fix most of the doxygen warnings

eo/src/eoContinue.h

@@ -50,11 +50,17 @@ class eoContinue : public eoUF<const eoPop<EOT>&, bool>, public eoPersistent
 public:
   virtual std::string className(void) const { return "eoContinue"; }
 
+  /** Read from a stream
+   * @param __is istream to read from
+   */
   void readFrom (std :: istream & __is) {
       (void)__is;
     /* It should be implemented by subclasses ! */
   }
   
+  /** Print on a stream
+   * @param __os ostream to print on
+   */
   void printOn (std :: ostream & __os) const {
       (void)__os;
     /* It should be implemented by subclasses ! */

eo/src/eoFixedInertiaWeightedVelocity.h

@@ -58,7 +58,7 @@ public:
     * @param _c2 - The second learning factor used for the local/global best(s). Type must be POT::ParticleVelocityType 
     * @param _bounds - An eoRealBaseVectorBounds: real bounds for real velocities. 
     * If the velocities are not real, they won't be bounded by default. Should have a eoBounds ?
-    * @param _boundsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
+    * @param _bndsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
     * @param _gen - The eo random generator, default=rng
     */
     eoFixedInertiaWeightedVelocity (eoTopology < POT > & _topology,

eo/src/eoGenContinue.h

@@ -86,11 +86,17 @@ public:
   
   virtual std::string className(void) const { return "eoGenContinue"; }
 
+  /** Read from a stream
+   * @param __is the istream to read from
+   */
   void readFrom (std :: istream & __is) {
     
     __is >> thisGeneration; /* Loading the number of generations counted */
   }
   
+  /** Print on a stream
+   * @param __os the ostream to print on
+   */
   void printOn (std :: ostream & __os) const {
     
     __os << thisGeneration << std :: endl; /* Saving the number of generations counted */   

eo/src/eoInit.h

@@ -191,7 +191,7 @@ class eoInitPermutation: public eoInit<EOT>
     eoInitAdaptor changes the place in the hierarchy
     from eoInit to eoMonOp. This is mainly a type conversion,
     nothing else
-    .
+    
     @see eoInit, eoMonOp
 */
 template <class EOT>

eo/src/eoInitializer.h

@@ -66,6 +66,7 @@ public:
     //! @param _proc Evaluation function
     //! @param _initVelo Initialization of the velocity
     //! @param _initBest Initialization of the best
+    //! @param _topology the topology to use
     //! @param _pop Population
     eoInitializer(
         eoUF<POT&, void>& _proc,
@@ -80,6 +81,7 @@ public:
     //! @param _proc Evaluation function
     //! @param _initVelo Initialization of the velocity
     //! @param _initBest Initialization of the best
+    //! @param _topology the topology to use
     //! @param _pop Population
     eoInitializer(
         eoPopEvalFunc <POT>& _proc,

eo/src/eoInt.h

@@ -43,6 +43,7 @@ template <class FitT> class eoInt: public eoVector<FitT, int>
   /**
    * (Default) Constructor.
    * @param size Size of the std::vector
+   * @param value fill the vector with this value
    */
   eoInt(unsigned size = 0, int value = 0):
     eoVector<FitT, int>(size, value) {}

eo/src/eoIntegerVelocity.h

@@ -60,7 +60,7 @@ public:
     * @param _c3 - The third learning factor used for the local/global best(s). Type must be POT::ParticleVelocityType 
     * @param _bounds - An eoRealBaseVectorBounds: real bounds for real velocities. 
     * If the velocities are not real, they won't be bounded by default. Should have a eoBounds ?
-    * @param _boundsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
+    * @param _bndsModifier - An eoRealBoundModifier used to modify the bounds (for real bounds only).
     * @param _gen - The eo random generator, default=rng
     */
     eoIntegerVelocity (eoTopology < POT > & _topology,
@@ -104,6 +104,7 @@ public:
 
 
     /** Constructor: Neither bounds nor bound updater required <-> free velocity
+     * @param _topology the topology to use
        * @param _c1 - The first learning factor quantify how much the particle trusts itself. Type must be POT::ParticleVelocityType 
        * @param _c2 - The second learning factor used for the particle's best. Type must be POT::ParticleVelocityType 
        * @param _c3 - The third learning factor used for the local/global best(s). Type must be POT::ParticleVelocityType 

eo/src/eoLinearTopology.h

@@ -48,7 +48,7 @@ public:
 
     /**
      * Build the topology made of _neighborhoodSize neighborhoods.
-     * @param _neighborhoods - The size of each neighborhood. 
+     * @param _neighborhoodSize - The size of each neighborhood. 
      */
     eoLinearTopology (unsigned _neighborhoodSize):neighborhoodSize (_neighborhoodSize),isSetup(false){}
 

eo/src/eoOneToOneBreeder.h

@@ -55,7 +55,6 @@ class eoOneToOneBreeder: public eoBreed<EOT>
   /** Ctor:
    * @param _op       a general operator (must MODIFY only ONE parent)
    * @param _eval     an eoEvalFunc to evaluate the offspring 
-   * @param _select   a selectoOne, to be used for all selections [sequential]
    * @param _pReplace probability that the best of parent/offspring wins [1]
    * @param _howMany  eoHowMany offpsring to generate [100%]
    */

eo/src/eoOpSelMason.h

@@ -59,7 +59,7 @@ public:
 	Stores all operators built in a database (#allocMap#), so that somebody 
 	can destroy them later. The Mason is in charge or destroying the operators,
 	since the built object can´t do it itself. The objects built must be destroyed
-	from outside, using the #destroy# method
+	from outside, using the "destroy" method
 	*/
 	virtual eoOpSelector<eoClass>* make(std::istream& _is) {
 

