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NCBI C++ ToolKit: CAutoDefFeatureClause_Base Class Reference

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#include <objmgr/util/autodef_feature_clause_base.hpp>

CAutoDefFeatureClause_Base (const CAutoDefOptions &opts) virtual ~CAutoDefFeatureClause_Base () virtual void AddSubclause (CRef< CAutoDefFeatureClause_Base > subclause) string PrintClause (bool print_typeword, bool typeword_is_plural, bool suppress_allele) virtual CSeqFeatData::ESubtype GetMainFeatureSubtype () const size_t GetNumSubclauses () virtual void Label (bool suppress_allele) virtual bool AddmRNA (CAutoDefFeatureClause_Base *mRNAClause) virtual bool AddGene (CAutoDefFeatureClause_Base *gene_clause, bool suppress_allele) virtual sequence::ECompare CompareLocation (const CSeq_loc &loc) const virtual void AddToOtherLocation (CRef< CSeq_loc > loc) virtual void AddToLocation (CRef< CSeq_loc > loc, bool also_set_partials=true) virtual bool SameStrand (const CSeq_loc &loc) const virtual bool IsPartial () const virtual bool IsMobileElement () const virtual bool IsInsertionSequence () const virtual bool IsControlRegion () const virtual bool IsEndogenousVirusSourceFeature () const virtual bool IsGeneCluster () const virtual bool IsNoncodingProductFeat () const virtual bool IsSatelliteClause () const virtual bool IsExonList () const virtual CAutoDefFeatureClause_Base * FindBestParentClause (CAutoDefFeatureClause_Base *subclause, bool gene_cluster_opp_strand) void GroupClauses (bool gene_cluster_opp_strand) void GroupAltSplicedExons (CBioseq_Handle bh) virtual CRef< CSeq_loc > GetLocation () const string ListClauses (bool allow_semicolons, bool suppress_final_and, bool suppress_allele) bool IsGeneMentioned (CAutoDefFeatureClause_Base *gene_clause) const bool IsUnattachedGene () const bool IsTypewordFirst () const bool DisplayAlleleName () const const string & GetInterval () const const string & GetTypeword () const const string & GetDescription () const const string & GetProductName () const const string & GetGeneName () const const string & GetAlleleName () const virtual void SetProductName (string product_name) bool GetGeneIsPseudo () const bool NeedPlural () const bool IsAltSpliced () const void SetAltSpliced (string splice_name) bool IsMarkedForDeletion () const void MarkForDeletion () void SetMakePlural () bool HasmRNA () const void SetInfoOnly (bool info_only) void PluralizeInterval () void PluralizeDescription () void ShowSubclauses () void RemoveDeletedSubclauses () void GroupmRNAs (bool suppress_allele) void GroupGenes (bool suppress_allele) void GroupConsecutiveExons (CBioseq_Handle bh) void GroupSegmentedCDSs (bool suppress_allele) void RemoveGenesMentionedElsewhere () void RemoveuORFs () void RemoveOptionalMobileElements () void ConsolidateRepeatedClauses (bool suppress_allele) void FindAltSplices (bool suppress_allele) void TransferSubclauses (TClauseList &other_clause_list) void CountUnknownGenes () void ExpandExonLists () virtual void ReverseCDSClauseLists () virtual bool OkToGroupUnderByType (const CAutoDefFeatureClause_Base *) const virtual bool OkToGroupUnderByLocation (const CAutoDefFeatureClause_Base *, bool) const virtual void SuppressMobileElementAndInsertionSequenceSubfeatures () void SuppressSubfeatures () string FindGeneProductName (CAutoDefFeatureClause_Base *gene_clause) void AssignGeneProductNames (CAutoDefFeatureClause_Base *main_clause, bool suppress_allele) void RemoveFeaturesByType (unsigned int feature_type, bool except_promoter=false) bool IsFeatureTypeLonely (unsigned int feature_type) const void RemoveFeaturesInmRNAsByType (unsigned int feature_type, bool except_promoter=false) void RemoveFeaturesUnderType (unsigned int feature_type) void RemoveFeaturesInLocation (const CSeq_loc &loc) virtual bool ShouldRemoveExons () const virtual bool IsExonWithNumber () const void RemoveUnwantedExons () virtual bool IsBioseqPrecursorRNA () const void RemoveBioseqPrecursorRNAs () virtual bool IsPromoter () const void Consolidate (CAutoDefFeatureClause_Base &other, bool suppress_allele) void TakeSubclauses (CAutoDefFeatureClause_Base &other) CObject (void) Constructor. More...
CObject (const CObject &src) Copy constructor. More...
virtual ~CObject (void) Destructor. More...
CObject & operator= (const CObject &src) THROWS_NONE Assignment operator. More...
bool CanBeDeleted (void) const THROWS_NONE Check if object can be deleted. More...
bool IsAllocatedInPool (void) const THROWS_NONE Check if object is allocated in memory pool (not system heap) More...
bool Referenced (void) const THROWS_NONE Check if object is referenced. More...
bool ReferencedOnlyOnce (void) const THROWS_NONE Check if object is referenced only once. More...
void AddReference (void) const Add reference to object. More...
void RemoveReference (void) const Remove reference to object. More...
void ReleaseReference (void) const Remove reference without deleting object. More...
virtual void DoNotDeleteThisObject (void) Mark this object as not allocated in heap – do not delete this object. More...
virtual void DoDeleteThisObject (void) Mark this object as allocated in heap – object can be deleted. More...
void * operator new (size_t size) Define new operator for memory allocation. More...
void * operator new[] (size_t size) Define new[] operator for 'array' memory allocation. More...
void operator delete (void *ptr) Define delete operator for memory deallocation. More...
void operator delete[] (void *ptr) Define delete[] operator for memory deallocation. More...
void * operator new (size_t size, void *place) Define new operator. More...
void operator delete (void *ptr, void *place) Define delete operator. More...
void * operator new (size_t size, CObjectMemoryPool *place) Define new operator using memory pool. More...
void operator delete (void *ptr, CObjectMemoryPool *place) Define delete operator. More...
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const Define method for dumping debug information. More...
CDebugDumpable (void) virtual ~CDebugDumpable (void) void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const void DumpToConsole (void) const

