Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 1234567]

bpp::AdaptiveKernelDensityEstimation	Density estimation using the adaptive kernel method
bpp::ApplicationTools	This class provides some common tools for developping applications
bpp::AttributesTools	Some functions to deal with attributes, i.e. parameters passed to a program/method
bpp::BppApplication
bpp::Bracket
bpp::BracketPoint
bpp::Clonable	The Clonable interface (allow an object to be cloned)
bpp::BppBoolean	The BppBoolean object class
bpp::BppString	The BppString object class
bpp::BppVector< TYPE >	The BppVector object class
bpp::Constraint	The constraint interface
bpp::IntervalConstraint	An interval, either bounded or not, which can also have infinite bounds
bpp::DataTable	This class corresponds to a 'dataset', i.e. a table with data by rows and variable by columns
bpp::DualityDiagram	The core class of a multivariate analysis
bpp::CorrespondenceAnalysis
bpp::PrincipalComponentAnalysis	This class allows to perform a principal component analysis
bpp::Font	Data structure for fonts
bpp::Matrix< Scalar >	The matrix template interface
bpp::LinearMatrix< Scalar >	Matrix storage in one vector
bpp::RowMatrix< Scalar >	Matrix storage by row
bpp::RowMatrix< double >
bpp::RowMatrix< Real >
bpp::MetaOptimizerInfos	Provide a list of optimizer and corresponding options to be used with the MetaOptimizer class
bpp::Number< T >	The Number object template class
bpp::OptimizationStopCondition	Interface for otimization stop condition objet
bpp::AbstractOptimizationStopCondition	Partial implementation of the OptimizationStopCondition interface
bpp::BrentOneDimension::BODStopCondition
bpp::DownhillSimplexMethod::DSMStopCondition
bpp::FunctionStopCondition	Stop condition on function value
bpp::GoldenSectionSearch::GSSStopCondition
bpp::NewtonBacktrackOneDimension::NBODStopCondition
bpp::ParametersStopCondition	Stop condition on parameters
bpp::PowellMultiDimensions::PMDStopCondition
bpp::Optimizer	This is the basal interface for all optimization methods
bpp::AbstractOptimizer	Partial implementation of the Optimizer interface
bpp::BfgsMultiDimensions	Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization method
bpp::BrentOneDimension	Brent's optimization for one parameter
bpp::ConjugateGradientMultiDimensions	Conjugate gradient optimization method
bpp::DownhillSimplexMethod	This implements the Downhill Simplex method in multidimensions
bpp::GoldenSectionSearch	Golden Section Search optimization algorithm for one parameter
bpp::MetaOptimizer	Meta-optimizer
bpp::NewtonBacktrackOneDimension	Newton's backtrack nearly optimization for one parameter
bpp::NewtonOneDimension	Newton's optimization for one parameter
bpp::PowellMultiDimensions	Powell's multi-dimensions optimization algorithm for one parameter
bpp::SimpleMultiDimensions	This Optimizer is a very simple multi-dimensions optimizer, calling a one dimensional optimizer on each parameter
bpp::SimpleNewtonMultiDimensions	This Optimizer is a simple multi-dimensions optimizer, calling the Newton one dimensional optimizer on each parameter
bpp::OutputStream	OutputStream interface
bpp::AbstractOutputStream	Helper implementation of the OutputStream interface
bpp::NullOutputStream	Null output stream (swich off output)
bpp::StdErr	Standard error stream
bpp::StdOut	Standard output stream
bpp::StlOutputStream	STL output stream
bpp::StlOutputStreamWrapper	STL wrapper for output stream
bpp::StdStr	String output stream
bpp::Parameter	This class is designed to facilitate the manipulation of parameters
bpp::AutoParameter	The AutoParameter class
bpp::TransformedParameter	The TransformedParameter abstract class
bpp::IntervalTransformedParameter	Parameter transformation from ] a, b [ to ]-inf, + inf [
bpp::PlaceboTransformedParameter	'Placebo' parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [
bpp::RTransformedParameter	Parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [
bpp::ParameterEvent
bpp::ParameterList	The parameter list object
bpp::ParameterListener	The parameter listener interface
bpp::AliasParameterListener	Inner listener class used by AbstractParameterAliasable
bpp::Parametrizable	This is the interface for all objects that imply parameters
