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CCSraDb_Impl Class Reference

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

+ Inheritance diagram for CCSraDb_Impl:
+ Collaboration diagram for CCSraDb_Impl:

Classes

struct  SAlnTableCursor
 
struct  SRefInfo
 
struct  SRefTableCursor
 
struct  SSeqTableCursor
 

Public Types

typedef list< SRefInfoTRefInfoList
 
typedef map< string, TRefInfoList::iterator, PNocaseTRefInfoMapByName
 
typedef map< CSeq_id_Handle, TRefInfoList::iterator > TRefInfoMapBySeq_id
 
typedef vector< stringTSpotGroups
 
- 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 Types inherited from SCSraDb_Defs
enum  ERefIdType { eRefId_SEQ_ID, eRefId_gnl_NAME }
 
enum  EPathInIdType { ePathInId_config, ePathInId_yes, ePathInId_no }
 

Public Member Functions

 CCSraDb_Impl (CVDBMgr &mgr, const string &csra_path, IIdMapper *ref_id_mapper, ERefIdType ref_id_type, const string &sra_id_part)
 
virtual ~CCSraDb_Impl (void)
 
const TRefInfoListGetRefInfoList (void) const
 
const TRefInfoMapByNameGetRefInfoMapByName (void) const
 
const TRefInfoMapBySeq_idGetRefInfoMapBySeq_id (void) const
 
TSeqPos GetRowSize (void) const
 
void GetSpotGroups (TSpotGroups &spot_groups)
 
const stringGetCSraPath (void) const
 
const stringGetSraIdPart (void) const
 
void SetSraIdPart (const string &s)
 
CRef< CSeq_idMakeShortReadId (TVDBRowId id1, INSDC_coord_one id2) const
 
void SetShortReadId (string &str, TVDBRowId id1, INSDC_coord_one id2) 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
 

Protected Member Functions

void x_CalcSeqLength (const SRefInfo &info)
 
CRef< SRefTableCursorRef (void)
 
CRef< SAlnTableCursorAln (bool is_secondary)
 
CRef< SSeqTableCursorSeq (void)
 
void Put (CRef< SRefTableCursor > &curs)
 
void Put (CRef< SAlnTableCursor > &curs)
 
void Put (CRef< SSeqTableCursor > &curs)
 
void OpenRefTable (void)
 
void OpenAlnTable (bool is_secondary)
 
void OpenSeqTable (void)
 
const CVDBTableRefTable (void)
 
const CVDBTableAlnTable (bool is_secondary)
 
const CVDBTableSeqTable (void)
 
void x_MakeRefSeq_ids (SRefInfo &info, IIdMapper *ref_id_mapper, int ref_id_type)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Private Attributes

CVDBMgr m_Mgr
 
CVDB m_Db
 
string m_CSraPath
 
string m_SraIdPart
 
CFastMutex m_TableMutex
 
CVDBTable m_RefTable
 
CVDBTable m_AlnTable [2]
 
CVDBTable m_SeqTable
 
CVDBObjectCache< SRefTableCursorm_Ref
 
CVDBObjectCache< SAlnTableCursorm_Aln [2]
 
CVDBObjectCache< SSeqTableCursorm_Seq
 
TSeqPos m_RowSize
 
TRefInfoList m_RefList
 
TRefInfoMapByName m_RefMapByName
 
TRefInfoMapBySeq_id m_RefMapBySeq_id
 

Friends

class CCSraRefSeqIterator
 
class CCSraAlignIterator
 
class CCSraShortReadIterator
 
struct SSeqTableCursor
 

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 80 of file csraread.hpp.

Member Typedef Documentation

Definition at line 108 of file csraread.hpp.

typedef map<string, TRefInfoList::iterator, PNocase> CCSraDb_Impl::TRefInfoMapByName

Definition at line 109 of file csraread.hpp.

typedef map<CSeq_id_Handle, TRefInfoList::iterator> CCSraDb_Impl::TRefInfoMapBySeq_id

Definition at line 110 of file csraread.hpp.

Definition at line 126 of file csraread.hpp.

