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CSeq_feat_Handle Class Reference

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CSeq_feat_Handle –. More...

#include <objmgr/seq_feat_handle.hpp>

+ Inheritance diagram for CSeq_feat_Handle:
+ Collaboration diagram for CSeq_feat_Handle:

Public Types

typedef CRange< TSeqPosTRange
 
typedef SSNP_Info::TSNPId TSNPId
 
typedef SSNP_Info::TWeight TWeight
 

Public Member Functions

 CSeq_feat_Handle (void)
 
 ~CSeq_feat_Handle (void)
 
void Reset (void)
 
 DECLARE_OPERATOR_BOOL (m_Seq_annot &&!IsRemoved())
 
bool operator== (const CSeq_feat_Handle &feat) const
 
bool operator!= (const CSeq_feat_Handle &feat) const
 
bool operator< (const CSeq_feat_Handle &feat) const
 
CScopeGetScope (void) const
 Get scope this handle belongs to. More...
 
const CSeq_annot_HandleGetAnnot (void) const
 Get handle to seq-annot for this feature. More...
 
CConstRef< CSeq_featGetPlainSeq_feat (void) const
 Get current seq-feat. More...
 
CConstRef< CSeq_featGetOriginalSeq_feat (void) const
 
virtual CConstRef< CSeq_featGetSeq_feat (void) const
 
bool IsPlainFeat (void) const
 Check if this is plain feature. More...
 
bool IsTableFeat (void) const
 Check if this is non-SNP table feature. More...
 
bool IsSortedTableFeat (void) const
 Check if this is a simple feature from sorted Seq-table. More...
 
bool IsTableSNP (void) const
 Check if this is SNP table feature. More...
 
virtual TRange GetRange (void) const
 Get range for current seq-feat. More...
 
virtual CSeq_id_Handle GetLocationId (void) const
 
TRange GetLocationTotalRange (void) const
 
virtual CSeq_id_Handle GetProductId (void) const
 
virtual TRange GetProductTotalRange (void) const
 
bool IsSetId (void) const
 
const CFeat_idGetId (void) const
 
bool IsSetData (void) const
 
const CSeqFeatDataGetData (void) const
 
virtual bool IsSetPartial (void) const
 
virtual bool GetPartial (void) const
 
bool IsSetExcept (void) const
 
bool GetExcept (void) const
 
bool IsSetComment (void) const
 
const stringGetComment (void) const
 
bool IsSetProduct (void) const
 
virtual const CSeq_locGetProduct (void) const
 
virtual const CSeq_locGetLocation (void) const
 
bool IsSetQual (void) const
 
const CSeq_feat::TQualGetQual (void) const
 
bool IsSetTitle (void) const
 
const stringGetTitle (void) const
 
bool IsSetExt (void) const
 
const CUser_objectGetExt (void) const
 
bool IsSetCit (void) const
 
const CPub_setGetCit (void) const
 
bool IsSetExp_ev (void) const
 
CSeq_feat::EExp_ev GetExp_ev (void) const
 
bool IsSetXref (void) const
 
const CSeq_feat::TXrefGetXref (void) const
 
bool IsSetDbxref (void) const
 
const CSeq_feat::TDbxrefGetDbxref (void) const
 
bool IsSetPseudo (void) const
 
bool GetPseudo (void) const
 
bool IsSetExcept_text (void) const
 
const stringGetExcept_text (void) const
 
bool IsSetIds (void) const
 
const CSeq_feat::TIdsGetIds (void) const
 
bool IsSetExts (void) const
 
const CSeq_feat::TExtsGetExts (void) const
 
CSeqFeatData::E_Choice GetFeatType (void) const
 
CSeqFeatData::ESubtype GetFeatSubtype (void) const
 
TSNPId GetSNPId (void) const
 
const CSeq_idGetSNPSeq_id (void) const
 
CSeq_id::TGi GetSNPGi (void) const
 
bool IsSNPMinusStrand (void) const
 
TWeight GetSNPWeight (void) const
 
size_t GetSNPAllelesCount (void) const
 
const stringGetSNPAllele (size_t index) const
 
bool IsSetSNPComment (void) const
 
const stringGetSNPComment (void) const
 
bool IsSetSNPQualityCode (void) const
 
CUser_field::TData::E_Choice GetSNPQualityCodeWhich (void) const
 
const stringGetSNPQualityCodeStr (void) const
 
void GetSNPQualityCodeOs (vector< char > &os) const
 
bool IsSetSNPExtra (void) const
 
const stringGetSNPExtra (void) const
 
bool IsRemoved (void) const
 Return true if this feature was removed already. More...
 
