more doc groups, cleaner modules hierarchy

eo/src/PO.h

@@ -35,6 +35,8 @@
     defined. A best fitness also belongs to the particle.Fitness says how
     good is the particle for a current iteration whereas the best fitness can be saved for
     many iterations.
+
+    @ingroup Core
 */
 template < class F > class PO:public EO < F >
 {

eo/src/eoBreed.h

@@ -41,6 +41,8 @@ eoBreed derived class rather than relying on a seperate select and
 transform function.
 
 @see eoSelect, eoTransform, eoSelectTransform
+
+@ingroup Combination
 */
 template<class EOT>
 class eoBreed : public eoBF<const eoPop<EOT>&, eoPop<EOT>&, void>
@@ -52,6 +54,8 @@ class eoBreed : public eoBF<const eoPop<EOT>&, eoPop<EOT>&, void>
 
 Special breeder that is just an application of an embedded select,
 followed by an embedded transform
+
+@ingroup Combination
 */
 template <class EOT>
 class eoSelectTransform : public eoBreed<EOT>

eo/src/eoOp.h

@@ -30,7 +30,7 @@
 #include <eoFunctor.h>
 #include <utils/eoRNG.h>
 /**
-@defgroup Operators Operators
+@defgroup Operators Evolutionary Operators
 
 in EO, an operator is any functors that modifies objects and inherits from an eoOp.
 
@@ -59,9 +59,12 @@ how to build them from a description in a file.
 Variators are operators that modify individuals.
 
 @defgroup Selectors Selection operators
+
 Selectors are operators that select a subset of a population.
 
+
 @defgroup Replacors Replacement operators
+
 Replacors are operators that replace a subset of a population by another set of individuals.
 */
 

eo/src/eoProportionalCombinedOp.h

@@ -30,13 +30,26 @@
 #include <eoOp.h>
 #include <utils/eoRNG.h>
 #include <utils/eoLogger.h>
+
 /**
-\defgroup PropCombinedOperators
-Combination of same-type Genetic Operators - Proportional choice
+\defgroup Utilities Utilities
+
+Classes that may help you write elegant code.
+*/
+
+/**
+@defgroup Combination Operators combination
+
+Classes that permits to combine several operators in a single one.
+
+@ingroup Utilities
+@{
 */
 
 /** @name PropCombined Genetic operators
 
+Combination of same-type Genetic Operators.
+
 This files contains the classes eoPropCombinedXXXOp (XXX in {Mon, Bin, Quad})
 that allow to use more than a single operator of a specific class
 into an algorithm, chosing by a roulette wheel based on user-defined rates
@@ -214,3 +227,4 @@ std::vector<double> rates;
 // for General Ops, it's another story - see eoOpContainer
 #endif
 
+/** @} */

eo/src/eoVector.h

@@ -30,7 +30,13 @@ Old contact: todos@geneura.ugr.es, http://geneura.ugr.es
 
 
 /**
- @addtogroup Core
+ @defgroup Representations Representations
+
+ Solution to a given optimization problem are using a given representation, and are called individuals.
+
+ Some of the most classical representations are proposed, but you can create your own one, providing
+ that it inherits from the EO base class. It will be used as a template parameter in almost all operators.
+
  @{
 */
 

eo/src/eoVectorParticle.h

@@ -29,7 +29,7 @@
 
 
 /**
- @addtogroup Core
+ @addtogroup Representations
  @{
 */
 

eo/src/ga/eoBit.h

@@ -42,9 +42,11 @@
 
 #include "eoVector.h"
 
-/** @defgroup bitstring
+/** @defgroup bitstring Bit strings
 
 Various functions for a bitstring representation
+
+@ingroup Representations
 */
 
 /** Implementation of bitstring chromosome.

eo/src/gp/eoParseTree.h

@@ -40,8 +40,9 @@ using namespace gp_parse_tree;
 /** @defgroup ParseTree
 
 Various functions for tree-based Genetic Programming
-*/
 
+@ingroup Representations
+*/
 
 
 /** Implementation of parse-tree for genetic programming

eo/src/gp/eoStParseTreeDepthInit.h

@@ -51,6 +51,8 @@ using namespace gp_parse_tree;
   \li int type(int child) which returns the required type for child 0, 1 or 2
   
   Pruning strongly typed trees is not possible at the moment.
+
+  \ingroup Representations
 */
 
 /** eoStParseTreeDepthInit : the initializer class for strongly typed tree-based genetic programming

eo/src/utils/eoRealBounds.h

@@ -31,7 +31,9 @@
 #include <utils/eoRNG.h>
 
 /**
-\defgroup EvolutionStrategies
+\defgroup EvolutionStrategies Continuous vector
+
+@ingroup Representations
 
 */