|
class | AbstractColorSet |
| Partial implementation of the ColorSet interface. More...
|
|
class | AbstractDiscreteDistribution |
| Partial implementation of the DiscreteDistribution interface. More...
|
|
class | AbstractFontManager |
|
class | AbstractGraphicDevice |
| Partial implementation of the GraphicDevice interface. More...
|
|
class | AbstractHmmLikelihood |
| partial impmementation of Hmm Likelihoods. More...
|
|
class | AbstractHmmTransitionMatrix |
| Partial implementation of HmmTransitionMatrix. More...
|
|
class | AbstractNumericalDerivative |
| Numerical derivative function wrapper, partial implementation. More...
|
|
class | AbstractOptimizationStopCondition |
| Partial implementation of the OptimizationStopCondition interface. More...
|
|
class | AbstractOptimizer |
| Partial implementation of the Optimizer interface. More...
|
|
class | AbstractOutputStream |
| Helper implementation of the OutputStream interface. More...
|
|
class | AbstractParameterAliasable |
| A partial implementation of the Parametrizable interface. More...
|
|
class | AbstractParametrizable |
| A partial implementation of the Parametrizable interface. More...
|
|
class | AdaptiveKernelDensityEstimation |
| Density estimation using the adaptive kernel method. More...
|
|
class | AliasParameterListener |
| Inner listener class used by AbstractParameterAliasable. More...
|
|
class | ApplicationTools |
| This class provides some common tools for developping applications. More...
|
|
class | AssociationDAGraphImplObserver |
|
class | AssociationDAGraphObserver |
| Defines a DA Graph Associator. It is a template which follows (subscribed to) a Graph. More...
|
|
class | AssociationGraphImplObserver |
|
class | AssociationGraphObserver |
| Defines a Graph Associator. It is a template which follows (subscribed to) a Graph. More...
|
|
class | AssociationTreeGraphImplObserver |
|
class | AssociationTreeGraphObserver |
| Defines a Tree Graph Associator. It is a template which follows (subscribed to) a Graph. More...
|
|
class | AttributesTools |
| Some functions to deal with attributes, i.e. parameters passed to a program/method. More...
|
|
class | AutoCorrelationTransitionMatrix |
| Describe the auto-correlation probabilities inside hidden states of a Hidden Markov Model. More...
|
|
class | AutoParameter |
| The AutoParameter class. More...
|
|
class | BackupListener |
| Save intermediate optimization results to file. More...
|
|
class | BadIntegerException |
| Number exception: integers. More...
|
|
class | BadNumberException |
| Number exception: doubles. More...
|
|
class | BadSizeException |
| Wrong size exception class. More...
|
|
class | BetaDiscreteDistribution |
| Discretized Beta distribution with parameters alpha and beta, on a given interval. On default, the interval is , but it can be restricted. More...
|
|
class | BfgsMultiDimensions |
| Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization method. More...
|
|
class | BinaryOperator |
| Binary arithmetic operator for numerical computation. More...
|
|
class | BppApplication |
|
class | BppBoolean |
| The BppBoolean object class. This class extends the bool type to support the Clonable interface. More...
|
|
class | BppDouble |
| An object wrapper for double values. More...
|
|
class | BppInteger |
| An object wrapper for integer values. More...
|
|
class | BppNotANumber |
|
class | BppNumberI |
| The Number interface. More...
|
|
class | BppODiscreteDistributionFormat |
| Discrete Distribution I/O in BppO format. More...
|
|
class | BppOParametrizableFormat |
| Parametrizable output in BppO format. More...
|
|
class | BppString |
| The BppString object class. This class extends the stl::string class to support the Clonable interface. More...
|
|
class | BppUnsignedInteger |
| An object wrapper for unsigned integer values. More...
|
|
class | BppVector |
| The BppVector object class. This class extends the std::vector class to support the Clonable interface. More...
|
|
class | Bracket |
|
class | BracketPoint |
|
class | BrentOneDimension |
| Brent's optimization for one parameter. More...
|
|
class | Clonable |
| The Clonable interface (allow an object to be cloned). More...
|
|
class | ColMatrix |
| Matrix storage by column. More...
|
|
class | ColorManager |
| Associate special colors to a code. More...
|
|
class | ColorSet |
| Specify a set of color definitions. More...
|
|
class | ColorTools |
| Provide tools to deal with color objects. More...
|
|
class | ComputationTree |
| Defines a Computation Tree based on Operators. More...
