An asymmetric two-dimensional matrix. More...

#include <fullmatrix.h>

Public Member Functions
void	Reset ()
	Empties the matrix and deallocates all associated memory.
tType **const	Get () const
	Return the two-dimensional array backing the matrix.
tType *	Get (size_t iY) const
	Return a single row of the matrix.
tType &	Get (size_t iY, size_t iX) const
	Returns the value at the requested matrix position.
void	Set (size_t iY, size_t iX, const tType &Value)
	Set the value at the requested matrix position.
void	Set (size_t iY, const tType *aValues)
	Set a single row of the matrix.
void	Initialize (const CFullMatrix &Mat)
	Create a new matrix using a reference to the given matrix.
virtual void	Initialize (size_t iR, size_t iC, tType **aaData=NULL)
	Create a new matrix of the requested size and, optionally, referencing the given data.
size_t	GetRows () const
	Return the number of rows in the matrix.
size_t	GetColumns () const
	Return the number of columns in the matrix.
bool	Open (std::istream &istm, bool fBinary)
	Loads a matrix from the given stream.
bool	Open (const char *szFile)
	Loads a matrix from the given filename, or standard input if null.
bool	Open (const CFullMatrix &Mat)
	Creates a copy of the given matrix's data.
bool	Save (std::ostream &ostm, bool fBinary) const
	Saves a matrix to the given stream in either binary or tab-delimited text format.
bool	Save (const char *szFile) const
	Saves a matrix to the given file in binary form; if null, save text to standard output.
bool	Save (const char *szFile, bool fBinary) const
	Saves a matrix to the given stream in either binary or tab-delimited text format.
void	Clear ()
	Sets all entries of the matrix to 0 without changing its size.
bool	AddRows (size_t iR, bool fClear=false)
	Increases the number of rows in the matrix by the requested amount.
bool	Multiply (std::vector< tType > &vecRight)
	Performs matrix multiplication by applying the given vector on the right of the current matrix.
bool	Multiply (const CFullMatrix &MatRight, bool fTranspose=false)
	Performs matrix multiplication by applying the given matrix on the right of the current matrix.
bool	SVD (CFullMatrix< tType > &MatU, CFullMatrix< tType > &MatV, std::vector< tType > &vecS) const
	Performs singular value decomposition of the current matrix.

Detailed Description

template<class tType>
class Sleipnir::CFullMatrix< tType >

An asymmetric two-dimensional matrix.

Parameters:

tType Type of element contained by the matrix.

Remarks:: Essentially nothing except a lack of bounds checking for efficiency's sake separates this from every other 2D matrix implementation known to man.

See also:: CCompactMatrix | CHalfMatrix

Definition at line 52 of file fullmatrix.h.

Member Function Documentation

template<class tType>

bool Sleipnir::CFullMatrix< tType >::AddRows	(	size_t	iR,
		bool	fClear = `false`
	)		`[inline]`

Increases the number of rows in the matrix by the requested amount.

Parameters:

iR	Number of rows to append to the matrix.
fClear	If true, set all values in the new rows to zero.

Returns:: True if the rows were appended successfully.

Remarks:: On success, GetRows will be increased by the requested amount. The news rows are not initialized to any particular value.

Definition at line 421 of file fullmatrix.h.

Referenced by Sleipnir::CPCL::AddGenes().

template<class tType>

tType** const Sleipnir::CFullMatrix< tType >::Get ( ) const [inline]

Return the two-dimensional array backing the matrix.

Returns:: Two-dimensional array backing the matrix.

Definition at line 82 of file fullmatrix.h.

Referenced by Sleipnir::CHMM::Add(), Sleipnir::CStatistics::CholeskyDecomposition(), Sleipnir::CClustKMeans::Cluster(), Sleipnir::CBayesNetMinimal::Evaluate(), Sleipnir::CPCLSet::Get(), Sleipnir::CHMM::Get(), Sleipnir::CPCL::Get(), Sleipnir::CDataSubset::GetContinuous(), Sleipnir::CDataSubset::GetDiscrete(), Sleipnir::CCoalesceMotifLibrary::GetKnown(), Sleipnir::CCoalesceMotifLibrary::GetPWM(), Sleipnir::CPST::GetPWM(), Sleipnir::CPCL::Impute(), Sleipnir::CDataSubset::IsExample(), Sleipnir::CStatistics::MatrixLUDecompose(), Sleipnir::CStatistics::MatrixLUDeterminant(), Sleipnir::CFullMatrix< CExampleImpl >::Multiply(), Sleipnir::CStatistics::MultivariateNormalCDF(), Sleipnir::CBayesNetSmile::Open(), Sleipnir::CPCL::Open(), Sleipnir::CFullMatrix< CExampleImpl >::Open(), Sleipnir::CDataSubset::Open(), Sleipnir::CPCL::OpenBinary(), Sleipnir::CSeekTools::ReadPlatforms(), Sleipnir::CDataSubset::Remove(), Sleipnir::CHMM::Save(), Sleipnir::CPCL::SortGenes(), and Sleipnir::CFullMatrix< CExampleImpl >::SVD().

template<class tType>

tType* Sleipnir::CFullMatrix< tType >::Get ( size_t iY ) const [inline]

Return a single row of the matrix.

