bpp-core3  3.0.0
Public Member Functions | List of all members
bpp::Matrix< Scalar > Class Template Referenceabstract

The matrix template interface. More...

#include <Bpp/Numeric/Matrix/Matrix.h>

+ Inheritance diagram for bpp::Matrix< Scalar >:
+ Collaboration diagram for bpp::Matrix< Scalar >:

Public Member Functions

 Matrix ()
 
virtual ~Matrix ()
 
virtual const Scalar & operator() (size_t i, size_t j) const =0
 
virtual Scalar & operator() (size_t i, size_t j)=0
 
virtual bool equals (const Matrix &m, double threshold=NumConstants::TINY())
 
virtual size_t getNumberOfRows () const =0
 
virtual size_t getNumberOfColumns () const =0
 
virtual std::vector< Scalar > row (size_t i) const =0
 
virtual std::vector< Scalar > col (size_t j) const =0
 
virtual void resize (size_t nRows, size_t nCols)=0
 Resize the matrix. More...
 
virtual Clonable * clone () const =0
 Create a copy of this object and send a pointer to it. More...
 

Detailed Description

template<class Scalar>
class bpp::Matrix< Scalar >

The matrix template interface.

Definition at line 59 of file Matrix.h.

Constructor & Destructor Documentation

◆ Matrix()

template<class Scalar >
bpp::Matrix< Scalar >::Matrix ( )
inline

Definition at line 63 of file Matrix.h.

◆ ~Matrix()

template<class Scalar >
virtual bpp::Matrix< Scalar >::~Matrix ( )
inlinevirtual

Definition at line 64 of file Matrix.h.

Member Function Documentation

◆ clone()

virtual Clonable* bpp::Clonable::clone ( ) const
pure virtualinherited

Create a copy of this object and send a pointer to it.

Returns
A pointer toward the copy object.

Implemented in bpp::TransformedParameter, bpp::MultipleDiscreteDistribution, bpp::DiscreteDistribution, bpp::ParameterListener, bpp::BppNumberI, bpp::HmmLikelihood, bpp::HmmEmissionProbabilities, bpp::Optimizer, bpp::OptimizationStopCondition, bpp::DerivableSecondOrder, bpp::DerivableFirstOrder, bpp::AbstractNumericalDerivative, bpp::Constraint, bpp::OutputStream, bpp::PlaceboTransformedParameter, bpp::IntervalTransformedParameter, bpp::RTransformedParameter, bpp::Table< T >, bpp::PrincipalComponentAnalysis, bpp::DualityDiagram, bpp::CorrespondenceAnalysis, bpp::ContingencyTableTest, bpp::Range< T >, bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::Simplex, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::ConstantDistribution, bpp::BetaDiscreteDistribution, bpp::ParametrizableCollection< N >, bpp::ParameterList, bpp::Parameter, bpp::ParameterEvent, bpp::BppUnsignedInteger, bpp::BppInteger, bpp::BppDouble, bpp::Number< T >, bpp::Number< double >, bpp::Number< int >, bpp::Number< unsigned int >, bpp::BppNotANumber, bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, bpp::FullHmmTransitionMatrix, bpp::AutoCorrelationTransitionMatrix, bpp::TwoPointsNumericalDerivative, bpp::ThreePointsNumericalDerivative, bpp::SimpleNewtonMultiDimensions, bpp::SimpleMultiDimensions, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::ReparametrizationFunctionWrapper, bpp::PowellMultiDimensions, bpp::PowellMultiDimensions::PMDStopCondition, bpp::FunctionStopCondition, bpp::ParametersStopCondition, bpp::NegativeOperator, bpp::MathOperator, bpp::FunctionOperator< F >, bpp::ConstantOperator, bpp::ComputationTree, bpp::BinaryOperator, bpp::NewtonOneDimension, bpp::NewtonBacktrackOneDimension, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::MetaOptimizer, bpp::MetaOptimizerInfos, bpp::GoldenSectionSearch, bpp::GoldenSectionSearch::GSSStopCondition, bpp::TestFunction, bpp::InfinityDerivableSecondOrderWrapper, bpp::InfinityDerivableFirstOrderWrapper, bpp::InfinityFunctionWrapper, bpp::FivePointsNumericalDerivative, bpp::DownhillSimplexMethod, bpp::DownhillSimplexMethod::DSMStopCondition, bpp::DirectionFunction, bpp::ConjugateGradientMultiDimensions, bpp::BrentOneDimension, bpp::BrentOneDimension::BODStopCondition, bpp::BfgsMultiDimensions, bpp::DataTable, bpp::IntervalConstraint, bpp::AutoParameter, bpp::AliasParameterListener, bpp::StdErr, bpp::StdOut, bpp::StlOutputStreamWrapper, bpp::StlOutputStream, bpp::NullOutputStream, bpp::RGBColor, bpp::Point2D< T >, bpp::Font, bpp::GlobalGraph, bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl >, bpp::BppVector< T >, bpp::BppString, and bpp::BppBoolean.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), and bpp::LogsumHmmLikelihood::operator=().

◆ col()

template<class Scalar >
virtual std::vector<Scalar> bpp::Matrix< Scalar >::col ( size_t  j) const
pure virtual
Returns
the column at position j as a vector.
Parameters
jThe index of the column.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

◆ equals()

template<class Scalar >
virtual bool bpp::Matrix< Scalar >::equals ( const Matrix< Scalar > &  m,
double  threshold = NumConstants::TINY() 
)
inlinevirtual

Definition at line 81 of file Matrix.h.