void Remove (void) const
 Remove the feature from Seq-annot. More...
 
void Replace (const CSeq_feat &new_feat) const
 Replace the feature with new Seq-feat object. More...
 
const CGene_refGetGeneXref (void) const
 get gene (if present) from Seq-feat.xref list More...
 
const CProt_refGetProtXref (void) const
 get protein (if present) from Seq-feat.xref list More...
 
CConstRef< CDbtagGetNamedDbxref (const CTempString &db) const
 Return a specified DB xref. More...
 
const stringGetNamedQual (const CTempString &qual_name) const
 Return a named qualifier. More...
 
- Public Member Functions inherited from ISeq_feat
virtual ~ISeq_feat (void)
 

Protected Types

enum  { kNoAnnotObjectInfo = 0x80000000, kFeatIndexMask = 0x7fffffff }
 
typedef Int4 TFeatIndex
 

Protected Member Functions

bool x_HasAnnotObjectInfo () const
 
TFeatIndex x_GetFeatIndex () const
 
const CSeq_annot_Infox_GetSeq_annot_Info (void) const
 
const CSeq_annot_SNP_Infox_GetSNP_annot_Info (void) const
 
const CAnnotObject_Infox_GetAnnotObject_InfoAny (void) const
 
const CAnnotObject_Infox_GetAnnotObject_Info (void) const
 
const CSeq_featx_GetPlainSeq_feat (void) const
 
const SSNP_Infox_GetSNP_InfoAny (void) const
 
const SSNP_Infox_GetSNP_Info (void) const
 
 CSeq_feat_Handle (const CSeq_annot_Handle &annot, TFeatIndex feat_index)
 
 CSeq_feat_Handle (const CSeq_annot_Handle &annot, const SSNP_Info &snp_info, CCreatedFeat_Ref &created_ref)
 
 CSeq_feat_Handle (CScope &scope, CAnnotObject_Info *info)
 

Private Attributes

CSeq_annot_Handle m_Seq_annot
 
TFeatIndex m_FeatIndex
 
CConstRef< CSeq_featm_CreatedOriginalFeat
 
CRef< CCreatedFeat_Refm_CreatedFeat
 

Friends

class CMappedFeat
 
class CFeat_CI
 
class CCreatedFeat_Ref
 
class CSeq_annot_Info
 
class CSeq_annot_Handle
 
class CSeq_annot_ftable_CI
 
class CSeq_annot_ftable_I
 
class CTSE_Handle
 
class CScope_Impl
 

Detailed Description

CSeq_feat_Handle –.

Proxy to access the seq-feat objects data

Definition at line 75 of file seq_feat_handle.hpp.

Member Typedef Documentation

Definition at line 228 of file seq_feat_handle.hpp.

Definition at line 112 of file seq_feat_handle.hpp.

Definition at line 166 of file seq_feat_handle.hpp.

Definition at line 167 of file seq_feat_handle.hpp.

Constructor & Destructor Documentation

CSeq_feat_Handle::~CSeq_feat_Handle ( void  )

Definition at line 90 of file seq_feat_handle.cpp.

CSeq_feat_Handle::CSeq_feat_Handle ( const CSeq_annot_Handle annot,
TFeatIndex  feat_index 
)
protected

Definition at line 57 of file seq_feat_handle.cpp.

References _ASSERT.

CSeq_feat_Handle::CSeq_feat_Handle ( const CSeq_annot_Handle annot,
const SSNP_Info snp_info,
CCreatedFeat_Ref created_ref 
)
protected

Definition at line 68 of file seq_feat_handle.cpp.

References _ASSERT, IsRemoved(), and IsTableSNP().

