Search Toolkit Book for CVariation_ref

#include <objects/seqfeat/Variation_ref.hpp>

Inheritance diagram for CVariation_ref:

Collaboration diagram for CVariation_ref:

Public Types
enum	ESeqType { eSeqType_na , eSeqType_aa }
	Enum governing sequence types for supplied sequence strings. More...

Public Types inherited from CVariation_ref_Base
enum	EMethod_E { eMethod_E_unknown = 0 , eMethod_E_bac_acgh = 1 , eMethod_E_computational = 2 , eMethod_E_curated = 3 , eMethod_E_digital_array = 4 , eMethod_E_expression_array = 5 , eMethod_E_fish = 6 , eMethod_E_flanking_sequence = 7 , eMethod_E_maph = 8 , eMethod_E_mcd_analysis = 9 , eMethod_E_mlpa = 10 , eMethod_E_oea_assembly = 11 , eMethod_E_oligo_acgh = 12 , eMethod_E_paired_end = 13 , eMethod_E_pcr = 14 , eMethod_E_qpcr = 15 , eMethod_E_read_depth = 16 , eMethod_E_roma = 17 , eMethod_E_rt_pcr = 18 , eMethod_E_sage = 19 , eMethod_E_sequence_alignment = 20 , eMethod_E_sequencing = 21 , eMethod_E_snp_array = 22 , eMethod_E_snp_genoytyping = 23 , eMethod_E_southern = 24 , eMethod_E_western = 25 , eMethod_E_optical_mapping = 26 , eMethod_E_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_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 DEPRECATED: new field = VariantProperties.allele-origin 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 DEPRECATED: new field = VariantProperties.allele-state More...

enum class	E_memberIndex { e__allMandatory = 0 , e_id , e_parent_id , e_sample_id , e_other_ids , e_name , e_synonyms , e_description , e_phenotype , e_method , e_population_data , e_variant_prop , e_validated , e_clinical_test , e_allele_origin , e_allele_state , e_allele_frequency , e_is_ancestral_allele , e_pub , e_data , e_consequence , e_location , e_ext_locs , e_ext , e_somatic_origin }

typedef CDbtag	TId

typedef CDbtag	TParent_id

typedef CObject_id	TSample_id

typedef list< CRef< CDbtag > >	TOther_ids

typedef string	TName

typedef list< string >	TSynonyms

typedef string	TDescription

typedef list< CRef< CPhenotype > >	TPhenotype

typedef list< int >	TMethod

typedef list< CRef< CPopulation_data > >	TPopulation_data

typedef CVariantProperties	TVariant_prop

typedef bool	TValidated

typedef list< CRef< CDbtag > >	TClinical_test

typedef int	TAllele_origin

typedef int	TAllele_state

typedef double	TAllele_frequency

typedef bool	TIs_ancestral_allele

typedef CPub	TPub

typedef C_Data	TData

typedef C_E_Consequence	C_E

typedef list< CRef< C_E_Consequence > >	TConsequence

typedef CSeq_loc	TLocation

typedef list< CRef< CExt_loc > >	TExt_locs

typedef CUser_object	TExt

typedef list< CRef< C_E_Somatic_origin > >	TSomatic_origin

typedef Tparent::CMemberIndex< E_memberIndex, 25 >	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...

Public Member Functions
	CVariation_ref (void)

	~CVariation_ref (void)

void	PostRead ()
	PostRead() hooks to establish correct, non-deprecated data layout. More...

void	SetSNV (const CSeq_data &nucleotide, CRef< CDelta_item > offset=null)

void	SetMNP (const CSeq_data &nucleotide, TSeqPos length, CRef< CDelta_item > offset=null)

void	SetMissense (const CSeq_data &amino_acid)

void	SetDuplication (CRef< CDelta_item > start_offset=null, CRef< CDelta_item > stop_offset=null)

void	SetIdentity (CRef< CSeq_literal > seq_literal, CRef< CDelta_item > start_offset=null, CRef< CDelta_item > stop_offset=null)

void	SetSNV (const vector< string > &replaces, ESeqType seq_type)
	Set a standard single nucleotide variant. More...

bool	IsSNV () const

void	SetMNP (const vector< string > &replaces, ESeqType seq_type)
	Set a standard multinucleotide variant. More...

bool	IsMNP () const

void	SetDeletion ()
	Make this variant a deletion. More...

bool	IsDeletion () const

void	SetInsertion (const string &sequence, ESeqType seq_type)
	Make this variant an insertion. More...

bool	IsInsertion () const

void	SetInsertion ()
	Make this variant an insertion of unknown sequence. More...

void	SetDeletionInsertion (const string &sequence, ESeqType seq_type)
	Make this variant an insertion. More...

bool	IsDeletionInsertion () const

void	SetMicrosatellite (const string &nucleotide_seq, TSeqPos min_repeats, TSeqPos max_repeats)
	Set the standard fields for a microsatellite. More...

bool	IsMicrosatellite () const

void	SetMicrosatellite (const string &nucleotide_seq, const vector< TSeqPos > &observed_repeats)
	Set the standard fields for a microsatellite. More...

void	SetCNV ()
	Make this variant a copy number variant. More...

bool	IsCNV () const

void	SetGain ()
	Special subtype of CNV: 'gain' - an unspecified increase in copy number. More...

bool	IsGain () const

void	SetLoss ()
	Special subtype of CNV: 'loss' - an unspecified decrease in copy number. More...

bool	IsLoss () const

void	SetCNV (TSeqPos min_copy, TSeqPos max_copy)
	Make this variant a copy number variant. More...

void	SetCNV (const vector< TSeqPos > &observed_copies)
	Make this variant a copy number variant. More...

void	SetInversion (const CSeq_loc &other_loc)
	The feature represents an inversion at the specified location The provided location should be upstream and on the opposite strand. More...

bool	IsInversion () const

void	SetEversion (const CSeq_loc &other_loc)
	The feature represents an eversion at the specified location The provided location should be downstream and on the opposite strand. More...

bool	IsEversion () const

void	SetTranslocation (const CSeq_loc &other_loc)
	The feature represents a translocation event The provided location can be anywhere; a special case exists when the provided location is on a different chromosome, in which case the feature is considered a transchromosomal rearrangement. More...

bool	IsTranslocation () const

void	SetUniparentalDisomy ()
	Establish a uniparental disomy mark-up. More...

bool	IsUniparentalDisomy () const

void	SetComplex ()
	Create a complex undescribed variant. More...

bool	IsComplex () const

void	SetUnknown ()
	Create a variant of unknown type. More...

bool	IsUnknown () const

void	SetOther ()
	Create a variant of type 'other'. More...

bool	IsOther () const

void	Validate ()
	Validate that all semantic fields are correct. More...

