Represents ASN.1 type Pubdesc defined in file seq.asn

how sequence presented in pub More...

#include <objects/seq/Pubdesc_.hpp>

Inheritance diagram for CPubdesc_Base:

Collaboration diagram for CPubdesc_Base:

Public Types
enum	EReftype { eReftype_seq = 0 , eReftype_sites = 1 , eReftype_feats = 2 , eReftype_no_target = 3 }
	type of reference in a GenBank record More...

enum class	E_memberIndex { e__allMandatory = 0 , e_pub , e_name , e_fig , e_num , e_numexc , e_poly_a , e_maploc , e_seq_raw , e_align_group , e_comment , e_reftype }

typedef CPub_equiv	TPub

typedef string	TName

typedef string	TFig

typedef CNumbering	TNum

typedef bool	TNumexc

typedef bool	TPoly_a

typedef string	TMaploc

typedef string	TSeq_raw

typedef int	TAlign_group

typedef string	TComment

typedef int	TReftype

typedef Tparent::CMemberIndex< E_memberIndex, 12 >	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
	CPubdesc_Base (void)

virtual	~CPubdesc_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetPub (void) const
	the citation(s) 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	IsSetName (void) const
	name used in paper 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	IsSetFig (void) const
	figure in paper Check if a value has been assigned to Fig data member. More...

bool	CanGetFig (void) const
	Check if it is safe to call GetFig method. More...

void	ResetFig (void)
	Reset Fig data member. More...

const TFig &	GetFig (void) const
	Get the Fig member data. More...

void	SetFig (const TFig &value)
	Assign a value to Fig data member. More...

void	SetFig (TFig &&value)

TFig &	SetFig (void)
	Assign a value to Fig data member. More...

bool	IsSetNum (void) const
	numbering from paper Check if a value has been assigned to Num data member. More...

bool	CanGetNum (void) const
	Check if it is safe to call GetNum method. More...

void	ResetNum (void)
	Reset Num data member. More...

const TNum &	GetNum (void) const
	Get the Num member data. More...

void	SetNum (TNum &value)
	Assign a value to Num data member. More...

TNum &	SetNum (void)
	Assign a value to Num data member. More...

bool	IsSetNumexc (void) const
	numbering problem with paper Check if a value has been assigned to Numexc data member. More...

bool	CanGetNumexc (void) const
	Check if it is safe to call GetNumexc method. More...

void	ResetNumexc (void)
	Reset Numexc data member. More...

TNumexc	GetNumexc (void) const
	Get the Numexc member data. More...

void	SetNumexc (TNumexc value)
	Assign a value to Numexc data member. More...

TNumexc &	SetNumexc (void)
	Assign a value to Numexc data member. More...

bool	IsSetPoly_a (void) const
	poly A tail indicated in figure? 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	IsSetMaploc (void) const
	map location reported in paper Check if a value has been assigned to Maploc data member. More...

bool	CanGetMaploc (void) const
	Check if it is safe to call GetMaploc method. More...

void	ResetMaploc (void)
	Reset Maploc data member. More...

const TMaploc &	GetMaploc (void) const
	Get the Maploc member data. More...

void	SetMaploc (const TMaploc &value)
	Assign a value to Maploc data member. More...

void	SetMaploc (TMaploc &&value)

TMaploc &	SetMaploc (void)
	Assign a value to Maploc data member. More...

bool	IsSetSeq_raw (void) const
	original sequence from paper Check if a value has been assigned to Seq_raw data member. More...

bool	CanGetSeq_raw (void) const
	Check if it is safe to call GetSeq_raw method. More...

void	ResetSeq_raw (void)
	Reset Seq_raw data member. More...

const TSeq_raw &	GetSeq_raw (void) const
	Get the Seq_raw member data. More...

void	SetSeq_raw (const TSeq_raw &value)
	Assign a value to Seq_raw data member. More...

void	SetSeq_raw (TSeq_raw &&value)

TSeq_raw &	SetSeq_raw (void)
	Assign a value to Seq_raw data member. More...

bool	IsSetAlign_group (void) const
	this seq aligned with others in paper Check if a value has been assigned to Align_group data member. More...

bool	CanGetAlign_group (void) const
	Check if it is safe to call GetAlign_group method. More...

void	ResetAlign_group (void)
	Reset Align_group data member. More...

TAlign_group	GetAlign_group (void) const
	Get the Align_group member data. More...

void	SetAlign_group (TAlign_group value)
	Assign a value to Align_group data member. More...

TAlign_group &	SetAlign_group (void)
	Assign a value to Align_group data member. More...

bool	IsSetComment (void) const
	any comment on this pub in context 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	IsSetReftype (void) const
	Check if a value has been assigned to Reftype data member. More...

bool	CanGetReftype (void) const
	Check if it is safe to call GetReftype method. More...

void	ResetReftype (void)
	Reset Reftype data member. More...

void	SetDefaultReftype (void)
	Assign default value to Reftype data member. More...

TReftype	GetReftype (void) const
	Get the Reftype member data. More...

void	SetReftype (TReftype value)
	Assign a value to Reftype data member. More...

TReftype &	SetReftype (void)
	Assign a value to Reftype 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()	EReftype (void)
	Access to EReftype'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
	CPubdesc_Base (const CPubdesc_Base &)

CPubdesc_Base &	operator= (const CPubdesc_Base &)

Private Attributes
Uint4	m_set_State [1]

CRef< TPub >	m_Pub

string	m_Name

string	m_Fig

CRef< TNum >	m_Num

bool	m_Numexc

bool	m_Poly_a

string	m_Maploc

string	m_Seq_raw

int	m_Align_group

string	m_Comment

int	m_Reftype

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

how sequence presented in pub

CPubdesc_Base –

Definition at line 78 of file Pubdesc_.hpp.

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

include/objects/seq/Pubdesc_.hpp
src/objects/seq/Pubdesc_.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description