  bpp | This class allows to perform a correspondence analysis |
   ApplicationTools | This class provides some common tools for developping applications |
| BppApplication | |
| NumCalcApplicationTools | |
| BppBoolean | The BppBoolean object class |
| BppString | The BppString object class |
| BppVector | The BppVector object class |
| Clonable | The Clonable interface (allow an object to be cloned) |
| Exception | Exception base class |
| IOException | The base class exception for IO error |
| NullPointerException | The base class exception for NULL pointer error |
| ZeroDivisionException | The base class exception for zero division error |
| BadIntegerException | Number exception: integers |
| BadNumberException | Number exception: doubles |
| NumberFormatException | Number format exception |
| IndexOutOfBoundsException | Index out of bounds exception class |
| BadSizeException | Wrong size exception class |
| OutOfRangeException | Out of range exception class |
| NotImplementedException | This expeption is sent when a given method is not implemented |
| BasicONode | Simple implementation of ONode |
| BasicTNode | Simple implementation of TNode |
| ONode | Oriented Node interface |
| TNode | Tree Node interface |
| UNode | Unoriented node interface |
| AbstractGraphicDevice | Partial implementation of the GraphicDevice interface |
| ColorManager | Associate special colors to a code |
| XFigColorManager | Color manager for the XFig format |
| ColorSet | Specify a set of color definitions |
| AbstractColorSet | Partial implementation of the ColorSet interface |
| ColorTools | Provide tools to deal with color objects |
| DefaultColorSet | Default color definitions |
| XFigGraphicDevice | XFig plotting format |
| XFigLaTeXFontManager | LaTeX font manager for the XFig format |
| XFigPostscriptFontManager | Postscript font manager for the XFig format |
| Font | Data structure for fonts |
| FontManager | Associate special fonts to a code |
| AbstractFontManager | |
| UnvalidFlagException | |
| GraphicDevice | Interface for all plotting devices |
| DvipsColorSet | The dvips color definitions |
| PgfGraphicDevice | LaTeX Portable Graphic Format (Pgf) plotting format |
| MolscriptColorSet | Molscript color definitions |
| Point2D | The Point2D class |
| CoordsTools | Some functions to deal with Point2D |
| RColorSet | R color definitions |
| RGBColor | Describe a color according to its red, green and blue componants |
| SvgGraphicDevice | SVG plotting format |
| BppODiscreteDistributionFormat | Discrete Distribution I/O in BppO format |
| BppOParametrizableFormat | Parametrizable output in BppO format |
| FileTools | Some utilitary functions to deal with files |
| IoDiscreteDistribution | General interface for model I/O |
| IDiscreteDistribution | General interface for distance matrix readers |
| ODiscreteDistribution | General interface writers |
| IoDiscreteDistributionFactory | Utilitary class for creating discrete distribution readers and writers |
| IOFormat | The IOFormat interface |
| IOParametrizable | General interface for parametrizable Output |
| OParametrizable | General interface writers |
| OutputStream | OutputStream interface |
| AbstractOutputStream | Helper implementation of the OutputStream interface |
| NullOutputStream | Null output stream (swich off output) |
| StlOutputStream | STL output stream |
| StlOutputStreamWrapper | STL wrapper for output stream |
| StdOut | Standard output stream |
| StdErr | Standard error stream |
| StdStr | String output stream |
| AliasParameterListener | Inner listener class used by AbstractParameterAliasable |
| AbstractParameterAliasable | A partial implementation of the Parametrizable interface |
| AbstractParametrizable | A partial implementation of the Parametrizable interface |
| AdaptiveKernelDensityEstimation | Density estimation using the adaptive kernel method |
| AutoParameter | The AutoParameter class |
| Constraint | The constraint interface |
| IntervalConstraint | An interval, either bounded or not, which can also have infinite bounds |
| DataTable | This class corresponds to a 'dataset', i.e. a table with data by rows and variable by columns |
| TableNameNotFoundException | Exception thrown when a given name is not found is a DataTable object |
| TableRowNameNotFoundException | Exception thrown when a given row name is not found is a DataTable object |
| TableColumnNameNotFoundException | Exception thrown when a given column name is not found is a DataTable object |
| NoTableRowNamesException | Exception thrown when trying to retrieve a row by its name and no row names have been specified |
| NoTableColumnNamesException | Exception thrown when trying to retrieve a column by its name and no column names have been specified |
| TableRowNamesException | General exception class dealing with row names |
| TableColumnNamesException | General exception class dealing with column names |
| DuplicatedTableRowNameException | Exception thrown when attempting to duplicate a row name |
