CSeq_feat_Base Class Reference

Represents ASN.1 type Seq-feat defined in file seqfeat.asn

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*** Seq-feat ******************************************* * sequence feature generalization More...

#include <objects/seqfeat/Seq_feat_.hpp>

Inheritance diagram for CSeq_feat_Base:

Collaboration diagram for CSeq_feat_Base:

Public Types
enum	EExp_ev { eExp_ev_experimental = 1 , eExp_ev_not_experimental = 2 }
	evidence for existence of feature More...
enum class	E_memberIndex {   e__allMandatory = 0 , e_id , e_data , e_partial ,   e_except , e_comment , e_product , e_location ,   e_qual , e_title , e_ext , e_cit ,   e_exp_ev , e_xref , e_dbxref , e_pseudo ,   e_except_text , e_ids , e_exts , e_support }
typedef CFeat_id	TId
typedef CSeqFeatData	TData
typedef bool	TPartial
typedef bool	TExcept
typedef string	TComment
typedef CSeq_loc	TProduct
typedef CSeq_loc	TLocation
typedef vector< CRef< CGb_qual > >	TQual
typedef string	TTitle
typedef CUser_object	TExt
typedef CPub_set	TCit
typedef EExp_ev	TExp_ev
typedef vector< CRef< CSeqFeatXref > >	TXref
typedef vector< CRef< CDbtag > >	TDbxref
typedef bool	TPseudo
typedef string	TExcept_text
typedef list< CRef< CFeat_id > >	TIds
typedef list< CRef< CUser_object > >	TExts
typedef CSeqFeatSupport	TSupport
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
	CSeq_feat_Base (void)
virtual	~CSeq_feat_Base (void)
	DECLARE_INTERNAL_TYPE_INFO ()
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	IsSetData (void) const
	the specific data 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	IsSetPartial (void) const
	incomplete in some way? Check if a value has been assigned to Partial data member. More...
bool	CanGetPartial (void) const
	Check if it is safe to call GetPartial method. More...
void	ResetPartial (void)
	Reset Partial data member. More...
TPartial	GetPartial (void) const
	Get the Partial member data. More...
void	SetPartial (TPartial value)
	Assign a value to Partial data member. More...
TPartial &	SetPartial (void)
	Assign a value to Partial data member. More...
bool	IsSetExcept (void) const
	something funny about this? Check if a value has been assigned to Except data member. More...
bool	CanGetExcept (void) const
	Check if it is safe to call GetExcept method. More...
void	ResetExcept (void)
	Reset Except data member. More...
TExcept	GetExcept (void) const
	Get the Except member data. More...
void	SetExcept (TExcept value)
	Assign a value to Except data member. More...
TExcept &	SetExcept (void)
	Assign a value to Except data member. More...
bool	IsSetComment (void) const
	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	IsSetProduct (void) const
	product of process Check if a value has been assigned to Product data member. More...
bool	CanGetProduct (void) const
	Check if it is safe to call GetProduct method. More...
void	ResetProduct (void)
	Reset Product data member. More...
const TProduct &	GetProduct (void) const
	Get the Product member data. More...
void	SetProduct (TProduct &value)
	Assign a value to Product data member. More...
TProduct &	SetProduct (void)
	Assign a value to Product data member. More...
bool	IsSetLocation (void) const
	feature made from Check if a value has been assigned to Location data member. 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	IsSetQual (void) const
	qualifiers Check if a value has been assigned to Qual data member. More...
bool	CanGetQual (void) const
	Check if it is safe to call GetQual method. More...
void	ResetQual (void)
	Reset Qual data member. More...
const TQual &	GetQual (void) const
	Get the Qual member data. More...
TQual &	SetQual (void)
	Assign a value to Qual data member. More...
bool	IsSetTitle (void) const
	for user defined label Check if a value has been assigned to Title data member. More...
bool	CanGetTitle (void) const
	Check if it is safe to call GetTitle method. More...
void	ResetTitle (void)
	Reset Title data member. More...
const TTitle &	GetTitle (void) const
	Get the Title member data. More...
void	SetTitle (const TTitle &value)
	Assign a value to Title data member. More...
void	SetTitle (TTitle &&value)
TTitle &	SetTitle (void)
	Assign a value to Title data member. More...
bool	IsSetExt (void) const
	user defined structure extension 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	IsSetCit (void) const
	citations for this feature Check if a value has been assigned to Cit data member. More...
bool	CanGetCit (void) const
	Check if it is safe to call GetCit method. More...
void	ResetCit (void)
	Reset Cit data member. More...
const TCit &	GetCit (void) const
	Get the Cit member data. More...
void	SetCit (TCit &value)
	Assign a value to Cit data member. More...
TCit &	SetCit (void)
