NCBI C++ ToolKit
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CSeqDBExtFile Class Reference

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Database component file. More...

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

+ Inheritance diagram for CSeqDBExtFile:
+ Collaboration diagram for CSeqDBExtFile:

Public Types

typedef CSeqDBAtlas::TIndx TIndx
 Type which spans possible file offsets. 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

 CSeqDBExtFile (CSeqDBAtlas &atlas, const string &dbfilename, char prot_nucl)
 Constructor. More...
 
virtual ~CSeqDBExtFile ()
 Destructor. More...
 
void UnLease ()
 Release memory held in the atlas layer by this object. 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
 

Protected Member Functions

void x_ReadBytes (char *buf, TIndx start, TIndx end) const
 Read part of the file into a buffer. More...
 
template<class T >
TIndx x_ReadSwapped (CSeqDBFileMemMap &lease, TIndx offset, T *value)
 Read a numerical object from the file. More...
 
char x_GetSeqType () const
 Get the volume's sequence data type. More...
 
void x_SetFileType (char prot_nucl)
 Sets the sequence data type. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CSeqDBAtlasm_Atlas
 The memory layer management object. More...
 
string m_FileName
 The name of this file. More...
 
char m_ProtNucl
 Either 'p' for protein or 'n' for nucleotide. More...
 
CSeqDBFileMemMap m_Lease
 A memory lease used by this file. More...
 
CSeqDBRawFile m_File
 The raw file object. More...
 

Additional Inherited Members

- 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

Database component file.

This represents any database component file with an extension like "pxx" or "nxx". This finds the correct type (protein or nucleotide) if that is unknown, and computes the filename based on a filename template like "path/to/file/basename.-in".

This also provides a 'protected' interface to the specific db files, and defines a few useful methods.

Definition at line 258 of file seqdbfile.hpp.

Member Typedef Documentation

◆ TIndx

Type which spans possible file offsets.

Definition at line 261 of file seqdbfile.hpp.

Constructor & Destructor Documentation

◆ CSeqDBExtFile()

CSeqDBExtFile::CSeqDBExtFile ( CSeqDBAtlas atlas,
const string dbfilename,
char  prot_nucl 
)

Constructor.

This builds an object which has a few properties required by most or all database volume component files. This object keeps a lease on the file from the first access until instructed not to, moving and expanding that lease to cover incoming requests. By keeping a lease, lookups, file opens, and other expensive operations are usually avoided on subsequent calls. This object also provides some methods to read data in a byte swapped or direct way.

Parameters
atlasThe memory management layer object.
dbfilenameThe name of the managed file.
prot_nuclThe sequence data type.
lockedThe lock holder object for this thread.

Definition at line 106 of file seqdbfile.cpp.

References CSeqDBFileMemMap::Init(), m_File, m_FileName, m_Lease, NCBI_THROW, CSeqDBRawFile::Open(), string, and x_SetFileType().

◆ ~CSeqDBExtFile()

virtual CSeqDBExtFile::~CSeqDBExtFile ( )
inlinevirtual

Destructor.

Definition at line 287 of file seqdbfile.hpp.

Member Function Documentation

◆ UnLease()

void CSeqDBExtFile::UnLease ( )
inline

Release memory held in the atlas layer by this object.

Definition at line 293 of file seqdbfile.hpp.

References CSeqDBFileMemMap::Clear(), and m_Lease.

Referenced by CSeqDBVol::UnLease().

◆ x_GetSeqType()

char CSeqDBExtFile::x_GetSeqType ( ) const
inlineprotected

Get the volume's sequence data type.

This object knows which type of sequence data it deals with - this method returns that information.

Returns
The type of sequence data in use.

Definition at line 353 of file seqdbfile.hpp.

References m_ProtNucl.

Referenced by CSeqDBIdxFile::CSeqDBIdxFile(), CSeqDBIdxFile::GetAmbStartEnd(), CSeqDBIdxFile::GetSeqStartEnd(), CSeqDBIdxFile::GetSeqType(), and CSeqDBIdxFile::x_GetAmb().

◆ x_ReadBytes()

void CSeqDBExtFile::x_ReadBytes ( char *  buf,
TIndx  start,
TIndx  end 
) const
inlineprotected

Read part of the file into a buffer.

Copy the file data from offsets start to end into the array at buf, which is assumed to already have been allocated. This method assumes the atlas lock is held.

Parameters
bufThe destination for the data to be read.
startThe starting offset for the first byte to read.
endThe offset for the first byte after the area to read.

Definition at line 312 of file seqdbfile.hpp.

References buf, m_File, m_Lease, and CSeqDBRawFile::ReadBytes().

Referenced by CSeqDBSeqFile::ReadBytes(), and CSeqDBHdrFile::ReadBytes().

◆ x_ReadSwapped()

template<class T >
TIndx CSeqDBExtFile::x_ReadSwapped ( CSeqDBFileMemMap lease,
TIndx  offset,
T value 
)
inlineprotected

Read a numerical object from the file.

Given a pointer to an object in memory, this reads a numerical value for it from the file. The data in the file is assumed to be in network byte order, and the user version in the local default byte order (host order). The offset of the data is provided, and the size of the object is taken as sizeof(T).

Parameters
leaseA memory lease object to use for the read.
offsetThe starting offset of the object in the file.
valueA pointer to the object.
lockedThe lock holder object for this thread.
Returns
The offset of the first byte after the object.

Definition at line 338 of file seqdbfile.hpp.

References m_File, offset, CSeqDBRawFile::ReadSwapped(), and rapidjson::value.

Referenced by CSeqDBIdxFile::CSeqDBIdxFile().

◆ x_SetFileType()

void CSeqDBExtFile::x_SetFileType ( char  prot_nucl)
inlineprotected

Sets the sequence data type.

The sequence data will be set as protein or nucleotide. An exception is thrown if an invalid type is provided. The first character of the file extension will be modified to reflect the sequence data type.

Parameters
prot_nuclEither 'p' or 'n' for protein or nucleotide.

Definition at line 387 of file seqdbfile.hpp.

References _ASSERT, m_FileName, m_ProtNucl, and NCBI_THROW.

Referenced by CSeqDBExtFile().

Member Data Documentation

◆ m_Atlas

CSeqDBAtlas& CSeqDBExtFile::m_Atlas
protected

The memory layer management object.

Definition at line 372 of file seqdbfile.hpp.

◆ m_File

CSeqDBRawFile CSeqDBExtFile::m_File
protected

The raw file object.

Definition at line 384 of file seqdbfile.hpp.

Referenced by CSeqDBExtFile(), x_ReadBytes(), and x_ReadSwapped().

◆ m_FileName

string CSeqDBExtFile::m_FileName
protected

The name of this file.

Definition at line 375 of file seqdbfile.hpp.

Referenced by CSeqDBExtFile(), CSeqDBIdxFile::x_GetAmb(), CSeqDBIdxFile::x_GetHdr(), CSeqDBIdxFile::x_GetSeq(), and x_SetFileType().

◆ m_Lease

CSeqDBFileMemMap CSeqDBExtFile::m_Lease
mutableprotected

◆ m_ProtNucl

char CSeqDBExtFile::m_ProtNucl
protected

Either 'p' for protein or 'n' for nucleotide.

Definition at line 378 of file seqdbfile.hpp.

Referenced by x_GetSeqType(), and x_SetFileType().


The documentation for this class was generated from the following files:
Modified on Mon Jun 24 05:25:24 2024 by modify_doxy.py rev. 669887