Cbpp::AdaptiveKernelDensityEstimation | Density estimation using the adaptive kernel method |
Cbpp::Graph::ALLGRAPHITER | Define categories of iterators |
Cbpp::ApplicationTools | This class provides some common tools for developping applications |
Cbpp::AttributesTools | Some functions to deal with attributes, i.e. parameters passed to a program/method |
Cbpp::BppApplication | |
Cbpp::Bracket | |
Cbpp::BracketPoint | |
►Cbpp::Clonable | The Clonable interface (allow an object to be cloned) |
Cbpp::BppBoolean | The BppBoolean object class. This class extends the bool type to support the Clonable interface |
►Cbpp::BppNumberI | The Number interface |
Cbpp::BppNotANumber | |
Cbpp::Number< T > | The Number object template class |
►Cbpp::Number< double > | |
Cbpp::BppDouble | An object wrapper for double values |
►Cbpp::Number< int > | |
Cbpp::BppInteger | An object wrapper for integer values |
►Cbpp::Number< unsigned int > | |
Cbpp::BppUnsignedInteger | An object wrapper for unsigned integer values |
Cbpp::BppString | The BppString object class. This class extends the stl::string class to support the Clonable interface |
Cbpp::BppVector< T > | The BppVector object class. This class extends the std::vector class to support the Clonable interface |
►Cbpp::ConstraintInterface | The constraint interface |
Cbpp::IntervalConstraint | An interval, either bounded or not, which can also have infinite bounds |
Cbpp::DataTable | This class corresponds to a 'dataset', i.e. a table with data by rows and variable by columns |
►Cbpp::DualityDiagram | The core class of a multivariate analysis |
Cbpp::CorrespondenceAnalysis | This class allows to perform a correspondence analysis |
Cbpp::PrincipalComponentAnalysis | This class allows to perform a principal component analysis |
Cbpp::Font | Data structure for fonts |
Cbpp::GlobalGraph | |
►Cbpp::GraphObserver | Defines a Graph Observer. It is a template which follows (subscribed to) a Graph. The graph and the graph observer communicate to keep them up-to-date each other. The observer is also an actor, since it can change the structure of the observed Graph |
►Cbpp::AssociationGraphObserver< N, E > | Defines a Graph Associator. It is a template which follows (subscribed to) a Graph |
►Cbpp::AssociationGraphImplObserver< N, E, DAGraphImpl > | |
Cbpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl > | |
►Cbpp::AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
►Cbpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > | |
Cbpp::ComputationTree | Defines a Computation Tree based on Operators |
►Cbpp::AssociationDAGraphObserver< N, E > | Defines a DA Graph Associator. It is a template which follows (subscribed to) a Graph |
Cbpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl > | |
Cbpp::AssociationGraphImplObserver< N, E, GraphImpl > | |
►Cbpp::AssociationTreeGraphObserver< N, E > | Defines a Tree Graph Associator. It is a template which follows (subscribed to) a Graph |
Cbpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > | |
►Cbpp::Matrix< Scalar > | The matrix template interface |
Cbpp::ColMatrix< Scalar > | Matrix storage by column |
Cbpp::LinearMatrix< Scalar > | Matrix storage in one vector |
Cbpp::RowMatrix< Scalar > | Matrix storage by row |
Cbpp::RowMatrix< double > | |
Cbpp::RowMatrix< Real > | |
Cbpp::MetaOptimizerInfos | Provide a list of optimizer and corresponding options to be used with the MetaOptimizer class |
►Cbpp::Operator | Interface of operator for numerical computation |
Cbpp::BinaryOperator | Binary arithmetic operator for numerical computation |
Cbpp::ConstantOperator | Constant (ie leaf) operator |
Cbpp::FunctionOperator< F > | Implements a double operator (ie leaf in the computation tree) where value comes from a function |
