Search Toolkit Book for CSeqEntryIndex

#include <objmgr/util/indexer.hpp>

Inheritance diagram for CSeqEntryIndex:

Collaboration diagram for CSeqEntryIndex:

Public Types
enum	EPolicy { eAdaptive = 0 , eInternal = 1 , eExternal = 2 , eExhaustive = 3 , eFtp = 4 , eWeb = 5 , eGenomes = 6 }

enum	EFlags { fDefault = 0 , fHideImpFeats = 1 , fHideSNPFeats = 2 , fHideCDDFeats = 4 , fHideSTSFeats = 8 , fHideExonFeats = 16 , fHideIntronFeats = 32 , fHideMiscFeats = 64 , fShowSNPFeats = 128 , fShowCDDFeats = 256 , fGeneRNACDSOnly = 512 , fHideGapFeats = 1024 }

typedef int	TFlags

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
	CSeqEntryIndex (CSeq_entry_Handle &topseh, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CBioseq_Handle &bsh, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CSeq_entry &topsep, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CBioseq_set &seqset, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CBioseq &bioseq, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CSeq_submit &submit, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CSeq_entry &topsep, CSubmit_block &sblock, EPolicy policy=eAdaptive, TFlags flags=fDefault)

	CSeqEntryIndex (CSeq_entry &topsep, CSeq_descr &descr, EPolicy policy=eAdaptive, TFlags flags=fDefault)

template<typename Fnc >
size_t	IterateBioseqs (Fnc m)

CRef< CBioseqIndex >	GetBioseqIndex (void)

CRef< CBioseqIndex >	GetBioseqIndex (int n)

CRef< CBioseqIndex >	GetBioseqIndex (const string &accn)

CRef< CBioseqIndex >	GetBioseqIndex (CBioseq_Handle bsh)

CRef< CBioseqIndex >	GetBioseqIndex (const CMappedFeat &mf)

CRef< CBioseqIndex >	GetBioseqIndex (const CSeq_loc &loc)

template<typename Fnc >
size_t	IterateSeqsets (Fnc m)

const vector< CRef< CBioseqIndex > > &	GetBioseqIndices (void)

const vector< CRef< CSeqsetIndex > > &	GetSeqsetIndices (void)

bool	DistributedReferences (void)

void	SetSnpFunc (FAddSnpFunc *snp)

FAddSnpFunc *	GetSnpFunc (void)

void	SetFeatDepth (int featDepth)

int	GetFeatDepth (void)

void	SetGapDepth (int gapDepth)

int	GetGapDepth (void)

bool	IsFetchFailure (void)

bool	IsIndexFailure (void)

CRef< CSeqMasterIndex >	GetMasterIndex (void) const

Public Member Functions inherited from CObjectEx
	CObjectEx (void)

virtual	~CObjectEx (void)

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...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. 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

Public Member Functions inherited from CWeakObject
	CWeakObject (void)

virtual	~CWeakObject (void)

CPtrToObjectProxy *	GetPtrProxy (void) const
	Get pointer to proxy object containing pointer to this object. More...

Private Member Functions
	CSeqEntryIndex (const CSeqEntryIndex &)=delete

CSeqEntryIndex &	operator= (const CSeqEntryIndex &)=delete

Private Attributes
CRef< CSeqMasterIndex >	m_Idx

Additional Inherited Members
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 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...

Protected Member Functions inherited from CWeakObject
void	CleanWeakRefs (void) const
	Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More...

Detailed Description

Definition at line 87 of file indexer.hpp.

Member Typedef Documentation

◆ TFlags

typedef int CSeqEntryIndex::TFlags

Definition at line 116 of file indexer.hpp.

Member Enumeration Documentation

◆ EFlags

enum CSeqEntryIndex::EFlags

Enumerator
fDefault
fHideImpFeats
fHideSNPFeats
fHideCDDFeats
fHideSTSFeats
fHideExonFeats
fHideIntronFeats
fHideMiscFeats
fShowSNPFeats
fShowCDDFeats
fGeneRNACDSOnly
fHideGapFeats