Commit 6ab7693c authored by Pierre-Henri Wuillemin's avatar Pierre-Henri Wuillemin

synchronized with master

parents 89c28cc1 ed34ac13
This diff is collapsed.
......@@ -34,7 +34,7 @@ namespace gum {
namespace samplers {
/**
* @class Gibbs Gibbs.h <agrum/BN/particle/Gibbs.h>
* @class GibbsSampler Gibbs.h <agrum/BN/samplers/Gibbs.h>
* @brief class for particle using GIBBS sampling
* @ingroup bn_particles
*
......@@ -58,17 +58,17 @@ namespace gum {
*/
/**
* Insert new evidence in the sampler.
* @warning if an evidence already w.r.t. a given node and a new
* evidence w.r.t. this node is inserted, the old evidence is removed.
*/
* Insert new evidence in the sampler.
* @warning if an evidence already w.r.t. a given node and a new
* evidence w.r.t. this node is inserted, the old evidence is removed.
*/
virtual void addSoftEvidenceSampler( const Potential<GUM_SCALAR>& pot );
/**
* Insert new hard evidence in the sampler.
* @warning if an evidence already w.r.t. a given node and a new
* evidence w.r.t. this node is inserted, the old evidence is removed.
*/
* Insert new hard evidence in the sampler.
* @warning if an evidence already w.r.t. a given node and a new
* evidence w.r.t. this node is inserted, the old evidence is removed.
*/
virtual void addHardEvidenceSampler( NodeId id, Idx pos );
/**
......
......@@ -51,7 +51,7 @@
namespace gum {
/**
* @class sdyna sdyna.h <agrum/FMDP/SDyna/sdyna.h>
* @class SDYNA sdyna.h <agrum/FMDP/SDyna/sdyna.h>
* @brief
* @ingroup fmdp_group
*
......@@ -59,7 +59,6 @@ namespace gum {
* Instance of SDyna architecture should inherit
*
*/
class SDYNA {
// ###################################################################
......
......@@ -68,15 +68,14 @@ namespace gum {
PutDown = 5,
FillUp = 6
};
// clang-format off
/**
* @class Factory factorySimulator.h
* <agrum/FMDP/simulation/factorySimulator.h>
* @class FactorySimulator factorySimulator.h <agrum/FMDP/simulation/factorySimulator.h>
* @brief A class to simulate the Factory problem
* @ingroup fmdp_group
*
*
*
*/
// clang-format on
class FactorySimulator : public AbstractSimulator {
public:
......
......@@ -68,14 +68,14 @@ namespace gum {
PutDown = 6,
FillUp = 7
};
// clang-format off
/**
* @class Taxi taxiSimulator.h <agrum/FMDP/simulation/taxiSimulator.h>
* @class TaxiSimulator taxiSimulator.h <agrum/FMDP/simulation/taxiSimulator.h>
* @brief A class to simulate the Taxi problem
* @ingroup fmdp_group
*
*
*
*/
// clang-format on
class TaxiSimulator : public AbstractSimulator {
public:
......
......@@ -34,26 +34,24 @@
namespace gum {
namespace prm {
// clang-format off
/**
* @class ClassBayesNet<GUM_SCALAR> classBayesNet.h
*<agrum/PRM/classBayesNet.h>
* @class ClassBayesNet classBayesNet.h <agrum/PRM/classBayesNet.h>
* @brief This class decorates a gum::prm::Class<GUM_SCALAR> has an
*IBaseBayesNet.
* IBaseBayesNet.
* @tparam GUM_SCALAR The type of scalar to use.
*
* This class filters PRMAttribute and PRMAggregate in a way it can be
*interpreted
*as
* a IBayesNet. SlotChains and PRMReferenceSlot are not represented.
* interpreted as a IBayesNet.
*
* SlotChains and PRMReferenceSlot are not represented.
*
* Remember that a ClassBayesNet<GUM_SCALAR> does not contain input nodes
*parents
*and
* output nodes children. Thus you should be careful when using one of the
* BayesNetInference over a ClassBayesNet<GUM_SCALAR> since some variables
*are
*missing in
* the DAG but not in the nodes CPT.
