Search Toolkit Book for CGene_ref
#include <objects/seqfeat/Gene_ref.hpp>
Inheritance diagram for CGene_ref:
Collaboration diagram for CGene_ref:
Public Member Functions | |
| CGene_ref (void) | |
| ~CGene_ref (void) | |
| void | GetLabel (string *label) const |
| bool | IsSuppressed (void) const |
| bool | RefersToSameGene (const CGene_ref &xref) const |
| Public Member Functions inherited from CGene_ref_Base | |
| CGene_ref_Base (void) | |
| virtual | ~CGene_ref_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetLocus (void) const |
| Official gene symbol Check if a value has been assigned to Locus data member. More... | |
| bool | CanGetLocus (void) const |
| Check if it is safe to call GetLocus method. More... | |
| void | ResetLocus (void) |
| Reset Locus data member. More... | |
| const TLocus & | GetLocus (void) const |
| Get the Locus member data. More... | |
| void | SetLocus (const TLocus &value) |
| Assign a value to Locus data member. More... | |
| void | SetLocus (TLocus &&value) |
| TLocus & | SetLocus (void) |
| Assign a value to Locus data member. More... | |
| bool | IsSetAllele (void) const |
| Official allele designation Check if a value has been assigned to Allele data member. More... | |
| bool | CanGetAllele (void) const |
| Check if it is safe to call GetAllele method. More... | |
| void | ResetAllele (void) |
| Reset Allele data member. More... | |
| const TAllele & | GetAllele (void) const |
| Get the Allele member data. More... | |
| void | SetAllele (const TAllele &value) |
| Assign a value to Allele data member. More... | |
| void | SetAllele (TAllele &&value) |
| TAllele & | SetAllele (void) |
| Assign a value to Allele data member. More... | |
| bool | IsSetDesc (void) const |
| descriptive name Check if a value has been assigned to Desc data member. More... | |
| bool | CanGetDesc (void) const |
| Check if it is safe to call GetDesc method. More... | |
| void | ResetDesc (void) |
| Reset Desc data member. More... | |
| const TDesc & | GetDesc (void) const |
| Get the Desc member data. More... | |
| void | SetDesc (const TDesc &value) |
| Assign a value to Desc data member. More... | |
| void | SetDesc (TDesc &&value) |
| TDesc & | SetDesc (void) |
| Assign a value to Desc data member. More... | |
| bool | IsSetMaploc (void) const |
| descriptive map location Check if a value has been assigned to Maploc data member. More... | |
| bool | CanGetMaploc (void) const |
| Check if it is safe to call GetMaploc method. More... | |
| void | ResetMaploc (void) |
| Reset Maploc data member. More... | |
| const TMaploc & | GetMaploc (void) const |
| Get the Maploc member data. More... | |
| void | SetMaploc (const TMaploc &value) |
| Assign a value to Maploc data member. More... | |
| void | SetMaploc (TMaploc &&value) |
| TMaploc & | SetMaploc (void) |
| Assign a value to Maploc data member. More... | |
| bool | IsSetPseudo (void) const |
| pseudogene Check if a value has been assigned to Pseudo data member. More... | |
| bool | CanGetPseudo (void) const |
| Check if it is safe to call GetPseudo method. More... | |
| void | ResetPseudo (void) |
| Reset Pseudo data member. More... | |
| void | SetDefaultPseudo (void) |
| Assign default value to Pseudo data member. More... | |
| TPseudo | GetPseudo (void) const |
| Get the Pseudo member data. More... | |
| void | SetPseudo (TPseudo value) |
| Assign a value to Pseudo data member. More... | |
| TPseudo & | SetPseudo (void) |
| Assign a value to Pseudo data member. More... | |
| bool | IsSetDb (void) const |
| ids in other dbases Check if a value has been assigned to Db data member. More... | |
| bool | CanGetDb (void) const |
| Check if it is safe to call GetDb method. More... | |
| void | ResetDb (void) |
| Reset Db data member. More... | |
| const TDb & | GetDb (void) const |
| Get the Db member data. More... | |
| TDb & | SetDb (void) |
| Assign a value to Db data member. More... | |
| bool | IsSetSyn (void) const |
| synonyms for locus Check if a value has been assigned to Syn data member. More... | |
| bool | CanGetSyn (void) const |
| Check if it is safe to call GetSyn method. More... | |
| void | ResetSyn (void) |