Cbpp::MathOperator | Implements a unary operator that applies a math (described in cmath) operator |
Cbpp::NegativeOperator | Negative value for an operator |
►Cbpp::OptimizationStopCondition | Interface for otimization stop condition objet |
►Cbpp::AbstractOptimizationStopCondition | Partial implementation of the OptimizationStopCondition interface |
Cbpp::BrentOneDimension::BODStopCondition | |
Cbpp::DownhillSimplexMethod::DSMStopCondition | |
Cbpp::FunctionStopCondition | Stop condition on function value |
Cbpp::GoldenSectionSearch::GSSStopCondition | |
Cbpp::NewtonBacktrackOneDimension::NBODStopCondition | |
Cbpp::ParametersStopCondition | Stop condition on parameters |
Cbpp::PowellMultiDimensions::PMDStopCondition | |
►Cbpp::OptimizerInterface | This is the basal interface for all optimization methods |
►Cbpp::AbstractOptimizer | Partial implementation of the Optimizer interface |
Cbpp::BfgsMultiDimensions | Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization method |
Cbpp::BrentOneDimension | Brent's optimization for one parameter |
Cbpp::ConjugateGradientMultiDimensions | Conjugate gradient optimization method |
Cbpp::DownhillSimplexMethod | This implements the Downhill Simplex method in multidimensions |
Cbpp::GoldenSectionSearch | Golden Section Search optimization algorithm for one parameter |
Cbpp::MetaOptimizer | Meta-optimizer |
Cbpp::NewtonBacktrackOneDimension | Newton's backtrack nearly optimization for one parameter |
Cbpp::NewtonOneDimension | Newton's optimization for one parameter |
Cbpp::PowellMultiDimensions | Powell's multi-dimensions optimization algorithm for one parameter |
Cbpp::SimpleMultiDimensions | This Optimizer is a very simple multi-dimensions optimizer, calling a one dimensional optimizer on each parameter |
Cbpp::SimpleNewtonMultiDimensions | This Optimizer is a simple multi-dimensions optimizer, calling the Newton one dimensional optimizer on each parameter |
►Cbpp::OutputStream | OutputStream interface |
►Cbpp::AbstractOutputStream | Helper implementation of the OutputStream interface |
Cbpp::NullOutputStream | Null output stream (swich off output) |
Cbpp::StdErr | Standard error stream |
Cbpp::StdOut | Standard output stream |
Cbpp::StlOutputStream | STL output stream |
►Cbpp::StlOutputStreamWrapper | STL wrapper for output stream |
Cbpp::StdStr | String output stream |
►Cbpp::Parameter | This class is designed to facilitate the manipulation of parameters |
Cbpp::AutoParameter | The AutoParameter class |
►Cbpp::TransformedParameter | The TransformedParameter abstract class |
Cbpp::IntervalTransformedParameter | Parameter transformation from ] a, b [ to ]-inf, + inf [ |
Cbpp::PlaceboTransformedParameter | 'Placebo' parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [ |
Cbpp::RTransformedParameter | Parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [ |
Cbpp::ParameterEvent | |
Cbpp::ParameterList | The parameter list object |
►Cbpp::ParameterListener | The parameter listener interface |
Cbpp::AliasParameterListener | Inner listener class used by AbstractParameterAliasable |
►Cbpp::Parametrizable | This is the interface for all objects that imply parameters |
►Cbpp::AbstractParametrizable | A partial implementation of the Parametrizable interface |
►Cbpp::AbstractParameterAliasable | A partial implementation of the Parametrizable interface |
►Cbpp::AbstractDiscreteDistribution | Partial implementation of the DiscreteDistribution interface |
Cbpp::BetaDiscreteDistribution | Discretized Beta distribution with parameters alpha and beta, on a given interval. On default, the interval is , but it can be restricted |
Cbpp::ConstantDistribution | Constant discrete distribution |
Cbpp::ExponentialDiscreteDistribution | Discretized Exponential distribution |
Cbpp::GammaDiscreteDistribution | Discretized Gamma distribution with an offset |