Constructor & Destructor Documentation

CCSraDb_Impl::CCSraDb_Impl ( CVDBMgr mgr,
const string csra_path,
IIdMapper ref_id_mapper,
ERefIdType  ref_id_type,
const string sra_id_part 
)
CCSraDb_Impl::~CCSraDb_Impl ( void  )
virtual

Definition at line 370 of file csraread.cpp.

Member Function Documentation

CRef< CCSraDb_Impl::SAlnTableCursor > CCSraDb_Impl::Aln ( bool  is_secondary)
protected

Definition at line 543 of file csraread.cpp.

References AlnTable(), and m_Aln.

Referenced by CCSraShortReadIterator::GetRefSeqIter(), and CCSraAlignIterator::x_Settle().

const CVDBTable& CCSraDb_Impl::AlnTable ( bool  is_secondary)
inlineprotected

Definition at line 179 of file csraread.hpp.

References m_AlnTable, OpenAlnTable(), and table.

Referenced by Aln().

const string& CCSraDb_Impl::GetCSraPath ( void  ) const
inline

Definition at line 129 of file csraread.hpp.

References m_CSraPath.

Referenced by OpenSeqTable().

const TRefInfoList& CCSraDb_Impl::GetRefInfoList ( void  ) const
inline

Definition at line 112 of file csraread.hpp.

References m_RefList.

const TRefInfoMapByName& CCSraDb_Impl::GetRefInfoMapByName ( void  ) const
inline

Definition at line 115 of file csraread.hpp.

References m_RefMapByName.

const TRefInfoMapBySeq_id& CCSraDb_Impl::GetRefInfoMapBySeq_id ( void  ) const
inline

Definition at line 118 of file csraread.hpp.

References m_RefMapBySeq_id.

TSeqPos CCSraDb_Impl::GetRowSize ( void  ) const
inline
void CCSraDb_Impl::GetSpotGroups ( TSpotGroups spot_groups)

Definition at line 420 of file csraread.cpp.

References CKMDataNode::GetUint8(), i, m_Db, names, and CKNameList::size().

Referenced by CCSraDb::GetSpotGroups().

const string& CCSraDb_Impl::GetSraIdPart ( void  ) const
inline

Definition at line 133 of file csraread.hpp.

References m_SraIdPart.

CRef< CSeq_id > CCSraDb_Impl::MakeShortReadId ( TVDBRowId  id1,
INSDC_coord_one  id2 
) const
void CCSraDb_Impl::OpenAlnTable ( bool  is_secondary)
protected

Definition at line 508 of file csraread.cpp.

References m_AlnTable, m_Db, and m_TableMutex.

Referenced by AlnTable().

void CCSraDb_Impl::OpenRefTable ( void  )
protected

Definition at line 499 of file csraread.cpp.

References m_Db, m_RefTable, and m_TableMutex.

Referenced by RefTable().

void CCSraDb_Impl::OpenSeqTable ( void  )
protected

Definition at line 519 of file csraread.cpp.

References GetCSraPath(), m_Db, m_Mgr, m_SeqTable, and m_TableMutex.

Referenced by SeqTable().

void CCSraDb_Impl::Put ( CRef< SRefTableCursor > &  curs)
protected
void CCSraDb_Impl::Put ( CRef< SAlnTableCursor > &  curs)
protected

Definition at line 569 of file csraread.cpp.

References m_Aln.

void CCSraDb_Impl::Put ( CRef< SSeqTableCursor > &  curs)
protected

Definition at line 577 of file csraread.cpp.

References m_Seq.

CRef< CCSraDb_Impl::SRefTableCursor > CCSraDb_Impl::Ref ( void  )
protected

Definition at line 533 of file csraread.cpp.

References m_Ref, and RefTable().

Referenced by CCSraDb_Impl(), and x_CalcSeqLength().

const CVDBTable& CCSraDb_Impl::RefTable ( void  )
inlineprotected

Definition at line 172 of file csraread.hpp.

References m_RefTable, OpenRefTable(), and table.

Referenced by Ref().

CRef< CCSraDb_Impl::SSeqTableCursor > CCSraDb_Impl::Seq ( void  )
protected

Definition at line 553 of file csraread.cpp.

