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NCBI C++ ToolKit: COrgMod Class Reference
Represents ASN.1 type OrgMod defined in file seqfeat.asn
Search Toolkit Book for COrgMod
@OrgMod.hpp User-defined methods of the data storage class. More...
#include <objects/seqfeat/OrgMod.hpp>
enum EVocabulary { eVocabulary_raw , eVocabulary_insdc } typedef map< string, string, PNocase > TInstitutionCodeMap enum ESubtype {
eSubtype_strain = 2 , eSubtype_substrain = 3 , eSubtype_type = 4 , eSubtype_subtype = 5 ,
eSubtype_variety = 6 , eSubtype_serotype = 7 , eSubtype_serogroup = 8 , eSubtype_serovar = 9 ,
eSubtype_cultivar = 10 , eSubtype_pathovar = 11 , eSubtype_chemovar = 12 , eSubtype_biovar = 13 ,
eSubtype_biotype = 14 , eSubtype_group = 15 , eSubtype_subgroup = 16 , eSubtype_isolate = 17 ,
eSubtype_common = 18 , eSubtype_acronym = 19 , eSubtype_dosage = 20 , eSubtype_nat_host = 21 ,
eSubtype_sub_species = 22 , eSubtype_specimen_voucher = 23 , eSubtype_authority = 24 , eSubtype_forma = 25 ,
eSubtype_forma_specialis = 26 , eSubtype_ecotype = 27 , eSubtype_synonym = 28 , eSubtype_anamorph = 29 ,
eSubtype_teleomorph = 30 , eSubtype_breed = 31 , eSubtype_gb_acronym = 32 , eSubtype_gb_anamorph = 33 ,
eSubtype_gb_synonym = 34 , eSubtype_culture_collection = 35 , eSubtype_bio_material = 36 , eSubtype_metagenome_source = 37 ,
eSubtype_type_material = 38 , eSubtype_nomenclature = 39 , eSubtype_old_lineage = 253 , eSubtype_old_name = 254 ,
eSubtype_other = 255
} enum class E_memberIndex { e__allMandatory = 0 , e_subtype , e_subname , e_attrib } typedef int TSubtype typedef string TSubname typedef string TAttrib typedef Tparent::CMemberIndex< E_memberIndex, 4 > TmemberIndex 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...
COrgMod (void) COrgMod (TSubtype subtype, const TSubname &subname) COrgMod (const string &subtype, const TSubname &subname) ~COrgMod (void) void FixCapitalization () void AutoFix () bool IsDeprecated () const bool RemoveAbbreviation () bool IsUnexpectedViralOrgModQualifier () const COrgMod_Base (void) virtual ~COrgMod_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetSubtype (void) const Check if a value has been assigned to Subtype data member. More...
bool CanGetSubtype (void) const Check if it is safe to call GetSubtype method. More...
void ResetSubtype (void) Reset Subtype data member. More...
TSubtype GetSubtype (void) const Get the Subtype member data. More...
void SetSubtype (TSubtype value) Assign a value to Subtype data member. More...
TSubtype & SetSubtype (void) Assign a value to Subtype data member. More...
bool IsSetSubname (void) const Check if a value has been assigned to Subname data member. More...
bool CanGetSubname (void) const Check if it is safe to call GetSubname method. More...
void ResetSubname (void) Reset Subname data member. More...
const TSubname & GetSubname (void) const Get the Subname member data. More...
void SetSubname (const TSubname &value) Assign a value to Subname data member. More...
void SetSubname (TSubname &&value) TSubname & SetSubname (void) Assign a value to Subname data member. More...
bool IsSetAttrib (void) const attribution/source 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...
virtual void Reset (void) Reset the whole object. More...
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...
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...
