CCompareFeats represens a result of comparison of two features. More...

#include <algo/sequence/compare_feats.hpp>

Inheritance diagram for CCompareFeats:

Collaboration diagram for CCompareFeats:

Public Member Functions
	CCompareFeats (const CSeq_feat &feat1, const CSeq_loc &feat1_mapped_loc, double mapped_identity, const CSeq_loc &feat1_self_loc, CScope scope1, const CSeq_feat &feat2, const CSeq_loc &feat2_self_loc, CScope scope2)

	CCompareFeats (const CSeq_feat &feat1, const CSeq_loc &feat1_mapped_loc, double mapped_identity, const CSeq_loc &feat1_self_loc, CScope *scope1)
	No matching feat2. More...

	CCompareFeats (const CSeq_feat &feat2, const CSeq_loc &feat2_self_loc, double mapped_identity, CScope *scope2)
	No matching feat1. More...

double	GetMappedIdentity () const

bool	IsSameSubtype () const

bool	IsSameType () const

bool	IsIdentical () const

CConstRef< CSeq_feat >	GetFeatQ () const

CConstRef< CSeq_feat >	GetFeatT () const

CConstRef< CSeq_loc >	GetMappedLocQ () const

CConstRef< CSeq_loc >	GetSelfLocQ () const

CConstRef< CSeq_loc >	GetSelfLocT () const

bool	IsMatch () const

CConstRef< CCompareSeq_locs >	GetComparison () const

int	GetIrrelevance () const

void	SetIrrelevance (int val)

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 string	s_GetLocLabel (const CSeq_loc &loc, bool merged=false)

static string	s_GetFeatLabel (const CSeq_feat &gene_feat, feature::TFeatLabelFlags type=feature::fFGL_Both)

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)

Private Attributes
CConstRef< CSeq_feat >	m_feat1

CConstRef< CSeq_loc >	m_feat1_mapped_loc

CConstRef< CSeq_loc >	m_feat1_self_loc

CScope *	m_scope_q

CConstRef< CSeq_feat >	m_feat2

CConstRef< CSeq_loc >	m_feat2_self_loc

CScope *	m_scope_t

CRef< CCompareSeq_locs >	m_compare

int	m_irrelevance

bool	m_unmatched

double	m_mapped_identity

Friends
CNcbiOstream &	operator<< (CNcbiOstream &out, const CCompareFeats &cf)

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...

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

Detailed Description

CCompareFeats represens a result of comparison of two features.

(CCompareFeats::m_compare stores the actual result) These comparisons will be produces by CCompare_Regions

Definition at line 349 of file compare_feats.hpp.

Constructor & Destructor Documentation

◆ CCompareFeats() [1/3]

CCompareFeats::CCompareFeats	(	const CSeq_feat &	feat1,
		const CSeq_loc &	feat1_mapped_loc,
		double	mapped_identity,
		const CSeq_loc &	feat1_self_loc,
		CScope *	scope1,
		const CSeq_feat &	feat2,
		const CSeq_loc &	feat2_self_loc,
		CScope *	scope2
	)

inline

Definition at line 352 of file compare_feats.hpp.

◆ CCompareFeats() [2/3]

CCompareFeats::CCompareFeats	(	const CSeq_feat &	feat1,
		const CSeq_loc &	feat1_mapped_loc,
		double	mapped_identity,
		const CSeq_loc &	feat1_self_loc,
		CScope *	scope1
	)

inline

No matching feat2.

Parameters

feat1_mapped_loc mapped to feat2's coordinate system

Definition at line 374 of file compare_feats.hpp.

◆ CCompareFeats() [3/3]

CCompareFeats::CCompareFeats	(	const CSeq_feat &	feat2,
		const CSeq_loc &	feat2_self_loc,
		double	mapped_identity,
		CScope *	scope2
	)

inline

No matching feat1.

Definition at line 388 of file compare_feats.hpp.

Member Function Documentation

◆ GetComparison()

CConstRef<CCompareSeq_locs> CCompareFeats::GetComparison ( ) const

inline

Definition at line 461 of file compare_feats.hpp.

References m_compare.

◆ GetFeatQ()

CConstRef<CSeq_feat> CCompareFeats::GetFeatQ ( ) const

inline

Definition at line 453 of file compare_feats.hpp.

References m_feat1.

◆ GetFeatT()

CConstRef<CSeq_feat> CCompareFeats::GetFeatT ( ) const

inline

Definition at line 454 of file compare_feats.hpp.

References m_feat2.

◆ GetIrrelevance()

int CCompareFeats::GetIrrelevance ( ) const

inline

Definition at line 464 of file compare_feats.hpp.

References m_irrelevance.

◆ GetMappedIdentity()

double CCompareFeats::GetMappedIdentity ( ) const

inline

Definition at line 402 of file compare_feats.hpp.

References m_mapped_identity.

Referenced by operator<<().

◆ GetMappedLocQ()

CConstRef<CSeq_loc> CCompareFeats::GetMappedLocQ ( ) const

inline

Definition at line 456 of file compare_feats.hpp.

References m_feat1_mapped_loc.

◆ GetSelfLocQ()

CConstRef<CSeq_loc> CCompareFeats::GetSelfLocQ ( ) const

inline

Definition at line 457 of file compare_feats.hpp.

References m_feat1_self_loc.

◆ GetSelfLocT()

CConstRef<CSeq_loc> CCompareFeats::GetSelfLocT ( ) const

inline

Definition at line 458 of file compare_feats.hpp.

References m_feat2_self_loc.

