Search Toolkit Book for CGC_SeqIdAlias

#include <objects/genomecoll/GC_SeqIdAlias.hpp>

Inheritance diagram for CGC_SeqIdAlias:

Collaboration diagram for CGC_SeqIdAlias:

Public Types
enum	E_AliasTypes { e_None = 0 , e_Public , e_Gpipe , e_Gi }

Public Types inherited from CGC_SeqIdAlias_Base
enum	ESimilarity { eSimilarity_unknown = 0 , eSimilarity_identical = 1 , eSimilarity_different = 255 }

enum class	E_memberIndex { e__allMandatory = 0 , e_public , e_gpipe , e_gi , e_similarity }

typedef CSeq_id	TPublic

typedef CSeq_id	TGpipe

typedef CSeq_id	TGi

typedef int	TSimilarity

typedef Tparent::CMemberIndex< E_memberIndex, 5 >	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
	CGC_SeqIdAlias (void)

	~CGC_SeqIdAlias (void)

Public Member Functions inherited from CGC_SeqIdAlias_Base
	CGC_SeqIdAlias_Base (void)

virtual	~CGC_SeqIdAlias_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetPublic (void) const
	the refseq/genbank accession Check if a value has been assigned to Public data member. More...

bool	CanGetPublic (void) const
	Check if it is safe to call GetPublic method. More...

void	ResetPublic (void)
	Reset Public data member. More...

const TPublic &	GetPublic (void) const
	Get the Public member data. More...

void	SetPublic (TPublic &value)
	Assign a value to Public data member. More...

TPublic &	SetPublic (void)
	Assign a value to Public data member. More...

bool	IsSetGpipe (void) const
	the gpipe accession Check if a value has been assigned to Gpipe data member. More...

bool	CanGetGpipe (void) const
	Check if it is safe to call GetGpipe method. More...

void	ResetGpipe (void)
	Reset Gpipe data member. More...

const TGpipe &	GetGpipe (void) const
	Get the Gpipe member data. More...

void	SetGpipe (TGpipe &value)
	Assign a value to Gpipe data member. More...

TGpipe &	SetGpipe (void)
	Assign a value to Gpipe data member. More...

bool	IsSetGi (void) const
	optional since not all sequences have GIs Similarity: relationship between this synonym to main seqid of the GC-Sequence Can be expanded to multiple level of identicality can use bitmap to flag ambiguity between different levels Check if a value has been assigned to Gi data member. More...

bool	CanGetGi (void) const
	Check if it is safe to call GetGi method. More...

void	ResetGi (void)
	Reset Gi data member. More...

const TGi &	GetGi (void) const
	Get the Gi member data. More...

void	SetGi (TGi &value)
	Assign a value to Gi data member. More...

TGi &	SetGi (void)
	Assign a value to Gi data member. More...

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

bool	CanGetSimilarity (void) const
	Check if it is safe to call GetSimilarity method. More...

void	ResetSimilarity (void)
	Reset Similarity data member. More...

TSimilarity	GetSimilarity (void) const
	Get the Similarity member data. More...

void	SetSimilarity (TSimilarity value)
	Assign a value to Similarity data member. More...

TSimilarity &	SetSimilarity (void)
	Assign a value to Similarity 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

Private Types
typedef CGC_SeqIdAlias_Base	Tparent

Private Member Functions
	CGC_SeqIdAlias (const CGC_SeqIdAlias &value)

CGC_SeqIdAlias &	operator= (const CGC_SeqIdAlias &value)

Additional Inherited Members
Static Public Member Functions inherited from CGC_SeqIdAlias_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ESimilarity (void)
	Access to ESimilarity'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)

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 53 of file GC_SeqIdAlias.hpp.

Member Typedef Documentation

◆ Tparent

typedef CGC_SeqIdAlias_Base CGC_SeqIdAlias::Tparent

private

Definition at line 55 of file GC_SeqIdAlias.hpp.

Member Enumeration Documentation

◆ E_AliasTypes

enum CGC_SeqIdAlias::E_AliasTypes

Enumerator
e_None
e_Public
e_Gpipe
e_Gi

Definition at line 57 of file GC_SeqIdAlias.hpp.

Constructor & Destructor Documentation

◆ CGC_SeqIdAlias() [1/2]

CGC_SeqIdAlias::CGC_SeqIdAlias ( void )

inline

Definition at line 82 of file GC_SeqIdAlias.hpp.

◆ ~CGC_SeqIdAlias()

CGC_SeqIdAlias::~CGC_SeqIdAlias ( void )

Definition at line 50 of file GC_SeqIdAlias.cpp.

◆ CGC_SeqIdAlias() [2/2]

CGC_SeqIdAlias::CGC_SeqIdAlias ( const CGC_SeqIdAlias & value )

private

Member Function Documentation

◆ operator=()

CGC_SeqIdAlias& CGC_SeqIdAlias::operator= ( const CGC_SeqIdAlias & value )

private

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

include/objects/genomecoll/GC_SeqIdAlias.hpp
src/objects/genomecoll/GC_SeqIdAlias.cpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Tparent

Member Enumeration Documentation

◆ E_AliasTypes

Constructor & Destructor Documentation

◆ CGC_SeqIdAlias() [1/2]

◆ ~CGC_SeqIdAlias()

◆ CGC_SeqIdAlias() [2/2]

Member Function Documentation

◆ operator=()