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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__dataspec__NCBI__Protein.html below:

Code generated by DATATOOL from 'seqfeat.asn' (module 'NCBI-Protein')

class   CProt_ref_Base   *** Prot-ref *********************************************** * * Reference to a protein name * More...
  enum   CProt_ref_Base::EProcessed {
  CProt_ref_Base::eProcessed_not_set = 0 , CProt_ref_Base::eProcessed_preprotein = 1 , CProt_ref_Base::eProcessed_mature = 2 , CProt_ref_Base::eProcessed_signal_peptide = 3 ,
  CProt_ref_Base::eProcessed_transit_peptide = 4 , CProt_ref_Base::eProcessed_propeptide = 5
}   processing status More...
  enum class   CProt_ref_Base::E_memberIndex {
  CProt_ref_Base::e__allMandatory = 0 , CProt_ref_Base::e_name , CProt_ref_Base::e_desc , CProt_ref_Base::e_ec ,
  CProt_ref_Base::e_activity , CProt_ref_Base::e_db , CProt_ref_Base::e_processed
}   ◆ TActivity ◆ TDb ◆ TDesc ◆ TEc ◆ TmemberIndex ◆ TName ◆ Tparent ◆ TProcessed ◆ E_memberIndex Enumerator e__allMandatory  e_name  e_desc  e_ec  e_activity  e_db  e_processed 

Definition at line 116 of file Prot_ref_.hpp.

◆ EProcessed

processing status

Enumerator eProcessed_not_set  eProcessed_preprotein  eProcessed_mature  eProcessed_signal_peptide  eProcessed_transit_peptide  eProcessed_propeptide 

Definition at line 95 of file Prot_ref_.hpp.

◆ CanGetActivity() bool CProt_ref_Base::CanGetActivity ( void  ) const inline

Check if it is safe to call GetActivity method.

Returns

Definition at line 469 of file Prot_ref_.hpp.

◆ CanGetDb() bool CProt_ref_Base::CanGetDb ( void  ) const inline

Check if it is safe to call GetDb method.

Returns

Definition at line 494 of file Prot_ref_.hpp.

◆ CanGetDesc() bool CProt_ref_Base::CanGetDesc ( void  ) const inline ◆ CanGetEc() bool CProt_ref_Base::CanGetEc ( void  ) const inline

Check if it is safe to call GetEc method.

Returns

Definition at line 444 of file Prot_ref_.hpp.

◆ CanGetName() bool CProt_ref_Base::CanGetName ( void  ) const inline

Check if it is safe to call GetName method.

Returns

Definition at line 372 of file Prot_ref_.hpp.

Referenced by GetProduct().

◆ CanGetProcessed() bool CProt_ref_Base::CanGetProcessed ( void  ) const inline

Check if it is safe to call GetProcessed method.

Returns

Definition at line 519 of file Prot_ref_.hpp.

◆ CProt_ref_Base() [1/2] ◆ CProt_ref_Base() [2/2] ◆ DECLARE_INTERNAL_TYPE_INFO() CProt_ref_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ EProcessed()

Access to EProcessed's attributes (values, names) as defined in spec.

◆ GetActivity() ◆ GetDb() ◆ GetDesc()

Get the Desc member data.

Returns
Reference to the member data.

Definition at line 403 of file Prot_ref_.hpp.

References CProt_ref_Base::CanGetDesc(), CProt_ref_Base::m_Desc, and CSerialObject::ThrowUnassigned().

Referenced by CDescriptionColumn::AddToFeature(), CConvertCDSToProt::Convert(), CCdsToMatPeptide::ConvertInner(), CEntrezgene::GetDescription(), CDescriptionColumn::GetFromFeat(), CProt_ref::GetLabel(), CEditingActionFeatDesc::GetValue(), CNewCleanup_imp::PostProtFeatfBC(), CNewCleanup_imp::ProtrefBC(), CNewCleanup_imp::ProtRefEC(), CFindASN1Dlg::ReplaceInFeature(), s_AppendProtRefInfo(), CFeatureItem::x_AddFTableProtQuals(), CGeneFeatFromOtherFeatDlg::x_AddGeneQuals(), CFeatureItem::x_AddQualProtDesc(), CFeatureItem::x_AddQualsProt(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

◆ GetEc() ◆ GetName()

Get the Name member data.