| Reset Syn data member. More... | |
| const TSyn & | GetSyn (void) const |
| Get the Syn member data. More... | |
| TSyn & | SetSyn (void) |
| Assign a value to Syn data member. More... | |
| bool | IsSetLocus_tag (void) const |
| systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data member. More... | |
| bool | CanGetLocus_tag (void) const |
| Check if it is safe to call GetLocus_tag method. More... | |
| void | ResetLocus_tag (void) |
| Reset Locus_tag data member. More... | |
| const TLocus_tag & | GetLocus_tag (void) const |
| Get the Locus_tag member data. More... | |
| void | SetLocus_tag (const TLocus_tag &value) |
| Assign a value to Locus_tag data member. More... | |
| void | SetLocus_tag (TLocus_tag &&value) |
| TLocus_tag & | SetLocus_tag (void) |
| Assign a value to Locus_tag data member. More... | |
| bool | IsSetFormal_name (void) const |
| Check if a value has been assigned to Formal_name data member. More... | |
| bool | CanGetFormal_name (void) const |
| Check if it is safe to call GetFormal_name method. More... | |
| void | ResetFormal_name (void) |
| Reset Formal_name data member. More... | |
| const TFormal_name & | GetFormal_name (void) const |
| Get the Formal_name member data. More... | |
| void | SetFormal_name (TFormal_name &value) |
| Assign a value to Formal_name data member. More... | |
| TFormal_name & | SetFormal_name (void) |
| Assign a value to Formal_name data member. More... | |
| virtual void | Reset (void) |
| Reset the whole object. More... | |
| Public Member Functions inherited from CSerialObject | |
| CSerialObject (void) | |
| virtual | ~CSerialObject (void) |
| virtual const CTypeInfo * | GetThisTypeInfo (void) const =0 |
| virtual void | Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive) |
| Set object to copy of another one. More... | |
| virtual bool | Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const |
| Check if both objects contain the same values. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| void | ThrowUnassigned (TMemberIndex index) const |
| void | ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const |
| bool | HasNamespaceName (void) const |
| Check if object data type has namespace name. More... | |
| const string & | GetNamespaceName (void) const |
| Get namespace name. More... | |
| bool | HasNamespacePrefix (void) const |
| Check if data type has namespace prefix. More... | |
| const string & | GetNamespacePrefix (void) const |
| Get namespace prefix. More... | |
| Public Member Functions inherited from CObject | |
| 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... | |
| Public Member Functions inherited from CDebugDumpable | |
| 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 |
Private Types | |
| typedef CGene_ref_Base | Tparent |
Private Member Functions | |
| CGene_ref (const CGene_ref &value) | |
| CGene_ref & | operator= (const CGene_ref &value) |
Additional Inherited Members | |
| Public Types inherited from CGene_ref_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_locus , e_allele , e_desc , e_maploc , e_pseudo , e_db , e_syn , e_locus_tag , e_formal_name } |
| typedef string | TLocus |
| typedef string | TAllele |
| typedef string | TDesc |
| typedef string | TMaploc |
| typedef bool | TPseudo |
| typedef vector< CRef< CDbtag > > | TDb |
| typedef list< string > | TSyn |
| typedef string | TLocus_tag |
| typedef CGene_nomenclature | TFormal_name |
| typedef Tparent::CMemberIndex< E_memberIndex, 10 > | TmemberIndex |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CSerialObject | |
| static void | SetVerifyDataThread (ESerialVerifyData verify) |
| static void | SetVerifyDataGlobal (ESerialVerifyData verify) |
| static string | UnassignedString (void) |
| static CStringUTF8 | UnassignedStringUTF8 (void) |
| static char | UnassignedByte (void) |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CSerialObject | |
| static const char * | ms_UnassignedStr = "<*unassigned*>" |
| static const char | ms_UnassignedByte = char(0xcd) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
Definition at line 51 of file Gene_ref.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 53 of file Gene_ref.hpp.
