Search Toolkit Book for CEntrezgene
#include <objects/entrezgene/Entrezgene.hpp>
Inheritance diagram for CEntrezgene:
Collaboration diagram for CEntrezgene:
Public Member Functions | |
| CEntrezgene (void) | |
| ~CEntrezgene (void) | |
| CRef< CGene_nomenclature > | GetNomenclature () const |
| string | GetDescription () const |
| string | GetSymbol () const |
| CRef< CGene_commentary > | FindComment (const string &heading) const |
| void | GetPubs (set< ncbi::TEntrezId > &pubs) const |
| Public Member Functions inherited from CEntrezgene_Base | |
| CEntrezgene_Base (void) | |
| virtual | ~CEntrezgene_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetTrack_info (void) const |
| not in submission, but in retrieval Check if a value has been assigned to Track_info data member. More... | |
| bool | CanGetTrack_info (void) const |
| Check if it is safe to call GetTrack_info method. More... | |
| void | ResetTrack_info (void) |
| Reset Track_info data member. More... | |
| const TTrack_info & | GetTrack_info (void) const |
| Get the Track_info member data. More... | |
| void | SetTrack_info (TTrack_info &value) |
| Assign a value to Track_info data member. More... | |
| TTrack_info & | SetTrack_info (void) |
| Assign a value to Track_info data member. More... | |
| bool | IsSetType (void) const |
| Check if a value has been assigned to Type data member. More... | |
| bool | CanGetType (void) const |
| Check if it is safe to call GetType method. More... | |
| void | ResetType (void) |
| Reset Type data member. More... | |
| TType | GetType (void) const |
| Get the Type member data. More... | |
| void | SetType (TType value) |
| Assign a value to Type data member. More... | |
| TType & | SetType (void) |
| Assign a value to Type data member. More... | |
| bool | IsSetSource (void) const |
| Check if a value has been assigned to Source data member. More... | |
| bool | CanGetSource (void) const |
| Check if it is safe to call GetSource method. More... | |
| void | ResetSource (void) |
| Reset Source data member. More... | |
| const TSource & | GetSource (void) const |
| Get the Source member data. More... | |
| void | SetSource (TSource &value) |
| Assign a value to Source data member. More... | |
| TSource & | SetSource (void) |
| Assign a value to Source data member. More... | |
| bool | IsSetGene (void) const |
| for locus-tag see note 3 Check if a value has been assigned to Gene data member. More... | |
| bool | CanGetGene (void) const |
| Check if it is safe to call GetGene method. More... | |
| void | ResetGene (void) |
| Reset Gene data member. More... | |
| const TGene & | GetGene (void) const |
| Get the Gene member data. More... | |
| void | SetGene (TGene &value) |
| Assign a value to Gene data member. More... | |
| TGene & | SetGene (void) |
| Assign a value to Gene data member. More... | |
| bool | IsSetProt (void) const |
| Check if a value has been assigned to Prot data member. More... | |
| bool | CanGetProt (void) const |
| Check if it is safe to call GetProt method. More... | |
| void | ResetProt (void) |
| Reset Prot data member. More... | |
| const TProt & | GetProt (void) const |
| Get the Prot member data. More... | |
| void | SetProt (TProt &value) |
| Assign a value to Prot data member. More... | |
| TProt & | SetProt (void) |
| Assign a value to Prot data member. More... | |
| bool | IsSetRna (void) const |
| Check if a value has been assigned to Rna data member. More... | |
| bool | CanGetRna (void) const |
| Check if it is safe to call GetRna method. More... | |
| void | ResetRna (void) |
| Reset Rna data member. More... | |
| const TRna & | GetRna (void) const |
| Get the Rna member data. More... | |
| void | SetRna (TRna &value) |
| Assign a value to Rna data member. More... | |
| TRna & | SetRna (void) |
| Assign a value to Rna data member. More... | |
| bool | IsSetSummary (void) const |
| short summary Check if a value has been assigned to Summary data member. More... | |
| bool | CanGetSummary (void) const |
| Check if it is safe to call GetSummary method. More... | |
| void | ResetSummary (void) |
| Reset Summary data member. More... | |
| const TSummary & | GetSummary (void) const |
| Get the Summary member data. More... | |
| void | SetSummary (const TSummary &value) |
| Assign a value to Summary data member. More... | |
| void | SetSummary (TSummary &&value) |
