Represents ASN.1 type Prot-ref defined in file seqfeat.asn

#include <objects/seqfeat/Prot_ref.hpp>

Inheritance diagram for CProt_ref:

Collaboration diagram for CProt_ref:

Public Types
enum	EECNumberStatus { eEC_specific , eEC_ambiguous , eEC_replaced , eEC_deleted , eEC_unknown }
	Enzyme Commission number status. More...

enum	EECNumberFileStatus { eECFile_not_attempted , eECFile_not_found , eECFile_not_read , eECFile_read }
	Enzyme Commission file status. More...

Public Types inherited from CProt_ref_Base
enum	EProcessed { eProcessed_not_set = 0 , eProcessed_preprotein = 1 , eProcessed_mature = 2 , eProcessed_signal_peptide = 3 , eProcessed_transit_peptide = 4 , eProcessed_propeptide = 5 }
	processing status More...

enum class	E_memberIndex { e__allMandatory = 0 , e_name , e_desc , e_ec , e_activity , e_db , e_processed }

typedef list< string >	TName

typedef string	TDesc

typedef list< string >	TEc

typedef list< string >	TActivity

typedef vector< CRef< CDbtag > >	TDb

typedef EProcessed	TProcessed

typedef Tparent::CMemberIndex< E_memberIndex, 7 >	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
	CProt_ref (void)

	~CProt_ref (void)

void	GetLabel (string *label) const

void	AutoFixEC ()

void	RemoveBadEC ()

Public Member Functions inherited from CProt_ref_Base
	CProt_ref_Base (void)

virtual	~CProt_ref_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetName (void) const
	protein name 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...

TName &	SetName (void)
	Assign a value to Name data member. More...

bool	IsSetDesc (void) const
	description (instead of name) Check if a value has been assigned to Desc data member. More...

bool	CanGetDesc (void) const
	Check if it is safe to call GetDesc method. More...

void	ResetDesc (void)
	Reset Desc data member. More...

const TDesc &	GetDesc (void) const
	Get the Desc member data. More...

void	SetDesc (const TDesc &value)
	Assign a value to Desc data member. More...

void	SetDesc (TDesc &&value)

TDesc &	SetDesc (void)
	Assign a value to Desc data member. More...

bool	IsSetEc (void) const
	E.C. More...

bool	CanGetEc (void) const
	Check if it is safe to call GetEc method. More...

void	ResetEc (void)
	Reset Ec data member. More...

const TEc &	GetEc (void) const
	Get the Ec member data. More...

TEc &	SetEc (void)
	Assign a value to Ec data member. More...

bool	IsSetActivity (void) const
	activities Check if a value has been assigned to Activity data member. More...

bool	CanGetActivity (void) const
	Check if it is safe to call GetActivity method. More...

void	ResetActivity (void)
	Reset Activity data member. More...

const TActivity &	GetActivity (void) const
	Get the Activity member data. More...

TActivity &	SetActivity (void)
	Assign a value to Activity data member. More...

bool	IsSetDb (void) const
	ids in other dbases Check if a value has been assigned to Db data member. More...

bool	CanGetDb (void) const
	Check if it is safe to call GetDb method. More...

void	ResetDb (void)
	Reset Db data member. More...

const TDb &	GetDb (void) const
	Get the Db member data. More...

TDb &	SetDb (void)
	Assign a value to Db data member. More...

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

bool	CanGetProcessed (void) const
	Check if it is safe to call GetProcessed method. More...

void	ResetProcessed (void)
	Reset Processed data member. More...

void	SetDefaultProcessed (void)
	Assign default value to Processed data member. More...

TProcessed	GetProcessed (void) const
	Get the Processed member data. More...

void	SetProcessed (TProcessed value)
	Assign a value to Processed data member. More...

TProcessed &	SetProcessed (void)
	Assign a value to Processed 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 EECNumberStatus	GetECNumberStatus (const string &ecno)
	Determine an EC number's validity and specificity. More...

static const string &	GetECNumberReplacement (const string &old_ecno)
	Return a replaced EC number's replacement. More...

static bool	IsECNumberSplit (const string &old_ecno)

static bool	IsValidECNumberFormat (const string &ecno)
	Verify correct form of EC number. More...

static EECNumberFileStatus	GetECNumAmbiguousStatus ()

static EECNumberFileStatus	GetECNumDeletedStatus ()

static EECNumberFileStatus	GetECNumReplacedStatus ()

static EECNumberFileStatus	GetECNumSpecificStatus ()

Static Public Member Functions inherited from CProt_ref_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EProcessed (void)
	Access to EProcessed'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 CProt_ref_Base	Tparent

Private Member Functions
	CProt_ref (const CProt_ref &value)

CProt_ref &	operator= (const CProt_ref &value)

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

Definition at line 50 of file Prot_ref.hpp.

Member Typedef Documentation

◆ Tparent

typedef CProt_ref_Base CProt_ref::Tparent

private

Definition at line 52 of file Prot_ref.hpp.

Member Enumeration Documentation

◆ EECNumberFileStatus

enum CProt_ref::EECNumberFileStatus

Enzyme Commission file status.

Enumerator
eECFile_not_attempted	No attempt has been made to read the file.
eECFile_not_found	File was not found in expected directory.
eECFile_not_read	File was found but could not be read.
eECFile_read	File was read successfully (and is being instead of the compiled fallback data.

Definition at line 72 of file Prot_ref.hpp.

◆ EECNumberStatus

enum CProt_ref::EECNumberStatus

Enzyme Commission number status.

Enumerator
eEC_specific	Specifically identifies a valid classification.
eEC_ambiguous	Valid wildcard for a broader family.
eEC_replaced	Obsolete synonym for some other EC number.
eEC_deleted	Withdrawn, with no (single?) replacement.
eEC_unknown	Unrecognized; possibly malformed.