Constructor & Destructor Documentation
◆ CGene_ref() [1/2]
|
inline |
Definition at line 81 of file Gene_ref.hpp.
◆ ~CGene_ref()
| CGene_ref::~CGene_ref | ( | void | ) |
Definition at line 52 of file Gene_ref.cpp.
◆ CGene_ref() [2/2]
Member Function Documentation
◆ GetLabel()
| void CGene_ref::GetLabel | ( | string * | label | ) | const |
Definition at line 57 of file Gene_ref.cpp.
References ctll::empty(), CGene_ref_Base::GetDb(), CGene_ref_Base::GetDesc(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::GetMaploc(), CGene_ref_Base::GetSyn(), CGene_ref_Base::IsSetDb(), CGene_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CGene_ref_Base::IsSetMaploc(), CGene_ref_Base::IsSetSyn(), label, and ncbi::grid::netcache::search::fields::size.
Referenced by CFeatureGenePanel::CreateControls(), CGeneFinder::GetAssociatedGeneInfo(), GetBestGeneForCds(), GetBestGeneForMrna(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), CEntrezgeneHandler::GetLabel(), GetMrnasForGene(), CReadBlastApp::overlaps_na(), CReadBlastApp::overlaps_prot_na(), CGFFReader::Read(), s_GetCdregionContentLabel(), s_GetCdregionLabel(), s_GetContentLabel(), CValidError_bioseq::ValidateRawConst(), CFeatureItem::x_AddFTableQuals(), and CGFFReader::x_CreateGeneFeatures().
◆ IsSuppressed()
| bool CGene_ref::IsSuppressed | ( | void | ) | const |
Definition at line 75 of file Gene_ref.cpp.
References ctll::empty(), CGene_ref_Base::GetAllele(), CGene_ref_Base::GetDb(), CGene_ref_Base::GetDesc(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::GetMaploc(), CGene_ref_Base::GetSyn(), CGene_ref_Base::IsSetAllele(), CGene_ref_Base::IsSetDb(), CGene_ref_Base::IsSetDesc(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CGene_ref_Base::IsSetMaploc(), CGene_ref_Base::IsSetSyn(), and ncbi::grid::netcache::search::fields::size.
Referenced by CGeneFinder::GetAssociatedGeneInfo(), GetBestGeneForCds(), GetBestGeneForMrna(), GetGeneForFeature(), NMacroUtil::GetLocusTagFromGene(), GetMrnasForGene(), CGeneFinder::GetSuppressionCheckGeneRef(), CCleanup::IsGeneXrefUnnecessary(), CGeneFinder::ResolveGeneObjectId(), CMacroFunction_RemoveGeneXref::s_GeneXrefMatchesSuppression(), CMacroFunction_RemoveQual::s_RemoveFields(), CMacroFunction_SwapQual::TheFunction(), CValidError_bioseq::ValidateBadGeneOverlap(), CFeatureItem::x_AddFTableQuals(), CFeatureItem::x_AddQualOperon(), CFeatureItem::x_AddQuals(), CFeatureItem::x_AddQualsGene(), CFeatureItem::x_AddQualsIdx(), CAutoDefFeatureClause::x_GetGeneName(), CSingleFeatValidator::x_ValidateGeneXRef(), and CSingleFeatValidator::x_ValidateLocusTagGeneralMatch().
◆ operator=()
◆ RefersToSameGene()
Definition at line 91 of file Gene_ref.cpp.
References NStr::Equal(), ctll::front(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CGene_ref_Base::GetSyn(), NStr::IsBlank(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CGene_ref_Base::IsSetSyn(), and ncbi::grid::netcache::search::fields::size.
Referenced by CCleanup::IsGeneXrefUnnecessary().
The documentation for this class was generated from the following files:
- include/objects/seqfeat/Gene_ref.hpp
- src/objects/seqfeat/Gene_ref.cpp