	Assign a value to Cit data member. More...
bool	IsSetExp_ev (void) const
	Check if a value has been assigned to Exp_ev data member. More...
bool	CanGetExp_ev (void) const
	Check if it is safe to call GetExp_ev method. More...
void	ResetExp_ev (void)
	Reset Exp_ev data member. More...
TExp_ev	GetExp_ev (void) const
	Get the Exp_ev member data. More...
void	SetExp_ev (TExp_ev value)
	Assign a value to Exp_ev data member. More...
TExp_ev &	SetExp_ev (void)
	Assign a value to Exp_ev data member. More...
bool	IsSetXref (void) const
	cite other relevant features Check if a value has been assigned to Xref data member. More...
bool	CanGetXref (void) const
	Check if it is safe to call GetXref method. More...
void	ResetXref (void)
	Reset Xref data member. More...
const TXref &	GetXref (void) const
	Get the Xref member data. More...
TXref &	SetXref (void)
	Assign a value to Xref data member. More...
bool	IsSetDbxref (void) const
	support for xref to other databases Check if a value has been assigned to Dbxref data member. More...
bool	CanGetDbxref (void) const
	Check if it is safe to call GetDbxref method. More...
void	ResetDbxref (void)
	Reset Dbxref data member. More...
const TDbxref &	GetDbxref (void) const
	Get the Dbxref member data. More...
TDbxref &	SetDbxref (void)
	Assign a value to Dbxref data member. More...
bool	IsSetPseudo (void) const
	annotated on pseudogene? Check if a value has been assigned to Pseudo data member. More...
bool	CanGetPseudo (void) const
	Check if it is safe to call GetPseudo method. More...
void	ResetPseudo (void)
	Reset Pseudo data member. More...
TPseudo	GetPseudo (void) const
	Get the Pseudo member data. More...
void	SetPseudo (TPseudo value)
	Assign a value to Pseudo data member. More...
TPseudo &	SetPseudo (void)
	Assign a value to Pseudo data member. More...
bool	IsSetExcept_text (void) const
	explain if except=TRUE Check if a value has been assigned to Except_text data member. More...
bool	CanGetExcept_text (void) const
	Check if it is safe to call GetExcept_text method. More...
void	ResetExcept_text (void)
	Reset Except_text data member. More...
const TExcept_text &	GetExcept_text (void) const
	Get the Except_text member data. More...
void	SetExcept_text (const TExcept_text &value)
	Assign a value to Except_text data member. More...
void	SetExcept_text (TExcept_text &&value)
TExcept_text &	SetExcept_text (void)
	Assign a value to Except_text data member. More...
bool	IsSetIds (void) const
	set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member. More...
bool	CanGetIds (void) const
	Check if it is safe to call GetIds method. More...
void	ResetIds (void)
	Reset Ids data member. More...
const TIds &	GetIds (void) const
	Get the Ids member data. More...
TIds &	SetIds (void)
	Assign a value to Ids data member. More...
bool	IsSetExts (void) const
	set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member. More...
bool	CanGetExts (void) const
	Check if it is safe to call GetExts method. More...
void	ResetExts (void)
	Reset Exts data member. More...
const TExts &	GetExts (void) const
	Get the Exts member data. More...
TExts &	SetExts (void)
	Assign a value to Exts data member. More...
bool	IsSetSupport (void) const
	will replace /experiment, /inference, model-evidence Check if a value has been assigned to Support data member. More...
bool	CanGetSupport (void) const
	Check if it is safe to call GetSupport method. More...
void	ResetSupport (void)
	Reset Support data member. More...
const TSupport &	GetSupport (void) const
	Get the Support member data. More...
void	SetSupport (TSupport &value)
	Assign a value to Support data member. More...
TSupport &	SetSupport (void)
	Assign a value to Support 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()	EExp_ev (void)
	Access to EExp_ev'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
	CSeq_feat_Base (const CSeq_feat_Base &)
CSeq_feat_Base &	operator= (const CSeq_feat_Base &)

Private Attributes
Uint4	m_set_State [2]
CRef< TId >	m_Id
CRef< TData >	m_Data
bool	m_Partial
bool	m_Except
string	m_Comment
CRef< TProduct >	m_Product
CRef< TLocation >	m_Location
vector< CRef< CGb_qual > >	m_Qual
string	m_Title
CRef< TExt >	m_Ext
CRef< TCit >	m_Cit
EExp_ev	m_Exp_ev
vector< CRef< CSeqFeatXref > >	m_Xref
vector< CRef< CDbtag > >	m_Dbxref
bool	m_Pseudo
string	m_Except_text
list< CRef< CFeat_id > >	m_Ids
list< CRef< CUser_object > >	m_Exts
CRef< TSupport >	m_Support

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

*** Seq-feat ******************************************* * sequence feature generalization

CSeq_feat_Base –

Definition at line 88 of file Seq_feat_.hpp.

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

• include/objects/seqfeat/Seq_feat_.hpp
• src/objects/seqfeat/Seq_feat_.cpp