Cbpp::GaussianDiscreteDistribution | Discretized Gaussian distribution |
Cbpp::InvariantMixedDiscreteDistribution | Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution |
Cbpp::MixtureOfDiscreteDistributions | A Discrete distribution object defined by a vector of Discrete Distributions and a set of probabilities for these Discrete Distributions |
Cbpp::SimpleDiscreteDistribution | A Discrete distribution object, where some specific probabilities are assigned to a finite set of values |
Cbpp::TruncatedExponentialDiscreteDistribution | Discretized Truncated (on the right) Exponential distribution, where the probabilities are given the exponential, conditioned by the upper limit |
Cbpp::UniformDiscreteDistribution | Discretized Uniform distribution. All categories are equidistributed all along a given interval |
Cbpp::DirichletDiscreteDistribution | Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex |
Cbpp::ParametrizableCollection< N > | Plain collection of parametrizable objects |
►Cbpp::Simplex | A Simplex object, used to define sets of probabilities that sum 1 |
Cbpp::OrderedSimplex | Simplex where all values are in decreasing order |
Cbpp::AutoCorrelationTransitionMatrix | Describe the auto-correlation probabilities inside hidden states of a Hidden Markov Model |
Cbpp::FullHmmTransitionMatrix | Describe the transition probabilities between hidden states of a Hidden Markov Model |
Cbpp::LogsumHmmLikelihood | A simple implementation of hidden Markov models recursion |
Cbpp::LowMemoryRescaledHmmLikelihood | A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage |
►Cbpp::ReparametrizationFunctionWrapper | Function wrapper that remove simple constraints on parameters |
►Cbpp::ReparametrizationDerivableFirstOrderWrapper | Function wrapper that remove simple constraints on parameters. Also transform first order derivatives |
Cbpp::ReparametrizationDerivableSecondOrderWrapper | Function wrapper that remove simple constraints on parameters. Also transform first and second order derivatives |
Cbpp::RescaledHmmLikelihood | A simple implementation of hidden Markov models recursion |
Cbpp::TestFunction | A simple function with two parameters, mostly for testing and debugging :) |
►Cbpp::FunctionInterface | This is the function abstract class |
Cbpp::DirectionFunction | |
►Cbpp::FirstOrderDerivable | This is the abstract class for first order derivable functions |
►Cbpp::FirstOrderDerivableWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
Cbpp::SecondOrderDerivableWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
Cbpp::ReparametrizationDerivableFirstOrderWrapper | Function wrapper that remove simple constraints on parameters. Also transform first order derivatives |
►Cbpp::SecondOrderDerivable | This is the abstract class for second order derivable functions |
►Cbpp::HmmLikelihood | Basal interface for Hidden Markov Models likelihood computation |
►Cbpp::AbstractHmmLikelihood | Partial impmementation of Hmm Likelihoods |
Cbpp::LogsumHmmLikelihood | A simple implementation of hidden Markov models recursion |
Cbpp::LowMemoryRescaledHmmLikelihood | A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage |
Cbpp::RescaledHmmLikelihood | A simple implementation of hidden Markov models recursion |
►Cbpp::NumericalDerivativeInterface | Numerical derivative function wrapper |
►Cbpp::AbstractNumericalDerivative | Numerical derivative function wrapper, partial implementation |
Cbpp::FivePointsNumericalDerivative | Five points numerical derivative function wrapper |
Cbpp::ThreePointsNumericalDerivative | Three points numerical derivative function wrapper |
Cbpp::TwoPointsNumericalDerivative | Two points numerical derivative function wrapper |
Cbpp::ReparametrizationDerivableSecondOrderWrapper | Function wrapper that remove simple constraints on parameters. Also transform first and second order derivatives |