bpp::AbstractParametrizable	A partial implementation of the Parametrizable interface
bpp::AbstractParameterAliasable	A partial implementation of the Parametrizable interface
bpp::AbstractDiscreteDistribution	Partial implementation of the DiscreteDistribution interface
bpp::BetaDiscreteDistribution	Discretized Beta distribution with parameters alpha and beta, on a given interval. On default, the interval is , but it can be restricted
bpp::ConstantDistribution	Constant discrete distribution
bpp::ExponentialDiscreteDistribution	Discretized Exponential distribution
bpp::GammaDiscreteDistribution	Discretized Gamma distribution
bpp::GaussianDiscreteDistribution	Discretized Gaussian distribution
bpp::InvariantMixedDiscreteDistribution	Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution
bpp::MixtureOfDiscreteDistributions	A Discrete distribution object defined by a vector of Discrete Distributions and a set of probabilities for these Discrete Distributions
bpp::SimpleDiscreteDistribution	A Discrete distribution object, where some specific probabilities are assigned to a finite set of values
bpp::TruncatedExponentialDiscreteDistribution	Discretized Truncated (on the right) Exponential distribution, where the probabilities are given the exponential, conditioned by the upper limit
bpp::UniformDiscreteDistribution	Discretized Uniform distribution. All categories are equidistributed all along a given interval
bpp::DirichletDiscreteDistribution	Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex
bpp::Simplex	A Simplex object, used to define sets of probabilities that sum 1
bpp::LogsumHmmLikelihood	A simple implementation of hidden Markov models recursion
bpp::LowMemoryRescaledHmmLikelihood	A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage
bpp::ReparametrizationFunctionWrapper	Function wrapper that remove simple constraints on parameters
bpp::ReparametrizationDerivableFirstOrderWrapper	Function wrapper that remove simple constraints on parameters. Also transform first order derivatives
bpp::ReparametrizationDerivableSecondOrderWrapper	Function wrapper that remove simple constraints on parameters. Also transform first and second order derivatives
bpp::RescaledHmmLikelihood	A simple implementation of hidden Markov models recursion
bpp::TestFunction	A simple funciton with two parameters, mostly for testing and debugging :)
bpp::Function	This is the function abstract class
bpp::DerivableFirstOrder	This is the abstract class for first order derivable functions
bpp::DerivableFirstOrderWrapper	General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework
bpp::DerivableSecondOrderWrapper	General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework
bpp::DerivableSecondOrder	This is the abstract class for second order derivable functions
bpp::AbstractNumericalDerivative	Numerical derivative function wrapper, partial implementation
bpp::FivePointsNumericalDerivative	Five points numerical derivative function wrapper
bpp::ThreePointsNumericalDerivative	Three points numerical derivative function wrapper
bpp::TwoPointsNumericalDerivative	Two points numerical derivative function wrapper
bpp::DerivableSecondOrderWrapper	General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework
bpp::ReparametrizationDerivableSecondOrderWrapper	Function wrapper that remove simple constraints on parameters. Also transform first and second order derivatives
bpp::ReparametrizationDerivableFirstOrderWrapper	Function wrapper that remove simple constraints on parameters. Also transform first order derivatives
bpp::DirectionFunction
bpp::FunctionWrapper	General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework
bpp::AbstractNumericalDerivative	Numerical derivative function wrapper, partial implementation
bpp::DerivableFirstOrderWrapper	General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework
bpp::InfinityFunctionWrapper	Wrapper class for optimization under constraints
bpp::InfinityDerivableFirstOrderWrapper	Wrapper class for optimization under constraints
bpp::InfinityDerivableSecondOrderWrapper	Wrapper class for optimization under constraints
bpp::HmmLikelihood	Basal interface for Hidden Markov Models likelihood computation