|
|
class | ConjugateGradientMultiDimensions |
| Conjugate gradient optimization method. More...
|
|
class | ConstantDistribution |
| Constant discrete distribution. More...
|
|
class | ConstantOperator |
| Constant (ie leaf) operator. More...
|
|
class | ConstraintException |
| Exception thrown when a value do not match a given constraint. More...
|
|
class | ConstraintInterface |
| The constraint interface. More...
|
|
class | ContingencyTableGenerator |
| Generate a random contingency matrix with given marginal counts. More...
|
|
class | ContingencyTableTest |
| Implements tests on contingency tables. More...
|
|
class | CoordsTools |
| Some functions to deal with Point2D. More...
|
|
class | CorrespondenceAnalysis |
| This class allows to perform a correspondence analysis. More...
|
|
class | DAGraph |
|
class | DAGraphImpl |
|
class | DataTable |
| This class corresponds to a 'dataset', i.e. a table with data by rows and variable by columns. More...
|
|
class | DefaultColorSet |
| Default color definitions. More...
|
|
class | DimensionException |
| Exception thrown when a dimension problem occured. More...
|
|
class | DirectionFunction |
|
class | DirichletDiscreteDistribution |
| Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex. More...
|
|
class | DiscreteDistributionInterface |
| Interface for discrete distribution objects. More...
|
|
class | DownhillSimplexMethod |
| This implements the Downhill Simplex method in multidimensions. More...
|
|
class | DualityDiagram |
| The core class of a multivariate analysis. More...
|
|
class | DuplicatedTableColumnNameException |
| Excpetion thrown when attempting to duplicate a column name. More...
|
|
class | DuplicatedTableRowNameException |
| Exception thrown when attempting to duplicate a row name. More...
|
|
class | DvipsColorSet |
| The dvips color definitions. More...
|
|
class | EdgesIteratorClass |
|
class | EdgesIteratorClass< Graph::ALLGRAPHITER, is_const > |
|
class | EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > |
|
class | EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > |
|
class | EigenValue |
| Computes eigenvalues and eigenvectors of a real (non-complex) matrix. More...
|
|
class | ElementNotFoundException |
| Exception thrown when a given element was not found in the vector. More...
|
|
class | EmptyVectorException |
| Exception thrown when an empty vector was found. More...
|
|
class | Exception |
| Exception base class. Overload exception constructor (to control the exceptions mechanism). Destructor is already virtual (from std::exception) More...
|
|
class | ExponentialDiscreteDistribution |
| Discretized Exponential distribution. More...
|
|
class | FileTools |
| Some utilitary functions to deal with files. More...
|
|
class | FirstOrderDerivable |
| This is the abstract class for first order derivable functions. More...
|
|
class | FirstOrderDerivableWrapper |
| General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework. More...
|
|
class | FivePointsNumericalDerivative |
| Five points numerical derivative function wrapper. More...
|
|
class | Font |
| Data structure for fonts. More...
|
|
class | FontManager |
| Associate special fonts to a code. More...
|
|
class | FullHmmTransitionMatrix |
| Describe the transition probabilities between hidden states of a Hidden Markov Model. More...
|
|
class | FunctionInterface |
| This is the function abstract class. More...
|
|
class | FunctionOperator |
| Implements a double operator (ie leaf in the computation tree) where value comes from a function. More...
|
|
class | FunctionStopCondition |
| Stop condition on function value. More...
|
|
class | FunctionTools |
| This class contains static methods to deal with Function objects. More...
|
|
class | FunctionWrapper |
| General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework. More...
|
|
class | GammaDiscreteDistribution |
| Discretized Gamma distribution with an offset. More...
|
|
class | GaussianDiscreteDistribution |
| Discretized Gaussian distribution. More...
|
|
class | GlobalGraph |
|
class | GoldenSectionSearch |
| Golden Section Search optimization algorithm for one parameter. More...
|
|
class | Graph |
|
class | GraphicDevice |
| Interface for all plotting devices. More...
|
|
class | 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. More...
|
|
class | HmmBadStateException |
| Exception thrown when an unvalid state is requested. More...
|
|
class | HmmEmissionProbabilities |
| Interface for computing emission probabilities in a Hidden Markov Model. More...
|
|
class | HmmLikelihood |
| Basal interface for Hidden Markov Models likelihood computation. More...
|
|
class | HmmStateAlphabet |
| Hidden states alphabet. More...