◆ IsIdentical()

bool CCompareFeats::IsIdentical ( ) const

inline

Definition at line 425 of file compare_feats.hpp.

References CCompareSeq_locs::fCmp_Match, CCompareSeq_locs::GetResult(), IsMatch(), m_compare, m_feat1, m_feat2, and s_GetFeatLabel().

◆ IsMatch()

bool CCompareFeats::IsMatch ( ) const

inline

Definition at line 460 of file compare_feats.hpp.

References CConstRef< C, Locker >::IsNull(), m_feat1, and m_feat2.

Referenced by IsIdentical(), IsSameSubtype(), and IsSameType().

◆ IsSameSubtype()

bool CCompareFeats::IsSameSubtype ( ) const

inline

Definition at line 408 of file compare_feats.hpp.

References CSeq_feat_Base::CanGetData(), CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), IsMatch(), m_feat1, and m_feat2.

◆ IsSameType()

bool CCompareFeats::IsSameType ( ) const

inline

Definition at line 416 of file compare_feats.hpp.

References CSeq_feat_Base::CanGetData(), CSeq_feat_Base::GetData(), IsMatch(), m_feat1, m_feat2, and CSeqFeatData_Base::Which().

◆ s_GetFeatLabel()

static string CCompareFeats::s_GetFeatLabel	(	const CSeq_feat &	gene_feat,
		feature::TFeatLabelFlags	type = `feature::fFGL_Both`
	)

inlinestatic

Definition at line 445 of file compare_feats.hpp.

References GetLabel(), and NULL.

Referenced by IsIdentical(), and operator<<().

◆ s_GetLocLabel()

static string CCompareFeats::s_GetLocLabel	(	const CSeq_loc &	loc,
		bool	merged = `false`
	)

inlinestatic

Definition at line 432 of file compare_feats.hpp.

References CSeq_loc::fMerge_SingleRange, CSeq_loc::GetLabel(), NULL, and Seq_loc_Merge().

Referenced by operator<<().

◆ SetIrrelevance()

void CCompareFeats::SetIrrelevance ( int val )

inline

Definition at line 465 of file compare_feats.hpp.

References m_irrelevance, and val.

Friends And Related Function Documentation

◆ operator<<

CNcbiOstream& operator<<	(	CNcbiOstream &	out,
		const CCompareFeats &	cf
	)

friend

Definition at line 134 of file compare_feats.cpp.

Member Data Documentation

◆ m_compare

CRef<CCompareSeq_locs> CCompareFeats::m_compare

private

Definition at line 478 of file compare_feats.hpp.

Referenced by GetComparison(), IsIdentical(), and operator<<().

◆ m_feat1

CConstRef<CSeq_feat> CCompareFeats::m_feat1

private

Definition at line 467 of file compare_feats.hpp.

Referenced by GetFeatQ(), IsIdentical(), IsMatch(), IsSameSubtype(), IsSameType(), and operator<<().

◆ m_feat1_mapped_loc

CConstRef<CSeq_loc> CCompareFeats::m_feat1_mapped_loc

private

Definition at line 468 of file compare_feats.hpp.

Referenced by GetMappedLocQ(), and operator<<().

◆ m_feat1_self_loc

CConstRef<CSeq_loc> CCompareFeats::m_feat1_self_loc

private

Definition at line 469 of file compare_feats.hpp.

Referenced by GetSelfLocQ().

◆ m_feat2

CConstRef<CSeq_feat> CCompareFeats::m_feat2

private

Definition at line 473 of file compare_feats.hpp.

Referenced by GetFeatT(), IsIdentical(), IsMatch(), IsSameSubtype(), IsSameType(), and operator<<().

◆ m_feat2_self_loc

CConstRef<CSeq_loc> CCompareFeats::m_feat2_self_loc

private

Definition at line 474 of file compare_feats.hpp.

Referenced by GetSelfLocT().

◆ m_irrelevance

int CCompareFeats::m_irrelevance

private

Definition at line 479 of file compare_feats.hpp.

Referenced by GetIrrelevance(), and SetIrrelevance().

◆ m_mapped_identity

double CCompareFeats::m_mapped_identity

private

Definition at line 481 of file compare_feats.hpp.

Referenced by GetMappedIdentity().

◆ m_scope_q

CScope* CCompareFeats::m_scope_q

private

Definition at line 470 of file compare_feats.hpp.

◆ m_scope_t

CScope* CCompareFeats::m_scope_t

private

Definition at line 475 of file compare_feats.hpp.

◆ m_unmatched

bool CCompareFeats::m_unmatched

private

Definition at line 480 of file compare_feats.hpp.

Referenced by operator<<().

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

include/algo/sequence/compare_feats.hpp

Public Member Functions

Static Public Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CCompareFeats() [1/3]

◆ CCompareFeats() [2/3]

◆ CCompareFeats() [3/3]

Member Function Documentation

◆ GetComparison()

◆ GetFeatQ()

◆ GetFeatT()

◆ GetIrrelevance()

◆ GetMappedIdentity()

◆ GetMappedLocQ()

◆ GetSelfLocQ()

◆ GetSelfLocT()

◆ IsIdentical()

◆ IsMatch()

◆ IsSameSubtype()

◆ IsSameType()

◆ s_GetFeatLabel()

◆ s_GetLocLabel()

◆ SetIrrelevance()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ m_compare

◆ m_feat1

◆ m_feat1_mapped_loc

◆ m_feat1_self_loc

◆ m_feat2

◆ m_feat2_self_loc

◆ m_irrelevance

◆ m_mapped_identity

◆ m_scope_q

◆ m_scope_t

◆ m_unmatched