CSpliced_seg_Base Class Reference

Represents ASN.1 type Spliced-seg defined in file seqalign.asn

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CSpliced_seg_Base –. More...

#include <objects/seqalign/Spliced_seg_.hpp>

Inheritance diagram for CSpliced_seg_Base:

Collaboration diagram for CSpliced_seg_Base:

Public Types
enum	EProduct_type { eProduct_type_transcript = 0 , eProduct_type_protein = 1 }
enum class	E_memberIndex {   e__allMandatory = 0 , e_product_id , e_genomic_id , e_product_strand ,   e_genomic_strand , e_product_type , e_exons , e_poly_a ,   e_product_length , e_modifiers }
typedef CSeq_id	TProduct_id
typedef CSeq_id	TGenomic_id
typedef ENa_strand	TProduct_strand
typedef ENa_strand	TGenomic_strand
typedef EProduct_type	TProduct_type
typedef list< CRef< CSpliced_exon > >	TExons
typedef TSeqPos	TPoly_a
typedef TSeqPos	TProduct_length
typedef list< CRef< CSpliced_seg_modifier > >	TModifiers
typedef Tparent::CMemberIndex< E_memberIndex, 10 >	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
	CSpliced_seg_Base (void)
virtual	~CSpliced_seg_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
bool	IsSetProduct_id (void) const
	product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data member. More...
bool	CanGetProduct_id (void) const
	Check if it is safe to call GetProduct_id method. More...
void	ResetProduct_id (void)
	Reset Product_id data member. More...
const TProduct_id &	GetProduct_id (void) const
	Get the Product_id member data. More...
void	SetProduct_id (TProduct_id &value)
	Assign a value to Product_id data member. More...
TProduct_id &	SetProduct_id (void)
	Assign a value to Product_id data member. More...
bool	IsSetGenomic_id (void) const
	Check if a value has been assigned to Genomic_id data member. More...
bool	CanGetGenomic_id (void) const
	Check if it is safe to call GetGenomic_id method. More...
void	ResetGenomic_id (void)
	Reset Genomic_id data member. More...
const TGenomic_id &	GetGenomic_id (void) const
	Get the Genomic_id member data. More...
void	SetGenomic_id (TGenomic_id &value)
	Assign a value to Genomic_id data member. More...
TGenomic_id &	SetGenomic_id (void)
	Assign a value to Genomic_id data member. More...
bool	IsSetProduct_strand (void) const
	should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member. More...
bool	CanGetProduct_strand (void) const
	Check if it is safe to call GetProduct_strand method. More...
void	ResetProduct_strand (void)
	Reset Product_strand data member. More...
TProduct_strand	GetProduct_strand (void) const
	Get the Product_strand member data. More...
void	SetProduct_strand (TProduct_strand value)
	Assign a value to Product_strand data member. More...
TProduct_strand &	SetProduct_strand (void)
	Assign a value to Product_strand data member. More...
bool	IsSetGenomic_strand (void) const
	Check if a value has been assigned to Genomic_strand data member. More...
bool	CanGetGenomic_strand (void) const
	Check if it is safe to call GetGenomic_strand method. More...
void	ResetGenomic_strand (void)
	Reset Genomic_strand data member. More...
TGenomic_strand	GetGenomic_strand (void) const
	Get the Genomic_strand member data. More...
void	SetGenomic_strand (TGenomic_strand value)
	Assign a value to Genomic_strand data member. More...
TGenomic_strand &	SetGenomic_strand (void)
	Assign a value to Genomic_strand data member. More...
bool	IsSetProduct_type (void) const
	Check if a value has been assigned to Product_type data member. More...
bool	CanGetProduct_type (void) const
	Check if it is safe to call GetProduct_type method. More...
void	ResetProduct_type (void)
	Reset Product_type data member. More...
TProduct_type	GetProduct_type (void) const
	Get the Product_type member data. More...
void	SetProduct_type (TProduct_type value)
	Assign a value to Product_type data member. More...
TProduct_type &	SetProduct_type (void)
	Assign a value to Product_type data member. More...
bool	IsSetExons (void) const
	set of segments involved each segment corresponds to one exon exons are always in biological order Check if a value has been assigned to Exons data member. More...
bool	CanGetExons (void) const
	Check if it is safe to call GetExons method. More...
void	ResetExons (void)
	Reset Exons data member. More...
const TExons &	GetExons (void) const
	Get the Exons member data. More...
TExons &	SetExons (void)
	Assign a value to Exons data member. More...
bool	IsSetPoly_a (void) const
	start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= product-length poly-a == product-length indicates inferred poly(A) tail at transcript's end For antisense transcripts: -1 <= poly-a < aligned product positions poly-a == -1 indicates inferred poly(A) tail at transcript's start Check if a value has been assigned to Poly_a data member. More...
bool	CanGetPoly_a (void) const
	Check if it is safe to call GetPoly_a method. More...
void	ResetPoly_a (void)
	Reset Poly_a data member. More...
TPoly_a	GetPoly_a (void) const
	Get the Poly_a member data. More...
void	SetPoly_a (TPoly_a value)
	Assign a value to Poly_a data member. More...
TPoly_a &	SetPoly_a (void)
	Assign a value to Poly_a data member. More...
bool	IsSetProduct_length (void) const
	length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length can be extracted Check if a value has been assigned to Product_length data member. More...
bool	CanGetProduct_length (void) const
	Check if it is safe to call GetProduct_length method. More...
void	ResetProduct_length (void)
	Reset Product_length data member. More...
TProduct_length	GetProduct_length (void) const
	Get the Product_length member data. More...
void	SetProduct_length (TProduct_length value)
	Assign a value to Product_length data member. More...
TProduct_length &	SetProduct_length (void)
	Assign a value to Product_length data member. More...
bool	IsSetModifiers (void) const
	alignment descriptors / modifiers this provides us a set for extension Check if a value has been assigned to Modifiers data member. More...
bool	CanGetModifiers (void) const
	Check if it is safe to call GetModifiers method. More...
void	ResetModifiers (void)
	Reset Modifiers data member. More...
const TModifiers &	GetModifiers (void) const
	Get the Modifiers member data. More...
TModifiers &	SetModifiers (void)
	Assign a value to Modifiers 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()	EProduct_type (void)
	Access to EProduct_type'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
	CSpliced_seg_Base (const CSpliced_seg_Base &)
CSpliced_seg_Base &	operator= (const CSpliced_seg_Base &)

Private Attributes
Uint4	m_set_State [1]
CRef< TProduct_id >	m_Product_id
CRef< TGenomic_id >	m_Genomic_id
ENa_strand	m_Product_strand
ENa_strand	m_Genomic_strand
EProduct_type	m_Product_type
list< CRef< CSpliced_exon > >	m_Exons
TSeqPos	m_Poly_a
TSeqPos	m_Product_length
list< CRef< CSpliced_seg_modifier > >	m_Modifiers

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

CSpliced_seg_Base –.

Definition at line 79 of file Spliced_seg_.hpp.

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

• include/objects/seqalign/Spliced_seg_.hpp
• src/objects/seqalign/Spliced_seg_.cpp