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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Variation__ref___8cpp_source.html below:

NCBI C++ ToolKit: src/objects/seqfeat/Variation_ref_.cpp Source File

(

, eMethod_E_flanking_sequence);

(

, eMethod_E_sequence_alignment);

(

, eAllele_origin_tested_inconclusive);

->RandomOrder();

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

,

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

->RandomOrder();

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

: m_Phase(0), m_X_length(0)

->RandomOrder();

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

->RandomOrder();

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

(*m_Condition);

->RandomOrder();

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

->RandomOrder();

->CodeVersion(22400);

->DataSpec(ncbi::EDataSpec::eASN);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

BEGIN_NAMED_CHOICE_INFO("", CVariation_ref_Base::C_Data)

BEGIN_NAMED_BASE_CLASS_INFO("Variation-ref", CVariation_ref)

BEGIN_NAMED_CLASS_INFO("", CVariation_ref_Base::C_Data::C_Set)

BEGIN_NAMED_ENUM_IN_INFO("", CVariation_ref_Base::, EMethod_E, true)

Set of related Variations.

see http://www.hgvs.org/mutnomen/recs-prot.html

C_Loss_of_heterozygosity –.

condition related to this origin's type

#define DIAG_COMPILE_INFO

Make compile time diagnostic information object to use in CNcbiDiag and CException.

#define MEMBER_PTR(MemberName)

#define SET_ENUM_INTERNAL_NAME(OwnerName, MemberName)

#define ADD_NAMED_MEMBER(MemberAlias, MemberName, TypeMacro, TypeMacroArgs)

#define ADD_NAMED_REF_MEMBER(MemberAlias, MemberName, ClassName)

#define SET_ENUM_MODULE(ModuleName)

#define ADD_NAMED_REF_CHOICE_VARIANT(MemberAlias, MemberName, ClassName)

#define ADD_NAMED_STD_MEMBER(MemberAlias, MemberName)

#define SET_CLASS_MODULE(ModuleName)

#define ADD_NAMED_ENUM_MEMBER(MemberAlias, MemberName, EnumName)

#define ADD_ENUM_VALUE(EnumValueName, EnumValueValue)

#define SET_INTERNAL_NAME(OwnerName, MemberName)

#define SET_CHOICE_MODULE(ModuleName)

#define ADD_NAMED_NULL_CHOICE_VARIANT(MemberAlias, TypeMacro, TypeMacroArgs)

#define ADD_NAMED_BUF_CHOICE_VARIANT(MemberAlias, MemberName, TypeMacro, TypeMacroArgs)

void AddReference(void) const

Add reference to object.

void Reset(void)

Reset reference object.

bool IsAllocatedInPool(void) const THROWS_NONE

Check if object is allocated in memory pool (not system heap)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

virtual void Reset(void)

Reset the whole object.

void ResetClinical_test(void)

Reset Clinical_test data member.

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

TNote & SetNote(void)

Select the variant.

const TInstance & GetInstance(void) const

Get the variant data.

void ResetPopulation_data(void)

Reset Population_data data member.

list< CRef< CDbtag > > m_Clinical_test

void ResetId(void)

Reset Id data member.

TSource & SetSource(void)

Assign a value to Source data member.

void ResetSource(void)

Reset Source data member.

void ResetMethod(void)

Reset Method data member.

CVariation_ref_Base(void)

void ResetSelection(void)

Reset the selection (set it to e_not_set).

virtual ~CVariation_ref_Base(void)

const TVariation & GetVariation(void) const

Get the variant data.

void ResetValidated(void)

Reset Validated data member.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

CRef< TParent_id > m_Parent_id

const TSet & GetSet(void) const

Get the variant data.

void Reset(void)

Reset the whole object.

void Reset(void)

Reset the whole object.

void ResetAllele_frequency(void)

Reset Allele_frequency data member.

void ThrowInvalidSelection(E_Choice index) const

Throw 'InvalidSelection' exception.

TFrameshift & SetFrameshift(void)

Select the variant.

list< CRef< CPhenotype > > m_Phenotype

void ResetTest(void)

Reset Test data member.

void DoSelect(E_Choice index, CObjectMemoryPool *pool=0)

list< CRef< C_E_Consequence > > m_Consequence

double m_Allele_frequency

list< CRef< CPopulation_data > > m_Population_data

static const char *const sm_SelectionNames[]

list< CRef< CDbtag > > m_Other_ids

void ThrowInvalidSelection(E_Choice index) const

Throw 'InvalidSelection' exception.

void Reset(void)

Reset the whole object.

