Search Toolkit Book for COrg_ref
#include <objects/seqfeat/Org_ref.hpp>
Inheritance diagram for COrg_ref:
Collaboration diagram for COrg_ref:
Public Types | |
| enum | EOrgref_part { eOrgref_nothing = 0 , eOrgref_taxname = 0x0010 , eOrgref_common = 0x0040 , eOrgref_mod = 0x0800 , eOrgref_db = 0x2000 , eOrgref_db_taxid = 0x0001 , eOrgref_db_all = (eOrgref_db | eOrgref_db_taxid) , eOrgref_syn = 0x4000 , eOrgref_orgname = 0x0008 , eOrgref_on_name = 0x0080 , eOrgref_on_attr = 0x1000 , eOrgref_on_attr_spec = 0x00010000 , eOrgref_on_attr_nofwd = 0x00040000 , eOrgref_on_attr_uncult = 0x00080000 , eOrgref_on_attr_all = (eOrgref_on_attr | eOrgref_on_attr_spec | eOrgref_on_attr_nofwd | eOrgref_on_attr_uncult) , eOrgref_on_mod = 0x0200 , eOrgref_on_mod_nom = 0x00020000 , eOrgref_on_mod_oldname = 0x00100000 , eOrgref_on_mod_tm = 0x00200000 , eOrgref_on_mod_all = (eOrgref_on_mod | eOrgref_on_mod_nom | eOrgref_on_mod_oldname | eOrgref_on_mod_tm) , eOrgref_on_lin = 0x0020 , eOrgref_on_gc = 0x0002 , eOrgref_on_mgc = 0x0004 , eOrgref_on_pgc = 0x0400 , eOrgref_on_div = 0x0100 , eOrgref_on_all , eOrgref_all , eOrgref_all_but_syn = (eOrgref_all ^ eOrgref_syn) , eOrgref_all_but_spec = (eOrgref_all ^ eOrgref_on_attr_spec) , eOrgref_default = eOrgref_all } |
| typedef unsigned int | fOrgref_parts |
| Public Types inherited from COrg_ref_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_taxname , e_common , e_mod , e_db , e_syn , e_orgname } |
| typedef string | TTaxname |
| typedef string | TCommon |
| typedef list< string > | TMod |
| typedef vector< CRef< CDbtag > > | TDb |
| typedef list< string > | TSyn |
| typedef COrgName | TOrgname |
| typedef Tparent::CMemberIndex< E_memberIndex, 7 > | 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... | |
Public Member Functions | |
| COrg_ref (void) | |
| ~COrg_ref (void) | |
| void | GetLabel (string *label) const |
| TTaxId | GetTaxId () const |
| TTaxId | SetTaxId (TTaxId tax_id) |
| bool | IsSetLineage (void) const |
| const string & | GetLineage (void) const |
| bool | IsSetGcode (void) const |
| int | GetGcode (void) const |
| bool | IsSetMgcode (void) const |
| int | GetMgcode (void) const |
| bool | IsSetPgcode (void) const |
| int | GetPgcode (void) const |
| bool | IsSetDivision (void) const |
| const string & | GetDivision (void) const |
| bool | IsSetOrgMod (void) const |
| bool | IsVarietyValid (const string &variety) const |
| bool | HasValidVariety () const |
| bool | IsSubspeciesValid (const string &subspecies) const |
| CRef< COrg_ref > | MakeCommon (const COrg_ref &other) const |
| bool | UpdateFromTable () |
| void | CleanForGenBank () |
| void | FilterOutParts (fOrgref_parts to_remain) |
| Public Member Functions inherited from COrg_ref_Base | |
| COrg_ref_Base (void) | |
| virtual | ~COrg_ref_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetTaxname (void) const |
| preferred formal name Check if a value has been assigned to Taxname data member. More... | |
| bool | CanGetTaxname (void) const |
| Check if it is safe to call GetTaxname method. More... | |
| void | ResetTaxname (void) |
| Reset Taxname data member. More... | |
| const TTaxname & | GetTaxname (void) const |
| Get the Taxname member data. More... | |
| void | SetTaxname (const TTaxname &value) |
| Assign a value to Taxname data member. More... | |
| void | SetTaxname (TTaxname &&value) |
| TTaxname & | SetTaxname (void) |
| Assign a value to Taxname data member. More... | |
| bool | IsSetCommon (void) const |
| common name Check if a value has been assigned to Common data member. More... | |
| bool | CanGetCommon (void) const |
| Check if it is safe to call GetCommon method. More... | |
| void | ResetCommon (void) |
| Reset Common data member. More... | |
| const TCommon & | GetCommon (void) const |
| Get the Common member data. More... | |
| void | SetCommon (const TCommon &value) |
| Assign a value to Common data member. More... | |
| void | SetCommon (TCommon &&value) |
