#include <algo/blast/dbindex_search/sr_search.hpp>

Inheritance diagram for CSRSearch:

Collaboration diagram for CSRSearch:

Classes
class	CMismatchResultsInfo

class	CResCache

class	InternalException

struct	SHKData

struct	SMismatchInfo

struct	SMismatchResultsEntry

struct	SResultData

struct	SResults

struct	SSearchData

struct	SSRResult

Public Types
enum	ELevel { PE , PM , SE , SM , EM }

typedef CDbIndex::TSeqNum	TSeqNum

typedef SResults	TResults

typedef vector< SSRResult >	TSRResults

typedef pair< SSRResult, SSRResult >	TSRPairedResult

typedef vector< TSRPairedResult >	TSRPairedResults

typedef vector< SMismatchResultsEntry >	TMismatchResults

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
virtual void	search (const SSearchData &sdata, TResults &results)=0

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

Static Public Member Functions
static CRef< CSRSearch >	MakeSRSearch (CRef< CDbIndex > index, TSeqPos d=0, TSeqPos dfuzz=0)

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 Uint4	TSRRESULTS_INISIZE = 1000000UL

static const Uint4	TSRPAIRS_INISIZE = 10000UL

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
	CSRSearch (CRef< CDbIndex > index, TSeqPos d, TSeqPos dfuzz)

vector< TSeqPos >	GetQNmerPositions (TSeqPos sz) const

Uint4	getNMer (const CSeqVector &seq, TSeqPos pos, bool fw, bool &ambig) const

Uint4	getNMer (const CSeqVector &seq, TSeqPos pos, bool fw, bool &ambig, TSeqPos sub_pos, Uint1 sub_letter) const

pair< TSeqPos, TSeqPos >	Pos2Index (TSeqPos pos, TSeqPos sz, SMismatchInfo &mismatch_info) const

void	mergeResults (TSRResults &results, const TSRResults &src, Int4 step)

void	combine (const TSRResults &results_1, const TSRResults &results_2, TSRPairedResults &results, Int4 adjust=0)

pair< TSeqNum, TSeqPos >	MapSOff (TSeqNum lid, TSeqPos loff, TSeqPos sz, bool &overlap) const

bool	reportResults (TResults &r, Uint4 nr, TSeqPos qsz1, TSeqPos qsz2, const TSRPairedResults &results, bool fw1, bool fw2, bool mismatch1=false, bool mismatch2=false, TSeqPos mismatch_pos1=0, TSeqPos mismatch_pos2=0, Uint1 mismatch_letter1=(Uint1)'-', Uint1 mismatch_letter2=(Uint1)'-', Uint4 adjustment1=0, Uint4 adjustment2=0)

bool	reportResults (TResults &r, Uint4 nr, TSeqPos qsz, const TSRResults &results, bool fw, bool mismatch=false, TSeqPos mismatch_pos=0, Uint1 mismatch_letter=(Uint1)'-', Uint4 adjustment=0, Uint4 pos_in_pair=0)

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

Protected Attributes
unsigned long	hkey_width_

SHKData	hk_data_

Private Attributes
CRef< CDbIndex >	index_

TSeqPos	dmax_

TSeqPos	dmin_

Detailed Description

Definition at line 46 of file sr_search.hpp.

Member Typedef Documentation

◆ TMismatchResults

typedef vector< SMismatchResultsEntry > CSRSearch::TMismatchResults

Definition at line 268 of file sr_search.hpp.

◆ TResults

typedef SResults CSRSearch::TResults

Definition at line 152 of file sr_search.hpp.

◆ TSeqNum

typedef CDbIndex::TSeqNum CSRSearch::TSeqNum

Definition at line 52 of file sr_search.hpp.

◆ TSRPairedResult

typedef pair< SSRResult, SSRResult > CSRSearch::TSRPairedResult

Definition at line 176 of file sr_search.hpp.

◆ TSRPairedResults

typedef vector< TSRPairedResult > CSRSearch::TSRPairedResults

Definition at line 177 of file sr_search.hpp.

◆ TSRResults

typedef vector< SSRResult > CSRSearch::TSRResults

Definition at line 175 of file sr_search.hpp.

Member Enumeration Documentation

◆ ELevel

enum CSRSearch::ELevel

Enumerator
PE
PM
SE
SM
EM

Definition at line 50 of file sr_search.hpp.

Constructor & Destructor Documentation

◆ CSRSearch()

CSRSearch::CSRSearch	(	CRef< CDbIndex >	index,
		TSeqPos	d,
		TSeqPos	dfuzz
	)

inlineprotected

Definition at line 370 of file sr_search.hpp.

References ASSERT.

Member Function Documentation

◆ combine()

void CSRSearch::combine	(	const TSRResults &	results_1,
		const TSRResults &	results_2,
		TSRPairedResults &	results,
		Int4	adjust = `0`
	)

protected

Definition at line 273 of file sr_search.cpp.

References chunk_size, dmax_, dmin_, CDbIndex::getChunkOverlap(), CDbIndex::getMaxChunkSize(), CDbIndex::getSIdOffByLIdOff(), i, and index_.

◆ getNMer() [1/2]

Uint4 CSRSearch::getNMer	(	const CSeqVector &	seq,
		TSeqPos	pos,
		bool	fw,
		bool &	ambig
	)		const

protected

Definition at line 82 of file sr_search.cpp.

References ambig(), hkey_width_, letter(), result, and CSeqVector::size().

◆ getNMer() [2/2]

Uint4 CSRSearch::getNMer	(	const CSeqVector &	seq,
		TSeqPos	pos,
		bool	fw,
		bool &	ambig,
		TSeqPos	sub_pos,
		Uint1	sub_letter
	)		const

protected

Definition at line 128 of file sr_search.cpp.