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 TSubtype GetSubtypeValue (const string &str, EVocabulary vocabulary=eVocabulary_raw) static string GetSubtypeName (TSubtype stype, EVocabulary vocabulary=eVocabulary_raw) static bool IsValidSubtypeName (const string &str, EVocabulary vocabulary=eVocabulary_raw) static bool IsDiscouraged (const TSubtype stype, bool indexer=false) static bool IsMultipleValuesAllowed (TSubtype) static bool HoldsInstitutionCode (const TSubtype stype) This indicates if the given Org-mod subtype is supposed to hold an institution code (Example: "ATCC:27305") More...
static bool ParseStructuredVoucher (const string &str, string &inst, string &coll, string &id) static bool IsInstitutionCodeValid (const string &inst_coll, string &voucher_type, bool &is_miscapitalized, string &correct_cap, bool &needs_country, bool &erroneous_country) static string IsCultureCollectionValid (const string &culture_collection) static string IsSpecimenVoucherValid (const string &specimen_voucher) static string IsBiomaterialValid (const string &biomaterial) static string IsStructuredVoucherValid (const string &val, const string &voucher_type) static string MakeStructuredVoucher (const string &inst, const string &coll, const string &id) static bool FixStructuredVoucher (string &val, const string &voucher_type) static bool AddStructureToVoucher (string &val, const string &voucher_type) static bool RescueInstFromParentheses (string &val, const string &voucher_type) static string CheckMultipleVouchers (const vector< string > &) static const string & GetInstitutionFullName (const string &short_name) static const string & GetInstitutionShortName (const string &full_name) static string FixStrain (const string &strain) static bool FuzzyStrainMatch (const string &strain1, const string &strain2) static bool IsStrainValid (const string &strain) static bool IsIsolateValid (const string &isolate) static string FixHost (const string &value) static string FixHostCapitalization (const string &value) static string FixCapitalization (TSubtype subtype, const string &value) static string AutoFix (TSubtype subtype, const string &value) static bool IsDeprecated (TSubtype subtype) static bool IsUnexpectedViralOrgModQualifier (TSubtype subtype) static bool IsValidTypeMaterial (const string &type_material) static bool IsINSDCValidTypeMaterial (const string &type_material) static bool NCBI_ValidateForMultipleIsolates (void) static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() ESubtype (void) Access to ESubtype's attributes (values, names) as defined in spec. More...
static void SetVerifyDataThread (ESerialVerifyData verify) static void SetVerifyDataGlobal (ESerialVerifyData verify) static string UnassignedString (void) static CStringUTF8 UnassignedStringUTF8 (void) static char UnassignedByte (void) 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 void EnableDebugDump (bool on)
@OrgMod.hpp User-defined methods of the data storage class.
This file was originally generated by application DATATOOL using the following specifications: 'seqfeat.asn'.
New methods or data members can be added to it if needed. See also: OrgMod_.hpp
Definition at line 53 of file OrgMod.hpp.
◆ TInstitutionCodeMap ◆ Tparent ◆ EVocabulary Enumerator eVocabulary_raw eVocabulary_insdc
Definition at line 67 of file OrgMod.hpp.
◆ COrgMod() [1/4] COrgMod::COrgMod ( void ) inline
Definition at line 154 of file OrgMod.hpp.
◆ COrgMod() [2/4] ◆ COrgMod() [3/4] ◆ ~COrgMod() COrgMod::~COrgMod ( void )
Definition at line 57 of file OrgMod.cpp.
◆ COrgMod() [4/4] ◆ AddStructureToVoucher() ◆ AutoFix() [1/2] void COrgMod::AutoFix ( ) ◆ AutoFix() [2/2] ◆ CheckMultipleVouchers() ◆ FindInstitutionCode() ◆ FixCapitalization() [1/2] void COrgMod::FixCapitalization ( ) ◆ FixCapitalization() [2/2] ◆ FixHost() ◆ FixHostCapitalization() ◆ FixStrain() ◆ FixStructuredVoucher()
Definition at line 663 of file OrgMod.cpp.
References AddStructureToVoucher(), map_checker< Container >::begin(), map_checker< Container >::end(), NStr::Equal(), NStr::EqualNocase(), NStr::Find(), NStr::IsBlank(), MakeStructuredVoucher(), ParseStructuredVoucher(), RescueInstFromParentheses(), s_InitializeInstitutionCollectionCodeMaps(), s_InstitutionCodeTypeMap, NStr::StartsWith(), and val.