Parameters:

iY	Matrix row.

Returns:: Requested matrix row.

Remarks:: For efficiency, no bounds checking is performed. The given row must be smaller than the size. The returned array will contain a number of elements equal to the number of columns.

See also:: Set

Definition at line 103 of file fullmatrix.h.

template<class tType>

tType& Sleipnir::CFullMatrix< tType >::Get	(	size_t	iY,
		size_t	iX
	)		const `[inline]`

Returns the value at the requested matrix position.

Parameters:

iY	Matrix row.
iX	Matrix column.

Returns:: Value at the requested matrix position.

Remarks:: For efficiency, no bounds checking is performed. The given row and column must be smaller than the size.

See also:: Set

Definition at line 127 of file fullmatrix.h.

template<class tType>

size_t Sleipnir::CFullMatrix< tType >::GetColumns ( ) const [inline]

Return the number of columns in the matrix.

Returns:: Number of columns in the matrix.

See also:: GetRows

Definition at line 243 of file fullmatrix.h.

Referenced by Sleipnir::CPCL::AddGenes(), Sleipnir::CFullMatrix< CExampleImpl >::AddRows(), Sleipnir::CStatistics::CholeskyDecomposition(), Sleipnir::CFullMatrix< CExampleImpl >::Clear(), Sleipnir::CClustKMeans::Cluster(), Sleipnir::CBayesNetMinimal::Evaluate(), Sleipnir::CHMM::Get(), Sleipnir::CCoalesceMotifLibrary::GetKnown(), Sleipnir::CCoalesceMotifLibrary::GetPWM(), Sleipnir::CFullMatrix< CExampleImpl >::Initialize(), Sleipnir::CStatistics::MatrixLUDecompose(), Sleipnir::CStatistics::MatrixLUDeterminant(), Sleipnir::CStatistics::MatrixLUInvert(), Sleipnir::CFullMatrix< CExampleImpl >::Multiply(), Sleipnir::CStatistics::MultivariateNormalCDF(), Sleipnir::CStatistics::MultivariateNormalPDF(), Sleipnir::CBayesNetSmile::Open(), Sleipnir::CPCL::Open(), Sleipnir::CFullMatrix< CExampleImpl >::Open(), Sleipnir::CDataSubset::Open(), Sleipnir::CSeekTools::ReadPlatforms(), Sleipnir::CHMM::Save(), Sleipnir::CFullMatrix< CExampleImpl >::Set(), Sleipnir::CHMM::SetUniform(), and Sleipnir::CFullMatrix< CExampleImpl >::SVD().

template<class tType>

size_t Sleipnir::CFullMatrix< tType >::GetRows ( ) const [inline]

Return the number of rows in the matrix.

Returns:: Number of rows in the matrix.

See also:: GetColumns

Definition at line 229 of file fullmatrix.h.

Referenced by Sleipnir::CPCL::AddGenes(), Sleipnir::CFullMatrix< CExampleImpl >::AddRows(), Sleipnir::CStatistics::CholeskyDecomposition(), Sleipnir::CFullMatrix< CExampleImpl >::Clear(), Sleipnir::CClustQTC::Cluster(), Sleipnir::CClustKMeans::Cluster(), Sleipnir::CBayesNetMinimal::Evaluate(), Sleipnir::CHMM::Get(), Sleipnir::CCoalesceMotifLibrary::GetKnown(), Sleipnir::CCoalesceMotifLibrary::GetPWM(), Sleipnir::CPST::GetPWM(), Sleipnir::CFullMatrix< CExampleImpl >::Initialize(), Sleipnir::CStatistics::MatrixLUDecompose(), Sleipnir::CStatistics::MatrixLUDeterminant(), Sleipnir::CStatistics::MatrixLUInvert(), Sleipnir::CFullMatrix< CExampleImpl >::Multiply(), Sleipnir::CStatistics::MultivariateNormalCDF(), Sleipnir::CStatistics::MultivariateNormalPDF(), Sleipnir::CBayesNetSmile::Open(), Sleipnir::CPCL::Open(), Sleipnir::CBayesNetMinimal::Open(), Sleipnir::CFullMatrix< CExampleImpl >::Open(), Sleipnir::CDataSubset::Open(), Sleipnir::CPCL::OpenBinary(), Sleipnir::CBayesNetMinimal::OpenCounts(), Sleipnir::CSeekTools::ReadPlatforms(), Sleipnir::CFullMatrix< CExampleImpl >::Reset(), Sleipnir::CHMM::Save(), Sleipnir::CHMM::SetUniform(), Sleipnir::CPCL::SortGenes(), and Sleipnir::CFullMatrix< CExampleImpl >::SVD().

