Search Toolkit Book for CSubjectRangesSet

Set of ranges of subject sequence offsets to fetch during the traceback stage. More...

#include <algo/blast/api/subj_ranges_set.hpp>

Inheritance diagram for CSubjectRangesSet:

Collaboration diagram for CSubjectRangesSet:

Public Member Functions
	CSubjectRangesSet (int expand_hsp=kHspExpandSize, int min_gap=kMinGap)
	Construct a set of sequence ranges. More...

void	AddRange (int q_oid, int s_oid, int begin, int end)
	Add new offset range for subject HSP. More...

void	RemoveSubject (int s_oid)
	Remove a given subject OID from the set. More...

void	ApplyRanges (CSeqDB &db) const
	Apply existing ranges to a database. 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

Static Public Attributes
static const int	kHspExpandSize = 1024
	Default number of letters to expand for each HSP after all merging has taken place. More...

static const int	kMinGap = 1024
	Default minimum gap size to avoid merge. More...

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 Types
typedef map< int, CRef< CSubjectRanges > >	TSubjOid2RangesMap
	List of OIDs and sequence ranges. More...

Private Member Functions
	CSubjectRangesSet (const CSubjectRangesSet &other)
	Prevent copy constructor. More...

CSubjectRangesSet &	operator= (const CSubjectRangesSet &rhs)
	Prevent assignment operator. More...

void	x_ExpandHspRange (int &begin, int &end)
	Add, expand, and merge new range. More...

void	x_TranslateOffsets (int &begin, int &end)
	Translate subject offsets from protein to DNA coordinates. More...

Private Attributes
TSubjOid2RangesMap	m_SubjRanges
	Set of query ids and ranges for an OID. More...

int	m_ExpandHSP
	Expansion amount for each HSP range. More...

int	m_MinGap
	Minimum gap between sequences to avoid merging. More...

Additional Inherited Members
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...

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)

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

Detailed Description

Set of ranges of subject sequence offsets to fetch during the traceback stage.

This is applicable only to nucleotide sequences and improves performance during the traceback stage when dealing with large subject sequences.

Definition at line 100 of file subj_ranges_set.hpp.

Member Typedef Documentation

◆ TSubjOid2RangesMap

typedef map<int, CRef<CSubjectRanges> > CSubjectRangesSet::TSubjOid2RangesMap

private

List of OIDs and sequence ranges.

Definition at line 170 of file subj_ranges_set.hpp.

Constructor & Destructor Documentation

◆ CSubjectRangesSet() [1/2]

CSubjectRangesSet::CSubjectRangesSet	(	int	expand_hsp = `kHspExpandSize`,
		int	min_gap = `kMinGap`
	)

inline

Construct a set of sequence ranges.

Create a new sequence map set, specifying that expand_hsp letters should be fetched on either side of every region of a database sequence. The min_gap value is applied to the results of extension, and joins any ranges where the intervening gap is smaller than the specified value.

These numbers have not (yet) been 'tuned' to find an optimal value for performance; it is expected that few searches will hit the 'fence' at the current default values.

It may be unsafe to specify either of these values at very small numbers (less than 10 or so).

Parameters

expand_hsp	Expand each range by at least this much.
min_gap	Join ranges if gap is smaller than this.

Definition at line 127 of file subj_ranges_set.hpp.

◆ CSubjectRangesSet() [2/2]

CSubjectRangesSet::CSubjectRangesSet ( const CSubjectRangesSet & other )

private

Prevent copy constructor.

Member Function Documentation

◆ AddRange()

void CSubjectRangesSet::AddRange	(	int	q_oid,
		int	s_oid,
		int	begin,
		int	end
	)

Add new offset range for subject HSP.

Parameters

q_oid	Query OID or index.
s_oid	Subject OID.
begin	Start offset in subject HSP.
begin	End offset in subject HSP.

Definition at line 118 of file subj_ranges_set.cpp.