| TSummary & | SetSummary (void) |
| Assign a value to Summary data member. More... | |
| bool | IsSetLocation (void) const |
| Check if a value has been assigned to Location data member. More... | |
| bool | CanGetLocation (void) const |
| Check if it is safe to call GetLocation method. More... | |
| void | ResetLocation (void) |
| Reset Location data member. More... | |
| const TLocation & | GetLocation (void) const |
| Get the Location member data. More... | |
| TLocation & | SetLocation (void) |
| Assign a value to Location data member. More... | |
| bool | IsSetGene_source (void) const |
| NCBI source to Entrez Check if a value has been assigned to Gene_source data member. More... | |
| bool | CanGetGene_source (void) const |
| Check if it is safe to call GetGene_source method. More... | |
| void | ResetGene_source (void) |
| Reset Gene_source data member. More... | |
| const TGene_source & | GetGene_source (void) const |
| Get the Gene_source member data. More... | |
| void | SetGene_source (TGene_source &value) |
| Assign a value to Gene_source data member. More... | |
| TGene_source & | SetGene_source (void) |
| Assign a value to Gene_source data member. More... | |
| bool | IsSetLocus (void) const |
| location of gene on chromosome (if known) and all information about products (mRNA, proteins and so on) 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... | |
| TLocus & | SetLocus (void) |
| Assign a value to Locus data member. More... | |
| bool | IsSetProperties (void) const |
| Check if a value has been assigned to Properties data member. More... | |
| bool | CanGetProperties (void) const |
| Check if it is safe to call GetProperties method. More... | |
| void | ResetProperties (void) |
| Reset Properties data member. More... | |
| const TProperties & | GetProperties (void) const |
| Get the Properties member data. More... | |
| TProperties & | SetProperties (void) |
| Assign a value to Properties data member. More... | |
| bool | IsSetRefgene (void) const |
| NG for this? Check if a value has been assigned to Refgene data member. More... | |
| bool | CanGetRefgene (void) const |
| Check if it is safe to call GetRefgene method. More... | |
| void | ResetRefgene (void) |
| Reset Refgene data member. More... | |
| const TRefgene & | GetRefgene (void) const |
| Get the Refgene member data. More... | |
| TRefgene & | SetRefgene (void) |
| Assign a value to Refgene data member. More... | |
| bool | IsSetHomology (void) const |
| Check if a value has been assigned to Homology data member. More... | |
| bool | CanGetHomology (void) const |
| Check if it is safe to call GetHomology method. More... | |
| void | ResetHomology (void) |
| Reset Homology data member. More... | |
| const THomology & | GetHomology (void) const |
| Get the Homology member data. More... | |
| THomology & | SetHomology (void) |
| Assign a value to Homology data member. More... | |
| bool | IsSetComments (void) const |
| Check if a value has been assigned to Comments data member. More... | |
| bool | CanGetComments (void) const |
| Check if it is safe to call GetComments method. More... | |
| void | ResetComments (void) |
| Reset Comments data member. More... | |
| const TComments & | GetComments (void) const |
| Get the Comments member data. More... | |
| TComments & | SetComments (void) |
| Assign a value to Comments data member. More... | |
| bool | IsSetUnique_keys (void) const |
| see note 3 Check if a value has been assigned to Unique_keys data member. More... | |
| bool | CanGetUnique_keys (void) const |
| Check if it is safe to call GetUnique_keys method. More... | |
| void | ResetUnique_keys (void) |
| Reset Unique_keys data member. More... | |
| const TUnique_keys & | GetUnique_keys (void) const |
| Get the Unique_keys member data. More... | |
| TUnique_keys & | SetUnique_keys (void) |
| Assign a value to Unique_keys data member. More... | |
| bool | IsSetXtra_index_terms (void) const |
| see note 2 Check if a value has been assigned to Xtra_index_terms data member. More... | |
| bool | CanGetXtra_index_terms (void) const |
| Check if it is safe to call GetXtra_index_terms method. More... | |
| void | ResetXtra_index_terms (void) |
| Reset Xtra_index_terms data member. More... | |
| const TXtra_index_terms & | GetXtra_index_terms (void) const |
| Get the Xtra_index_terms member data. More... | |
