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NCBI C++ ToolKit: CConvertFeatureBase Class Reference

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#include <gui/objutils/convert_feat.hpp>

CConvertFeatureBase (objects::CSeqFeatData::ESubtype feat_to=objects::CSeqFeatData::eSubtype_bad, objects::CSeqFeatData::ESubtype feat_from=objects::CSeqFeatData::eSubtype_bad) ~CConvertFeatureBase () virtual string GetDescription () virtual bool CanConvertFrom (objects::CSeqFeatData::ESubtype subtype) virtual bool CanConvertTo (objects::CSeqFeatData::ESubtype subtype) virtual CRef< CCmdComposite > Convert (const objects::CSeq_feat &orig, bool keep_orig, objects::CScope &scope) TOptions & SetOptions () const TOptions & GetOptions () const CRef< CConversionOption > FindRemoveTranscriptId () string x_GetCDSProduct (const objects::CSeq_feat &orig, objects::CScope &scope) void SetCreateGeneralOnly (bool flag) void SetOffset (int *offset) 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 CRef< CCmdComposite > x_SimpleConversion (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope) CRef< CCmdComposite > x_ConvertToCDS (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope, vector< string > product) bool x_MoveFeatureToProtein (const objects::CSeq_feat &orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope &scope) vector< string > x_ExtractQuals (CRef< objects::CSeq_feat > new_feat, string qual_name) vector< string > x_ExtractProductQuals (CRef< objects::CSeq_feat > new_feat) void x_AddToComment (string comment, CRef< objects::CSeq_feat > new_feat, objects::edit::EExistingText existing_text=objects::edit::eExistingText_prefix_semi) void x_ClearGenericFields (CRef< objects::CSeq_feat > new_feat) void x_AddCDSSourceConversionOptions () void x_AddCDSDestinationConversionOptions () void x_AddRnaDestinationConversionOptions () void x_AddSiteDestinationConversionOptions () void x_AddBondDestinationConversionOptions () void x_AddRegionDestionationConversionOptions () CRef< CConversionOption > x_FindOption (const string &label) CRef< CConversionOption > x_FindRemoveGene () CRef< CConversionOption > x_FindRemovemRNA () CRef< CConversionOption > x_FindNcrnaClass () CRef< CConversionOption > x_FindSiteType () CRef< CConversionOption > x_FindBondType () CRef< CConversionOption > x_FindPlaceOnProt () CRef< CConversionOption > x_FindPseudo () bool x_IsImportSubtype (objects::CSeqFeatData::ESubtype subtype) bool x_IsProtSubtype (objects::CSeqFeatData::ESubtype subtype) bool x_IsRnaSubtype (objects::CSeqFeatData::ESubtype subtype) string GetSiteName (objects::CSeqFeatData::TSite site_type) virtual void DeleteThis (void) Virtual method "deleting" this object. More...

Definition at line 121 of file convert_feat.hpp.

◆ TOptions ◆ CConvertFeatureBase() CConvertFeatureBase::CConvertFeatureBase ( objects::CSeqFeatData::ESubtype feat_to = objects::CSeqFeatData::eSubtype_bad, objects::CSeqFeatData::ESubtype feat_from = objects::CSeqFeatData::eSubtype_bad )

Definition at line 65 of file convert_feat.cpp.

References CSeqFeatData_Base::e_Rna, CSeqFeatData::eSubtype_bond, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, CSeqFeatData::GetTypeFromSubtype(), m_From, m_Options, m_To, x_AddBondDestinationConversionOptions(), x_AddCDSDestinationConversionOptions(), x_AddCDSSourceConversionOptions(), x_AddRegionDestionationConversionOptions(), x_AddRnaDestinationConversionOptions(), x_AddSiteDestinationConversionOptions(), and x_IsProtSubtype().

◆ ~CConvertFeatureBase() CConvertFeatureBase::~CConvertFeatureBase ( ) inline

Definition at line 126 of file convert_feat.hpp.

◆ CanConvertFrom() bool CConvertFeatureBase::CanConvertFrom ( objects::CSeqFeatData::ESubtype subtype ) virtual ◆ CanConvertTo() bool CConvertFeatureBase::CanConvertTo ( objects::CSeqFeatData::ESubtype subtype ) virtual

Reimplemented in CConvertCDSToProt, CConvertProtToProt, CConvertRNAToRNA, CConvertGeneToRNA, CConvertCDSToRNA, CConvertImpToImp, CConvertRegionToProt, CConvertSiteToImp, CConvertRnaToImp, CConvertGeneToImp, CConvertCommentToImp, CConvertRegionToRna, CConvertRegionToImp, CConvertImpToRNA, CConvertProtToImp, and CConvertImpToProt.

