and finally... still more grouping in documentation.

eo/src/do/make_algo_easea.h

@@ -68,8 +68,10 @@
  *
  * This is why the template is the complete EOT even though only the fitness
  * is actually templatized here
+ *
+ *
+ * @ingroup Builders
 */
-
 template <class EOT>
 eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoPopEvalFunc<EOT>& _popeval, eoContinue<EOT>& _continue, eoGenOp<EOT>& _op)
 {

eo/src/do/make_algo_scalar.h

@@ -73,9 +73,9 @@
  *
  * This is why the template is the complete EOT even though only the fitness
  * is actually templatized here
+ *
+ * @ingroup Builders
 */
-
-
 template <class EOT>
 eoAlgo<EOT> & do_make_algo_scalar(eoParser& _parser, eoState& _state, eoEvalFunc<EOT>& _eval, eoContinue<EOT>& _continue, eoGenOp<EOT>& _op, eoDistance<EOT> * _dist = NULL)
 {

eo/src/do/make_checkpoint.h

@@ -69,6 +69,8 @@ bool testDirRes(std::string _dirName, bool _erase);
  *
  * CHANGE (March 2008): now receiving an eoValueParam instead of an eoEvalFuncCounter. This function is just interested
  * in the value of the parameter calculated on the evaluation function, not in the actual function itself!!
+ *
+ * @ingroup Builders
 */
 template <class EOT>
 eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoValueParam<unsigned long>& _eval, eoContinue<EOT>& _continue)

eo/src/do/make_checkpoint_FDC.h

@@ -41,6 +41,9 @@ bool testDirRes(std::string _dirName, bool _erase);
 /////////////////// The checkpoint and other I/O //////////////
 
 
+/**
+ * @ingroup Builders
+ */
 template <class EOT>
 eoCheckPoint<EOT>& do_make_checkpoint(eoParser& _parser, eoState& _state, eoEvalFuncCounter<EOT>& _eval, eoContinue<EOT>& _continue)
 {

eo/src/do/make_checkpoint_assembled.h

@@ -49,7 +49,11 @@
 bool testDirRes(std::string _dirName, bool _erase);
 /////////////////// The checkpoint and other I/O //////////////
 
-/** Of course, Fitness needs to be an eoScalarFitnessAssembled!!! */
+/** Of course, Fitness needs to be an eoScalarFitnessAssembled!!! 
+ *
+ *
+ * @ingroup Builders
+ * */
 template <class EOT>
 eoCheckPoint<EOT>& do_make_checkpoint_assembled(eoParser& _parser, eoState& _state, eoEvalFuncCounter<EOT>& _eval, eoContinue<EOT>& _continue)
 {

eo/src/do/make_continue.h

@@ -49,6 +49,9 @@ It can then be instantiated, and compiled on its own for a given EOType
 
 
 /////////////////// the stopping criterion ////////////////
+ /**
+ * @ingroup Builders
+ */
 template <class Indi>
 eoCombinedContinue<Indi> * make_combinedContinue(eoCombinedContinue<Indi> *_combined, eoContinue<Indi> *_cont)
 {
@@ -59,7 +62,10 @@ eoCombinedContinue<Indi> * make_combinedContinue(eoCombinedContinue<Indi> *_comb
   return _combined;
 }
 
-
+/**
+ *
+ * @ingroup Builders
+ */
 template <class Indi>
 eoContinue<Indi> & do_make_continue(eoParser& _parser, eoState& _state, eoEvalFuncCounter<Indi> & _eval)
 {

eo/src/do/make_general_replacement.h

@@ -39,6 +39,8 @@
 
 /** a helper function that decodes a parameter read by the parser into an
  * eoReduce<EOT> & (allocates the pointer and stores it into an eoState)
+ *
+ * @ingroup Builders
  */
 template <class EOT>
 eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
@@ -129,8 +131,9 @@ eoReduce<EOT> & decode_reduce(eoParamParamType & _ppReduce, eoState & _state)
  *  eoHowMany _surviveOffspring   number of offspring after offspring recuction
  *  eoParamParamType & _reduceOffspringType   how the offspring are reduced
  *  eoParamParamType & _reduceFinalType       how the final population is reduced to initial population size
+ *
+ * @ingroup Builders
  */
-
 template <class EOT>
 eoReplacement<EOT> & make_general_replacement(
     eoParser& _parser, eoState& _state, 

eo/src/do/make_pop.h

@@ -34,17 +34,25 @@
 #include <utils/eoParser.h>
 #include <utils/eoState.h>
 
+/** @defgroup Builders Automatic builders
+ *
+ * Automatic builders are functions that automagically builds most commons instances for you.
+ *
+ * All the options you needs are set in the command-line parser.
+ * Those functions all start with the "do_make_" prefix.
+ *
+ * @ingroup Utilities
+ */
 
