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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/Variation___8hpp_source.html below:

NCBI C++ ToolKit: include/objects/variation/Variation_.hpp Source File

eData_set_type_unknown = 0,

eData_set_type_compound = 1,

eData_set_type_products = 2,

eData_set_type_haplotype = 3,

eData_set_type_genotype = 4,

eData_set_type_mosaic = 5,

eData_set_type_individual = 6,

eData_set_type_population = 7,

eData_set_type_alleles = 8,

eData_set_type_package = 9,

eData_set_type_chimeric = 10,

eData_set_type_other = 255

IsSetType(

)

;

CanGetType(

)

;

ResetType(

);

GetType(

)

;

& SetType(

);

IsSetVariations(

)

;

CanGetVariations(

)

;

ResetVariations(

);

IsSetName(

)

;

CanGetName(

)

;

ResetName(

);

& GetName(

)

;

& SetName(

);

ResetSelection(

);

E_Choice Which(

)

;

CheckSelected(E_Choice index)

;

NCBI_NORETURN

ThrowInvalidSelection(E_Choice index)

;

SelectionName(E_Choice index);

IsUnknown(

)

;

SetUnknown(

);

IsNote(

)

;

& GetNote(

)

;

& SetNote(

);

IsUniparental_disomy(

)

;

SetUniparental_disomy(

);

IsInstance(

)

;

& GetInstance(

)

;

IsSet(

)

;

& GetSet(

)

;

& SetSet(

);

IsComplex(

)

;

SetComplex(

);

IsSeq(

)

;

& GetSeq(

)

;

& SetSeq(

);

*

sm_SelectionNames[];

NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string>

;

IsSetReference(

)

;

CanGetReference(

)

;

ResetReference(

);

& GetReference(

)

;

IsSetTest(

)

;

CanGetTest(

)

;

ResetTest(

);

& GetTest(

)

;

e_Loss_of_heterozygosity

ResetSelection(

);

E_Choice Which(

)

;

CheckSelected(E_Choice index)

;

NCBI_NORETURN

ThrowInvalidSelection(E_Choice index)

;

SelectionName(E_Choice index);

IsUnknown(

)

;

SetUnknown(

);

IsSplicing(

)

;

SetSplicing(

);

IsNote(

)

;

& GetNote(

)

;

& SetNote(

);

IsVariation(

)

;

& GetVariation(

)

;

IsLoss_of_heterozygosity(

)

;

*

sm_SelectionNames[];

NCBI_NS_NCBI::CUnionBuffer<NCBI_NS_STD::string>

;

IsSetPhase(

)

;

CanGetPhase(

)

;

ResetPhase(

);

GetPhase(

)

;

& SetPhase(

);

IsSetX_length(

)

;

CanGetX_length(

)

;

ResetX_length(

);

e__allMandatory = 0,

IsSetDescription(

)

;

CanGetDescription(

)

;

ResetDescription(

);

IsSetObject_id(

)

;

CanGetObject_id(

)

;

ResetObject_id(

);

& GetObject_id(

)

;

e__allMandatory = 0,

IsSetSource(

)

;

CanGetSource(

)

;

ResetSource(

);

& GetSource(

)

;

IsSetCondition(

)

;

CanGetCondition(

)

;

ResetCondition(

);

& GetCondition(

)

;

list< CRef< CUser_object > >

;

e__allMandatory = 0,

IsSetId(

)

;

CanGetId(

)

;

ResetId(

);

& SetId(

);

IsSetParent_id(

)

;

CanGetParent_id(

)

;

ResetParent_id(

);

& GetParent_id(

)

;

IsSetSample_id(

)

;

CanGetSample_id(

)

;

ResetSample_id(

);

& GetSample_id(

)

;

IsSetOther_ids(

)

;

CanGetOther_ids(

)

;

ResetOther_ids(

);

& GetOther_ids(

)

;

IsSetName(

)

;

CanGetName(

)

;

ResetName(

);

& GetName(

)

;

& SetName(

);

IsSetSynonyms(

)

;

CanGetSynonyms(

)

;

ResetSynonyms(

);

& GetSynonyms(

)

;

IsSetDescription(

)

;

CanGetDescription(

)

;

ResetDescription(

);

IsSetPlacements(

)

;

CanGetPlacements(

)

;

ResetPlacements(

);

IsSetPhenotype(

)

;

CanGetPhenotype(

)

;

ResetPhenotype(

);

& GetPhenotype(

)

;

IsSetMethod(

)

;

CanGetMethod(

)

