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)
     {

eo/src/eoSimpleEDA.h

@@ -49,8 +49,8 @@ template<class EOT> class eoSimpleEDA: public eoEDA<EOT>
 {
  public:
 
-  /** Ctor from an eoDistribUpdater
-   * ... plus an eoEval and eoContinue of course 
+  /** Ctor from an eoDistribUpdater,
+   *  plus an eoEval and eoContinue of course.
    */
   eoSimpleEDA(eoDistribUpdater<EOT>& _update,
 	   eoEvalFunc<EOT>& _eval,

eo/src/eoStandardVelocity.h

@@ -60,7 +60,7 @@ public:
     * @param _c2 - 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
     */
     eoStandardVelocity (eoTopology < POT > & _topology,

eo/src/eoStarTopology.h

@@ -122,8 +122,6 @@ public:
 
    /**
      * Print the structure of the topology on the standard output.
-     * @param
-     * @return
      */
     void printOn()
     {

eo/src/eoTruncatedSelectOne.h

@@ -93,8 +93,8 @@ public:
   /**
      The implementation selects an individual from the fertile pop
 
-     @param _source the source population
-     @param _dest the selected guy
+     @param _pop the source population
+     @return the selected guy
   */
   const EOT& operator()(const eoPop<EOT>& _pop) 
   {

eo/src/eoTwoOptMutation.h

@@ -49,7 +49,7 @@ public:
 
     /**
     *
-    * @param eo The cromosome which is going to be changed.
+    * @param _eo The cromosome which is going to be changed.
     */
     bool operator()(EOT& _eo) {
         // generate two different indices

eo/src/es/eoEsChromInit.h

@@ -107,7 +107,7 @@ public:
     Specify individual initial sigmas for each variable.
 
     @param _bounds bounds for uniform initialization
-    @param _sigma initial value for the stddev
+    @param _vecSigma initial value for the stddev
     */
     eoEsChromInit(eoRealVectorBounds& _bounds, const std::vector<double>& _vecSigma)
         : eoRealInitBounded<EOT>(_bounds), uniqueSigma(_vecSigma[0]), vecSigma(_vecSigma)

eo/src/es/eoEsGlobalXover.h

@@ -65,7 +65,7 @@ public:
    * modifies one parents in the populator
    *     using 2 new parents for each component!
    *
-   * @param _pop a POPULATOR (not a simple population)
+   * @param _plop a POPULATOR (not a simple population)
    */
   void apply(eoPopulator<EOT>& _plop)
   {

eo/src/es/eoEsMutationInit.h

@@ -52,7 +52,7 @@ public :
     /** Constructor
 
     @param _parser Parser to read parameters from.
-    @param _section Parser section for \tau-parameters.
+    @param _section Parser section for \f$\tau\f$-parameters.
     */
     eoEsMutationInit(eoParser& _parser,
 		     std::string _section="ES mutation parameters" ) :
@@ -62,7 +62,7 @@ public :
     /** Virtual destructor */
     virtual ~eoEsMutationInit() {}
 
-    /** local \tau */
+    /** local tau */
     double TauLcl(void)
     {
         if (TauLclParam == 0)

eo/src/es/eoNormalMutation.h

@@ -192,11 +192,11 @@ public:
   /**
    * (Default) Constructor.
    *
-   * @param eval the evaluation function, needed to recompute the fitmess
+   * @param _eval the evaluation function, needed to recompute the fitmess
    * @param _sigmaInit the initial value for uniform mutation
    * @param _windowSize the size of the window for statistics
-   * @param _threshold the threshold (the 1/5 - 0.2)
    * @param _updateFactor multiplicative update factor for sigma
+   * @param _threshold the threshold (the 1/5 - 0.2)
    */
   eoOneFifthMutation(eoEvalFunc<EOT> & _eval, double & _sigmaInit,
 		     unsigned _windowSize = 10, double _updateFactor=0.83,

eo/src/es/eoReal.h

@@ -43,6 +43,7 @@ template <class FitT> class eoReal: public eoVector<FitT, double>
   /**
    * (Default) Constructor.
    * @param size Size of the std::vector
+   * @param value fill the vector with this value
    */
   eoReal(unsigned size = 0, double value = 0.0):
     eoVector<FitT, double>(size, value) {}

