NCBI C++ ToolKit
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
CModifySeqId Class Reference

Search Toolkit Book for CModifySeqId

#include <gui/packages/pkg_sequence_edit/edit_seq_id.hpp>

+ Inheritance diagram for CModifySeqId:
+ Collaboration diagram for CModifySeqId:

Public Member Functions

 CModifySeqId ()
 
 CModifySeqId (objects::CSeq_entry_Handle seh, const string &name)
 
virtual ~CModifySeqId ()
 
virtual CRef< CCmdComposite > GetCommand (void)
 

Protected Member Functions

void x_ChangeId (objects::CSeq_id &id)
 
virtual void x_UpdateBioseq (CRef< CBioseq > new_seq)
 
void x_GetRemoveOriginalIdCommand (CRef< CCmdComposite > cmd)
 
void x_UpdateSeqAnnot (objects::CSeq_annot &annot)
 
void x_UpdateSeqAlign (objects::CSeq_align &align)
 
void x_UpdateLoc (objects::CSeq_loc &loc)
 
void x_UpdateFeat (objects::CSeq_feat &feat)
 
void x_UpdateVariation (objects::CVariation_ref &var)
 

Protected Attributes

objects::CSeq_entry_Handle m_TopSeqEntry
 
vector< pair< CConstRef< CSeq_id >, CRef< CSeq_id > > > m_old_to_new_id
 
string m_cmd_name
 
set< string > m_remove_ids
 

Detailed Description

CEditSeqId class declaration

Definition at line 82 of file edit_seq_id.hpp.

Constructor & Destructor Documentation

◆ CModifySeqId() [1/2]

CModifySeqId::CModifySeqId ( )
inline

Definition at line 85 of file edit_seq_id.hpp.

◆ CModifySeqId() [2/2]

CModifySeqId::CModifySeqId ( objects::CSeq_entry_Handle  seh,
const string &  name 
)
inline

Definition at line 86 of file edit_seq_id.hpp.

◆ ~CModifySeqId()

virtual CModifySeqId::~CModifySeqId ( )
inlinevirtual

Definition at line 87 of file edit_seq_id.hpp.

Member Function Documentation

◆ GetCommand()

CRef< CCmdComposite > CModifySeqId::GetCommand ( void  )
virtual

Reimplemented in CRemoveGeneralId, and CEditSeqId.

Definition at line 426 of file edit_seq_id.cpp.

References CSerialObject::Assign(), cmd, EDIT_EACH_SEQANNOT_ON_BIOSEQ, CSeq_entry_CI::fIncludeGivenEntry, CSeq_entry_CI::fRecursive, CBioseq_Handle::GetBioseqCore(), CSeq_ext_Base::GetDelta(), CBioseq_Base::GetInst(), CSeq_ext_Base::GetMap(), CSeq_hist_Base::GetReplaced_by(), CSeq_hist_Base::GetReplaces(), CSeq_ext_Base::GetSeg(), CSeq_entry_Handle::GetSeq(), CSeq_ext_Base::IsDelta(), CSeq_ext_Base::IsMap(), CSeq_ext_Base::IsRef(), CSeq_ext_Base::IsSeg(), CSeq_entry_Handle::IsSeq(), CDelta_ext_Base::IsSet(), CMap_ext_Base::IsSet(), CSeg_ext_Base::IsSet(), CSeq_hist_Base::IsSetAssembly(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetHist(), CSeq_hist_rec_Base::IsSetIds(), CBioseq_Base::IsSetInst(), CSeq_graph_Base::IsSetLoc(), CSeq_hist_Base::IsSetReplaced_by(), CSeq_hist_Base::IsSetReplaces(), m_cmd_name, m_TopSeqEntry, CDelta_ext_Base::Set(), CMap_ext_Base::Set(), CRef_ext_Base::Set(), CSeg_ext_Base::Set(), CSeq_hist_Base::SetAssembly(), CSeq_ext_Base::SetDelta(), CBioseq_Base::SetInst(), CSeq_graph_Base::SetLoc(), CSeq_ext_Base::SetMap(), CSeq_ext_Base::SetRef(), CSeq_hist_Base::SetReplaced_by(), CSeq_hist_Base::SetReplaces(), CSeq_ext_Base::SetSeg(), CSeq_entry_Base::SetSeq(), x_ChangeId(), x_UpdateBioseq(), x_UpdateFeat(), x_UpdateLoc(), x_UpdateSeqAlign(), and x_UpdateSeqAnnot().