References ambig(), hkey_width_, letter(), result, and CSeqVector::size().

◆ GetQNmerPositions()

vector< TSeqPos > CSRSearch::GetQNmerPositions ( TSeqPos sz ) const

protected

Definition at line 62 of file sr_search.cpp.

References hkey_width_, and result.

◆ MakeSRSearch()

CRef< CSRSearch > CSRSearch::MakeSRSearch	(	CRef< CDbIndex >	index,
		TSeqPos	d = `0`,
		TSeqPos	dfuzz = `0`
	)

static

Definition at line 46 of file sr_search.cpp.

Referenced by CSRSearchApplication::Run().

◆ MapSOff()

pair< TSeqNum, TSeqPos > CSRSearch::MapSOff	(	TSeqNum	lid,
		TSeqPos	loff,
		TSeqPos	sz,
		bool &	overlap
	)		const

protected

Definition at line 380 of file sr_search.cpp.

References CDbIndex::getCIdOffByLIdOff(), CDbIndex::getOIdBySId(), CDbIndex::getSIdByCId(), CDbIndex::getSIdOffByCIdOff(), and index_.

Referenced by reportResults().

◆ mergeResults()

void CSRSearch::mergeResults	(	TSRResults &	results,
		const TSRResults &	src,
		Int4	step
	)

protected

Definition at line 238 of file sr_search.cpp.

References test().

◆ Pos2Index()

pair< TSeqPos, TSeqPos > CSRSearch::Pos2Index	(	TSeqPos	pos,
		TSeqPos	sz,
		SMismatchInfo &	mismatch_info
	)		const

protected

Definition at line 197 of file sr_search.cpp.

References hkey_width_, CSRSearch::SMismatchInfo::idx, CSRSearch::SMismatchInfo::key_pos, min(), CSRSearch::SMismatchInfo::num_keys, and result.

◆ reportResults() [1/2]

bool CSRSearch::reportResults	(	TResults &	r,
		Uint4	nr,
		TSeqPos	qsz,
		const TSRResults &	results,
		bool	fw,
		bool	mismatch = `false`,
		TSeqPos	mismatch_pos = `0`,
		Uint1	mismatch_letter = `(Uint1)'-'`,
		Uint4	adjustment = `0`,
		Uint4	pos_in_pair = `0`
	)

protected

Definition at line 400 of file sr_search.cpp.

References hkey_width_, MapSOff(), r(), and CSRSearch::SResults::res.

◆ reportResults() [2/2]

bool CSRSearch::reportResults	(	TResults &	r,
		Uint4	nr,
		TSeqPos	qsz1,
		TSeqPos	qsz2,
		const TSRPairedResults &	results,
		bool	fw1,
		bool	fw2,
		bool	mismatch1 = `false`,
		bool	mismatch2 = `false`,
		TSeqPos	mismatch_pos1 = `0`,
		TSeqPos	mismatch_pos2 = `0`,
		Uint1	mismatch_letter1 = `(Uint1)'-'`,
		Uint1	mismatch_letter2 = `(Uint1)'-'`,
		Uint4	adjustment1 = `0`,
		Uint4	adjustment2 = `0`
	)

protected

Definition at line 429 of file sr_search.cpp.

References hkey_width_, MapSOff(), r(), CSRSearch::SResults::res, CSRSearch::SSRResult::seqnum, and CSRSearch::SSRResult::soff.

◆ search()

virtual void CSRSearch::search	(	const SSearchData &	sdata,
		TResults &	results
	)

pure virtual

Implemented in CSRSearch_Impl< index_t >.

Member Data Documentation

◆ dmax_

TSeqPos CSRSearch::dmax_

private

Definition at line 425 of file sr_search.hpp.

Referenced by combine().

◆ dmin_

TSeqPos CSRSearch::dmin_

private

Definition at line 425 of file sr_search.hpp.

Referenced by combine().

◆ hk_data_

SHKData CSRSearch::hk_data_

protected

Definition at line 420 of file sr_search.hpp.

◆ hkey_width_

unsigned long CSRSearch::hkey_width_

protected

Definition at line 419 of file sr_search.hpp.

Referenced by getNMer(), GetQNmerPositions(), Pos2Index(), and reportResults().

◆ index_

CRef< CDbIndex > CSRSearch::index_

private

Definition at line 424 of file sr_search.hpp.

Referenced by combine(), and MapSOff().

◆ TSRPAIRS_INISIZE

const Uint4 CSRSearch::TSRPAIRS_INISIZE = 10000UL

static

Definition at line 163 of file sr_search.hpp.

◆ TSRRESULTS_INISIZE

const Uint4 CSRSearch::TSRRESULTS_INISIZE = 1000000UL

static

Definition at line 162 of file sr_search.hpp.

The documentation for this class was generated from the following files:

include/algo/blast/dbindex_search/sr_search.hpp
src/algo/blast/dbindex_search/sr_search.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

◆ TMismatchResults

◆ TResults

◆ TSeqNum

◆ TSRPairedResult

◆ TSRPairedResults

◆ TSRResults

Member Enumeration Documentation

◆ ELevel

Constructor & Destructor Documentation

◆ CSRSearch()

Member Function Documentation

◆ combine()

◆ getNMer() [1/2]

◆ getNMer() [2/2]

◆ GetQNmerPositions()

◆ MakeSRSearch()

◆ MapSOff()

◆ mergeResults()

◆ Pos2Index()

◆ reportResults() [1/2]

◆ reportResults() [2/2]

◆ search()

Member Data Documentation

◆ dmax_

◆ dmin_

◆ hk_data_

◆ hkey_width_

◆ index_

◆ TSRPAIRS_INISIZE

◆ TSRRESULTS_INISIZE