 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 , 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 |