eo/src/es/eoRealOp.h

@@ -153,7 +153,7 @@ template<class EOT> class eoDetUniformMutation: public eoMonOp<EOT>
    * it's there mostly for backward compatibility
    *
    * @param _epsilon the range for uniform nutation
-   * @param number of coordinate to modify
+   * @param _no number of coordinate to modify
    */
   eoDetUniformMutation(const double& _epsilon, const unsigned& _no = 1):
     homogeneous(true), bounds(eoDummyVectorNoBounds),
@@ -163,7 +163,7 @@ template<class EOT> class eoDetUniformMutation: public eoMonOp<EOT>
    * Constructor with bounds
    * @param _bounds an eoRealVectorBounds that contains the bounds
    * @param _epsilon the range for uniform nutation (to be scaled if necessary)
-   * @param number of coordinate to modify
+   * @param _no number of coordinate to modify
    */
   eoDetUniformMutation(eoRealVectorBounds & _bounds,
 		       const double& _epsilon, const unsigned& _no = 1):
@@ -180,7 +180,7 @@ template<class EOT> class eoDetUniformMutation: public eoMonOp<EOT>
    * Constructor with bounds and full std::vector of epsilon
    * @param _bounds an eoRealVectorBounds that contains the bounds
    * @param _epsilon the VECTOR of ranges for uniform mutation
-   * @param number of coordinate to modify
+   * @param _no number of coordinates to modify
    */
   eoDetUniformMutation(eoRealVectorBounds & _bounds,
 		       const std::vector<double>& _epsilon,
@@ -257,7 +257,7 @@ template<class EOT> class eoSegmentCrossover: public eoQuadOp<EOT>
    * (Default) Constructor.
    * The bounds are initialized with the global object that says: no bounds.
    *
-   * @param _alphaMin the amount of exploration OUTSIDE the parents
+   * @param _alpha the amount of exploration OUTSIDE the parents
    *               as in BLX-alpha notation (Eshelman and Schaffer)
    *               0 == contractive application
    *               Must be positive
@@ -268,7 +268,7 @@ template<class EOT> class eoSegmentCrossover: public eoQuadOp<EOT>
   /**
    * Constructor with bounds
    * @param _bounds an eoRealVectorBounds that contains the bounds
-   * @param _alphaMin the amount of exploration OUTSIDE the parents
+   * @param _alpha the amount of exploration OUTSIDE the parents
    *               as in BLX-alpha notation (Eshelman and Schaffer)
    *               0 == contractive application
    *               Must be positive
@@ -348,7 +348,7 @@ template<class EOT> class eoHypercubeCrossover: public eoQuadOp<EOT>
    * (Default) Constructor.
    * The bounds are initialized with the global object that says: no bounds.
    *
-   * @param _alphaMin the amount of exploration OUTSIDE the parents
+   * @param _alpha the amount of exploration OUTSIDE the parents
    *               as in BLX-alpha notation (Eshelman and Schaffer)
    *               0 == contractive application
    *               Must be positive
@@ -363,7 +363,7 @@ template<class EOT> class eoHypercubeCrossover: public eoQuadOp<EOT>
   /**
    * Constructor with bounds
    * @param _bounds an eoRealVectorBounds that contains the bounds
-   * @param _alphaMin the amount of exploration OUTSIDE the parents
+   * @param _alpha the amount of exploration OUTSIDE the parents
    *               as in BLX-alpha notation (Eshelman and Schaffer)
    *               0 == contractive application
    *               Must be positive
@@ -483,7 +483,7 @@ template<class EOT> class eoRealUXover: public eoQuadOp<EOT>
    * Uniform crossover for real std::vectors
    * @param _eo1 The first parent
    * @param _eo2 The second parent
-   *    @std::runtime_error if sizes don't match
+   *    @exception std::runtime_error if sizes don't match
    */
   bool operator()(EOT& _eo1, EOT& _eo2)
     {

eo/src/es/eoSBXcross.h

@@ -54,7 +54,7 @@ template<class EOT> class eoSBXCrossover: public eoQuadOp<EOT>
   /**
    * Constructor with bounds
    * @param _bounds an eoRealVectorBounds that contains the bounds
-   * @param _alphaMin the amount of exploration OUTSIDE the parents 
+   * @param _eta the amount of exploration OUTSIDE the parents 
    *               as in BLX-alpha notation (Eshelman and Schaffer)
    *               0 == contractive application
    *               Must be positive

eo/src/gp/eoParseTreeDepthInit.h

@@ -61,7 +61,7 @@ class eoParseTreeDepthInit : public eoInit< eoParseTree<FType, Node> >
     
