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< CBlastKmerResults >	value_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< TBlastKmerPrelimScoreVector >	TBlastKmerPrelimScoreVectorSet
	Vector of TBlastKmerScoreVector (scores) More...

typedef vector< BlastKmerStats >	TBlastKmerStatsVector
	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< Uint8 >	TCounter
	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...

CBlastKmerResults &	operator[] (size_type i)

const CBlastKmerResults &	operator[] (size_type i) const

CRef< CBlastKmerResults >	operator[] (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...

CObject &	operator= (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

typedef vector<value_type>::const_iterator CBlastKmerResultsSet::const_iterator

const_iterator type definition

Definition at line 149 of file blastkmerresults.hpp.

◆ iterator

typedef vector<value_type>::iterator CBlastKmerResultsSet::iterator

iterator type definition

Definition at line 152 of file blastkmerresults.hpp.

◆ size_type

typedef vector<value_type>::size_type CBlastKmerResultsSet::size_type

size_type type definition

Definition at line 146 of file blastkmerresults.hpp.

◆ TBlastKmerPrelimScoreVectorSet

typedef vector<TBlastKmerPrelimScoreVector> CBlastKmerResultsSet::TBlastKmerPrelimScoreVectorSet

Vector of TBlastKmerScoreVector (scores)

Definition at line 158 of file blastkmerresults.hpp.

◆ TBlastKmerStatsVector

typedef vector<BlastKmerStats> CBlastKmerResultsSet::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

typedef CRef<CBlastKmerResults> CBlastKmerResultsSet::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

ids	vector of Query IDs
scores	vector of TBlastKmerScoreVector
stats	vector of Statistics
seqdb	CSeqDB object for search.
msg_vec	vector 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

ident query 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

element to 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

ids	vector of Query IDs
scores	vector of TBlastKmerScoreVector
stats	vector of Statistics
seqdb	CSeqDB object for search.
msg_vec	vector 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:

include/algo/blast/proteinkmer/blastkmerresults.hpp
src/algo/blast/proteinkmer/blastkmerresults.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ iterator

◆ size_type

◆ TBlastKmerPrelimScoreVectorSet

◆ TBlastKmerStatsVector

◆ TQueryIdVector

◆ value_type

Constructor & Destructor Documentation

◆ CBlastKmerResultsSet() [1/2]

◆ CBlastKmerResultsSet() [2/2]

◆ ~CBlastKmerResultsSet()

Member Function Documentation

◆ GetNumQueries()

◆ operator[]() [1/3]

◆ operator[]() [2/3]

◆ operator[]() [3/3]

◆ push_back()

◆ x_Init()

Member Data Documentation

◆ m_NumQueries

◆ m_Results