| TXtra_index_terms & | SetXtra_index_terms (void) |
| Assign a value to Xtra_index_terms data member. More... | |
| bool | IsSetXtra_properties (void) const |
| see note 2 Check if a value has been assigned to Xtra_properties data member. More... | |
| bool | CanGetXtra_properties (void) const |
| Check if it is safe to call GetXtra_properties method. More... | |
| void | ResetXtra_properties (void) |
| Reset Xtra_properties data member. More... | |
| const TXtra_properties & | GetXtra_properties (void) const |
| Get the Xtra_properties member data. More... | |
| TXtra_properties & | SetXtra_properties (void) |
| Assign a value to Xtra_properties data member. More... | |
| bool | IsSetXtra_iq (void) const |
| see note 2 Check if a value has been assigned to Xtra_iq data member. More... | |
| bool | CanGetXtra_iq (void) const |
| Check if it is safe to call GetXtra_iq method. More... | |
| void | ResetXtra_iq (void) |
| Reset Xtra_iq data member. More... | |
| const TXtra_iq & | GetXtra_iq (void) const |
| Get the Xtra_iq member data. More... | |
| TXtra_iq & | SetXtra_iq (void) |
| Assign a value to Xtra_iq data member. More... | |
| bool | IsSetNon_unique_keys (void) const |
| Check if a value has been assigned to Non_unique_keys data member. More... | |
| bool | CanGetNon_unique_keys (void) const |
| Check if it is safe to call GetNon_unique_keys method. More... | |
| void | ResetNon_unique_keys (void) |
| Reset Non_unique_keys data member. More... | |
| const TNon_unique_keys & | GetNon_unique_keys (void) const |
| Get the Non_unique_keys member data. More... | |
| TNon_unique_keys & | SetNon_unique_keys (void) |
| Assign a value to Non_unique_keys 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) noexcept |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const noexcept |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const noexcept |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const noexcept |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const noexcept |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const noexcept |
| 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 CEntrezgene_Base | Tparent |
Private Member Functions | |
| CEntrezgene (const CEntrezgene &value) | |
| CEntrezgene & | operator= (const CEntrezgene &value) |
Additional Inherited Members | |
| Public Types inherited from CEntrezgene_Base | |
| enum | EType { eType_unknown = 0 , eType_tRNA = 1 , eType_rRNA = 2 , eType_snRNA = 3 , eType_scRNA = 4 , eType_snoRNA = 5 , eType_protein_coding = 6 , eType_pseudo = 7 , eType_transposon = 8 , eType_miscRNA = 9 , eType_ncRNA = 10 , eType_biological_region = 11 , eType_other = 255 } |
| type of Gene More... | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_track_info , e_type , e_source , e_gene , e_prot , e_rna , e_summary , e_location , e_gene_source , e_locus , e_properties , e_refgene , e_homology , e_comments , e_unique_keys , e_xtra_index_terms , e_xtra_properties , e_xtra_iq , e_non_unique_keys } |
| typedef CGene_track | TTrack_info |
| typedef int | TType |
| typedef CBioSource | TSource |
| typedef CGene_ref | TGene |
| typedef CProt_ref | TProt |
| typedef CRNA_ref | TRna |
| typedef string | TSummary |
| typedef list< CRef< CMaps > > | TLocation |
| typedef CGene_source | TGene_source |
| typedef list< CRef< CGene_commentary > > | TLocus |
| typedef list< CRef< CGene_commentary > > | TProperties |
| typedef list< CRef< CGene_commentary > > | TRefgene |
| typedef list< CRef< CGene_commentary > > | THomology |
| typedef list< CRef< CGene_commentary > > | TComments |
| typedef list< CRef< CDbtag > > | TUnique_keys |
| typedef list< string > | TXtra_index_terms |
| typedef list< CRef< CXtra_Terms > > | TXtra_properties |
| typedef list< CRef< CXtra_Terms > > | TXtra_iq |
| typedef list< CRef< CDbtag > > | TNon_unique_keys |
| typedef Tparent::CMemberIndex< E_memberIndex, 20 > | 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 std::atomic<> More... | |
| typedef TCounter::value_type | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CEntrezgene_Base | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EType (void) |
| Access to EType's attributes (values, names) as defined in spec. 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 55 of file Entrezgene.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 57 of file Entrezgene.hpp.
