Search Toolkit Book for CDbtag
#include <objects/general/Dbtag.hpp>
Inheritance diagram for CDbtag:
Collaboration diagram for CDbtag:
Public Member Functions | |
| CDbtag (void) | |
| ~CDbtag (void) | |
| int | Compare (const CDbtag &dbt2) const |
| bool | Match (const CDbtag &dbt2) const |
| bool | SetAsMatchingTo (const CDbtag &dbt2) |
| void | GetLabel (string *label) const |
| bool | IsApproved (EIsRefseq refseq=eIsRefseq_No, EIsSource is_source=eIsSource_No, EIsEstOrGss is_est_or_gss=eIsEstOrGss_No) const |
| const char * | IsApprovedNoCase (EIsRefseq refseq=eIsRefseq_No, EIsSource is_source=eIsSource_No) const |
| bool | IsApproved (TDbtagGroup group) const |
| bool | IsSkippable (void) const |
| EDbtagType | GetType (void) const |
| bool | GetDBFlags (bool &is_refseq, bool &is_src, string &correct_caps) const |
| TDbtagGroup | GetDBFlags (string &correct_caps) const |
| void | InvalidateType (void) |
| string | GetUrl (void) const |
| string | GetUrl (TTaxId taxid) const |
| string | GetUrl (const string &taxname) const |
| string | GetUrl (const string &genus, const string &species, const string &subspecies=kEmptyStr) const |
| Public Member Functions inherited from CDbtag_Base | |
| CDbtag_Base (void) | |
| virtual | ~CDbtag_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetDb (void) const |
| name of database or system 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... | |
| void | SetDb (const TDb &value) |
| Assign a value to Db data member. More... | |
| void | SetDb (TDb &&value) |
| TDb & | SetDb (void) |
| Assign a value to Db data member. More... | |
| bool | IsSetTag (void) const |
| appropriate tag Check if a value has been assigned to Tag data member. More... | |
| bool | CanGetTag (void) const |
| Check if it is safe to call GetTag method. More... | |
| void | ResetTag (void) |
| Reset Tag data member. More... | |
| const TTag & | GetTag (void) const |
| Get the Tag member data. More... | |
| void | SetTag (TTag &value) |
| Assign a value to Tag data member. More... | |
| TTag & | SetTag (void) |
| Assign a value to Tag 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 CDbtag_Base | Tparent |
Private Member Functions | |
| CDbtag (const CDbtag &) | |
| CDbtag & | operator= (const CDbtag &) |
Static Private Member Functions | |
| static bool | x_LooksLikeAccession (const string &tag, int &out_num_alpha, int &out_num_digit, int &out_num_unscr) |
Private Attributes | |
| EDbtagType | m_Type |
Additional Inherited Members | |
| 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
Member Typedef Documentation
◆ TDbtagGroup
| typedef int CDbtag::TDbtagGroup |
◆ Tparent
|
private |
Member Enumeration Documentation
◆ EDbtagGroup
| enum CDbtag::EDbtagGroup |
◆ EDbtagType
| enum CDbtag::EDbtagType |
◆ EIsEstOrGss
| enum CDbtag::EIsEstOrGss |
◆ EIsRefseq
| enum CDbtag::EIsRefseq |
◆ EIsSource
| enum CDbtag::EIsSource |
Constructor & Destructor Documentation
◆ CDbtag() [1/2]
◆ ~CDbtag()
◆ CDbtag() [2/2]
Member Function Documentation
◆ Compare()
Definition at line 176 of file Dbtag.cpp.
References CObject_id::Compare(), PNocase_Generic< T >::Compare(), CDbtag_Base::GetDb(), and CDbtag_Base::GetTag().
Referenced by CSeq_id::CompareOrdered(), SSortReferenceByName::operator()(), SChildLess::operator()(), s_DbtagCompare(), and s_DbtagEqual().
◆ GetDBFlags() [1/2]
Definition at line 327 of file Dbtag.cpp.
References fNone, fRefSeq, and fSrc.
Referenced by BOOST_AUTO_TEST_CASE(), CValidator::IsValidDbxref(), and CValidError_imp::ValidateDbxref().
◆ GetDBFlags() [2/2]
| CDbtag::TDbtagGroup CDbtag::GetDBFlags | ( | string & | correct_caps | ) | const |
Definition at line 305 of file Dbtag.cpp.
References CDbtag_Base::CanGetDb(), fNone, and CDbtag_Base::GetDb().
◆ GetLabel()
| void CDbtag::GetLabel | ( | string * | label | ) | const |
Definition at line 187 of file Dbtag.cpp.
