NCBI C++ ToolKit
Public Types | Public Member Functions | List of all members
CSeqDBSeqFile Class Reference

Search Toolkit Book for CSeqDBSeqFile

Sequence data file. More...

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

+ Inheritance diagram for CSeqDBSeqFile:
+ Collaboration diagram for CSeqDBSeqFile:

Public Types

typedef CSeqDBAtlas::TIndx TIndx
 Type which spans possible file offsets. More...
 
- Public Types inherited from CSeqDBExtFile
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

 CSeqDBSeqFile (CSeqDBAtlas &atlas, const string &dbname, char prot_nucl)
 Constructor. More...
 
virtual ~CSeqDBSeqFile ()
 Destructor. More...
 
void ReadBytes (char *buf, TIndx start, TIndx end) const
 Read part of the file into a buffer. More...
 
const char * GetFileDataPtr (TIndx start) const
 Get a pointer into the file contents. More...
 
- Public Member Functions inherited from CSeqDBExtFile
 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
 

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...
 
- Protected Member Functions inherited from CSeqDBExtFile
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 inherited from CSeqDBExtFile
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...
 

Detailed Description

Sequence data file.

This is the .psq or .nsq file; it provides the raw sequence data, and for nucleotide sequences, ambiguity data. For nucleotide sequences, the last byte will contain a two bit marker with a number from 0-3, which indicates how much of the rest of that byte is filled with base information (0-3 bases, which is 0-6 bits). For ambiguous regions, the sequence data is normally randomized in this file, to reduce the number of accidental false positives during the search. The ambiguity data encodes the location of, and actual data for, those regions.

Definition at line 748 of file seqdbfile.hpp.

Member Typedef Documentation

◆ TIndx

Type which spans possible file offsets.

Definition at line 751 of file seqdbfile.hpp.

Constructor & Destructor Documentation

◆ CSeqDBSeqFile()

CSeqDBSeqFile::CSeqDBSeqFile ( CSeqDBAtlas atlas,
const string dbname,
char  prot_nucl 
)
inline

Constructor.

This builds an object which provides access to the sequence data file for a volume. This file is simply a concatenation of all the sequence data for the database sequences. In a protein file, these are just the database sequences seperated by NUL bytes. In a nucleotide volume, the packed data for each sequence is followed by ambiguity data for that sequence (if any such data exists).

Parameters
atlasThe memory management layer object.
dbnameThe name of the database volume.
prot_nuclThe sequence data type.
lockedThe lock holder object for this thread.

Definition at line 771 of file seqdbfile.hpp.

◆ ~CSeqDBSeqFile()

virtual CSeqDBSeqFile::~CSeqDBSeqFile ( )
inlinevirtual

Destructor.

Definition at line 779 of file seqdbfile.hpp.

Member Function Documentation

◆ GetFileDataPtr()

const char* CSeqDBSeqFile::GetFileDataPtr ( TIndx  start) const
inline

Get a pointer into the file contents.

Copy the sequence 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. If the user will take ownership of the memory region hold, the keep argument should be specified as true.

Parameters
startThe starting offset for the first byte to read.
endThe offset for the first byte after the area to read.
keepTrue if an extra hold should be acquired on the data.
holdSpecify true to get a request-duration hold.
lockedThe lock holder object for this thread.
Returns
A pointer into the file data.

Definition at line 822 of file seqdbfile.hpp.

References CSeqDBFileMemMap::GetFileDataPtr(), and CSeqDBExtFile::m_Lease.

Referenced by CSeqDBVol::GetRawSeqAndAmbig(), CSeqDBVol::x_GetAmbChar(), and CSeqDBVol::x_GetSequence().

◆ ReadBytes()

void CSeqDBSeqFile::ReadBytes ( char *  buf,
TIndx  start,
TIndx  end 
) const
inline

Read part of the file into a buffer.

Copy the sequence 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 795 of file seqdbfile.hpp.

References buf, and CSeqDBExtFile::x_ReadBytes().

Referenced by CSeqDBVol::GetSeqLengthExact().


The documentation for this class was generated from the following file:
Modified on Tue Feb 27 05:55:14 2024 by modify_doxy.py rev. 669887