References m_Seq, SeqTable(), and SSeqTableCursor.

Referenced by CCSraShortReadIterator::x_Init().

const CVDBTable& CCSraDb_Impl::SeqTable ( void  )
inlineprotected

Definition at line 186 of file csraread.hpp.

References m_SeqTable, OpenSeqTable(), and table.

Referenced by CCSraDb_Impl(), and Seq().

void CCSraDb_Impl::SetShortReadId ( string str,
TVDBRowId  id1,
INSDC_coord_one  id2 
) const

Definition at line 1220 of file csraread.cpp.

References m_SraIdPart.

Referenced by CCSraAlignIterator::GetMatchAlign(), and MakeShortReadId().

void CCSraDb_Impl::SetSraIdPart ( const string s)
inline

Definition at line 136 of file csraread.hpp.

References m_SraIdPart.

void CCSraDb_Impl::x_CalcSeqLength ( const SRefInfo info)
protected
void CCSraDb_Impl::x_MakeRefSeq_ids ( SRefInfo info,
IIdMapper ref_id_mapper,
int  ref_id_type 
)
protected

Friends And Related Function Documentation

friend class CCSraAlignIterator
friend

Definition at line 145 of file csraread.hpp.

friend class CCSraRefSeqIterator
friend

Definition at line 144 of file csraread.hpp.

friend class CCSraShortReadIterator
friend

Definition at line 146 of file csraread.hpp.

friend struct SSeqTableCursor
friend

Definition at line 155 of file csraread.hpp.

Referenced by Seq().

Member Data Documentation

CVDBObjectCache<SAlnTableCursor> CCSraDb_Impl::m_Aln[2]
private

Definition at line 210 of file csraread.hpp.

Referenced by Aln(), and Put().

CVDBTable CCSraDb_Impl::m_AlnTable[2]
private

Definition at line 206 of file csraread.hpp.

Referenced by AlnTable(), and OpenAlnTable().

string CCSraDb_Impl::m_CSraPath
private

Definition at line 201 of file csraread.hpp.

Referenced by GetCSraPath().

CVDB CCSraDb_Impl::m_Db
private

Definition at line 200 of file csraread.hpp.

Referenced by CCSraDb_Impl(), GetSpotGroups(), OpenAlnTable(), OpenRefTable(), and OpenSeqTable().

CVDBMgr CCSraDb_Impl::m_Mgr
private

Definition at line 199 of file csraread.hpp.

Referenced by OpenSeqTable().

CVDBObjectCache<SRefTableCursor> CCSraDb_Impl::m_Ref
private

Definition at line 209 of file csraread.hpp.

Referenced by Put(), and Ref().

TRefInfoList CCSraDb_Impl::m_RefList
private

Definition at line 214 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRefInfoList().

TRefInfoMapByName CCSraDb_Impl::m_RefMapByName
private

Definition at line 215 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRefInfoMapByName().

TRefInfoMapBySeq_id CCSraDb_Impl::m_RefMapBySeq_id
private

Definition at line 216 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRefInfoMapBySeq_id().

CVDBTable CCSraDb_Impl::m_RefTable
private

Definition at line 205 of file csraread.hpp.

Referenced by OpenRefTable(), and RefTable().

TSeqPos CCSraDb_Impl::m_RowSize
private

Definition at line 213 of file csraread.hpp.

Referenced by CCSraDb_Impl(), and GetRowSize().

CVDBObjectCache<SSeqTableCursor> CCSraDb_Impl::m_Seq
private

Definition at line 211 of file csraread.hpp.

Referenced by Put(), and Seq().

CVDBTable CCSraDb_Impl::m_SeqTable
private

Definition at line 207 of file csraread.hpp.

Referenced by OpenSeqTable(), and SeqTable().

string CCSraDb_Impl::m_SraIdPart
private
CFastMutex CCSraDb_Impl::m_TableMutex
private

Definition at line 204 of file csraread.hpp.

Referenced by OpenAlnTable(), OpenRefTable(), and OpenSeqTable().


The documentation for this class was generated from the following files:
Modified on Fri Sep 22 15:40:27 2017 by modify_doxy.py rev. 546573