CSeq_feat_Handle::CSeq_feat_Handle ( CScope scope,
CAnnotObject_Info info 
)
protected

Definition at line 81 of file seq_feat_handle.cpp.

Member Function Documentation

CSeq_feat_Handle::DECLARE_OPERATOR_BOOL ( m_Seq_annot &&!  IsRemoved())
CSeqFeatData::ESubtype CSeq_feat_Handle::GetFeatSubtype ( void  ) const

Definition at line 435 of file seq_feat_handle.cpp.

References CSeqFeatData::eSubtype_variation, SAnnotTypeSelector::GetFeatSubtype(), CAnnotObject_Info::GetFeatSubtype(), CSeq_annot_Info::GetTableInfo(), CSeqTableInfo::GetType(), IsTableSNP(), x_GetAnnotObject_Info(), x_GetSeq_annot_Info(), and x_HasAnnotObjectInfo().

Referenced by CFeatTree::AddFeaturesFor(), BOOST_AUTO_TEST_CASE(), CEditingActionFeatGeneLocusRna::Find(), CGffFeatureContext::FindBestGeneParent(), IEditingActionFeat::FindRelated(), CGeneFinder::GetAssociatedGeneInfo(), GetBestCdsForMrna(), GetBestGeneForCds(), GetBestGeneForMrna(), GetBestMrnaForCds(), GetBestOverlappingFeat(), GetCdssForGene(), CGeneXrefsFromFeats::GetCommand(), CValidator::CCacheImpl::GetFeatFromCache(), CSeqTextDataSourceInterval::GetFeatureData(), CGffIdGenerator::GetGffId(), GetMrnasForGene(), CFeatTree::GetParent(), GetParentFeature(), CFeatTree::CFeatInfo::GetSubtype(), CSeqTextDataSourceInterval::GetSubtypesForAlternatingExons(), CFeatTableEdit::InstantiateProducts(), IsMicroSatellite(), MapSeq_feat(), CEditingActionRelatedFeatureConstraint::Match(), operator<<(), CEditObjectSeq_feat::RemapOtherProtFeats(), CDemoApp::Run(), s_CoincidingGapFeatures(), s_IsDuplicateFeatures(), IEditingActionFeat::SetFeatForAnotherFeat(), sFeatureGetChildrenOfSubtype(), sFeatureGetChildrenOfSubtypeFaster(), sFeatureHasChildOfSubtype(), sGetFeatureGeneBiotypeWrapper(), CGff3WriteRecordFeature::x_AssignAttributeCodeBreak(), CGff3WriteRecordFeature::x_AssignAttributeName(), CGff3WriteRecordFeature::x_AssignAttributeProduct(), CGff3WriteRecordFeature::x_AssignAttributeTranslationTable(), CGffWriteRecordFeature::x_AssignPhase(), CGffWriteRecordFeature::x_AssignType(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CFlatGatherer::x_GatherFeaturesOnWholeLocation(), CFlatGatherer::x_GatherFeaturesOnWholeLocationIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CSGAlignmentJob::x_LoadAlignmentFeats(), CSeqTextJob::x_LoadFeatureTypes(), CGtfRecord::x_MrnaFeatureToGeneParent(), CReportTrim::x_RetranslateCDS(), CGff3Writer::xAssignFeatureAttributeCodeBreak(), CGff3Writer::xAssignFeatureAttributeName(), CGff3Writer::xAssignFeatureAttributeNote(), CGff3Writer::xAssignFeatureAttributeParent(), CGff3Writer::xAssignFeatureAttributeParentMrna(), CGff3Writer::xAssignFeatureAttributeProduct(), CGff3Writer::xAssignFeatureAttributePseudoGene(), CGff3Writer::xAssignFeatureAttributeRptFamily(), CGff3Writer::xAssignFeatureAttributesQualifiers(), CGff3Writer::xAssignFeatureAttributeTranslationTable(), CGff3Writer::xAssignFeaturePhase(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), CFeatTableEdit::xGenerateLocusIdsUseExisting(), CFeatTableEdit::xGenerateTranscriptOrProteinId(), CFeatTableEdit::xGetCurrentLocusTagPrefix(), CFeatTableEdit::xPutErrorDifferingProteinIds(), CFeatTableEdit::xPutErrorDifferingTranscriptIds(), CFeatTableEdit::xPutErrorMissingLocustag(), CFeatTableEdit::xPutErrorMissingProteinId(), CFeatTableEdit::xPutErrorMissingTranscriptId(), CGvfWriter::xWriteFeature(), CGtfWriter::xWriteFeature(), CGff3Writer::xWriteFeature(), CGff3Writer::xWriteFeatureCDJVSegment(), and CGff3Writer::xWriteFeatureRna().

