Represents ASN.1 type Hit defined in file blastxml.asn

A generalized representation of a pairwise alignment. More...

#include <algo/cobalt/hit.hpp>

Inheritance diagram for CHit:

Collaboration diagram for CHit:

Public Types
typedef vector< CHit * >	TSubHit
	Hits can be grouped hierarchically. More...

Public Types inherited from CHit_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_num , e_id , e_def , e_accession , e_len , e_hsps , e__allMandatory = 0 , e_num , e_description , e_len , e_hsps }

enum class	E_memberIndex { e__allMandatory = 0 , e_num , e_id , e_def , e_accession , e_len , e_hsps , e__allMandatory = 0 , e_num , e_description , e_len , e_hsps }

typedef int	TNum

typedef string	TId

typedef string	TDef

typedef string	TAccession

typedef int	TLen

typedef list< CRef< CHsp > >	THsps

typedef Tparent::CMemberIndex< E_memberIndex, 7 >	TmemberIndex

typedef int	TNum

typedef list< CRef< CHitDescr > >	TDescription

typedef int	TLen

typedef list< CRef< CHsp > >	THsps

typedef Tparent::CMemberIndex< E_memberIndex, 5 >	TmemberIndex

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
	CHit (int seq1_index, int seq2_index)
	Create an empty alignment. More...

	CHit (int seq1_index, int seq2_index, BlastHSP *hsp)
	Create an alignment from a BLAST hit. More...

	CHit (int seq1_index, int seq2_index, int score, const objects::CDense_seg &denseg)
	Create an alignment from a Dense_seg. More...

	CHit (int seq1_index, int seq2_index, int score, const objects::CDense_diag &dendiag)
	Create an alignment from a Dense_diag. More...

	CHit (int seq1_index, int seq2_index, TRange seq_range1, TRange seq_range2, int score, CEditScript edit_script)
	Create an alignment with all specified parameters. More...

	~CHit ()
	Destructor. More...

void	InsertSubHit (CHit *hit)
	Add a to a CHit's list of subhits. More...

TSubHit &	GetSubHit ()
	Retrieve a list of subhits. More...

CEditScript &	GetEditScript ()
	Retrieve the traceback associated with a CHit. More...

bool	HasSubHits ()
	Query if a CHit has a hierarchy of subhits available. More...

void	AddUpSubHits ()
	Sum the score of all subhits, and make the sequence ranges the union of the ranges of all subhits. More...

CHit *	Clone ()
	Produce an independent copy of a CHit. More...

void	GetRangeFromSeq2 (TRange seq_range2, TRange &seq_range1, TRange &new_seq_range2, TRange &traceback_range)
	Retrieve the seq1 range corresponding to a specified seq2 range. More...

void	GetRangeFromSeq1 (TRange seq_range1, TRange &new_seq_range1, TRange &seq_range2, TRange &traceback_range)
	Retrieve the seq2 range corresponding to a specified seq1 range. More...

void	VerifyHit ()
	Perform basic integrity checks on a CHit. More...

void	ResolveSubHitConflicts (CSequence &seq1, int **seq2_pssm, CNWAligner::TScore gap_open, CNWAligner::TScore gap_extend)
	If pairs of subhits have overlapping ranges, either delete one or change one so that the overlap is avoided. More...

	CHit (void)

	~CHit (void)

	CHit (void)

	~CHit (void)

Public Member Functions inherited from CHit_Base
	CHit_Base (void)

virtual	~CHit_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetNum (void) const
	hit number Check if a value has been assigned to Num data member. More...

bool	CanGetNum (void) const
	Check if it is safe to call GetNum method. More...

void	ResetNum (void)
	Reset Num data member. More...

TNum	GetNum (void) const
	Get the Num member data. More...

void	SetNum (TNum value)
	Assign a value to Num data member. More...

