Search Toolkit Book for CCompareSeqRegions

Compare multiple feature annotations on the specified seq_locs. More...

#include <algo/sequence/compare_feats.hpp>

Inheritance diagram for CCompareSeqRegions:

Collaboration diagram for CCompareSeqRegions:

Public Types
enum	EScoreMethod { eScore_SymmetricPctOverlap , eScore_Feat1PctOverlap , eScore_Feat2PctOverlap }

enum	EComparisonOptions { fSelectBest = (1<<0) , fMergeExons = (1<<1) , fDifferentGenesOnly = (1<<2) , fCreateSentinelGenes = (1<<3) , fSameTypeOnly = (1<<4) }

typedef int	TComparisonOptions

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
	CCompareSeqRegions (const CSeq_loc &query_loc, CScope q_scope, CScope t_scope, ILocMapper &mapper, const SAnnotSelector &q_sel, const SAnnotSelector &t_sel, const CSeq_id &target_id, TComparisonOptions options=fSelectBest\|fMergeExons, EScoreMethod score_method=eScore_SymmetricPctOverlap)

void	Rewind ()

TComparisonOptions &	SetOptions ()

TComparisonOptions	GetOptions () const

const CSeq_loc &	GetQueryLoc () const

bool	NextComparisonGroup (vector< CRef< CCompareFeats > > &v)
	Return the next group of comparisons on the region (return true iff found any) A group is a set of features on the query region where each feature overlaps at least one other feature in the group. More...

void	SelectMatches (vector< CRef< CCompareFeats > > &v)

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 int	s_GetGeneId (const CSeq_feat &feat)

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 Member Functions
void	x_GetPutativeMatches (vector< CRef< CCompareFeats > > &v, CConstRef< CSeq_feat > q_feat)

CConstRef< CSeq_loc >	x_GetSelfLoc (const CSeq_loc &loc, CScope *scope, bool merge_single_range)

Private Attributes
CConstRef< CSeq_loc >	m_loc_q

CScope *	m_scope_q

CScope *	m_scope_t

CRef< ILocMapper >	m_mapper

const SAnnotSelector &	m_selector_q

const SAnnotSelector &	m_selector_t

CConstRef< CSeq_id >	m_target_id

CRef< CSeq_loc_Mapper >	m_self_mapper_q

CRef< CSeq_loc_Mapper >	m_self_mapper_t

TComparisonOptions	m_comp_options

EScoreMethod	m_score_method

CFeat_CI	m_loc_q_ci

std::set< std::string >	m_seen_targets

bool	m_already_processed_unmatched_targets

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...

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

Detailed Description

Compare multiple feature annotations on the specified seq_locs.

Definition at line 487 of file compare_feats.hpp.

Member Typedef Documentation

◆ TComparisonOptions

typedef int CCompareSeqRegions::TComparisonOptions

Definition at line 504 of file compare_feats.hpp.

Member Enumeration Documentation

◆ EComparisonOptions

enum CCompareSeqRegions::EComparisonOptions

Enumerator
fSelectBest
fMergeExons
fDifferentGenesOnly
fCreateSentinelGenes
fSameTypeOnly

Definition at line 496 of file compare_feats.hpp.

◆ EScoreMethod

enum CCompareSeqRegions::EScoreMethod

Enumerator
eScore_SymmetricPctOverlap	length of overlap / (sum of lengths - overlaps)
eScore_Feat1PctOverlap	length of overlap / (length of 1st feat)
eScore_Feat2PctOverlap	length of overlap / (length of 2nd feat)

Definition at line 490 of file compare_feats.hpp.

Constructor & Destructor Documentation

◆ CCompareSeqRegions()

CCompareSeqRegions::CCompareSeqRegions	(	const CSeq_loc &	query_loc,
		CScope *	q_scope,
		CScope *	t_scope,
		ILocMapper &	mapper,
		const SAnnotSelector &	q_sel,
		const SAnnotSelector &	t_sel,
		const CSeq_id &	target_id,
		TComparisonOptions	options = `fSelectBest\|fMergeExons`,
		EScoreMethod	score_method = `eScore_SymmetricPctOverlap`
	)

inline

Definition at line 507 of file compare_feats.hpp.

References CSeq_id::Assign(), GetId(), m_scope_q, m_scope_t, m_seen_targets, m_self_mapper_q, m_self_mapper_t, CRef< C, Locker >::Reset(), and CSeq_loc::SetInt().

Member Function Documentation

◆ GetOptions()

TComparisonOptions CCompareSeqRegions::GetOptions ( void ) const

inline

Definition at line 561 of file compare_feats.hpp.

References m_comp_options.

Referenced by CXcompareAnnotsApplication::x_ProcessComparison().

◆ GetQueryLoc()

const CSeq_loc& CCompareSeqRegions::GetQueryLoc ( ) const

inline

Definition at line 563 of file compare_feats.hpp.

References m_loc_q.

Referenced by CXcompareAnnotsApplication::x_ProcessComparison().

◆ NextComparisonGroup()

bool CCompareSeqRegions::NextComparisonGroup ( vector< CRef< CCompareFeats > > & vComparisons )

Return the next group of comparisons on the region (return true iff found any) A group is a set of features on the query region where each feature overlaps at least one other feature in the group.

(normally related gene, introns, exons, mRNAs and CDSes). Comparison for each feature contains best match from the other sequence and their relationship. (may be more than one best) If cannot find matching (overlapping) feature of the same type on the target, choose the one(s) of the semantically closest type. TODO: need to report features on target unaccounted for in the reported comparisons

Definition at line 731 of file compare_feats.cpp.