CSeqFeatData::E_Choice CSeq_feat_Handle::GetFeatType ( void  ) const
const CGene_ref * CSeq_feat_Handle::GetGeneXref ( void  ) const
virtual
const CSeq_loc & CSeq_feat_Handle::GetLocation ( void  ) const
virtual

Reimplemented in CMappedFeat.

Definition at line 252 of file seq_feat_handle.cpp.

References CSeq_feat_Base::GetLocation(), and GetSeq_feat().

Referenced by AddColumnsToFeatureTable(), CStrandPanel::AddCommand(), CFeatGapInfo::AdjustForRelevantGapIntervals(), CSplitCDSwithTooManyXs::AdjustSingleCDS(), CExplodeRNAFeats::apply(), ApplyFeatureSeqTableToSeqEntry(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), IEditingActionFeat::FindFeatForAnotherFeat(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedFeatForAnotherFeat(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CGeneFinder::GetAssociatedGeneInfo(), CFuseFeaturesDlg::GetCommand(), CBulkEditFeatDlg::GetCommand(), GetLocationId(), IEditingAction::GetUpdateMRNAProductNameCmd(), IsDuplicate(), IsLocationInFrame(), CLocationConstraintMatcher::Match(), CEditingActionRelatedFeatureConstraint::Match(), IEditingActionFeat::MatchBioseqConstraintForFeatHandle(), CCleanup::MoveFeatToProtein(), CAdjustFeaturesForGaps::RemapOtherProtFeats(), CGeneFinder::ResolveGeneXref(), RestoreModelReadingFrame(), s_AreFullLengthCodingRegionsWithDifferentFrames(), s_AreLinkedToDifferentFeats(), s_GetFeatDesc(), s_IsDuplicateFeatures(), CSameConstraintMatcher::SetFeat(), IEditingActionFeat::SetFeatForAnotherFeat(), TestUpdateCDS(), CAdjustFeaturesForGaps::x_DoOne(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), x_GetDivisionProcIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), and CSequenceUpdater::x_ShouldRemoveFeature().

CSeq_id_Handle CSeq_feat_Handle::GetLocationId ( void  ) const
virtual
TRange CSeq_feat_Handle::GetLocationTotalRange ( void  ) const
inline

Definition at line 118 of file seq_feat_handle.hpp.

CConstRef< CDbtag > CSeq_feat_Handle::GetNamedDbxref ( const CTempString db) const
virtual

Return a specified DB xref.

This will find the *first* item in the given referenced database. If no item is found, an empty CConstRef<> is returned.

Implements ISeq_feat.

Definition at line 461 of file seq_feat_handle.cpp.

References CSeq_feat::GetNamedDbxref(), and GetSeq_feat().

Referenced by CScore_GeneID::Get().

const string & CSeq_feat_Handle::GetNamedQual ( const CTempString qual_name) const
virtual

Return a named qualifier.

This will return the first item matching the qualifier name. If no such qualifier is found, an empty string is returned.

Implements ISeq_feat.

Definition at line 467 of file seq_feat_handle.cpp.

References CSeq_feat::GetNamedQual(), and GetSeq_feat().

