#include <algo/align/nw/nw_aligner.hpp>

Inheritance diagram for CNWAligner:

Collaboration diagram for CNWAligner:

Classes
class	CBacktraceMatrix4

struct	SAlignInOut

struct	SProgressInfo

Public Types
enum	EGapPreference { eEarlier , eLater }

enum	ETranscriptSymbol { eTS_None = 0 , eTS_Delete = 'D' , eTS_Insert = 'I' , eTS_Match = 'M' , eTS_Replace = 'R' , eTS_Intron = 'Z' , eTS_SlackDelete , eTS_SlackInsert }

typedef int	TScore

typedef bool(*	FProgressCallback) (SProgressInfo *)

typedef vector< ETranscriptSymbol >	TTranscript

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
	CNWAligner (void)

	CNWAligner (const char seq1, size_t len1, const char seq2, size_t len2, const SNCBIPackedScoreMatrix *scoremat=0)

	CNWAligner (const string &seq1, const string &seq2, const SNCBIPackedScoreMatrix *scoremat=0)

virtual	~CNWAligner (void)

virtual TScore	Run (void)

CRef< objects::CSeq_align >	Run (objects::CScope &scope, const objects::CSeq_loc &loc1, const objects::CSeq_loc &loc2, bool trim_end_gaps=true)

CRef< objects::CSeq_align >	Run (objects::CScope &scope, const objects::CSeq_id &id1, const objects::CSeq_id &id2, bool trim_end_gaps=true)

virtual void	SetSequences (const char seq1, size_t len1, const char seq2, size_t len2, bool verify=true)

void	SetSequences (const string &seq1, const string &seq2, bool verify=true)

void	SetScoreMatrix (const SNCBIPackedScoreMatrix *scoremat)

const SNCBIFullScoreMatrix &	GetScoreMatrix (void) const

void	SetWm (TScore value)

void	SetWms (TScore value)

void	SetWg (TScore value)

void	SetWs (TScore value)

void	SetEndSpaceFree (bool Left1, bool Right1, bool Left2, bool Right2)

void	SetSmithWaterman (bool SW)

void	SetGapPreference (EGapPreference p)
	Control preference for where to place a gap if there is a choice; default is eLater, placing the gap as late as possible. More...

void	SetPattern (const vector< size_t > &pattern)

void	SetSpaceLimit (const size_t &maxmem)

void	SetProgressCallback (FProgressCallback prg_callback, void *data)

TScore	GetWm (void) const

TScore	GetWms (void) const

TScore	GetWg (void) const

TScore	GetWs (void) const

const char *	GetSeq1 (void) const

size_t	GetSeqLen1 (void) const

const char *	GetSeq2 (void) const

size_t	GetSeqLen2 (void) const

void	GetEndSpaceFree (bool L1, bool R1, bool L2, bool R2) const

bool	IsSmithWaterman () const

EGapPreference	GetGapPreference () const

TScore	GetScore (void) const

size_t	GetSpaceLimit (void) const

TTranscript	GetTranscript (bool reversed=true) const

void	SetTranscript (const TTranscript &transcript)

string	GetTranscriptString (void) const

void	SetPositivesAsMatches (bool positives_as_matches=true)

bool	GetPositivesAsMatches (void) const

size_t	GetLeftSeg (size_t q0, size_t q1, size_t s0, size_t s1, size_t min_size) const

size_t	GetRightSeg (size_t q0, size_t q1, size_t s0, size_t s1, size_t min_size) const

size_t	GetLongestSeg (size_t q0, size_t q1, size_t s0, size_t s1) const

virtual size_t	GetElemSize (void) const

virtual TScore	ScoreFromTranscript (const TTranscript &transcript, size_t start1=kMax_UInt, size_t start2=kMax_UInt) const

void	EnableMultipleThreads (bool enable=true)

size_t	MakePattern (const size_t hit_size=100, const size_t core_size=28)

CRef< objects::CDense_seg >	GetDense_seg (TSeqPos query_start, objects::ENa_strand query_strand, TSeqPos subj_start, objects::ENa_strand subj_strand, bool trim_end_gaps=false) const

CRef< objects::CDense_seg >	GetDense_seg (TSeqPos query_start, objects::ENa_strand query_strand, const objects::CSeq_id &query_id, TSeqPos subj_start, objects::ENa_strand subj_strand, const objects::CSeq_id &subj_id, bool trim_end_gaps=false) const

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 TScore	GetDefaultWm (void)

static TScore	GetDefaultWms (void)

static TScore	GetDefaultWg (void)

static TScore	GetDefaultWs (void)

static size_t	GetDefaultSpaceLimit (void)

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
size_t	x_CheckSequence (const char *seq, size_t len) const

virtual bool	x_CheckMemoryLimit (void)

unsigned char	x_CalcFingerPrint64 (const char beg, const char end, size_t &err_index)

const char *	x_FindFingerPrint64 (const char beg, const char end, unsigned char fingerprint, size_t size, size_t &err_index)

virtual TScore	x_Run (void)

virtual TScore	x_Align (SAlignInOut *data)

void	x_DoBackTrace (const CBacktraceMatrix4 &backtrace, SAlignInOut *data)

virtual ETranscriptSymbol	x_GetDiagTS (size_t i1, size_t i2) const

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

Protected Attributes
TScore	m_Wm

TScore	m_Wms

TScore	m_Wg

TScore	m_Ws

bool	m_esf_L1

bool	m_esf_R1

bool	m_esf_L2

bool	m_esf_R2

bool	m_SmithWaterman

EGapPreference	m_GapPreference

const char *	m_abc

SNCBIFullScoreMatrix	m_ScoreMatrix

bool	m_ScoreMatrixInvalid

FProgressCallback	m_prg_callback

SProgressInfo	m_prg_info

bool	m_terminate

vector< char >	m_Seq1Vec

const char *	m_Seq1

size_t	m_SeqLen1

vector< char >	m_Seq2Vec

const char *	m_Seq2

size_t	m_SeqLen2

TTranscript	m_Transcript

bool	m_PositivesAsMatches

TScore	m_score

vector< size_t >	m_guides

bool	m_mt

size_t	m_maxthreads

size_t	m_MaxMem

Private Member Functions
void	x_SWDoBackTrace (const CBacktraceMatrix4 &backtrace, SAlignInOut *data)

Friends
class	CNWAlignerThread_Align

Additional Inherited Members
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

Definition at line 69 of file nw_aligner.hpp.

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

include/algo/align/nw/nw_aligner.hpp
src/algo/align/nw/nw_aligner.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description