| TCommon & | SetCommon (void) |
| Assign a value to Common data member. More... | |
| bool | IsSetMod (void) const |
| unstructured modifiers 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 | IsSetDb (void) const |
| ids in taxonomic or culture 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 taxname or common 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 | IsSetOrgname (void) const |
| Check if a value has been assigned to Orgname data member. More... | |
| bool | CanGetOrgname (void) const |
| Check if it is safe to call GetOrgname method. More... | |
| void | ResetOrgname (void) |
| Reset Orgname data member. More... | |
| const TOrgname & | GetOrgname (void) const |
| Get the Orgname member data. More... | |
| void | SetOrgname (TOrgname &value) |
| Assign a value to Orgname data member. More... | |
| TOrgname & | SetOrgname (void) |
| Assign a value to Orgname 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 |
Static Public Member Functions | |
| static CConstRef< COrg_ref > | TableLookup (const string &taxname) |
| static const vector< string > & | GetTaxnameList () |
| 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) |
Private Types | |
| typedef COrg_ref_Base | Tparent |
Private Member Functions | |
| COrg_ref (const COrg_ref &value) | |
| COrg_ref & | operator= (const COrg_ref &value) |
| string | x_GetTaxnameAfterFirstTwoWords () const |
Additional Inherited Members | |
| 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 Org_ref.hpp.
Member Typedef Documentation
◆ fOrgref_parts
| typedef unsigned int COrg_ref::fOrgref_parts |
Definition at line 94 of file Org_ref.hpp.
◆ Tparent
|
private |
Definition at line 52 of file Org_ref.hpp.
Member Enumeration Documentation
◆ EOrgref_part
Definition at line 54 of file Org_ref.hpp.
Constructor & Destructor Documentation
◆ COrg_ref() [1/2]
|
inline |
Definition at line 156 of file Org_ref.hpp.
Referenced by MakeCommon().
◆ ~COrg_ref()
| COrg_ref::~COrg_ref | ( | void | ) |
Definition at line 52 of file Org_ref.cpp.
◆ COrg_ref() [2/2]
Member Function Documentation
◆ CleanForGenBank()
| void COrg_ref::CleanForGenBank | ( | ) |
Definition at line 510 of file Org_ref.cpp.
References COrg_ref_Base::ResetSyn().
Referenced by CTaxValidationAndCleanup::AdjustOrgRefsWithTaxLookupReply().
◆ FilterOutParts()
| void COrg_ref::FilterOutParts | ( | fOrgref_parts | to_remain | ) |
Definition at line 517 of file Org_ref.cpp.
References COrgName::EnableModifierForwarding(), eOrgref_all, eOrgref_common, eOrgref_db_all, eOrgref_db_taxid, eOrgref_mod, eOrgref_nothing, eOrgref_on_all, eOrgref_on_attr_all, eOrgref_on_attr_nofwd, eOrgref_on_div, eOrgref_on_gc, eOrgref_on_lin, eOrgref_on_mgc, eOrgref_on_mod, eOrgref_on_mod_nom, eOrgref_on_mod_oldname, eOrgref_on_mod_tm, eOrgref_on_name, eOrgref_on_pgc, eOrgref_syn, eOrgref_taxname, COrgMod_Base::eSubtype_old_name, COrgMod_Base::eSubtype_type_material, i, COrgName::IsModifierForwardingDisabled(), COrgName_Base::IsSetAttrib(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), COrgName_Base::IsSetDiv(), COrgName_Base::IsSetGcode(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMgcode(), COrg_ref_Base::IsSetMod(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetName(), COrg_ref_Base::IsSetOrgname(), COrgName_Base::IsSetPgcode(), COrg_ref_Base::IsSetSyn(), COrg_ref_Base::IsSetTaxname(), NO_FLAG, COrgName::RemoveModBySubtype(), COrg_ref_Base::Reset(), COrgName_Base::ResetAttrib(), COrg_ref_Base::ResetCommon(), COrg_ref_Base::ResetDb(), COrgName_Base::ResetDiv(), COrgName_Base::ResetGcode(), COrgName_Base::ResetLineage(), COrgName_Base::ResetMgcode(), COrg_ref_Base::ResetMod(), COrgName_Base::ResetMod(), COrgName_Base::ResetName(), COrgName::ResetNomenclature(), COrg_ref_Base::ResetOrgname(), COrgName_Base::ResetPgcode(), COrg_ref_Base::ResetSyn(), COrg_ref_Base::ResetTaxname(), s_taxonName, COrg_ref_Base::SetDb(), and COrg_ref_Base::SetOrgname().