;

ResetMethod(

);

& GetMethod(

)

;

IsSetPopulation_data(

)

;

CanGetPopulation_data(

)

;

ResetPopulation_data(

);

IsSetVariant_prop(

)

;

CanGetVariant_prop(

)

;

ResetVariant_prop(

);

IsSetPub(

)

;

CanGetPub(

)

;

ResetPub(

);

& GetPub(

)

;

& SetPub(

);

IsSetClinical_test(

)

;

CanGetClinical_test(

)

;

ResetClinical_test(

);

IsSetData(

)

;

CanGetData(

)

;

ResetData(

);

& GetData(

)

;

& SetData(

);

IsSetConsequence(

)

;

CanGetConsequence(

)

;

ResetConsequence(

);

IsSetFrameshift(

)

;

CanGetFrameshift(

)

;

ResetFrameshift(

);

IsSetExt(

)

;

CanGetExt(

)

;

ResetExt(

);

& GetExt(

)

;

& SetExt(

);

IsSetSomatic_origin(

)

;

CanGetSomatic_origin(

)

;

ResetSomatic_origin(

);

IsSetExceptions(

)

;

CanGetExceptions(

)

;

ResetExceptions(

);

IsSetSo_terms(

)

;

CanGetSo_terms(

)

;

ResetSo_terms(

);

& GetSo_terms(

)

;

Reset(

);

(!CanGetType()) {

m_Variations;

m_Variations;

= std::forward<CVariation_Base::C_Data::C_Set::TName>(

);

(index, reset, 0);

IsSetReference();

(!CanGetReference()) {

m_Reference =

;

m_Reference = std::forward<CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::TReference>(

);

(!IsSetReference()) {

(!CanGetTest()) {

m_Test = std::forward<CVariation_Base::C_E_Consequence::C_Loss_of_heterozygosity::TTest>(

);

(index, reset, 0);

== e_Loss_of_heterozygosity;

IsSetPhase();

(!CanGetPhase()) {

(!IsSetPhase()) {

IsSetX_length();

(!CanGetX_length()) {

m_X_length =

;

(!IsSetX_length()) {

= std::forward<CVariation_Base::C_E_Somatic_origin::C_Condition::TDescription>(

);

m_Source.NotEmpty();

IsSetSource();

(!CanGetSource()) {

m_Condition.NotEmpty();

IsSetCondition();

(!CanGetCondition()) {

(*m_Condition);

.NotEmpty();

= std::forward<CVariation_Base::TName>(

);

.NotEmpty();

Base class for all serializable objects.

Set of related Variations.

C_Loss_of_heterozygosity –.

condition related to this origin's type

static char UnassignedByte(void)

void ThrowUnassigned(TMemberIndex index) const

#define ENUM_METHOD_NAME(EnumName)

static string UnassignedString(void)

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_VARIATION_EXPORT

bool CanGetVariant_prop(void) const

Check if it is safe to call GetVariant_prop method.

bool CanGetCondition(void) const

Check if it is safe to call GetCondition method.

bool CanGetMethod(void) const

Check if it is safe to call GetMethod method.

C_Frameshift & operator=(const C_Frameshift &)

bool IsSetName(void) const

names and synonyms some variants have well-known canonical names and possible accepted synonyms Check...

bool CanGetReference(void) const

Check if it is safe to call GetReference method.

C_Loss_of_heterozygosity(const C_Loss_of_heterozygosity &)

void ResetSelection(void)

Reset the selection (set it to e_not_set).

C_E_Consequence(const C_E_Consequence &)

const TSo_terms & GetSo_terms(void) const

Get the So_terms member data.

Tparent::CMemberIndex< E_memberIndex, 3 > TmemberIndex

C_Loss_of_heterozygosity TLoss_of_heterozygosity

bool IsSetOther_ids(void) const

Check if a value has been assigned to Other_ids data member.

TSomatic_origin & SetSomatic_origin(void)

Assign a value to Somatic_origin data member.

bool IsUnknown(void) const

Check if variant Unknown is selected.

bool IsComplex(void) const

Check if variant Complex is selected.

list< CRef< CVariantPlacement > > TPlacements

bool IsNote(void) const

Check if variant Note is selected.