Referenced by CGffIdGenerator::GetGffId(), CFeatTableEdit::InstantiateProducts(), s_CheckQuals_assembly_gap(), s_CheckQuals_bind(), s_CheckQuals_gap(), s_CheckQuals_mod_base(), s_CheckQuals_ncRNA(), s_CheckQuals_regulatory(), s_GetTranscriptIdFromMrna(), s_HasCompareOrCitation(), CFeatTableEdit::SubmitFixProducts(), CGtfRecord::x_CdsToProteinId(), CGtfRecord::x_GeneToGeneId(), CGtfRecord::x_MrnaToProduct(), CGtfRecord::x_MrnaToTranscriptId(), CFeatTableEdit::xAddTranscriptAndProteinIdsToCdsAndParentMrna(), CFeatTableEdit::xAddTranscriptAndProteinIdsToMrna(), CFeatTableEdit::xAddTranscriptAndProteinIdsToUnmatchedMrna(), CGff3Writer::xAssignFeatureAttributeExperiment(), CGff3Writer::xAssignFeatureAttributeFunction(), CGff3Writer::xAssignFeatureAttributeNote(), CGff3Writer::xAssignFeatureAttributePseudoGene(), CGff3Writer::xAssignFeatureAttributesGoMarkup(), CFeatTableEdit::xFeatureAddProteinIdCds(), CFeatTableEdit::xFeatureAddProteinIdDefault(), CFeatTableEdit::xFeatureAddProteinIdMrna(), CFeatTableEdit::xFeatureAddTranscriptIdCds(), CFeatTableEdit::xFeatureAddTranscriptIdDefault(), CFeatTableEdit::xFeatureAddTranscriptIdMrna(), CFeatTableEdit::xFeatureSetQualifier(), CFeatTableEdit::xGenerateLocusIdsRegenerate(), CFeatTableEdit::xGenerateLocusIdsUseExisting(), CFeatTableEdit::xGenerateTranscriptOrProteinId(), CFeatTableEdit::xGetCurrentLocusTagPrefix(), CGffIdGenerator::xGetIdForCds(), and CGffIdGenerator::xGetIdForMrna().

CConstRef< CSeq_feat > CSeq_feat_Handle::GetOriginalSeq_feat ( void  ) const

Definition at line 197 of file seq_feat_handle.cpp.

References ConstRef(), CCreatedFeat_Ref::GetOriginalFeature(), IsPlainFeat(), m_CreatedFeat, and x_GetPlainSeq_feat().

Referenced by AddColumnsToFeatureTable(), CFeatGapInfo::AdjustForRelevantGapIntervals(), ApplyFeatureSeqTableToSeqEntry(), CNewCleanup_imp::BasicCleanupSeqFeatHandle(), CmRNACDSLinker::CompleteHalfFormedXrefPairs(), IEditingActionBiosource::Find(), IEditingActionFeat::Find(), CEditingActionFeatGeneLocusPlain::Find(), CEditingActionFeatGeneLocusRna::Find(), CEditingActionFeatGeneLocusCdsGeneProt::Find(), IEditingActionFeat::FindFeatForAnotherFeat(), IEditingActionFeat::FindOrCreateProtFeat(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedFeatForAnotherFeat(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CProductColumn::GetApplyObjects(), CFuseFeaturesDlg::GetCommand(), CBulkEditFeatDlg::GetCommand(), CFlatFileViewContext::GetEditObject(), GetGeneForFeature(), CMappedFeat::GetLocation(), CCreatedFeat_Ref::GetMappedFeature(), CCreatedFeat_Ref::GetMappedLocation(), CFeatureSeqTableColumnBase::GetObjects(), CMappedFeat::GetOriginalFeature(), CMappedFeat::GetProduct(), CMiscSeqTableColumn::GetRelatedApplyObjects(), CMappedFeat::GetSeq_feat(), GetSeq_feat(), IEditingActionFeat::GoToProtFeature(), CmRNACDSLinker::LinkByLabelAndLocation(), MapSeq_feat(), CLocationConstraintMatcher::Match(), CBioseqEditor::OnEditBiosourceFeat(), CFindASN1Dlg::OnReplaceButton(), CNewCleanup_imp::ProtSeqBC(), CAdjustFeaturesForGaps::RemapOtherProtFeats(), RestoreModelAttributes(), RestoreModelFromInternalGnomonFeature(), CDemoApp::Run(), s_GetFeatureLabel(), s_GetProtApplyObjectsFeatures(), s_GetProtFeatures(), IEditingActionFeat::SetFeat(), IEditingActionBiosource::SetFeat(), IEditingActionFeat::SetFeatForAnotherFeat(), CCleanup::TaxonomyLookup(), CValidError_bioseq::ValidateFeatPartialInContext(), CFeatureItem::x_AddQuals(), CCreateGeneModelTask::x_AssignIDsAndUpdateGenes(), CSGAlignmentJob::x_CreateFeatGlyph(), CAdjustFeaturesForGaps::x_DoOne(), CFlatGatherer::x_GatherFeatures(), CSortedProteins::x_GatherProteinNames(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CmRNACDSLinker::x_LinkBasedOnGbQualifiers(), CSequenceUpdater::x_ShouldImportFeature(), and CVcfWriter::x_WriteData().