References bpp::Matrix< Scalar >::getNumberOfColumns(), and bpp::Matrix< Scalar >::getNumberOfRows().

◆ getNumberOfColumns()

template<class Scalar >
virtual size_t bpp::Matrix< Scalar >::getNumberOfColumns ( ) const
pure virtual
Returns
The number of columns.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

Referenced by bpp::PrincipalComponentAnalysis::center(), bpp::DualityDiagram::check_(), bpp::ColMatrix< Scalar >::ColMatrix(), bpp::DualityDiagram::compute_(), bpp::CorrespondenceAnalysis::CorrespondenceAnalysis(), bpp::MatrixTools::covar(), bpp::MatrixTools::det(), bpp::MatrixTools::diag(), bpp::MatrixTools::directSum(), bpp::Matrix< Scalar >::equals(), bpp::MatrixTools::exp(), bpp::MatrixTools::fill(), bpp::MatrixTools::hadamardMult(), bpp::MatrixTools::inv(), bpp::MatrixTools::isSquare(), bpp::MatrixTools::kroneckerMult(), bpp::MatrixTools::lap(), bpp::MatrixTools::max(), bpp::MatrixTools::min(), bpp::MatrixTools::mult(), bpp::RowMatrix< Scalar >::operator=(), bpp::ColMatrix< Scalar >::operator=(), bpp::LinearMatrix< Scalar >::operator=(), bpp::operator==(), bpp::MatrixTools::pow(), bpp::PrincipalComponentAnalysis::PrincipalComponentAnalysis(), bpp::MatrixTools::print(), bpp::MatrixTools::printForR(), bpp::RowMatrix< Scalar >::RowMatrix(), bpp::AdaptiveKernelDensityEstimation::sampleMean_(), bpp::MatrixTools::scale(), bpp::PrincipalComponentAnalysis::scale(), bpp::LUDecomposition< Real >::solve(), bpp::MatrixTools::sumElements(), bpp::MatrixTools::Taylor(), bpp::MatrixTools::toVVdouble(), bpp::MatrixTools::whichMax(), and bpp::MatrixTools::whichMin().

◆ getNumberOfRows()

template<class Scalar >
virtual size_t bpp::Matrix< Scalar >::getNumberOfRows ( ) const
pure virtual
Returns
The number of rows.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

Referenced by bpp::PrincipalComponentAnalysis::center(), bpp::DualityDiagram::check_(), bpp::ColMatrix< Scalar >::ColMatrix(), bpp::DualityDiagram::compute_(), bpp::CorrespondenceAnalysis::CorrespondenceAnalysis(), bpp::MatrixTools::covar(), bpp::MatrixTools::det(), bpp::MatrixTools::diag(), bpp::MatrixTools::directSum(), bpp::Matrix< Scalar >::equals(), bpp::MatrixTools::exp(), bpp::MatrixTools::fill(), bpp::MatrixTools::fillDiag(), bpp::MatrixTools::hadamardMult(), bpp::MatrixTools::inv(), bpp::MatrixTools::isSquare(), bpp::MatrixTools::kroneckerMult(), bpp::MatrixTools::lap(), bpp::MatrixTools::max(), bpp::MatrixTools::min(), bpp::MatrixTools::mult(), bpp::RowMatrix< Scalar >::operator=(), bpp::ColMatrix< Scalar >::operator=(), bpp::LinearMatrix< Scalar >::operator=(), bpp::operator==(), bpp::MatrixTools::pow(), bpp::PrincipalComponentAnalysis::PrincipalComponentAnalysis(), bpp::MatrixTools::print(), bpp::MatrixTools::printForR(), bpp::RowMatrix< Scalar >::RowMatrix(), bpp::AdaptiveKernelDensityEstimation::sampleMean_(), bpp::MatrixTools::scale(), bpp::PrincipalComponentAnalysis::scale(), bpp::FullHmmTransitionMatrix::setTransitionProbabilities(), bpp::LUDecomposition< Real >::solve(), bpp::MatrixTools::sumElements(), bpp::MatrixTools::Taylor(), bpp::MatrixTools::toVVdouble(), bpp::MatrixTools::whichMax(), and bpp::MatrixTools::whichMin().

◆ operator()() [1/2]

template<class Scalar >
virtual const Scalar& bpp::Matrix< Scalar >::operator() ( size_t  i,
size_t  j 
) const
pure virtual
Returns
$m_{i,j}$.
Parameters
irow index.
jcolumn index.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

◆ operator()() [2/2]

template<class Scalar >
virtual Scalar& bpp::Matrix< Scalar >::operator() ( size_t  i,
size_t  j 
)
pure virtual
Returns
$m_{i,j}$.
Parameters
irow index.
jcolumn index.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

◆ resize()

template<class Scalar >
virtual void bpp::Matrix< Scalar >::resize ( size_t  nRows,
size_t  nCols 
)
pure virtual

Resize the matrix.

Parameters
nRowsThe new number of rows.
nColsThe new number of columns.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

Referenced by bpp::MatrixTools::covar(), bpp::MatrixTools::diag(), bpp::MatrixTools::directSum(), bpp::MatrixTools::getId(), bpp::MatrixTools::hadamardMult(), bpp::MatrixTools::kroneckerMult(), bpp::MatrixTools::mult(), and bpp::LUDecomposition< Real >::permuteCopy().

◆ row()

template<class Scalar >
virtual std::vector<Scalar> bpp::Matrix< Scalar >::row ( size_t  i) const
pure virtual
Returns
the row at position i as a vector.
Parameters
iThe index of the row.

Implemented in bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, and bpp::RowMatrix< Real >.

Referenced by bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

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