template<class tType>

void Sleipnir::CFullMatrix< tType >::Initialize ( const CFullMatrix< tType > & Mat ) [inline]

Create a new matrix using a reference to the given matrix.

Parameters:

Mat	Matrix to duplicate in the created matrix.

Remarks:: A reference is held to the given matrix; it is not copied, so it should not be destroyed before the newly initialized matrix.

Definition at line 187 of file fullmatrix.h.

Referenced by Sleipnir::CClustKMeans::Cluster(), Sleipnir::CPST::GetPWM(), Sleipnir::CFullMatrix< CExampleImpl >::Initialize(), Sleipnir::CDataSubset::Initialize(), Sleipnir::CStatistics::MatrixLUInvert(), Sleipnir::CFullMatrix< CExampleImpl >::Multiply(), Sleipnir::CStatistics::MultivariateNormalPDF(), Sleipnir::CPCLSet::Open(), Sleipnir::CHMM::Open(), Sleipnir::CPCL::Open(), Sleipnir::CFullMatrix< CExampleImpl >::Open(), Sleipnir::CPCL::OpenBinary(), Sleipnir::CBayesNetMinimal::OpenCounts(), and Sleipnir::CFullMatrix< CExampleImpl >::SVD().

template<class tType>

virtual void Sleipnir::CFullMatrix< tType >::Initialize	(	size_t	iR,
		size_t	iC,
		tType **	aaData = `NULL`
	)		`[inline, virtual]`

Create a new matrix of the requested size and, optionally, referencing the given data.

Parameters:

iR	Matrix rows.
iC	Matrix columns.
aaData	If non-null, the memory that will back the newly created matrix.

Remarks:: A reference is held to the given memory; it is not copied, so it should not be destroyed before the newly initialized matrix.

Definition at line 208 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Multiply ( std::vector< tType > & vecRight ) [inline]

Performs matrix multiplication by applying the given vector on the right of the current matrix.

Parameters:

vecRight Vector by which current matrix is multiplied on the right.

Returns:: True on success, false if the given vector is of an inappropriate size.

Remarks:: vecRight must have the same number of entries as the current matrix has columns.

See also:: Multiply

Definition at line 456 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Multiply	(	const CFullMatrix< tType > &	MatRight,
		bool	fTranspose = `false`
	)		`[inline]`

Performs matrix multiplication by applying the given matrix on the right of the current matrix.

Parameters:

MatRight	Matrix by which current matrix is multiplied on the right.
fTranspose	If true, transpose MatRight prior to multiplication.

Returns:: True on success, false if MatRight is of inappropriate dimensions.

Remarks:: If fTranspose is false, MatRight must have the same number of rows as the current matrix has columns; if it is true, MatRight and the current matrix must have the same number of columns.

See also:: Multiply

Definition at line 488 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Open	(	std::istream &	istm,
		bool	fBinary
	)		`[inline]`

Loads a matrix from the given stream.

Parameters:

istm	Stream from which matrix is loaded.
fBinary	If true, matrix and stream are in binary format.

Returns:: True if matrix was loaded successfully.

Remarks:: A binary matrix is saved in row-major order and should have been produced using Save. A text matrix is a simple tab-delimited file from which matrix elements are read using >>.

Definition at line 264 of file fullmatrix.h.

Referenced by Sleipnir::CFullMatrix< CExampleImpl >::Multiply(), Sleipnir::CStatistics::MultivariateNormalPDF(), Sleipnir::CFullMatrix< CExampleImpl >::Open(), Sleipnir::CBayesNetMinimal::Open(), Sleipnir::CSeekTools::ReadPlatforms(), and Sleipnir::CFullMatrix< CExampleImpl >::SVD().

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Open ( const char * szFile ) [inline]

Loads a matrix from the given filename, or standard input if null.

Parameters:

szFile File from which binary matrix is opened; if null, use text from standard input.

Returns:: True if open was successful, false otherwise.

