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NCBI C++ ToolKit: CVariantProperties_Base Class Reference
Historically, the dbSNP definitions document data structures used in the processing and annotation of variations by the dbSNP group. More...
enum EResource_link {
eResource_link_preserved = 1 , eResource_link_provisional = 2 , eResource_link_has3D = 4 , eResource_link_submitterLinkout = 8 ,
eResource_link_clinical = 16 , eResource_link_genotypeKit = 32
} NOTE: The format for most of these values is as an integer Unless otherwise noted, these integers represent a bitwise OR (= simple sum) of the possible values, and as such, these values represent the specific bit flags that may be set for each of the possible attributes here. More...
enum EGene_location {
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
} enum EEffect {
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
} enum EMapping { eMapping_has_other_snp = 1 , eMapping_has_assembly_conflict = 2 , eMapping_is_assembly_specific = 4 } enum EMap_weight { 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 } map-weight captures specificity of placement NOTE: This is *NOT* a bitfield More...
enum EFrequency_based_validation {
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
} enum EGenotype { eGenotype_in_haplotype_set = 1 , eGenotype_has_genotypes = 2 } enum EQuality_check {
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
} enum EConfidence { eConfidence_unknown = 0 , eConfidence_likely_artifact = 1 , eConfidence_other = 255 } enum EAllele_origin {
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
} origin of this allele, if known note that these are powers-of-two, and represent bits; thus, we can represent more than one state simultaneously through a bitwise OR More...
enum EAllele_state {
eAllele_state_unknown = 0 , eAllele_state_homozygous = 1 , eAllele_state_heterozygous = 2 , eAllele_state_hemizygous = 3 ,
eAllele_state_nullizygous = 4 , eAllele_state_other = 255
} observed allele state, if known NOTE: THIS IS NOT A BITFIELD! More...
enum class E_memberIndex {
e__allMandatory = 0 , e_version , e_resource_link , e_gene_location ,
e_effect , e_mapping , e_map_weight , e_frequency_based_validation ,
e_genotype , e_project_data , e_quality_check , e_confidence ,
e_other_validation , e_allele_origin , e_allele_state , e_allele_frequency ,
e_is_ancestral_allele
} typedef int TVersion typedef int TResource_link typedef int TGene_location typedef int TEffect typedef int TMapping typedef int TMap_weight typedef int TFrequency_based_validation typedef int TGenotype typedef list< int > TProject_data typedef int TQuality_check typedef int TConfidence typedef bool TOther_validation typedef int TAllele_origin typedef int TAllele_state typedef double TAllele_frequency typedef bool TIs_ancestral_allele typedef Tparent::CMemberIndex< E_memberIndex, 17 > 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...
CVariantProperties_Base (void) virtual ~CVariantProperties_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetVersion (void) const Check if a value has been assigned to Version data member. More...
bool CanGetVersion (void) const Check if it is safe to call GetVersion method. More...
void ResetVersion (void) Reset Version data member. More...
TVersion GetVersion (void) const Get the Version member data. More...
void SetVersion (TVersion value) Assign a value to Version data member. More...
TVersion & SetVersion (void) Assign a value to Version data member. More...
bool IsSetResource_link (void) const Check if a value has been assigned to Resource_link data member. More...
bool CanGetResource_link (void) const Check if it is safe to call GetResource_link method. More...
void ResetResource_link (void) Reset Resource_link data member. More...
TResource_link GetResource_link (void) const Get the Resource_link member data. More...
void SetResource_link (TResource_link value) Assign a value to Resource_link data member. More...
TResource_link & SetResource_link (void) Assign a value to Resource_link data member. More...
bool IsSetGene_location (void) const Check if a value has been assigned to Gene_location data member. More...
bool CanGetGene_location (void) const Check if it is safe to call GetGene_location method. More...
void ResetGene_location (void) Reset Gene_location data member. More...
TGene_location GetGene_location (void) const Get the Gene_location member data. More...
void SetGene_location (TGene_location value) Assign a value to Gene_location data member. More...