Definition at line 47 of file autodef_feature_clause_base.hpp.

◆ TClauseList ◆ ERnaMiscWord Enumerator eMiscRnaWordType_InternalSpacer eMiscRnaWordType_ExternalSpacer eMiscRnaWordType_RNAIntergenicSpacer eMiscRnaWordType_RNA eMiscRnaWordType_IntergenicSpacer eMiscRnaWordType_tRNA eMiscRnaWordType_Unrecognized

Definition at line 204 of file autodef_feature_clause_base.hpp.

◆ ETRNAIntergenicSpacerType Enumerator eTRNAIntergenicSpacerType_Gene eTRNAIntergenicSpacerType_Spacer eTRNAIntergenicSpacerType_Unrecognized

Definition at line 218 of file autodef_feature_clause_base.hpp.

◆ CAutoDefFeatureClause_Base() ◆ ~CAutoDefFeatureClause_Base() ◆ AddGene() ◆ AddmRNA() ◆ AddSubclause() ◆ AddToLocation() void CAutoDefFeatureClause_Base::AddToLocation ( CRef< CSeq_loc > loc, bool also_set_partials = true ) virtual ◆ AddToOtherLocation() ◆ AssignGeneProductNames() ◆ ClauseFromPhrase() ◆ CompareLocation() ◆ Consolidate() ◆ ConsolidateRepeatedClauses() void CAutoDefFeatureClause_Base::ConsolidateRepeatedClauses ( bool suppress_allele ) ◆ CountUnknownGenes() void CAutoDefFeatureClause_Base::CountUnknownGenes ( ) ◆ DisplayAlleleName() bool CAutoDefFeatureClause_Base::DisplayAlleleName ( ) const ◆ ExpandExonLists() void CAutoDefFeatureClause_Base::ExpandExonLists ( ) ◆ FindAltSplices() void CAutoDefFeatureClause_Base::FindAltSplices ( bool suppress_allele ) ◆ FindBestParentClause()

Reimplemented in CAutoDefFeatureClause.

Definition at line 1020 of file autodef_feature_clause_base.cpp.

References CompareLocation(), eContained, eSame, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, GetLocation(), GetMainFeatureSubtype(), m_ClauseList, and NULL.

Referenced by CAutoDefFeatureClause::FindBestParentClause(), and GroupClauses().