bpp::LogsumHmmLikelihood	A simple implementation of hidden Markov models recursion
bpp::LowMemoryRescaledHmmLikelihood	A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage
bpp::RescaledHmmLikelihood	A simple implementation of hidden Markov models recursion
bpp::ReparametrizationFunctionWrapper	Function wrapper that remove simple constraints on parameters
bpp::TestFunction	A simple funciton with two parameters, mostly for testing and debugging :)
bpp::HmmEmissionProbabilities	Interface for computing emission probabilities in a Hidden Markov Model
bpp::HmmStateAlphabet	Hidden states alphabet
bpp::HmmTransitionMatrix	Describe the transition probabilities between hidden states of a Hidden Markov Model
bpp::ParameterAliasable	Extend the Parametrizable interface with support for parameter aliases
bpp::AbstractParameterAliasable	A partial implementation of the Parametrizable interface
bpp::DiscreteDistribution	Interface for discrete distribution objects
bpp::AbstractDiscreteDistribution	Partial implementation of the DiscreteDistribution interface
bpp::MultipleDiscreteDistribution	Interface for multiple discrete distribution objects
bpp::DirichletDiscreteDistribution	Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex
bpp::ParametrizableAdapter	A low-level implementation of the Parametrizable interface with void functions
bpp::DirectionFunction
bpp::ParameterAliasableAdapter	A low-level implementation of the ParameterAliasable interface with void functions
bpp::Point2D< T >	The Point2D class
bpp::Range< T >	The Range class, defining an interval
bpp::RGBColor	Describe a color according to its red, green and blue componants
bpp::StatTest	Interface for statistical test results
bpp::ContingencyTableTest	Implements tests on contingency tables
bpp::UNode	Unoriented node interface
bpp::ONode	Oriented Node interface
bpp::BasicONode	Simple implementation of ONode
bpp::TNode	Tree Node interface
bpp::BasicTNode	Simple implementation of TNode
bpp::ColorManager< CodeType >	Associate special colors to a code
bpp::ColorManager< unsigned int >
bpp::XFigColorManager	Color manager for the XFig format
bpp::ColorSet	Specify a set of color definitions
bpp::AbstractColorSet	Partial implementation of the ColorSet interface
bpp::DefaultColorSet	Default color definitions
bpp::DvipsColorSet	The dvips color definitions
bpp::MolscriptColorSet	Molscript color definitions
bpp::RColorSet	R color definitions
bpp::ColorTools	Provide tools to deal with color objects
bpp::ContingencyTableGenerator	Generate a random contingency matrix with given marginal counts
bpp::CoordsTools	Some functions to deal with Point2D
bpp::EigenValue< Real >	Computes eigenvalues and eigenvectors of a real (non-complex) matrix
std::exception	STL class
bpp::Exception	Exception base class
bpp::BadIntegerException	Number exception: integers
bpp::BadNumberException	Number exception: doubles
bpp::BadSizeException	Wrong size exception class
bpp::DimensionException	Exception thrown when a dimension problem occured
bpp::DuplicatedTableColumnNameException	Excpetion thrown when attempting to duplicate a column name
bpp::DuplicatedTableRowNameException	Exception thrown when attempting to duplicate a row name
bpp::HmmBadStateException	Exception thrown when an unvalid state is requested
bpp::HmmUnvalidAlphabetException	Exception thrown when an unvalid alphabet is specified
bpp::IndexOutOfBoundsException	Index out of bounds exception class
bpp::IOException	The base class exception for IO error
bpp::KeyvalException	Exception thrown by the Keyval parser
bpp::NoTableColumnNamesException	Exception thrown when trying to retrieve a column by its name and no column names have been specified
bpp::NoTableRowNamesException	Exception thrown when trying to retrieve a row by its name and no row names have been specified
bpp::NotImplementedException	This expeption is sent when a given method is not implemented
bpp::NullPointerException	The base class exception for NULL pointer error
bpp::NumberFormatException	Number format exception
bpp::OutOfRangeException	Out of range exception class
bpp::ParameterException	The parameter exception base class
bpp::ConstraintException	Exception thrown when a value do not match a given constraint