* parents and output nodes children. Thus you should be careful when using
* one of the BayesNetInference over a ClassBayesNet<GUM_SCALAR> since some
* variables are missing in the DAG but not in the nodes CPT.
*/
// clang-format on
template <typename GUM_SCALAR>
class ClassBayesNet : public IBayesNet<GUM_SCALAR> {
public:
......
......@@ -46,12 +46,11 @@ namespace gum {
namespace prm {
/**
* @class Class<GUM_SCALAR> class.h <agrum/PRM/class.h>
* @brief A Class<GUM_SCALAR> is an object of a PRM representing a fragment
*of a
* Bayesian Network which can be instantiated in PRMInstance.
* @class PRMClass PRMClass.h <agrum/PRM/elements/PRMClass.h>
* @brief A PRMClass is an object of a PRM representing a fragment
* of a Bayesian Network which can be instantiated in PRMInstance.
*
* @see PRM Class<GUM_SCALAR> PRMClassElement<GUM_SCALAR>
* @see PRMClassElement
* @ingroup prm_group
*/
template <typename GUM_SCALAR>
......
......@@ -40,23 +40,20 @@ namespace gum {
/**
* @class PRMInstance<GUM_SCALAR> instance.h <agrum/PRM/elements/instance.h>
* @class PRMInstance instance.h <agrum/PRM/elements/instance.h>
*
* @brief An PRMInstance<GUM_SCALAR> is a Bayesian Network fragment defined
*by
*a Class<GUM_SCALAR> and
* used in a PRMSystem.
* @brief An PRMInstance is a Bayesian Network fragment defined by a Class
* and used in a PRMSystem.
*
* Before using an PRMInstance<GUM_SCALAR> for inference YOU MUST call
* PRMInstance<GUM_SCALAR>::instantiateSlotChains() and
*PRMInstance<GUM_SCALAR>::instantiate() on it before,
* otherwise DiscreteVariable pointers will be inconsistent and inference
*will
* be erroneous. Of course, this must be done once you have set all
*reference
* in the current system.
* Before using an PRMInstance for inference YOU MUST call
* PRMInstance::instantiateSlotChains() and PRMInstance::instantiate() on
* it before, otherwise DiscreteVariable pointers will be inconsistent and
* inference will be erroneous. Of course, this must be done once you have
* set all reference in the current system.
*
* @see Class<GUM_SCALAR> PRM PRMClassElement @ingroup prm_group
* @see PRMClass PRM PRMClassElement
*
* @ingroup prm_group
*/
template <typename GUM_SCALAR>
class PRMInstance : public PRMObject {
......
......@@ -61,8 +61,7 @@ namespace gum {
* @class DFSTree DFSTree.h <agrum/PRM/gspan/DFSTree.h>
*
* A DFSTree is used by gspan to sort lexicographically patterns
*discovered
* in an interface graph.
* discovered in an interface graph.
*/
template <typename GUM_SCALAR>
class DFSTree : private DiGraph {
......@@ -144,12 +143,6 @@ namespace gum {
*/
void addRoot( LabelData& data );
/**
* @class EdgeGrowth DFSTree.h <agrum/PRM/DFSTree.h>
* This class is used to define an edge growth of a pattern
* in this DFSTree.
*/
/**
* @brief Add a one edge growth of p as one of its child.
*
......
......@@ -50,6 +50,11 @@ namespace gum {
template <typename GUM_SCALAR>
class DFSTree;
/**
* @class EdgeGrowth DFSTree.h <agrum/PRM/DFSTree.h>
* This class is used to define an edge growth of a pattern
* in this DFSTree.
*/
template <typename GUM_SCALAR>
class EdgeGrowth {
public:
......
......@@ -73,8 +73,7 @@ namespace gum {
std::ostream& operator<<( std::ostream& out, const LabelData& data );
/**
* @struct NodeData<GUM_SCALAR> interfaceGraph.h
* <agrum/PRM/gspan/interfaceGraph.h>
* @struct NodeData interfaceGraph.h <agrum/PRM/gspan/interfaceGraph.h>
* Inner class to handle data about nodes in __graph.