| DuplicatedTableColumnNameException | Excpetion thrown when attempting to duplicate a column name |
| AbstractNumericalDerivative | Numerical derivative function wrapper, partial implementation |
| AbstractOptimizer | Partial implementation of the Optimizer interface |
| BfgsMultiDimensions | Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization method |
 BrentOneDimension | Brent's optimization for one parameter |
  BODStopCondition | |
| ConjugateGradientMultiDimensions | Conjugate gradient optimization method |
| DirectionFunction | |
| DownhillSimplexMethod | This implements the Downhill Simplex method in multidimensions |
| DSMStopCondition | |
| Simplex | |
| FivePointsNumericalDerivative | Five points numerical derivative function wrapper |
| Function | This is the function abstract class |
| DerivableFirstOrder | This is the abstract class for first order derivable functions |
| DerivableSecondOrder | This is the abstract class for second order derivable functions |
| FunctionWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
| DerivableFirstOrderWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
| DerivableSecondOrderWrapper | General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework |
| InfinityFunctionWrapper | Wrapper class for optimization under constraints |
| InfinityDerivableFirstOrderWrapper | Wrapper class for optimization under constraints |
| InfinityDerivableSecondOrderWrapper | Wrapper class for optimization under constraints |
| TestFunction | A simple funciton with two parameters, mostly for testing and debugging :) |
| ParameterGrid | This class is a data structure to specify a set of parameter values (most likely for evaluation by a Function) |
| FunctionTools | This class contains static methods to deal with Function objects |
| GoldenSectionSearch | Golden Section Search optimization algorithm for one parameter |
| GSSStopCondition | |
| MetaOptimizerInfos | Provide a list of optimizer and corresponding options to be used with the MetaOptimizer class |
| MetaOptimizer | Meta-optimizer |
| NewtonBacktrackOneDimension | Newton's backtrack nearly optimization for one parameter |
| NBODStopCondition | |
| NewtonOneDimension | Newton's optimization for one parameter |
| BracketPoint | |
| Bracket | |
| OneDimensionOptimizationTools | Tools of one parameter-functions optimizations |
| OptimizationStopCondition | Interface for otimization stop condition objet |
| AbstractOptimizationStopCondition | Partial implementation of the OptimizationStopCondition interface |
| ParametersStopCondition | Stop condition on parameters |
| FunctionStopCondition | Stop condition on function value |
| OptimizationEvent | An event object which indicates that an optimization event occured |
| OptimizationListener | The listener interface for receiving optimization events |
| Optimizer | This is the basal interface for all optimization methods |
| BackupListener | Save intermediate optimization results to file |
| PowellMultiDimensions | Powell's multi-dimensions optimization algorithm for one parameter |
| PMDStopCondition | |
| ReparametrizationFunctionWrapper | Function wrapper that remove simple constraints on parameters |
| ReparametrizationDerivableFirstOrderWrapper | Function wrapper that remove simple constraints on parameters. Also transform first order derivatives |
| ReparametrizationDerivableSecondOrderWrapper | Function wrapper that remove simple constraints on parameters. Also transform first and second order derivatives |
| SimpleMultiDimensions | This Optimizer is a very simple multi-dimensions optimizer, calling a one dimensional optimizer on each parameter |
| SimpleNewtonMultiDimensions | This Optimizer is a simple multi-dimensions optimizer, calling the Newton one dimensional optimizer on each parameter |
| ThreePointsNumericalDerivative | Three points numerical derivative function wrapper |
| TwoPointsNumericalDerivative | Two points numerical derivative function wrapper |
| HmmEmissionProbabilities | Interface for computing emission probabilities in a Hidden Markov Model |
| HmmBadStateException | Exception thrown when an unvalid state is requested |
| HmmUnvalidAlphabetException | Exception thrown when an unvalid alphabet is specified |
| HmmLikelihood | Basal interface for Hidden Markov Models likelihood computation |
| HmmStateAlphabet | Hidden states alphabet |
| StateListener | |
| StateChangedEvent | |
| HmmTransitionMatrix | Describe the transition probabilities between hidden states of a Hidden Markov Model |
| LogsumHmmLikelihood | A simple implementation of hidden Markov models recursion |
| LowMemoryRescaledHmmLikelihood | A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage |
| RescaledHmmLikelihood | A simple implementation of hidden Markov models recursion |
| EigenValue | Computes eigenvalues and eigenvectors of a real (non-complex) matrix |
| LUDecomposition | LU Decomposition |
| Matrix | The matrix template interface |
| RowMatrix | Matrix storage by row |
| LinearMatrix | Matrix storage in one vector |
| MatrixTools | Functions dealing with matrices |