bpp::ParameterNotFoundException	Exception thrown when a parameter is not found, for instance in a ParameterList
bpp::TableColumnNamesException	General exception class dealing with column names
bpp::TableNameNotFoundException	Exception thrown when a given name is not found is a DataTable object
bpp::TableColumnNameNotFoundException	Exception thrown when a given column name is not found is a DataTable object
bpp::TableRowNameNotFoundException	Exception thrown when a given row name is not found is a DataTable object
bpp::TableRowNamesException	General exception class dealing with row names
bpp::UnvalidFlagException
bpp::VectorException< T >	General Exception dealing with vectors
bpp::ElementNotFoundException< T >	Exception thrown when a given element was not found in the vector
bpp::EmptyVectorException< T >	Exception thrown when an empty vector was found
bpp::ZeroDivisionException	The base class exception for zero division error
bpp::FileTools	Some utilitary functions to deal with files
bpp::FontManager< CodeType >	Associate special fonts to a code
bpp::AbstractFontManager< CodeType >
bpp::FontManager< int >
bpp::AbstractFontManager< int >
bpp::XFigLaTeXFontManager	LaTeX font manager for the XFig format
bpp::XFigPostscriptFontManager	Postscript font manager for the XFig format
bpp::FunctionTools	This class contains static methods to deal with Function objects
bpp::GraphicDevice	Interface for all plotting devices
bpp::AbstractGraphicDevice	Partial implementation of the GraphicDevice interface
bpp::PgfGraphicDevice	LaTeX Portable Graphic Format (Pgf) plotting format
bpp::SvgGraphicDevice	SVG plotting format
bpp::XFigGraphicDevice	XFig plotting format
bpp::IoDiscreteDistributionFactory	Utilitary class for creating discrete distribution readers and writers
bpp::IOFormat	The IOFormat interface
bpp::IoDiscreteDistribution	General interface for model I/O
bpp::IDiscreteDistribution	General interface for distance matrix readers
bpp::BppODiscreteDistributionFormat	Discrete Distribution I/O in BppO format
bpp::ODiscreteDistribution	General interface writers
bpp::BppODiscreteDistributionFormat	Discrete Distribution I/O in BppO format
bpp::IOParametrizable	General interface for parametrizable Output
bpp::OParametrizable	General interface writers
bpp::BppOParametrizableFormat	Parametrizable output in BppO format
bpp::KeyvalTools	Tools to deal with the keyval syntax
bpp::LUDecomposition< Real >	LU Decomposition
bpp::MapTools	A fiew tools working on map objects
bpp::MatrixTools	Functions dealing with matrices
bpp::NumCalcApplicationTools
bpp::NumConstants	This static class contains several useful constant values
bpp::NumTools	Some utilitary function for numerical calculus
bpp::OneDimensionOptimizationTools	Tools of one parameter-functions optimizations
bpp::OptimizationEvent	An event object which indicates that an optimization event occured
bpp::OptimizationListener	The listener interface for receiving optimization events
bpp::BackupListener	Save intermediate optimization results to file
bpp::AbstractDiscreteDistribution::Order	Comparator class for AbstractDiscreteDistribution
bpp::VectorTools::order_Cmp_< T >
bpp::ParameterGrid	This class is a data structure to specify a set of parameter values (most likely for evaluation by a Function)
bpp::StatTools::PValue_
bpp::RandomFactory	This is the interface for the Random Number Generators
bpp::Uniform01K	A uniform random number generator
bpp::Uniform01QD	A quick and dirty uniform random number generator
bpp::Uniform01WH	A uniform random number generator
bpp::RandomTools	Utilitary function dealing with random numbers
bpp::RangeCollection< T >	Interface discribing a collection of Range objects
bpp::MultiRange< T >	This class implements a data structure describing a set of non-overlapping intervales
bpp::RangeSet< T >	This class implements a data structure describing a set of intervales
bpp::rangeComp_< T >	A special class used inside RangeCollection
bpp::DownhillSimplexMethod::Simplex
bpp::StateChangedEvent
bpp::StateListener
bpp::StatTools	Statistics tools and utilitary functions
bpp::StringTokenizer	A tokenizer for strings
bpp::NestedStringTokenizer	An improved tokenizer for strings
bpp::TextTools	Some utilitary functions that work on strings
bpp::VectorTools