Deprecated Methods
bool	IsSetLocation (void) const
	NOTE: THESE ARE GOING AWAY SOON!! More...

bool	CanGetLocation (void) const

void	ResetLocation (void)

const TLocation &	GetLocation (void) const

void	SetLocation (TLocation &value)

TLocation &	SetLocation (void)

bool	IsSetExt_locs (void) const

bool	CanGetExt_locs (void) const

void	ResetExt_locs (void)

const TExt_locs &	GetExt_locs (void) const

TExt_locs &	SetExt_locs (void)

bool	IsSetExt (void) const

bool	CanGetExt (void) const

void	ResetExt (void)

const TExt &	GetExt (void) const

void	SetExt (TExt &value)

TExt &	SetExt (void)

bool	IsSetValidated (void) const

bool	CanGetValidated (void) const

void	ResetValidated (void)

TValidated	GetValidated (void) const

void	SetValidated (TValidated value)

TValidated &	SetValidated (void)

bool	IsSetClinical_test (void) const

bool	CanGetClinical_test (void) const

void	ResetClinical_test (void)

const TClinical_test &	GetClinical_test (void) const

TClinical_test &	SetClinical_test (void)

bool	IsSetAllele_origin (void) const

bool	CanGetAllele_origin (void) const

void	ResetAllele_origin (void)

TAllele_origin	GetAllele_origin (void) const

void	SetAllele_origin (TAllele_origin value)

TAllele_origin &	SetAllele_origin (void)

bool	IsSetAllele_state (void) const

bool	CanGetAllele_state (void) const

void	ResetAllele_state (void)

TAllele_state	GetAllele_state (void) const

void	SetAllele_state (TAllele_state value)

TAllele_state &	SetAllele_state (void)

bool	IsSetAllele_frequency (void) const

bool	CanGetAllele_frequency (void) const

void	ResetAllele_frequency (void)

TAllele_frequency	GetAllele_frequency (void) const

void	SetAllele_frequency (TAllele_frequency value)

TAllele_frequency &	SetAllele_frequency (void)

bool	IsSetIs_ancestral_allele (void) const

bool	CanGetIs_ancestral_allele (void) const

void	ResetIs_ancestral_allele (void)

TIs_ancestral_allele	GetIs_ancestral_allele (void) const

void	SetIs_ancestral_allele (TIs_ancestral_allele value)

TIs_ancestral_allele &	SetIs_ancestral_allele (void)

Public Member Functions inherited from CVariation_ref_Base
	CVariation_ref_Base (void)

virtual	~CVariation_ref_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetId (void) const
	ids (i.e., SNP rsid / ssid, dbVar nsv/nssv) expected values include 'dbSNP\|rs12334', 'dbSNP\|ss12345', 'dbVar\|nsv1' More...

bool	CanGetId (void) const
	Check if it is safe to call GetId method. More...

void	ResetId (void)
	Reset Id data member. More...

const TId &	GetId (void) const
	Get the Id member data. More...

void	SetId (TId &value)
	Assign a value to Id data member. More...

TId &	SetId (void)
	Assign a value to Id data member. More...

bool	IsSetParent_id (void) const
	Check if a value has been assigned to Parent_id data member. More...

bool	CanGetParent_id (void) const
	Check if it is safe to call GetParent_id method. More...

void	ResetParent_id (void)
	Reset Parent_id data member. More...

const TParent_id &	GetParent_id (void) const
	Get the Parent_id member data. More...

void	SetParent_id (TParent_id &value)
	Assign a value to Parent_id data member. More...

TParent_id &	SetParent_id (void)
	Assign a value to Parent_id data member. More...

bool	IsSetSample_id (void) const
	Check if a value has been assigned to Sample_id data member. More...

bool	CanGetSample_id (void) const
	Check if it is safe to call GetSample_id method. More...

void	ResetSample_id (void)
	Reset Sample_id data member. More...

const TSample_id &	GetSample_id (void) const
	Get the Sample_id member data. More...

void	SetSample_id (TSample_id &value)
	Assign a value to Sample_id data member. More...

TSample_id &	SetSample_id (void)
	Assign a value to Sample_id data member. More...

bool	IsSetOther_ids (void) const
	Check if a value has been assigned to Other_ids data member. More...

bool	CanGetOther_ids (void) const
	Check if it is safe to call GetOther_ids method. More...

void	ResetOther_ids (void)
	Reset Other_ids data member. More...

const TOther_ids &	GetOther_ids (void) const
	Get the Other_ids member data. More...

TOther_ids &	SetOther_ids (void)
	Assign a value to Other_ids data member. More...

bool	IsSetName (void) const
	names and synonyms some variants have well-known canonical names and possible accepted synonyms Check if a value has been assigned to Name data member. More...

bool	CanGetName (void) const
	Check if it is safe to call GetName method. More...

void	ResetName (void)
	Reset Name data member. More...

const TName &	GetName (void) const
	Get the Name member data. More...

void	SetName (const TName &value)
	Assign a value to Name data member. More...

void	SetName (TName &&value)

TName &	SetName (void)
	Assign a value to Name data member. More...

bool	IsSetSynonyms (void) const
	Check if a value has been assigned to Synonyms data member. More...

bool	CanGetSynonyms (void) const
	Check if it is safe to call GetSynonyms method. More...

void	ResetSynonyms (void)
	Reset Synonyms data member. More...

const TSynonyms &	GetSynonyms (void) const
	Get the Synonyms member data. More...

TSynonyms &	SetSynonyms (void)
	Assign a value to Synonyms data member. More...

bool	IsSetDescription (void) const
	tag for comment and descriptions Check if a value has been assigned to Description data member. More...

bool	CanGetDescription (void) const
	Check if it is safe to call GetDescription method. More...

void	ResetDescription (void)
	Reset Description data member. More...

const TDescription &	GetDescription (void) const
	Get the Description member data. More...

void	SetDescription (const TDescription &value)
	Assign a value to Description data member. More...

void	SetDescription (TDescription &&value)

TDescription &	SetDescription (void)
	Assign a value to Description data member. More...

bool	IsSetPhenotype (void) const
	phenotype Check if a value has been assigned to Phenotype data member. More...

bool	CanGetPhenotype (void) const
	Check if it is safe to call GetPhenotype method. More...

void	ResetPhenotype (void)
	Reset Phenotype data member. More...

const TPhenotype &	GetPhenotype (void) const
	Get the Phenotype member data. More...

TPhenotype &	SetPhenotype (void)
	Assign a value to Phenotype data member. More...

bool	IsSetMethod (void) const
	Check if a value has been assigned to Method data member. More...

bool	CanGetMethod (void) const
	Check if it is safe to call GetMethod method. More...

void	ResetMethod (void)
	Reset Method data member. More...

const TMethod &	GetMethod (void) const
	Get the Method member data. More...

