#include <util/math/matrix.hpp>

Inheritance diagram for CNcbiMatrix< T >:

Collaboration diagram for CNcbiMatrix< T >:

Public Types
typedef vector< T >	TData

typedef TData::iterator	iterator

typedef TData::const_iterator	const_iterator

Public Member Functions
	CNcbiMatrix ()
	default ctor More...

	CNcbiMatrix (size_t r, size_t c, T val=T())

void	Identity (size_t size)
	make this matrix an identity matrix of a given size More...

void	Identity ()
	make this matrix an identity matrix More...

void	Diagonal (size_t size, T val)
	make this matrix a diagonal matrix of a given size, with a given value on the diagonal More...

void	Diagonal (T val)
	make this matrix a diagonal matrix, with a given value on the diagonal More...

void	Transpose ()
	transpose this matrix More...

void	Resize (size_t i, size_t j, T val=T())
	resize this matrix, filling the empty cells with a known value More...

void	SwapRows (size_t i, size_t j)
	swap two rows in the matrix More...

void	RemoveRow (size_t i)
	remove a given row in the matrix More...

void	RemoveCol (size_t i)
	remove a given column in the matrix More...

size_t	GetRows () const
	get the number of rows in this matrix More...

size_t	GetCols () const
	get the number of columns in this matrix More...

TData &	GetData ()
	retrieve the data associated with this matrix More...

const TData &	GetData () const

iterator	begin ()
	iterators More...

iterator	end ()

const_iterator	begin () const

const_iterator	end () const

void	Set (T val)
	set all values in the matrix to a known value More...

void	Swap (CNcbiMatrix< T > &M)
	swap two matrices efficiently More...

const T &	operator[] (size_t i) const
	operator[] for raw data indexing More...

T &	operator[] (size_t i)

const T &	operator() (size_t i, size_t j) const
	operator() for row/column indexing More...

T &	operator() (size_t i, size_t j)

Protected Attributes
TData	m_Data
	the data strip we use More...

size_t	m_Rows
	size of this matrix More...

size_t	m_Cols

Detailed Description

template<class T>
class CNcbiMatrix< T >

Definition at line 46 of file matrix.hpp.

Member Typedef Documentation

◆ const_iterator

template<class T >

typedef TData::const_iterator CNcbiMatrix< T >::const_iterator

Definition at line 51 of file matrix.hpp.

◆ iterator

template<class T >

typedef TData::iterator CNcbiMatrix< T >::iterator

Definition at line 50 of file matrix.hpp.

◆ TData

template<class T >

typedef vector<T> CNcbiMatrix< T >::TData

Definition at line 49 of file matrix.hpp.

Constructor & Destructor Documentation

◆ CNcbiMatrix() [1/2]

template<class T >

CNcbiMatrix< T >::CNcbiMatrix

inline

default ctor

Definition at line 281 of file matrix.hpp.

◆ CNcbiMatrix() [2/2]

template<class T >

CNcbiMatrix< T >::CNcbiMatrix	(	size_t	r,
		size_t	c,
		T	val = `T()`
	)

inline

Definition at line 289 of file matrix.hpp.

References CNcbiMatrix< T >::m_Data, r(), and val.

Member Function Documentation

◆ begin() [1/2]

template<class T >

CNcbiMatrix< T >::iterator CNcbiMatrix< T >::begin ( void )

inline

iterators

Definition at line 325 of file matrix.hpp.

Referenced by operator*(), operator*=(), operator+(), operator+=(), operator-(), operator-=(), operator/=(), and CClusterer::SetDistMatrix().

◆ begin() [2/2]

template<class T >

CNcbiMatrix< T >::const_iterator CNcbiMatrix< T >::begin ( void ) const

inline

Definition at line 339 of file matrix.hpp.

◆ Diagonal() [1/2]

template<class T >

void CNcbiMatrix< T >::Diagonal	(	size_t	size,
		T	val
	)

inline

make this matrix a diagonal matrix of a given size, with a given value on the diagonal

Definition at line 461 of file matrix.hpp.

References i, ncbi::grid::netcache::search::fields::size, T, and val.

◆ Diagonal() [2/2]

template<class T >

void CNcbiMatrix< T >::Diagonal ( T val )

inline

make this matrix a diagonal matrix, with a given value on the diagonal

Definition at line 449 of file matrix.hpp.

References _ASSERT, i, T, and val.

◆ end() [1/2]

template<class T >

CNcbiMatrix< T >::iterator CNcbiMatrix< T >::end ( void )

inline

Definition at line 332 of file matrix.hpp.

Referenced by operator*(), operator*=(), operator+(), operator+=(), operator-(), operator-=(), operator/=(), and CClusterer::SetDistMatrix().

◆ end() [2/2]

template<class T >

CNcbiMatrix< T >::const_iterator CNcbiMatrix< T >::end ( void ) const

inline

Definition at line 346 of file matrix.hpp.