*/
template <typename GUM_SCALAR>
......@@ -107,8 +106,7 @@ namespace gum {
const NodeData<GUM_SCALAR>& data );
/**
* @struct EdgeData<GUM_SCALAR> interfaceGraph.h
* <agrum/PRM/gspan/interfaceGraph.h>
* @struct EdgeData interfaceGraph.h <agrum/PRM/gspan/interfaceGraph.h>
* Inner class to handle data about edges in __graph.
*/
template <typename GUM_SCALAR>
......
......@@ -55,14 +55,16 @@ namespace gum {
template <typename GUM_SCALAR>
class DFSTree;
// clang_format off
/**
* @class SearchStrategy<GUM_SCALAR> DFSTree.h <agrum/PRM/gspan/DFSTree.h>
* @class SearchStrategy searchStrategy.h <agrum/PRM/gspan/searchStrategy.h>
*
* This is an abstract class used to tune search strategies in the gspan
* algorithm. Since GSpan uses a DFS to expand the search tree, this class
* works as a stack regarding adding and removing informations about the
*growths.
* growths.
*/
// clang_format on
template <typename GUM_SCALAR>
class SearchStrategy {
......
......@@ -43,7 +43,7 @@
namespace gum {
/**
* @struct maximizes functors.h <agrum/multidim/patterns/functors.h>
* @struct Maximizes functors.h <agrum/core/functors.h>
* @brief Maximization function object class
* @ingroup core
*
......@@ -69,7 +69,7 @@ namespace gum {
};
/**
* @struct minimizes functors.h <agrum/multidim/patterns/functors.h>
* @struct Minimizes functors.h <agrum/core/functors.h>
* @brief Minimization function object class
* @ingroup core
*
......@@ -95,7 +95,7 @@ namespace gum {
};
/**
* @struct argmax functors.h <agrum/multidim/patterns/functors.h>
* @struct ArgumentMaximises functors.h <agrum/core/functors.h>
* @brief Arg Max function object class
* @ingroup core
*
......
#ifndef DOXYGEN_SHOULD_SKIP_THIS
/* lrslib.hpp (vertex enumeration using lexicographic reverse search) */
#define TITLE "lrslib "
#define VERSION "v.6.2 2016.3.28"
......@@ -483,3 +485,5 @@ void lrs_set_obj_mp(
lrs_mp_vector num,
lrs_mp_vector den,
int64_t max ); /* same as lrs_set_obj but num/den has lrs_mp type */
#endif // DOXYGEN_SHOULD_SKIP_THIS
#ifndef DOXYGEN_SHOULD_SKIP_THIS
/* lrslong.h (lrs long integer arithmetic library */
/* Copyright: David Avis 2000, avis@cs.mcgill.ca */
/* Version 4.0, February 17, 2000 */
......@@ -269,3 +271,5 @@ void* xcalloc( int64_t n, int64_t s, int64_t l, char* f );
void lrs_default_digits_overflow();
/* end of lrs_mp.h (vertex enumeration using lexicographic reverse search) */
#endif // DOXYGEN_SHOULD_SKIP_THIS
#ifndef DOXYGEN_SHOULD_SKIP_THIS
/* lrsmp.h (lrs extended precision arithmetic library) */
/* Copyright: David Avis 2000, avis@cs.mcgill.ca */
/* Version 4.1, February 17, 2000 */
......@@ -279,3 +281,5 @@ void lrs_default_digits_overflow();
void digits_overflow();
/* end of lrsmp.h (vertex enumeration using lexicographic reverse search) */
#endif // DOXYGEN_SHOULD_SKIP_THIS
......@@ -10,6 +10,8 @@
#ifndef DIRENT_H
#define DIRENT_H
#ifndef DOXYGEN_SHOULD_SKIP_THIS
/*
* Define architecture flags so we don't need to include windows.h.