◆ FindGeneProductName() ◆ GetAlleleName() const string& CAutoDefFeatureClause_Base::GetAlleleName ( ) const inline ◆ GetDescription() const string& CAutoDefFeatureClause_Base::GetDescription ( void ) const inline ◆ GetFeatureClausePhrases() vector< string > CAutoDefFeatureClause_Base::GetFeatureClausePhrases ( string comment ) static ◆ GetGeneIsPseudo() bool CAutoDefFeatureClause_Base::GetGeneIsPseudo ( ) const inline ◆ GetGeneName() const string& CAutoDefFeatureClause_Base::GetGeneName ( ) const inline ◆ GetInterval() const string& CAutoDefFeatureClause_Base::GetInterval ( void ) const inline ◆ GetLocation() CRef< CSeq_loc > CAutoDefFeatureClause_Base::GetLocation ( void ) const virtual ◆ GetMainFeatureSubtype()

Reimplemented in CAutoDefExonListClause, CAutoDefPromoterAnd5UTRClause, CAutoDefFakePromoterClause, CAutoDefParsedtRNAClause, and CAutoDefFeatureClause.

Definition at line 74 of file autodef_feature_clause_base.cpp.

References CSeqFeatData::eSubtype_bad, and m_ClauseList.

Referenced by CAutoDefFeatureClause::AddGene(), FindAltSplices(), FindBestParentClause(), GroupAltSplicedExons(), GroupConsecutiveExons(), GroupGenes(), GroupmRNAs(), GroupSegmentedCDSs(), IsGeneMentioned(), IsUnattachedGene(), ListClauses(), CAutoDefFeatureClause::OkToGroupUnderByLocation(), CAutoDefFeatureClause::OkToGroupUnderByType(), CAutoDefFakePromoterClause::OkToGroupUnderByType(), CAutoDefExonListClause::OkToGroupUnderByType(), RemoveFeaturesByType(), RemoveFeaturesInmRNAsByType(), RemoveFeaturesUnderType(), RemoveGenesMentionedElsewhere(), RemoveUnwantedExons(), x_OkToConsolidate(), and CAutoDef::x_RemoveOptionalFeatures().

◆ GetMiscRNAElements() vector< string > CAutoDefFeatureClause_Base::GetMiscRNAElements ( const string & product ) static ◆ GetNumSubclauses() size_t CAutoDefFeatureClause_Base::GetNumSubclauses ( ) inline ◆ GetProductName() const string& CAutoDefFeatureClause_Base::GetProductName ( void ) const inline ◆ GetTrnaIntergenicSpacerClausePhrases() vector< string > CAutoDefFeatureClause_Base::GetTrnaIntergenicSpacerClausePhrases ( const string & comment ) static ◆ GetTypeword() const string& CAutoDefFeatureClause_Base::GetTypeword ( ) const inline ◆ GroupAltSplicedExons() void CAutoDefFeatureClause_Base::GroupAltSplicedExons ( CBioseq_Handle bh )

Definition at line 1176 of file autodef_feature_clause_base.cpp.

References CAutoDefExonListClause::AddSubclause(), CompareLocation(), eNoOverlap, eOverlap, CSeqFeatData::eSubtype_exon, GetLocation(), GetMainFeatureSubtype(), IsAltSpliced(), IsMarkedForDeletion(), m_ClauseList, m_Opts, and NULL.

Referenced by CAutoDef::x_GetFeatureClauses().

◆ GroupClauses() void CAutoDefFeatureClause_Base::GroupClauses ( bool gene_cluster_opp_strand ) ◆ GroupConsecutiveExons() void CAutoDefFeatureClause_Base::GroupConsecutiveExons ( CBioseq_Handle bh )

Definition at line 1273 of file autodef_feature_clause_base.cpp.

References CAutoDefExonListClause::AddSubclause(), CSeqFeatData::eSubtype_exon, GetMainFeatureSubtype(), IsAltSpliced(), IsMarkedForDeletion(), CAutoDefExonListClause::Label(), m_ClauseList, m_Opts, NULL, CAutoDefExonListClause::SetSuppressFinalAnd(), and NStr::StringToUInt().

Referenced by CAutoDef::x_GetFeatureClauses().