TNum &	SetNum (void)
	Assign a value to Num data member. More...

bool	IsSetId (void) const
	SeqId of subject Check if a value has been assigned to Id data member. More...

bool	CanGetId (void) const
	Check if it is safe to call GetId method. More...

void	ResetId (void)
	Reset Id data member. More...

const TId &	GetId (void) const
	Get the Id member data. More...

void	SetId (const TId &value)
	Assign a value to Id data member. More...

void	SetId (TId &&value)

TId &	SetId (void)
	Assign a value to Id data member. More...

bool	IsSetDef (void) const
	definition line of subject Check if a value has been assigned to Def data member. More...

bool	CanGetDef (void) const
	Check if it is safe to call GetDef method. More...

void	ResetDef (void)
	Reset Def data member. More...

const TDef &	GetDef (void) const
	Get the Def member data. More...

void	SetDef (const TDef &value)
	Assign a value to Def data member. More...

void	SetDef (TDef &&value)

TDef &	SetDef (void)
	Assign a value to Def data member. More...

bool	IsSetAccession (void) const
	accession Check if a value has been assigned to Accession data member. More...

bool	CanGetAccession (void) const
	Check if it is safe to call GetAccession method. More...

void	ResetAccession (void)
	Reset Accession data member. More...

const TAccession &	GetAccession (void) const
	Get the Accession member data. More...

void	SetAccession (const TAccession &value)
	Assign a value to Accession data member. More...

void	SetAccession (TAccession &&value)

TAccession &	SetAccession (void)
	Assign a value to Accession data member. More...

bool	IsSetLen (void) const
	length of subject Check if a value has been assigned to Len data member. More...

bool	CanGetLen (void) const
	Check if it is safe to call GetLen method. More...

void	ResetLen (void)
	Reset Len data member. More...

TLen	GetLen (void) const
	Get the Len member data. More...

void	SetLen (TLen value)
	Assign a value to Len data member. More...

TLen &	SetLen (void)
	Assign a value to Len data member. More...

bool	IsSetHsps (void) const
	all HSP regions for the given subject Check if a value has been assigned to Hsps data member. More...

bool	CanGetHsps (void) const
	Check if it is safe to call GetHsps method. More...

void	ResetHsps (void)
	Reset Hsps data member. More...

const THsps &	GetHsps (void) const
	Get the Hsps member data. More...

THsps &	SetHsps (void)
	Assign a value to Hsps data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

	CHit_Base (void)

virtual	~CHit_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetNum (void) const
	hit number Check if a value has been assigned to Num data member. More...

bool	CanGetNum (void) const
	Check if it is safe to call GetNum method. More...

void	ResetNum (void)
	Reset Num data member. More...

TNum	GetNum (void) const
	Get the Num member data. More...

void	SetNum (TNum value)
	Assign a value to Num data member. More...

TNum &	SetNum (void)
	Assign a value to Num data member. More...

bool	IsSetDescription (void) const
	ID, title, and taxonomy for each entry in the PIG Check if a value has been assigned to Description data member. More...

bool	CanGetDescription (void) const
	Check if it is safe to call GetDescription method. More...

void	ResetDescription (void)
	Reset Description data member. More...

const TDescription &	GetDescription (void) const
	Get the Description member data. More...

TDescription &	SetDescription (void)
	Assign a value to Description data member. More...

bool	IsSetLen (void) const
	length of subject Check if a value has been assigned to Len data member. More...

bool	CanGetLen (void) const
	Check if it is safe to call GetLen method. More...

void	ResetLen (void)
	Reset Len data member. More...

TLen	GetLen (void) const
	Get the Len member data. More...

void	SetLen (TLen value)
	Assign a value to Len data member. More...

TLen &	SetLen (void)
	Assign a value to Len data member. More...

bool	IsSetHsps (void) const
	all HSP regions for the given subject Check if a value has been assigned to Hsps data member. More...

bool	CanGetHsps (void) const
	Check if it is safe to call GetHsps method. More...

void	ResetHsps (void)
	Reset Hsps data member. More...

const THsps &	GetHsps (void) const
	Get the Hsps member data. More...

THsps &	SetHsps (void)
	Assign a value to Hsps data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...

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...

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

Public Attributes
int	m_SeqIndex1
	Numerical identifier for first sequence in alignment. More...

int	m_SeqIndex2
	Numerical identifier for second sequence in alignment. More...

int	m_Score
	Score of alignment. More...

TRange	m_SeqRange1
	The range of offsets on the first sequence. More...