* Avoiding windows.h makes it simpler to use windows sockets in conjunction
......@@ -870,4 +872,7 @@ static void dirent_set_errno( int error ) {
#ifdef __cplusplus
}
#endif
#endif /* DOXYGEN_SHOULD_SKIP_THIS */
#endif /*DIRENT_H*/
#ifndef _UNISTD_H
#define _UNISTD_H 1
#ifndef DOXYGEN_SHOULD_SKIP_THIS
/* This file intended to serve as a drop-in replacement for
* unistd.h on Windows
* Please add functionality as neeeded
......@@ -52,4 +54,6 @@ typedef unsigned __int16 uint16_t;
typedef unsigned __int32 uint32_t;
typedef unsigned __int64 uint64_t;
#endif /* unistd.h */
\ No newline at end of file
#endif /* DOXYGEN_SHOULD_SKIP_THIS */
#endif /* unistd.h */
......@@ -53,8 +53,9 @@ namespace gum {
*/
class FixedAllocator {
// clang-format off
/**
* @struct Chunk fixedAllocator.h <agrum/core/fixedAllocator.h>
* @struct __Chunk fixedAllocator.h <agrum/core/smallobjectallocator/fixedAllocator.h>
*
* @brief Allocates objects of one given size. Has a fixed limit of
* allocation
......@@ -72,6 +73,7 @@ namespace gum {
*
* @ingroup core
*/
// clang-format on
struct __Chunk {
// ============================================================================
......
......@@ -39,25 +39,25 @@ namespace gum {
namespace learning {
/* =========================================================================
*/
/* === INDEP TEST G2 CLASS ===
*/
/* =========================================================================
*/
/** @class ScoreG2
// clang-format off
/* ========================================================================= */
/* === INDEP TEST G2 CLASS === */
/* ========================================================================= */
/**
* @class IndepTestG2 indepTestG2.h <agrum/learning/scores_and_tests/indepTestG2.h>
* @brief the class for computing G2 independence test scores
* @ingroup learning_group
*
* The class should be used as follows: first, to speed-up computations, you
* should consider computing all the independence tests you need in one
*pass.
* The class should be used as follows: first, to speed-up computations,
* you should consider computing all the independence tests you need in one
* pass.
*
* To do so, use the appropriate addNodeSet methods. These will compute
* everything you need. Use method score to retrieve the scores related to
* the independence test that were computed. See the IndependenceTest class
*for
* details.
* for details.
*/
// clang-format on
template <typename IdSetAlloc = std::allocator<Idx>,
typename CountAlloc = std::allocator<double>>
class IndepTestG2 : public IndependenceTest<IdSetAlloc, CountAlloc> {
......
......@@ -43,7 +43,7 @@ namespace gum {
// ===========================================================================
// clang-format off
/**
* @class MultiDimCIModel
* @class MultiDimICIModel
* @headerfile multiDimICIModel.h <agrum/multidim/ICIModels/multiDimICIModel.h>
* @ingroup multidim_group
*
......
......@@ -55,7 +55,7 @@ namespace gum {
class MultiDimFunctionGraphTreeManager;
/**
* @class MultiDimFunctionGraph
* @class MultiDimFunctionGraph
* @ingroup multidim_group
*
* @warning Doxygen does not like spanning command on multiple line, so we
......
......@@ -764,6 +764,7 @@ WARN_LOGFILE = warning.txt
# Note: If this tag is empty the current directory is searched.
INPUT = @AGRUM_SOURCE_DIR@/agrum \
@AGRUM_SOURCE_DIR@/docs/mainpage.dox \
@AGRUM_SOURCE_DIR@/docs/howtos \
@AGRUM_SOURCE_DIR@/docs/modules
......@@ -834,7 +835,8 @@ EXCLUDE_PATTERNS = */cocoR/*
EXCLUDE_SYMBOLS = IApproximationPolicy \
ICPTDisturber \
ICPTGenerator \
SetIteratorStaticEnd
SetIteratorStaticEnd \
TerminalNodePolicy
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
......
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