◆ GroupGenes() void CAutoDefFeatureClause_Base::GroupGenes ( bool suppress_allele ) ◆ GroupmRNAs() void CAutoDefFeatureClause_Base::GroupmRNAs ( bool suppress_allele ) ◆ GroupSegmentedCDSs() void CAutoDefFeatureClause_Base::GroupSegmentedCDSs ( bool suppress_allele )

Definition at line 1369 of file autodef_feature_clause_base.cpp.

References NStr::Equal(), CSeqFeatData::eSubtype_cdregion, GetAlleleName(), GetGeneName(), GetLocation(), GetMainFeatureSubtype(), GetProductName(), NStr::IsBlank(), IsMarkedForDeletion(), m_ClauseList, n, and NULL.

Referenced by CAutoDef::x_GetFeatureClauses().

◆ HasmRNA() bool CAutoDefFeatureClause_Base::HasmRNA ( ) const inline ◆ IsAltSpliced() bool CAutoDefFeatureClause_Base::IsAltSpliced ( ) const inline ◆ IsBioseqPrecursorRNA() bool CAutoDefFeatureClause_Base::IsBioseqPrecursorRNA ( ) const virtual ◆ IsControlRegion() virtual bool CAutoDefFeatureClause_Base::IsControlRegion ( ) const inlinevirtual ◆ IsEndogenousVirusSourceFeature() virtual bool CAutoDefFeatureClause_Base::IsEndogenousVirusSourceFeature ( ) const inlinevirtual ◆ IsExonList() virtual bool CAutoDefFeatureClause_Base::IsExonList ( ) const inlinevirtual ◆ IsExonWithNumber() virtual bool CAutoDefFeatureClause_Base::IsExonWithNumber ( ) const inlinevirtual ◆ IsFeatureTypeLonely() bool CAutoDefFeatureClause_Base::IsFeatureTypeLonely ( unsigned int feature_type ) const ◆ IsGeneCluster() virtual bool CAutoDefFeatureClause_Base::IsGeneCluster ( ) const inlinevirtual ◆ IsGeneMentioned() ◆ IsInsertionSequence() virtual bool CAutoDefFeatureClause_Base::IsInsertionSequence ( ) const inlinevirtual ◆ IsMarkedForDeletion() bool CAutoDefFeatureClause_Base::IsMarkedForDeletion ( ) const inline ◆ IsMobileElement() virtual bool CAutoDefFeatureClause_Base::IsMobileElement ( ) const inlinevirtual ◆ IsNoncodingProductFeat() virtual bool CAutoDefFeatureClause_Base::IsNoncodingProductFeat ( ) const inlinevirtual ◆ IsPartial() virtual bool CAutoDefFeatureClause_Base::IsPartial ( void ) const inlinevirtual ◆ IsPromoter() virtual bool CAutoDefFeatureClause_Base::IsPromoter ( ) const inlinevirtual ◆ IsSatelliteClause() virtual bool CAutoDefFeatureClause_Base::IsSatelliteClause ( ) const inlinevirtual ◆ IsTypewordFirst() bool CAutoDefFeatureClause_Base::IsTypewordFirst ( ) const inline ◆ IsUnattachedGene() bool CAutoDefFeatureClause_Base::IsUnattachedGene ( ) const ◆ IsuORF() ◆ IsValidFeatureClausePhrase() bool CAutoDefFeatureClause_Base::IsValidFeatureClausePhrase ( const string & phrase ) static ◆ Label() void CAutoDefFeatureClause_Base::Label ( bool suppress_allele ) virtual

Reimplemented in CAutoDefExonListClause, CAutoDefUnknownGeneList, CAutoDefPromoterAnd5UTRClause, CAutoDefFakePromoterClause, CAutoDefParsedRegionClause, CAutoDefMiscCommentClause, CAutoDefGeneClusterClause, CAutoDefIntergenicSpacerClause, CAutoDefPromoterClause, CAutoDefSatelliteClause, CAutoDefMobileElementClause, and CAutoDefFeatureClause.

Definition at line 260 of file autodef_feature_clause_base.cpp.

References m_ClauseList.

Referenced by Consolidate(), ConsolidateRepeatedClauses(), and CAutoDef::x_GetFeatureClauses().

◆ ListClauses() string CAutoDefFeatureClause_Base::ListClauses ( bool allow_semicolons, bool suppress_final_and, bool suppress_allele )

Definition at line 357 of file autodef_feature_clause_base.cpp.