| Number | The Number object template class |
| NumConstants | This static class contains several useful constant values |
| NumTools | Some utilitary function for numerical calculus |
| ParameterEvent | |
| ParameterListener | The parameter listener interface |
| Parameter | This class is designed to facilitate the manipulation of parameters |
| ParameterAliasable | Extend the Parametrizable interface with support for parameter aliases |
| ParameterAliasableAdapter | A low-level implementation of the ParameterAliasable interface with void functions |
| ParameterException | The parameter exception base class |
| ConstraintException | Exception thrown when a value do not match a given constraint |
| ParameterNotFoundException | Exception thrown when a parameter is not found, for instance in a ParameterList |
| ParameterList | The parameter list object |
| Parametrizable | This is the interface for all objects that imply parameters |
| ParametrizableAdapter | A low-level implementation of the Parametrizable interface with void functions |
| AbstractDiscreteDistribution | Partial implementation of the DiscreteDistribution interface |
| Order | Comparator class for AbstractDiscreteDistribution |
| BetaDiscreteDistribution | Discretized Beta distribution with parameters alpha and beta, on a given interval. On default, the interval is ![$ [0;1] $](form_77.png) , but it can be restricted |
| ConstantDistribution | Constant discrete distribution |
| DirichletDiscreteDistribution | Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex |
| DiscreteDistribution | Interface for discrete distribution objects |
| ExponentialDiscreteDistribution | Discretized Exponential distribution |
| GammaDiscreteDistribution | Discretized Gamma distribution |
| GaussianDiscreteDistribution | Discretized Gaussian distribution |
| InvariantMixedDiscreteDistribution | Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution |
| MixtureOfDiscreteDistributions | A Discrete distribution object defined by a vector of Discrete Distributions and a set of probabilities for these Discrete Distributions |
| MultipleDiscreteDistribution | Interface for multiple discrete distribution objects |
| SimpleDiscreteDistribution | A Discrete distribution object, where some specific probabilities are assigned to a finite set of values |
| Simplex | A Simplex object, used to define sets of probabilities that sum 1 |
| TruncatedExponentialDiscreteDistribution | Discretized Truncated (on the right) Exponential distribution, where the probabilities are given the exponential, conditioned by the upper limit |
| UniformDiscreteDistribution | Discretized Uniform distribution. All categories are equidistributed all along a given interval |
| ContingencyTableGenerator | Generate a random contingency matrix with given marginal counts |
| RandomFactory | This is the interface for the Random Number Generators |
| RandomTools | Utilitary function dealing with random numbers |
| Uniform01K | A uniform random number generator |
| Uniform01QD | A quick and dirty uniform random number generator |
| Uniform01WH | A uniform random number generator |
| Range | The Range class, defining an interval |
| RangeCollection | Interface discribing a collection of Range objects |
| rangeComp_ | A special class used inside RangeCollection |
| RangeSet | This class implements a data structure describing a set of intervales |
| MultiRange | This class implements a data structure describing a set of non-overlapping intervales |
| ContingencyTableTest | Implements tests on contingency tables |
| CorrespondenceAnalysis | |
| DualityDiagram | The core class of a multivariate analysis |
| PrincipalComponentAnalysis | This class allows to perform a principal component analysis |
| StatTest | Interface for statistical test results |
| StatTools | Statistics tools and utilitary functions |
| PValue_ | |
| TransformedParameter | The TransformedParameter abstract class |
| RTransformedParameter | Parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [ |
| IntervalTransformedParameter | Parameter transformation from ] a, b [ to ]-inf, + inf [ |
| PlaceboTransformedParameter | 'Placebo' parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [ |
| VectorException | General Exception dealing with vectors |
| EmptyVectorException | Exception thrown when an empty vector was found |
| DimensionException | Exception thrown when a dimension problem occured |
| ElementNotFoundException | Exception thrown when a given element was not found in the vector |
| VectorTools | |
| order_Cmp_ | |
| KeyvalException | Exception thrown by the Keyval parser |
| KeyvalTools | Tools to deal with the keyval syntax |
| NestedStringTokenizer | An improved tokenizer for strings |
| StringTokenizer | A tokenizer for strings |
| TextTools | Some utilitary functions that work on strings |
| AttributesTools | Some functions to deal with attributes, i.e. parameters passed to a program/method |
| MapTools | A fiew tools working on map objects |
1.8.3.1-20130209 
