CVariantPlacement_Base Class Reference

Represents ASN.1 type VariantPlacement defined in file variation.asn

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CVariantPlacement_Base –. More...

#include <objects/variation/VariantPlacement_.hpp>

Inheritance diagram for CVariantPlacement_Base:

Collaboration diagram for CVariantPlacement_Base:

Public Types
enum	EMol {   eMol_unknown = 0 , eMol_genomic = 1 , eMol_cdna = 2 , eMol_rna = 3 ,   eMol_protein = 4 , eMol_mitochondrion = 5 }
enum	EPlacement_method { ePlacement_method_projected = 1 , ePlacement_method_asserted = 2 , ePlacement_method_aligned = 3 }
	location flags More...
enum class	E_memberIndex {   e__allMandatory = 0 , e_loc , e_mol , e_placement_method ,   e_start_offset , e_start_offset_fuzz , e_stop_offset , e_stop_offset_fuzz ,   e_frame , e_seq , e_assembly , e_hgvs_name ,   e_comment , e_exceptions , e_dbxrefs , e_ext ,   e_gene_location , e_id , e_parent_id , e_so_terms }
typedef CSeq_loc	TLoc
typedef int	TMol
typedef int	TPlacement_method
typedef int	TStart_offset
typedef CInt_fuzz	TStart_offset_fuzz
typedef int	TStop_offset
typedef CInt_fuzz	TStop_offset_fuzz
typedef int	TFrame
typedef CSeq_literal	TSeq
typedef CDbtag	TAssembly
typedef string	THgvs_name
typedef string	TComment
typedef list< CRef< CVariationException > >	TExceptions
typedef list< CRef< CDbtag > >	TDbxrefs
typedef list< CRef< CUser_object > >	TExt
typedef int	TGene_location
typedef CObject_id	TId
typedef CObject_id	TParent_id
typedef list< int >	TSo_terms
typedef Tparent::CMemberIndex< E_memberIndex, 20 >	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
	CVariantPlacement_Base (void)
virtual	~CVariantPlacement_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetLoc (void) const
	actual concrete placement we are considering Check if a value has been assigned to Loc data member. More...
bool	CanGetLoc (void) const
	Check if it is safe to call GetLoc method. More...
void	ResetLoc (void)
	Reset Loc data member. More...
const TLoc &	GetLoc (void) const
	Get the Loc member data. More...
void	SetLoc (TLoc &value)
	Assign a value to Loc data member. More...
TLoc &	SetLoc (void)
	Assign a value to Loc data member. More...
bool	IsSetMol (void) const
	Check if a value has been assigned to Mol data member. More...
bool	CanGetMol (void) const
	Check if it is safe to call GetMol method. More...
void	ResetMol (void)
	Reset Mol data member. More...
TMol	GetMol (void) const
	Get the Mol member data. More...
void	SetMol (TMol value)
	Assign a value to Mol data member. More...
TMol &	SetMol (void)
	Assign a value to Mol data member. More...
bool	IsSetPlacement_method (void) const
	Check if a value has been assigned to Placement_method data member. More...
bool	CanGetPlacement_method (void) const
	Check if it is safe to call GetPlacement_method method. More...
void	ResetPlacement_method (void)
	Reset Placement_method data member. More...
TPlacement_method	GetPlacement_method (void) const
	Get the Placement_method member data. More...
void	SetPlacement_method (TPlacement_method value)
	Assign a value to Placement_method data member. More...
TPlacement_method &	SetPlacement_method (void)
	Assign a value to Placement_method data member. More...
bool	IsSetStart_offset (void) const
	location refinements, describing offsets into introns from product coordinates. More...
bool	CanGetStart_offset (void) const
	Check if it is safe to call GetStart_offset method. More...
void	ResetStart_offset (void)
	Reset Start_offset data member. More...
TStart_offset	GetStart_offset (void) const
	Get the Start_offset member data. More...
void	SetStart_offset (TStart_offset value)
	Assign a value to Start_offset data member. More...
TStart_offset &	SetStart_offset (void)
	Assign a value to Start_offset data member. More...
bool	IsSetStart_offset_fuzz (void) const
	Check if a value has been assigned to Start_offset_fuzz data member. More...
bool	CanGetStart_offset_fuzz (void) const
	Check if it is safe to call GetStart_offset_fuzz method. More...
void	ResetStart_offset_fuzz (void)
	Reset Start_offset_fuzz data member. More...
const TStart_offset_fuzz &	GetStart_offset_fuzz (void) const
	Get the Start_offset_fuzz member data. More...
void	SetStart_offset_fuzz (TStart_offset_fuzz &value)
	Assign a value to Start_offset_fuzz data member. More...
TStart_offset_fuzz &	SetStart_offset_fuzz (void)
	Assign a value to Start_offset_fuzz data member. More...
bool	IsSetStop_offset (void) const
	Check if a value has been assigned to Stop_offset data member. More...
bool	CanGetStop_offset (void) const
	Check if it is safe to call GetStop_offset method. More...
void	ResetStop_offset (void)
	Reset Stop_offset data member. More...
TStop_offset	GetStop_offset (void) const
	Get the Stop_offset member data. More...
void	SetStop_offset (TStop_offset value)
	Assign a value to Stop_offset data member. More...
TStop_offset &	SetStop_offset (void)
	Assign a value to Stop_offset data member. More...
bool	IsSetStop_offset_fuzz (void) const
	Check if a value has been assigned to Stop_offset_fuzz data member. More...
bool	CanGetStop_offset_fuzz (void) const
	Check if it is safe to call GetStop_offset_fuzz method. More...
void	ResetStop_offset_fuzz (void)
	Reset Stop_offset_fuzz data member. More...
const TStop_offset_fuzz &	GetStop_offset_fuzz (void) const
	Get the Stop_offset_fuzz member data. More...
void	SetStop_offset_fuzz (TStop_offset_fuzz &value)
	Assign a value to Stop_offset_fuzz data member. More...
TStop_offset_fuzz &	SetStop_offset_fuzz (void)
	Assign a value to Stop_offset_fuzz data member. More...
bool	IsSetFrame (void) const
	0-based position of bio-start relative to containing codon Check if a value has been assigned to Frame data member. More...
bool	CanGetFrame (void) const
	Check if it is safe to call GetFrame method. More...
void	ResetFrame (void)
	Reset Frame data member. More...
TFrame	GetFrame (void) const
	Get the Frame member data. More...
void	SetFrame (TFrame value)
	Assign a value to Frame data member. More...
TFrame &	SetFrame (void)
	Assign a value to Frame data member. More...
bool	IsSetSeq (void) const
	for situations in which a raw location isn't sufficient Check if a value has been assigned to Seq data member. More...
bool	CanGetSeq (void) const
	Check if it is safe to call GetSeq method. More...
void	ResetSeq (void)
	Reset Seq data member. More...
const TSeq &	GetSeq (void) const
	Get the Seq member data. More...
void	SetSeq (TSeq &value)
	Assign a value to Seq data member. More...
TSeq &	SetSeq (void)
	Assign a value to Seq data member. More...
bool	IsSetAssembly (void) const
	reference to the assembly (GenColl ID) for this location Check if a value has been assigned to Assembly data member. More...
bool	CanGetAssembly (void) const
	Check if it is safe to call GetAssembly method. More...
void	ResetAssembly (void)
	Reset Assembly data member. More...
const TAssembly &	GetAssembly (void) const
	Get the Assembly member data. More...
void	SetAssembly (TAssembly &value)
	Assign a value to Assembly data member. More...
TAssembly &	SetAssembly (void)
	Assign a value to Assembly data member. More...
bool	IsSetHgvs_name (void) const
	Check if a value has been assigned to Hgvs_name data member. More...
bool	CanGetHgvs_name (void) const
	Check if it is safe to call GetHgvs_name method. More...
void	ResetHgvs_name (void)
	Reset Hgvs_name data member. More...
const THgvs_name &	GetHgvs_name (void) const
	Get the Hgvs_name member data. More...
void	SetHgvs_name (const THgvs_name &value)
	Assign a value to Hgvs_name data member. More...
void	SetHgvs_name (THgvs_name &&value)
THgvs_name &	SetHgvs_name (void)
	Assign a value to Hgvs_name data member. More...
bool	IsSetComment (void) const
	the reference location for this variant Check if a value has been assigned to Comment data member. More...
bool	CanGetComment (void) const
	Check if it is safe to call GetComment method. More...
void	ResetComment (void)
	Reset Comment data member. More...
const TComment &	GetComment (void) const
	Get the Comment member data. More...
void	SetComment (const TComment &value)
	Assign a value to Comment data member. More...
void	SetComment (TComment &&value)
TComment &	SetComment (void)
	Assign a value to Comment 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	IsSetDbxrefs (void) const
	e.g. More...
bool	CanGetDbxrefs (void) const
	Check if it is safe to call GetDbxrefs method. More...
void	ResetDbxrefs (void)
	Reset Dbxrefs data member. More...
const TDbxrefs &	GetDbxrefs (void) const
	Get the Dbxrefs member data. More...
TDbxrefs &	SetDbxrefs (void)
	Assign a value to Dbxrefs data member. More...
bool	IsSetExt (void) const
	for process-specific placement tags/labels 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	IsSetGene_location (void) const
	Same semantics as VariantProperties.gene-location, except placement-specific 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	IsSetId (void) const
	Check if a value has been assigned to Id data member. 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
	id of the placement from which this one was derived 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	IsSetSo_terms (void) const
	Sequence Ontology terms for this placement 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