◆ GetCols()

template<class T >

size_t CNcbiMatrix< T >::GetCols

inline

get the number of columns in this matrix

Definition at line 305 of file matrix.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CMatrixScoringMethod::CalculateScores(), CDistanceMatrix::FromMatrix(), CBDB_BlobDeMux::GetCoordinates(), CDistMethods::GrishinDist(), CDistMethods::GrishinGeneralDist(), CDistMethods::JukesCantorDist(), CDistMethods::KimuraDist(), CBDB_BlobDeMuxPersistent::Load(), CBDB_BlobDeMux::NewPlane(), operator*(), operator*=(), operator+(), operator+=(), operator-(), operator-=(), operator<<(), operator==(), operator>>(), CDistMethods::PoissonDist(), s_CheckAgainstNullData(), s_CheckDistMatrix(), CBDB_BlobDeMuxPersistent::Save(), CClusterer::SetDistMatrix(), SNcbiMatrix2DoubleMatrix::SNcbiMatrix2DoubleMatrix(), CMultiAligner::x_AddRpsFreqsToCluster(), CMultiAligner::x_AlignMSAs(), CMatrixScoringMethod::x_CalculateConsensusRange(), CMatrixScoringMethod::x_CalculateNonConsensusRange(), CMultiAligner::x_ComputeTree(), and CTreeBuilderJob::x_CreateProjectItems().

◆ GetData() [1/2]

template<class T >

CNcbiMatrix< T >::TData & CNcbiMatrix< T >::GetData ( void )

inline

retrieve the data associated with this matrix

Definition at line 312 of file matrix.hpp.

Referenced by CDistMethods::AllFinite(), operator*(), operator==(), and CBlastTabularInfo::SetFields().

◆ GetData() [2/2]

template<class T >

const CNcbiMatrix< T >::TData & CNcbiMatrix< T >::GetData ( void ) const

inline

Definition at line 319 of file matrix.hpp.

◆ GetRows()

template<class T >

size_t CNcbiMatrix< T >::GetRows ( void ) const

inline

get the number of rows in this matrix

Definition at line 298 of file matrix.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CMatrixScoringMethod::CalculateScores(), CDistMethods::FastMeTree(), CDistanceMatrix::FromMatrix(), CBDB_BlobDeMux::GetCoordinates(), CDistMethods::GrishinDist(), CDistMethods::GrishinGeneralDist(), CSequence::InsertGaps(), CDistMethods::JukesCantorDist(), CDistMethods::KimuraDist(), CBDB_BlobDeMuxPersistent::Load(), CBDB_BlobDeMux::NewPlane(), CDistMethods::NjTree(), operator*(), operator*=(), operator+(), operator+=(), operator-(), operator-=(), operator<<(), operator==(), operator>>(), CDistMethods::PoissonDist(), s_CheckAgainstNullData(), s_CheckDistMatrix(), s_FindDistAsMax(), s_FindDistAsMean(), s_FindMaxDistFromElem(), s_FindSumDistFromElem(), CBDB_BlobDeMuxPersistent::Save(), CClusterer::SetDistMatrix(), SNcbiMatrix2DoubleMatrix::SNcbiMatrix2DoubleMatrix(), CMultiAligner::x_AddRpsFreqsToCluster(), CMultiAligner::x_AlignMSAs(), CPhyTreeCalc::x_CalcDistMatrix(), CMatrixScoringMethod::x_CalculateConsensusRange(), CMatrixScoringMethod::x_CalculateNonConsensusRange(), CMultiAligner::x_ComputeTree(), CPhyTreeCalc::x_ComputeTree(), and CMultiAligner::x_MakeClusterResidueFrequencies().

◆ Identity() [1/2]

template<class T >

void CNcbiMatrix< T >::Identity

inline

make this matrix an identity matrix

Definition at line 425 of file matrix.hpp.

References _ASSERT, i, and T.

◆ Identity() [2/2]

template<class T >

void CNcbiMatrix< T >::Identity ( size_t size )

inline

make this matrix an identity matrix of a given size

Definition at line 437 of file matrix.hpp.

References i, ncbi::grid::netcache::search::fields::size, and T.

◆ operator()() [1/2]

template<class T >

T & CNcbiMatrix< T >::operator()	(	size_t	i,
		size_t	j
	)

inline

Definition at line 380 of file matrix.hpp.

References _ASSERT, and i.

◆ operator()() [2/2]

template<class T >

const T & CNcbiMatrix< T >::operator()	(	size_t	i,
		size_t	j
	)		const

inline

operator() for row/column indexing

Definition at line 370 of file matrix.hpp.

References _ASSERT, and i.

◆ operator[]() [1/2]

template<class T >

T & CNcbiMatrix< T >::operator[] ( size_t i )

inline

Definition at line 362 of file matrix.hpp.

References _ASSERT, and i.