DECLARE_INTERNAL_TYPE_INFO()

Tparent::CMemberIndex< E_memberIndex, 3 > TmemberIndex

CRef< TFrameshift > m_Frameshift

C_Data & operator=(const C_Data &)

void Select(E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)

Select the requested variant if needed, allocating CObject variants from memory pool.

list< CRef< C_E_Consequence > > m_Consequence

bool CanGetTest(void) const

Check if it is safe to call GetTest method.

bool IsSetPhenotype(void) const

phenotype Check if a value has been assigned to Phenotype data member.

bool IsSetFrameshift(void) const

Check if a value has been assigned to Frameshift data member.

DECLARE_INTERNAL_TYPE_INFO()

E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

void Select(E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)

Select the requested variant if needed, allocating CObject variants from memory pool.

TObject_id & SetObject_id(void)

Assign a value to Object_id data member.

bool CanGetOther_ids(void) const

Check if it is safe to call GetOther_ids method.

bool CanGetFrameshift(void) const

Check if it is safe to call GetFrameshift method.

const TPopulation_data & GetPopulation_data(void) const

Get the Population_data member data.

bool CanGetPopulation_data(void) const

Check if it is safe to call GetPopulation_data method.

list< CRef< CVariation > > TVariations

CVariation_inst TInstance

bool CanGetType(void) const

Check if it is safe to call GetType method.

DECLARE_INTERNAL_TYPE_INFO()

TExt & SetExt(void)

Assign a value to Ext data member.

bool IsVariation(void) const

Check if variant Variation is selected.

bool CanGetData(void) const

Check if it is safe to call GetData method.

bool IsSetPlacements(void) const

where this beast is seen note that this is a set of locations, and there are no restrictions to the c...

const TClinical_test & GetClinical_test(void) const

Get the Clinical_test member data.

Tparent::CMemberIndex< E_memberIndex, 3 > TmemberIndex

TExceptions & SetExceptions(void)

Assign a value to Exceptions data member.

bool IsLoss_of_heterozygosity(void) const

Check if variant Loss_of_heterozygosity is selected.

C_Frameshift(const C_Frameshift &)

const TName & GetName(void) const

Get the Name member data.

bool IsSplicing(void) const

Check if variant Splicing is selected.

NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string

bool CanGetPlacements(void) const

Check if it is safe to call GetPlacements method.

const TExceptions & GetExceptions(void) const

Get the Exceptions member data.

TTest & SetTest(void)

Assign a value to Test data member.

list< CRef< CDbtag > > m_Other_ids

DECLARE_INTERNAL_TYPE_INFO()

bool IsUnknown(void) const

Check if variant Unknown is selected.

bool CanGetSo_terms(void) const

Check if it is safe to call GetSo_terms method.

bool CanGetSomatic_origin(void) const

Check if it is safe to call GetSomatic_origin method.

void ResetX_length(void)

Reset X_length data member.

C_Loss_of_heterozygosity & operator=(const C_Loss_of_heterozygosity &)

TSample_id & SetSample_id(void)

Assign a value to Sample_id data member.

bool IsSetPub(void) const

publication support; same type as in seq-feat Check if a value has been assigned to Pub data member.

TX_length GetX_length(void) const

Get the X_length member data.

list< CRef< CPopulation_data > > m_Population_data

TReference & SetReference(void)

Assign a value to Reference data member.

list< string > m_Synonyms

bool IsInstance(void) const

Check if variant Instance is selected.

const TSample_id & GetSample_id(void) const

Get the Sample_id member data.

TPhase & SetPhase(void)

Assign a value to Phase data member.

bool CanGetDescription(void) const

Check if it is safe to call GetDescription method.

bool CanGetName(void) const

Check if it is safe to call GetName method.

TName & SetName(void)

Assign a value to Name data member.

bool CanGetId(void) const

Check if it is safe to call GetId method.

bool IsSetSource(void) const

description of the somatic origin itself Check if a value has been assigned to Source data member.

const TExt & GetExt(void) const

Get the Ext member data.

TSo_terms & SetSo_terms(void)

Assign a value to So_terms data member.

list< CRef< CObject_id > > m_Sample_id

list< CRef< CPhenotype > > m_Phenotype

list< CRef< CPhenotype > > TPhenotype

list< CRef< CVariantPlacement > > m_Placements

bool CanGetPhase(void) const

Check if it is safe to call GetPhase method.

const TPhenotype & GetPhenotype(void) const

Get the Phenotype member data.

CRef< TClinical_test > m_Clinical_test

NCBI_NS_NCBI::CSerialObject * m_object

const TCondition & GetCondition(void) const

Get the Condition member data.

bool CanGetExceptions(void) const

Check if it is safe to call GetExceptions method.

