NCBI C++ ToolKit
gap_trim.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <objtools/edit/gap_trim.hpp>
#include <objtools/edit/loc_edit.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/seq_map.hpp>
#include <objmgr/seq_map_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
+ Include dependency graph for gap_trim.cpp:

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void s_FixPartial (CSeq_feat &feat)
TGappedFeatList ListGappedFeatures (CFeat_CI &feat_it, CScope &scope)
void ProcessForTrimAndSplitUpdates (CSeq_feat_Handle cds, vector< CRef< CSeq_feat > > updates)
void FixFeatureIdsForUpdates (CSeq_feat &feat, CObject_id::TId &next_id)
void FixFeatureIdsForUpdates (vector< CRef< CSeq_feat > > updates, CObject_id::TId &next_id)
bool s_IsRelated (const CSeq_feat &f1, CObject_id::TId search)
bool s_IsRelated (const CSeq_feat &f1, const CSeq_feat &f2)
void s_ReplaceFeatureIdXref (CSeq_feat &f, CObject_id::TId orig_id, CObject_id::TId new_id)
void FixFeatureIdsForUpdatePair (vector< CRef< CSeq_feat > > &updates1, vector< CRef< CSeq_feat > > &updates2)

Function Documentation

◆ FixFeatureIdsForUpdatePair()

void FixFeatureIdsForUpdatePair ( vector< CRef< CSeq_feat > > &  updates1,
vector< CRef< CSeq_feat > > &  updates2 

Definition at line 743 of file gap_trim.cpp.

References s_ReplaceFeatureIdXref().

Referenced by CAdjustFeaturesForGaps::x_DoGroup().

◆ FixFeatureIdsForUpdates() [1/2]

void FixFeatureIdsForUpdates ( CSeq_feat feat,
CObject_id::TId next_id 

◆ FixFeatureIdsForUpdates() [2/2]

void FixFeatureIdsForUpdates ( vector< CRef< CSeq_feat > >  updates,
CObject_id::TId next_id 

Definition at line 684 of file gap_trim.cpp.

References FixFeatureIdsForUpdates(), and i.

◆ ListGappedFeatures()

TGappedFeatList ListGappedFeatures ( CFeat_CI feat_it,
CScope scope 

◆ ProcessForTrimAndSplitUpdates()

void ProcessForTrimAndSplitUpdates ( CSeq_feat_Handle  cds,
vector< CRef< CSeq_feat > >  updates 

◆ s_FixPartial()

void s_FixPartial ( CSeq_feat feat)

◆ s_IsRelated() [1/2]

bool s_IsRelated ( const CSeq_feat f1,
CObject_id::TId  search 

◆ s_IsRelated() [2/2]

bool s_IsRelated ( const CSeq_feat f1,
const CSeq_feat f2 

◆ s_ReplaceFeatureIdXref()

void s_ReplaceFeatureIdXref ( CSeq_feat f,
CObject_id::TId  orig_id,
CObject_id::TId  new_id 

Definition at line 729 of file gap_trim.cpp.

References f(), and NON_CONST_ITERATE.

Referenced by FixFeatureIdsForUpdatePair().

Modified on Thu Jul 18 16:04:29 2024 by rev. 669887