Search Toolkit Book for COrgName
#include <objects/seqfeat/OrgName.hpp>
Inheritance diagram for COrgName:
Collaboration diagram for COrgName:
Public Member Functions | |
| COrgName (void) | |
| ~COrgName (void) | |
| bool | GetFlatName (string &name_out, string *lineage=0) const |
| bool | IsFormalName () const |
| void | SetFormalNameFlag (bool bFormalName) |
| bool | IsUncultured () const |
| void | SetUncultured (bool bUncultured) |
| bool | IsModifierForwardingDisabled () const |
| void | DisableModifierForwarding () |
| void | EnableModifierForwarding () |
| CRef< COrgName > | MakeCommon (const COrgName &other) const |
| bool | GetNomenclature (string &result) const |
| bool | SetNomenclature (const string &nomenclature) |
| void | ResetNomenclature () |
| unsigned int | RemoveModBySubtype (COrgMod::ESubtype to_remove) |
| Public Member Functions inherited from COrgName_Base | |
| COrgName_Base (void) | |
| virtual | ~COrgName_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetName (void) const |
| Check if a value has been assigned to Name data member. More... | |
| bool | CanGetName (void) const |
| Check if it is safe to call GetName method. More... | |
| void | ResetName (void) |
| Reset Name data member. More... | |
| const TName & | GetName (void) const |
| Get the Name member data. More... | |
| void | SetName (TName &value) |
| Assign a value to Name data member. More... | |
| TName & | SetName (void) |
| Assign a value to Name data member. More... | |
| bool | IsSetAttrib (void) const |
| attribution of name Check if a value has been assigned to Attrib data member. More... | |
| bool | CanGetAttrib (void) const |
| Check if it is safe to call GetAttrib method. More... | |
| void | ResetAttrib (void) |
| Reset Attrib data member. More... | |
| const TAttrib & | GetAttrib (void) const |
| Get the Attrib member data. More... | |
| void | SetAttrib (const TAttrib &value) |
| Assign a value to Attrib data member. More... | |
| void | SetAttrib (TAttrib &&value) |
| TAttrib & | SetAttrib (void) |
| Assign a value to Attrib data member. More... | |
| bool | IsSetMod (void) const |
| Check if a value has been assigned to Mod data member. More... | |
| bool | CanGetMod (void) const |
| Check if it is safe to call GetMod method. More... | |
| void | ResetMod (void) |
| Reset Mod data member. More... | |
| const TMod & | GetMod (void) const |
| Get the Mod member data. More... | |
| TMod & | SetMod (void) |
| Assign a value to Mod data member. More... | |
| bool | IsSetLineage (void) const |
| lineage with semicolon separators Check if a value has been assigned to Lineage data member. More... | |
| bool | CanGetLineage (void) const |
| Check if it is safe to call GetLineage method. More... | |
| void | ResetLineage (void) |
| Reset Lineage data member. More... | |
| const TLineage & | GetLineage (void) const |
| Get the Lineage member data. More... | |
| void | SetLineage (const TLineage &value) |
| Assign a value to Lineage data member. More... | |
| void | SetLineage (TLineage &&value) |
| TLineage & | SetLineage (void) |
| Assign a value to Lineage data member. More... | |
| bool | IsSetGcode (void) const |
| genetic code (see CdRegion) Check if a value has been assigned to Gcode data member. More... | |
| bool | CanGetGcode (void) const |
| Check if it is safe to call GetGcode method. More... | |
| void | ResetGcode (void) |
| Reset Gcode data member. More... | |
| TGcode | GetGcode (void) const |
| Get the Gcode member data. More... | |
| void | SetGcode (TGcode value) |
| Assign a value to Gcode data member. More... | |
| TGcode & | SetGcode (void) |
| Assign a value to Gcode data member. More... | |
| bool | IsSetMgcode (void) const |
| mitochondrial genetic code Check if a value has been assigned to Mgcode data member. More... | |
| bool | CanGetMgcode (void) const |
| Check if it is safe to call GetMgcode method. More... | |
| void | ResetMgcode (void) |
| Reset Mgcode data member. More... | |
| TMgcode | GetMgcode (void) const |
| Get the Mgcode member data. More... | |
| void | SetMgcode (TMgcode value) |
| Assign a value to Mgcode data member. More... | |
| TMgcode & | SetMgcode (void) |