CVariation_Base(const CVariation_Base &)

NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string

bool IsSetId(void) const

ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP|rs12334',...

const TNote & GetNote(void) const

Get the variant data.

CVariantProperties TVariant_prop

NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string

DECLARE_INTERNAL_TYPE_INFO()

DECLARE_INTERNAL_TYPE_INFO()

CRef< TVariant_prop > m_Variant_prop

DECLARE_INTERNAL_TYPE_INFO()

Tparent::CMemberIndex< E_memberIndex, 4 > TmemberIndex

const TOther_ids & GetOther_ids(void) const

Get the Other_ids member data.

bool IsSetParent_id(void) const

Check if a value has been assigned to Parent_id data member.

const TDescription & GetDescription(void) const

Get the Description member data.

const TSomatic_origin & GetSomatic_origin(void) const

Get the Somatic_origin member data.

bool IsSetDescription(void) const

Check if a value has been assigned to Description data member.

bool IsSetVariations(void) const

Check if a value has been assigned to Variations data member.

void SetUnknown(void)

Select the variant.

bool CanGetParent_id(void) const

Check if it is safe to call GetParent_id method.

bool CanGetVariations(void) const

Check if it is safe to call GetVariations method.

list< CRef< CObject_id > > TSample_id

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

const TNote & GetNote(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the Pub member data.

const TVariations & GetVariations(void) const

Get the Variations member data.

bool CanGetDescription(void) const

Check if it is safe to call GetDescription method.

bool IsSetReference(void) const

In germline comparison, it will be reference genome assembly (default) or reference/normal population...

bool IsSetExceptions(void) const

Check if a value has been assigned to Exceptions data member.

const TFrameshift & GetFrameshift(void) const

Get the Frameshift member data.

bool IsSetType(void) const

Check if a value has been assigned to Type data member.

E_ChoiceStopper

Maximum+1 value of the choice variant enumerator.

DECLARE_INTERNAL_TYPE_INFO()

bool IsSetData(void) const

Check if a value has been assigned to Data data member.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

Check if a value has been assigned to Name data member.

list< CRef< CPopulation_data > > TPopulation_data

bool CanGetX_length(void) const

Check if it is safe to call GetX_length method.

void SetUniparental_disomy(void)

Select the variant.

bool IsNote(void) const

Check if variant Note is selected.

bool CanGetClinical_test(void) const

Check if it is safe to call GetClinical_test method.

TType & SetType(void)

Assign a value to Type data member.

const TMethod & GetMethod(void) const

Get the Method member data.

const TPlacements & GetPlacements(void) const

Get the Placements member data.

bool IsSetVariant_prop(void) const

variant properties bit fields Check if a value has been assigned to Variant_prop data member.

bool IsSetSample_id(void) const

Check if a value has been assigned to Sample_id data member.

C_Set & operator=(const C_Set &)

list< CRef< CUser_object > > TExt

bool CanGetPub(void) const

Check if it is safe to call GetPub method.

bool IsSetSo_terms(void) const

Check if a value has been assigned to So_terms data member.

const TDescription & GetDescription(void) const

Get the Description member data.

C_E_Somatic_origin(const C_E_Somatic_origin &)

Tparent::CMemberIndex< E_memberIndex, 22 > TmemberIndex

const TSynonyms & GetSynonyms(void) const

Get the Synonyms member data.

list< CRef< CVariation > > m_Variations

TPhenotype & SetPhenotype(void)

Assign a value to Phenotype data member.

void SetComplex(void)

Select the variant.

TPlacements & SetPlacements(void)

Assign a value to Placements data member.

bool CanGetName(void) const

Check if it is safe to call GetName method.

CRef< TCondition > m_Condition

CVariation_Base & operator=(const CVariation_Base &)

const TSource & GetSource(void) const

Get the Source member data.

const TTest & GetTest(void) const

Get the Test member data.

bool CanGetSource(void) const

Check if it is safe to call GetSource method.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetPhase(void) const

Check if a value has been assigned to Phase data member.

void ResetType(void)

Reset Type data member.

const TData & GetData(void) const

Get the Data member data.

TData & SetData(void)

Assign a value to Data data member.

bool CanGetSynonyms(void) const

Check if it is safe to call GetSynonyms method.

E_Choice

Choice variants.

void ResetData(void)

Reset Data data member.

void SetSplicing(void)

Select the variant.

bool IsSetCondition(void) const

Check if a value has been assigned to Condition data member.

E_Choice Which(void) const

Which variant is currently selected.

