#include <algo/align/util/blast_tabular.hpp>

Inheritance diagram for CBlastTabular:

Collaboration diagram for CBlastTabular:

Public Types
typedef CAlignShadow	TParent

typedef TParent::TCoord	TCoord

typedef int(*	SCORE_FUNC) (const CRef< objects::CSeq_id > &id)
	Construct CBlastTabular from m8 line, use score_func to select seq-id from FASTA-style ids. More...

Public Types inherited from CAlignShadow
typedef CConstRef< objects::CSeq_id >	TId

typedef TSeqPos	TCoord

typedef string	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
	CBlastTabular (void)

	CBlastTabular (const objects::CSeq_align &seq_align, bool save_xcript=false)

	CBlastTabular (const TId &idquery, TCoord qstart, bool qstrand, const TId &idsubj, TCoord sstart, bool sstrand, const string &xcript)

	CBlastTabular (const char *m8, bool force_local_ids=false)

	CBlastTabular (const char *m8, SCORE_FUNC score_func)

void	SetLength (TCoord length)

TCoord	GetLength (void) const

void	SetMismatches (TCoord mismatches)

TCoord	GetMismatches (void) const

void	SetGaps (TCoord gaps)

TCoord	GetGaps (void) const

void	SetRawScore (TCoord score)

TCoord	GetRawScore (void) const

void	SetEValue (double evalue)

double	GetEValue (void) const

void	SetIdentity (float identity)

float	GetIdentity (void) const

void	SetScore (float score)

float	GetScore (void) const

virtual void	Modify (Uint1 where, TCoord new_pos)

Public Member Functions inherited from CAlignShadow
	CAlignShadow (void)

	CAlignShadow (const objects::CSeq_align &seq_align, bool save_xcript=false)
	Create the object from a seq-align structure. More...

	CAlignShadow (const TId &idquery, TCoord qstart, bool qstrand, const TId &idsubj, TCoord sstart, bool sstrand, const string &xcript)
	Create the object from a transcript. More...

virtual	~CAlignShadow ()

const TId &	GetId (Uint1 where) const

const TId &	GetQueryId (void) const

const TId &	GetSubjId (void) const

void	SetId (Uint1 where, const TId &id)

void	SetQueryId (const TId &id)

void	SetSubjId (const TId &id)

bool	GetStrand (Uint1 where) const

bool	GetQueryStrand (void) const

bool	GetSubjStrand (void) const

void	SetStrand (Uint1 where, bool strand)

void	SetQueryStrand (bool strand)

void	SetSubjStrand (bool strand)

void	FlipStrands (void)

void	SwapQS (void)

const TCoord *	GetBox (void) const

void	SetBox (const TCoord box[4])

TCoord	GetMin (Uint1 where) const

TCoord	GetMax (Uint1 where) const

TCoord	GetQueryMin (void) const

TCoord	GetQueryMax (void) const

TCoord	GetSubjMin (void) const

TCoord	GetSubjMax (void) const

void	SetMax (Uint1 where, TCoord pos)

void	SetMin (Uint1 where, TCoord pos)

void	SetQueryMin (TCoord pos)

void	SetQueryMax (TCoord pos)

void	SetSubjMin (TCoord pos)

void	SetSubjMax (TCoord pos)

TCoord	GetQuerySpan (void) const

TCoord	GetSubjSpan (void) const

TCoord	GetStart (Uint1 where) const

TCoord	GetStop (Uint1 where) const

TCoord	GetQueryStart (void) const

TCoord	GetQueryStop (void) const

TCoord	GetSubjStart (void) const

TCoord	GetSubjStop (void) const

void	SetStop (Uint1 where, TCoord pos)

void	SetStart (Uint1 where, TCoord pos)

void	SetQueryStart (TCoord pos)

void	SetQueryStop (TCoord pos)

void	SetSubjStart (TCoord pos)

void	SetSubjStop (TCoord pos)

void	Shift (Int4 shift_query, Int4 shift_subj)

const TTranscript &	GetTranscript (void) 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

Protected Member Functions
template<class F >
void	x_Deserialize (const char *m8, F seq_id_extractor)

virtual void	x_PartialSerialize (CNcbiOstream &os) const

virtual void	x_PartialDeserialize (const char *m8)

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

Static Protected Member Functions
static void	sx_MineSegment (size_t where, const objects::CStd_seg::TLoc &locs, TSeqPos delta, TSeqPos prev)

Protected Attributes
TCoord	m_Length

TCoord	m_Mismatches

TCoord	m_Gaps

TCoord	m_RawScore

double	m_EValue

float	m_Identity

float	m_Score

Protected Attributes inherited from CAlignShadow
std::pair< TId, TId >	m_Id

TCoord	m_Box [4]

TTranscript	m_Transcript

Additional Inherited Members
Static Public Member Functions inherited from CAlignShadow
static string	s_RunLengthEncode (const string &in)

static string	s_RunLengthDecode (const string &in)

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...

