Search Toolkit Book for CVariantProperties

#include <objects/seqfeat/VariantProperties.hpp>

Inheritance diagram for CVariantProperties:

Collaboration diagram for CVariantProperties:

Public Member Functions
	CVariantProperties (void)

	~CVariantProperties (void)

Public Member Functions inherited from CVariantProperties_Base
	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...

Public Member Functions inherited from CSerialObject
	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...

Public Member Functions inherited from CObject
	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...

Public Member Functions inherited from CDebugDumpable
	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

Private Types
typedef CVariantProperties_Base	Tparent

Private Member Functions
	CVariantProperties (const CVariantProperties &value)

CVariantProperties &	operator= (const CVariantProperties &value)

const TProject_data &	GetProject_data () const
	Poisoned APIs - abandoned, do not use!! These APIs reference a data element caught up in a breaking spec change; use of these APIs will cause problems for many applications NOTE: ResetProject_data() / IsSetProject_data() / CanGetProject_data() are deliberately NOT poisoned, since they legitimately repairs data to a usable state. More...

TProject_data &	SetProject_data ()

Additional Inherited Members
Public Types inherited from CVariantProperties_Base
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

Public Types inherited from CObject
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...

Static Public Member Functions inherited from CVariantProperties_Base
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 Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

Static Public Member Functions inherited from CObject
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 Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 53 of file VariantProperties.hpp.

Member Typedef Documentation

◆ Tparent

typedef CVariantProperties_Base CVariantProperties::Tparent

private

Definition at line 55 of file VariantProperties.hpp.

Constructor & Destructor Documentation

◆ CVariantProperties() [1/2]

CVariantProperties::CVariantProperties ( void )

Definition at line 50 of file VariantProperties.cpp.

References CVariantProperties_Base::SetVersion().

◆ ~CVariantProperties()

CVariantProperties::~CVariantProperties ( void )

Definition at line 59 of file VariantProperties.cpp.

◆ CVariantProperties() [2/2]

CVariantProperties::CVariantProperties ( const CVariantProperties & value )

private

Member Function Documentation

◆ GetProject_data()

const CVariantProperties::TProject_data & CVariantProperties::GetProject_data ( void ) const

private

Poisoned APIs - abandoned, do not use!! These APIs reference a data element caught up in a breaking spec change; use of these APIs will cause problems for many applications NOTE: ResetProject_data() / IsSetProject_data() / CanGetProject_data() are deliberately NOT poisoned, since they legitimately repairs data to a usable state.

Definition at line 64 of file VariantProperties.cpp.

References eUnknown, and NCBI_THROW.

◆ operator=()

CVariantProperties& CVariantProperties::operator= ( const CVariantProperties & value )

private

◆ SetProject_data()

CVariantProperties::TProject_data & CVariantProperties::SetProject_data ( void )

private

Definition at line 73 of file VariantProperties.cpp.

References eUnknown, and NCBI_THROW.

The documentation for this class was generated from the following files:

include/objects/seqfeat/VariantProperties.hpp
src/objects/seqfeat/VariantProperties.cpp

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CVariantProperties() [1/2]

◆ ~CVariantProperties()

◆ CVariantProperties() [2/2]

Member Function Documentation

◆ GetProject_data()

◆ operator=()

◆ SetProject_data()