TRange	m_SeqRange2
	The range of offsets on the second sequence. More...

Static Public Attributes
static const int	kMinHitSize = 2
	Not always used, but useful to avoid extremely small hits. More...

Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

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...

Private Types
typedef CHit_Base	Tparent

typedef CHit_Base	Tparent

Private Member Functions
	CHit (const CHit &value)

CHit &	operator= (const CHit &value)

	CHit (const CHit &value)

CHit &	operator= (const CHit &value)

Private Attributes
CEditScript	m_EditScript
	Traceback for this alignment. More...

vector< CHit * >	m_SubHit
	Subhits for this alignment. More...

Additional Inherited Members
Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (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 inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

A generalized representation of a pairwise alignment.

CHit –.

Definition at line 85 of file hit.hpp.

Member Typedef Documentation

◆ TSubHit

typedef vector<CHit *> CHit::TSubHit

Hits can be grouped hierarchically.

Definition at line 93 of file hit.hpp.

Constructor & Destructor Documentation

◆ CHit() [1/5]

CHit::CHit	(	int	seq1_index,
		int	seq2_index
	)

inline

Create an empty alignment.

Parameters

seq1_index	Numerical identifier for first sequence [in]
seq2_index	Numerical identifier for second sequence [in]

Definition at line 116 of file hit.hpp.

◆ CHit() [2/5]

CHit::CHit	(	int	seq1_index,
		int	seq2_index,
		BlastHSP *	hsp
	)

inline

Create an alignment from a BLAST hit.

Parameters

seq1_index	Numerical identifier for first sequence [in]
seq2_index	Numerical identifier for second sequence [in]
hsp	A single pairwise alignment from a blast hit [in]

Definition at line 125 of file hit.hpp.

◆ CHit() [3/5]

CHit::CHit	(	int	seq1_index,
		int	seq2_index,
		int	score,
		const objects::CDense_seg &	denseg
	)

Create an alignment from a Dense_seg.

Parameters

seq1_index	Numerical identifier for first sequence [in]
seq2_index	Numerical identifier for second sequence [in]
score	The score of the pairwise alignment [in]
denseg	Dense_seg representing a single pairwise alignment from a blast hit [in]

◆ CHit() [4/5]

CHit::CHit	(	int	seq1_index,
		int	seq2_index,
		int	score,
		const objects::CDense_diag &	dendiag
	)

Create an alignment from a Dense_diag.

Parameters

seq1_index	Numerical identifier for first sequence [in]
seq2_index	Numerical identifier for second sequence [in]
score	The score of the pairwise alignment [in]
dendiag	Dense_seg representing a single ungapped pairwise alignment from a blast hit [in]

◆ CHit() [5/5]

CHit::CHit	(	int	seq1_index,
		int	seq2_index,
		TRange	seq_range1,
		TRange	seq_range2,
		int	score,
		CEditScript	edit_script
	)

inline

Create an alignment with all specified parameters.

Parameters

seq1_index	Numerical identifier for first sequence [in]
seq2_index	Numerical identifier for second sequence [in]
seq_range1	Offsets on the first sequence [in]
seq_range2	Offsets on the second sequence [in]
score	The score of the alignment [in]
edit_script	Traceback for the alignment (may be empty) [in]

Definition at line 160 of file hit.hpp.

◆ ~CHit()

BEGIN_blastxml2_SCOPE CHit::~CHit ( void )

inline

Destructor.

Definition at line 170 of file hit.hpp.

References i, and int.

Member Function Documentation

◆ AddUpSubHits()

void CHit::AddUpSubHits ( )

Sum the score of all subhits, and make the sequence ranges the union of the ranges of all subhits.

Traceback is ignored

Definition at line 87 of file hit.cpp.

References _ASSERT, COpenRange< Position >::CombineWith(), HasSubHits(), i, int, m_Score, m_SeqRange1, m_SeqRange2, and m_SubHit.

Referenced by CHitList::MatchOverlappingSubHits(), and CMultiAligner::x_RealignBlocks().

◆ Clone()

CHit * CHit::Clone ( )

Produce an independent copy of a CHit.