|
|
class | HmmTransitionMatrix |
| Describe the transition probabilities between hidden states of a Hidden Markov Model. More...
|
|
class | HmmUnvalidAlphabetException |
| Exception thrown when an unvalid alphabet is specified. More...
|
|
class | IDiscreteDistribution |
| General interface for distance matrix readers. More...
|
|
class | IndexOutOfBoundsException |
| Index out of bounds exception class. More...
|
|
class | InfinityDerivableFirstOrderWrapper |
| Wrapper class for optimization under constraints. More...
|
|
class | InfinityDerivableSecondOrderWrapper |
| Wrapper class for optimization under constraints. More...
|
|
class | InfinityFunctionWrapper |
| Wrapper class for optimization under constraints. More...
|
|
class | IntervalConstraint |
| An interval, either bounded or not, which can also have infinite bounds. More...
|
|
class | IntervalTransformedParameter |
| Parameter transformation from ] a, b [ to ]-inf, + inf [. More...
|
|
class | InvariantMixedDiscreteDistribution |
| Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution. More...
|
|
class | IoDiscreteDistribution |
| General interface for model I/O. More...
|
|
class | IoDiscreteDistributionFactory |
| Utilitary class for creating discrete distribution readers and writers. More...
|
|
class | IOException |
| The base class exception for IO error. More...
|
|
class | IOFormat |
| The IOFormat interface. More...
|
|
class | IOParametrizable |
| General interface for parametrizable Output. More...
|
|
class | KeyvalException |
| Exception thrown by the Keyval parser. More...
|
|
class | KeyvalTools |
| Tools to deal with the keyval syntax. More...
|
|
class | LinearMatrix |
| Matrix storage in one vector. More...
|
|
class | LogsumHmmLikelihood |
| A simple implementation of hidden Markov models recursion. More...
|
|
class | LowMemoryRescaledHmmLikelihood |
| A modified implementation of the RescaledHmmLikelihood implementation, with lower memory usage. More...
|
|
class | LUDecomposition |
| LU Decomposition. More...
|
|
class | MapTools |
| A fiew tools working on map objects. More...
|
|
class | MathOperator |
| Implements a unary operator that applies a math (described in cmath) operator. More...
|
|
class | Matrix |
| The matrix template interface. More...
|
|
class | MatrixTools |
| Functions dealing with matrices. More...
|
|
class | MetaOptimizer |
| Meta-optimizer. More...
|
|
class | MetaOptimizerInfos |
| Provide a list of optimizer and corresponding options to be used with the MetaOptimizer class. More...
|
|
class | MixtureOfDiscreteDistributions |
| A Discrete distribution object defined by a vector of Discrete Distributions and a set of probabilities for these Discrete Distributions. More...
|
|
class | MolscriptColorSet |
| Molscript color definitions. More...
|
|
class | MultipleDiscreteDistribution |
| Interface for multiple discrete distribution objects. More...
|
|
class | MultiRange |
| This class implements a data structure describing a set of non-overlapping intervals. More...
|
|
class | NegativeOperator |
| Negative value for an operator. More...
|
|
class | NeighborIteratorClass |
| Abstract class for neighbor iterators. More...
|
|
class | NestedStringTokenizer |
| An improved tokenizer for strings. More...
|
|
class | NewtonBacktrackOneDimension |
| Newton's backtrack nearly optimization for one parameter. More...
|
|
class | NewtonOneDimension |
| Newton's optimization for one parameter. More...
|
|
class | NodesIteratorClass |
|
class | NodesIteratorClass< Graph::ALLGRAPHITER, is_const > |
|
class | NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > |
|
class | NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > |
|
class | NoTableColumnNamesException |
| Exception thrown when trying to retrieve a column by its name and no column names have been specified. More...
|
|
class | NoTableRowNamesException |
| Exception thrown when trying to retrieve a row by its name and no row names have been specified. More...
|
|
class | NotImplementedException |
| This exception is sent when a given method is not implemented. More...
|
|
class | NullOutputStream |
| Null output stream (swich off output). More...
|
|
class | NullPointerException |
| The base class exception for NULL pointer error. This exception may be thrown when an unexpected NULL pointer is found. More...
|
|
class | Number |
| The Number object template class. More...
|
|
class | NumberFormatException |
| Number format exception. More...
|
|
class | NumCalcApplicationTools |
|
class | NumConstants |
| this static class contains several useful constant values. More...
|
|
class | NumericalDerivativeInterface |
| Numerical derivative function wrapper. More...