Referenced by BOOST_AUTO_TEST_CASE(), and CFixStructuredVouchers::x_ApplyToBioSource().
◆ FuzzyStrainMatch() ◆ GetInstitutionFullName() ◆ GetInstitutionShortName() ◆ GetSubtypeName()
Definition at line 108 of file OrgMod.cpp.
References ENUM_METHOD_NAME, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_other, COrgMod_Base::eSubtype_substrain, eVocabulary_insdc, and NStr::Replace().
Referenced by AddBioSourceToAttributes(), CFieldChoicePanel::AutoMatchSrc(), CAutoDefAvailableModifier::GetOrgModLabel(), GetOrgModName(), CWriteUtil::GetOrgModSubType(), GetSeqTableFromSeqEntry(), CQualLookupMap::IncrementalUpdate(), UpdateBiosourceFromBiosample(), CValidError_imp::ValidateBioSource(), CValidError_imp::ValidateOrgRef(), CSourceFieldNamePanel::x_ChooseTextQualifier(), CSrcModListPanel::x_FillDataList(), CMacroEditorContext::x_GetBsrcTextFieldnames(), CBioSource::x_GetOrgModNameValPairs(), and CAutoDefOptions::x_MakeModifierList().
◆ GetSubtypeValue()
Definition at line 62 of file OrgMod.cpp.
References ENUM_METHOD_NAME, NStr::EqualNocase(), COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_other, COrgMod_Base::eSubtype_substrain, eVocabulary_insdc, str(), NStr::ToLower(), and NStr::TruncateSpaces().
Referenced by CFieldChoicePanel::AutoMatchSrc(), COrgMod(), COrgModQual::COrgModQual(), CSrcTableColumnBaseFactory::Create(), CreateActionBiosource(), CAutoColValidatorsubtype::DoValidate(), SrcEditDialog::GetLabelForTitle(), CColumnValidator::IsDiscouraged(), CCompareWithBiosample::OnClickOk(), CNewCleanup_imp::OrgnameBC(), s_SetBioSourceField(), s_StringHasOrgModPrefix(), CSourceFieldNamePanel::SetFieldName(), CBioSource::ShouldIgnoreConflict(), CMacroFunction_ApplyStrucVoucherPart::TheFunction(), CBioSource::UpdateWithBioSample(), CMacroFunction_AddorSetContElement::x_AddBioSrcModifier(), CMacroFunction_Autodef::x_IsRequested(), CMacroFunction_AutodefComplete::x_IsRequested(), CSrcModListPanel::x_SetBioSourceModifier(), CAutoDefOptions::x_SetModifierList(), and CSrcWriter::xGatherOrgModFeat().
◆ HoldsInstitutionCode() ◆ IsBiomaterialValid() ◆ IsCultureCollectionValid() ◆ IsDeprecated() [1/2] bool COrgMod::IsDeprecated ( ) const ◆ IsDeprecated() [2/2]
Definition at line 1087 of file OrgMod.cpp.
References COrgMod_Base::eSubtype_acronym, COrgMod_Base::eSubtype_anamorph, COrgMod_Base::eSubtype_authority, COrgMod_Base::eSubtype_biotype, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_chemovar, COrgMod_Base::eSubtype_common, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_group, COrgMod_Base::eSubtype_pathovar, COrgMod_Base::eSubtype_serogroup, COrgMod_Base::eSubtype_subgroup, COrgMod_Base::eSubtype_substrain, COrgMod_Base::eSubtype_subtype, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_teleomorph, and COrgMod_Base::eSubtype_type.
◆ IsDiscouraged()
Definition at line 160 of file OrgMod.cpp.
References COrgMod_Base::eSubtype_dosage, COrgMod_Base::eSubtype_gb_acronym, COrgMod_Base::eSubtype_gb_anamorph, COrgMod_Base::eSubtype_gb_synonym, COrgMod_Base::eSubtype_metagenome_source, COrgMod_Base::eSubtype_old_lineage, and COrgMod_Base::eSubtype_old_name.