Definition at line 88 of file convert_feat.cpp.

References m_To.

Referenced by CConvertFeatureBaseFactory::Create().

◆ Convert()

Reimplemented in CConvertCDSToPseudoGene, CConvertCDSToGene, CConvertCDSToProt, CConvertToRegion, CConvertToSite, CConvertToBond, CConvertRNAToRNA, CConvertRegionToProt, CConvertSiteToImp, CConverttRNAToGene, CConvertmRNAToCDS, CConvertRnaToImp, CConvertGeneToImp, CConvertCommentToImp, CConvertRegionToRna, CConvertRegionToImp, CConvertImpToGene, CConvertImpToCDS, CConvertImpToRNA, CConvertProtToImp, CConvertImpToProt, CConvertCDSToMiscFeat, CConvertBioSrcToRptRegion, CConvertGeneToRNA, CConvertCDSToRNA, CConvertImpToImp, and CConvertMiscFeatToGene.

Definition at line 110 of file convert_feat.cpp.

References CSerialObject::Assign(), cmd, orig, and x_SimpleConversion().

Referenced by CCdsToMatPeptide::ConvertEach(), CConvertCdsToMiscFeat::GetCommand(), CConvertFeatDlg::GetCommand(), and CMacroFunction_ConvertFeature::TheFunction().

◆ FindRemoveTranscriptId() ◆ GetDescription() virtual string CConvertFeatureBase::GetDescription ( void ) inlinevirtual

Reimplemented in CConvertCDSToPseudoGene, CConvertCDSToGene, CConvertCDSToProt, CConvertProtToProt, CConvertToRegion, CConvertToSite, CConvertToBond, CConvertRNAToRNA, CConvertRegionToProt, CConvertSiteToImp, CConverttRNAToGene, CConvertmRNAToCDS, CConvertRnaToImp, CConvertGeneToImp, CConvertCommentToImp, CConvertRegionToRna, CConvertRegionToImp, CConvertImpToGene, CConvertImpToCDS, CConvertImpToRNA, CConvertProtToImp, CConvertImpToProt, CConvertCDSToMiscFeat, CConvertBioSrcToRptRegion, CConvertGeneToRNA, CConvertCDSToRNA, CConvertImpToImp, and CConvertMiscFeatToGene.

Definition at line 129 of file convert_feat.hpp.

References kConversionNotSupported.

Referenced by CConvertCdsToMiscFeat::GetCommand(), CConvertFeatDlg::GetCommand(), CMacroEditorContext::GetConversionDescr(), CMacroFunction_ConvertFeature::TheFunction(), and CConvertFeatDlg::UpdateEditor().

◆ GetOptions() ◆ GetSiteName() string CConvertFeatureBase::GetSiteName ( objects::CSeqFeatData::TSite site_type ) protected ◆ SetCreateGeneralOnly() void CConvertFeatureBase::SetCreateGeneralOnly ( bool flag ) inline ◆ SetOffset() void CConvertFeatureBase::SetOffset ( int * offset ) inline ◆ SetOptions() TOptions& CConvertFeatureBase::SetOptions ( void ) inline ◆ x_AddBondDestinationConversionOptions() void CConvertFeatureBase::x_AddBondDestinationConversionOptions ( ) protected ◆ x_AddCDSDestinationConversionOptions() void CConvertFeatureBase::x_AddCDSDestinationConversionOptions ( ) protected ◆ x_AddCDSSourceConversionOptions() void CConvertFeatureBase::x_AddCDSSourceConversionOptions ( ) protected ◆ x_AddRegionDestionationConversionOptions() void CConvertFeatureBase::x_AddRegionDestionationConversionOptions ( ) protected ◆ x_AddRnaDestinationConversionOptions() void CConvertFeatureBase::x_AddRnaDestinationConversionOptions ( ) protected ◆ x_AddSiteDestinationConversionOptions() void CConvertFeatureBase::x_AddSiteDestinationConversionOptions ( ) protected ◆ x_AddToComment()

Definition at line 422 of file convert_feat.cpp.

