Search Toolkit Book for CGeneralScoreMatrix

Score matrix that can take any value. More...

#include <algo/blast/gumbel_params/general_score_matrix.hpp>

Inheritance diagram for CGeneralScoreMatrix:

Collaboration diagram for CGeneralScoreMatrix:

Public Types
enum	EScoreMatrixName { eBlosum45 , eBlosum62 , eBlosum80 , ePam30 , ePam70 , ePam250 }
	Names of standard scoring matrices. More...

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
	CGeneralScoreMatrix (EScoreMatrixName type, unsigned int sub_size=25)
	Creates a standard score matrix. More...

	CGeneralScoreMatrix (const Int4 *matrix, unsigned int size, const char alphabet=NULL)
	Creates user defined score matrix. More...

	CGeneralScoreMatrix (const vector< Int4 > &vals, const char *alphabet=NULL)
	Creates score matrix from values in a given vector. More...

	CGeneralScoreMatrix (const CGeneralScoreMatrix &matrix)
	Copy constructor. More...

	~CGeneralScoreMatrix ()
	Destructor. More...

const Int4 **	GetMatrix (void) const
	Access matrix values. More...

const char *	GetResidueOrder (void) const
	Get order of residues in the score matrix. More...

unsigned int	GetNumResidues (void) const
	Get number of residues. More...

Int4	GetScore (Uint4 i, Uint4 j) const
	Get score matrix entry for at specified position. More...

Int4	GetScore (char a, char b) const
	Return score matrix entry for a given pair of residues. 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...

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 Attributes
Int4 **	m_ScoreMatrix

char *	m_ResidueOrder

unsigned int	m_NumResidues

Private Member Functions
CGeneralScoreMatrix &	operator= (const CGeneralScoreMatrix &)
	Forbid assignment operator. More...

Additional Inherited Members
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...

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

Detailed Description

Score matrix that can take any value.

Definition at line 51 of file general_score_matrix.hpp.

Member Enumeration Documentation

◆ EScoreMatrixName

enum CGeneralScoreMatrix::EScoreMatrixName

Names of standard scoring matrices.

Enumerator
eBlosum45
eBlosum62
eBlosum80
ePam30
ePam70
ePam250

Definition at line 56 of file general_score_matrix.hpp.

Constructor & Destructor Documentation

◆ CGeneralScoreMatrix() [1/4]

CGeneralScoreMatrix::CGeneralScoreMatrix	(	CGeneralScoreMatrix::EScoreMatrixName	type,
		unsigned int	sub_size = `25`
	)

Creates a standard score matrix.

Parameters

type	Standard score matrix type [in]
sub_size	Number of rows and columns to copy [in]

Definition at line 48 of file general_score_matrix.cpp.

References eBlosum45, eBlosum62, eBlosum80, ePam250, ePam30, ePam70, i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, min(), NCBI_THROW, NCBISM_Blosum45, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, NCBISM_Unpack(), SNCBIFullScoreMatrix::s, and SNCBIPackedScoreMatrix::symbols.

◆ CGeneralScoreMatrix() [2/4]

CGeneralScoreMatrix::CGeneralScoreMatrix	(	const Int4 **	matrix,
		unsigned int	size,
		const char *	alphabet = `NULL`
	)

Creates user defined score matrix.

Matrix and alphabet are copied.

Parameters

matrix	Matrix values [in]
size	Number of alphabet elements [in]
alphabet	Alphabel symbols [in]

Definition at line 102 of file general_score_matrix.cpp.

References i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NULL.

◆ CGeneralScoreMatrix() [3/4]

CGeneralScoreMatrix::CGeneralScoreMatrix	(	const vector< Int4 > &	vals,
		const char *	alphabet = `NULL`
	)

Creates score matrix from values in a given vector.

Parameters

vals	Values for the score matrix as consecutive rows [in]
alphabet	Order of residues for the score matrix or NULL

Definition at line 125 of file general_score_matrix.cpp.

References _ASSERT, i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NULL.