|
|
class | NumTools |
| Some utilitary function for numerical calculus. More...
|
|
class | ODiscreteDistribution |
| General interface writers. More...
|
|
class | OneDimensionOptimizationTools |
| Tools of one parameter-functions optimizations. More...
|
|
class | OParametrizable |
| General interface writers. More...
|
|
class | Operator |
| Interface of operator for numerical computation. More...
|
|
class | OptimizationEvent |
| An event object which indicates that an optimization event occured. More...
|
|
class | OptimizationListener |
| The listener interface for receiving optimization events. More...
|
|
class | OptimizationStopCondition |
| Interface for otimization stop condition objet. More...
|
|
class | OptimizerInterface |
| This is the basal interface for all optimization methods. More...
|
|
class | OrderedSimplex |
| Simplex where all values are in decreasing order. More...
|
|
class | OutOfRangeException |
| Out of range exception class. More...
|
|
class | OutputStream |
| OutputStream interface. More...
|
|
class | Parameter |
| This class is designed to facilitate the manipulation of parameters. More...
|
|
class | ParameterAliasable |
| Extend the Parametrizable interface with support for parameter aliases. More...
|
|
class | ParameterAliasableAdapter |
| A low-level implementation of the ParameterAliasable interface with void functions. More...
|
|
class | ParameterEvent |
|
class | ParameterException |
| The parameter exception base class. More...
|
|
class | ParameterGrid |
| This class is a data structure to specify a set of parameter values (most likely for evaluation by a Function) More...
|
|
class | ParameterList |
| The parameter list object. More...
|
|
class | ParameterListener |
| The parameter listener interface. More...
|
|
class | ParameterNotFoundException |
| Exception thrown when a parameter is not found, for instance in a ParameterList. More...
|
|
class | ParametersStopCondition |
| Stop condition on parameters. More...
|
|
class | Parametrizable |
| This is the interface for all objects that imply parameters. More...
|
|
class | ParametrizableAdapter |
| A low-level implementation of the Parametrizable interface with void functions. More...
|
|
class | ParametrizableCollection |
| Plain collection of parametrizable objects. More...
|
|
class | PgfGraphicDevice |
| LaTeX Portable Graphic Format (Pgf) plotting format. More...
|
|
class | PlaceboTransformedParameter |
| 'Placebo' parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [. More...
|
|
class | Point2D |
| The Point2D class. More...
|
|
class | PowellMultiDimensions |
| Powell's multi-dimensions optimization algorithm for one parameter. More...
|
|
class | PrincipalComponentAnalysis |
| This class allows to perform a principal component analysis. More...
|
|
class | RandomTools |
| Utilitary function dealing with random numbers. More...
|
|
class | Range |
| The Range class, defining an interval. More...
|
|
class | RangeCollection |
| Interface discribing a collection of Range objects. More...
|
|
class | rangeComp_ |
| A special class used inside RangeCollection. More...
|
|
class | RangeSet |
| This class implements a data structure describing a set of intervals. More...
|
|
class | RColorSet |
| R color definitions. More...
|
|
class | ReparametrizationDerivableFirstOrderWrapper |
| Function wrapper that remove simple constraints on parameters. Also transform first order derivatives. More...
|
|
class | ReparametrizationDerivableSecondOrderWrapper |
| Function wrapper that remove simple constraints on parameters. Also transform first and second order derivatives. More...
|
|
class | ReparametrizationFunctionWrapper |
| Function wrapper that remove simple constraints on parameters. More...
|
|
class | RescaledHmmLikelihood |
| A simple implementation of hidden Markov models recursion. More...
|
|
class | RGBColor |
| Describe a color according to its red, green and blue componants. More...
|
|
class | RowMatrix |
| Matrix storage by row. More...
|
|
class | RTransformedParameter |
| Parameter transformation from ] b, +inf [ or ] -inf, b [ to ]-inf, + inf [. More...
|
|
class | SecondOrderDerivable |
| This is the abstract class for second order derivable functions. More...
|
|
class | SecondOrderDerivableWrapper |
| General class that wraps a function into another one. This class is meant to be derivated and just provides a general framework. More...
|
|
class | SimpleDiscreteDistribution |
| A Discrete distribution object, where some specific probabilities are assigned to a finite set of values. More...
|
|
class | SimpleMultiDimensions |
| This Optimizer is a very simple multi-dimensions optimizer, calling a one dimensional optimizer on each parameter. More...