Referenced by CSequenceEditingEventHandler::ConvertAccessionToLocalIdsAll(), CSequenceEditingEventHandler::ConvertAccessionToLocalIdsName(), CSequenceEditingEventHandler::ConvertAccessionToLocalIdsNuc(), CSequenceEditingEventHandler::ConvertAccessionToLocalIdsProt(), CSequenceEditingEventHandler::GeneralToLocalId(), CEditSeqId::GetCommand(), CRemoveGeneralId::GetCommand(), CSequenceEditingEventHandler::LocalToGeneralId(), CSequenceEditingEventHandler::RemoveGenbankSeqIdsFromAll(), CSequenceEditingEventHandler::RemoveGenbankSeqIdsFromProt(), CSequenceEditingEventHandler::RemoveGiSeqIdsFromAll(), CSequenceEditingEventHandler::RemoveLocalSeqIdsFromAll(), CSequenceEditingEventHandler::RemoveLocalSeqIdsFromNuc(), CSequenceEditingEventHandler::RemoveLocalSeqIdsFromProt(), and CSequenceEditingEventHandler::RemoveSeqIdNamesFromProtFeats().

◆ x_ChangeId()

void CModifySeqId::x_ChangeId ( objects::CSeq_id &  id)
protected

Definition at line 851 of file edit_seq_id.cpp.

References first(), i, and m_old_to_new_id.

Referenced by GetCommand(), x_UpdateBioseq(), x_UpdateFeat(), x_UpdateLoc(), x_UpdateSeqAlign(), and x_UpdateSeqAnnot().

◆ x_GetRemoveOriginalIdCommand()

void CModifySeqId::x_GetRemoveOriginalIdCommand ( CRef< CCmdComposite >  cmd)
protected

Definition at line 393 of file edit_seq_id.cpp.

References cmd, CSeqdesc_Base::e_User, set< Key, Compare >::end(), NStr::Equal(), NStr::EqualNocase(), set< Key, Compare >::find(), FOR_EACH_USERFIELD_ON_USEROBJECT, CUser_field_Base::GetData(), CUser_field_Base::GetLabel(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_field_Base::IsSetData(), CObject_id_Base::IsStr(), CUser_field_Base::C_Data::IsStr(), m_remove_ids, m_TopSeqEntry, and rapidjson::value.

Referenced by CRemoveSeqId::GetRemoveOriginalIdCommand(), and CEditSeqId::GetRemoveOriginalIdCommand().

◆ x_UpdateBioseq()

void CModifySeqId::x_UpdateBioseq ( CRef< CBioseq >  new_seq)
protectedvirtual

Reimplemented in CRemoveSeqId.

Definition at line 548 of file edit_seq_id.cpp.

References CBioseq_Base::IsSetId(), CBioseq_Base::SetId(), and x_ChangeId().

Referenced by GetCommand(), and CRemoveSeqId::x_UpdateBioseq().

◆ x_UpdateFeat()

void CModifySeqId::x_UpdateFeat ( objects::CSeq_feat &  feat)
protected

Definition at line 560 of file edit_seq_id.cpp.

References EDIT_EACH_CODEBREAK_ON_CDREGION, CSeqFeatData_Base::GetClone(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CSeqFeatData_Base::GetRna(), CSeq_feat_Base::GetSupport(), CRNA_ref_Base::C_Ext::GetTRNA(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsClone(), CSeqFeatData_Base::IsRna(), CClone_seq_set_Base::IsSet(), CTrna_ext_Base::IsSetAnticodon(), CClone_ref_Base::IsSetClone_seq(), CSeq_feat_Base::IsSetData(), CRNA_ref_Base::IsSetExt(), CSeqFeatSupport_Base::IsSetInference(), CSeq_feat_Base::IsSetLocation(), CSeqFeatSupport_Base::IsSetModel_evidence(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Base::IsSetSupport(), CRNA_ref_Base::C_Ext::IsTRNA(), CSeqFeatData_Base::IsVariation(), CClone_seq_set_Base::Set(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_feat_Base::SetSupport(), x_ChangeId(), x_UpdateLoc(), and x_UpdateVariation().

Referenced by GetCommand(), and x_UpdateSeqAnnot().

◆ x_UpdateLoc()

void CModifySeqId::x_UpdateLoc ( objects::CSeq_loc &  loc)
protected

Definition at line 840 of file edit_seq_id.cpp.

References CSeq_loc::Assign(), CSeq_loc::GetId(), CSeq_loc::SetId(), and x_ChangeId().