◆ GetDivision()
Definition at line 164 of file Org_ref.cpp.
References COrgName_Base::GetDiv(), and COrg_ref_Base::GetOrgname().
Referenced by CCleanup::FixViralMolInfo(), CBioSource::GetDivision(), s_CompleteGenomeNeedsChromosome(), s_IsPhage(), CSourceOtherPanel::TransferFromOrgRef(), CAutoDef::x_GetFeatureClauses(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), and CSrcWriter::xGatherDivision().
◆ GetGcode()
| int COrg_ref::GetGcode | ( | void | ) | const |
Definition at line 134 of file Org_ref.cpp.
References COrgName_Base::GetGcode(), and COrg_ref_Base::GetOrgname().
Referenced by BOOST_AUTO_TEST_CASE(), CProteinAlignText::CProteinAlignText(), CProSplign::CImplementation::FindGlobalAlignment_stage1(), CScoreBuilder::GetBlastScoreProtToNucl(), CBioSource::GetGcode(), s_GetGeneticCode(), and CSFTranslationJob::x_InitGeneticCode().
◆ GetLabel()
| void COrg_ref::GetLabel | ( | string * | label | ) | const |
Definition at line 57 of file Org_ref.cpp.
References COrg_ref_Base::GetCommon(), COrg_ref_Base::GetDb(), COrg_ref_Base::GetTaxname(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), COrg_ref_Base::IsSetTaxname(), and label.
Referenced by CEntrezgeneHandler::GetLabel(), IAlignRowHandle::GetOrgLabel(), CSequenceTrack::GetTooltip(), CGuiObjectInfoComponent::GetToolTip(), s_GetContentLabel(), CAlnVecRow::x_GetDescrTooltip(), and CAlignSeqTableModel::x_GetOrganism().
◆ GetLineage()
Definition at line 124 of file Org_ref.cpp.
References COrgName_Base::GetLineage(), and COrg_ref_Base::GetOrgname().
Referenced by CSpecificHostRequest::AddReply(), CStrainRequest::Check(), CSpecificHostRequest::CSpecificHostRequest(), CCleanup::FixViralMolInfo(), CBioSource::GetBioprojectLocation(), CBioSource::GetBioprojectType(), CBioSource::GetLineage(), CValidError_imp::IsSyntheticConstruct(), CTaxValidationAndCleanup::ListTaxLookupErrors(), s_CompleteGenomeNeedsChromosome(), CStrainRequest::StrainContainsTaxonInfo(), CSourceOtherPanel::TransferFromOrgRef(), CStrainRequest::x_AddOneStrain(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CStrainRequest::x_CheckOneStrain(), and CValidError_bioseq::x_ValidateMolInfoForBioSource().
◆ GetMgcode()
| int COrg_ref::GetMgcode | ( | void | ) | const |
Definition at line 144 of file Org_ref.cpp.
References COrgName_Base::GetMgcode(), and COrg_ref_Base::GetOrgname().
Referenced by CBioSource::GetMgcode(), and CSFTranslationJob::x_InitGeneticCode().
◆ GetPgcode()
| int COrg_ref::GetPgcode | ( | void | ) | const |
Definition at line 154 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), and COrgName_Base::GetPgcode().
Referenced by CBioSource::GetPgcode(), and CSFTranslationJob::x_InitGeneticCode().
◆ GetTaxId()
| TTaxId COrg_ref::GetTaxId | ( | void | ) | const |
Definition at line 72 of file Org_ref.cpp.
References COrg_ref_Base::GetDb(), GetId(), i, COrg_ref_Base::IsSetDb(), s_taxonName, TAX_ID_FROM, and ZERO_TAX_ID.