Cbpp::SecondOrderDerivableWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
►Cbpp::FunctionWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
Cbpp::AbstractNumericalDerivative | Numerical derivative function wrapper, partial implementation |
Cbpp::FirstOrderDerivableWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
►Cbpp::InfinityFunctionWrapper | Wrapper class for optimization under constraints |
►Cbpp::InfinityDerivableFirstOrderWrapper | Wrapper class for optimization under constraints |
Cbpp::InfinityDerivableSecondOrderWrapper | Wrapper class for optimization under constraints |
Cbpp::ReparametrizationFunctionWrapper | Function wrapper that remove simple constraints on parameters |
Cbpp::TestFunction | A simple function with two parameters, mostly for testing and debugging :) |
Cbpp::HmmEmissionProbabilities | Interface for computing emission probabilities in a Hidden Markov Model |
Cbpp::HmmStateAlphabet | Hidden states alphabet |
►Cbpp::HmmTransitionMatrix | Describe the transition probabilities between hidden states of a Hidden Markov Model |
►Cbpp::AbstractHmmTransitionMatrix | Partial implementation of HmmTransitionMatrix |
Cbpp::AutoCorrelationTransitionMatrix | Describe the auto-correlation probabilities inside hidden states of a Hidden Markov Model |
Cbpp::FullHmmTransitionMatrix | Describe the transition probabilities between hidden states of a Hidden Markov Model |
►Cbpp::ParameterAliasable | Extend the Parametrizable interface with support for parameter aliases |
Cbpp::AbstractParameterAliasable | A partial implementation of the Parametrizable interface |
►Cbpp::DiscreteDistributionInterface | Interface for discrete distribution objects |
Cbpp::AbstractDiscreteDistribution | Partial implementation of the DiscreteDistribution interface |
►Cbpp::MultipleDiscreteDistribution | Interface for multiple discrete distribution objects |
Cbpp::DirichletDiscreteDistribution | Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex |
►Cbpp::ParametrizableAdapter | A low-level implementation of the Parametrizable interface with void functions |
Cbpp::DirectionFunction | |
Cbpp::ParameterAliasableAdapter | A low-level implementation of the ParameterAliasable interface with void functions |
Cbpp::Point2D< T > | The Point2D class |
Cbpp::Range< T > | The Range class, defining an interval |
Cbpp::RGBColor | Describe a color according to its red, green and blue componants |
►Cbpp::StatTest | Interface for statistical test results |
Cbpp::ContingencyTableTest | Implements tests on contingency tables |
Cbpp::Table< T > | This class corresponds to a 'dataset', i.e. a table with data by rows and variable by columns |
Cbpp::ColorManager< CodeType > | Associate special colors to a code |
►Cbpp::ColorManager< unsigned int > | |
Cbpp::XFigColorManager | Color manager for the XFig format |
►Cbpp::ColorSet | Specify a set of color definitions |
►Cbpp::AbstractColorSet | Partial implementation of the ColorSet interface |
Cbpp::DefaultColorSet | Default color definitions |
Cbpp::DvipsColorSet | The dvips color definitions |
Cbpp::MolscriptColorSet | Molscript color definitions |
Cbpp::RColorSet | R color definitions |
Cbpp::ColorTools | Provide tools to deal with color objects |
Cbpp::ContingencyTableGenerator | Generate a random contingency matrix with given marginal counts |
Cbpp::CoordsTools | Some functions to deal with Point2D |
►Cbpp::AssociationGraphObserver< N, E >::EdgeIterator | |
Cbpp::AssociationGraphImplObserver< N, E, GraphImpl >::EdgeIteratorClass< GraphIterator, is_const > | |
►Cbpp::Graph::EdgeIterator | |
Cbpp::EdgesIteratorClass< T, is_const > | |
Cbpp::EdgesIteratorClass< Graph::ALLGRAPHITER, is_const > | |
Cbpp::EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > | |
Cbpp::EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > | |
Cbpp::EdgesIteratorClass< GraphIterator, is_const > | |
Cbpp::EigenValue< Real > | Computes eigenvalues and eigenvectors of a real (non-complex) matrix |
►Cstd::exception | STL class |
►Cbpp::Exception | Exception base class. Overload exception constructor (to control the exceptions mechanism). Destructor is already virtual (from std::exception) |
Cbpp::BadIntegerException | Number exception: integers |
Cbpp::BadNumberException | Number exception: doubles |
Cbpp::BadSizeException | Wrong size exception class |
Cbpp::DimensionException | Exception thrown when a dimension problem occured |
Cbpp::DuplicatedTableColumnNameException | Excpetion thrown when attempting to duplicate a column name |
Cbpp::DuplicatedTableRowNameException | Exception thrown when attempting to duplicate a row name |
Cbpp::HmmBadStateException | Exception thrown when an unvalid state is requested |
Cbpp::HmmUnvalidAlphabetException | Exception thrown when an unvalid alphabet is specified |
Cbpp::IndexOutOfBoundsException | Index out of bounds exception class |
Cbpp::IOException | The base class exception for IO error |
Cbpp::KeyvalException | Exception thrown by the Keyval parser |
Cbpp::NoTableColumnNamesException | Exception thrown when trying to retrieve a column by its name and no column names have been specified |
Cbpp::NoTableRowNamesException | Exception thrown when trying to retrieve a row by its name and no row names have been specified |
Cbpp::NotImplementedException | This exception is sent when a given method is not implemented |
Cbpp::NullPointerException | The base class exception for NULL pointer error. This exception may be thrown when an unexpected NULL pointer is found |
Cbpp::NumberFormatException | Number format exception |
Cbpp::OutOfRangeException | Out of range exception class |
►Cbpp::ParameterException | The parameter exception base class |
Cbpp::ConstraintException | Exception thrown when a value do not match a given constraint |
Cbpp::ParameterNotFoundException | Exception thrown when a parameter is not found, for instance in a ParameterList |
Cbpp::TableColumnNamesException | General exception class dealing with column names |
►Cbpp::TableNameNotFoundException | Exception thrown when a given name is not found is a DataTable object |
Cbpp::TableColumnNameNotFoundException | Exception thrown when a given column name is not found is a DataTable object |
Cbpp::TableRowNameNotFoundException | Exception thrown when a given row name is not found is a DataTable object |
Cbpp::TableRowNamesException | General exception class dealing with row names |
Cbpp::UnvalidFlagException | |
►Cbpp::VectorException< T > | General Exception dealing with vectors |
Cbpp::ElementNotFoundException< T > | Exception thrown when a given element was not found in the vector |
Cbpp::EmptyVectorException< T > | Exception thrown when an empty vector was found |
Cbpp::ZeroDivisionException | The base class exception for zero division error |
Cbpp::FileTools | Some utilitary functions to deal with files |
►Cbpp::FontManager< CodeType > | Associate special fonts to a code |
Cbpp::AbstractFontManager< CodeType > | |
►Cbpp::FontManager< int > | |
►Cbpp::AbstractFontManager< int > | |
Cbpp::XFigLaTeXFontManager | LaTeX font manager for the XFig format |
Cbpp::XFigPostscriptFontManager | Postscript font manager for the XFig format |
Cbpp::FunctionTools | This class contains static methods to deal with Function objects |
►Cbpp::Graph | |
►Cbpp::DAGraph | |
Cbpp::DAGraphImpl< GraphImpl > | |
Cbpp::GlobalGraph | |
►Cbpp::TreeGraph | |
Cbpp::TreeGraphImpl< GraphImpl > | |
►Cbpp::GraphicDevice | Interface for all plotting devices |
►Cbpp::AbstractGraphicDevice | Partial implementation of the GraphicDevice interface |