References AddValueToString(), CSeq_feat_Base::GetComment(), NStr::IsBlank(), CSeq_feat_Base::IsSetComment(), and CSeq_feat_Base::SetComment().

Referenced by CConvertCDSToRNA::Convert(), CConvertCDSToMiscFeat::Convert(), CConvertImpToRNA::Convert(), CConvertRegionToImp::Convert(), CConvertRegionToRna::Convert(), CConvertGeneToImp::Convert(), CConvertRnaToImp::Convert(), CConvertSiteToImp::Convert(), CConvertRNAToRNA::Convert(), CConvertCDSToGene::Convert(), CConvertCDSToPseudoGene::Convert(), and x_ConvertToCDS().

◆ x_ClearGenericFields() void CConvertFeatureBase::x_ClearGenericFields ( CRef< objects::CSeq_feat > new_feat ) protected

Definition at line 438 of file convert_feat.cpp.

References eExtreme_Biological, CSeq_feat_Base::ResetCit(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::ResetDbxref(), CSeq_feat_Base::ResetExcept(), CSeq_feat_Base::ResetExcept_text(), CSeq_feat_Base::ResetId(), CSeq_feat_Base::ResetProduct(), CSeq_feat_Base::ResetPseudo(), CSeq_feat_Base::ResetQual(), CSeq_feat_Base::ResetTitle(), and CSeq_feat_Base::SetLocation().

Referenced by CConvertToBond::Convert(), CConvertToSite::Convert(), and CConvertToRegion::Convert().

◆ x_ConvertToCDS() CRef< CCmdComposite > CConvertFeatureBase::x_ConvertToCDS ( const objects::CSeq_feat & orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope & scope, vector< string > product ) protected

Definition at line 272 of file convert_feat.cpp.

References AddProteinFeatureToProtein(), cmd, CreateTranslatedProteinSequence(), eExtreme_Biological, CScope::GetBioseqHandle(), GetDeleteFeatureCommand(), CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetSeq_entry_Handle(), CScope::GetSeq_featHandle(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), ITERATE, m_create_general_only, m_offset, NULL, orig, prot, CSeq_feat_Base::SetPseudo(), x_AddToComment(), x_FindPseudo(), and x_SimpleConversion().

Referenced by CConvertImpToCDS::Convert(), and CConvertmRNAToCDS::Convert().

◆ x_ExtractProductQuals() vector< string > CConvertFeatureBase::x_ExtractProductQuals ( CRef< objects::CSeq_feat > new_feat ) protected ◆ x_ExtractQuals() vector< string > CConvertFeatureBase::x_ExtractQuals ( CRef< objects::CSeq_feat > new_feat, string qual_name ) protected ◆ x_FindBondType() ◆ x_FindNcrnaClass() ◆ x_FindOption()

Definition at line 539 of file convert_feat.cpp.

References NStr::Equal(), ITERATE, label, m_Options, and NULL.

Referenced by FindRemoveTranscriptId(), x_FindBondType(), x_FindNcrnaClass(), x_FindPlaceOnProt(), x_FindPseudo(), x_FindRemoveGene(), x_FindRemovemRNA(), and x_FindSiteType().

◆ x_FindPlaceOnProt() ◆ x_FindPseudo() ◆ x_FindRemoveGene() ◆ x_FindRemovemRNA() ◆ x_FindSiteType() ◆ x_GetCDSProduct() string CConvertFeatureBase::x_GetCDSProduct ( const objects::CSeq_feat & orig, objects::CScope & scope ) ◆ x_IsImportSubtype() bool CConvertFeatureBase::x_IsImportSubtype ( objects::CSeqFeatData::ESubtype subtype ) protected

Definition at line 598 of file convert_feat.cpp.

References CSeqFeatData_Base::e_Imp, and CSeqFeatData::GetTypeFromSubtype().

Referenced by CConvertImpToProt::CanConvertFrom(), CConvertImpToRNA::CanConvertFrom(), CConvertImpToCDS::CanConvertFrom(), CConvertImpToGene::CanConvertFrom(), CConvertImpToImp::CanConvertFrom(), CConvertProtToImp::CanConvertTo(), CConvertRegionToImp::CanConvertTo(), CConvertCommentToImp::CanConvertTo(), CConvertGeneToImp::CanConvertTo(), CConvertRnaToImp::CanConvertTo(), CConvertSiteToImp::CanConvertTo(), CConvertImpToImp::CanConvertTo(), and x_SimpleConversion().