TGene_location & SetGene_location (void) Assign a value to Gene_location data member. More...
bool IsSetEffect (void) const Check if a value has been assigned to Effect data member. More...
bool CanGetEffect (void) const Check if it is safe to call GetEffect method. More...
void ResetEffect (void) Reset Effect data member. More...
TEffect GetEffect (void) const Get the Effect member data. More...
void SetEffect (TEffect value) Assign a value to Effect data member. More...
TEffect & SetEffect (void) Assign a value to Effect data member. More...
bool IsSetMapping (void) const Check if a value has been assigned to Mapping data member. More...
bool CanGetMapping (void) const Check if it is safe to call GetMapping method. More...
void ResetMapping (void) Reset Mapping data member. More...
TMapping GetMapping (void) const Get the Mapping member data. More...
void SetMapping (TMapping value) Assign a value to Mapping data member. More...
TMapping & SetMapping (void) Assign a value to Mapping data member. More...
bool IsSetMap_weight (void) const Check if a value has been assigned to Map_weight data member. More...
bool CanGetMap_weight (void) const Check if it is safe to call GetMap_weight method. More...
void ResetMap_weight (void) Reset Map_weight data member. More...
TMap_weight GetMap_weight (void) const Get the Map_weight member data. More...
void SetMap_weight (TMap_weight value) Assign a value to Map_weight data member. More...
TMap_weight & SetMap_weight (void) Assign a value to Map_weight data member. More...
bool IsSetFrequency_based_validation (void) const Check if a value has been assigned to Frequency_based_validation data member. More...
bool CanGetFrequency_based_validation (void) const Check if it is safe to call GetFrequency_based_validation method. More...
void ResetFrequency_based_validation (void) Reset Frequency_based_validation data member. More...
TFrequency_based_validation GetFrequency_based_validation (void) const Get the Frequency_based_validation member data. More...
void SetFrequency_based_validation (TFrequency_based_validation value) Assign a value to Frequency_based_validation data member. More...
TFrequency_based_validation & SetFrequency_based_validation (void) Assign a value to Frequency_based_validation data member. More...
bool IsSetGenotype (void) const Check if a value has been assigned to Genotype data member. More...
bool CanGetGenotype (void) const Check if it is safe to call GetGenotype method. More...
void ResetGenotype (void) Reset Genotype data member. More...
TGenotype GetGenotype (void) const Get the Genotype member data. More...
void SetGenotype (TGenotype value) Assign a value to Genotype data member. More...
TGenotype & SetGenotype (void) Assign a value to Genotype data member. More...
bool IsSetProject_data (void) const project IDs are IDs from BioProjects in order to report information about project relationships, we require projects to be registered This field in many ways duplicates dbxrefs; however, the intention of this field is to more adequately reflect ownership and data source More...
bool CanGetProject_data (void) const Check if it is safe to call GetProject_data method. More...
void ResetProject_data (void) Reset Project_data data member. More...
const TProject_data & GetProject_data (void) const Get the Project_data member data. More...
TProject_data & SetProject_data (void) Assign a value to Project_data data member. More...
bool IsSetQuality_check (void) const Check if a value has been assigned to Quality_check data member. More...
bool CanGetQuality_check (void) const Check if it is safe to call GetQuality_check method. More...
void ResetQuality_check (void) Reset Quality_check data member. More...
TQuality_check GetQuality_check (void) const Get the Quality_check member data. More...
void SetQuality_check (TQuality_check value) Assign a value to Quality_check data member. More...
TQuality_check & SetQuality_check (void) Assign a value to Quality_check data member. More...
bool IsSetConfidence (void) const Check if a value has been assigned to Confidence data member. More...
bool CanGetConfidence (void) const Check if it is safe to call GetConfidence method. More...
void ResetConfidence (void) Reset Confidence data member. More...
TConfidence GetConfidence (void) const Get the Confidence member data. More...
void SetConfidence (TConfidence value) Assign a value to Confidence data member. More...
