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CVDBGraphDb_Impl Class Reference

Search Toolkit Book for CVDBGraphDb_Impl

#include <sra/readers/sra/graphread.hpp>

+ Inheritance diagram for CVDBGraphDb_Impl:
+ Collaboration diagram for CVDBGraphDb_Impl:

Classes

struct  SGraphTableCursor
 
struct  SSeqInfo
 

Public Member Functions

 CVDBGraphDb_Impl (CVDBMgr &mgr, CTempString path, ELookupType lookup_type=eLookupDefault)
 
virtual ~CVDBGraphDb_Impl (void)
 
bool HasMidZoomGraphs (void)
 
bool LookupIsInVDB () const
 
bool LookupIsInMemory () const
 
- 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 bool LookupIsInMemory (ELookupType lookup_type)
 
- 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)
 

Protected Types

typedef list< SSeqInfoTSeqInfoList
 
typedef map< CSeq_id_Handle, TSeqInfoList::iterator > TSeqInfoMapBySeq_id
 
typedef map< TVDBRowId, TSeqInfoList::iterator > TSeqInfoMapByFirstRow
 

Protected Member Functions

const stringGetPath (void) const
 
const TSeqInfoListGetSeqInfoList (void) const
 
const TSeqInfoMapBySeq_idGetSeqInfoMapBySeq_id (void) const
 
const CVDBTableGraphTable (void)
 
CRef< SGraphTableCursorGraph (void)
 
void Put (CRef< SGraphTableCursor > &curs)
 
SSeqInfo GetSeqInfoAtRow (TVDBRowId row)
 
SSeqInfo GetSeqInfo (const CSeq_id_Handle &seq_id)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Attributes

CVDBMgr m_Mgr
 
string m_Path
 
CVDBTable m_GraphTable
 
CVDBTableIndex m_LookupIndex
 
CVDBObjectCache< SGraphTableCursorm_Graph
 
CMutex m_SeqInfoMutex
 
TSeqInfoList m_SeqList
 
TSeqInfoMapBySeq_id m_SeqMapBySeq_id
 
TSeqInfoMapByFirstRow m_SeqMapByFirstRow
 

Friends

class CVDBGraphSeqIterator
 

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...
 
- Public Types inherited from SVDBGraphDb_Base
enum  ELookupType { eLookupDefault , eLookupInMemory , eLookupInVDB }
 
- 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...
 

Detailed Description

Definition at line 62 of file graphread.hpp.

Member Typedef Documentation

◆ TSeqInfoList

typedef list<SSeqInfo> CVDBGraphDb_Impl::TSeqInfoList
protected

Definition at line 131 of file graphread.hpp.

◆ TSeqInfoMapByFirstRow

typedef map<TVDBRowId, TSeqInfoList::iterator> CVDBGraphDb_Impl::TSeqInfoMapByFirstRow
protected

Definition at line 133 of file graphread.hpp.

◆ TSeqInfoMapBySeq_id

typedef map<CSeq_id_Handle, TSeqInfoList::iterator> CVDBGraphDb_Impl::TSeqInfoMapBySeq_id
protected

Definition at line 132 of file graphread.hpp.

Constructor & Destructor Documentation

◆ CVDBGraphDb_Impl()

CVDBGraphDb_Impl::CVDBGraphDb_Impl ( CVDBMgr mgr,
CTempString  path,
ELookupType  lookup_type = eLookupDefault 
)

◆ ~CVDBGraphDb_Impl()

CVDBGraphDb_Impl::~CVDBGraphDb_Impl ( void  )
virtual

Definition at line 203 of file graphread.cpp.

Member Function Documentation

◆ GetPath()

const string& CVDBGraphDb_Impl::GetPath ( void  ) const
inlineprotected

Definition at line 111 of file graphread.hpp.

References m_Path.

◆ GetSeqInfo()

CVDBGraphDb_Impl::SSeqInfo CVDBGraphDb_Impl::GetSeqInfo ( const CSeq_id_Handle seq_id)
protected

◆ GetSeqInfoAtRow()

CVDBGraphDb_Impl::SSeqInfo CVDBGraphDb_Impl::GetSeqInfoAtRow ( TVDBRowId  row)
protected

◆ GetSeqInfoList()

const TSeqInfoList& CVDBGraphDb_Impl::GetSeqInfoList ( void  ) const
inlineprotected

Definition at line 135 of file graphread.hpp.