References DisplayAlleleName(), NStr::EndsWith(), NStr::Equal(), CSeqFeatData::eSubtype_biosrc, NStr::Find(), GetDescription(), GetInterval(), GetMainFeatureSubtype(), GetTypeword(), HasAlleleChange(), IsAltSpliced(), NStr::IsBlank(), IsExonList(), IsMobileElement(), IsTypewordFirst(), m_ClauseList, NeedPlural(), and x_LastIntervalChangeBeforeEnd().

Referenced by CAutoDefExonListClause::Label(), CAutoDef::x_GetFeatureClauses(), and CAutoDefFeatureClause::x_GetGenericInterval().

◆ MarkForDeletion() void CAutoDefFeatureClause_Base::MarkForDeletion ( ) inline ◆ NeedPlural() bool CAutoDefFeatureClause_Base::NeedPlural ( ) const inline ◆ OkToGroupUnderByLocation() ◆ OkToGroupUnderByType() ◆ PluralizeDescription() void CAutoDefFeatureClause_Base::PluralizeDescription ( ) ◆ PluralizeInterval() void CAutoDefFeatureClause_Base::PluralizeInterval ( ) ◆ PrintClause() string CAutoDefFeatureClause_Base::PrintClause ( bool print_typeword, bool typeword_is_plural, bool suppress_allele ) ◆ RemoveBioseqPrecursorRNAs() void CAutoDefFeatureClause_Base::RemoveBioseqPrecursorRNAs ( ) ◆ RemoveDeletedSubclauses() void CAutoDefFeatureClause_Base::RemoveDeletedSubclauses ( ) ◆ RemoveFeaturesByType() void CAutoDefFeatureClause_Base::RemoveFeaturesByType ( unsigned int feature_type, bool except_promoter = false ) ◆ RemoveFeaturesInLocation() void CAutoDefFeatureClause_Base::RemoveFeaturesInLocation ( const CSeq_loc & loc ) ◆ RemoveFeaturesInmRNAsByType() void CAutoDefFeatureClause_Base::RemoveFeaturesInmRNAsByType ( unsigned int feature_type, bool except_promoter = false ) ◆ RemoveFeaturesUnderType() void CAutoDefFeatureClause_Base::RemoveFeaturesUnderType ( unsigned int feature_type ) ◆ RemoveGenesMentionedElsewhere() void CAutoDefFeatureClause_Base::RemoveGenesMentionedElsewhere ( ) ◆ RemoveOptionalMobileElements() void CAutoDefFeatureClause_Base::RemoveOptionalMobileElements ( ) ◆ RemoveUnwantedExons() void CAutoDefFeatureClause_Base::RemoveUnwantedExons ( ) ◆ RemoveuORFs() void CAutoDefFeatureClause_Base::RemoveuORFs ( ) ◆ ReverseCDSClauseLists() void CAutoDefFeatureClause_Base::ReverseCDSClauseLists ( ) virtual ◆ SameStrand() ◆ SetAltSpliced() void CAutoDefFeatureClause_Base::SetAltSpliced ( string splice_name ) ◆ SetInfoOnly() void CAutoDefFeatureClause_Base::SetInfoOnly ( bool info_only ) inline ◆ SetMakePlural() void CAutoDefFeatureClause_Base::SetMakePlural ( ) inline ◆ SetProductName() void CAutoDefFeatureClause_Base::SetProductName ( string product_name ) virtual ◆ ShouldRemoveExons() virtual bool CAutoDefFeatureClause_Base::ShouldRemoveExons ( ) const inlinevirtual ◆ ShowSubclauses() void CAutoDefFeatureClause_Base::ShowSubclauses ( ) ◆ SuppressMobileElementAndInsertionSequenceSubfeatures() void CAutoDefFeatureClause_Base::SuppressMobileElementAndInsertionSequenceSubfeatures ( ) virtual ◆ SuppressSubfeatures() void CAutoDefFeatureClause_Base::SuppressSubfeatures ( ) inline ◆ TakeSubclauses() ◆ TransferSubclauses() void CAutoDefFeatureClause_Base::TransferSubclauses ( TClauseList & other_clause_list ) ◆ x_AddOneMiscWordElement() bool CAutoDefFeatureClause_Base::x_AddOneMiscWordElement ( const string & phrase, vector< string > & elements ) staticprotected ◆ x_AddOnetRNAIntergenicSpacerElement() bool CAutoDefFeatureClause_Base::x_AddOnetRNAIntergenicSpacerElement ( const string & phrase, vector< string > & elements ) staticprotected ◆ x_GetRnaMiscWord() ◆ x_GetRnaMiscWordType() ◆ x_GetTRNAIntergenicSpacerType() ◆ x_LastIntervalChangeBeforeEnd() size_t CAutoDefFeatureClause_Base::x_LastIntervalChangeBeforeEnd ( ) const protected ◆ x_MeetAltSpliceRules() bool CAutoDefFeatureClause_Base::x_MeetAltSpliceRules ( size_t clause1, size_t clause2, string & splice_name ) const protected