◆ operator[]() [2/2]

template<class T >

const T & CNcbiMatrix< T >::operator[] ( size_t i ) const

inline

operator[] for raw data indexing

Definition at line 354 of file matrix.hpp.

References _ASSERT, and i.

◆ RemoveCol()

template<class T >

void CNcbiMatrix< T >::RemoveCol ( size_t i )

inline

remove a given column in the matrix

Definition at line 525 of file matrix.hpp.

References _ASSERT, and r().

◆ RemoveRow()

template<class T >

void CNcbiMatrix< T >::RemoveRow ( size_t i )

inline

remove a given row in the matrix

Definition at line 510 of file matrix.hpp.

References _ASSERT, and r().

◆ Resize()

template<class T >

void CNcbiMatrix< T >::Resize	(	size_t	i,
		size_t	j,
		T	val = `T()`
	)

inline

resize this matrix, filling the empty cells with a known value

Definition at line 390 of file matrix.hpp.

References i, min(), r(), and val.

Referenced by CDistanceMatrix::AsMatrix(), BOOST_AUTO_TEST_CASE(), CMatrixScoringMethod::CMatrixScoringMethod(), TKmerMethods< TKmerCounts >::ComputeDistMatrix(), CDistances::ComputeMatrix(), CAlignFormatUtil::GetAsciiProteinMatrix(), CClusterer::GetClusterDistMatrix(), CBDB_BlobDeMux::GetCoordinates(), CSequence::InsertGaps(), CBDB_BlobDeMuxPersistent::Load(), CMatrixScoringMethod::Load(), CBDB_BlobDeMux::NewPlane(), CDistMethods::NjTree(), NodeToDistMat(), operator>>(), CSequence::Reset(), s_ReadDistMatrix(), CPhyTreeCalc::x_CalcDistMatrix(), CMultiAligner::x_ComputeTree(), and CPhyTreeCalc::x_ComputeTree().

◆ Set()

template<class T >

void CNcbiMatrix< T >::Set ( T val )

inline

set all values in the matrix to a known value

Definition at line 417 of file matrix.hpp.

References val.

Referenced by CDistanceMatrix::AsMatrix(), CDistances::ComputeMatrix(), and CSequence::Reset().

◆ Swap()

template<class T >

void CNcbiMatrix< T >::Swap ( CNcbiMatrix< T > & M )

inline

swap two matrices efficiently

Definition at line 501 of file matrix.hpp.

References CNcbiMatrix< T >::m_Cols, CNcbiMatrix< T >::m_Data, CNcbiMatrix< T >::m_Rows, and swap().

Referenced by CSequence::InsertGaps(), operator>>(), and CSequence::PropagateGaps().

◆ SwapRows()

template<class T >

void CNcbiMatrix< T >::SwapRows	(	size_t	i,
		size_t	j
	)

inline

swap two rows in the matrix

Definition at line 489 of file matrix.hpp.

References i, and swap().

◆ Transpose()

template<class T >

void CNcbiMatrix< T >::Transpose

inline

transpose this matrix

Definition at line 473 of file matrix.hpp.

References i, and swap().

Member Data Documentation

◆ m_Cols

template<class T >

size_t CNcbiMatrix< T >::m_Cols

protected

Definition at line 121 of file matrix.hpp.

Referenced by CNcbiMatrix< T >::Swap().

◆ m_Data

template<class T >

TData CNcbiMatrix< T >::m_Data

protected

the data strip we use

Definition at line 117 of file matrix.hpp.

Referenced by CNcbiMatrix< T >::CNcbiMatrix(), and CNcbiMatrix< T >::Swap().

◆ m_Rows

template<class T >

size_t CNcbiMatrix< T >::m_Rows

protected

size of this matrix

Definition at line 120 of file matrix.hpp.

Referenced by CNcbiMatrix< T >::Swap().

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

include/util/math/matrix.hpp

Public Types

Public Member Functions

Protected Attributes

Detailed Description

template<class T> class CNcbiMatrix< T >

Member Typedef Documentation

◆ const_iterator

◆ iterator

◆ TData

Constructor & Destructor Documentation

◆ CNcbiMatrix() [1/2]

◆ CNcbiMatrix() [2/2]

Member Function Documentation

◆ begin() [1/2]

◆ begin() [2/2]

◆ Diagonal() [1/2]

◆ Diagonal() [2/2]

◆ end() [1/2]

◆ end() [2/2]

◆ GetCols()

◆ GetData() [1/2]

◆ GetData() [2/2]

◆ GetRows()

◆ Identity() [1/2]

◆ Identity() [2/2]

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ RemoveCol()

◆ RemoveRow()

◆ Resize()

◆ Set()

◆ Swap()

◆ SwapRows()

◆ Transpose()

Member Data Documentation

◆ m_Cols

◆ m_Data

◆ m_Rows

template<class T>
class CNcbiMatrix< T >