Referenced by GetCommand(), x_UpdateFeat(), x_UpdateSeqAlign(), x_UpdateSeqAnnot(), and x_UpdateVariation().

◆ x_UpdateSeqAlign()

void CModifySeqId::x_UpdateSeqAlign ( objects::CSeq_align &  align)
protected

Definition at line 795 of file edit_seq_id.cpp.

References EDIT_EACH_DENDIAG_ON_SEQALIGN, EDIT_EACH_RECURSIVE_SEQALIGN_ON_SEQALIGN, EDIT_EACH_SEQID_ON_DENDIAG, EDIT_EACH_SEQID_ON_DENSEG, EDIT_EACH_STDSEG_ON_SEQALIGN, CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_align_Base::IsSetSegs(), CSeq_align_Base::C_Segs::IsStd(), CSeq_align_Base::SetSegs(), x_ChangeId(), and x_UpdateLoc().

Referenced by GetCommand(), and x_UpdateSeqAnnot().

◆ x_UpdateSeqAnnot()

void CModifySeqId::x_UpdateSeqAnnot ( objects::CSeq_annot &  annot)
protected

Definition at line 701 of file edit_seq_id.cpp.

References EDIT_EACH_ANNOTDESC_ON_SEQANNOT, EDIT_EACH_SEQALIGN_ON_SEQANNOT, EDIT_EACH_SEQFEAT_ON_SEQANNOT, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetSeq_table(), CSeq_annot_Base::C_Data::IsGraph(), CSeq_annot_Base::C_Data::IsIds(), CSeq_annot_Base::C_Data::IsLocs(), CSeq_annot_Base::C_Data::IsSeq_table(), CSeq_table_Base::IsSetColumns(), CSeq_annot_Base::IsSetData(), CSeq_annot_Base::SetData(), x_ChangeId(), x_UpdateFeat(), x_UpdateLoc(), and x_UpdateSeqAlign().

Referenced by GetCommand().

◆ x_UpdateVariation()

void CModifySeqId::x_UpdateVariation ( objects::CVariation_ref &  var)
protected

Definition at line 670 of file edit_seq_id.cpp.

References CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_ref_Base::C_Data::GetSet(), CVariation_ref_Base::C_Data::IsInstance(), CVariation_ref_Base::C_Data::IsSet(), CVariation_ref_Base::IsSetConsequence(), CVariation_ref_Base::IsSetData(), CVariation_inst_Base::IsSetDelta(), CVariation_ref_Base::C_Data::C_Set::IsSetVariations(), CVariation_ref_Base::SetConsequence(), CVariation_ref_Base::SetData(), and x_UpdateLoc().

Referenced by x_UpdateFeat().

Member Data Documentation

◆ m_cmd_name

string CModifySeqId::m_cmd_name
protected

Definition at line 102 of file edit_seq_id.hpp.

Referenced by GetCommand().

◆ m_old_to_new_id

vector<pair<CConstRef<CSeq_id>, CRef<CSeq_id> > > CModifySeqId::m_old_to_new_id
protected

Definition at line 101 of file edit_seq_id.hpp.

Referenced by CGeneralToLocalId::CGeneralToLocalId(), CLocalToGeneralId::CLocalToGeneralId(), CRemoveSeqId::CRemoveSeqId(), x_ChangeId(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), CRemoveName::x_GetReplacementIds(), CAccessionToLocalId::x_GetReplacementIds(), and CRemoveSeqId::x_UpdateBioseq().

◆ m_remove_ids

set<string> CModifySeqId::m_remove_ids
protected

Definition at line 103 of file edit_seq_id.hpp.

Referenced by CRemoveSeqId::CRemoveSeqId(), CRemoveSeqId::GetRemoveOriginalIdCommand(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), and x_GetRemoveOriginalIdCommand().

◆ m_TopSeqEntry

objects::CSeq_entry_Handle CModifySeqId::m_TopSeqEntry
protected

Definition at line 100 of file edit_seq_id.hpp.

Referenced by CAccessionToLocalId::CAccessionToLocalId(), CGeneralToLocalId::CGeneralToLocalId(), CLocalToGeneralId::CLocalToGeneralId(), CRemoveName::CRemoveName(), CRemoveSeqId::CRemoveSeqId(), GetCommand(), CEditSeqId::x_CollectChangedIds(), CRemoveGeneralId::x_CollectChangedIds(), and x_GetRemoveOriginalIdCommand().

The documentation for this class was generated from the following files:
Generated by doxygen 1.9.0
Modified on Thu May 02 14:31:43 2024 by modify_doxy.py rev. 669887