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CCSRAFileInfo Class Reference

Search Toolkit Book for CCSRAFileInfo

#include <sra/data_loaders/csra/impl/csraloader_impl.hpp>

+ Inheritance diagram for CCSRAFileInfo:
+ Collaboration diagram for CCSRAFileInfo:

Public Types

typedef CCSRADataLoader::TAnnotNames TAnnotNames
 
- 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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CCSRAFileInfo (CCSRADataLoader_Impl &impl, const string &csra, CCSraDb::ERefIdType ref_id_type)
 
const stringGetCSRAName (void) const
 
const stringGetBaseAnnotName (void) const
 
string GetAnnotName (const string &spot_group, ECSRAAnnotChunkIdType type) const
 
string GetAlignAnnotName (void) const
 
string GetAlignAnnotName (const string &spot_group) const
 
string GetPileupAnnotName (void) const
 
string GetPileupAnnotName (const string &spot_group) const
 
CCSraDb::ERefIdType GetRefIdType (void) const
 
int GetMinMapQuality (void) const
 
bool GetPileupGraphs (void) const
 
bool GetQualityGraphs (void) const
 
bool IsValidReadId (TVDBRowId spot_id, Uint4 read_id, CRef< CCSRARefSeqInfo > *ref_ptr=0, TSeqPos *ref_pos_ptr=0)
 
void GetAnnotBlobId (CRef< CCSRABlobId > &ret, const CSeq_id_Handle &idh)
 
CRef< CCSRARefSeqInfoGetRefSeqInfo (const CSeq_id_Handle &seq_id)
 
CRef< CCSRARefSeqInfoGetRefSeqInfo (const CCSRABlobId &blob_id)
 
CCSraDbGetDb (void)
 
 operator CCSraDb & (void)
 
void AddRefSeq (const string &refseq_label, const CSeq_id_Handle &refseq_id)
 
const vector< string > & GetSeparateSpotGroups (void) const
 
void GetPossibleAnnotNames (TAnnotNames &names) const
 
void LoadReadsBlob (const CCSRABlobId &blob_id, CTSE_LoadLock &load_lock)
 
void LoadReadsChunk (const CCSRABlobId &blob_id, CTSE_Chunk_Info &chunk_info)
 
void LoadReadsMainEntry (const CCSRABlobId &blob_id, CTSE_LoadLock &load_lock)
 
- 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< CCSRARefSeqInfo > > TRefSeqs
 

Protected Member Functions

void x_Initialize (CCSRADataLoader_Impl &impl, const string &csra, CCSraDb::ERefIdType ref_id_type)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

string m_CSRAName
 
CCSraDb::ERefIdType m_RefIdType
 
string m_AnnotName
 
int m_MinMapQuality
 
bool m_PileupGraphs
 
bool m_QualityGraphs
 
CCSraDb m_CSRADb
 
vector< stringm_SeparateSpotGroups
 
TRefSeqs m_RefSeqs
 

Friends

class CCSRADataLoader_Impl
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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 375 of file csraloader_impl.hpp.

Member Typedef Documentation

Definition at line 445 of file csraloader_impl.hpp.

Definition at line 459 of file csraloader_impl.hpp.

Constructor & Destructor Documentation

CCSRAFileInfo::CCSRAFileInfo ( CCSRADataLoader_Impl impl,
const string csra,
CCSraDb::ERefIdType  ref_id_type 
)

Definition at line 915 of file csraloader_impl.cpp.

References AddRefSeq(), CSeq_id_Handle::AsString(), m_CSRADb, and x_Initialize().

Member Function Documentation

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

Definition at line 1035 of file csraloader_impl.cpp.

References GetDebugLevel(), Info(), LOG_POST_X, m_CSRAName, and m_RefSeqs.

Referenced by CCSRAFileInfo(), and GetRefSeqInfo().

string CCSRAFileInfo::GetAlignAnnotName ( void  ) const
string CCSRAFileInfo::GetAlignAnnotName ( const string spot_group) const

Definition at line 996 of file csraloader_impl.cpp.

References eCSRAAnnotChunk_align, and GetAnnotName().

void CCSRAFileInfo::GetAnnotBlobId ( CRef< CCSRABlobId > &  ret,
const CSeq_id_Handle idh 
)
string CCSRAFileInfo::GetAnnotName ( const string spot_group,
ECSRAAnnotChunkIdType  type 
) const
const string& CCSRAFileInfo::GetBaseAnnotName ( void  ) const
inline

Definition at line 386 of file csraloader_impl.hpp.

References m_AnnotName.

Referenced by GetAnnotName().

const string& CCSRAFileInfo::GetCSRAName ( void  ) const
inline

Definition at line 382 of file csraloader_impl.hpp.

References m_CSRAName.

Referenced by GetRefSeqInfo(), and CCSRARefSeqInfo::LoadAnnotAlignChunk().