◆ x_IsProtSubtype() bool CConvertFeatureBase::x_IsProtSubtype ( objects::CSeqFeatData::ESubtype subtype ) protected ◆ x_IsRnaSubtype() bool CConvertFeatureBase::x_IsRnaSubtype ( objects::CSeqFeatData::ESubtype subtype ) protected ◆ x_MoveFeatureToProtein() bool CConvertFeatureBase::x_MoveFeatureToProtein ( const objects::CSeq_feat & orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope & scope ) protected

Definition at line 359 of file convert_feat.cpp.

References AdjustMappedStop(), CSeq_loc_Base::e_Null, CSeq_loc_Mapper_Base::eLocationToProduct, eOverlap_Contained, CSeqFeatData::eSubtype_cdregion, fBestFeat_Defaults, fBestFeat_FavorLonger, GetBestOverlappingFeat(), CConstRef< C, Locker >::GetPointer(), CSeq_feat_Base::GetProduct(), CSeq_feat_Base::IsSetProduct(), CSeq_loc_Mapper_Base::Map(), orig, CSeq_feat_Base::SetLocation(), CSeq_loc_Mapper_Base::SetMergeAbutting(), and CSeq_loc_Base::Which().

Referenced by CConvertImpToProt::Convert(), CConvertRegionToProt::Convert(), CConvertCDSToProt::Convert(), and x_SimpleConversion().

◆ x_SimpleConversion() CRef< CCmdComposite > CConvertFeatureBase::x_SimpleConversion ( const objects::CSeq_feat & orig, CRef< objects::CSeq_feat > new_feat, bool keep_orig, objects::CScope & scope ) protected

Definition at line 193 of file convert_feat.cpp.

References cmd, CSeqFeatData::eSubtype_bond, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_site, FindRemoveTranscriptId(), CScope::GetBioseqHandle(), GetDeleteFeatureCommand(), CSeq_feat_Base::GetLocation(), GetOverlappingGene(), GetOverlappingmRNA(), GetProtProcessedFromFeatureSubtype(), GetRnaTypeFromFeatureSubtype(), CBioseq_Handle::GetSeq_entry_Handle(), CScope::GetSeq_featHandle(), NStr::IsBlank(), CSeq_feat_Base::IsSetProduct(), m_BondList, m_SiteList, m_To, NULL, orig, CSeq_feat_Base::ResetProduct(), CSeq_feat_Base::SetData(), CSeqFeatData::SubtypeValueToName(), x_FindBondType(), x_FindNcrnaClass(), x_FindPlaceOnProt(), x_FindRemoveGene(), x_FindRemovemRNA(), x_FindSiteType(), x_IsImportSubtype(), x_IsProtSubtype(), x_IsRnaSubtype(), and x_MoveFeatureToProtein().

◆ m_BondList objects::CBondList CConvertFeatureBase::m_BondList protected ◆ m_create_general_only bool CConvertFeatureBase::m_create_general_only = false protected ◆ m_From objects::CSeqFeatData::ESubtype CConvertFeatureBase::m_From protected ◆ m_offset ◆ m_Options

Definition at line 160 of file convert_feat.hpp.

Referenced by CConvertCDSToPseudoGene::CConvertCDSToPseudoGene(), CConvertFeatureBase(), GetOptions(), SetOptions(), x_AddBondDestinationConversionOptions(), x_AddCDSDestinationConversionOptions(), x_AddCDSSourceConversionOptions(), x_AddRegionDestionationConversionOptions(), x_AddRnaDestinationConversionOptions(), x_AddSiteDestinationConversionOptions(), and x_FindOption().

◆ m_SiteList objects::CSiteList CConvertFeatureBase::m_SiteList protected ◆ m_To objects::CSeqFeatData::ESubtype CConvertFeatureBase::m_To protected

Definition at line 158 of file convert_feat.hpp.

◆ s_BondType ◆ s_IsPseudo ◆ s_NcrnaClass ◆ s_PlaceOnProt ◆ s_RemoveGene ◆ s_RemovemRNA ◆ s_RemoveTranscriptID ◆ s_SiteType

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

include/gui/objutils/convert_feat.hpp
src/gui/objutils/convert_feat.cpp

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