NCBI C++ ToolKit
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CFeatureIndex Class Reference

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#include <objmgr/util/indexer.hpp>

+ Inheritance diagram for CFeatureIndex:
+ Collaboration diagram for CFeatureIndex:

Public Member Functions

 CFeatureIndex (CSeq_feat_Handle sfh, const CMappedFeat mf, CConstRef< CSeq_loc > feat_loc, CBioseqIndex &bsx)
 
CSeq_feat_Handle GetSeqFeatHandle (void) const
 
const CMappedFeat GetMappedFeat (void) const
 
CRef< CSeqVectorGetSeqVector (void) const
 
CConstRef< CSeq_locGetMappedLocation (void) const
 
CWeakRef< CBioseqIndexGetBioseqIndex (void) const
 
CSeqFeatData::E_Choice GetType (void) const
 
CSeqFeatData::ESubtype GetSubtype (void) const
 
TSeqPos GetStart (void) const
 
TSeqPos GetEnd (void) const
 
string GetSequence (void)
 
void GetSequence (string &buffer)
 
string GetSequence (int from, int to)
 
void GetSequence (int from, int to, string &buffer)
 
CRef< CFeatureIndexGetBestGene (void)
 
CRef< CFeatureIndexGetBestParent (void)
 
CRef< CFeatureIndexGetOverlappingSource (void)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (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
 

Private Member Functions

 CFeatureIndex (const CFeatureIndex &)=delete
 
CFeatureIndexoperator= (const CFeatureIndex &)=delete
 
void SetFetchFailure (bool fails)
 

Private Attributes

CSeq_feat_Handle m_Sfh
 
const CMappedFeat m_Mf
 
CConstRef< CSeq_locm_Fl
 
CRef< CSeqVectorm_SeqVec
 
CWeakRef< CBioseqIndexm_Bsx
 
CSeqFeatData::E_Choice m_Type
 
CSeqFeatData::ESubtype m_Subtype
 
TSeqPos m_Start
 
TSeqPos m_End
 

Additional Inherited Members

- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- 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...
 

Detailed Description

Definition at line 880 of file indexer.hpp.

Constructor & Destructor Documentation

◆ CFeatureIndex() [1/2]

CFeatureIndex::CFeatureIndex ( CSeq_feat_Handle  sfh,
const CMappedFeat  mf,
CConstRef< CSeq_loc feat_loc,
CBioseqIndex bsx 
)

◆ CFeatureIndex() [2/2]

CFeatureIndex::CFeatureIndex ( const CFeatureIndex )
privatedelete

Member Function Documentation

◆ GetBestGene()

CRef< CFeatureIndex > CFeatureIndex::GetBestGene ( void  )

◆ GetBestParent()

CRef< CFeatureIndex > CFeatureIndex::GetBestParent ( void  )

◆ GetBioseqIndex()

CWeakRef<CBioseqIndex> CFeatureIndex::GetBioseqIndex ( void  ) const
inline

◆ GetEnd()

TSeqPos CFeatureIndex::GetEnd ( void  ) const
inline

Definition at line 912 of file indexer.hpp.

References m_End.

Referenced by CExploreProcess::DoOneBioseq().

◆ GetMappedFeat()

const CMappedFeat CFeatureIndex::GetMappedFeat ( void  ) const
inline

◆ GetMappedLocation()

CConstRef<CSeq_loc> CFeatureIndex::GetMappedLocation ( void  ) const
inline

◆ GetOverlappingSource()

CRef< CFeatureIndex > CFeatureIndex::GetOverlappingSource ( void  )

◆ GetSeqFeatHandle()

CSeq_feat_Handle CFeatureIndex::GetSeqFeatHandle ( void  ) const
inline

◆ GetSequence() [1/4]

string CFeatureIndex::GetSequence ( int  from,
int  to 
)

Definition at line 3348 of file indexer.cpp.

References buffer, and GetSequence().

◆ GetSequence() [2/4]

void CFeatureIndex::GetSequence ( int  from,
int  to,
string buffer 
)

◆ GetSequence() [3/4]

void CFeatureIndex::GetSequence ( string buffer)

Definition at line 3358 of file indexer.cpp.

References buffer, and GetSequence().

◆ GetSequence() [4/4]

string CFeatureIndex::GetSequence ( void  )

Definition at line 3364 of file indexer.cpp.

References buffer.

Referenced by CExploreProcess::DoOneBioseq(), and GetSequence().

◆ GetSeqVector()

CRef<CSeqVector> CFeatureIndex::GetSeqVector ( void  ) const
inline

Definition at line 898 of file indexer.hpp.

References m_SeqVec.

◆ GetStart()

TSeqPos CFeatureIndex::GetStart ( void  ) const
inline

Definition at line 911 of file indexer.hpp.

References m_Start.

Referenced by CExploreProcess::DoOneBioseq().

◆ GetSubtype()

CSeqFeatData::ESubtype CFeatureIndex::GetSubtype ( void  ) const
inline

◆ GetType()

CSeqFeatData::E_Choice CFeatureIndex::GetType ( void  ) const
inline

Definition at line 906 of file indexer.hpp.

References m_Type.

Referenced by CBioseqIndex::x_InitFeats().

◆ operator=()

CFeatureIndex& CFeatureIndex::operator= ( const CFeatureIndex )
privatedelete

◆ SetFetchFailure()

void CFeatureIndex::SetFetchFailure ( bool  fails)
private

Definition at line 3264 of file indexer.cpp.

References GetBioseqIndex(), and CWeakRef< C, Locker >::Lock().

Referenced by GetSequence().

Member Data Documentation

◆ m_Bsx

CWeakRef<CBioseqIndex> CFeatureIndex::m_Bsx
private

Definition at line 938 of file indexer.hpp.

Referenced by GetBioseqIndex().

◆ m_End

TSeqPos CFeatureIndex::m_End
private

Definition at line 944 of file indexer.hpp.

Referenced by CFeatureIndex(), and GetEnd().

◆ m_Fl

CConstRef<CSeq_loc> CFeatureIndex::m_Fl
private

Definition at line 936 of file indexer.hpp.

Referenced by CFeatureIndex(), and GetMappedLocation().

◆ m_Mf

const CMappedFeat CFeatureIndex::m_Mf
private

◆ m_SeqVec

CRef<CSeqVector> CFeatureIndex::m_SeqVec
private

Definition at line 937 of file indexer.hpp.

Referenced by GetSequence(), and GetSeqVector().

◆ m_Sfh

CSeq_feat_Handle CFeatureIndex::m_Sfh
private

Definition at line 934 of file indexer.hpp.

Referenced by GetSeqFeatHandle().

◆ m_Start

TSeqPos CFeatureIndex::m_Start
private

Definition at line 943 of file indexer.hpp.

Referenced by CFeatureIndex(), and GetStart().

◆ m_Subtype

CSeqFeatData::ESubtype CFeatureIndex::m_Subtype
private

Definition at line 941 of file indexer.hpp.

Referenced by CFeatureIndex(), and GetSubtype().

◆ m_Type

CSeqFeatData::E_Choice CFeatureIndex::m_Type
private

Definition at line 940 of file indexer.hpp.

Referenced by CFeatureIndex(), and GetType().


The documentation for this class was generated from the following files:
Modified on Mon Jun 17 05:06:12 2024 by modify_doxy.py rev. 669887