Returns
Reference to the member data.

Definition at line 378 of file Prot_ref_.hpp.

References CProt_ref_Base::m_Name.

Referenced by CProductColumn::AddToFeature(), CProtRefColumn::AddToFeature(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), ConvertProteinToImp(), CTruncateCDS::GetCommand(), CEntrezgene::GetDescription(), CProductColumn::GetFromFeat(), CProtRefColumn::GetFromFeat(), CProt_ref::GetLabel(), GetProduct(), LookForProductName(), s_AppendProtRefInfo(), s_NotPeptideException(), s_RemoveTaxnameFromProtRef(), s_TitleFromSegment(), CCleanup::SetProteinName(), CMacroFunction_SwapRelFeatQual::TheFunction(), CMacroFunction_SetRelFeatQual::TheFunction(), CMacroFunction_ConvertFeatQual::TheFunction(), CMacroFunction_ParseFeatQual::TheFunction(), CMacroFunction_CopyFeatQual::TheFunction(), CMacroFunction_RemoveOutside::TheFunction(), CMacroFunction_RmvOutsideRelFeatQual::TheFunction(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), UpdatemRNAProduct(), CValidError_bioseq::ValidateRawConst(), CFeatureItem::x_AddFTableProtQuals(), CGeneFeatFromOtherFeatDlg::x_AddGeneQuals(), CFastaOstreamEx::x_AddProteinNameAttribute(), CFeatureItem::x_AddQualCdsProduct(), CFeatureItem::x_AddQualsProt(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), CAutoDefFeatureClause::x_GetProductName(), CProtValidator::x_ReportUninformativeNames(), CEditObjectSeq_feat::x_UpdatemRNA(), CGff2Writer::xAssignFeatureAttributeProduct(), CFeatTableEdit::xGenerate_mRNA_Product(), CFeatureTableReader::xTranslateProtein(), and CGff3Writer::xWriteProteinFeature().

◆ GetProcessed()

Get the Processed member data.

Returns
Copy of the member data.

Definition at line 538 of file Prot_ref_.hpp.

References CProt_ref_Base::m_Processed.

Referenced by BOOST_AUTO_TEST_CASE(), ConvertProteinToImp(), CValidErrorFormat::GetFeatureContentLabel(), GetProteinWeight(), CCleanup::MoveFeatToProtein(), CNewCleanup_imp::ResynchPeptidePartials(), s_AppendProtRefInfo(), s_FindKeyFromFeatDefType(), s_GetBestProtFeature(), s_IsPreprotein(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_feat::ValidateSeqFeatContext(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CFeatureItem::x_AddQualProtNote(), CFeatureItem::x_AddQualsProt(), CDeflineGenerator::x_GetLongestProtein(), and CBioseqIndex::x_InitFeats().

◆ IsSetActivity() bool CProt_ref_Base::IsSetActivity ( void  ) const inline ◆ IsSetDb() bool CProt_ref_Base::IsSetDb ( void  ) const inline ◆ IsSetDesc() bool CProt_ref_Base::IsSetDesc ( void  ) const inline

description (instead of name) Check if a value has been assigned to Desc data member.

Data member Desc is optional; its type is defined as 'typedef string TDesc'

Returns

Definition at line 391 of file Prot_ref_.hpp.

References CProt_ref_Base::m_set_State.