bool CSeq_feat_Handle::GetPartial ( void  ) const
virtual

Reimplemented in CMappedFeat.

Definition at line 230 of file seq_feat_handle.cpp.

References CSeq_feat_Base::GetPartial(), GetSeq_feat(), IsTableSNP(), and x_HasAnnotObjectInfo().

Referenced by CMappedFeat::GetPartial().

CConstRef< CSeq_feat > CSeq_feat_Handle::GetPlainSeq_feat ( void  ) const

Get current seq-feat.

Definition at line 191 of file seq_feat_handle.cpp.

References ConstRef(), and x_GetPlainSeq_feat().

Referenced by CCreatedFeat_Ref::GetOriginalFeature().

const CSeq_loc & CSeq_feat_Handle::GetProduct ( void  ) const
virtual
CSeq_id_Handle CSeq_feat_Handle::GetProductId ( void  ) const
virtual
CSeq_feat_Handle::TRange CSeq_feat_Handle::GetProductTotalRange ( void  ) const
virtual
const CProt_ref * CSeq_feat_Handle::GetProtXref ( void  ) const
virtual
CSeq_feat_Handle::TRange CSeq_feat_Handle::GetRange ( void  ) const
virtual
CConstRef< CSeq_feat > CSeq_feat_Handle::GetSeq_feat ( void  ) const
virtual

Reimplemented in CMappedFeat.

Definition at line 208 of file seq_feat_handle.cpp.

References GetOriginalSeq_feat().

Referenced by AddCodeBreak(), AddColumnsToFeatureTable(), CSeq_feat_EditHandle::AddDbxref(), CSeq_feat_EditHandle::AddExceptText(), CSeq_feat_EditHandle::AddQualifier(), ApplyFeatureSeqTableToSeqEntry(), ConvertProteinToImp(), CCreateProteinId::create_protein_ids(), CGeneFinder::GetAssociatedGeneInfo(), GetCit(), GetComment(), AnnotDataResolver< CSeq_feat_EditHandle >::GetData(), GetData(), GetDbxref(), GetExcept(), GetExcept_text(), GetExp_ev(), GetExt(), GetExts(), GetGeneXref(), GetId(), GetIds(), GetLocation(), GetModelEvidenceUserObject(), GetmRNAforCDS(), GetNamedDbxref(), GetNamedQual(), GetPartial(), GetProduct(), GetProtXref(), GetPseudo(), GetQual(), GetRange(), CmRNACDSLinker::GetReferencedmRNA_CDS(), GetTitle(), GetXref(), CFeatGapInfo::IsRelatedByCrossRef(), IsSetCit(), IsSetComment(), IsSetData(), IsSetDbxref(), IsSetExcept(), IsSetExcept_text(), IsSetExp_ev(), IsSetExt(), IsSetExts(), IsSetId(), IsSetIds(), IsSetPartial(), IsSetProduct(), IsSetPseudo(), IsSetQual(), IsSetTitle(), IsSetXref(), CCleanup::MoveFeatToProtein(), ProcessForTrimAndSplitUpdates(), CPromote::PromoteCdregion(), CPromote::PromotePub(), CPromote::PromoteRna(), CFeatureGenerator::SImplementation::RecomputePartialFlags(), CSeq_feat_EditHandle::RemoveExceptText(), CSeq_feat_EditHandle::RemoveQualifier(), CCleanup::RepairXrefs(), CEditsSaver::Replace(), RestoreModelMethod(), CDemoApp::Run(), s_AreFeatureLabelsSame(), s_AreLinkedToDifferentFeats(), s_GetCDSformRNA(), s_GetFeatDesc(), s_GetmRNAForCDS(), s_IsDuplicateFeatures(), CSeq_feat_EditHandle::SetGeneXref(), CSeq_feat_EditHandle::SetProtXref(), CSeq_annot_EditHandle::TakeFeat(), CCmdPropagateFeat::x_CdsAttachNucProt(), CSequenceUpdater::x_ChangeIDInFeature(), CNewCleanup_imp::x_ExtendFeatureToCoverSequence(), CSequenceUpdater::x_MappedFeature_ChangeId(), CSequenceUpdater::x_MappedFeature_ThroughAlign(), CValidError_bioseq::x_ReportDupOverlapFeaturePair(), and CValidError_bioseq::x_ReportOverlappingPeptidePair().