TLocation & SetLocation(void)

Assign a value to Location data member.

~C_Loss_of_heterozygosity(void)

NCBI_NS_NCBI::CSerialObject * m_object

list< CRef< CVariation_ref > > m_Variations

TVariation & SetVariation(void)

Select the variant.

void ResetLocation(void)

Reset Location data member.

void ResetExt(void)

Reset Ext data member.

void Reset(void)

Reset the whole object.

void ResetAllele_state(void)

Reset Allele_state data member.

const TFrameshift & GetFrameshift(void) const

Get the variant data.

void CheckSelected(E_Choice index) const

Verify selection, throw exception if it differs from the expected.

void ResetName(void)

Reset Name data member.

TData & SetData(void)

Assign a value to Data data member.

TCondition & SetCondition(void)

Assign a value to Condition data member.

void ResetData(void)

Reset Data data member.

TSample_id & SetSample_id(void)

Assign a value to Sample_id data member.

NCBI_NS_NCBI::CSerialObject * m_object

void ResetObject_id(void)

Reset Object_id data member.

E_Choice

Choice variants.

void ResetOther_ids(void)

Reset Other_ids data member.

static const char *const sm_SelectionNames[]

TVariant_prop & SetVariant_prop(void)

Assign a value to Variant_prop data member.

E_Choice

Choice variants.

~C_E_Somatic_origin(void)

void ResetExt_locs(void)

Reset Ext_locs data member.

TLoss_of_heterozygosity & SetLoss_of_heterozygosity(void)

Select the variant.

void ResetConsequence(void)

Reset Consequence data member.

CRef< TLocation > m_Location

void ResetCondition(void)

Reset Condition data member.

const TLoss_of_heterozygosity & GetLoss_of_heterozygosity(void) const

Get the variant data.

EAllele_state

observed allele state, if known DEPRECATED: new field = VariantProperties.allele-state

TNote & SetNote(void)

Select the variant.

void CheckSelected(E_Choice index) const

Verify selection, throw exception if it differs from the expected.

EAllele_origin

origin of this allele, if known note that these are powers-of-two, and represent bits; thus,...

virtual void Reset(void)

Reset the whole object.

list< CRef< CExt_loc > > m_Ext_locs

static string SelectionName(E_Choice index)

Retrieve selection name (for diagnostic purposes).

CRef< TVariant_prop > m_Variant_prop

void ResetSomatic_origin(void)

Reset Somatic_origin data member.

CVariantProperties TVariant_prop

C_Loss_of_heterozygosity(void)

void ResetAllele_origin(void)

Reset Allele_origin data member.

NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string

TSet & SetSet(void)

Select the variant.

void ResetSynonyms(void)

Reset Synonyms data member.

void ResetPub(void)

Reset Pub data member.

void Reset(void)

Reset the whole object.

bool m_Is_ancestral_allele

CRef< TSample_id > m_Sample_id

void ResetDescription(void)

Reset Description data member.

void ResetParent_id(void)

Reset Parent_id data member.

void ResetIs_ancestral_allele(void)

Reset Is_ancestral_allele data member.

TId & SetId(void)

Assign a value to Id data member.

void DoSelect(E_Choice index, CObjectMemoryPool *pool=0)

TInstance & SetInstance(void)

Select the variant.

void Reset(void)

Reset the whole object.

void ResetSample_id(void)

Reset Sample_id data member.

TPub & SetPub(void)

Assign a value to Pub data member.

void ResetName(void)

Reset Name data member.

void ResetDescription(void)

Reset Description data member.

void ResetVariations(void)

Reset Variations data member.

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

void ResetVariant_prop(void)

Reset Variant_prop data member.

list< string > m_Synonyms

NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string

TExt & SetExt(void)

Assign a value to Ext data member.

void ResetPhenotype(void)

Reset Phenotype data member.

void ResetReference(void)

Reset Reference data member.

list< CRef< C_E_Somatic_origin > > m_Somatic_origin

void Reset(void)

Reset the whole object.

TParent_id & SetParent_id(void)

Assign a value to Parent_id data member.

void ResetSelection(void)

Reset the selection (set it to e_not_set).

@ e_not_set

No variant selected.

@ e_Variation

Describe resulting variation in the product, e.g. missense, nonsense, silent, neutral,...

@ e_Loss_of_heterozygosity

@ e_Instance

actual sequence-edit at feat.location

@ e_not_set

No variant selected.

const GenericPointer< typename T::ValueType > T2 value

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