| Assign a value to Mgcode data member. More... | |
| bool | IsSetDiv (void) const |
| GenBank division code Check if a value has been assigned to Div data member. More... | |
| bool | CanGetDiv (void) const |
| Check if it is safe to call GetDiv method. More... | |
| void | ResetDiv (void) |
| Reset Div data member. More... | |
| const TDiv & | GetDiv (void) const |
| Get the Div member data. More... | |
| void | SetDiv (const TDiv &value) |
| Assign a value to Div data member. More... | |
| void | SetDiv (TDiv &&value) |
| TDiv & | SetDiv (void) |
| Assign a value to Div data member. More... | |
| bool | IsSetPgcode (void) const |
| plastid genetic code Check if a value has been assigned to Pgcode data member. More... | |
| bool | CanGetPgcode (void) const |
| Check if it is safe to call GetPgcode method. More... | |
| void | ResetPgcode (void) |
| Reset Pgcode data member. More... | |
| TPgcode | GetPgcode (void) const |
| Get the Pgcode member data. More... | |
| void | SetPgcode (TPgcode value) |
| Assign a value to Pgcode data member. More... | |
| TPgcode & | SetPgcode (void) |
| Assign a value to Pgcode 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 COrgName_Base | Tparent |
Private Member Functions | |
| COrgName (const COrgName &value) | |
| COrgName & | operator= (const COrgName &value) |
| void | x_SetAttribFlag (const string &name, bool bStartsWith=false) |
| void | x_ResetAttribFlag (const string &name, bool bStartsWith=false) |
| bool | x_GetAttribFlag (const string &name, bool bStartsWith=false) const |
| bool | x_GetAttribValue (const string &name, string &sValue) const |
Additional Inherited Members | |
| Public Types inherited from COrgName_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_name , e_attrib , e_mod , e_lineage , e_gcode , e_mgcode , e_div , e_pgcode } |
| typedef C_Name | TName |
| typedef string | TAttrib |
| typedef list< CRef< COrgMod > > | TMod |
| typedef string | TLineage |
| typedef int | TGcode |
| typedef int | TMgcode |
| typedef string | TDiv |
| typedef int | TPgcode |
| typedef Tparent::CMemberIndex< E_memberIndex, 9 > | 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 50 of file OrgName.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 52 of file OrgName.hpp.
Constructor & Destructor Documentation
◆ COrgName() [1/2]
|
inline |
Definition at line 117 of file OrgName.hpp.
Referenced by MakeCommon().
◆ ~COrgName()
| COrgName::~COrgName | ( | void | ) |
Definition at line 53 of file OrgName.cpp.
◆ COrgName() [2/2]
Member Function Documentation
◆ DisableModifierForwarding()
| void COrgName::DisableModifierForwarding | ( | ) |
Definition at line 310 of file OrgName.cpp.
References x_SetAttribFlag().
◆ EnableModifierForwarding()
| void COrgName::EnableModifierForwarding | ( | ) |
Definition at line 315 of file OrgName.cpp.
References x_ResetAttribFlag().
Referenced by COrg_ref::FilterOutParts().
◆ GetFlatName()
Definition at line 58 of file OrgName.cpp.
References COrgName_Base::C_Name::e_Binomial, COrgName_Base::C_Name::e_Hybrid, COrgName_Base::C_Name::e_Namedhybrid, COrgName_Base::C_Name::e_Partial, COrgName_Base::C_Name::e_Virus, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_variety, CMultiOrgName_Base::Get(), CPartialOrgName_Base::Get(), COrgName_Base::C_Name::GetBinomial(), CBinomialOrgName_Base::GetGenus(), COrgName_Base::C_Name::GetHybrid(), COrgName_Base::GetLineage(), COrgName_Base::GetMod(), COrgName_Base::GetName(), COrgName_Base::C_Name::GetNamedhybrid(), GetNomenclature(), COrgName_Base::C_Name::GetPartial(), CBinomialOrgName_Base::GetSpecies(), CBinomialOrgName_Base::GetSubspecies(), COrgName_Base::C_Name::GetVirus(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetName(), CBinomialOrgName_Base::IsSetSpecies(), CBinomialOrgName_Base::IsSetSubspecies(), ITERATE, NcbiEmptyString, NStr::StartsWith(), tmp, NStr::TruncateSpaces(), and COrgName_Base::C_Name::Which().
Referenced by s_MatchOrgname().
◆ GetNomenclature()
Definition at line 371 of file OrgName.cpp.
References COrgMod_Base::eSubtype_nomenclature, COrgName_Base::GetMod(), COrgName_Base::IsSetMod(), ITERATE, and result.
Referenced by GetFlatName(), and SetNomenclature().
