NCBI C++ ToolKit
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CSeqEntryIndex Class Reference

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#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< Uint8TCounter
 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< CBioseqIndexGetBioseqIndex (void)
 
CRef< CBioseqIndexGetBioseqIndex (int n)
 
CRef< CBioseqIndexGetBioseqIndex (const string &accn)
 
CRef< CBioseqIndexGetBioseqIndex (CBioseq_Handle bsh)
 
CRef< CBioseqIndexGetBioseqIndex (const CMappedFeat &mf)
 
CRef< CBioseqIndexGetBioseqIndex (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)
 
FAddSnpFuncGetSnpFunc (void)
 
void SetFeatDepth (int featDepth)
 
int GetFeatDepth (void)
 
void SetGapDepth (int gapDepth)
 
int GetGapDepth (void)
 
bool IsFetchFailure (void)
 
bool IsIndexFailure (void)
 
CRef< CSeqMasterIndexGetMasterIndex (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...
 
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
 
- Public Member Functions inherited from CWeakObject
 CWeakObject (void)
 
virtual ~CWeakObject (void)
 
CPtrToObjectProxyGetPtrProxy (void) const
 Get pointer to proxy object containing pointer to this object. More...
 

Private Member Functions

 CSeqEntryIndex (const CSeqEntryIndex &)=delete
 
CSeqEntryIndexoperator= (const CSeqEntryIndex &)=delete
 

Private Attributes

CRef< CSeqMasterIndexm_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

Definition at line 116 of file indexer.hpp.

Member Enumeration Documentation

◆ EFlags

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

Definition at line 102 of file indexer.hpp.

◆ EPolicy

Enumerator
eAdaptive 
eInternal 
eExternal 
eExhaustive 
eFtp 
eWeb 
eGenomes 

Definition at line 91 of file indexer.hpp.

Constructor & Destructor Documentation

◆ CSeqEntryIndex() [1/9]

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

Definition at line 57 of file indexer.cpp.

References flags.

◆ CSeqEntryIndex() [2/9]

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

Definition at line 64 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [3/9]

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

Definition at line 71 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [4/9]

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

Definition at line 78 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [5/9]

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

Definition at line 85 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [6/9]

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

Definition at line 92 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [7/9]

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

Definition at line 99 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [8/9]

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

Definition at line 106 of file indexer.cpp.

References flags, m_Idx, CRef< C, Locker >::Reset(), and CSeqMasterIndex::x_Initialize().

◆ CSeqEntryIndex() [9/9]

CSeqEntryIndex::CSeqEntryIndex ( const CSeqEntryIndex )
privatedelete

Member Function Documentation

◆ DistributedReferences()

bool CSeqEntryIndex::DistributedReferences ( void  )

◆ GetBioseqIndex() [1/6]

CRef< CBioseqIndex > CSeqEntryIndex::GetBioseqIndex ( CBioseq_Handle  bsh)

Definition at line 135 of file indexer.cpp.

References CSeqMasterIndex::GetBioseqIndex(), and m_Idx.

◆ GetBioseqIndex() [2/6]

CRef< CBioseqIndex > CSeqEntryIndex::GetBioseqIndex ( const CMappedFeat mf)

Definition at line 142 of file indexer.cpp.

References CSeqMasterIndex::GetBioseqIndex(), and m_Idx.

◆ GetBioseqIndex() [3/6]

CRef< CBioseqIndex > CSeqEntryIndex::GetBioseqIndex ( const CSeq_loc loc)

Definition at line 149 of file indexer.cpp.

References CSeqMasterIndex::GetBioseqIndex(), and m_Idx.

◆ GetBioseqIndex() [4/6]

CRef< CBioseqIndex > CSeqEntryIndex::GetBioseqIndex ( const string accn)

Definition at line 128 of file indexer.cpp.

References CSeqMasterIndex::GetBioseqIndex(), and m_Idx.

◆ GetBioseqIndex() [5/6]

CRef< CBioseqIndex > CSeqEntryIndex::GetBioseqIndex ( int  n)

Definition at line 121 of file indexer.cpp.

References CSeqMasterIndex::GetBioseqIndex(), m_Idx, and n.

◆ GetBioseqIndex() [6/6]

CRef< CBioseqIndex > CSeqEntryIndex::GetBioseqIndex ( void  )

◆ GetBioseqIndices()

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

Definition at line 155 of file indexer.cpp.

References CSeqMasterIndex::GetBioseqIndices(), and m_Idx.

◆ GetFeatDepth()

int CSeqEntryIndex::GetFeatDepth ( void  )

Definition at line 191 of file indexer.cpp.

References CSeqMasterIndex::GetFeatDepth(), and m_Idx.

◆ GetGapDepth()

int CSeqEntryIndex::GetGapDepth ( void  )

Definition at line 203 of file indexer.cpp.

References CSeqMasterIndex::GetGapDepth(), and m_Idx.

◆ GetMasterIndex()

CRef<CSeqMasterIndex> CSeqEntryIndex::GetMasterIndex ( void  ) const
inline

Definition at line 189 of file indexer.hpp.

References m_Idx.

Referenced by CFlatFileGenerator::Generate(), and CFeatureItem::x_AddQualsIdx().

◆ GetSeqsetIndices()

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

Definition at line 161 of file indexer.cpp.

References CSeqMasterIndex::GetSeqsetIndices(), and m_Idx.

◆ GetSnpFunc()

FAddSnpFunc * CSeqEntryIndex::GetSnpFunc ( void  )

Definition at line 179 of file indexer.cpp.

References CSeqMasterIndex::GetSnpFunc(), and m_Idx.

◆ IsFetchFailure()

bool CSeqEntryIndex::IsFetchFailure ( void  )

Definition at line 209 of file indexer.cpp.

References CSeqMasterIndex::IsFetchFailure(), and m_Idx.

◆ IsIndexFailure()

bool CSeqEntryIndex::IsIndexFailure ( void  )

Definition at line 215 of file indexer.cpp.

References CSeqMasterIndex::IsIndexFailure(), and m_Idx.

Referenced by CFlatFileGenerator::Generate().

◆ IterateBioseqs()

template<typename Fnc >
size_t CSeqEntryIndex::IterateBioseqs ( Fnc  m)
inline

Definition at line 990 of file indexer.hpp.

References CSeqMasterIndex::IterateBioseqs(), and m_Idx.

Referenced by CExploreProcess::SeqEntryProcess().

◆ IterateSeqsets()

template<typename Fnc >
size_t CSeqEntryIndex::IterateSeqsets ( Fnc  m)
inline

Definition at line 1012 of file indexer.hpp.

References CSeqMasterIndex::IterateSeqsets(), and m_Idx.

◆ operator=()

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

◆ SetFeatDepth()

void CSeqEntryIndex::SetFeatDepth ( int  featDepth)

◆ SetGapDepth()

void CSeqEntryIndex::SetGapDepth ( int  gapDepth)

Definition at line 197 of file indexer.cpp.

References m_Idx, and CSeqMasterIndex::SetGapDepth().

Referenced by CFlatFileGenerator::Generate().

◆ SetSnpFunc()

void CSeqEntryIndex::SetSnpFunc ( FAddSnpFunc snp)

Definition at line 173 of file indexer.cpp.

References m_Idx, and CSeqMasterIndex::SetSnpFunc().

Member Data Documentation

◆ m_Idx

CRef<CSeqMasterIndex> CSeqEntryIndex::m_Idx
private

The documentation for this class was generated from the following files:
Modified on Sat May 18 11:40:20 2024 by modify_doxy.py rev. 669887