Referenced by CDescriptionColumn::AddToFeature(), CProt_ref_Base::CanGetDesc(), CConvertCDSToProt::Convert(), CCdsToMatPeptide::ConvertInner(), CDescriptionColumn::GetFromFeat(), CProt_ref::GetLabel(), CEditingActionFeatDesc::GetValue(), CEditingActionFeatDesc::IsSetValue(), CNewCleanup_imp::PostProtFeatfBC(), CNewCleanup_imp::ProtrefBC(), CNewCleanup_imp::ProtRefEC(), CFindASN1Dlg::ReplaceInFeature(), s_AppendProtRefInfo(), CProt_ref_Base::SetDesc(), CFeatureItem::x_AddFTableProtQuals(), CGeneFeatFromOtherFeatDlg::x_AddGeneQuals(), CFeatureItem::x_AddQualProtDesc(), CFeatureItem::x_AddQualsProt(), CAutogeneratedCleanup::x_BasicCleanupProtRef(), CDeflineGenerator::x_SetTitleFromProtein(), and CDeflineGenerator::x_SetTitleFromProteinIdx().

◆ IsSetEc() bool CProt_ref_Base::IsSetEc ( void  ) const inline

E.C.

number(s) Check if a value has been assigned to Ec data member.

Data member Ec is optional; its type is defined as 'typedef list< string > TEc'

Returns

Definition at line 438 of file Prot_ref_.hpp.

References CProt_ref_Base::m_set_State.

Referenced by CProtRefColumn::AddToFeature(), CProt_ref::AutoFixEC(), CProtRefColumn::GetFromFeat(), CUpdateECNumbers::operator()(), CNewCleanup_imp::ProtRefEC(), CProt_ref::RemoveBadEC(), CFindASN1Dlg::ReplaceInFeature(), s_AppendProtRefInfo(), CFeatureItem::x_AddQualProtEcNumber(), CFeatureItem::x_AddQualsProt(), CAutogeneratedCleanup::x_BasicCleanupProtRef(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), CProtValidator::x_ValidateECNumbers(), and CCdregionValidator::x_ValidateFeatComment().

◆ IsSetName() bool CProt_ref_Base::IsSetName ( void  ) const inline

protein name Check if a value has been assigned to Name data member.

Data member Name is optional; its type is defined as 'typedef list< string > TName'

Returns

Definition at line 366 of file Prot_ref_.hpp.

References CProt_ref_Base::m_set_State.

Referenced by CProductColumn::AddToFeature(), CProtRefColumn::AddToFeature(), CFixProductNames::apply(), CProductColumn::ClearInFeature(), ConvertProteinToImp(), CTruncateCDS::GetCommand(), CProductColumn::GetFromFeat(), CProtRefColumn::GetFromFeat(), CProt_ref::GetLabel(), LookForProductName(), CCleanup::MoveFeatToProtein(), CSuspectProductRulesEditor::OnApplyFixes(), CSuspectProductRulesEditor::OnListMatches(), CNewCleanup_imp::ProtrefBC(), CFindASN1Dlg::ReplaceInFeature(), RescueProtProductQual(), s_AppendProtRefInfo(), s_NotPeptideException(), s_RemoveTaxnameFromProtRef(), s_SetProtRef(), s_TitleFromSegment(), CCleanup::SetProteinName(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), UpdatemRNAProduct(), CGeneFeatFromOtherFeatDlg::x_AddGeneQuals(), CFastaOstreamEx::x_AddProteinNameAttribute(), CFeatureItem::x_AddQualsProt(), CAutogeneratedCleanup::x_BasicCleanupProtRef(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CValidErrorFormat::x_FormatECNumberForSubmitterReport(), CAutoDefFeatureClause::x_GetProductName(), CEditObjectSeq_feat::x_UpdatemRNA(), CGff2Writer::xAssignFeatureAttributeProduct(), CFeatTableEdit::xGenerate_mRNA_Product(), CFeatureTableReader::xTranslateProtein(), and CGff3Writer::xWriteProteinFeature().

◆ IsSetProcessed() bool CProt_ref_Base::IsSetProcessed ( void  ) const inline

Check if a value has been assigned to Processed data member.

Data member Processed is optional with default eProcessed_not_set; its type is defined as 'typedef EProcessed TProcessed'

Returns

Definition at line 513 of file Prot_ref_.hpp.

