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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/VariantProperties___8hpp_source.html below:

NCBI C++ ToolKit: include/objects/seqfeat/VariantProperties_.hpp Source File

eResource_link_preserved = 1,

eResource_link_provisional = 2,

eResource_link_has3D = 4,

eResource_link_submitterLinkout = 8,

eResource_link_clinical = 16,

eResource_link_genotypeKit = 32

eGene_location_in_gene = 1,

eGene_location_near_gene_5 = 2,

eGene_location_near_gene_3 = 4,

eGene_location_intron = 8,

eGene_location_donor = 16,

eGene_location_acceptor = 32,

eGene_location_utr_5 = 64,

eGene_location_utr_3 = 128,

eGene_location_in_start_codon = 256,

eGene_location_in_stop_codon = 512,

eGene_location_intergenic = 1024,

eGene_location_conserved_noncoding = 2048

eEffect_no_change = 0,

eEffect_synonymous = 1,

eEffect_nonsense = 2,

eEffect_missense = 4,

eEffect_frameshift = 8,

eEffect_up_regulator = 16,

eEffect_down_regulator = 32,

eEffect_methylation = 64,

eEffect_stop_gain = 128,

eEffect_stop_loss = 256

eMapping_has_other_snp = 1,

eMapping_has_assembly_conflict = 2,

eMapping_is_assembly_specific = 4

eMap_weight_is_uniquely_placed = 1,

eMap_weight_placed_twice_on_same_chrom = 2,

eMap_weight_placed_twice_on_diff_chrom = 3,

eMap_weight_many_placements = 10

eFrequency_based_validation_is_mutation = 1,

eFrequency_based_validation_above_5pct_all = 2,

eFrequency_based_validation_above_5pct_1plus = 4,

eFrequency_based_validation_validated = 8,

eFrequency_based_validation_above_1pct_all = 16,

eFrequency_based_validation_above_1pct_1plus = 32

eGenotype_in_haplotype_set = 1,

eGenotype_has_genotypes = 2

eQuality_check_contig_allele_missing = 1,

eQuality_check_withdrawn_by_submitter = 2,

eQuality_check_non_overlapping_alleles = 4,

eQuality_check_strain_specific = 8,

eQuality_check_genotype_conflict = 16

eConfidence_unknown = 0,

eConfidence_likely_artifact = 1,

eConfidence_other = 255

eAllele_origin_unknown = 0,

eAllele_origin_germline = 1,

eAllele_origin_somatic = 2,

eAllele_origin_inherited = 4,

eAllele_origin_paternal = 8,

eAllele_origin_maternal = 16,

eAllele_origin_de_novo = 32,

eAllele_origin_biparental = 64,

eAllele_origin_uniparental = 128,

eAllele_origin_not_tested = 256,

eAllele_origin_tested_inconclusive = 512,

eAllele_origin_not_reported = 1024,

eAllele_origin_other = 1073741824

eAllele_state_unknown = 0,

eAllele_state_homozygous = 1,

eAllele_state_heterozygous = 2,

eAllele_state_hemizygous = 3,

eAllele_state_nullizygous = 4,

eAllele_state_other = 255

e_frequency_based_validation,

e_is_ancestral_allele

IsSetVersion(

)

;

CanGetVersion(

)

;

ResetVersion(

);

IsSetResource_link(

)

;

CanGetResource_link(

)

;

ResetResource_link(

);

IsSetGene_location(

)

;

CanGetGene_location(

)

;

ResetGene_location(

);

IsSetEffect(

)

;

CanGetEffect(

)

;

ResetEffect(

);

GetEffect(

)

;

IsSetMapping(

)

;

CanGetMapping(

)

;

ResetMapping(

);

IsSetMap_weight(

)

;

CanGetMap_weight(

)

;

ResetMap_weight(

);

IsSetFrequency_based_validation(

)

;

CanGetFrequency_based_validation(

)

;

ResetFrequency_based_validation(

);

IsSetGenotype(

)

;

CanGetGenotype(

)

;

ResetGenotype(

);