Detailed Description

Definition at line 43 of file blast_tabular.hpp.

Member Typedef Documentation

◆ SCORE_FUNC

typedef int(* CBlastTabular::SCORE_FUNC) (const CRef< objects::CSeq_id > &id)

Construct CBlastTabular from m8 line, use score_func to select seq-id from FASTA-style ids.

Definition at line 63 of file blast_tabular.hpp.

◆ TCoord

typedef TParent::TCoord CBlastTabular::TCoord

Definition at line 48 of file blast_tabular.hpp.

◆ TParent

typedef CAlignShadow CBlastTabular::TParent

Definition at line 47 of file blast_tabular.hpp.

Constructor & Destructor Documentation

◆ CBlastTabular() [1/5]

CBlastTabular::CBlastTabular ( void )

inline

Definition at line 51 of file blast_tabular.hpp.

◆ CBlastTabular() [2/5]

CBlastTabular::CBlastTabular	(	const objects::CSeq_align &	seq_align,
		bool	save_xcript = `false`
	)

◆ CBlastTabular() [3/5]

CBlastTabular::CBlastTabular	(	const TId &	idquery,
		TCoord	qstart,
		bool	qstrand,
		const TId &	idsubj,
		TCoord	sstart,
		bool	sstrand,
		const string &	xcript
	)

Definition at line 233 of file blast_tabular.cpp.

References i, m_EValue, m_Gaps, m_Length, m_Mismatches, m_RawScore, m_Score, and SetIdentity().

◆ CBlastTabular() [4/5]

CBlastTabular::CBlastTabular	(	const char *	m8,
		bool	force_local_ids = `false`
	)

Definition at line 306 of file blast_tabular.cpp.

References x_Deserialize().

◆ CBlastTabular() [5/5]

CBlastTabular::CBlastTabular	(	const char *	m8,
		SCORE_FUNC	score_func
	)

Definition at line 314 of file blast_tabular.cpp.

References x_Deserialize().

Member Function Documentation

◆ GetEValue()

double CBlastTabular::GetEValue ( void ) const

Definition at line 418 of file blast_tabular.cpp.

References m_EValue.

Referenced by x_PartialSerialize().

◆ GetGaps()

CBlastTabular::TCoord CBlastTabular::GetGaps ( void ) const

Definition at line 390 of file blast_tabular.cpp.

References m_Gaps.

Referenced by Modify(), and x_PartialSerialize().

◆ GetIdentity()

float CBlastTabular::GetIdentity ( void ) const

Definition at line 445 of file blast_tabular.cpp.

References m_Identity.

Referenced by Modify(), and x_PartialSerialize().

◆ GetLength()

CBlastTabular::TCoord CBlastTabular::GetLength ( void ) const

Definition at line 362 of file blast_tabular.cpp.

References m_Length.

Referenced by Modify(), CElementaryMatching::x_CompartPair(), and x_PartialSerialize().

◆ GetMismatches()

CBlastTabular::TCoord CBlastTabular::GetMismatches ( void ) const

Definition at line 376 of file blast_tabular.cpp.

References m_Mismatches.

Referenced by Modify(), and x_PartialSerialize().

◆ GetRawScore()

CBlastTabular::TCoord CBlastTabular::GetRawScore ( void ) const

Definition at line 404 of file blast_tabular.cpp.

References m_RawScore.

Referenced by Modify().

◆ GetScore()

float CBlastTabular::GetScore ( void ) const

Definition at line 432 of file blast_tabular.cpp.

References m_Score.

Referenced by Modify(), CHitFilter< THit >::SHitEnd::operator<(), CCleanupAlignmentsJob::x_CreateProjectItems(), CAppHitFilter::x_DumpOutput(), and x_PartialSerialize().

◆ Modify()

void CBlastTabular::Modify	(	Uint1	where,
		TCoord	new_pos
	)

virtual

Reimplemented from CAlignShadow.

Definition at line 512 of file blast_tabular.cpp.

References GetGaps(), GetIdentity(), GetLength(), GetMismatches(), CAlignShadow::GetQuerySpan(), GetRawScore(), GetScore(), CAlignShadow::GetTranscript(), ITERATE, CAlignShadow::Modify(), NCBI_THROW, CAlignShadow::s_RunLengthDecode(), SetGaps(), SetLength(), SetMismatches(), SetRawScore(), and SetScore().

◆ SetEValue()

void CBlastTabular::SetEValue ( double evalue )

Definition at line 411 of file blast_tabular.cpp.

References m_EValue.

◆ SetGaps()

void CBlastTabular::SetGaps ( TCoord gaps )

Definition at line 383 of file blast_tabular.cpp.

References m_Gaps.

Referenced by Modify().

◆ SetIdentity()

void CBlastTabular::SetIdentity ( float identity )

Definition at line 438 of file blast_tabular.cpp.

References m_Identity.

Referenced by CBlastTabular().

◆ SetLength()

void CBlastTabular::SetLength ( TCoord length )

Definition at line 355 of file blast_tabular.cpp.