Referenced by BOOST_AUTO_TEST_CASE(), CSrcModPanel::DoNotListOrgMod(), CColumnValidator::IsDiscouraged(), s_StringHasOrgModPrefix(), and CSrcWriter::xIsOrgmodTypeSuppressed().
◆ IsINSDCValidTypeMaterial() ◆ IsInstitutionCodeValid() ◆ IsIsolateValid() ◆ IsMultipleValuesAllowed()
Definition at line 127 of file OrgMod.cpp.
References COrgMod_Base::eSubtype_biotype, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_breed, COrgMod_Base::eSubtype_chemovar, COrgMod_Base::eSubtype_cultivar, COrgMod_Base::eSubtype_ecotype, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_gb_acronym, COrgMod_Base::eSubtype_gb_anamorph, COrgMod_Base::eSubtype_gb_synonym, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_metagenome_source, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_nomenclature, COrgMod_Base::eSubtype_old_name, COrgMod_Base::eSubtype_pathovar, COrgMod_Base::eSubtype_serogroup, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, COrgMod_Base::eSubtype_substrain, and COrgMod_Base::eSubtype_variety.
◆ IsSpecimenVoucherValid() ◆ IsStrainValid() ◆ IsStructuredVoucherValid()
Definition at line 461 of file OrgMod.cpp.
References NStr::eNocase, NStr::Equal(), NStr::EqualNocase(), NStr::FindNoCase(), NStr::IsBlank(), IsInstitutionCodeValid(), kEmptyStr, kMissingId, kMissingInst, ParseStructuredVoucher(), NStr::StartsWith(), and val.
Referenced by IsBiomaterialValid(), IsCultureCollectionValid(), and IsSpecimenVoucherValid().
◆ IsUnexpectedViralOrgModQualifier() [1/2] bool COrgMod::IsUnexpectedViralOrgModQualifier ( ) const ◆ IsUnexpectedViralOrgModQualifier() [2/2] ◆ IsValidSubtypeName()
Definition at line 86 of file OrgMod.cpp.
References ENUM_METHOD_NAME, eVocabulary_insdc, str(), NStr::ToLower(), and NStr::TruncateSpaces().
Referenced by CFieldChoicePanel::AutoMatchSrc(), CSrcTableColumnBaseFactory::Create(), CreateActionBiosource(), NMItemData::GetEditableFieldForPair(), SrcEditDialog::GetLabelForTitle(), CSourceFieldNamePanel::GetMacroFieldName(), NMacroUtil::IsBiosourceModifier(), s_SetBioSourceField(), CSourceFieldNamePanel::SetFieldName(), CMacroFunction_AddorSetContElement::x_AddBioSrcModifier(), CMacroEditorContext::x_GetAsnPathToBsrcText(), CMacroEditorContext::x_GetGUIFieldForBsrcText(), CMacroFunction_Autodef::x_IsRequested(), CMacroFunction_AutodefComplete::x_IsRequested(), and CSrcModListPanel::x_SetBioSourceModifier().
◆ IsValidTypeMaterial() ◆ MakeStructuredVoucher() ◆ NCBI_ValidateForMultipleIsolates() bool COrgMod::NCBI_ValidateForMultipleIsolates ( void ) static ◆ operator=() ◆ ParseStructuredVoucher()
Definition at line 189 of file OrgMod.cpp.
References NStr::Find(), NStr::IsBlank(), kEmptyStr, and str().
Referenced by CheckMultipleVouchers(), FixStructuredVoucher(), IsStructuredVoucherValid(), s_GetSpecimenVoucherText(), s_ParseValues(), CMacroFunction_ApplyStrucVoucherPart::x_ApplyPart(), CFixOrgModInst::x_ApplyToBioSource(), CSrcStructuredVoucherPartColumn::x_ParsePartsFromStructuredVoucher(), and CMacroFunction_ApplyStrucVoucherPart::x_RemovePart().
◆ RemoveAbbreviation() bool COrgMod::RemoveAbbreviation ( ) ◆ RescueInstFromParentheses()
The documentation for this class was generated from the following files:
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