-///////////////////////////////// INIT POP ///////////////////////////////
 /**
  * Templatized version of parser-based construct of the population
  * + other initializations that are NOT representation-dependent.
  *
  * It must then be instantiated, and compiled on its own for a given EOType
  * (see e.g. ga.h and ga.pp in dir ga)
+ *
+ * @ingroup Builders
 */
-
-
 template <class EOT>
 eoPop<EOT>&  do_make_pop(eoParser & _parser, eoState& _state, eoInit<EOT> & _init)
 {

eo/src/do/make_run.h

@@ -34,8 +34,9 @@
  * A trivial function - only here to allow instanciation with a give EOType
  *      and separate compilation - see in ga dir, make_run_ga
  *
+ *
+ * @ingroup Builders
 */
-
 template <class EOT>
 void do_run(eoAlgo<EOT>& _algo, eoPop<EOT>& _pop)
 {

eo/src/eoScalarFitnessAssembled.h

@@ -36,6 +36,10 @@
 #include <vector>
 #include <string>
 
+/** @addtogroup Evaluation
+ * @{
+ */
+
 //! Defines properties of eoScalarFitnessAssembled.
 /*! Properties that are hold in this traits class:
     - std::vector<std::string> to hold descriptions of the different fitness terms
@@ -270,7 +274,6 @@ std::istream& operator>>(std::istream& is, eoScalarFitnessAssembled<F, Cmp, Fitn
   return is;
 }
 
+/** @} */
 #endif
 
-
-

eo/src/es/eoEsChromInit.h

@@ -40,7 +40,8 @@ Contact: http://eodev.sourceforge.net
 
 /** Random Es-chromosome initializer (therefore derived from eoInit)
 
-@ingroup EvolutionStrategies
+@ingroup Real
+@ingroup Initializators
 
 
 This class can initialize four types of real-valued genotypes thanks

eo/src/es/eoEsFull.h

@@ -30,7 +30,7 @@
 #include <eoVector.h>
 
 /**
-\ingroup EvolutionStrategies
+\ingroup Real
 
   The most complex evolutionary strategy representation. Co-evolving mutation
 rates and correlated mutations.

eo/src/es/eoEsGlobalXover.h

@@ -36,9 +36,12 @@
 // needs a selector - here random
 #include <eoRandomSelect.h>
 
-/** Gloabl crossover operator for ES genotypes.
+/** Global crossover operator for ES genotypes.
   *  Uses some Atom crossovers to handle both the object variables
   *  and the mutation strategy parameters
+  *
+  *  @ingroup Real
+  *  @ingroup Variators
   */
 template<class EOT>
 class eoEsGlobalXover: public eoGenOp<EOT>

eo/src/es/eoEsMutate.h

@@ -45,7 +45,8 @@
 
 /** ES-style mutation in the large
 
-@ingroup EvolutionStrategies
+@ingroup Real
+@ingroup Variators
 
 Obviously, valid only for eoES*. It is currently valid for three types
 of ES chromosomes:

eo/src/es/eoEsMutationInit.h

@@ -31,7 +31,8 @@
 
 /** Initialize Mutation operator
 
-@ingroup EvolutionStrategies
+@ingroup Real
+@ingroup Variators
 
 Proxy class that is used for initializing the mutation operator. It provides an
 interface between eoEsMutate and the abstract parameterLoader. It also provides

eo/src/es/eoEsSimple.h

@@ -30,7 +30,7 @@ Contact: http://eodev.sourceforge.net
 
 /** Simple Evolution Strategy
 
-@ingroup EvolutionStrategies
+@ingroup Real
 
 One of the more simple evolution strategies, sporting just a single stdeviation
 for the entire chromosome. For more advanced versions see also eoEsStdev

eo/src/es/eoEsStandardXover.h

@@ -41,6 +41,9 @@
  *  and the mutation strategy parameters
  *  It is an  eoBinOp and has to be wrapped into an eoGenOp before being used
  *  like the global version
+ *
+ *  @ingroup Real
+ *  @ingroup Variators
  */
 template<class EOT> 
 class eoEsStandardXover: public eoBinOp<EOT>

eo/src/es/eoEsStdev.h

@@ -28,10 +28,10 @@ Contact: http://eodev.sourceforge.net
 
 /** Evolutionary Strategy with a standard deviation per parameter
 
-@ingroup EvolutionStrategies
-
 Evolutionary strategie style representation, supporting co-evolving
 standard deviations.
+
+@ingroup Real
 */
 template <class Fit>
 class eoEsStdev : public eoVector<Fit, double>

eo/src/es/eoNormalMutation.h

@@ -43,8 +43,10 @@
  * As for the bounds, the values are here folded back into the bounds.
  * The other possiblity would be to iterate until we fall inside the bounds -
  *     but this sometimes takes a long time!!!
+ *
+ * @ingroup Real
+ * @ingroup Variators
  */
-
 template<class EOT> class eoNormalVecMutation: public eoMonOp<EOT>
 {
  public:
@@ -111,8 +113,10 @@ private:
  * As for the bounds, the values are here folded back into the bounds.
  * The other possiblity would be to iterate until we fall inside the bounds -
  *     but this sometimes takes a long time!!!
+ *
+ * @ingroup Real
+ * @ingroup Variators
  */
-
 template<class EOT> class eoNormalMutation
     : public eoMonOp<EOT>
 {
@@ -172,8 +176,10 @@ private:
  *  and write the update() method!
  *  here the 1 fifth rule: count the proportion of successful mutations, and
  *  increase sigma if more than threshold (1/5 !)
+ *
+ * @ingroup Real
+ * @ingroup Variators
  */
-
 template<class EOT> class eoOneFifthMutation :
   public eoNormalMutation<EOT>, public eoUpdatable
 {

eo/src/es/eoReal.h

@@ -33,6 +33,8 @@
 
 /** eoReal: implementation of simple real-valued chromosome.
   * based on eoVector class
+ *
+ * @ingroup Real
 */
 template <class FitT> class eoReal: public eoVector<FitT, double>
 {