const string & CSeq_feat_Handle::GetSNPAllele ( size_t  index) const
size_t CSeq_feat_Handle::GetSNPAllelesCount ( void  ) const

Definition at line 352 of file seq_feat_handle.cpp.

References SSNP_Info::GetAllelesCount(), and x_GetSNP_Info().

const string & CSeq_feat_Handle::GetSNPComment ( void  ) const
const string & CSeq_feat_Handle::GetSNPExtra ( void  ) const
CSeq_id::TGi CSeq_feat_Handle::GetSNPGi ( void  ) const
void CSeq_feat_Handle::GetSNPQualityCodeOs ( vector< char > &  os) const
const string & CSeq_feat_Handle::GetSNPQualityCodeStr ( void  ) const
CUser_field::TData::E_Choice CSeq_feat_Handle::GetSNPQualityCodeWhich ( void  ) const

Definition at line 371 of file seq_feat_handle.cpp.

References SSNP_Info::GetQualityCodesWhich(), and x_GetSNP_Info().

const CSeq_id & CSeq_feat_Handle::GetSNPSeq_id ( void  ) const

Definition at line 334 of file seq_feat_handle.cpp.

References CSeq_annot_SNP_Info::GetSeq_id(), and x_GetSNP_annot_Info().

Referenced by GetLocationId().

bool CSeq_feat_Handle::IsPlainFeat ( void  ) const
bool CSeq_feat_Handle::IsRemoved ( void  ) const
bool CSeq_feat_Handle::IsSetData ( void  ) const

Definition at line 258 of file seq_feat_handle.cpp.

References GetSeq_feat(), CSeq_feat_Base::IsSetData(), and x_HasAnnotObjectInfo().

Referenced by CReportTrim::AdjustAndTranslate(), CRemoveGenomeProjectsDB::apply_to_seq_and_feat(), CRemoveStructuredComment::apply_to_seq_and_feat(), CModifyStructuredComment::apply_to_seq_and_feat(), CApplyObject::ApplyChange(), CMolInfoEditDlg::compute_peptide_completeness(), CConvertCDSToGene::Convert(), CConvertCDSToPseudoGene::Convert(), DeleteProteinAndRenormalizeNucProtSet(), CAsn2FastaApp::HandleSeqEntry(), IsLocationInFrame(), CDesktopViewContext::OnCutSelection(), s_IsPreprotein(), CValidError_bioseq::ValidateCDSAndProtPartials(), CFastaOstreamEx::x_AddProteinNameAttribute(), CGff3WriteRecordFeature::x_AssignAttributeCodeBreak(), CGff3WriteRecordFeature::x_AssignAttributeGene(), CGff3WriteRecordFeature::x_AssignAttributeProduct(), CGff3WriteRecordFeature::x_AssignAttributeTranslationTable(), CGff3WriteRecordFeature::x_AssignType(), CNewCleanup_imp::x_ExtendSingleGeneOnMrna(), CConvertFeatureBase::x_GetCDSProduct(), CConvertCDSToMiscFeat::x_GetProteinDesc(), CBioseqIndex::x_InitFeats(), CNewCleanup_imp::x_RemoveOldFeatures(), CVectorTrimPanel::x_TrimSelected(), CGff3Writer::xAssignFeatureAttributeCodeBreak(), CGff3Writer::xAssignFeatureAttributeDbXref(), CGff3Writer::xAssignFeatureAttributeGene(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), CGff3Writer::xAssignFeatureAttributeNote(), CGff3Writer::xAssignFeatureAttributeProduct(), and CGff3Writer::xAssignFeatureAttributeTranslationTable().