References m_SeqList.

◆ GetSeqInfoMapBySeq_id()

const TSeqInfoMapBySeq_id& CVDBGraphDb_Impl::GetSeqInfoMapBySeq_id ( void  ) const
inlineprotected

Definition at line 138 of file graphread.hpp.

References m_SeqMapBySeq_id.

◆ Graph()

CRef< CVDBGraphDb_Impl::SGraphTableCursor > CVDBGraphDb_Impl::Graph ( void  )
protected

Definition at line 208 of file graphread.cpp.

References GraphTable(), and m_Graph.

Referenced by CVDBGraphDb_Impl(), GetSeqInfo(), GetSeqInfoAtRow(), and HasMidZoomGraphs().

◆ GraphTable()

const CVDBTable& CVDBGraphDb_Impl::GraphTable ( void  )
inlineprotected

Definition at line 143 of file graphread.hpp.

References m_GraphTable.

Referenced by CVDBGraphDb_Impl(), and Graph().

◆ HasMidZoomGraphs()

bool CVDBGraphDb_Impl::HasMidZoomGraphs ( void  )

Definition at line 219 of file graphread.cpp.

References Graph(), and Put().

◆ LookupIsInMemory() [1/2]

bool CVDBGraphDb_Impl::LookupIsInMemory ( ) const
inline

Definition at line 75 of file graphread.hpp.

References m_LookupIndex.

Referenced by CVDBGraphDb_Impl().

◆ LookupIsInMemory() [2/2]

bool CVDBGraphDb_Impl::LookupIsInMemory ( ELookupType  lookup_type)
static

◆ LookupIsInVDB()

bool CVDBGraphDb_Impl::LookupIsInVDB ( ) const
inline

Definition at line 71 of file graphread.hpp.

References m_LookupIndex.

◆ Put()

void CVDBGraphDb_Impl::Put ( CRef< SGraphTableCursor > &  curs)
inlineprotected

Friends And Related Function Documentation

◆ CVDBGraphSeqIterator

friend class CVDBGraphSeqIterator
friend

Definition at line 82 of file graphread.hpp.

Member Data Documentation

◆ m_Graph

CVDBObjectCache<SGraphTableCursor> CVDBGraphDb_Impl::m_Graph
private

Definition at line 163 of file graphread.hpp.

Referenced by Graph(), and Put().

◆ m_GraphTable

CVDBTable CVDBGraphDb_Impl::m_GraphTable
private

Definition at line 160 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), and GraphTable().

◆ m_LookupIndex

CVDBTableIndex CVDBGraphDb_Impl::m_LookupIndex
private

◆ m_Mgr

CVDBMgr CVDBGraphDb_Impl::m_Mgr
private

Definition at line 157 of file graphread.hpp.

◆ m_Path

string CVDBGraphDb_Impl::m_Path
private

Definition at line 158 of file graphread.hpp.

Referenced by GetPath().

◆ m_SeqInfoMutex

CMutex CVDBGraphDb_Impl::m_SeqInfoMutex
private

Definition at line 165 of file graphread.hpp.

Referenced by GetSeqInfo(), and GetSeqInfoAtRow().

◆ m_SeqList

TSeqInfoList CVDBGraphDb_Impl::m_SeqList
private

Definition at line 166 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), and GetSeqInfoList().

◆ m_SeqMapByFirstRow

TSeqInfoMapByFirstRow CVDBGraphDb_Impl::m_SeqMapByFirstRow
private

Definition at line 168 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), and GetSeqInfoAtRow().

◆ m_SeqMapBySeq_id

TSeqInfoMapBySeq_id CVDBGraphDb_Impl::m_SeqMapBySeq_id
private

Definition at line 167 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), GetSeqInfo(), and GetSeqInfoMapBySeq_id().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:04:04 2024 by modify_doxy.py rev. 669887