◆ IsFormalName()
| bool COrgName::IsFormalName | ( | ) | const |
Definition at line 273 of file OrgName.cpp.
References x_GetAttribFlag().
◆ IsModifierForwardingDisabled()
| bool COrgName::IsModifierForwardingDisabled | ( | ) | const |
Definition at line 305 of file OrgName.cpp.
References x_GetAttribFlag().
Referenced by COrg_ref::FilterOutParts().
◆ IsUncultured()
| bool COrgName::IsUncultured | ( | ) | const |
Definition at line 287 of file OrgName.cpp.
References x_GetAttribFlag().
◆ MakeCommon()
Definition at line 323 of file OrgName.cpp.
References CSerialObject::Assign(), COrgName(), CSerialObject::Equals(), COrgName_Base::GetMod(), COrgName_Base::GetName(), COrgName_Base::IsSetAttrib(), COrgName_Base::IsSetDiv(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMgcode(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetName(), COrgName_Base::IsSetPgcode(), ITERATE, MAKE_COMMON, MAKE_COMMON_INT, NULL, CRef< C, Locker >::Reset(), COrgName_Base::SetMod(), and COrgName_Base::SetName().
Referenced by BOOST_AUTO_TEST_CASE(), and COrg_ref::MakeCommon().
◆ operator=()
◆ RemoveModBySubtype()
| unsigned int COrgName::RemoveModBySubtype | ( | COrgMod::ESubtype | to_remove | ) |
Definition at line 428 of file OrgName.cpp.
References i, COrgName_Base::IsSetMod(), result, and COrgName_Base::SetMod().
Referenced by COrg_ref::FilterOutParts(), and ResetNomenclature().
◆ ResetNomenclature()
| void COrgName::ResetNomenclature | ( | ) |
Definition at line 422 of file OrgName.cpp.
References COrgMod_Base::eSubtype_nomenclature, and RemoveModBySubtype().
Referenced by COrg_ref::FilterOutParts(), and SetNomenclature().
◆ SetFormalNameFlag()
| void COrgName::SetFormalNameFlag | ( | bool | bFormalName | ) |
Definition at line 278 of file OrgName.cpp.
References x_ResetAttribFlag(), and x_SetAttribFlag().
◆ SetNomenclature()
Definition at line 385 of file OrgName.cpp.
References COrgMod_Base::eSubtype_nomenclature, GetNomenclature(), i, ITERATE, ResetNomenclature(), and COrgName_Base::SetMod().
◆ SetUncultured()
| void COrgName::SetUncultured | ( | bool | bUncultured | ) |
Definition at line 292 of file OrgName.cpp.
References x_ResetAttribFlag(), and x_SetAttribFlag().
◆ x_GetAttribFlag()
Definition at line 233 of file OrgName.cpp.
References NStr::eNocase, NStr::EqualNocase(), NStr::fSplit_Tokenize, COrgName_Base::GetAttrib(), i, COrgName_Base::IsSetAttrib(), NON_CONST_ITERATE, s_flagDelim, NStr::Split(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().
Referenced by IsFormalName(), IsModifierForwardingDisabled(), IsUncultured(), and x_SetAttribFlag().
◆ x_GetAttribValue()
Definition at line 252 of file OrgName.cpp.
References NStr::eNocase, NStr::fSplit_Tokenize, COrgName_Base::GetAttrib(), i, COrgName_Base::IsSetAttrib(), NON_CONST_ITERATE, s_flagDelim, NStr::Split(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().
◆ x_ResetAttribFlag()
Definition at line 211 of file OrgName.cpp.
References ctll::empty(), NStr::eNocase, NStr::EqualNocase(), NStr::fSplit_Tokenize, COrgName_Base::GetAttrib(), i, COrgName_Base::IsSetAttrib(), NStr::Join(), COrgName_Base::ResetAttrib(), s_flagDelim, COrgName_Base::SetAttrib(), NStr::Split(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().
Referenced by EnableModifierForwarding(), SetFormalNameFlag(), and SetUncultured().
◆ x_SetAttribFlag()
Definition at line 200 of file OrgName.cpp.
References ctll::empty(), COrgName_Base::GetAttrib(), COrgName_Base::IsSetAttrib(), s_flagDelim, COrgName_Base::SetAttrib(), and x_GetAttribFlag().
Referenced by DisableModifierForwarding(), SetFormalNameFlag(), and SetUncultured().
The documentation for this class was generated from the following files:
- include/objects/seqfeat/OrgName.hpp
- src/objects/seqfeat/OrgName.cpp
