NCBI C++ ToolKit
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CWriteDB_HeaderFile Class Reference

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This class builds the volume header file (phr or nhr). More...

#include <objtools/blast/seqdb_writer/writedb_files.hpp>

+ Inheritance diagram for CWriteDB_HeaderFile:
+ Collaboration diagram for CWriteDB_HeaderFile:

Public Member Functions

 CWriteDB_HeaderFile (const string &dbname, bool protein, int index, Uint8 max_file_size)
 Constructor. More...
 
bool CanFit (int size)
 Returns true if the specified amount of data would fit. More...
 
void AddSequence (const string &binhdr, unsigned int &offset)
 Add binary header data to this file. More...
 
- Public Member Functions inherited from CWriteDB_File
 CWriteDB_File (const string &basename, const string &extension, int index, Uint8 max_file_size, bool always_create)
 Constructor. More...
 
void Create ()
 Create and open the file. More...
 
unsigned int Write (const CTempString &data)
 Write contents of a string to the file. More...
 
unsigned int Write (const char *data, int length)
 
unsigned int WriteInt4 (int data)
 Write an Int4 (in bigendian order) to the file. More...
 
unsigned int WriteInt8 (Int8 data)
 Write an Int8 (in bigendian order) to the file. More...
 
unsigned int WriteWithNull (const CTempString &data)
 Write contents of a string to the file, appending a NUL. More...
 
void Close ()
 Close the file, flushing any remaining data to disk. More...
 
virtual void RenameSingle ()
 Rename this file, disincluding the volume index. More...
 
virtual void RenameFileIndex (unsigned int num_digits)
 
const stringGetFilename () const
 Get the current filename for this file. 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
 

Private Member Functions

virtual void x_Flush ()
 Flush unwritten data to the output file. More...
 

Private Attributes

Uint8 m_DataSize
 Amount of data written so far. More...
 

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 CWriteDB_File
static string MakeShortName (const string &base, int index)
 Construct the short name for a volume. 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...
 
- Protected Types inherited from CWriteDB_File
typedef ofstream TFile
 Underlying 'output file' type used here. More...
 
- Protected Member Functions inherited from CWriteDB_File
Uint8 x_DefaultByteLimit ()
 The default value for max_file_size. More...
 
void x_MakeFileName ()
 Build the filename for this file. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 
- Protected Attributes inherited from CWriteDB_File
bool m_Created
 True if the file has already been opened. More...
 
string m_Nul
 For convenience, a string containing one NUL character. More...
 
string m_BaseName
 Database base name for all files. More...
 
string m_Extension
 File extension for this file. More...
 
int m_Index
 Volume index. More...
 
unsigned int m_Offset
 Stream position. More...
 
Uint8 m_MaxFileSize
 Maximum file size in bytes. More...
 
bool m_UseIndex
 True if filenames should use volume index. More...
 
string m_Fname
 Current filename for output file. More...
 
TFile m_RealFile
 Actual stream implementing the output file. More...
 

Detailed Description

This class builds the volume header file (phr or nhr).

Definition at line 346 of file writedb_files.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_HeaderFile()

CWriteDB_HeaderFile::CWriteDB_HeaderFile ( const string dbname,
bool  protein,
int  index,
Uint8  max_file_size 
)

Constructor.

Parameters
dbnameDatabase base name.
proteinTrue for protein volumes.
indexIndex of this volume.
max_file_sizeMaximum file size in bytes (or zero).

Definition at line 450 of file writedb_files.cpp.

Member Function Documentation

◆ AddSequence()

void CWriteDB_HeaderFile::AddSequence ( const string binhdr,
unsigned int offset 
)
inline

Add binary header data to this file.

Parameters
binhdrBinary ASN.1 version of header data. [in]
offsetOffset of end of header data. [out]

Definition at line 379 of file writedb_files.hpp.

References m_DataSize, offset, and CWriteDB_File::Write().

Referenced by CWriteDB_Volume::WriteSequence().

◆ CanFit()

bool CWriteDB_HeaderFile::CanFit ( int  size)
inline

Returns true if the specified amount of data would fit.

If the specified amount of data (in bytes) would fit in the file without exceeding the max_file_size, this method returns true.

Parameters
sizeSize of new data in bytes.

Definition at line 365 of file writedb_files.hpp.

References _ASSERT, m_DataSize, CWriteDB_File::m_MaxFileSize, and ncbi::grid::netcache::search::fields::size.

Referenced by CWriteDB_Volume::WriteSequence().

◆ x_Flush()

virtual void CWriteDB_HeaderFile::x_Flush ( void  )
inlineprivatevirtual

Flush unwritten data to the output file.

Implements CWriteDB_File.

Definition at line 386 of file writedb_files.hpp.

Member Data Documentation

◆ m_DataSize

Uint8 CWriteDB_HeaderFile::m_DataSize
private

Amount of data written so far.

Definition at line 393 of file writedb_files.hpp.

Referenced by AddSequence(), and CanFit().


The documentation for this class was generated from the following files:
Modified on Sat Apr 13 11:45:25 2024 by modify_doxy.py rev. 669887