IsSetProject_data(

)

;

CanGetProject_data(

)

;

ResetProject_data(

);

IsSetQuality_check(

)

;

CanGetQuality_check(

)

;

ResetQuality_check(

);

IsSetConfidence(

)

;

CanGetConfidence(

)

;

ResetConfidence(

);

IsSetOther_validation(

)

;

CanGetOther_validation(

)

;

ResetOther_validation(

);

IsSetAllele_origin(

)

;

CanGetAllele_origin(

)

;

ResetAllele_origin(

);

IsSetAllele_state(

)

;

CanGetAllele_state(

)

;

ResetAllele_state(

);

IsSetAllele_frequency(

)

;

CanGetAllele_frequency(

)

;

ResetAllele_frequency(

);

IsSetIs_ancestral_allele(

)

;

CanGetIs_ancestral_allele(

)

;

ResetIs_ancestral_allele(

);

Reset(

);

Base class for all serializable objects.

Historically, the dbSNP definitions document data structures used in the processing and annotation of...

static char UnassignedByte(void)

void ThrowUnassigned(TMemberIndex index) const

#define ENUM_METHOD_NAME(EnumName)

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_SEQFEAT_EXPORT

void ResetResource_link(void)

Reset Resource_link data member.

TMapping & SetMapping(void)

Assign a value to Mapping data member.

bool IsSetFrequency_based_validation(void) const

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

bool IsSetResource_link(void) const

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

TFrequency_based_validation GetFrequency_based_validation(void) const

Get the Frequency_based_validation member data.

bool CanGetIs_ancestral_allele(void) const

Check if it is safe to call GetIs_ancestral_allele method.

void ResetGene_location(void)

Reset Gene_location data member.

list< int > TProject_data

TEffect & SetEffect(void)

Assign a value to Effect data member.

TAllele_state & SetAllele_state(void)

Assign a value to Allele_state data member.

void ResetOther_validation(void)

Reset Other_validation data member.

TAllele_state GetAllele_state(void) const

Get the Allele_state member data.

bool IsSetAllele_state(void) const

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

TGenotype GetGenotype(void) const

Get the Genotype member data.

bool IsSetMapping(void) const

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

void ResetAllele_state(void)

Reset Allele_state data member.

bool CanGetMap_weight(void) const

Check if it is safe to call GetMap_weight method.

void ResetAllele_frequency(void)

Reset Allele_frequency data member.

void ResetAllele_origin(void)

Reset Allele_origin data member.

EFrequency_based_validation

bool IsSetAllele_origin(void) const

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

TIs_ancestral_allele GetIs_ancestral_allele(void) const

Get the Is_ancestral_allele member data.

TEffect GetEffect(void) const

Get the Effect member data.

bool IsSetVersion(void) const

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

bool CanGetGene_location(void) const

Check if it is safe to call GetGene_location method.

list< int > m_Project_data

TMapping GetMapping(void) const

Get the Mapping member data.

bool IsSetMap_weight(void) const

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

bool CanGetQuality_check(void) const

Check if it is safe to call GetQuality_check method.

void ResetMapping(void)

Reset Mapping data member.

bool CanGetOther_validation(void) const

Check if it is safe to call GetOther_validation method.

bool CanGetFrequency_based_validation(void) const

Check if it is safe to call GetFrequency_based_validation method.

void ResetMap_weight(void)

Reset Map_weight data member.

CVariantProperties_Base & operator=(const CVariantProperties_Base &)

void ResetConfidence(void)

Reset Confidence data member.

bool CanGetAllele_origin(void) const

Check if it is safe to call GetAllele_origin method.

bool CanGetAllele_state(void) const

Check if it is safe to call GetAllele_state method.

EResource_link

NOTE: The format for most of these values is as an integer Unless otherwise noted,...

double m_Allele_frequency

TResource_link GetResource_link(void) const

Get the Resource_link member data.

TOther_validation GetOther_validation(void) const

Get the Other_validation member data.

void ResetFrequency_based_validation(void)

Reset Frequency_based_validation data member.

bool CanGetAllele_frequency(void) const

Check if it is safe to call GetAllele_frequency method.