bool CSeq_feat_Handle::IsSetPartial ( void  ) const
virtual
bool CSeq_feat_Handle::IsSortedTableFeat ( void  ) const

Check if this is a simple feature from sorted Seq-table.

Definition at line 117 of file seq_feat_handle.cpp.

References CSeq_annot_Info::IsSortedTable(), x_GetSeq_annot_Info(), and x_HasAnnotObjectInfo().

Referenced by CMappedFeat::Set().

bool CSeq_feat_Handle::IsTableFeat ( void  ) const
bool CSeq_feat_Handle::IsTableSNP ( void  ) const
void CSeq_feat_Handle::Remove ( void  ) const

Remove the feature from Seq-annot.

Deprecated:
Use CSeq_feat_EditHandle

Definition at line 405 of file seq_feat_handle.cpp.

References CSeq_feat_EditHandle::Remove().

void CSeq_feat_Handle::Replace ( const CSeq_feat new_feat) const

Replace the feature with new Seq-feat object.

All indexes are updated correspondingly.

Deprecated:
Use CSeq_feat_EditHandle

Definition at line 411 of file seq_feat_handle.cpp.

References CSeq_feat_EditHandle::Replace().

void CSeq_feat_Handle::Reset ( void  )
const CAnnotObject_Info & CSeq_feat_Handle::x_GetAnnotObject_Info ( void  ) const
protected
const CAnnotObject_Info & CSeq_feat_Handle::x_GetAnnotObject_InfoAny ( void  ) const
protected
const CSeq_feat & CSeq_feat_Handle::x_GetPlainSeq_feat ( void  ) const
protected
const CSeq_annot_SNP_Info & CSeq_feat_Handle::x_GetSNP_annot_Info ( void  ) const
protected
const SSNP_Info & CSeq_feat_Handle::x_GetSNP_Info ( void  ) const
protected
const SSNP_Info & CSeq_feat_Handle::x_GetSNP_InfoAny ( void  ) const
protected

Friends And Related Function Documentation

friend class CCreatedFeat_Ref
friend

Definition at line 221 of file seq_feat_handle.hpp.

friend class CFeat_CI
friend

Definition at line 220 of file seq_feat_handle.hpp.

friend class CMappedFeat
friend

Definition at line 219 of file seq_feat_handle.hpp.

friend class CScope_Impl
friend

Definition at line 227 of file seq_feat_handle.hpp.

friend class CSeq_annot_ftable_CI
friend

Definition at line 224 of file seq_feat_handle.hpp.

friend class CSeq_annot_ftable_I
friend

Definition at line 225 of file seq_feat_handle.hpp.

friend class CSeq_annot_Handle
friend

Definition at line 223 of file seq_feat_handle.hpp.

friend class CSeq_annot_Info
friend

Definition at line 222 of file seq_feat_handle.hpp.

friend class CTSE_Handle
friend

Definition at line 226 of file seq_feat_handle.hpp.

Member Data Documentation

CRef<CCreatedFeat_Ref> CSeq_feat_Handle::m_CreatedFeat
mutableprivate

Definition at line 259 of file seq_feat_handle.hpp.

Referenced by GetOriginalSeq_feat(), Reset(), and CMappedFeat::Set().

CConstRef<CSeq_feat> CSeq_feat_Handle::m_CreatedOriginalFeat
mutableprivate
TFeatIndex CSeq_feat_Handle::m_FeatIndex
private
CSeq_annot_Handle CSeq_feat_Handle::m_Seq_annot
private

The documentation for this class was generated from the following files:
Modified on Fri Apr 20 12:40:45 2018 by modify_doxy.py rev. 546573