NCBI C++ ToolKit
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CBamFileInfo Class Reference

Search Toolkit Book for CBamFileInfo

#include <sra/data_loaders/bam/impl/bamloader_impl.hpp>

+ Inheritance diagram for CBamFileInfo:
+ Collaboration diagram for CBamFileInfo:

Public Member Functions

 CBamFileInfo (const CBAMDataLoader_Impl &impl, const CBAMDataLoader::SBamFileName &bam, const string &refseq_label=kEmptyStr, const CSeq_id_Handle &seq_id=CSeq_id_Handle())
 
const stringGetBamName (void) const
 
const stringGetAnnotName (void) const
 
void GetShortSeqBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const
 
void GetRefSeqBlobId (CRef< CBAMBlobId > &ret, const CSeq_id_Handle &idh) const
 
CBamRefSeqInfoGetRefSeqInfo (const CSeq_id_Handle &seq_id) const
 
TSeqPos GetRefSeqLength (const string &id) const
 
CMutexGetMutex (void) const
 
CBamDbGetBamDb (void)
 
 operator CBamDb & (void)
 
void AddRefSeq (const string &refseq_label, const CSeq_id_Handle &refseq_id)
 
- 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
 

Protected Types

typedef map< CSeq_id_Handle, CRef< CBamRefSeqInfo > > TRefSeqs
 

Protected Member Functions

void x_Initialize (const CBAMDataLoader_Impl &impl, const CBAMDataLoader::SBamFileName &bam)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

string m_BamName
 
string m_AnnotName
 
CMutex m_BamMutex
 
CBamDb m_BamDb
 
TRefSeqs m_RefSeqs
 

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...
 

Detailed Description

Definition at line 208 of file bamloader_impl.hpp.

Member Typedef Documentation

◆ TRefSeqs

Definition at line 255 of file bamloader_impl.hpp.

Constructor & Destructor Documentation

◆ CBamFileInfo()

CBamFileInfo::CBamFileInfo ( const CBAMDataLoader_Impl impl,
const CBAMDataLoader::SBamFileName bam,
const string refseq_label = kEmptyStr,
const CSeq_id_Handle seq_id = CSeq_id_Handle() 
)

Member Function Documentation

◆ AddRefSeq()

void CBamFileInfo::AddRefSeq ( const string refseq_label,
const CSeq_id_Handle refseq_id 
)

◆ GetAnnotName()

const string& CBamFileInfo::GetAnnotName ( void  ) const
inline

◆ GetBamDb()

CBamDb& CBamFileInfo::GetBamDb ( void  )
inline

◆ GetBamName()

const string& CBamFileInfo::GetBamName ( void  ) const
inline

◆ GetMutex()

CMutex& CBamFileInfo::GetMutex ( void  ) const
inline

Definition at line 237 of file bamloader_impl.hpp.

References m_BamMutex.

◆ GetRefSeqBlobId()

void CBamFileInfo::GetRefSeqBlobId ( CRef< CBAMBlobId > &  ret,
const CSeq_id_Handle idh 
) const

Definition at line 802 of file bamloader_impl.cpp.

References GetRefSeqInfo(), and info.

◆ GetRefSeqInfo()

CBamRefSeqInfo * CBamFileInfo::GetRefSeqInfo ( const CSeq_id_Handle seq_id) const

◆ GetRefSeqLength()

TSeqPos CBamFileInfo::GetRefSeqLength ( const string id) const
inline

◆ GetShortSeqBlobId()

void CBamFileInfo::GetShortSeqBlobId ( CRef< CBAMBlobId > &  ret,
const CSeq_id_Handle idh 
) const

Definition at line 793 of file bamloader_impl.cpp.

References ITERATE, and m_RefSeqs.

◆ operator CBamDb &()

CBamFileInfo::operator CBamDb & ( void  )
inline

Definition at line 246 of file bamloader_impl.hpp.

References GetBamDb().

◆ x_Initialize()

void CBamFileInfo::x_Initialize ( const CBAMDataLoader_Impl impl,
const CBAMDataLoader::SBamFileName bam 
)
protected

Member Data Documentation

◆ m_AnnotName

string CBamFileInfo::m_AnnotName
protected

Definition at line 261 of file bamloader_impl.hpp.

Referenced by GetAnnotName(), and x_Initialize().

◆ m_BamDb

CBamDb CBamFileInfo::m_BamDb
protected

Definition at line 263 of file bamloader_impl.hpp.

Referenced by CBamFileInfo(), GetBamDb(), GetRefSeqLength(), and x_Initialize().

◆ m_BamMutex

CMutex CBamFileInfo::m_BamMutex
mutableprotected

Definition at line 262 of file bamloader_impl.hpp.

Referenced by GetMutex().

◆ m_BamName

string CBamFileInfo::m_BamName
protected

Definition at line 260 of file bamloader_impl.hpp.

Referenced by AddRefSeq(), GetBamName(), and x_Initialize().

◆ m_RefSeqs

TRefSeqs CBamFileInfo::m_RefSeqs
protected

Definition at line 264 of file bamloader_impl.hpp.

Referenced by AddRefSeq(), GetRefSeqInfo(), and GetShortSeqBlobId().


The documentation for this class was generated from the following files:
Modified on Fri Apr 12 17:14:36 2024 by modify_doxy.py rev. 669887