Referenced by CStrainRequest::AddReply(), BOOST_AUTO_TEST_CASE(), CAutoDefWithTaxonomy::GetDocsumOrgDescription(), CBioSource::GetNameValPairs(), CCachedTaxon3_impl::GetOrgReply(), GetSourceFields(), CBioseq::GetTaxId(), GetTaxId(), CPriorityTaxNodes::getTaxId(), CBioseq_Info::GetTaxId(), CLocalTaxon::GetTaxIdByOrgRef(), CTaxValidationAndCleanup::GetTaxonomyLookupRequest(), CTaxValidationAndCleanup::ListTaxLookupErrors(), MakeCommon(), MakeCommonBioSource(), s_GetTaxId(), CGenusSpeciesFixup::s_HasTaxId(), CUnculturedTool::s_HasTaxId(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_AdjustEnds(), CAdjustForConsensusSpliceSite::s_IsBioseqGood_Strict(), UpdateBiosourceFromBiosample(), CSrcDescEditorPanel::UpdateSeqdesc(), CCachedTaxon3::x_GetReplyForOrgRef(), CBioseqIndex::x_InitSource(), CPhyTreeFormatter::x_InitTreeFeatures(), CDeflineGenerator::x_SetBioSrc(), CSourceItem::x_SetSource(), CBlastTabularInfo::x_SetTaxInfoAll(), CTaxonomyUpdater::xUpdateOrgTaxname(), and CGff3Writer::xWriteSequenceHeader().
◆ GetTaxnameList()
Definition at line 503 of file Org_ref.cpp.
References s_CommonTaxnameList, and s_InitializeOrgRefMap().
◆ HasValidVariety()
| bool COrg_ref::HasValidVariety | ( | ) | const |
Definition at line 230 of file Org_ref.cpp.
References COrgMod_Base::eSubtype_variety, COrg_ref_Base::GetMod(), COrg_ref_Base::GetOrgname(), NStr::IsBlank(), COrg_ref_Base::IsSetMod(), COrg_ref_Base::IsSetOrgname(), IsVarietyValid(), and ITERATE.
Referenced by IsSubspeciesValid().
◆ IsSetDivision()
| bool COrg_ref::IsSetDivision | ( | void | ) | const |
Definition at line 159 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetDiv(), and COrg_ref_Base::IsSetOrgname().
Referenced by CBioSource::IsSetDivision(), s_CompleteGenomeNeedsChromosome(), s_IsPhage(), CSourceOtherPanel::TransferFromOrgRef(), CAutoDef::x_GetFeatureClauses(), CBioseqIndex::x_InitSource(), CDeflineGenerator::x_SetBioSrc(), and CSrcWriter::xGatherDivision().
◆ IsSetGcode()
| bool COrg_ref::IsSetGcode | ( | void | ) | const |
Definition at line 129 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetGcode(), and COrg_ref_Base::IsSetOrgname().
Referenced by BOOST_AUTO_TEST_CASE(), CBioSource::IsSetGcode(), and CSFTranslationJob::x_InitGeneticCode().
◆ IsSetLineage()
| bool COrg_ref::IsSetLineage | ( | void | ) | const |
Definition at line 119 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetLineage(), and COrg_ref_Base::IsSetOrgname().
Referenced by CSpecificHostRequest::AddReply(), CStrainRequest::Check(), CSpecificHostRequest::CSpecificHostRequest(), CCleanup::FixViralMolInfo(), CBioSource::IsSetLineage(), CValidError_imp::IsSyntheticConstruct(), CTaxValidationAndCleanup::ListTaxLookupErrors(), s_CompleteGenomeNeedsChromosome(), CStrainRequest::StrainContainsTaxonInfo(), CSourceOtherPanel::TransferFromOrgRef(), CValidError_imp::ValidateBioSourceForSeq(), CStrainRequest::x_AddOneStrain(), CValidError_bioseq::x_BadMetazoanMitochondrialLength(), CStrainRequest::x_CheckOneStrain(), and CValidError_bioseq::x_ValidateMolInfoForBioSource().
◆ IsSetMgcode()
| bool COrg_ref::IsSetMgcode | ( | void | ) | const |
Definition at line 139 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetMgcode(), and COrg_ref_Base::IsSetOrgname().
Referenced by CBioSource::IsSetMgcode(), and CSFTranslationJob::x_InitGeneticCode().
◆ IsSetOrgMod()
| bool COrg_ref::IsSetOrgMod | ( | void | ) | const |
Definition at line 169 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), COrgName_Base::IsSetMod(), and COrg_ref_Base::IsSetOrgname().
Referenced by AddBioSourceToAttributes(), CQualLookupMap::AddDesc(), CQualLookupMap::AddFeat(), AddMissingCommonOrgMods(), CQualLookupMap::AddOrg(), BOOST_AUTO_TEST_CASE(), CStrainRequest::Check(), CreateRawBioSources(), CBioSource::IsSetOrgMod(), CTaxValidationAndCleanup::ListTaxLookupErrors(), s_HasMetagenomeSource(), s_TitleEndsInOrganism(), SetCultureCollectionFromStrain(), CStrainRequest::StrainContainsTaxonInfo(), CValidError_imp::ValidateBioSource(), CStrainRequest::x_AddOneStrain(), CStrainRequest::x_CheckOneStrain(), and CBioSource::x_RemoveStopWords().
