NCBI C++ ToolKit
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
CWriteDB_GiMaskData Class Reference

Search Toolkit Book for CWriteDB_GiMaskData

CWriteDB_GiMaskData class. More...

#include "writedb_gimask.hpp"
(Private to src/objtools/blast/seqdb_writer.)

+ Inheritance diagram for CWriteDB_GiMaskData:
+ Collaboration diagram for CWriteDB_GiMaskData:

Public Types

typedef vector< pair< TSeqPos, TSeqPos > > TPairVector
 
typedef pair< int, intTOffset
 
- 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

 CWriteDB_GiMaskData (const string &maskname, const string &extn, int index, Uint8 max_file_size, bool le=false)
 Constructor for an gimask data file. More...
 
 ~CWriteDB_GiMaskData ()
 Destructor. More...
 
void WriteMask (const TPairVector &mask)
 Write a new data blob. More...
 
int GetIndex () const
 Get current index. More...
 
TOffset GetOffset () const
 Get current index/offset pair. More...
 
bool CanFit (int num_masks) const
 Tests whether there is room for another batch. 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

void x_Flush ()
 Flush any stored data. More...
 

Private Attributes

Uint8 m_DataLength
 Length of data written so far. More...
 
bool m_UseLE
 Use little endian? More...
 
int m_Index
 Current index. More...
 

Additional Inherited Members

- 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

CWriteDB_GiMaskData class.

Manufacture gi based mask data files from input data.

Definition at line 56 of file writedb_gimask.hpp.

Member Typedef Documentation

◆ TOffset

Definition at line 59 of file writedb_gimask.hpp.

◆ TPairVector

Definition at line 58 of file writedb_gimask.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_GiMaskData()

CWriteDB_GiMaskData::CWriteDB_GiMaskData ( const string maskname,
const string extn,
int  index,
Uint8  max_file_size,
bool  le = false 
)

Constructor for an gimask data file.

Parameters
masknameDatabase name (same for all volumes).
extnFile extension to use for index file.
max_file_sizeMaximum size of any generated file in bytes.
leUse little endian format

Definition at line 279 of file writedb_gimask.cpp.

◆ ~CWriteDB_GiMaskData()

CWriteDB_GiMaskData::~CWriteDB_GiMaskData ( )
inline

Destructor.

Definition at line 74 of file writedb_gimask.hpp.

Member Function Documentation

◆ CanFit()

bool CWriteDB_GiMaskData::CanFit ( int  num_masks) const
inline

Tests whether there is room for another batch.

Parameters
thenumber of masks to be added. [in]
Returns
Return TRUE if masks can fit into the volume.

Definition at line 96 of file writedb_gimask.hpp.

References m_DataLength, and CWriteDB_File::m_MaxFileSize.

Referenced by CWriteDB_GiMask::AddGiMask().

◆ GetIndex()

int CWriteDB_GiMaskData::GetIndex ( void  ) const
inline

Get current index.

Definition at line 81 of file writedb_gimask.hpp.

References m_Index.

Referenced by CWriteDB_GiMask::AddGiMask(), and CWriteDB_GiMask::Close().

◆ GetOffset()

TOffset CWriteDB_GiMaskData::GetOffset ( void  ) const
inline

Get current index/offset pair.

Returns
The current volume index and offset in byte

Definition at line 88 of file writedb_gimask.hpp.

References m_DataLength, and m_Index.

Referenced by CWriteDB_GiMask::AddGiMask().

◆ WriteMask()

void CWriteDB_GiMaskData::WriteMask ( const TPairVector mask)

◆ x_Flush()

void CWriteDB_GiMaskData::x_Flush ( void  )
inlineprivatevirtual

Flush any stored data.

Implements CWriteDB_File.

Definition at line 112 of file writedb_gimask.hpp.

Member Data Documentation

◆ m_DataLength

Uint8 CWriteDB_GiMaskData::m_DataLength
private

Length of data written so far.

Definition at line 103 of file writedb_gimask.hpp.

Referenced by CanFit(), GetOffset(), and WriteMask().

◆ m_Index

int CWriteDB_GiMaskData::m_Index
private

Current index.

Definition at line 109 of file writedb_gimask.hpp.

Referenced by GetIndex(), and GetOffset().

◆ m_UseLE

bool CWriteDB_GiMaskData::m_UseLE
private

Use little endian?

Definition at line 106 of file writedb_gimask.hpp.

Referenced by WriteMask().


The documentation for this class was generated from the following files:
Modified on Mon Feb 26 04:05:14 2024 by modify_doxy.py rev. 669887