#include <algo/blast/igblast/igblast.hpp>

Inheritance diagram for CIgBlast:

Collaboration diagram for CIgBlast:

Public Member Functions
	CIgBlast (CRef< CBlastQueryVector > query_factory, CRef< CLocalDbAdapter > blastdb, CRef< CBlastOptionsHandle > options, CConstRef< CIgBlastOptions > ig_options, CRef< CScope > scope)
	Local Igblast search API. More...

	CIgBlast (CRef< CBlastQueryVector > query_factory, CRef< CSearchDatabase > blastdb, CRef< IQueryFactory > subjects, CRef< CBlastOptionsHandle > options, CConstRef< CIgBlastOptions > ig_options, string entrez_query, CRef< CScope > scope)
	Remote Igblast search API. More...

	~CIgBlast ()
	Destructor. More...

CRef< CSearchResultSet >	Run ()
	Run the Ig-BLAST engine. More...

void	SetNumberOfThreads (size_t nthreads)
	Set MT mode. More...

string	GetRid ()

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

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

void	x_SetupVSearch (CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl)
	Prepare blast option handle and query for V germline database search. More...

void	x_SetupDJSearch (const vector< CRef< CIgAnnotation > > &annots, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl, int db_type)
	Prepare blast option handle and query for D, J germline database search. More...

void	x_SetupCRegionSearch (const vector< CRef< CIgAnnotation > > &annots, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl)

void	x_SetupNoOverlapDSearch (const vector< CRef< CIgAnnotation > > &annots, CRef< CSearchResultSet > &results, CRef< IQueryFactory > &qf, CRef< CBlastOptionsHandle > &opts_hndl, int db_type)

void	x_SetupDbSearch (vector< CRef< CIgAnnotation > > &annot, CRef< IQueryFactory > &qf)
	Prepare blast option handle and query for specified database search. More...

void	x_AnnotateV (CRef< CSearchResultSet > &results, vector< CRef< CIgAnnotation > > &annot)
	Annotate the V gene based on blast results. More...

void	x_AnnotateDJ (CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annot)
	Annotate the D and J genes based on blast results. More...

void	x_AnnotateD (CRef< CSearchResultSet > &results_D, vector< CRef< CIgAnnotation > > &annot)

void	x_AnnotateJ (CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annot)

void	x_AnnotateC (CRef< CSearchResultSet > &results_c, CRef< CSearchResultSet > &results_j, vector< CRef< CIgAnnotation > > &annot)

void	x_AnnotateDomain (CRef< CSearchResultSet > &gl_results, CRef< CSearchResultSet > &dm_results, vector< CRef< CIgAnnotation > > &annot)
	Annotate the query chaintype and domains based on blast results. More...

void	x_SetChainType (CRef< CSearchResultSet > &results, vector< CRef< CIgAnnotation > > &annot)
	Set the subject chain type and frame info. More...

void	x_ConvertResultType (CRef< CSearchResultSet > &results)
	Convert bl2seq result to database search mode. More...

void	x_SetAnnotation (vector< CRef< CIgAnnotation > > &annot, CRef< CSearchResultSet > &final_results)
	Append annotation info to the final results. More...

void	x_FindDJ (CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, CRef< CIgAnnotation > &annot, CRef< CSeq_align_set > &align_D, CRef< CSeq_align_set > &align_J, string q_ct, bool q_ms, ENa_strand q_st, int q_ve, int iq)

void	x_FindDJAln (CRef< CSeq_align_set > &align_D, CRef< CSeq_align_set > &align_J, string q_ct, bool q_ms, ENa_strand q_st, int q_ve, int iq, bool va_or_vd_as_heavy_chain)

void	x_ExtendAlign5end (CRef< CSearchResultSet > &results)

void	x_ExtendAlign3end (CRef< CSearchResultSet > &results)

void	x_ScreenByAlignLength (CRef< CSearchResultSet > &results, int length)

void	x_FillJDomain (CRef< CSeq_align > &align, CRef< CIgAnnotation > &annot)

void	x_ProcessDJResult (CRef< CSearchResultSet > &results_V, CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annots)

void	x_ProcessDGeneResult (CRef< CSearchResultSet > &results_V, CRef< CSearchResultSet > &results_D, CRef< CSearchResultSet > &results_J, vector< CRef< CIgAnnotation > > &annots)

void	x_ProcessCResult (CRef< CSearchResultSet > &results_C, vector< CRef< CIgAnnotation > > &annots)

Static Private Member Functions
static void	s_SortResultsByEvalue (CRef< CSearchResultSet > &results)
	Sort blast results according to evalue. More...

static void	s_AppendResults (CRef< CSearchResultSet > &results, int num_aligns, int gene, CRef< CSearchResultSet > &final_results)
	Append blast results to the final results. More...

Private Attributes
bool	m_IsLocal

size_t	m_NumThreads

CRef< CBlastQueryVector >	m_Query

CRef< IQueryFactory >	m_Subject

CRef< CLocalDbAdapter >	m_LocalDb

CRef< CSearchDatabase >	m_RemoteDb

CRef< CBlastOptionsHandle >	m_Options

CConstRef< CIgBlastOptions >	m_IgOptions

CIgAnnotationInfo	m_AnnotationInfo

string	m_EntrezQuery

CRef< CScope >	m_Scope

string	m_RID

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)

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

Definition at line 236 of file igblast.hpp.

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

include/algo/blast/igblast/igblast.hpp
src/algo/blast/igblast/igblast.cpp

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description