NCBI C++ ToolKit
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CSeqDBRangeList Class Reference

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CSeqDBRangeList. More...

#include <objtools/blast/seqdb_reader/impl/seqdbvol.hpp>

+ Inheritance diagram for CSeqDBRangeList:
+ Collaboration diagram for CSeqDBRangeList:

Public Types

typedef set< pair< int, int > > TRangeList
 List of sequence offset ranges. More...
 
- 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

 CSeqDBRangeList ()
 Constructor. More...
 
 ~CSeqDBRangeList ()
 Destructor. More...
 
bool IsCached ()
 Returns true if the sequence data is cached. More...
 
void SetRanges (const TRangeList &ranges, bool append_ranges, bool cache_data)
 Set ranges of the sequence that will be used. More...
 
const TRangeListGetRanges ()
 Get ranges of sequence offsets that will be used. More...
 
void FlushSequence ()
 Flush cached sequence data (if any). More...
 
- 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
 

Static Public Member Functions

static int ImmediateLength ()
 Sequences shorter than this will not use ranges in any case. 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)
 

Private Attributes

TRangeList m_Ranges
 Range of offsets needed for this sequence. More...
 
bool m_CacheData
 True if caching of sequence data is required for this sequence. More...
 

Additional Inherited Members

- 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

CSeqDBRangeList.

This class maintains a list of ranges of sequence offsets that are desired for performance optimization. For large sequences that need to be unpacked, this class describes the subsets of those sequences that will actually be used. Each instance of this class corresponds to sequence data for one OID.

Definition at line 100 of file seqdbvol.hpp.

Member Typedef Documentation

◆ TRangeList

List of sequence offset ranges.

Definition at line 125 of file seqdbvol.hpp.

Constructor & Destructor Documentation

◆ CSeqDBRangeList()

CSeqDBRangeList::CSeqDBRangeList ( )
inline

Constructor.

Parameters
atlasThe SeqDB memory management layer. [in]

Definition at line 104 of file seqdbvol.hpp.

◆ ~CSeqDBRangeList()

CSeqDBRangeList::~CSeqDBRangeList ( )
inline

Destructor.

Definition at line 113 of file seqdbvol.hpp.

References FlushSequence().

Member Function Documentation

◆ FlushSequence()

void CSeqDBRangeList::FlushSequence ( )
inline

Flush cached sequence data (if any).

Definition at line 142 of file seqdbvol.hpp.

Referenced by ~CSeqDBRangeList().

◆ GetRanges()

const TRangeList& CSeqDBRangeList::GetRanges ( void  )
inline

Get ranges of sequence offsets that will be used.

Definition at line 136 of file seqdbvol.hpp.

References m_Ranges.

◆ ImmediateLength()

static int CSeqDBRangeList::ImmediateLength ( )
inlinestatic

Sequences shorter than this will not use ranges in any case.

Definition at line 147 of file seqdbvol.hpp.

Referenced by CSeqDBVol::x_GetAmbigSeq().

◆ IsCached()

bool CSeqDBRangeList::IsCached ( )
inline

Returns true if the sequence data is cached.

Definition at line 119 of file seqdbvol.hpp.

◆ SetRanges()

void CSeqDBRangeList::SetRanges ( const TRangeList ranges,
bool  append_ranges,
bool  cache_data 
)

Set ranges of the sequence that will be used.

Parameters
rangesOffset ranges of the sequence that are needed. [in]
append_rangesIf true, combine new ranges with old. [in]
cache_dataIf true, SeqDB is allowed to cache data. [in]

Definition at line 3189 of file seqdbvol.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::end(), set< Key, Compare >::insert(), m_CacheData, and m_Ranges.

Member Data Documentation

◆ m_CacheData

bool CSeqDBRangeList::m_CacheData
private

True if caching of sequence data is required for this sequence.

Definition at line 157 of file seqdbvol.hpp.

Referenced by SetRanges().

◆ m_Ranges

TRangeList CSeqDBRangeList::m_Ranges
private

Range of offsets needed for this sequence.

Definition at line 154 of file seqdbvol.hpp.

Referenced by GetRanges(), and SetRanges().


The documentation for this class was generated from the following files:
Modified on Fri Apr 12 17:23:41 2024 by modify_doxy.py rev. 669887