References m_ExpandHSP, m_MinGap, m_SubjRanges, CRandom::Reset(), and x_ExpandHspRange().

Referenced by BOOST_AUTO_TEST_CASE().

◆ ApplyRanges()

void CSubjectRangesSet::ApplyRanges ( CSeqDB & db ) const

Apply existing ranges to a database.

Parameters

seqdb SeqDB object to modify.

Definition at line 156 of file subj_ranges_set.cpp.

References CSubjectRanges::GetRanges(), CSubjectRanges::IsUsedByMultipleQueries(), ITERATE, m_SubjRanges, and CSeqDB::SetOffsetRanges().

Referenced by BOOST_AUTO_TEST_CASE().

◆ operator=()

CSubjectRangesSet& CSubjectRangesSet::operator= ( const CSubjectRangesSet & rhs )

private

Prevent assignment operator.

◆ RemoveSubject()

void CSubjectRangesSet::RemoveSubject ( int s_oid )

Remove a given subject OID from the set.

Any ranges for the given subject oid are cleared, causing the entire offset range to be included. The normal use of this method is to remove ranges specified for query sequences that are also found in the subject database. If the OID is not found, there is no effect.

Parameters

s_oid Subject OID.

Definition at line 133 of file subj_ranges_set.cpp.

References map_checker< Container >::erase(), and m_SubjRanges.

Referenced by BOOST_AUTO_TEST_CASE().

◆ x_ExpandHspRange()

void CSubjectRangesSet::x_ExpandHspRange	(	int &	begin,
		int &	end
	)

private

Add, expand, and merge new range.

Definition at line 138 of file subj_ranges_set.cpp.

References m_ExpandHSP.

Referenced by AddRange().

◆ x_TranslateOffsets()

void CSubjectRangesSet::x_TranslateOffsets	(	int &	begin,
		int &	end
	)

private

Translate subject offsets from protein to DNA coordinates.

Parameters

begin	Starting offset.
end	Ending offset of desired sequence range.
length	Total length of sequence.
negative	Specify true for negative frames.

Member Data Documentation

◆ kHspExpandSize

const int CSubjectRangesSet::kHspExpandSize = 1024

static

Default number of letters to expand for each HSP after all merging has taken place.

Definition at line 104 of file subj_ranges_set.hpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ kMinGap

const int CSubjectRangesSet::kMinGap = 1024

static

Default minimum gap size to avoid merge.

Definition at line 107 of file subj_ranges_set.hpp.

◆ m_ExpandHSP

int CSubjectRangesSet::m_ExpandHSP

private

Expansion amount for each HSP range.

Definition at line 176 of file subj_ranges_set.hpp.

Referenced by AddRange(), and x_ExpandHspRange().

◆ m_MinGap

int CSubjectRangesSet::m_MinGap

private

Minimum gap between sequences to avoid merging.

Definition at line 179 of file subj_ranges_set.hpp.

Referenced by AddRange().

◆ m_SubjRanges

TSubjOid2RangesMap CSubjectRangesSet::m_SubjRanges

private

Set of query ids and ranges for an OID.

Definition at line 173 of file subj_ranges_set.hpp.

Referenced by AddRange(), ApplyRanges(), and RemoveSubject().

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

include/algo/blast/api/subj_ranges_set.hpp
src/algo/blast/api/subj_ranges_set.cpp

Public Member Functions

Static Public Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TSubjOid2RangesMap

Constructor & Destructor Documentation

◆ CSubjectRangesSet() [1/2]

◆ CSubjectRangesSet() [2/2]

Member Function Documentation

◆ AddRange()

◆ ApplyRanges()

◆ operator=()

◆ RemoveSubject()

◆ x_ExpandHspRange()

◆ x_TranslateOffsets()

Member Data Documentation

◆ kHspExpandSize

◆ kMinGap

◆ m_ExpandHSP

◆ m_MinGap

◆ m_SubjRanges