Returns: Pointer to the copy

Definition at line 378 of file hit.cpp.

References CHit(), GetSubHit(), HasSubHits(), InsertSubHit(), m_EditScript, m_Score, m_SeqIndex1, m_SeqIndex2, m_SeqRange1, m_SeqRange2, and NON_CONST_ITERATE.

◆ GetEditScript()

CEditScript& CHit::GetEditScript ( )

inline

Retrieve the traceback associated with a CHit.

Returns: The traceback

Definition at line 190 of file hit.hpp.

Referenced by CHitList::MakeCanonical(), ResolveSubHitConflicts(), CMultiAligner::x_AssignRPSResFreqs(), CMultiAligner::x_FindInClusterConstraints(), and CMultiAligner::x_RealignBlocks().

◆ GetRangeFromSeq1()

void CHit::GetRangeFromSeq1	(	TRange	seq_range1,
		TRange &	new_seq_range1,
		TRange &	seq_range2,
		TRange &	traceback_range
	)

Retrieve the seq2 range corresponding to a specified seq1 range.

Assumes traceback is valid

Parameters

seq_range1	The target range on the first sequence [in]
new_seq_range1	If seq_range1 starts or ends in a gap on seq_range2, the range is shortened to exclude the gap and seq_range1 is cropped to compensate [out]
seq_range2	The corresponding range on the second sequence [out]
traceback_range	The range of traceback operations corresponding to seq_range1 and new_seq_range2 [out]

Definition at line 145 of file hit.cpp.

References _ASSERT, CLocalRange< Position >::Contains(), CEditScript::FindOffsetFromSeq1(), CRange_Base::GetFrom(), CRange_Base::GetTo(), m_EditScript, m_SeqRange1, m_SeqRange2, CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by ResolveSubHitConflicts().

◆ GetRangeFromSeq2()

void CHit::GetRangeFromSeq2	(	TRange	seq_range2,
		TRange &	seq_range1,
		TRange &	new_seq_range2,
		TRange &	traceback_range
	)

Retrieve the seq1 range corresponding to a specified seq2 range.

Assumes traceback is valid

Parameters

seq_range2	The target range on the second sequence [in]
seq_range1	The corresponding range on the first sequence [out]
new_seq_range2	If seq_range2 starts or ends in a gap on seq_range1, the range is shortened to exclude the gap and seq_range2 is cropped to compensate [out]
traceback_range	The range of traceback operations corresponding to seq_range1 and new_seq_range2 [out]

Definition at line 109 of file hit.cpp.

References _ASSERT, CLocalRange< Position >::Contains(), CEditScript::FindOffsetFromSeq2(), CRange_Base::GetFrom(), CRange_Base::GetTo(), m_EditScript, m_SeqRange1, m_SeqRange2, CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by x_MatchSubHits(), and CMultiAligner::x_RealignBlocks().

◆ GetSubHit()

TSubHit& CHit::GetSubHit ( )

inline

Retrieve a list of subhits.

Returns: The list of subhits

Definition at line 185 of file hit.hpp.

Referenced by Clone(), CHitList::MakeCanonical(), CHitList::MatchOverlappingSubHits(), CMultiAligner::x_AssignRPSResFreqs(), CMultiAligner::x_FindConstraints(), CMultiAligner::x_FindDomainHits(), x_HitToConstraints(), and CMultiAligner::x_MakeFillerBlocks().

◆ HasSubHits()

bool CHit::HasSubHits ( )

inline

Query if a CHit has a hierarchy of subhits available.

Returns: true if subhits are available

Definition at line 195 of file hit.hpp.

Referenced by AddUpSubHits(), Clone(), CHitList::MakeCanonical(), CHitList::MatchOverlappingSubHits(), CMultiAligner::x_AssignRPSResFreqs(), CMultiAligner::x_FindConstraints(), x_HitToConstraints(), CMultiAligner::x_MakeFillerBlocks(), and CMultiAligner::x_RealignBlocks().

◆ InsertSubHit()

void CHit::InsertSubHit ( CHit * hit )

inline

Add a to a CHit's list of subhits.

Parameters

hit	The hit to add [in]

Definition at line 180 of file hit.hpp.