     /**
      * Constructor
-     * @parm _max_depth The maximum depth of a tree
+     * @param _max_depth The maximum depth of a tree
      * @param _initializor A std::vector containing the possible nodes
      * @param _grow False results in a full tree, True result is a randomly grown tree
      * @param _ramped_half_and_half True results in Ramped Half and Half Initialization

eo/src/gp/eoParseTreeOp.h

@@ -338,9 +338,9 @@ class eoHoistMutation: public eoMonOp< eoParseTree<FType, Node> >
 public:
 
   typedef eoParseTree<FType,Node> EoType;
+
   /**
    * Constructor
-   * @param none
    */
   eoHoistMutation()
     : eoMonOp<EoType>()

eo/src/gp/eoStParseTreeDepthInit.h

@@ -69,8 +69,9 @@ class eoStParseTreeDepthInit : public eoInit< eoParseTree<FType, Node> >
     
     /**
      * Constructor
-     * @parm _max_depth The maximum depth of a tree
-     * @param _initializor A std::vector containing the possible nodes
+     * @param _max_depth The maximum depth of a tree
+     * @param _node A std::vector containing the possible nodes
+     * @param _return_type (JD_2010-11-09: don't know the use of this parameter, maybe to force implicit template instanciation?)
      * @param _grow False results in a full tree, True result is a randomly grown tree
      */
 	eoStParseTreeDepthInit(

eo/src/gp/eoStParseTreeOp.h

@@ -203,7 +203,7 @@ public:
 
   /**
    * Constructor
-   * @param _initializor The std::vector of Nodes given to the eoGpDepthInitializer
+   * @param _node The std::vector of Nodes given to the eoGpDepthInitializer
    */
   eoStPointMutation( std::vector<Node>& _node)
     : eoMonOp<EoType>()

eo/src/utils/eoFileMonitor.h

@@ -55,6 +55,7 @@ public :
      * @param _delim delimiter string to use between each item of the registered vector (e.g. of eoStats)
      * @param _keep_existing if true, overwrite any existing file with the same name prior to any output
      * @param _header print the header (with the descriptions of registered eoStats) at the beginning of the file (WARNING: true will discards header printing)
+     * @param _overwrite if true, overwrite the existing file
      */
     eoFileMonitor(
         std::string _filename, 

eo/src/utils/eoGnuplot.h

@@ -44,7 +44,7 @@ public:
     /** Open pipe to Gnuplot.
 
     @param _title Title for gnuplot window.
-    @param _extra Extra parameters to gnuplot (default <none>).
+    @param _extra Extra parameters to gnuplot (default to none: "").
     */
     eoGnuplot(std::string _title, std::string _extra = std::string(""));
 

eo/src/utils/eoHowMany.h

@@ -77,7 +77,7 @@ class eoHowMany : public eoPersistent
 {
 public:
   /** Original Ctor from direct rate + bool
-      @param rate    the rate, OR the integer to store, depending on 2nd arg.
+      @param _rate    the rate, OR the integer to store, depending on 2nd arg.
       @param _interpret_as_rate to tell whether the rate actually is a rate
   */
   eoHowMany(double  _rate = 0.0, bool _interpret_as_rate = true):

eo/src/utils/eoParser.h

@@ -64,7 +64,7 @@ public :
      * @param _defaultValue       The default value
      * @param _longName           Long name of the argument
      * @param _description        Description of the parameter. What is useful for.
-     * @param _shortName          Short name of the argument (Optional)
+     * @param _shortHand          Short name of the argument (Optional)
      * @param _section            Name of the section where the parameter belongs
      * @param _required           If it is a necessary parameter or not
      */
@@ -128,8 +128,14 @@ public:
   */
   void processParam(eoParam& param, std::string section = "");
 
+  /** Read from a stream
+   * @param is the input stream
+   */
   void readFrom(std::istream& is);
 
+  /** Pint on a stream
+   * @param os the output stream
+   */
   void printOn(std::ostream& os) const;
 
   /// className for readibility
@@ -207,7 +213,7 @@ public:
     @param _defaultValue Default value.
     @param _longName     Long name of the argument.
     @param _description  Description of the parameter.
-    @param _shortName    Short name of the argument (Optional)
+    @param _shortHand    Short name of the argument (Optional)
     @param _section      Name of the section where the parameter belongs.
     @param _required     Is the parameter mandatory?
     @return Corresponding parameter.

eo/src/utils/eoRealVectorBounds.h

@@ -305,7 +305,7 @@ public:
 
   /**
    * Read object from a std::string
-   * @param _is A std::istream.
+   * @param _s A std::istream.
    */
   virtual void readFrom(std::string _s) ;
 

eo/src/utils/eoTimeCounter.h

@@ -35,7 +35,7 @@
     An eoStat that simply gives the user time since first generation
     It has to be tempatized by EOT because it must be an eoStat
 
-    @group Stats
+    @ingroup Stats
 */
 class eoTimeCounter : public eoUpdater, public eoValueParam<double>
 {