eo/src/eoOrderXover.h

@@ -58,6 +58,8 @@ template<class Chrom> class eoOrderXover: public eoQuadOp<Chrom>
 	  * @param _chrom2 The second parent chromosome.
 	  * @param _child The result chromosome.
 	  * @param _direction The direction of the OrderXover (left: -1 or right: 1)
+      * @param _cut1 index of the first cut 
+      * @param _cut2 index of the second cut
 	  */
 	 void cross(Chrom& _chrom1, Chrom& _chrom2, Chrom& _child, char _direction, unsigned _cut1, unsigned _cut2){
 	 		

eo/src/eoParticleFullInitializer.h

@@ -66,6 +66,7 @@ template <class POT> class eoParticleInitializer : public eoInitializerBase <POT
     //! @param _proc Evaluation function
     //! @param _initVelo Initialization of the velocity
     //! @param _initBest Initialization of the best
+    //! @param _topology Topology to use
     //! @param _pop Population
     eoParticleFullInitializer(
       eoUF<POT&, void>& _proc,
@@ -80,6 +81,7 @@ template <class POT> class eoParticleInitializer : public eoInitializerBase <POT
     //! @param _proc Evaluation function
     //! @param _initVelo Initialization of the velocity
     //! @param _initBest Initialization of the best
+    //! @param _topology Topology to use
     //! @param _pop Population
     eoParticleFullInitializer(
       eoPopEvalFunc <POT>& _proc,

eo/src/eoPop.h

@@ -87,10 +87,10 @@ public:
 	  }
 	};
 
-	/** appstd::ends random guys at end of pop.
+	/** appends random guys at end of pop.
 	    Can be used to initialize it pop is empty 
     
-	@param _popSize total population size
+	@param _newPopSize total population size
 	@param _chromInit Initialization routine, produces EO's, needs to be an eoInit 
 	*/
     void append( unsigned _newPopSize, eoInit<EOT>& _chromInit )

eo/src/eoPrintable.h

@@ -38,7 +38,7 @@ some objects (for instance, a #eoFactory# or a random number generator.
 /**
 Base class for objects that can print themselves
 (#printOn#). Besides, this file defines the standard output for all the objects; 
-if the objects define printOn there's no need to define #operator <<#.
+if the objects define printOn there's no need to define "operator<<".
 
   @ingroup Core
  */

eo/src/eoReduceMerge.h

@@ -48,10 +48,11 @@ eoReduceMerge: Replacement strategies that start by reducing the parents,
 This is the way to do SSGA: the offspring gets inserted in the population
 even if it is worse than anybody else.
 
-@classes: eoReduceMerge, eoSSGAWorseReplacement, 
-    eoSSGADetTournamentReplacement, eoSSGAStochTournamentReplacement
+@see eoReduceMerge
+@see eoSSGAWorseReplacement
+@see eoSSGADetTournamentReplacement
+@see eoSSGAStochTournamentReplacement
 */
-
 template <class EOT>
 class eoReduceMerge : public eoReplacement<EOT>
 {

eo/src/eoRingTopology.h

@@ -142,8 +142,6 @@ public:
 
     /**
      * Print the structure of the topology on the standard output.
-     * @param
-     * @return
      */
     void printOn()
     {

eo/src/eoSGATransform.h

@@ -59,7 +59,7 @@ template<class EOT> class eoSGATransform : public eoTransform<EOT>
 
   /**
    * Transforms a population.
-   * @param pop The population to be transformed.
+   * @param _pop The population to be transformed.
    */
   void operator()(eoPop<EOT>& _pop) 
   {
@@ -124,7 +124,7 @@ template<class EOT> class eoDynSGATransform : public eoTransform<EOT>
 
   /**
    * Transforms a population.
-   * @param pop The population to be transformed.
+   * @param _pop The population to be transformed.
    */
   void operator()(eoPop<EOT>& _pop) 
   {

eo/src/eoSecondsElapsedContinue.h

@@ -53,11 +53,17 @@ public:
   
   virtual std::string className(void) const { return "eoSecondsElapsedContinue"; }
 
+  /** REad from a stream
+   * @param __is the ostream to read from
+   */
   void readFrom (std :: istream & __is) {
     
     __is >> start >> seconds; 
   }
   
+  /** Print on a stream
+   * @param __os the ostream to print on
+   */
   void printOn (std :: ostream & __os) const {
     
     __os << start << ' ' << seconds << std :: endl;    

eo/src/eoSharingSelect.h

@@ -45,7 +45,8 @@ class eoSharingSelect: public eoRouletteWorthSelect<EOT, double>
 {
 public:
   /** Ctor:
-   *  @param _s the sigma_share
+   *  @param _sigma the sigma_share
+   *  @param _dist the distance object to use
    */
   eoSharingSelect(double _sigma, eoDistance<EOT> & _dist): 
     eoRouletteWorthSelect<EOT, double>(sharing), sharing(_sigma, _dist) {}

eo/src/eoShiftMutation.h

@@ -53,7 +53,7 @@ template<class EOT> class eoShiftMutation: public eoMonOp<EOT>
 
   /**
    * Shift two components of the given eoosome.
-   * @param eo The cromosome which is going to be changed.
+   * @param _eo The cromosome which is going to be changed.
    */
   bool operator()(EOT& _eo)
     {