TName & SetName(void)

Assign a value to Name data member.

bool IsSetSynonyms(void) const

Check if a value has been assigned to Synonyms data member.

bool IsSetExt(void) const

Additional undescribed extensions Check if a value has been assigned to Ext data member.

C_Condition(const C_Condition &)

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

bool IsSetMethod(void) const

sequencing / acuisition method Check if a value has been assigned to Method data member.

const TObject_id & GetObject_id(void) const

Get the Object_id member data.

const TParent_id & GetParent_id(void) const

Get the Parent_id member data.

bool CanGetConsequence(void) const

Check if it is safe to call GetConsequence method.

bool IsSetX_length(void) const

Check if a value has been assigned to X_length data member.

TNote & SetNote(void)

Select the variant.

bool CanGetSample_id(void) const

Check if it is safe to call GetSample_id method.

list< CRef< CDbtag > > TOther_ids

list< CRef< CVariationException > > m_Exceptions

C_E_Consequence & operator=(const C_E_Consequence &)

TVariations & SetVariations(void)

Assign a value to Variations data member.

bool IsSetSomatic_origin(void) const

Check if a value has been assigned to Somatic_origin data member.

const TId & GetId(void) const

Get the Id member data.

E_Choice Which(void) const

Which variant is currently selected.

TDescription & SetDescription(void)

Assign a value to Description data member.

TX_length & SetX_length(void)

Assign a value to X_length data member.

C_Condition & operator=(const C_Condition &)

list< CRef< C_E_Somatic_origin > > TSomatic_origin

list< CRef< C_E_Somatic_origin > > m_Somatic_origin

TOther_ids & SetOther_ids(void)

Assign a value to Other_ids data member.

const TVariant_prop & GetVariant_prop(void) const

Get the Variant_prop member data.

bool IsSetPopulation_data(void) const

Note about SNP representation and pretinent fields: allele-frequency, population, quality-codes: The ...

void CheckSelected(E_Choice index) const

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

bool IsSetObject_id(void) const

reference to BioTerm / other descriptive database Check if a value has been assigned to Object_id dat...

void ResetPhase(void)

Reset Phase data member.

list< CRef< CDbtag > > TObject_id

void CheckSelected(E_Choice index) const

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

C_E_Somatic_origin & operator=(const C_E_Somatic_origin &)

bool IsSet(void) const

Check if variant Set is selected.

TPopulation_data & SetPopulation_data(void)

Assign a value to Population_data data member.

TNote & SetNote(void)

Select the variant.

bool IsSetClinical_test(void) const

References to external Check if a value has been assigned to Clinical_test data member.

void SetUnknown(void)

Select the variant.

const TConsequence & GetConsequence(void) const

Get the Consequence member data.

const TReference & GetReference(void) const

Get the Reference member data.

TDescription & SetDescription(void)

Assign a value to Description data member.

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

bool IsSetTest(void) const

Name of the testing subject type or the testing tissue.

bool IsUniparental_disomy(void) const

Check if variant Uniparental_disomy is selected.

TSynonyms & SetSynonyms(void)

Assign a value to Synonyms data member.

TType GetType(void) const

Get the Type member data.

list< CRef< CDbtag > > m_Object_id

list< CRef< CVariationException > > TExceptions

bool CanGetObject_id(void) const

Check if it is safe to call GetObject_id method.

void ThrowInvalidSelection(E_Choice index) const

Throw 'InvalidSelection' exception.

bool IsSetDescription(void) const

tag for comment and descriptions Check if a value has been assigned to Description data member.

NCBI_NS_NCBI::CSerialObject * m_object

E_Choice

Choice variants.

bool CanGetPhenotype(void) const

Check if it is safe to call GetPhenotype method.

TConsequence & SetConsequence(void)

Assign a value to Consequence data member.

list< CRef< CUser_object > > m_Ext

list< CRef< C_E_Consequence > > TConsequence

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

bool IsSetConsequence(void) const

Check if a value has been assigned to Consequence data member.

TPhase GetPhase(void) const

Get the Phase member data.

Tparent::CMemberIndex< E_memberIndex, 3 > TmemberIndex

CRef< TParent_id > m_Parent_id

@ e_Splicing

some effect on splicing

@ e_Variation

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

@ e_Complex

variant is a complex and undescribed change at the location This type of variant is known to occur in...

@ e_Instance

actual sequence-edit at feat.location

@ e_not_set

No variant selected.

@ e_Seq

Sequnece as it exists post-alteration.

const GenericPointer< typename T::ValueType > T2 value

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