◆ IsSetPgcode()
| bool COrg_ref::IsSetPgcode | ( | void | ) | const |
Definition at line 149 of file Org_ref.cpp.
References COrg_ref_Base::GetOrgname(), COrg_ref_Base::IsSetOrgname(), and COrgName_Base::IsSetPgcode().
Referenced by CBioSource::IsSetPgcode(), and CSFTranslationJob::x_InitGeneticCode().
◆ IsSubspeciesValid()
Definition at line 246 of file Org_ref.cpp.
References HasValidVariety(), NStr::IsBlank(), s_FindWholeWord(), and x_GetTaxnameAfterFirstTwoWords().
Referenced by CValidError_imp::ValidateOrgRef().
◆ IsVarietyValid()
Definition at line 220 of file Org_ref.cpp.
References NStr::IsBlank(), s_FindWholeWord(), and x_GetTaxnameAfterFirstTwoWords().
Referenced by HasValidVariety(), and CValidError_imp::ValidateOrgRef().
◆ MakeCommon()
Definition at line 280 of file Org_ref.cpp.
References CSerialObject::Assign(), COrg_ref(), CSerialObject::Equals(), COrg_ref_Base::GetDb(), COrg_ref_Base::GetMod(), COrg_ref_Base::GetOrgname(), COrg_ref_Base::GetSyn(), GetTaxId(), COrg_ref_Base::IsSetDb(), COrg_ref_Base::IsSetMod(), COrg_ref_Base::IsSetOrgname(), COrg_ref_Base::IsSetSyn(), ITERATE, MAKE_COMMON, COrgName::MakeCommon(), COrg_ref_Base::ResetMod(), COrg_ref_Base::ResetSyn(), s_MakeCommonStringList(), COrg_ref_Base::SetDb(), COrg_ref_Base::SetMod(), COrg_ref_Base::SetOrgname(), and COrg_ref_Base::SetSyn().
Referenced by BOOST_AUTO_TEST_CASE(), and CBioSource::MakeCommon().
◆ operator=()
◆ SetTaxId()
Definition at line 93 of file Org_ref.cpp.
References GetId(), i, s_taxonName, CDbtag_Base::SetDb(), COrg_ref_Base::SetDb(), CDbtag_Base::SetTag(), TAX_ID_FROM, TAX_ID_TO, and ZERO_TAX_ID.
Referenced by TaxTreeData::addTaxToBioseq(), BOOST_AUTO_TEST_CASE(), COrgRefCache::Insert2(), CDUpdater::reformatBioseq(), s_CreateOrgRef(), UpdateFromTable(), and CBioSource::UpdateWithBioSample().
◆ TableLookup()
Definition at line 448 of file Org_ref.cpp.
References map_checker< Container >::end(), map_checker< Container >::find(), s_InitializeOrgRefMap(), and s_OrgRefMap.
Referenced by BOOST_AUTO_TEST_CASE(), UpdateFromTable(), and CSrcDescEditorPanel::UpdateSeqdesc().
◆ UpdateFromTable()
| bool COrg_ref::UpdateFromTable | ( | ) |
Definition at line 459 of file Org_ref.cpp.
References NStr::Equal(), COrg_ref_Base::GetTaxname(), NStr::IsBlank(), COrg_ref_Base::IsSetTaxname(), ITERATE, lookup(), COrg_ref_Base::SetCommon(), COrgName_Base::SetDiv(), COrgName_Base::SetGcode(), COrgName_Base::SetLineage(), COrgName_Base::SetMgcode(), COrg_ref_Base::SetOrgname(), SetTaxId(), TableLookup(), and TAX_ID_FROM.
Referenced by CTable2AsnContext::UpdateTaxonFromTable().
◆ x_GetTaxnameAfterFirstTwoWords()
|
private |
Definition at line 175 of file Org_ref.cpp.
References NStr::Find(), COrg_ref_Base::GetTaxname(), COrg_ref_Base::IsSetTaxname(), and NStr::TruncateSpacesInPlace().
Referenced by IsSubspeciesValid(), and IsVarietyValid().
The documentation for this class was generated from the following files:
- include/objects/seqfeat/Org_ref.hpp
- src/objects/seqfeat/Org_ref.cpp
