function Documentation

◆ AssignLocalIdIfEmpty()

static bool AssignLocalIdIfEmpty ( CSeq_feat feature,
unsigned &  id 

◆ idAlpha()

bool idAlpha ( const CSeq_id_Handle idh1,
const CSeq_id_Handle  idh2 

Definition at line 1328 of file feattable_edit.cpp.

References CSeq_id_Handle::AsString().

Referenced by CFeatTableEdit::GenerateLocusTags().

◆ OjectIdsAreEqual()

bool OjectIdsAreEqual ( const CObject_id lhs,
const CObject_id rhs 

◆ s_AppendProtRefInfo()

static void s_AppendProtRefInfo ( CProt_ref current_ref,
const CProt_ref other_ref 

◆ s_GetTranscriptIdFromMrna()

static string s_GetTranscriptIdFromMrna ( const CMappedFeat mrna)

◆ s_IsGenbankId()

static bool s_IsGenbankId ( const string id)

◆ s_IsGeneralId()

static bool s_IsGeneralId ( const string id)

◆ s_SetProtRef()

static void s_SetProtRef ( const CSeq_feat cds,
CConstRef< CSeq_feat pMrna,
CProt_ref prot_ref 

◆ s_ShouldConvertToGeneral()

static bool s_ShouldConvertToGeneral ( const string id)

Definition at line 491 of file feattable_edit.cpp.

References NStr::StartsWith().

Referenced by CFeatTableEdit::xConvertToGeneralIds().

◆ sGetCdsProductName()

string sGetCdsProductName ( const CSeq_feat cds,
CScope scope 

◆ sGetFeatMapKey()

string sGetFeatMapKey ( const CObject_id objectId)

◆ sProductFromString()

CRef<CSeq_loc> sProductFromString ( const string  str)
Modified on Thu Feb 29 12:22:28 2024 by rev. 669887