References _TRACE, CSeq_loc::Add(), Compare(), dummy, CSeq_loc_Base::e_not_set, eNoOverlap, fCompareOverlapping, fFGL_Both, CSeq_loc::fMerge_All, CSeq_loc::fMerge_SingleRange, fSelectBest, GetLabel(), CSeq_loc::GetLabel(), GetLength(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsNull(), ITERATE, label, CCompareSeq_locs::m_scope_t, Seq_loc_Add(), Seq_loc_Subtract(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), SAnnotSelector::SetOverlapIntervals(), and CSeq_loc_Base::Which().

Referenced by CXcompareAnnotsApplication::x_ProcessComparison().

◆ Rewind()

void CCompareSeqRegions::Rewind ( )

inline

Definition at line 555 of file compare_feats.hpp.

References m_loc_q_ci, m_seen_targets, and CFeat_CI::Rewind().

◆ s_GetGeneId()

int CCompareSeqRegions::s_GetGeneId ( const CSeq_feat & feat )

static

◆ SelectMatches()

void CCompareSeqRegions::SelectMatches ( vector< CRef< CCompareFeats > > & v )

Definition at line 1035 of file compare_feats.cpp.

References set< Key, Compare >::end(), ERR_POST, fFGL_Both, set< Key, Compare >::find(), GetLabel(), i, Info(), set< Key, Compare >::insert(), CRef< C, Locker >::IsNull(), CConstRef< C, Locker >::IsNull(), and ITERATE.

◆ SetOptions()

TComparisonOptions& CCompareSeqRegions::SetOptions ( void )

inline

Definition at line 560 of file compare_feats.hpp.

References m_comp_options.

◆ x_GetPutativeMatches()

void CCompareSeqRegions::x_GetPutativeMatches	(	vector< CRef< CCompareFeats > > &	v,
		CConstRef< CSeq_feat >	q_feat
	)

private

◆ x_GetSelfLoc()

CConstRef< CSeq_loc > CCompareSeqRegions::x_GetSelfLoc	(	const CSeq_loc &	loc,
		CScope *	scope,
		bool	merge_single_range
	)

private

Definition at line 943 of file compare_feats.cpp.

References CSeq_loc::fMerge_SingleRange, CRef< C, Locker >::IsNull(), IsOneBioseq(), CSeq_loc_Mapper_Base::Map(), and Seq_loc_Merge().

Member Data Documentation

◆ m_already_processed_unmatched_targets

bool CCompareSeqRegions::m_already_processed_unmatched_targets

private

Definition at line 592 of file compare_feats.hpp.

◆ m_comp_options

TComparisonOptions CCompareSeqRegions::m_comp_options

private

Definition at line 586 of file compare_feats.hpp.

Referenced by GetOptions(), and SetOptions().

◆ m_loc_q

CConstRef<CSeq_loc> CCompareSeqRegions::m_loc_q

private

Definition at line 577 of file compare_feats.hpp.

Referenced by GetQueryLoc().

◆ m_loc_q_ci

CFeat_CI CCompareSeqRegions::m_loc_q_ci

private

Definition at line 588 of file compare_feats.hpp.

Referenced by Rewind().

◆ m_mapper

CRef<ILocMapper> CCompareSeqRegions::m_mapper

private

Definition at line 580 of file compare_feats.hpp.

◆ m_scope_q

CScope* CCompareSeqRegions::m_scope_q

private

Definition at line 578 of file compare_feats.hpp.

Referenced by CCompareSeqRegions().

◆ m_scope_t

CScope* CCompareSeqRegions::m_scope_t

private

Definition at line 579 of file compare_feats.hpp.

Referenced by CCompareSeqRegions().

◆ m_score_method

EScoreMethod CCompareSeqRegions::m_score_method

private

Definition at line 587 of file compare_feats.hpp.

◆ m_seen_targets

std::set<std::string> CCompareSeqRegions::m_seen_targets

private

Definition at line 589 of file compare_feats.hpp.

Referenced by CCompareSeqRegions(), and Rewind().

◆ m_selector_q

const SAnnotSelector& CCompareSeqRegions::m_selector_q

private

Definition at line 581 of file compare_feats.hpp.

◆ m_selector_t

const SAnnotSelector& CCompareSeqRegions::m_selector_t

private

Definition at line 582 of file compare_feats.hpp.

◆ m_self_mapper_q

CRef<CSeq_loc_Mapper> CCompareSeqRegions::m_self_mapper_q

private

Definition at line 584 of file compare_feats.hpp.

Referenced by CCompareSeqRegions().

◆ m_self_mapper_t

CRef<CSeq_loc_Mapper> CCompareSeqRegions::m_self_mapper_t

private

Definition at line 585 of file compare_feats.hpp.

Referenced by CCompareSeqRegions().

◆ m_target_id

CConstRef<CSeq_id> CCompareSeqRegions::m_target_id

private

Definition at line 583 of file compare_feats.hpp.

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

include/algo/sequence/compare_feats.hpp
src/algo/sequence/compare_feats.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TComparisonOptions

Member Enumeration Documentation

◆ EComparisonOptions

◆ EScoreMethod

Constructor & Destructor Documentation

◆ CCompareSeqRegions()

Member Function Documentation

◆ GetOptions()

◆ GetQueryLoc()

◆ NextComparisonGroup()

◆ Rewind()

◆ s_GetGeneId()

◆ SelectMatches()

◆ SetOptions()

◆ x_GetPutativeMatches()

◆ x_GetSelfLoc()

Member Data Documentation

◆ m_already_processed_unmatched_targets

◆ m_comp_options

◆ m_loc_q

◆ m_loc_q_ci

◆ m_mapper

◆ m_scope_q

◆ m_scope_t

◆ m_score_method

◆ m_seen_targets

◆ m_selector_q

◆ m_selector_t

◆ m_self_mapper_q

◆ m_self_mapper_t

◆ m_target_id