TMethod &	SetMethod (void)
	Assign a value to Method data member. More...

bool	IsSetPopulation_data (void) const
	Note about SNP representation and pretinent fields: allele-frequency, population, quality-codes: The case of multiple alleles for a SNP would be described by parent-feature of type Variation-set.diff-alleles, where the child features of type Variation-inst, all at the same location, would describe individual alleles. More...

bool	CanGetPopulation_data (void) const
	Check if it is safe to call GetPopulation_data method. More...

void	ResetPopulation_data (void)
	Reset Population_data data member. More...

const TPopulation_data &	GetPopulation_data (void) const
	Get the Population_data member data. More...

TPopulation_data &	SetPopulation_data (void)
	Assign a value to Population_data data member. More...

bool	IsSetVariant_prop (void) const
	variant properties bit fields Check if a value has been assigned to Variant_prop data member. More...

bool	CanGetVariant_prop (void) const
	Check if it is safe to call GetVariant_prop method. More...

void	ResetVariant_prop (void)
	Reset Variant_prop data member. More...

const TVariant_prop &	GetVariant_prop (void) const
	Get the Variant_prop member data. More...

void	SetVariant_prop (TVariant_prop &value)
	Assign a value to Variant_prop data member. More...

TVariant_prop &	SetVariant_prop (void)
	Assign a value to Variant_prop data member. More...

bool	IsSetValidated (void) const
	has this variant been validated? DEPRECATED: new field = VariantProperties.other-validation Check if a value has been assigned to Validated data member. More...

bool	CanGetValidated (void) const
	Check if it is safe to call GetValidated method. More...

void	ResetValidated (void)
	Reset Validated data member. More...

TValidated	GetValidated (void) const
	Get the Validated member data. More...

void	SetValidated (TValidated value)
	Assign a value to Validated data member. More...

TValidated &	SetValidated (void)
	Assign a value to Validated data member. More...

bool	IsSetClinical_test (void) const
	link-outs to GeneTests database DEPRECATED - do not use Check if a value has been assigned to Clinical_test data member. More...

bool	CanGetClinical_test (void) const
	Check if it is safe to call GetClinical_test method. More...

void	ResetClinical_test (void)
	Reset Clinical_test data member. More...

const TClinical_test &	GetClinical_test (void) const
	Get the Clinical_test member data. More...

TClinical_test &	SetClinical_test (void)
	Assign a value to Clinical_test 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 DEPRECATED: new field = VariantProperties.allele-frequency 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? DEPRECATED: new field = VariantProperties.is-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...

bool	IsSetPub (void) const
	publication support. More...

bool	CanGetPub (void) const
	Check if it is safe to call GetPub method. More...

void	ResetPub (void)
	Reset Pub data member. More...

const TPub &	GetPub (void) const
	Get the Pub member data. More...

void	SetPub (TPub &value)
	Assign a value to Pub data member. More...

TPub &	SetPub (void)
	Assign a value to Pub data member. More...

bool	IsSetData (void) const
	Check if a value has been assigned to Data data member. More...

bool	CanGetData (void) const
	Check if it is safe to call GetData method. More...

void	ResetData (void)
	Reset Data data member. More...

const TData &	GetData (void) const
	Get the Data member data. More...

void	SetData (TData &value)
	Assign a value to Data data member. More...

TData &	SetData (void)
	Assign a value to Data data member. More...

bool	IsSetConsequence (void) const
	Check if a value has been assigned to Consequence data member. More...

bool	CanGetConsequence (void) const
	Check if it is safe to call GetConsequence method. More...

void	ResetConsequence (void)
	Reset Consequence data member. More...

const TConsequence &	GetConsequence (void) const
	Get the Consequence member data. More...

TConsequence &	SetConsequence (void)
	Assign a value to Consequence data member. More...

bool	IsSetLocation (void) const
	Observed location, if different from the parent set or feature.location. More...

bool	CanGetLocation (void) const
	Check if it is safe to call GetLocation method. More...

void	ResetLocation (void)
	Reset Location data member. More...

const TLocation &	GetLocation (void) const
	Get the Location member data. More...

void	SetLocation (TLocation &value)
	Assign a value to Location data member. More...

TLocation &	SetLocation (void)
	Assign a value to Location data member. More...

bool	IsSetExt_locs (void) const
	reference other locs, e.g. More...

bool	CanGetExt_locs (void) const
	Check if it is safe to call GetExt_locs method. More...

void	ResetExt_locs (void)
	Reset Ext_locs data member. More...

const TExt_locs &	GetExt_locs (void) const
	Get the Ext_locs member data. More...

TExt_locs &	SetExt_locs (void)
	Assign a value to Ext_locs data member. More...

bool	IsSetExt (void) const
	DEPRECATED - do not use; use Seq-feat.exts instead Check if a value has been assigned to Ext data member. More...

bool	CanGetExt (void) const
	Check if it is safe to call GetExt method. More...

void	ResetExt (void)
	Reset Ext data member. More...

const TExt &	GetExt (void) const
	Get the Ext member data. More...

void	SetExt (TExt &value)
	Assign a value to Ext data member. More...

TExt &	SetExt (void)
	Assign a value to Ext data member. More...

bool	IsSetSomatic_origin (void) const
	Check if a value has been assigned to Somatic_origin data member. More...

bool	CanGetSomatic_origin (void) const
	Check if it is safe to call GetSomatic_origin method. More...

void	ResetSomatic_origin (void)
	Reset Somatic_origin data member. More...

const TSomatic_origin &	GetSomatic_origin (void) const
	Get the Somatic_origin member data. More...

TSomatic_origin &	SetSomatic_origin (void)
	Assign a value to Somatic_origin 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 CVariation_ref_Base	Tparent

Private Member Functions
	CVariation_ref (const CVariation_ref &value)

CVariation_ref &	operator= (const CVariation_ref &value)


bool	IsSetPopulation_data (void) const
	Prohibited deprecated functions Due to limitations in ASN spec-land, we cannot officially remove these data elements from the spec. More...

bool	CanGetPopulation_data (void) const

void	ResetPopulation_data (void)

const TPopulation_data &	GetPopulation_data (void) const

TPopulation_data &	SetPopulation_data (void)

bool	IsSetPub (void) const

bool	CanGetPub (void) const

void	ResetPub (void)

const TPub &	GetPub (void) const

void	SetPub (TPub &value)

TPub &	SetPub (void)

Additional Inherited Members
Static Public Member Functions inherited from CVariation_ref_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EMethod_E (void)
	Access to EMethod_E'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 56 of file Variation_ref.hpp.

Member Typedef Documentation

◆ Tparent

typedef CVariation_ref_Base CVariation_ref::Tparent

private

Definition at line 58 of file Variation_ref.hpp.

Member Enumeration Documentation

◆ ESeqType

enum CVariation_ref::ESeqType

Enum governing sequence types for supplied sequence strings.