Static Public Member Functions
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EMol (void)
	Access to EMol's attributes (values, names) as defined in spec. More...
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EPlacement_method (void)
	Access to EPlacement_method'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)

Private Types
typedef CSerialObject	Tparent

Private Member Functions
	CVariantPlacement_Base (const CVariantPlacement_Base &)
CVariantPlacement_Base &	operator= (const CVariantPlacement_Base &)

Private Attributes
Uint4	m_set_State [2]
CRef< TLoc >	m_Loc
int	m_Mol
int	m_Placement_method
int	m_Start_offset
CRef< TStart_offset_fuzz >	m_Start_offset_fuzz
int	m_Stop_offset
CRef< TStop_offset_fuzz >	m_Stop_offset_fuzz
int	m_Frame
CRef< TSeq >	m_Seq
CRef< TAssembly >	m_Assembly
string	m_Hgvs_name
string	m_Comment
list< CRef< CVariationException > >	m_Exceptions
list< CRef< CDbtag > >	m_Dbxrefs
list< CRef< CUser_object > >	m_Ext
int	m_Gene_location
CRef< TId >	m_Id
CRef< TParent_id >	m_Parent_id
list< int >	m_So_terms

Additional Inherited Members
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

CVariantPlacement_Base –.

Definition at line 83 of file VariantPlacement_.hpp.

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

• include/objects/variation/VariantPlacement_.hpp
• src/objects/variation/VariantPlacement_.cpp