See also:: Save

Definition at line 281 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Open ( const CFullMatrix< tType > & Mat ) [inline]

Creates a copy of the given matrix's data.

Parameters:

Mat	Matrix from which data is copied.

Returns:: True if matrix was copied successfully.

Remarks:: Matrix will be resized if dimensions do not match exactly.

See also:: Initialize

Definition at line 307 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Save	(	std::ostream &	ostm,
		bool	fBinary
	)		const `[inline]`

Saves a matrix to the given stream in either binary or tab-delimited text format.

Parameters:

ostm	Stream to which matrix is saved.
fBinary	If true, matrix is saved in binary format; otherwise, matrix is saved as tab-delimited text.

Returns:: True if matrix was saved successfully.

Remarks:: A binary matrix is saved in row-major order; a text matrix is a simple tab-delimited file from which matrix elements are read using >>.

See also:: Open

Definition at line 338 of file fullmatrix.h.

Referenced by Sleipnir::CBayesNetMinimal::Save(), and Sleipnir::CFullMatrix< CExampleImpl >::Save().

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Save ( const char * szFile ) const [inline]

Saves a matrix to the given file in binary form; if null, save text to standard output.

Parameters:

szFile File in which binary matrix is saved; if null, text is saved to standard output.

Returns:: True if matrix was saved successfully.

See also:: Open

Definition at line 355 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::Save	(	const char *	szFile,
		bool	fBinary
	)		const `[inline]`

Saves a matrix to the given stream in either binary or tab-delimited text format.

Parameters:

szFile	File to which matrix is saved.
fBinary	If true, matrix is saved in binary format; otherwise, matrix is saved as tab-delimited text.

Returns:: True if matrix was saved successfully.

Remarks:: A binary matrix is saved in row-major order; a text matrix is a simple tab-delimited file from which matrix elements are read using >>.

See also:: Open

Definition at line 385 of file fullmatrix.h.

template<class tType>

void Sleipnir::CFullMatrix< tType >::Set	(	size_t	iY,
		size_t	iX,
		const tType &	Value
	)		`[inline]`

Set the value at the requested matrix position.

Parameters:

iY	Matrix row.
iX	Matrix column.
Value	Value to store.

Remarks:: For efficiency, no bounds checking is performed. The given row and column must be smaller than the size.

See also:: Get

Definition at line 151 of file fullmatrix.h.

Referenced by Sleipnir::CPCL::AddGenes(), Sleipnir::CStatistics::CholeskyDecomposition(), Sleipnir::CClustKMeans::Cluster(), Sleipnir::CStatistics::MatrixLUDecompose(), Sleipnir::CStatistics::MatrixLUInvert(), Sleipnir::CFullMatrix< CExampleImpl >::Multiply(), Sleipnir::CPCLSet::Open(), Sleipnir::CPCL::Open(), Sleipnir::CBayesNetMinimal::OpenCounts(), Sleipnir::CPCL::Set(), Sleipnir::CHMM::SetUniform(), and Sleipnir::CFullMatrix< CExampleImpl >::SVD().

template<class tType>

void Sleipnir::CFullMatrix< tType >::Set	(	size_t	iY,
		const tType *	aValues
	)		`[inline]`

Set a single row of the matrix.

Parameters:

iY	Matrix row.
aValues	Data to be copied into the requested row.

Remarks:: For efficiency, no bounds checking is performed. The given row must be smaller than the size, and the given data array must be at least as long as the number of columns.

See also:: Get

Definition at line 172 of file fullmatrix.h.

template<class tType>

bool Sleipnir::CFullMatrix< tType >::SVD	(	CFullMatrix< tType > &	MatU,
		CFullMatrix< tType > &	MatV,
		std::vector< tType > &	vecS
	)		const `[inline]`

Performs singular value decomposition of the current matrix.

Parameters:

MatU	Output U matrix of basis vectors.
MatV	Output V matrix of analysis vectors.
vecS	Output diagonal of Sigma matrix of singular values.

Returns:: True on success, false if the matrix cannot be decomposed.

Outputs a singular value decomposition of the current matrix M such that M = U * Sigma * V'. For a matrix of expression values, V behaves as eigengenes, U as eigenconditions, and S quantifies the variability (or weight) attributable to each eigengene.

Remarks:: Matrix must not contain any missing values. Implementation courtesy of AJ Sedgewick.

Definition at line 529 of file fullmatrix.h.

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

src/fullmatrix.h

Public Member Functions

Detailed Description

template<class tType> class Sleipnir::CFullMatrix< tType >

Member Function Documentation

template<class tType>
class Sleipnir::CFullMatrix< tType >