Enumerator
eSeqType_na
eSeqType_aa

Definition at line 66 of file Variation_ref.hpp.

Constructor & Destructor Documentation

◆ CVariation_ref() [1/2]

CVariation_ref::CVariation_ref ( void )

inline

Definition at line 288 of file Variation_ref.hpp.

◆ ~CVariation_ref()

CVariation_ref::~CVariation_ref ( void )

Definition at line 51 of file Variation_ref.cpp.

◆ CVariation_ref() [2/2]

CVariation_ref::CVariation_ref ( const CVariation_ref & value )

private

Member Function Documentation

◆ CanGetAllele_frequency()

bool CVariation_ref::CanGetAllele_frequency ( void ) const

Definition at line 479 of file Variation_ref.cpp.

References CVariantProperties_Base::CanGetAllele_frequency(), CVariation_ref_Base::CanGetAllele_frequency(), CVariation_ref_Base::CanGetVariant_prop(), and CVariation_ref_Base::GetVariant_prop().

◆ CanGetAllele_origin()

bool CVariation_ref::CanGetAllele_origin ( void ) const

Definition at line 347 of file Variation_ref.cpp.

References CVariantProperties_Base::CanGetAllele_origin(), CVariation_ref_Base::CanGetAllele_origin(), CVariation_ref_Base::CanGetVariant_prop(), and CVariation_ref_Base::GetVariant_prop().

◆ CanGetAllele_state()

bool CVariation_ref::CanGetAllele_state ( void ) const

Definition at line 413 of file Variation_ref.cpp.

References CVariantProperties_Base::CanGetAllele_state(), CVariation_ref_Base::CanGetAllele_state(), CVariation_ref_Base::CanGetVariant_prop(), and CVariation_ref_Base::GetVariant_prop().

◆ CanGetClinical_test()

bool CVariation_ref::CanGetClinical_test ( void ) const

Definition at line 304 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ CanGetExt()

bool CVariation_ref::CanGetExt ( void ) const

Definition at line 822 of file Variation_ref.cpp.

References CVariation_ref_Base::CanGetExt().

◆ CanGetExt_locs()

bool CVariation_ref::CanGetExt_locs ( void ) const

Definition at line 791 of file Variation_ref.cpp.

References CVariation_ref_Base::CanGetExt_locs().

◆ CanGetIs_ancestral_allele()

bool CVariation_ref::CanGetIs_ancestral_allele ( void ) const

Definition at line 544 of file Variation_ref.cpp.

References CVariantProperties_Base::CanGetIs_ancestral_allele(), CVariation_ref_Base::CanGetIs_ancestral_allele(), CVariation_ref_Base::CanGetVariant_prop(), and CVariation_ref_Base::GetVariant_prop().

◆ CanGetLocation()

bool CVariation_ref::CanGetLocation ( void ) const

Definition at line 753 of file Variation_ref.cpp.

References CVariation_ref_Base::CanGetLocation().

◆ CanGetPopulation_data()

bool CVariation_ref::CanGetPopulation_data ( void ) const

private

Definition at line 196 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ CanGetPub()

bool CVariation_ref::CanGetPub ( void ) const

private

Definition at line 608 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ CanGetValidated()

bool CVariation_ref::CanGetValidated ( void ) const

Definition at line 239 of file Variation_ref.cpp.

References CVariantProperties_Base::CanGetOther_validation(), CVariation_ref_Base::CanGetValidated(), CVariation_ref_Base::CanGetVariant_prop(), and CVariation_ref_Base::GetVariant_prop().

◆ GetAllele_frequency()

CVariation_ref::TAllele_frequency CVariation_ref::GetAllele_frequency ( void ) const

Definition at line 497 of file Variation_ref.cpp.

References CVariantProperties_Base::GetAllele_frequency(), CVariation_ref_Base::GetAllele_frequency(), CVariation_ref_Base::GetVariant_prop(), and CVariation_ref_Base::IsSetVariant_prop().

◆ GetAllele_origin()

CVariation_ref::TAllele_origin CVariation_ref::GetAllele_origin ( void ) const

Definition at line 365 of file Variation_ref.cpp.

References CVariantProperties_Base::GetAllele_origin(), CVariation_ref_Base::GetAllele_origin(), CVariation_ref_Base::GetVariant_prop(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ GetAllele_state()

CVariation_ref::TAllele_state CVariation_ref::GetAllele_state ( void ) const

Definition at line 431 of file Variation_ref.cpp.

References CVariantProperties_Base::GetAllele_state(), CVariation_ref_Base::GetAllele_state(), CVariation_ref_Base::GetVariant_prop(), and CVariation_ref_Base::IsSetVariant_prop().

◆ GetClinical_test()

const CVariation_ref::TClinical_test & CVariation_ref::GetClinical_test ( void ) const

Definition at line 320 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ GetExt()

const CVariation_ref::TExt & CVariation_ref::GetExt ( void ) const

Definition at line 834 of file Variation_ref.cpp.

References CVariation_ref_Base::GetExt().

◆ GetExt_locs()

const CVariation_ref::TExt_locs & CVariation_ref::GetExt_locs ( void ) const

Definition at line 803 of file Variation_ref.cpp.

References CVariation_ref_Base::GetExt_locs().

◆ GetIs_ancestral_allele()

CVariation_ref::TIs_ancestral_allele CVariation_ref::GetIs_ancestral_allele ( void ) const

Definition at line 562 of file Variation_ref.cpp.

References CVariantProperties_Base::GetIs_ancestral_allele(), CVariation_ref_Base::GetIs_ancestral_allele(), CVariation_ref_Base::GetVariant_prop(), and CVariation_ref_Base::IsSetVariant_prop().

◆ GetLocation()

const CVariation_ref::TLocation & CVariation_ref::GetLocation ( void ) const

Definition at line 765 of file Variation_ref.cpp.

References CVariation_ref_Base::GetLocation().

◆ GetPopulation_data()

const CVariation_ref::TPopulation_data & CVariation_ref::GetPopulation_data ( void ) const

private

Definition at line 212 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ GetPub()

const CVariation_ref::TPub & CVariation_ref::GetPub ( void ) const

private

Definition at line 624 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ GetValidated()

CVariation_ref::TValidated CVariation_ref::GetValidated ( void ) const

Definition at line 257 of file Variation_ref.cpp.

References CVariantProperties_Base::GetOther_validation(), CVariation_ref_Base::GetValidated(), CVariation_ref_Base::GetVariant_prop(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsCNV()

bool CVariation_ref::IsCNV ( ) const

Definition at line 1137 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_cnv, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CGvfWriteRecord::AssignType(), CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsComplex()

bool CVariation_ref::IsComplex ( ) const

Definition at line 1319 of file Variation_ref.cpp.

References CVariation_ref_Base::GetData(), and CVariation_ref_Base::C_Data::IsComplex().

Referenced by CGvfWriteRecord::AssignType(), CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsDeletion()

bool CVariation_ref::IsDeletion ( ) const

Definition at line 1003 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_del, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsDeletionInsertion()

bool CVariation_ref::IsDeletionInsertion ( ) const

Definition at line 1066 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_delins, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsEversion()

bool CVariation_ref::IsEversion ( ) const

Definition at line 1261 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_everted_copy, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsGain()

bool CVariation_ref::IsGain ( ) const

Definition at line 1159 of file Variation_ref.cpp.

References CInt_fuzz_Base::eLim_gt, CVariation_inst_Base::eType_cnv, CVariation_ref_Base::GetData(), CVariation_inst_Base::GetDelta(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), CVariation_inst_Base::IsSetDelta(), and CVariation_inst_Base::IsSetType().

Referenced by CGvfWriteRecord::AssignType(), CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsInsertion()

bool CVariation_ref::IsInsertion ( ) const

Definition at line 1027 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_ins, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsInversion()

bool CVariation_ref::IsInversion ( ) const

Definition at line 1241 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_inverted_copy, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsLoss()

bool CVariation_ref::IsLoss ( ) const

Definition at line 1187 of file Variation_ref.cpp.

References CInt_fuzz_Base::eLim_lt, CVariation_inst_Base::eType_cnv, CVariation_ref_Base::GetData(), CVariation_inst_Base::GetDelta(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), CVariation_inst_Base::IsSetDelta(), and CVariation_inst_Base::IsSetType().

Referenced by CGvfWriteRecord::AssignType(), CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsMicrosatellite()

bool CVariation_ref::IsMicrosatellite ( ) const

Definition at line 1094 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_microsatellite, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

◆ IsMNP()

bool CVariation_ref::IsMNP ( ) const

Definition at line 986 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_mnp, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

◆ IsOther()

bool CVariation_ref::IsOther ( void ) const

Definition at line 1344 of file Variation_ref.cpp.

References CVariation_ref_Base::C_Data::C_Set::eData_set_type_other, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetSet(), CVariation_ref_Base::C_Data::C_Set::GetType(), and CVariation_ref_Base::C_Data::IsSet().

◆ IsSetAllele_frequency()

bool CVariation_ref::IsSetAllele_frequency ( void ) const

Definition at line 470 of file Variation_ref.cpp.

References CVariation_ref_Base::GetVariant_prop(), CVariantProperties_Base::IsSetAllele_frequency(), CVariation_ref_Base::IsSetAllele_frequency(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by PostRead(), and SetAllele_frequency().

◆ IsSetAllele_origin()

bool CVariation_ref::IsSetAllele_origin ( void ) const

Definition at line 338 of file Variation_ref.cpp.

References CVariation_ref_Base::GetVariant_prop(), CVariantProperties_Base::IsSetAllele_origin(), CVariation_ref_Base::IsSetAllele_origin(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by CSeq_featHandler::GetLabel(), CGuiObjectInfoVariant::GetToolTip(), PostRead(), and SetAllele_origin().

◆ IsSetAllele_state()

bool CVariation_ref::IsSetAllele_state ( void ) const

Definition at line 404 of file Variation_ref.cpp.

References CVariation_ref_Base::GetVariant_prop(), CVariantProperties_Base::IsSetAllele_state(), CVariation_ref_Base::IsSetAllele_state(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by PostRead(), and SetAllele_state().

◆ IsSetClinical_test()

bool CVariation_ref::IsSetClinical_test ( void ) const

Definition at line 296 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ IsSetExt()

bool CVariation_ref::IsSetExt ( void ) const

Definition at line 816 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetExt().

◆ IsSetExt_locs()

bool CVariation_ref::IsSetExt_locs ( void ) const

Definition at line 785 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetExt_locs().

◆ IsSetIs_ancestral_allele()

bool CVariation_ref::IsSetIs_ancestral_allele ( void ) const

Definition at line 535 of file Variation_ref.cpp.

References CVariation_ref_Base::GetVariant_prop(), CVariantProperties_Base::IsSetIs_ancestral_allele(), CVariation_ref_Base::IsSetIs_ancestral_allele(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by PostRead().

◆ IsSetLocation()

bool CVariation_ref::IsSetLocation ( void ) const

NOTE: THESE ARE GOING AWAY SOON!!

Definition at line 747 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetLocation().

Referenced by variation_ref::CVariationUtil::CheckExonBoundary(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), variation_ref::CVariationUtil::s_PropagateLocsInPlace(), variation_ref::CVariationUtil::s_Remap(), variation_ref::CVariationUtil::s_ResolveIntronicOffsets(), variation_ref::CVariationUtil::SetReferenceSequence(), and variation_ref::CVariationUtil::SetVariantProperties().

◆ IsSetPopulation_data()

bool CVariation_ref::IsSetPopulation_data ( void ) const

private

Prohibited deprecated functions Due to limitations in ASN spec-land, we cannot officially remove these data elements from the spec.

We can, however, hide them from client access.

Definition at line 188 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ IsSetPub()

bool CVariation_ref::IsSetPub ( void ) const

private

Definition at line 600 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ IsSetValidated()

bool CVariation_ref::IsSetValidated ( void ) const

Definition at line 230 of file Variation_ref.cpp.

References CVariation_ref_Base::GetVariant_prop(), CVariantProperties_Base::IsSetOther_validation(), CVariation_ref_Base::IsSetValidated(), and CVariation_ref_Base::IsSetVariant_prop().

Referenced by CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsSNV()

bool CVariation_ref::IsSNV ( ) const

Definition at line 952 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_snv, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), CVariation_inst_Base::IsSetType(), and ITERATE.

Referenced by CGuiObjectInfoVariant::GetToolTip().

◆ IsTranslocation()

bool CVariation_ref::IsTranslocation ( ) const

Definition at line 1291 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_translocation, CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CVariation_inst_Base::GetType(), CVariation_ref_Base::C_Data::IsInstance(), and CVariation_inst_Base::IsSetType().

Referenced by CFeatGlyph::GetCustomColorIdx(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ IsUniparentalDisomy()

bool CVariation_ref::IsUniparentalDisomy ( ) const

Definition at line 1306 of file Variation_ref.cpp.

References CVariation_ref_Base::GetData(), and CVariation_ref_Base::C_Data::IsUniparental_disomy().

Referenced by CSeq_featHandler::GetLabel().

◆ IsUnknown()

bool CVariation_ref::IsUnknown ( ) const

Definition at line 1330 of file Variation_ref.cpp.

References CVariation_ref_Base::GetData(), and CVariation_ref_Base::C_Data::IsUnknown().

Referenced by CSeq_featHandler::GetLabel().

◆ operator=()

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

private

◆ PostRead()

void CVariation_ref::PostRead ( void )

PostRead() hooks to establish correct, non-deprecated data layout.

Definition at line 56 of file Variation_ref.cpp.

◆ ResetAllele_frequency()

void CVariation_ref::ResetAllele_frequency ( void )

Definition at line 488 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetVariant_prop(), CVariantProperties_Base::ResetAllele_frequency(), CVariation_ref_Base::ResetAllele_frequency(), and CVariation_ref_Base::SetVariant_prop().

◆ ResetAllele_origin()

void CVariation_ref::ResetAllele_origin ( void )

Definition at line 356 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetVariant_prop(), CVariantProperties_Base::ResetAllele_origin(), CVariation_ref_Base::ResetAllele_origin(), and CVariation_ref_Base::SetVariant_prop().

◆ ResetAllele_state()

void CVariation_ref::ResetAllele_state ( void )

Definition at line 422 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetVariant_prop(), CVariantProperties_Base::ResetAllele_state(), CVariation_ref_Base::ResetAllele_state(), and CVariation_ref_Base::SetVariant_prop().

◆ ResetClinical_test()

void CVariation_ref::ResetClinical_test ( void )

Definition at line 312 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ ResetExt()

void CVariation_ref::ResetExt ( void )

Definition at line 828 of file Variation_ref.cpp.

References CVariation_ref_Base::ResetExt().

Referenced by variation_ref::RepackageAssertedSequence().

◆ ResetExt_locs()

void CVariation_ref::ResetExt_locs ( void )

Definition at line 797 of file Variation_ref.cpp.

References CVariation_ref_Base::ResetExt_locs().

◆ ResetIs_ancestral_allele()

void CVariation_ref::ResetIs_ancestral_allele ( void )

Definition at line 553 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetVariant_prop(), CVariantProperties_Base::ResetIs_ancestral_allele(), CVariation_ref_Base::ResetIs_ancestral_allele(), and CVariation_ref_Base::SetVariant_prop().

◆ ResetLocation()

void CVariation_ref::ResetLocation ( void )

Definition at line 759 of file Variation_ref.cpp.

References CVariation_ref_Base::ResetLocation().

Referenced by variation_ref::CVariationUtil::ProtToPrecursor(), and variation_ref::CVariationUtil::s_FactorOutLocsInPlace().

◆ ResetPopulation_data()

void CVariation_ref::ResetPopulation_data ( void )

private

Definition at line 204 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ ResetPub()

void CVariation_ref::ResetPub ( void )

private

Definition at line 616 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ ResetValidated()

void CVariation_ref::ResetValidated ( void )

Definition at line 248 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetVariant_prop(), CVariantProperties_Base::ResetOther_validation(), CVariation_ref_Base::ResetValidated(), and CVariation_ref_Base::SetVariant_prop().

◆ SetAllele_frequency() [1/2]

void CVariation_ref::SetAllele_frequency ( TAllele_frequency value )

Definition at line 506 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetAllele_frequency(), CVariation_ref_Base::ResetAllele_frequency(), CVariantProperties_Base::SetAllele_frequency(), CVariation_ref_Base::SetVariant_prop(), and rapidjson::value.

◆ SetAllele_frequency() [2/2]

CVariation_ref::TAllele_frequency & CVariation_ref::SetAllele_frequency ( void )

Definition at line 515 of file Variation_ref.cpp.

References ERR_POST, Error(), CVariation_ref_Base::GetAllele_frequency(), IsSetAllele_frequency(), CVariation_ref_Base::IsSetAllele_frequency(), CVariation_ref_Base::ResetAllele_frequency(), CVariantProperties_Base::SetAllele_frequency(), and CVariation_ref_Base::SetVariant_prop().

◆ SetAllele_origin() [1/2]

void CVariation_ref::SetAllele_origin ( TAllele_origin value )

Definition at line 374 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetAllele_origin(), CVariation_ref_Base::ResetAllele_origin(), CVariantProperties_Base::SetAllele_origin(), CVariation_ref_Base::SetVariant_prop(), and rapidjson::value.

◆ SetAllele_origin() [2/2]

CVariation_ref::TAllele_origin & CVariation_ref::SetAllele_origin ( void )

Definition at line 383 of file Variation_ref.cpp.

References ERR_POST, Error(), CVariation_ref_Base::GetAllele_origin(), IsSetAllele_origin(), CVariation_ref_Base::IsSetAllele_origin(), CVariation_ref_Base::ResetAllele_origin(), CVariantProperties_Base::SetAllele_origin(), and CVariation_ref_Base::SetVariant_prop().

◆ SetAllele_state() [1/2]

void CVariation_ref::SetAllele_state ( TAllele_state value )

Definition at line 440 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetAllele_state(), CVariation_ref_Base::ResetAllele_state(), CVariantProperties_Base::SetAllele_state(), CVariation_ref_Base::SetVariant_prop(), and rapidjson::value.

◆ SetAllele_state() [2/2]

CVariation_ref::TAllele_state & CVariation_ref::SetAllele_state ( void )

Definition at line 449 of file Variation_ref.cpp.

References ERR_POST, Error(), CVariation_ref_Base::GetAllele_state(), IsSetAllele_state(), CVariation_ref_Base::IsSetAllele_state(), CVariation_ref_Base::ResetAllele_state(), CVariantProperties_Base::SetAllele_state(), and CVariation_ref_Base::SetVariant_prop().

◆ SetClinical_test()

CVariation_ref::TClinical_test & CVariation_ref::SetClinical_test ( void )

Definition at line 328 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ SetCNV() [1/3]

void CVariation_ref::SetCNV ( )

Make this variant a copy number variant.

NOTE: This API variant establishes a CNV of unknown copy number

Definition at line 1124 of file Variation_ref.cpp.

References CInt_fuzz_Base::eLim_unk, CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetCNV() [2/3]

void CVariation_ref::SetCNV ( const vector< TSeqPos > & observed_copies )

Make this variant a copy number variant.

NOTE: This API variant establishes a CNV with a fixed set of possible copies

Definition at line 1216 of file Variation_ref.cpp.

References copy(), CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetCNV() [3/3]

void CVariation_ref::SetCNV	(	TSeqPos	min_copy,
		TSeqPos	max_copy
	)

Make this variant a copy number variant.

NOTE: This API variant establishes a CNV with a range of possible copies

Definition at line 1201 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetComplex()

void CVariation_ref::SetComplex ( )

Create a complex undescribed variant.

Establish a complex undescribed variant.

Definition at line 1314 of file Variation_ref.cpp.

References CVariation_ref_Base::C_Data::SetComplex(), and CVariation_ref_Base::SetData().

◆ SetDeletion()

void CVariation_ref::SetDeletion ( void )

Make this variant a deletion.

Definition at line 995 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_del, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetDeletionInsertion()

void CVariation_ref::SetDeletionInsertion	(	const string &	sequence,
		ESeqType	seq_type
	)

Make this variant an insertion.

Definition at line 1048 of file Variation_ref.cpp.

References CDelta_item_Base::eAction_del_at, CVariation_inst_Base::eType_delins, CRef< C, Locker >::Reset(), s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

Referenced by NSNPVariationHelper::x_CommonConvertFeat().

◆ SetDuplication()

void CVariation_ref::SetDuplication	(	CRef< CDelta_item >	start_offset = `null`,
		CRef< CDelta_item >	stop_offset = `null`
	)

Definition at line 700 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_ins, CRef< C, Locker >::NotNull(), Ref(), CVariation_ref_Base::SetData(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetEversion()

void CVariation_ref::SetEversion ( const CSeq_loc & other_loc )

The feature represents an eversion at the specified location The provided location should be downstream and on the opposite strand.

Definition at line 1250 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_everted_copy, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetExt() [1/2]

void CVariation_ref::SetExt ( TExt & value )

Definition at line 840 of file Variation_ref.cpp.

References CVariation_ref_Base::SetExt(), and rapidjson::value.

Referenced by variation_ref::AttachAssertedSequence(), and NSNPVariationHelper::ConvertFeat().

◆ SetExt() [2/2]

CVariation_ref::TExt & CVariation_ref::SetExt ( void )

Definition at line 846 of file Variation_ref.cpp.

References CVariation_ref_Base::SetExt().

◆ SetExt_locs()

CVariation_ref::TExt_locs & CVariation_ref::SetExt_locs ( void )

Definition at line 809 of file Variation_ref.cpp.

References CVariation_ref_Base::SetExt_locs().

Referenced by variation_ref::CVariationUtil::Remap().

◆ SetGain()

void CVariation_ref::SetGain ( )

Special subtype of CNV: 'gain' - an unspecified increase in copy number.

Definition at line 1146 of file Variation_ref.cpp.

References CInt_fuzz_Base::eLim_gt, CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetIdentity()

void CVariation_ref::SetIdentity	(	CRef< CSeq_literal >	seq_literal,
		CRef< CDelta_item >	start_offset = `null`,
		CRef< CDelta_item >	stop_offset = `null`
	)

Definition at line 720 of file Variation_ref.cpp.

References CVariation_inst_Base::eObservation_asserted, CVariation_inst_Base::eType_identity, CSeq_literal_Base::IsSetSeq_data(), CRef< C, Locker >::NotNull(), Ref(), CVariation_ref_Base::SetData(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetInsertion() [1/2]

void CVariation_ref::SetInsertion ( )

Make this variant an insertion of unknown sequence.

Definition at line 1036 of file Variation_ref.cpp.

References CDelta_item_Base::eAction_ins_before, CVariation_inst_Base::eType_ins, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetInsertion() [2/2]

void CVariation_ref::SetInsertion	(	const string &	sequence,
		ESeqType	seq_type
	)

Make this variant an insertion.

Definition at line 1012 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_ins, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

◆ SetInversion()

void CVariation_ref::SetInversion ( const CSeq_loc & other_loc )

The feature represents an inversion at the specified location The provided location should be upstream and on the opposite strand.

Definition at line 1230 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_inverted_copy, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetIs_ancestral_allele() [1/2]

void CVariation_ref::SetIs_ancestral_allele ( TIs_ancestral_allele value )

Definition at line 571 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetIs_ancestral_allele(), CVariation_ref_Base::ResetIs_ancestral_allele(), CVariantProperties_Base::SetIs_ancestral_allele(), CVariation_ref_Base::SetVariant_prop(), and rapidjson::value.

◆ SetIs_ancestral_allele() [2/2]

CVariation_ref::TIs_ancestral_allele & CVariation_ref::SetIs_ancestral_allele ( void )

Definition at line 580 of file Variation_ref.cpp.

References ERR_POST, Error(), CVariation_ref_Base::GetIs_ancestral_allele(), CVariation_ref_Base::IsSetIs_ancestral_allele(), CVariation_ref_Base::ResetIs_ancestral_allele(), CVariantProperties_Base::SetIs_ancestral_allele(), and CVariation_ref_Base::SetVariant_prop().

◆ SetLocation() [1/2]

void CVariation_ref::SetLocation ( TLocation & value )

Definition at line 771 of file Variation_ref.cpp.

References CVariation_ref_Base::SetLocation(), and rapidjson::value.

Referenced by variation_ref::CVariationUtil::AdjustDelinsToInterval(), variation_ref::CVariationUtil::CheckExonBoundary(), variation_ref::CVariationUtil::ProtToPrecursor(), variation_ref::CVariationUtil::Remap(), variation_ref::CVariationUtil::s_AddIntronicOffsets(), variation_ref::CVariationUtil::s_FactorOutLocsInPlace(), variation_ref::CVariationUtil::s_PropagateLocsInPlace(), variation_ref::CVariationUtil::s_Remap(), and variation_ref::CVariationUtil::s_ResolveIntronicOffsets().

◆ SetLocation() [2/2]

CVariation_ref::TLocation & CVariation_ref::SetLocation ( void )

Definition at line 777 of file Variation_ref.cpp.

References CVariation_ref_Base::SetLocation().

◆ SetLoss()

void CVariation_ref::SetLoss ( )

Special subtype of CNV: 'loss' - an unspecified decrease in copy number.

Definition at line 1174 of file Variation_ref.cpp.

References CInt_fuzz_Base::eLim_lt, CVariation_inst_Base::eType_cnv, CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetMicrosatellite() [1/2]

void CVariation_ref::SetMicrosatellite	(	const string &	nucleotide_seq,
		const vector< TSeqPos > &	observed_repeats
	)

Set the standard fields for a microsatellite.

This API establishes a microsatellite with a fixed set of possible observed repeats

Definition at line 1103 of file Variation_ref.cpp.

References copy(), eSeqType_na, CVariation_inst_Base::eType_microsatellite, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

◆ SetMicrosatellite() [2/2]

void CVariation_ref::SetMicrosatellite	(	const string &	nucleotide_seq,
		TSeqPos	min_repeats,
		TSeqPos	max_repeats
	)

Set the standard fields for a microsatellite.

This API establishes a microsatellite with a range of possible observed repeats.

Definition at line 1075 of file Variation_ref.cpp.

References eSeqType_na, CVariation_inst_Base::eType_microsatellite, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

◆ SetMissense()

void CVariation_ref::SetMissense ( const CSeq_data & amino_acid )

Definition at line 687 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_prot_missense, Ref(), CVariation_ref_Base::SetData(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetMNP() [1/2]

void CVariation_ref::SetMNP	(	const CSeq_data &	nucleotide,
		TSeqPos	length,
		CRef< CDelta_item >	offset = `null`
	)

Definition at line 667 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_mnp, offset, Ref(), CVariation_ref_Base::SetData(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

Referenced by NSNPVariationHelper::x_CommonConvertFeat().

◆ SetMNP() [2/2]

void CVariation_ref::SetMNP	(	const vector< string > &	replaces,
		ESeqType	seq_type
	)

Set a standard multinucleotide variant.

The replaces set can include empty strings and/or '-' as a character to indicate a deletion.

Definition at line 974 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_mnp, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

◆ SetOther()

void CVariation_ref::SetOther ( void )

Create a variant of type 'other'.

Definition at line 1336 of file Variation_ref.cpp.

References CVariation_ref_Base::C_Data::C_Set::eData_set_type_other, CVariation_ref_Base::SetData(), CVariation_ref_Base::C_Data::SetSet(), CVariation_ref_Base::C_Data::C_Set::SetType(), and CVariation_ref_Base::C_Data::C_Set::SetVariations().

◆ SetPopulation_data()

CVariation_ref::TPopulation_data & CVariation_ref::SetPopulation_data ( void )

private

Definition at line 220 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ SetPub() [1/2]

void CVariation_ref::SetPub ( TPub & value )

private

Definition at line 632 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ SetPub() [2/2]

CVariation_ref::TPub & CVariation_ref::SetPub ( void )

private

Definition at line 640 of file Variation_ref.cpp.

References eUnknown, and NCBI_THROW.

◆ SetSNV() [1/2]

void CVariation_ref::SetSNV	(	const CSeq_data &	nucleotide,
		CRef< CDelta_item >	offset = `null`
	)

Definition at line 648 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_snv, offset, Ref(), CVariation_ref_Base::SetData(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

Referenced by NSNPVariationHelper::x_CommonConvertFeat().

◆ SetSNV() [2/2]

void CVariation_ref::SetSNV	(	const vector< string > &	replaces,
		ESeqType	seq_type
	)

Set a standard single nucleotide variant.

The replaces set can include empty strings and/or '-' as a character to indicate a deletion.

Definition at line 941 of file Variation_ref.cpp.

References CVariation_inst_Base::eType_snv, s_SetReplaces(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), and CVariation_ref_Base::C_Data::SetInstance().

◆ SetTranslocation()

void CVariation_ref::SetTranslocation ( const CSeq_loc & other_loc )

The feature represents a translocation event The provided location can be anywhere; a special case exists when the provided location is on a different chromosome, in which case the feature is considered a transchromosomal rearrangement.

The feature represents an eversion at the specified location The provided location can be anywhere; a special case exists when the provided location is on a different chromosome, in which case the feature is considered a transchromosomal rearrangement.

Definition at line 1274 of file Variation_ref.cpp.

References CDelta_item_Base::eAction_del_at, CVariation_inst_Base::eType_translocation, CRef< C, Locker >::Reset(), CVariation_ref_Base::SetData(), CVariation_inst_Base::SetDelta(), CVariation_ref_Base::C_Data::SetInstance(), and CVariation_inst_Base::SetType().

◆ SetUniparentalDisomy()

void CVariation_ref::SetUniparentalDisomy ( )

Establish a uniparental disomy mark-up.

Definition at line 1301 of file Variation_ref.cpp.

References CVariation_ref_Base::SetData(), and CVariation_ref_Base::C_Data::SetUniparental_disomy().

◆ SetUnknown()

void CVariation_ref::SetUnknown ( )

Create a variant of unknown type.

Definition at line 1325 of file Variation_ref.cpp.

References CVariation_ref_Base::SetData(), and CVariation_ref_Base::C_Data::SetUnknown().

◆ SetValidated() [1/2]

void CVariation_ref::SetValidated ( TValidated value )

Definition at line 266 of file Variation_ref.cpp.

References CVariation_ref_Base::IsSetValidated(), CVariation_ref_Base::ResetValidated(), CVariantProperties_Base::SetOther_validation(), CVariation_ref_Base::SetVariant_prop(), and rapidjson::value.

◆ SetValidated() [2/2]

CVariation_ref::TValidated & CVariation_ref::SetValidated ( void )

Definition at line 275 of file Variation_ref.cpp.

References ERR_POST, Error(), CVariation_ref_Base::GetValidated(), CVariation_ref_Base::IsSetValidated(), CVariation_ref_Base::ResetValidated(), CVariantProperties_Base::SetOther_validation(), and CVariation_ref_Base::SetVariant_prop().

◆ Validate()

void CVariation_ref::Validate ( void )

Validate that all semantic fields are correct.

perform necessary validation

Definition at line 1356 of file Variation_ref.cpp.

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

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

Public Types

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Member Enumeration Documentation

◆ ESeqType

Constructor & Destructor Documentation

◆ CVariation_ref() [1/2]

◆ ~CVariation_ref()

◆ CVariation_ref() [2/2]

Member Function Documentation

◆ CanGetAllele_frequency()

◆ CanGetAllele_origin()

◆ CanGetAllele_state()

◆ CanGetClinical_test()

◆ CanGetExt()

◆ CanGetExt_locs()

◆ CanGetIs_ancestral_allele()

◆ CanGetLocation()

◆ CanGetPopulation_data()

◆ CanGetPub()

◆ CanGetValidated()

◆ GetAllele_frequency()

◆ GetAllele_origin()

◆ GetAllele_state()

◆ GetClinical_test()

◆ GetExt()

◆ GetExt_locs()

◆ GetIs_ancestral_allele()

◆ GetLocation()

◆ GetPopulation_data()

◆ GetPub()

◆ GetValidated()

◆ IsCNV()

◆ IsComplex()

◆ IsDeletion()

◆ IsDeletionInsertion()

◆ IsEversion()

◆ IsGain()

◆ IsInsertion()

◆ IsInversion()

◆ IsLoss()

◆ IsMicrosatellite()

◆ IsMNP()

◆ IsOther()

◆ IsSetAllele_frequency()

◆ IsSetAllele_origin()

◆ IsSetAllele_state()

◆ IsSetClinical_test()

◆ IsSetExt()

◆ IsSetExt_locs()

◆ IsSetIs_ancestral_allele()

◆ IsSetLocation()

◆ IsSetPopulation_data()

◆ IsSetPub()

◆ IsSetValidated()

◆ IsSNV()

◆ IsTranslocation()

◆ IsUniparentalDisomy()

◆ IsUnknown()

◆ operator=()

◆ PostRead()

◆ ResetAllele_frequency()

◆ ResetAllele_origin()

◆ ResetAllele_state()

◆ ResetClinical_test()

◆ ResetExt()

◆ ResetExt_locs()

◆ ResetIs_ancestral_allele()

◆ ResetLocation()

◆ ResetPopulation_data()

◆ ResetPub()

◆ ResetValidated()

◆ SetAllele_frequency() [1/2]

◆ SetAllele_frequency() [2/2]

◆ SetAllele_origin() [1/2]