CCSraDb& CCSRAFileInfo::GetDb ( void  )
inline
int CCSRAFileInfo::GetMinMapQuality ( void  ) const
inline

Definition at line 401 of file csraloader_impl.hpp.

References m_MinMapQuality.

string CCSRAFileInfo::GetPileupAnnotName ( void  ) const
string CCSRAFileInfo::GetPileupAnnotName ( const string spot_group) const

Definition at line 1008 of file csraloader_impl.cpp.

References eCSRAAnnotChunk_pileup_graph, and GetAnnotName().

bool CCSRAFileInfo::GetPileupGraphs ( void  ) const
inline
void CCSRAFileInfo::GetPossibleAnnotNames ( TAnnotNames names) const
bool CCSRAFileInfo::GetQualityGraphs ( void  ) const
inline

Definition at line 409 of file csraloader_impl.hpp.

References m_QualityGraphs.

CCSraDb::ERefIdType CCSRAFileInfo::GetRefIdType ( void  ) const
inline

Definition at line 397 of file csraloader_impl.hpp.

References m_RefIdType.

CRef< CCSRARefSeqInfo > CCSRAFileInfo::GetRefSeqInfo ( const CSeq_id_Handle seq_id)
CRef<CCSRARefSeqInfo> CCSRAFileInfo::GetRefSeqInfo ( const CCSRABlobId blob_id)
inline

Definition at line 423 of file csraloader_impl.hpp.

References GetRefSeqInfo(), and CCSRABlobId::m_SeqId.

const vector<string>& CCSRAFileInfo::GetSeparateSpotGroups ( void  ) const
inline
bool CCSRAFileInfo::IsValidReadId ( TVDBRowId  spot_id,
Uint4  read_id,
CRef< CCSRARefSeqInfo > *  ref_ptr = 0,
TSeqPos ref_pos_ptr = 0 
)
void CCSRAFileInfo::LoadReadsBlob ( const CCSRABlobId blob_id,
CTSE_LoadLock load_lock 
)

Definition at line 1100 of file csraloader_impl.cpp.

References LoadReadsMainEntry().

void CCSRAFileInfo::LoadReadsChunk ( const CCSRABlobId blob_id,
CTSE_Chunk_Info chunk_info 
)

Definition at line 1107 of file csraloader_impl.cpp.

References _ASSERT.

void CCSRAFileInfo::LoadReadsMainEntry ( const CCSRABlobId blob_id,
CTSE_LoadLock load_lock 
)
CCSRAFileInfo::operator CCSraDb & ( void  )
inline

Definition at line 432 of file csraloader_impl.hpp.

References GetDb().

void CCSRAFileInfo::x_Initialize ( CCSRADataLoader_Impl impl,
const string csra,
CCSraDb::ERefIdType  ref_id_type 
)
protected

Friends And Related Function Documentation

friend class CCSRADataLoader_Impl
friend

Definition at line 457 of file csraloader_impl.hpp.

Member Data Documentation

string CCSRAFileInfo::m_AnnotName
protected

Definition at line 467 of file csraloader_impl.hpp.

Referenced by GetBaseAnnotName(), and x_Initialize().

CCSraDb CCSRAFileInfo::m_CSRADb
protected

Definition at line 471 of file csraloader_impl.hpp.

Referenced by CCSRAFileInfo(), GetDb(), IsValidReadId(), and x_Initialize().

string CCSRAFileInfo::m_CSRAName
protected

Definition at line 465 of file csraloader_impl.hpp.

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

int CCSRAFileInfo::m_MinMapQuality
protected

Definition at line 468 of file csraloader_impl.hpp.

Referenced by GetMinMapQuality(), and x_Initialize().

bool CCSRAFileInfo::m_PileupGraphs
protected

Definition at line 469 of file csraloader_impl.hpp.

Referenced by GetPileupGraphs(), and x_Initialize().

bool CCSRAFileInfo::m_QualityGraphs
protected

Definition at line 470 of file csraloader_impl.hpp.

Referenced by GetQualityGraphs(), LoadReadsMainEntry(), and x_Initialize().

CCSraDb::ERefIdType CCSRAFileInfo::m_RefIdType
protected

Definition at line 466 of file csraloader_impl.hpp.

Referenced by GetRefIdType(), and x_Initialize().

TRefSeqs CCSRAFileInfo::m_RefSeqs
protected

Definition at line 473 of file csraloader_impl.hpp.

Referenced by AddRefSeq(), and GetRefSeqInfo().

vector<string> CCSRAFileInfo::m_SeparateSpotGroups
protected

Definition at line 472 of file csraloader_impl.hpp.

Referenced by GetAnnotName(), GetSeparateSpotGroups(), and x_Initialize().


The documentation for this class was generated from the following files:
Modified on Mon Nov 20 15:48:31 2017 by modify_doxy.py rev. 546573