Constructor & Destructor Documentation
◆ CEntrezgene() [1/2]
|
inline |
Definition at line 93 of file Entrezgene.hpp.
◆ ~CEntrezgene()
| CEntrezgene::~CEntrezgene | ( | void | ) |
Definition at line 60 of file Entrezgene.cpp.
◆ CEntrezgene() [2/2]
|
private |
Member Function Documentation
◆ FindComment()
| CRef< CGene_commentary > CEntrezgene::FindComment | ( | const string & | heading | ) | const |
Definition at line 218 of file Entrezgene.cpp.
References CEntrezgene_Base::GetComments().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetDescription()
| string CEntrezgene::GetDescription | ( | void | ) | const |
Definition at line 152 of file Entrezgene.cpp.
References ctll::empty(), CGene_ref_Base::GetDesc(), CProt_ref_Base::GetDesc(), CRNA_ref_Base::GetExt(), CEntrezgene_Base::GetGene(), CProt_ref_Base::GetName(), CRNA_ref_Base::C_Ext::GetName(), CEntrezgene_Base::GetProt(), CEntrezgene_Base::GetRna(), CEntrezgene_Base::GetType(), CRNA_ref_Base::C_Ext::IsName(), CRNA_ref_Base::IsSetExt(), CEntrezgene_Base::IsSetProt(), and CEntrezgene_Base::IsSetRna().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetNomenclature()
| CRef< CGene_nomenclature > CEntrezgene::GetNomenclature | ( | ) | const |
Definition at line 68 of file Entrezgene.cpp.
References CSerialObject::Assign(), CGene_nomenclature_Base::eStatus_interim, CGene_nomenclature_Base::eStatus_official, CGene_nomenclature_Base::eStatus_unknown, CGene_commentary_Base::eType_comment, CGene_commentary_Base::eType_property, CGene_ref_Base::GetFormal_name(), CEntrezgene_Base::GetGene(), CEntrezgene_Base::GetProperties(), GetSymbol(), CGene_ref_Base::IsSetFormal_name(), CGene_nomenclature_Base::IsSetSymbol(), label, CGene_nomenclature_Base::SetName(), CGene_nomenclature_Base::SetStatus(), CGene_nomenclature_Base::SetSymbol(), and text().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetPubs()
| void CEntrezgene::GetPubs | ( | set< ncbi::TEntrezId > & | pubs | ) | const |
Definition at line 234 of file Entrezgene.cpp.
References set< Key, Compare >::insert().
Referenced by BOOST_AUTO_TEST_CASE().
◆ GetSymbol()
| string CEntrezgene::GetSymbol | ( | void | ) | const |
Definition at line 190 of file Entrezgene.cpp.
References ctll::empty(), CEntrezgene_Base::GetGene(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CEntrezgene_Base::GetTrack_info(), and CEntrezgene_Base::IsSetLocus().
Referenced by BOOST_AUTO_TEST_CASE(), and GetNomenclature().
◆ operator=()
|
private |
The documentation for this class was generated from the following files:
- include/objects/entrezgene/Entrezgene.hpp
- src/objects/entrezgene/Entrezgene.cpp