TConfidence & SetConfidence(void)

Assign a value to Confidence data member.

bool CanGetProject_data(void) const

Check if it is safe to call GetProject_data method.

TResource_link & SetResource_link(void)

Assign a value to Resource_link data member.

void ResetIs_ancestral_allele(void)

Reset Is_ancestral_allele data member.

void ResetEffect(void)

Reset Effect data member.

void ResetVersion(void)

Reset Version data member.

EAllele_origin

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

TOther_validation & SetOther_validation(void)

Assign a value to Other_validation data member.

bool IsSetIs_ancestral_allele(void) const

is this variant the ancestral allele? Check if a value has been assigned to Is_ancestral_allele data ...

bool IsSetOther_validation(void) const

has this variant been validated? While a boolean flag offers no subtle distinctions of validation met...

EMap_weight

map-weight captures specificity of placement NOTE: This is *NOT* a bitfield

TAllele_frequency & SetAllele_frequency(void)

Assign a value to Allele_frequency data member.

int TFrequency_based_validation

const TProject_data & GetProject_data(void) const

Get the Project_data member data.

TIs_ancestral_allele & SetIs_ancestral_allele(void)

Assign a value to Is_ancestral_allele data member.

DECLARE_INTERNAL_TYPE_INFO()

TGenotype & SetGenotype(void)

Assign a value to Genotype data member.

bool CanGetEffect(void) const

Check if it is safe to call GetEffect method.

TGene_location & SetGene_location(void)

Assign a value to Gene_location data member.

TAllele_frequency GetAllele_frequency(void) const

Get the Allele_frequency member data.

Tparent::CMemberIndex< E_memberIndex, 17 > TmemberIndex

TProject_data & SetProject_data(void)

Assign a value to Project_data data member.

bool IsSetProject_data(void) const

project IDs are IDs from BioProjects in order to report information about project relationships,...

TMap_weight GetMap_weight(void) const

Get the Map_weight member data.

void ResetQuality_check(void)

Reset Quality_check data member.

bool CanGetResource_link(void) const

Check if it is safe to call GetResource_link method.

TVersion GetVersion(void) const

Get the Version member data.

bool CanGetGenotype(void) const

Check if it is safe to call GetGenotype method.

TQuality_check GetQuality_check(void) const

Get the Quality_check member data.

bool IsSetEffect(void) const

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

bool IsSetGenotype(void) const

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

bool CanGetVersion(void) const

Check if it is safe to call GetVersion method.

int m_Frequency_based_validation

TVersion & SetVersion(void)

Assign a value to Version data member.

EAllele_state

observed allele state, if known NOTE: THIS IS NOT A BITFIELD!

bool IsSetQuality_check(void) const

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

void ResetGenotype(void)

Reset Genotype data member.

bool m_Is_ancestral_allele

TConfidence GetConfidence(void) const

Get the Confidence member data.

bool CanGetMapping(void) const

Check if it is safe to call GetMapping method.

TFrequency_based_validation & SetFrequency_based_validation(void)

Assign a value to Frequency_based_validation data member.

bool IsSetAllele_frequency(void) const

NOTE: 'allele-frequency' here refers to the minor allele frequency of the default population Check if...

bool TIs_ancestral_allele

TGene_location GetGene_location(void) const

Get the Gene_location member data.

bool IsSetGene_location(void) const

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

TAllele_origin GetAllele_origin(void) const

Get the Allele_origin member data.

TAllele_origin & SetAllele_origin(void)

Assign a value to Allele_origin data member.

TMap_weight & SetMap_weight(void)

Assign a value to Map_weight data member.

bool IsSetConfidence(void) const

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

CVariantProperties_Base(const CVariantProperties_Base &)

TQuality_check & SetQuality_check(void)

Assign a value to Quality_check data member.

bool CanGetConfidence(void) const

Check if it is safe to call GetConfidence method.

const GenericPointer< typename T::ValueType > T2 value

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