Runs the BLAST algorithm between 2 sequences. More...

#include <algo/blast/api/bl2seq.hpp>

Inheritance diagram for CBl2Seq:

Collaboration diagram for CBl2Seq:

Public Member Functions
	CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, EProgram p)
	Constructor to compare 2 sequences with default options. More...

	CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
	Constructor to compare query against all subject sequences with default options. More...

	CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, EProgram p, bool dbscan_mode=false)
	Constructor to allow query concatenation with default options. More...

	CBl2Seq (const SSeqLoc &query, const SSeqLoc &subject, CBlastOptionsHandle &opts)
	Constructor to compare 2 sequences with specified options. More...

	CBl2Seq (const SSeqLoc &query, const TSeqLocVector &subjects, CBlastOptionsHandle &opts, bool dbscan_mode=false)
	Constructor to compare query against all subject sequences with specified options. More...

	CBl2Seq (const TSeqLocVector &queries, const TSeqLocVector &subjects, CBlastOptionsHandle &opts, bool dbscan_mode=false)
	Constructor to allow query concatenation with specified options. More...

virtual	~CBl2Seq ()
	Destructor. More...

void	SetQuery (const SSeqLoc &query)
	Set the query. More...

const SSeqLoc &	GetQuery () const
	Retrieve the query sequence. More...

void	SetQueries (const TSeqLocVector &queries)
	Set a vector of query sequences for a concatenated search. More...

const TSeqLocVector &	GetQueries () const
	Retrieve a vector of query sequences. More...

void	SetSubject (const SSeqLoc &subject)
	Set the subject sequence. More...

const SSeqLoc &	GetSubject () const
	Retrieve the subject sequence. More...

void	SetSubjects (const TSeqLocVector &subjects)
	Set a vector of subject sequences. More...

const TSeqLocVector &	GetSubjects () const
	Retrieve a vector of subject sequences. More...

CBlastOptionsHandle &	SetOptionsHandle ()
	Set the options handle. More...

const CBlastOptionsHandle &	GetOptionsHandle () const
	Retrieve the options handle. More...

virtual TSeqAlignVector	Run ()
	Perform BLAST search Assuming N queries and M subjects, the structure of the returned vector is as follows, with types indicated in parenthesis: TSeqAlignVector = [ {Results for query 1 and subject 1 (Seq-align-set)}, {Results for query 1 and subject 2 (Seq-align-set)}, ... More...

CRef< CSearchResultSet >	RunEx ()
	Performs the same functionality as Run(), but it returns a different data type. More...

TSeqLocInfoVector	GetFilteredQueryRegions () const
	Retrieves regions filtered on the query/queries. More...

void	GetFilteredSubjectRegions (vector< TSeqLocInfoVector > &retval) const
	Retrieves regions filtered on the subject sequence(s) More...

BlastDiagnostics *	GetDiagnostics () const
	Retrieves the diagnostics information returned from the engine. More...

void	GetAncillaryResults (CSearchResultSet::TAncillaryVector &retval) const
	Get the ancillary results for a BLAST search (to be used with the Run() method) More...

void	GetMessages (TSearchMessages &messages) const
	Returns error messages/warnings. More...

TInterruptFnPtr	SetInterruptCallback (TInterruptFnPtr fnptr, void *user_data=NULL)
	Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in progress. 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 Member Functions
static TSeqAlignVector	CSearchResultSet2TSeqAlignVector (CRef< CSearchResultSet > res)
	Converts m_Results data member to a TSeqAlignVector. 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
void	x_BuildAncillaryData ()
	Populate the internal m_AncillaryData member. More...

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

Private Member Functions
void	x_Init (const TSeqLocVector &queries, const TSeqLocVector &subjs)
	Common initialization code for all c-tors. More...

void	x_InitCLocalBlast ()
	Common initialization of the CLocalBlast object. More...

	CBl2Seq (const CBl2Seq &rhs)
	Prohibit copy constructor. More...

CBl2Seq &	operator= (const CBl2Seq &rhs)
	Prohibit assignment operator. More...

void	x_ResetInternalDs ()
	Clean up structures and results from any previous search. More...

Private Attributes
TSeqLocVector	m_tQueries
	query sequence(s) More...

TSeqLocVector	m_tSubjects
	sequence(s) to BLAST against More...

CRef< CBlastOptionsHandle >	m_OptsHandle
	Blast options. More...

CRef< CLocalBlast >	m_Blast
	The actual BLAST instance. More...

bool	m_DbScanMode
	Scan like a databsase (as opposed to pairwise) More...

TSearchMessages	m_Messages
	Stores any warnings emitted during query setup. More...

BlastDiagnostics *	mi_pDiagnostics
	Return search statistics data. More...

CSearchResultSet::TAncillaryVector	m_AncillaryData
	Ancillary BLAST data. More...

CRef< CSearchResultSet >	m_Results
	CLocalBlast results. More...

TInterruptFnPtr	m_InterruptFnx
	Interrupt callback. More...

void *	m_InterruptUserData
	Interrupt user datacallback. More...

Friends
class	::CBlastFilterTest

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 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...

Detailed Description

Runs the BLAST algorithm between 2 sequences.

Note: this is a single-BLAST search run object (i.e.: it caches the results after a BLAST search is done). If multiple BLAST searches with different queries, subjects, or options are required, please create a separate object

Definition at line 57 of file bl2seq.hpp.

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

include/algo/blast/api/bl2seq.hpp
src/algo/blast/api/bl2seq.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description