Referenced by Clone(), CHitList::MatchOverlappingSubHits(), CMultiAligner::x_FindConstraints(), and CMultiAligner::x_RealignBlocks().

◆ ResolveSubHitConflicts()

void CHit::ResolveSubHitConflicts	(	CSequence &	seq1,
		int **	seq2_pssm,
		CNWAligner::TScore	gap_open,
		CNWAligner::TScore	gap_extend
	)

If pairs of subhits have overlapping ranges, either delete one or change one so that the overlap is avoided.

Only the sequence 1 range is checked for overlap; in practice, the hits refer to block alignments derived from RPS blast results, and sequence 2 is an RPS database sequence. It is sequence 1 that matters for later processing

Parameters

seq1	The sequence data corresponding to the first sequence [in]
seq2_pssm	The PSSM for the second sequence [in]
gap_open	Penalty for opening a gap [in]
gap_extend	Penalty for extending a gap [in]

Definition at line 285 of file hit.cpp.

References CHit(), GetEditScript(), CRange_Base::GetFrom(), GetRangeFromSeq1(), CEditScript::GetScore(), CRange_Base::GetTo(), i, m_Score, m_SeqIndex1, m_SeqIndex2, m_SeqRange1, m_SeqRange2, m_SubHit, CEditScript::MakeEditScript(), CLocalRange< Position >::StrictlyBelow(), and x_RemoveEnvelopedSubHits().

Referenced by CMultiAligner::x_RealignBlocks().

◆ VerifyHit()

void CHit::VerifyHit ( )

Perform basic integrity checks on a CHit.

Definition at line 180 of file hit.cpp.

References _ASSERT, COpenRange< Position >::Empty(), m_EditScript, m_SeqRange1, m_SeqRange2, and CEditScript::VerifyScript().

Member Data Documentation

◆ kMinHitSize

const int CHit::kMinHitSize = 2

static

Not always used, but useful to avoid extremely small hits.

Definition at line 90 of file hit.hpp.

Referenced by CMultiAligner::x_MakeFillerBlocks(), x_MatchSubHits(), and CMultiAligner::x_RealignBlocks().

◆ m_EditScript

CEditScript CHit::m_EditScript

private

Traceback for this alignment.

Definition at line 267 of file hit.hpp.

Referenced by Clone(), GetRangeFromSeq1(), GetRangeFromSeq2(), and VerifyHit().

◆ m_Score

◆ m_SeqIndex1

int CHit::m_SeqIndex1

Numerical identifier for first sequence in alignment.

Definition at line 97 of file hit.hpp.

◆ m_SeqIndex2

int CHit::m_SeqIndex2

Numerical identifier for second sequence in alignment.

Definition at line 101 of file hit.hpp.

◆ m_SeqRange1

TRange CHit::m_SeqRange1

The range of offsets on the first sequence.

Definition at line 107 of file hit.hpp.

◆ m_SeqRange2

TRange CHit::m_SeqRange2

The range of offsets on the second sequence.

Definition at line 110 of file hit.hpp.

◆ m_SubHit

vector<CHit *> CHit::m_SubHit

private

Subhits for this alignment.

Definition at line 268 of file hit.hpp.

Referenced by AddUpSubHits(), and ResolveSubHitConflicts().

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

include/algo/cobalt/hit.hpp
src/algo/cobalt/hit.cpp

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TSubHit

Constructor & Destructor Documentation

◆ CHit() [1/5]

◆ CHit() [2/5]

◆ CHit() [3/5]

◆ CHit() [4/5]

◆ CHit() [5/5]

◆ ~CHit()

Member Function Documentation

◆ AddUpSubHits()

◆ Clone()

◆ GetEditScript()

◆ GetRangeFromSeq1()

◆ GetRangeFromSeq2()

◆ GetSubHit()

◆ HasSubHits()

◆ InsertSubHit()

◆ ResolveSubHitConflicts()

◆ VerifyHit()

Member Data Documentation

◆ kMinHitSize

◆ m_EditScript

◆ m_Score

◆ m_SeqIndex1

◆ m_SeqIndex2

◆ m_SeqRange1

◆ m_SeqRange2

◆ m_SubHit