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CBlastKmerResultsSet Class Reference

Search Toolkit Book for CBlastKmerResultsSet

This class holds one or more CBlastKmerResults. More...

#include <algo/blast/proteinkmer/blastkmerresults.hpp>

+ Inheritance diagram for CBlastKmerResultsSet:
+ Collaboration diagram for CBlastKmerResultsSet:

Public Types

typedef CRef< CBlastKmerResultsvalue_type
 data type contained by this container More...
 
typedef vector< value_type >::size_type size_type
 size_type type definition More...
 
typedef vector< value_type >::const_iterator const_iterator
 const_iterator type definition More...
 
typedef vector< value_type >::iterator iterator
 iterator type definition More...
 
typedef vector< CConstRef< objects::CSeq_id > > TQueryIdVector
 List of query ids. More...
 
typedef vector< TBlastKmerPrelimScoreVectorTBlastKmerPrelimScoreVectorSet
 Vector of TBlastKmerScoreVector (scores) More...
 
typedef vector< BlastKmerStatsTBlastKmerStatsVector
 Vector of KmerStats. 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

 CBlastKmerResultsSet ()
 Default constructor. More...
 
 CBlastKmerResultsSet (TQueryIdVector &ids, TBlastKmerPrelimScoreVectorSet &scores, TBlastKmerStatsVector &stats, CRef< CSeqDB > seqdb, TSearchMessages msg_vec)
 Constructor. More...
 
 ~CBlastKmerResultsSet ()
 Destructor. More...
 
CBlastKmerResultsoperator[] (size_type i)
 
const CBlastKmerResultsoperator[] (size_type i) const
 
CRef< CBlastKmerResultsoperator[] (const CSeq_id &ident)
 Array like acces with CSeq_id indices. More...
 
size_t GetNumQueries () const
 Returns the number of queries. More...
 
void push_back (value_type &element)
 Add an element to m_Results. 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_Init (TQueryIdVector &ids, TBlastKmerPrelimScoreVectorSet &scores, TBlastKmerStatsVector &stats, CRef< CSeqDB > seqdb, TSearchMessages msg_vec)
 

Private Attributes

vector< CRef< CBlastKmerResults > > m_Results
 Vectors of results. More...
 
size_t m_NumQueries
 Number or queries. 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...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

This class holds one or more CBlastKmerResults.

Definition at line 138 of file blastkmerresults.hpp.

Member Typedef Documentation

◆ const_iterator

const_iterator type definition

Definition at line 149 of file blastkmerresults.hpp.

◆ iterator

iterator type definition

Definition at line 152 of file blastkmerresults.hpp.

◆ size_type

size_type type definition

Definition at line 146 of file blastkmerresults.hpp.

◆ TBlastKmerPrelimScoreVectorSet

Vector of TBlastKmerScoreVector (scores)

Definition at line 158 of file blastkmerresults.hpp.

◆ TBlastKmerStatsVector

Vector of KmerStats.

Definition at line 161 of file blastkmerresults.hpp.

◆ TQueryIdVector

typedef vector< CConstRef<objects::CSeq_id> > CBlastKmerResultsSet::TQueryIdVector

List of query ids.

Definition at line 155 of file blastkmerresults.hpp.

◆ value_type

data type contained by this container

Definition at line 143 of file blastkmerresults.hpp.

Constructor & Destructor Documentation

◆ CBlastKmerResultsSet() [1/2]

CBlastKmerResultsSet::CBlastKmerResultsSet ( )

Default constructor.

Definition at line 145 of file blastkmerresults.cpp.

References m_NumQueries.

◆ CBlastKmerResultsSet() [2/2]

CBlastKmerResultsSet::CBlastKmerResultsSet ( TQueryIdVector ids,
TBlastKmerPrelimScoreVectorSet scores,
TBlastKmerStatsVector stats,
CRef< CSeqDB seqdb,
TSearchMessages  msg_vec 
)

Constructor.

Parameters
idsvector of Query IDs
scoresvector of TBlastKmerScoreVector
statsvector of Statistics
seqdbCSeqDB object for search.
msg_vecvector of messages and warnings.

Definition at line 135 of file blastkmerresults.cpp.

References stats, and x_Init().

◆ ~CBlastKmerResultsSet()

CBlastKmerResultsSet::~CBlastKmerResultsSet ( )
inline

Destructor.

Definition at line 179 of file blastkmerresults.hpp.

Member Function Documentation

◆ GetNumQueries()

size_t CBlastKmerResultsSet::GetNumQueries ( void  ) const
inline

Returns the number of queries.

Definition at line 196 of file blastkmerresults.hpp.

References m_NumQueries.

Referenced by BOOST_AUTO_TEST_CASE().

◆ operator[]() [1/3]

CRef<CBlastKmerResults> CBlastKmerResultsSet::operator[] ( const CSeq_id ident)

Array like acces with CSeq_id indices.

Parameters
identquery sequence id [in]

◆ operator[]() [2/3]

CBlastKmerResults& CBlastKmerResultsSet::operator[] ( size_type  i)
inline

Definition at line 183 of file blastkmerresults.hpp.

References i, and m_Results.

◆ operator[]() [3/3]

const CBlastKmerResults& CBlastKmerResultsSet::operator[] ( size_type  i) const
inline

Definition at line 187 of file blastkmerresults.hpp.

References i, and m_Results.

◆ push_back()

void CBlastKmerResultsSet::push_back ( CBlastKmerResultsSet::value_type element)

Add an element to m_Results.

Parameters
elementto add [in]

Definition at line 152 of file blastkmerresults.cpp.

References m_NumQueries, and m_Results.

Referenced by BOOST_AUTO_TEST_CASE().

◆ x_Init()

void CBlastKmerResultsSet::x_Init ( TQueryIdVector ids,
TBlastKmerPrelimScoreVectorSet scores,
TBlastKmerStatsVector stats,
CRef< CSeqDB seqdb,
TSearchMessages  msg_vec 
)
private
Parameters
idsvector of Query IDs
scoresvector of TBlastKmerScoreVector
statsvector of Statistics
seqdbCSeqDB object for search.
msg_vecvector of messages and warnings.

Definition at line 119 of file blastkmerresults.cpp.

References i, m_NumQueries, m_Results, and stats.

Referenced by CBlastKmerResultsSet().

Member Data Documentation

◆ m_NumQueries

size_t CBlastKmerResultsSet::m_NumQueries
private

Number or queries.

Definition at line 219 of file blastkmerresults.hpp.

Referenced by CBlastKmerResultsSet(), GetNumQueries(), push_back(), and x_Init().

◆ m_Results

vector< CRef<CBlastKmerResults> > CBlastKmerResultsSet::m_Results
private

Vectors of results.

Definition at line 216 of file blastkmerresults.hpp.

Referenced by operator[](), push_back(), and x_Init().


The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:01:17 2024 by modify_doxy.py rev. 669887