|
|
class | SimpleNewtonMultiDimensions |
| This Optimizer is a simple multi-dimensions optimizer, calling the Newton one dimensional optimizer on each parameter. More...
|
|
class | Simplex |
| A Simplex object, used to define sets of probabilities that sum 1. More...
|
|
class | StateChangedEvent |
|
class | StateListener |
|
class | StatTest |
| Interface for statistical test results. More...
|
|
class | StatTools |
| Statistics tools and utilitary functions. More...
|
|
class | StdErr |
| Standard error stream. More...
|
|
class | StdOut |
| Standard output stream. More...
|
|
class | StdStr |
| String output stream. More...
|
|
class | StlOutputStream |
| STL output stream. More...
|
|
class | StlOutputStreamWrapper |
| STL wrapper for output stream. More...
|
|
class | StringTokenizer |
| A tokenizer for strings. More...
|
|
class | SvgGraphicDevice |
| SVG plotting format. More...
|
|
class | Table |
| This class corresponds to a 'dataset', i.e. a table with data by rows and variable by columns. More...
|
|
class | TableColumnNameNotFoundException |
| Exception thrown when a given column name is not found is a DataTable object. More...
|
|
class | TableColumnNamesException |
| General exception class dealing with column names. More...
|
|
class | TableNameNotFoundException |
| Exception thrown when a given name is not found is a DataTable object. More...
|
|
class | TableRowNameNotFoundException |
| Exception thrown when a given row name is not found is a DataTable object. More...
|
|
class | TableRowNamesException |
| General exception class dealing with row names. More...
|
|
class | TestFunction |
| A simple function with two parameters, mostly for testing and debugging :) More...
|
|
class | ThreePointsNumericalDerivative |
| Three points numerical derivative function wrapper. More...
|
|
class | TransformedParameter |
| The TransformedParameter abstract class. More...
|
|
class | TreeGraph |
|
class | TreeGraphImpl |
|
class | TruncatedExponentialDiscreteDistribution |
| Discretized Truncated (on the right) Exponential distribution, where the probabilities are given the exponential, conditioned by the upper limit. More...
|
|
class | TwoPointsNumericalDerivative |
| Two points numerical derivative function wrapper. More...
|
|
class | UniformDiscreteDistribution |
| Discretized Uniform distribution. All categories are equidistributed all along a given interval. More...
|
|
class | UnvalidFlagException |
|
class | VectorException |
| General Exception dealing with vectors. More...
|
|
class | VectorTools |
|
class | XFigColorManager |
| Color manager for the XFig format. More...
|
|
class | XFigGraphicDevice |
| XFig plotting format. More...
|
|
class | XFigLaTeXFontManager |
| LaTeX font manager for the XFig format. More...
|
|
class | XFigPostscriptFontManager |
| Postscript font manager for the XFig format. More...
|
|
class | ZeroDivisionException |
| The base class exception for zero division error. More...
|
|
|
std::ostream & | operator<< (std::ostream &out, const BppBoolean &s) |
|
std::ostream & | operator<< (std::ostream &out, const BppString &s) |
|
template<class Scalar > |
bool | operator== (const Matrix< Scalar > &m1, const Matrix< Scalar > &m2) |
|
|
template<class T > |
std::vector< T > | operator+ (const std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T > |
std::vector< T > | operator- (const std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T > |
std::vector< T > | operator* (const std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T > |
std::vector< T > | operator/ (const std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T , class C > |
std::vector< T > | operator+ (const std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
std::vector< T > | operator+ (const C &c, const std::vector< T > &v1) |
|
template<class T , class C > |
std::vector< T > | operator- (const std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
std::vector< T > | operator- (const C &c, const std::vector< T > &v1) |
|
template<class T , class C > |
std::vector< T > | operator* (const std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
std::vector< T > | operator* (const C &c, const std::vector< T > &v1) |
|
template<class T , class C > |
std::vector< T > | operator/ (const std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
std::vector< T > | operator/ (const C &c, const std::vector< T > &v1) |
|
template<class T > |
void | operator+= (std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T > |
void | operator-= (std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T > |
void | operator*= (std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T > |
void | operator/= (std::vector< T > &v1, const std::vector< T > &v2) |
|
template<class T , class C > |
void | operator &= (std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
void | operator+= (std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
void | operator-= (std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
void | operator*= (std::vector< T > &v1, const C &c) |
|
template<class T , class C > |
void | operator/= (std::vector< T > &v1, const C &c) |
|