Definition at line 862 of file autodef_feature_clause_base.cpp.

References NStr::Equal(), CSeqFeatData::eSubtype_cdregion, NStr::Find(), GetAlleleName(), GetGeneName(), IsAltSpliced(), NStr::IsBlank(), isspace(), m_ClauseList, ShareInterval(), NStr::TruncateSpacesInPlace(), and unwanted_words.

Referenced by FindAltSplices().

◆ x_OkToConsolidate() [1/2] ◆ x_OkToConsolidate() [2/2] bool CAutoDefFeatureClause_Base::x_OkToConsolidate ( unsigned int clause1, unsigned int clause2 ) const protected ◆ x_RemoveNullClauses() void CAutoDefFeatureClause_Base::x_RemoveNullClauses ( ) protected ◆ x_tRNAGeneFromProduct() ◆ m_AlleleName string CAutoDefFeatureClause_Base::m_AlleleName protected ◆ m_ClauseInfoOnly bool CAutoDefFeatureClause_Base::m_ClauseInfoOnly protected ◆ m_ClauseList

Definition at line 171 of file autodef_feature_clause_base.hpp.

Referenced by AddGene(), AddmRNA(), AddSubclause(), CAutoDefExonListClause::AddSubclause(), AssignGeneProductNames(), CAutoDefFeatureClause::CAutoDefFeatureClause(), ConsolidateRepeatedClauses(), CountUnknownGenes(), ExpandExonLists(), FindAltSplices(), FindBestParentClause(), FindGeneProductName(), GetMainFeatureSubtype(), GetNumSubclauses(), GroupAltSplicedExons(), GroupClauses(), GroupConsecutiveExons(), GroupGenes(), GroupmRNAs(), GroupSegmentedCDSs(), IsBioseqPrecursorRNA(), IsFeatureTypeLonely(), IsGeneMentioned(), IsUnattachedGene(), Label(), CAutoDefUnknownGeneList::Label(), CAutoDefExonListClause::Label(), ListClauses(), RemoveBioseqPrecursorRNAs(), RemoveDeletedSubclauses(), RemoveFeaturesByType(), RemoveFeaturesInLocation(), RemoveFeaturesInmRNAsByType(), RemoveFeaturesUnderType(), RemoveGenesMentionedElsewhere(), RemoveOptionalMobileElements(), RemoveUnwantedExons(), RemoveuORFs(), CAutoDefFeatureClause::ReverseCDSClauseLists(), ReverseCDSClauseLists(), CAutoDefFeatureClause::ShouldRemoveExons(), ShowSubclauses(), SuppressMobileElementAndInsertionSequenceSubfeatures(), TransferSubclauses(), CAutoDefFeatureClause::x_GetGenericInterval(), CAutoDefFeatureClause::x_GetOperonSubfeatures(), x_LastIntervalChangeBeforeEnd(), x_MeetAltSpliceRules(), x_OkToConsolidate(), and x_RemoveNullClauses().

