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CLocalVDBBlast Class Reference

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#include <algo/blast/vdb/vdbblast_local.hpp>

+ Inheritance diagram for CLocalVDBBlast:
+ Collaboration diagram for CLocalVDBBlast:

Classes

struct  SLocalVDBStruct
 

Public Types

enum  ESRASearchMode { eUnaligned = 0 , eAligned = 1 , eBoth = 2 }
 
- 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

 CLocalVDBBlast (CRef< CBlastQueryVector > query_vector, CRef< CBlastOptionsHandle > options, CLocalVDBBlast::SLocalVDBStruct &local_vdb, bool include_filtered_reads=false)
 
 CLocalVDBBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CBlastOptionsHandle > options, SLocalVDBStruct &local_vdb, bool include_filtered_reads=false)
 
CRef< CSearchResultSetRun ()
 
Int4 GetNumExtensions ()
 
 ~CLocalVDBBlast ()
 
- 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
 

Static Public Member Functions

static string PreprocessDBs (CLocalVDBBlast::SLocalVDBStruct &local_vdb, const string db_names, unsigned int num_threads=kDisableThreadedSearch, ESRASearchMode seach_mode=eAligned)
 
- 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

static const unsigned int kDisableThreadedSearch = 1
 
- 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...
 

Private Member Functions

 CLocalVDBBlast (const CLocalVDBBlast &)
 
CLocalVDBBlastoperator= (const CLocalVDBBlast &)
 
CRef< CSearchResultSetRunThreadedSearch ()
 
void x_AdjustDbSize (void)
 
void x_PrepareQuery (vector< CRef< IQueryFactory > > &qf_v)
 
void x_PreparePssm (vector< CRef< CPssmWithParameters > > &pssm)
 

Private Attributes

CRef< CBlastQueryVectorm_query_vector
 
CRef< CBlastOptionsHandlem_opt_handle
 
Uint8 m_total_num_seqs
 
Uint8 m_total_length
 
vector< vector< string > > & m_chunks_for_thread
 
unsigned int m_num_threads
 
Int4 m_num_extensions
 
bool m_include_filtered_reads
 
CRef< objects::CPssmWithParameters > m_pssm
 

Additional Inherited Members

- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 43 of file vdbblast_local.hpp.

Member Enumeration Documentation

◆ ESRASearchMode

Enumerator
eUnaligned 
eAligned 
eBoth 

Definition at line 102 of file vdbblast_local.hpp.

Constructor & Destructor Documentation

◆ CLocalVDBBlast() [1/3]

CLocalVDBBlast::CLocalVDBBlast ( const CLocalVDBBlast )
private

◆ CLocalVDBBlast() [2/3]

CLocalVDBBlast::CLocalVDBBlast ( CRef< CBlastQueryVector query_vector,
CRef< CBlastOptionsHandle options,
CLocalVDBBlast::SLocalVDBStruct local_vdb,
bool  include_filtered_reads = false 
)

Definition at line 365 of file vdbblast_local.cpp.

◆ CLocalVDBBlast() [3/3]

CLocalVDBBlast::CLocalVDBBlast ( CRef< objects::CPssmWithParameters >  pssm,
CRef< CBlastOptionsHandle options,
SLocalVDBStruct local_vdb,
bool  include_filtered_reads = false 
)

Definition at line 381 of file vdbblast_local.cpp.

◆ ~CLocalVDBBlast()

CLocalVDBBlast::~CLocalVDBBlast ( )
inline

Definition at line 122 of file vdbblast_local.hpp.

Member Function Documentation

◆ GetNumExtensions()

Int4 CLocalVDBBlast::GetNumExtensions ( )

Definition at line 849 of file vdbblast_local.cpp.

References m_num_extensions.

Referenced by CVDBBlastnApp::Run().

◆ operator=()

CLocalVDBBlast& CLocalVDBBlast::operator= ( const CLocalVDBBlast )
private

◆ PreprocessDBs()

string CLocalVDBBlast::PreprocessDBs ( CLocalVDBBlast::SLocalVDBStruct local_vdb,
const string  db_names,
unsigned int  num_threads = kDisableThreadedSearch,
ESRASearchMode  seach_mode = eAligned 
)
static

◆ Run()

CRef< CSearchResultSet > CLocalVDBBlast::Run ( void  )

◆ RunThreadedSearch()

CRef< CSearchResultSet > CLocalVDBBlast::RunThreadedSearch ( void  )
private

◆ x_AdjustDbSize()

void CLocalVDBBlast::x_AdjustDbSize ( void  )
private

◆ x_PreparePssm()

void CLocalVDBBlast::x_PreparePssm ( vector< CRef< CPssmWithParameters > > &  pssm)
private

Definition at line 754 of file vdbblast_local.cpp.

References m_num_threads, m_pssm, MSerial_AsnBinary, and CRef< C, Locker >::Reset().

Referenced by RunThreadedSearch().

◆ x_PrepareQuery()

void CLocalVDBBlast::x_PrepareQuery ( vector< CRef< IQueryFactory > > &  qf_v)
private

Member Data Documentation

◆ kDisableThreadedSearch

const unsigned int CLocalVDBBlast::kDisableThreadedSearch = 1
static

Definition at line 67 of file vdbblast_local.hpp.

Referenced by PreprocessDBs(), Run(), and x_AdjustDbSize().

◆ m_chunks_for_thread

vector<vector<string> >& CLocalVDBBlast::m_chunks_for_thread
private

Definition at line 59 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), and x_AdjustDbSize().

◆ m_include_filtered_reads

bool CLocalVDBBlast::m_include_filtered_reads
private

Definition at line 62 of file vdbblast_local.hpp.

Referenced by Run(), and RunThreadedSearch().

◆ m_num_extensions

Int4 CLocalVDBBlast::m_num_extensions
private

Definition at line 61 of file vdbblast_local.hpp.

Referenced by GetNumExtensions(), Run(), and RunThreadedSearch().

◆ m_num_threads

unsigned int CLocalVDBBlast::m_num_threads
private

◆ m_opt_handle

CRef<CBlastOptionsHandle> CLocalVDBBlast::m_opt_handle
private

Definition at line 56 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), x_AdjustDbSize(), and x_PrepareQuery().

◆ m_pssm

CRef<objects::CPssmWithParameters> CLocalVDBBlast::m_pssm
private

Definition at line 63 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), and x_PreparePssm().

◆ m_query_vector

CRef<CBlastQueryVector> CLocalVDBBlast::m_query_vector
private

Definition at line 55 of file vdbblast_local.hpp.

Referenced by Run(), and x_PrepareQuery().

◆ m_total_length

Uint8 CLocalVDBBlast::m_total_length
private

Definition at line 58 of file vdbblast_local.hpp.

Referenced by x_AdjustDbSize().

◆ m_total_num_seqs

Uint8 CLocalVDBBlast::m_total_num_seqs
private

Definition at line 57 of file vdbblast_local.hpp.

Referenced by x_AdjustDbSize().


The documentation for this class was generated from the following files:
Modified on Sat Apr 20 12:15:31 2024 by modify_doxy.py rev. 669887