References CObject_id_Base::e_Id, CObject_id_Base::e_Str, NStr::eNocase, CDbtag_Base::GetDb(), GetId(), CDbtag_Base::GetTag(), NStr::IntToString(), label, NStr::StartsWith(), and str().
Referenced by CVariationHandler::GetLabel(), CDiscrepancyObject::GetTextObjectDescription(), GetTextObjectDescription(), CGuiObjectInfoVariant::GetToolTip(), CGeneralIDField::GetVal(), CEditingActionEntireGeneralId::GetValue(), s_GetContentLabel(), CValidError_bioseq::ValidateIDSetAgainstDb(), CGvfWriteRecord::x_AssignAttributeID(), CGvfWriteRecord::x_AssignAttributeParent(), and CXcompareAnnotsApplication::x_ProcessComparison().
◆ GetType()
| CDbtag::EDbtagType CDbtag::GetType | ( | void | ) | const |
Definition at line 289 of file Dbtag.cpp.
References CDbtag_Base::CanGetDb(), eDbtagType_bad, CDbtag_Base::GetDb(), and m_Type.
Referenced by BOOST_AUTO_TEST_CASE(), CSeq_id::Set(), and CVcfWriter::x_WriteFeatureInfo().
◆ GetUrl() [1/4]
| string CDbtag::GetUrl | ( | const string & | genus, |
| const string & | species, | ||
| const string & | subspecies = kEmptyStr |
||
| ) | const |
◆ GetUrl() [2/4]
◆ GetUrl() [3/4]
◆ GetUrl() [4/4]
| string CDbtag::GetUrl | ( | void | ) | const |
Referenced by CFlatXrefQVal::Format().
◆ InvalidateType()
| void CDbtag::InvalidateType | ( | void | ) |
Definition at line 339 of file Dbtag.cpp.
References eDbtagType_bad, and m_Type.
◆ IsApproved() [1/2]
| bool CDbtag::IsApproved | ( | EIsRefseq | refseq = eIsRefseq_No, |
| EIsSource | is_source = eIsSource_No, |
||
| EIsEstOrGss | is_est_or_gss = eIsEstOrGss_No |
||
| ) | const |
Definition at line 215 of file Dbtag.cpp.
References CDbtag_Base::CanGetDb(), eIsEstOrGss_Yes, eIsRefseq_Yes, eIsSource_Yes, fGenBank, fRefSeq, fSrc, and CDbtag_Base::GetDb().
Referenced by BOOST_AUTO_TEST_CASE(), and CFlatXrefQVal::Format().
◆ IsApproved() [2/2]
| bool CDbtag::IsApproved | ( | TDbtagGroup | group | ) | const |
Definition at line 269 of file Dbtag.cpp.
References CDbtag_Base::CanGetDb(), and CDbtag_Base::GetDb().
◆ IsApprovedNoCase()
| const char * CDbtag::IsApprovedNoCase | ( | EIsRefseq | refseq = eIsRefseq_No, |
| EIsSource | is_source = eIsSource_No |
||
| ) | const |
Definition at line 245 of file Dbtag.cpp.
References CDbtag_Base::CanGetDb(), eIsRefseq_Yes, eIsSource_Yes, fRefSeq, fSrc, CDbtag_Base::GetDb(), and NULL.
Referenced by BOOST_AUTO_TEST_CASE().
◆ IsSkippable()
| bool CDbtag::IsSkippable | ( | void | ) | const |
Definition at line 281 of file Dbtag.cpp.
References CDbtag_Base::GetDb().
Referenced by CBioseqIndex::CBioseqIndex(), GetProteinId(), GetTitle(), CValidError_imp::Setup(), CEditSeqId::x_CollectChangedIds(), CDeflineGenerator::x_SetFlags(), and CSingleFeatValidator::x_ValidateLocusTagGeneralMatch().
◆ Match()
Definition at line 158 of file Dbtag.cpp.
References CSerialObject::Equals(), CDbtag_Base::GetDb(), and CDbtag_Base::GetTag().
Referenced by CDbEquals::operator()(), CValidError_bioseq::ValidateIDSetAgainstDb(), and CFlatXrefQVal::x_XrefInGeneXref().
◆ operator=()
◆ SetAsMatchingTo()
Definition at line 166 of file Dbtag.cpp.
References CDbtag_Base::GetDb(), CDbtag_Base::GetTag(), CDbtag_Base::SetDb(), and CDbtag_Base::SetTag().
◆ x_LooksLikeAccession()
|
staticprivate |
Member Data Documentation
◆ m_Type
|
mutableprivate |
Definition at line 328 of file Dbtag.hpp.
Referenced by GetType(), and InvalidateType().
The documentation for this class was generated from the following files:
