#include <objects/variation/Variation.hpp>

Inheritance diagram for CVariation:

Collaboration diagram for CVariation:

Public Member Functions
	CVariation (void)

	~CVariation (void)

const CVariation *	GetParent () const

CVariation *	SetParent ()

const CVariation *	GetConsequenceParent () const

CVariation *	SetConsequenceParent ()

void	Index ()

Public Member Functions inherited from CVariation_Base
	CVariation_Base (void)

virtual	~CVariation_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...

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	IsSetPlacements (void) const
	where this beast is seen note that this is a set of locations, and there are no restrictions to the contents to this set. More...

bool	CanGetPlacements (void) const
	Check if it is safe to call GetPlacements method. More...

void	ResetPlacements (void)
	Reset Placements data member. More...

const TPlacements &	GetPlacements (void) const
	Get the Placements member data. More...

TPlacements &	SetPlacements (void)
	Assign a value to Placements 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
	sequencing / acuisition method 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...

void	SetMethod (TMethod &value)
	Assign a value to Method data member. 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	IsSetPub (void) const
	publication support; same type as in seq-feat Check if a value has been assigned to Pub data member. 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	IsSetClinical_test (void) const
	References to external 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...

void	SetClinical_test (TClinical_test &value)
	Assign a value to Clinical_test data member. More...

TClinical_test &	SetClinical_test (void)
	Assign a value to Clinical_test 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	IsSetFrameshift (void) const
	Check if a value has been assigned to Frameshift data member. More...

bool	CanGetFrameshift (void) const
	Check if it is safe to call GetFrameshift method. More...

void	ResetFrameshift (void)
	Reset Frameshift data member. More...

const TFrameshift &	GetFrameshift (void) const
	Get the Frameshift member data. More...

void	SetFrameshift (TFrameshift &value)
	Assign a value to Frameshift data member. More...

TFrameshift &	SetFrameshift (void)
	Assign a value to Frameshift data member. More...

bool	IsSetExt (void) const
	Additional undescribed extensions 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...

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...

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

bool	CanGetExceptions (void) const
	Check if it is safe to call GetExceptions method. More...

void	ResetExceptions (void)
	Reset Exceptions data member. More...

const TExceptions &	GetExceptions (void) const
	Get the Exceptions member data. More...

TExceptions &	SetExceptions (void)
	Assign a value to Exceptions data member. More...

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

bool	CanGetSo_terms (void) const
	Check if it is safe to call GetSo_terms method. More...

void	ResetSo_terms (void)
	Reset So_terms data member. More...

const TSo_terms &	GetSo_terms (void) const
	Get the So_terms member data. More...

TSo_terms &	SetSo_terms (void)
	Assign a value to So_terms 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_Base	Tparent

Private Member Functions
	CVariation (const CVariation &value)

CVariation &	operator= (const CVariation &value)

Private Attributes
CVariation *	m_parent

CVariation *	m_consequence_parent

Additional Inherited Members
Public Types inherited from CVariation_Base
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_placements , e_phenotype , e_method , e_population_data , e_variant_prop , e_pub , e_clinical_test , e_data , e_consequence , e_frameshift , e_ext , e_somatic_origin , e_exceptions , e_so_terms }

typedef CDbtag	TId

typedef CDbtag	TParent_id

typedef list< CRef< CObject_id > >	TSample_id

typedef list< CRef< CDbtag > >	TOther_ids

typedef string	TName

typedef list< string >	TSynonyms

typedef string	TDescription

typedef list< CRef< CVariantPlacement > >	TPlacements

typedef list< CRef< CPhenotype > >	TPhenotype

typedef CVariationMethod	TMethod

typedef list< CRef< CPopulation_data > >	TPopulation_data

typedef CVariantProperties	TVariant_prop

typedef CPub_set	TPub

typedef CDbtag	TClinical_test

typedef C_Data	TData

typedef C_E_Consequence	C_E

typedef list< CRef< C_E_Consequence > >	TConsequence

typedef C_Frameshift	TFrameshift

typedef list< CRef< CUser_object > >	TExt

typedef list< CRef< C_E_Somatic_origin > >	TSomatic_origin

typedef list< CRef< CVariationException > >	TExceptions

typedef list< int >	TSo_terms

typedef Tparent::CMemberIndex< E_memberIndex, 22 >	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 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 Variation.hpp.

Member Typedef Documentation

◆ Tparent

typedef CVariation_Base CVariation::Tparent

private

Definition at line 55 of file Variation.hpp.

Constructor & Destructor Documentation

◆ CVariation() [1/2]

CVariation::CVariation ( void )

inline

Definition at line 85 of file Variation.hpp.

◆ ~CVariation()

CVariation::~CVariation ( void )

Definition at line 50 of file Variation.cpp.

◆ CVariation() [2/2]

CVariation::CVariation ( const CVariation & value )

private

Member Function Documentation

◆ GetConsequenceParent()

const CVariation * CVariation::GetConsequenceParent ( ) const

inline

Definition at line 103 of file Variation.hpp.

References m_consequence_parent.

◆ GetParent()

const CVariation * CVariation::GetParent ( void ) const

inline

Definition at line 92 of file Variation.hpp.

References m_parent.

Referenced by variation::CVariationUtil::s_FindAssertedLiteral(), and variation::CVariationUtil::s_GetPlacements().

◆ Index()

void CVariation::Index ( )

Definition at line 55 of file Variation.cpp.

References CVariation_Base::GetData(), Index(), CVariation_Base::IsSetConsequence(), CVariation_Base::IsSetData(), m_parent, NON_CONST_ITERATE, CVariation_Base::SetConsequence(), and CVariation_Base::SetData().

Referenced by variation::CHgvsParser::AttachHgvs(), variation::CVariationUtil::AttachProteinConsequences(), variation::CVariationUtil::AttachSeq(), variation::CVariationUtil::ChangeToDelins(), variation::CVariationUtil::FlipStrand(), Index(), and variation::CVariationUtil::SetVariantProperties().

◆ operator=()

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

private

◆ SetConsequenceParent()

CVariation * CVariation::SetConsequenceParent ( )

inline

Definition at line 108 of file Variation.hpp.

References m_consequence_parent.

◆ SetParent()

CVariation * CVariation::SetParent ( void )

inline

Definition at line 97 of file Variation.hpp.

References m_parent.

Member Data Documentation

◆ m_consequence_parent

CVariation* CVariation::m_consequence_parent

private

Definition at line 77 of file Variation.hpp.

Referenced by GetConsequenceParent(), and SetConsequenceParent().

◆ m_parent

CVariation* CVariation::m_parent

private

Definition at line 76 of file Variation.hpp.

Referenced by GetParent(), Index(), and SetParent().

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

include/objects/variation/Variation.hpp
src/objects/variation/Variation.cpp

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Constructor & Destructor Documentation

◆ CVariation() [1/2]

◆ ~CVariation()

◆ CVariation() [2/2]

Member Function Documentation

◆ GetConsequenceParent()

◆ GetParent()

◆ Index()

◆ operator=()

◆ SetConsequenceParent()

◆ SetParent()

Member Data Documentation

◆ m_consequence_parent

◆ m_parent