◆ CGeneralScoreMatrix() [4/4]

CGeneralScoreMatrix::CGeneralScoreMatrix ( const CGeneralScoreMatrix & matrix )

Copy constructor.

Parameters

matrix Score matrix

Definition at line 149 of file general_score_matrix.cpp.

References GetResidueOrder(), i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NULL.

◆ ~CGeneralScoreMatrix()

CGeneralScoreMatrix::~CGeneralScoreMatrix ( )

Destructor.

Definition at line 171 of file general_score_matrix.cpp.

References m_ResidueOrder, m_ScoreMatrix, and NULL.

Member Function Documentation

◆ GetMatrix()

const Int4** CGeneralScoreMatrix::GetMatrix ( void ) const

inline

Access matrix values.

Returns: Pointer to matrix values

Definition at line 97 of file general_score_matrix.hpp.

◆ GetNumResidues()

unsigned int CGeneralScoreMatrix::GetNumResidues ( void ) const

inline

Get number of residues.

Returns: Number of residues

Definition at line 107 of file general_score_matrix.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CGumbelParamsOptions::Validate().

◆ GetResidueOrder()

const char* CGeneralScoreMatrix::GetResidueOrder ( void ) const

inline

Get order of residues in the score matrix.

Returns: Pointer to alphabet symbols

Definition at line 102 of file general_score_matrix.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and CGeneralScoreMatrix().

◆ GetScore() [1/2]

Int4 CGeneralScoreMatrix::GetScore	(	char	a,
		char	b
	)		const

Return score matrix entry for a given pair of residues.

Throws exception for illegal residues

Parameters

a	Residue 1 [in]
b	Residue 2 [in]

Returns: Score matrix value for a given pair of residues

Definition at line 193 of file general_score_matrix.cpp.

References a, b, i, m_NumResidues, m_ResidueOrder, m_ScoreMatrix, and NCBI_THROW.

◆ GetScore() [2/2]

Int4 CGeneralScoreMatrix::GetScore	(	Uint4	i,
		Uint4	j
	)		const

Get score matrix entry for at specified position.

Throws exception if index out of bounds

Parameters

i	Matrix row number [in]
j	Matrix column number [in]

Returns: Score matrix value at position i, j

Definition at line 183 of file general_score_matrix.cpp.

References i, m_NumResidues, m_ScoreMatrix, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), and CGumbelParamsOptions::Validate().

◆ operator=()

CGeneralScoreMatrix& CGeneralScoreMatrix::operator= ( const CGeneralScoreMatrix & )

private

Forbid assignment operator.

Member Data Documentation

◆ m_NumResidues

unsigned int CGeneralScoreMatrix::m_NumResidues

protected

Definition at line 132 of file general_score_matrix.hpp.

Referenced by CGeneralScoreMatrix(), and GetScore().

◆ m_ResidueOrder

char* CGeneralScoreMatrix::m_ResidueOrder

protected

Definition at line 131 of file general_score_matrix.hpp.

Referenced by CGeneralScoreMatrix(), GetScore(), and ~CGeneralScoreMatrix().

◆ m_ScoreMatrix

Int4** CGeneralScoreMatrix::m_ScoreMatrix

protected

Definition at line 130 of file general_score_matrix.hpp.

Referenced by CGeneralScoreMatrix(), GetScore(), and ~CGeneralScoreMatrix().

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

include/algo/blast/gumbel_params/general_score_matrix.hpp
src/algo/blast/gumbel_params/general_score_matrix.cpp

Public Types

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ EScoreMatrixName

Constructor & Destructor Documentation

◆ CGeneralScoreMatrix() [1/4]

◆ CGeneralScoreMatrix() [2/4]

◆ CGeneralScoreMatrix() [3/4]

◆ CGeneralScoreMatrix() [4/4]

◆ ~CGeneralScoreMatrix()

Member Function Documentation

◆ GetMatrix()

◆ GetNumResidues()

◆ GetResidueOrder()

◆ GetScore() [1/2]

◆ GetScore() [2/2]

◆ operator=()

Member Data Documentation

◆ m_NumResidues

◆ m_ResidueOrder

◆ m_ScoreMatrix