◆ m_DeleteMe bool CAutoDefFeatureClause_Base::m_DeleteMe protected ◆ m_Description string CAutoDefFeatureClause_Base::m_Description protected

Definition at line 187 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefGeneClusterClause::CAutoDefGeneClusterClause(), CAutoDefMiscCommentClause::CAutoDefMiscCommentClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CAutoDefParsedRegionClause::CAutoDefParsedRegionClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CAutoDefPromoterClause::CAutoDefPromoterClause(), CAutoDefSatelliteClause::CAutoDefSatelliteClause(), CAutoDefUnknownGeneList::CAutoDefUnknownGeneList(), GetDescription(), CAutoDefIntergenicSpacerClause::InitWithString(), CAutoDefFeatureClause::Label(), CAutoDefUnknownGeneList::Label(), CAutoDefExonListClause::Label(), PluralizeDescription(), PrintClause(), CAutoDefParsedClause::SetDescription(), and CAutoDefParsedClause::SetMiscRNAWord().

◆ m_DescriptionChosen bool CAutoDefFeatureClause_Base::m_DescriptionChosen protected

Definition at line 188 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFeatureClause::AddGene(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefGeneClusterClause::CAutoDefGeneClusterClause(), CAutoDefMiscCommentClause::CAutoDefMiscCommentClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CAutoDefParsedRegionClause::CAutoDefParsedRegionClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CAutoDefPromoterClause::CAutoDefPromoterClause(), CAutoDefSatelliteClause::CAutoDefSatelliteClause(), CAutoDefUnknownGeneList::CAutoDefUnknownGeneList(), CAutoDefIntergenicSpacerClause::InitWithString(), CAutoDefFeatureClause::Label(), CAutoDefMobileElementClause::Label(), CAutoDefSatelliteClause::Label(), CAutoDefPromoterClause::Label(), CAutoDefIntergenicSpacerClause::Label(), CAutoDefGeneClusterClause::Label(), CAutoDefMiscCommentClause::Label(), CAutoDefUnknownGeneList::Label(), CAutoDefExonListClause::Label(), SetAltSpliced(), CAutoDefParsedClause::SetDescription(), CAutoDefParsedClause::SetMiscRNAWord(), and SetProductName().

◆ m_GeneIsPseudo bool CAutoDefFeatureClause_Base::m_GeneIsPseudo protected ◆ m_GeneName string CAutoDefFeatureClause_Base::m_GeneName protected

Definition at line 173 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFeatureClause::AddGene(), CAutoDefExonListClause::AddSubclause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefGeneClause::CAutoDefGeneClause(), CAutoDefParsedtRNAClause::CAutoDefParsedtRNAClause(), GetGeneName(), IsGeneMentioned(), CAutoDefFeatureClause::OkToGroupUnderByLocation(), CAutoDefParsedClause::SetMiscRNAWord(), CAutoDefFeatureClause::x_GetDescription(), and CAutoDefGeneClause::x_GetProductName().

◆ m_HasGene bool CAutoDefFeatureClause_Base::m_HasGene protected ◆ m_HasmRNA bool CAutoDefFeatureClause_Base::m_HasmRNA protected ◆ m_Interval string CAutoDefFeatureClause_Base::m_Interval protected

Definition at line 176 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefMiscCommentClause::CAutoDefMiscCommentClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CAutoDefParsedRegionClause::CAutoDefParsedRegionClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CAutoDefPromoterClause::CAutoDefPromoterClause(), GetInterval(), CAutoDefIntergenicSpacerClause::InitWithString(), CAutoDefFeatureClause::Label(), CAutoDefMobileElementClause::Label(), CAutoDefSatelliteClause::Label(), CAutoDefGeneClusterClause::Label(), and PluralizeInterval().

◆ m_IsAltSpliced bool CAutoDefFeatureClause_Base::m_IsAltSpliced protected ◆ m_IsUnknown bool CAutoDefFeatureClause_Base::m_IsUnknown protected ◆ m_MakePlural bool CAutoDefFeatureClause_Base::m_MakePlural protected ◆ m_Opts ◆ m_Pluralizable bool CAutoDefFeatureClause_Base::m_Pluralizable protected ◆ m_ProductName string CAutoDefFeatureClause_Base::m_ProductName protected

Definition at line 189 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFeatureClause::AddGene(), CAutoDefFeatureClause::AddmRNA(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefParsedtRNAClause::CAutoDefParsedtRNAClause(), CAutoDefFeatureClause::DoesmRNAProductNameMatch(), GetProductName(), CAutoDefFeatureClause::Label(), SetAltSpliced(), CAutoDefParsedClause::SetMiscRNAWord(), SetProductName(), and CAutoDefFeatureClause::x_GetDescription().