References CProt_ref_Base::m_set_State.

Referenced by BOOST_AUTO_TEST_CASE(), ConvertProteinToImp(), CValidErrorFormat::GetFeatureContentLabel(), CCleanup::MoveFeatToProtein(), CNewCleanup_imp::ResynchPeptidePartials(), s_FindKeyFromFeatDefType(), s_IsPreprotein(), CProt_ref_Base::SetProcessed(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_feat::ValidateSeqFeatContext(), CFeatureTableReader_Imp::x_AddQualifierToFeature(), CSequenceUpdater::x_AdjustProteinFeature(), CDeflineGenerator::x_GetLongestProtein(), and CBioseqIndex::x_InitFeats().

◆ operator=() ◆ Reset() void CProt_ref_Base::Reset ( void  ) virtual ◆ ResetActivity() void CProt_ref_Base::ResetActivity ( void  ) ◆ ResetDb() void CProt_ref_Base::ResetDb ( void  ) ◆ ResetDesc() void CProt_ref_Base::ResetDesc ( void  ) ◆ ResetEc() void CProt_ref_Base::ResetEc ( void  ) ◆ ResetName() ◆ ResetProcessed() void CProt_ref_Base::ResetProcessed ( void  ) inline ◆ SetActivity() ◆ SetDb() ◆ SetDefaultProcessed() void CProt_ref_Base::SetDefaultProcessed ( void  ) inline ◆ SetDesc() [1/3] void CProt_ref_Base::SetDesc ( const TDesc &  value ) inline ◆ SetDesc() [2/3] ◆ SetDesc() [3/3] ◆ SetEc() ◆ SetName()

Assign a value to Name data member.

Returns
Reference to the data value.

Definition at line 384 of file Prot_ref_.hpp.

References CProt_ref_Base::m_Name, and CProt_ref_Base::m_set_State.

Referenced by GetProtRefAnnot(), CNewCleanup_imp::ImpFeatBC(), LookForProductName(), CNewCleanup_imp::ProtrefBC(), s_AppendProtRefInfo(), s_ProcessCdsQuals(), s_SetProtRef(), CCleanup::SetProteinName(), CFeatureTableReader_Imp::x_AddQualifierToCdregion(), CAutogeneratedCleanup::x_BasicCleanupProtRef(), CFeatTableEdit::xGenerate_mRNA_Product(), and CFeatureTableReader::xTranslateProtein().

◆ SetProcessed() [1/2] ◆ SetProcessed() [2/2] ◆ ~CProt_ref_Base() CProt_ref_Base::~CProt_ref_Base ( void  ) virtual

Definition at line 127 of file Prot_ref_.cpp.

◆ m_Activity list< string > CProt_ref_Base::m_Activity private ◆ m_Db ◆ m_Desc ◆ m_Ec list< string > CProt_ref_Base::m_Ec private ◆ m_Name list< string > CProt_ref_Base::m_Name private ◆ m_Processed ◆ m_set_State Uint4 CProt_ref_Base::m_set_State[1] private

Definition at line 347 of file Prot_ref_.hpp.

Referenced by CProt_ref_Base::CProt_ref_Base(), CProt_ref_Base::IsSetActivity(), CProt_ref_Base::IsSetDb(), CProt_ref_Base::IsSetDesc(), CProt_ref_Base::IsSetEc(), CProt_ref_Base::IsSetName(), CProt_ref_Base::IsSetProcessed(), CProt_ref_Base::ResetActivity(), CProt_ref_Base::ResetDb(), CProt_ref_Base::ResetDesc(), CProt_ref_Base::ResetEc(), CProt_ref_Base::ResetName(), CProt_ref_Base::ResetProcessed(), CProt_ref_Base::SetActivity(), CProt_ref_Base::SetDb(), CProt_ref_Base::SetDesc(), CProt_ref_Base::SetEc(), CProt_ref_Base::SetName(), and CProt_ref_Base::SetProcessed().

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