dup_feats.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <corelib/ncbidiag.hpp>
#include <serial/objectinfo.hpp>
#include <serial/serialbase.hpp>
#include <objmgr/scope.hpp>
#include <map>

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Functions
void	GetProductToCDSMap (CScope &scope, map< CBioseq_Handle, set< CSeq_feat_Handle > > &product_to_cds)
set< CSeq_feat_Handle >	GetDuplicateFeaturesForRemoval (CSeq_entry_Handle seh)
set< CBioseq_Handle >	ListOrphanProteins (CSeq_entry_Handle seh, bool force_refseq=false)
bool	AllowOrphanedProtein (const CBioseq &seq, bool force_refseq=false)

Function Documentation

AllowOrphanedProtein()

bool AllowOrphanedProtein	(	const CBioseq &	seq,
		bool	force_refseq = false
	)

Definition at line 82 of file dup_feats.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CTextseq_id_Base::GetAccession(), CBioseq_Base::GetId(), CSeq_id::GetTextseq_Id(), CTextseq_id_Base::IsSetAccession(), CBioseq_Base::IsSetId(), NStr::StartsWith(), and CSeq_id_Base::Which().

Referenced by ListOrphanProteins(), and CValidError_bioseq::ValidateBioseqContext().

GetDuplicateFeaturesForRemoval()

set< CSeq_feat_Handle > GetDuplicateFeaturesForRemoval

(

CSeq_entry_Handle

seh

)

Definition at line 62 of file dup_feats.cpp.

References eDuplicate_Duplicate, eDuplicate_DuplicateDifferentTable, set< Key, Compare >::end(), set< Key, Compare >::find(), GetProductToCDSMap(), CSeq_entry_Handle::GetScope(), set< Key, Compare >::insert(), and IsDuplicate().

Referenced by BOOST_AUTO_TEST_CASE(), and CCleanupApp::x_RemoveDuplicateFeatures().

GetProductToCDSMap()

void GetProductToCDSMap	(	CScope &	scope,
		map< CBioseq_Handle, set< CSeq_feat_Handle > > &	product_to_cds
	)

Definition at line 146 of file util_cmds.cpp.

References CScope::eAllTSEs, CSeqFeatData::eSubtype_cdregion, CScope::GetAllTSEs(), CScope::GetBioseqHandle(), CSeq_feat_Handle::GetProductId(), and CSeq_id_Handle::GetSeqId().

Referenced by GetDeleteAllFeaturesCommand().

ListOrphanProteins()

set< CBioseq_Handle > ListOrphanProteins	(	CSeq_entry_Handle	seh,
		bool	force_refseq = false
	)

Definition at line 142 of file dup_feats.cpp.

References AllowOrphanedProtein(), CSeq_inst_Base::eMol_aa, set< Key, Compare >::end(), CSeqFeatData::eSubtype_cdregion, set< Key, Compare >::find(), CBioseq_Handle::GetBioseqCore(), CScope::GetBioseqHandle(), CBioseq_Handle::GetScope(), set< Key, Compare >::insert(), and CBioseq_Handle::IsProtein().

Referenced by BOOST_AUTO_TEST_CASE(), and CCleanupApp::x_RemoveDuplicateFeatures().