NCBI C++ ToolKit
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#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>
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Functions | |
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) |
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().
void FixFeatureIdsForUpdates | ( | CSeq_feat & | feat, |
CObject_id::TId & | next_id | ||
) |
Definition at line 673 of file gap_trim.cpp.
References CSeq_feat_Base::GetId(), CFeat_id_Base::GetLocal(), CObject_id_Base::IsId(), CFeat_id_Base::IsLocal(), CSeq_feat_Base::IsSetId(), and CSeq_feat_Base::SetId().
Referenced by FixFeatureIdsForUpdates().
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.
TGappedFeatList ListGappedFeatures | ( | CFeat_CI & | feat_it, |
CScope & | scope | ||
) |
Definition at line 625 of file gap_trim.cpp.
References CSeq_feat_Handle::GetData(), and CSeqFeatData_Base::IsProt().
Referenced by BOOST_AUTO_TEST_CASE(), CAdjustFeaturesForGaps::GetGappedFeatures(), MakeTrnaWithAnticodon(), TestTrimForFrame(), TryMiscWithNs(), TryOneCase(), TryOneCaseMixLoc(), and TryOneCDSCase().
void ProcessForTrimAndSplitUpdates | ( | CSeq_feat_Handle | cds, |
vector< CRef< CSeq_feat > > | updates | ||
) |
Definition at line 641 of file gap_trim.cpp.
References CSeq_annot_EditHandle::AddFeat(), CFeatGapInfo::AdjustProteinSeq(), CBioseq_set_EditHandle::AttachBioseq(), CSeq_feat_Handle::GetAnnot(), CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_annot_Handle::GetEditHandle(), CBioseq_Handle::GetParentBioseq_set(), CSeq_feat_Handle::GetProduct(), CSeq_feat_Handle::GetScope(), CSeq_feat_Handle::GetSeq_feat(), i, ITERATE, CBioseq_EditHandle::Remove(), CSeq_feat_EditHandle::Remove(), and CSeq_feat_EditHandle::Replace().
Referenced by TestUpdateCDS().
void s_FixPartial | ( | CSeq_feat & | feat | ) |
Definition at line 480 of file gap_trim.cpp.
References eExtreme_Biological, CSeq_feat_Base::GetLocation(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), and CSeq_feat_Base::SetPartial().
Referenced by CFeatGapInfo::AdjustForRelevantGapIntervals().
bool s_IsRelated | ( | const CSeq_feat & | f1, |
CObject_id::TId | search | ||
) |
Definition at line 692 of file gap_trim.cpp.
References CSeq_feat_Base::GetXref(), CSeq_feat_Base::IsSetXref(), and ITERATE.
Referenced by CFeatGapInfo::IsRelatedByCrossRef(), and s_IsRelated().
Definition at line 708 of file gap_trim.cpp.
References CObject_id_Base::GetId(), CSeq_feat_Base::GetId(), CFeat_id_Base::GetLocal(), CObject_id_Base::IsId(), CFeat_id_Base::IsLocal(), CSeq_feat_Base::IsSetId(), and s_IsRelated().
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().