References m_Length.

Referenced by Modify().

◆ SetMismatches()

void CBlastTabular::SetMismatches ( TCoord mismatches )

Definition at line 369 of file blast_tabular.cpp.

References m_Mismatches.

Referenced by Modify().

◆ SetRawScore()

void CBlastTabular::SetRawScore ( TCoord score )

Definition at line 397 of file blast_tabular.cpp.

References m_RawScore.

Referenced by Modify().

◆ SetScore()

void CBlastTabular::SetScore ( float score )

Definition at line 425 of file blast_tabular.cpp.

References m_Score.

Referenced by Modify().

◆ sx_MineSegment()

void CBlastTabular::sx_MineSegment	(	size_t	where,
		const objects::CStd_seg::TLoc &	locs,
		TSeqPos *	delta,
		TSeqPos *	prev
	)

staticprotected

Definition at line 193 of file blast_tabular.cpp.

References delta(), eNa_strand_minus, CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_loc::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::IsInt(), NCBI_THROW, and prev().

◆ x_Deserialize()

template<class F >

void CBlastTabular::x_Deserialize	(	const char *	m8,
		F	seq_id_extractor
	)

protected

Definition at line 320 of file blast_tabular.cpp.

References isspace(), CAlignShadow::m_Id, NCBI_THROW, and x_PartialDeserialize().

Referenced by CBlastTabular().

◆ x_PartialDeserialize()

void CBlastTabular::x_PartialDeserialize ( const char * m8 )

protectedvirtual

Definition at line 471 of file blast_tabular.cpp.

References a, b, m_EValue, m_Gaps, m_Identity, m_Length, m_Mismatches, m_RawScore, m_Score, CAlignShadow::m_Transcript, NCBI_THROW, CAlignShadow::SetQueryStart(), CAlignShadow::SetQueryStop(), CAlignShadow::SetSubjStart(), and CAlignShadow::SetSubjStop().

Referenced by x_Deserialize().

◆ x_PartialSerialize()

void CBlastTabular::x_PartialSerialize ( CNcbiOstream & os ) const

protectedvirtual

Reimplemented from CAlignShadow.

Definition at line 455 of file blast_tabular.cpp.

References GetEValue(), GetGaps(), GetIdentity(), GetLength(), GetMismatches(), CAlignShadow::GetQueryStart(), CAlignShadow::GetQueryStop(), GetScore(), CAlignShadow::GetSubjStart(), CAlignShadow::GetSubjStop(), and CAlignShadow::m_Transcript.

Member Data Documentation

◆ m_EValue

double CBlastTabular::m_EValue

protected

Definition at line 96 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetEValue(), SetEValue(), and x_PartialDeserialize().

◆ m_Gaps

TCoord CBlastTabular::m_Gaps

protected

Definition at line 94 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetGaps(), SetGaps(), and x_PartialDeserialize().

◆ m_Identity

float CBlastTabular::m_Identity

protected

Definition at line 97 of file blast_tabular.hpp.

Referenced by GetIdentity(), SetIdentity(), and x_PartialDeserialize().

◆ m_Length

TCoord CBlastTabular::m_Length

protected

Definition at line 92 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetLength(), SetLength(), and x_PartialDeserialize().

◆ m_Mismatches

TCoord CBlastTabular::m_Mismatches

protected

Definition at line 93 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetMismatches(), SetMismatches(), and x_PartialDeserialize().

◆ m_RawScore

TCoord CBlastTabular::m_RawScore

protected

Definition at line 95 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetRawScore(), SetRawScore(), and x_PartialDeserialize().

◆ m_Score

float CBlastTabular::m_Score

protected

Definition at line 98 of file blast_tabular.hpp.

Referenced by CBlastTabular(), GetScore(), SetScore(), and x_PartialDeserialize().

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

include/algo/align/util/blast_tabular.hpp
src/algo/align/util/blast_tabular.cpp

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SCORE_FUNC

◆ TCoord

◆ TParent

Constructor & Destructor Documentation

◆ CBlastTabular() [1/5]

◆ CBlastTabular() [2/5]

◆ CBlastTabular() [3/5]

◆ CBlastTabular() [4/5]

◆ CBlastTabular() [5/5]

Member Function Documentation

◆ GetEValue()

◆ GetGaps()

◆ GetIdentity()

◆ GetLength()

◆ GetMismatches()

◆ GetRawScore()

◆ GetScore()

◆ Modify()

◆ SetEValue()

◆ SetGaps()

◆ SetIdentity()

◆ SetLength()

◆ SetMismatches()

◆ SetRawScore()

◆ SetScore()

◆ sx_MineSegment()

◆ x_Deserialize()

◆ x_PartialDeserialize()

◆ x_PartialSerialize()

Member Data Documentation

◆ m_EValue

◆ m_Gaps

◆ m_Identity

◆ m_Length

◆ m_Mismatches

◆ m_RawScore

◆ m_Score