Cbpp::PgfGraphicDevice | LaTeX Portable Graphic Format (Pgf) plotting format |
Cbpp::SvgGraphicDevice | SVG plotting format |
Cbpp::XFigGraphicDevice | XFig plotting format |
►CGraphImpl | |
Cbpp::DAGraphImpl< GraphImpl > | |
Cbpp::TreeGraphImpl< GraphImpl > | |
Cbpp::Graph::INCOMINGNEIGHBORITER | |
Cbpp::IoDiscreteDistributionFactory | Utilitary class for creating discrete distribution readers and writers |
►Cbpp::IOFormat | The IOFormat interface |
►Cbpp::IoDiscreteDistribution | General interface for model I/O |
►Cbpp::IDiscreteDistribution | General interface for distance matrix readers |
Cbpp::BppODiscreteDistributionFormat | Discrete Distribution I/O in BppO format |
►Cbpp::ODiscreteDistribution | General interface writers |
Cbpp::BppODiscreteDistributionFormat | Discrete Distribution I/O in BppO format |
►Cbpp::IOParametrizable | General interface for parametrizable Output |
►Cbpp::OParametrizable | General interface writers |
Cbpp::BppOParametrizableFormat | Parametrizable output in BppO format |
Cbpp::KeyvalTools | Tools to deal with the keyval syntax |
Cbpp::LUDecomposition< Real > | LU Decomposition |
Cbpp::MapTools | A fiew tools working on map objects |
Cbpp::MatrixTools | Functions dealing with matrices |
►Cbpp::NeighborIteratorClass< is_const > | Abstract class for neighbor iterators |
Cbpp::EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > | |
Cbpp::EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > | |
Cbpp::NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > | |
Cbpp::NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > | |
►Cbpp::AssociationGraphObserver< N, E >::NodeIterator | |
Cbpp::AssociationGraphImplObserver< N, E, GraphImpl >::NodeIteratorClass< GraphIterator, is_const > | |
►Cbpp::Graph::NodeIterator | |
Cbpp::NodesIteratorClass< T, is_const > | |
Cbpp::NodesIteratorClass< Graph::ALLGRAPHITER, is_const > | |
Cbpp::NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > | |
Cbpp::NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > | |
Cbpp::NodesIteratorClass< GraphIterator, is_const > | |
Cbpp::NumCalcApplicationTools | |
Cbpp::NumConstants | This static class contains several useful constant values |
Cbpp::NumTools | Some utilitary function for numerical calculus |
Cbpp::OneDimensionOptimizationTools | Tools of one parameter-functions optimizations |
Cbpp::OptimizationEvent | An event object which indicates that an optimization event occured |
►Cbpp::OptimizationListener | The listener interface for receiving optimization events |
Cbpp::BackupListener | Save intermediate optimization results to file |
Cbpp::AbstractDiscreteDistribution::Order | Comparator class for AbstractDiscreteDistribution |
Cbpp::VectorTools::order_Cmp_< T > | |
Cbpp::Graph::OUTGOINGNEIGHBORITER | |
Cbpp::ParameterGrid | This class is a data structure to specify a set of parameter values (most likely for evaluation by a Function) |
Cbpp::StatTools::PValue_ | |
Cbpp::RandomTools | Utilitary function dealing with random numbers |
►Cbpp::RangeCollection< T > | Interface discribing a collection of Range objects |
Cbpp::MultiRange< T > | This class implements a data structure describing a set of non-overlapping intervals |
Cbpp::RangeSet< T > | This class implements a data structure describing a set of intervals |
Cbpp::rangeComp_< T > | A special class used inside RangeCollection |
Cbpp::DownhillSimplexMethod::Simplex | |
Cbpp::StateChangedEvent | |
Cbpp::StateListener | |
Cbpp::StatTools | Statistics tools and utilitary functions |
►Cbpp::StringTokenizer | A tokenizer for strings |
Cbpp::NestedStringTokenizer | An improved tokenizer for strings |
►Cstd::vector< T > | STL class |
Cbpp::BppVector< T > | The BppVector object class. This class extends the std::vector class to support the Clonable interface |
Cbpp::VectorTools | |