◆ m_ProductNameChosen bool CAutoDefFeatureClause_Base::m_ProductNameChosen protected

Definition at line 190 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFeatureClause::AddGene(), CAutoDefFeatureClause::AddmRNA(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefParsedtRNAClause::CAutoDefParsedtRNAClause(), CAutoDefFeatureClause::DoesmRNAProductNameMatch(), CAutoDefFeatureClause::Label(), SetAltSpliced(), CAutoDefParsedClause::SetMiscRNAWord(), SetProductName(), and CAutoDefFeatureClause::x_GetDescription().

◆ m_ShowTypewordFirst bool CAutoDefFeatureClause_Base::m_ShowTypewordFirst protected

Definition at line 184 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefExonListClause::CAutoDefExonListClause(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefGeneClusterClause::CAutoDefGeneClusterClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CAutoDefUnknownGeneList::CAutoDefUnknownGeneList(), CAutoDefIntergenicSpacerClause::InitWithString(), IsTypewordFirst(), CAutoDefFeatureClause::Label(), PrintClause(), CAutoDefParsedClause::SetMiscRNAWord(), and CAutoDefParsedClause::SetTypewordFirst().

◆ m_SuppressSubfeatures bool CAutoDefFeatureClause_Base::m_SuppressSubfeatures protected ◆ m_Typeword string CAutoDefFeatureClause_Base::m_Typeword protected

Definition at line 185 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFeatureClause::AddGene(), CAutoDefExonListClause::CAutoDefExonListClause(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefGeneClusterClause::CAutoDefGeneClusterClause(), CAutoDefMiscCommentClause::CAutoDefMiscCommentClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CAutoDefParsedRegionClause::CAutoDefParsedRegionClause(), CAutoDefParsedtRNAClause::CAutoDefParsedtRNAClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CAutoDefPromoterClause::CAutoDefPromoterClause(), CAutoDefSatelliteClause::CAutoDefSatelliteClause(), CAutoDefUnknownGeneList::CAutoDefUnknownGeneList(), DisplayAlleleName(), GetTypeword(), CAutoDefIntergenicSpacerClause::InitWithString(), CAutoDefMobileElementClause::IsOptional(), CAutoDefFeatureClause::Label(), CAutoDefParsedIntergenicSpacerClause::MakeRegion(), PluralizeDescription(), PrintClause(), CAutoDefParsedClause::SetTypeword(), CAutoDefFeatureClause::x_GetDescription(), CAutoDefFeatureClause::x_GetGenericInterval(), and CAutoDefFeatureClause::x_TypewordFromSequence().

◆ m_TypewordChosen bool CAutoDefFeatureClause_Base::m_TypewordChosen protected

Definition at line 186 of file autodef_feature_clause_base.hpp.

Referenced by CAutoDefFeatureClause::AddGene(), CAutoDefExonListClause::CAutoDefExonListClause(), CAutoDefFakePromoterClause::CAutoDefFakePromoterClause(), CAutoDefFeatureClause::CAutoDefFeatureClause(), CAutoDefGeneClusterClause::CAutoDefGeneClusterClause(), CAutoDefMiscCommentClause::CAutoDefMiscCommentClause(), CAutoDefMobileElementClause::CAutoDefMobileElementClause(), CAutoDefParsedIntergenicSpacerClause::CAutoDefParsedIntergenicSpacerClause(), CAutoDefParsedRegionClause::CAutoDefParsedRegionClause(), CAutoDefParsedtRNAClause::CAutoDefParsedtRNAClause(), CAutoDefPromoterAnd5UTRClause::CAutoDefPromoterAnd5UTRClause(), CAutoDefPromoterClause::CAutoDefPromoterClause(), CAutoDefSatelliteClause::CAutoDefSatelliteClause(), CAutoDefUnknownGeneList::CAutoDefUnknownGeneList(), CAutoDefIntergenicSpacerClause::InitWithString(), CAutoDefFeatureClause::Label(), CAutoDefParsedClause::SetMiscRNAWord(), CAutoDefParsedClause::SetTypeword(), and CAutoDefFeatureClause::x_TypewordFromSequence().

The documentation for this class was generated from the following files:

include/objmgr/util/autodef_feature_clause_base.hpp
src/objmgr/util/autodef_feature_clause_base.cpp

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