TConfidence & SetConfidence (void) Assign a value to Confidence data member. More...
bool IsSetOther_validation (void) const has this variant been validated? While a boolean flag offers no subtle distinctions of validation methods, occasionally it is only known as a single boolean value NOTE: this flag is redundant and should be omitted if more comprehensive validation information is present Check if a value has been assigned to Other_validation data member. More...
bool CanGetOther_validation (void) const Check if it is safe to call GetOther_validation method. More...
void ResetOther_validation (void) Reset Other_validation data member. More...
TOther_validation GetOther_validation (void) const Get the Other_validation member data. More...
void SetOther_validation (TOther_validation value) Assign a value to Other_validation data member. More...
TOther_validation & SetOther_validation (void) Assign a value to Other_validation data member. More...
bool IsSetAllele_origin (void) const Check if a value has been assigned to Allele_origin data member. More...
bool CanGetAllele_origin (void) const Check if it is safe to call GetAllele_origin method. More...
void ResetAllele_origin (void) Reset Allele_origin data member. More...
TAllele_origin GetAllele_origin (void) const Get the Allele_origin member data. More...
void SetAllele_origin (TAllele_origin value) Assign a value to Allele_origin data member. More...
TAllele_origin & SetAllele_origin (void) Assign a value to Allele_origin data member. More...
bool IsSetAllele_state (void) const Check if a value has been assigned to Allele_state data member. More...
bool CanGetAllele_state (void) const Check if it is safe to call GetAllele_state method. More...
void ResetAllele_state (void) Reset Allele_state data member. More...
TAllele_state GetAllele_state (void) const Get the Allele_state member data. More...
void SetAllele_state (TAllele_state value) Assign a value to Allele_state data member. More...
TAllele_state & SetAllele_state (void) Assign a value to Allele_state data member. More...
bool IsSetAllele_frequency (void) const NOTE: 'allele-frequency' here refers to the minor allele frequency of the default population Check if a value has been assigned to Allele_frequency data member. More...
bool CanGetAllele_frequency (void) const Check if it is safe to call GetAllele_frequency method. More...
void ResetAllele_frequency (void) Reset Allele_frequency data member. More...
TAllele_frequency GetAllele_frequency (void) const Get the Allele_frequency member data. More...
void SetAllele_frequency (TAllele_frequency value) Assign a value to Allele_frequency data member. More...
TAllele_frequency & SetAllele_frequency (void) Assign a value to Allele_frequency data member. More...
bool IsSetIs_ancestral_allele (void) const is this variant the ancestral allele? Check if a value has been assigned to Is_ancestral_allele data member. More...
bool CanGetIs_ancestral_allele (void) const Check if it is safe to call GetIs_ancestral_allele method. More...
void ResetIs_ancestral_allele (void) Reset Is_ancestral_allele data member. More...
TIs_ancestral_allele GetIs_ancestral_allele (void) const Get the Is_ancestral_allele member data. More...
void SetIs_ancestral_allele (TIs_ancestral_allele value) Assign a value to Is_ancestral_allele data member. More...
TIs_ancestral_allele & SetIs_ancestral_allele (void) Assign a value to Is_ancestral_allele 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 const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EResource_link (void) Access to EResource_link's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EGene_location (void) Access to EGene_location's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EEffect (void) Access to EEffect's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EMapping (void) Access to EMapping's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EMap_weight (void) Access to EMap_weight's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EFrequency_based_validation (void) Access to EFrequency_based_validation's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EGenotype (void) Access to EGenotype's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EQuality_check (void) Access to EQuality_check's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EConfidence (void) Access to EConfidence's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EAllele_origin (void) Access to EAllele_origin's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EAllele_state (void) Access to EAllele_state'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)
Historically, the dbSNP definitions document data structures used in the processing and annotation of variations by the dbSNP group.
The intention is to provide information to clients that reflect internal information produced during the mapping of SNPs
CVariantProperties_Base –
Definition at line 114 of file VariantProperties_.hpp.
RetroSearch is an open source project built by @garambo
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