and finally... still more grouping in documentation.

eo/src/utils/eoAssembledFitnessStat.h

@@ -36,6 +36,10 @@
 #include <utils/eoStat.h>
 #include <eoScalarFitnessAssembled.h>
 
+/** @addtogroup Stats
+ * @{
+ */
+
 /**
    Average fitness values of a population, where the fitness is
    of type eoScalarAssembledFitness. Specify in the constructor,
@@ -109,4 +113,5 @@ private:
     unsigned whichFitnessTerm;
 };
 
+/** @} */
 #endif

eo/src/utils/eoCheckPoint.h

@@ -32,6 +32,21 @@
 #include <utils/eoMonitor.h>
 #include <utils/eoStat.h>
 
+/** @defgroup Checkpoints Checkpointing
+ *
+ * Checkpoints are supposed to be called perodically (for instance at each generation) and
+ * will call every functors you put in them.
+ *
+ * Use them with eoStats, eoUpdater and eoMonitor to get statistics at each generation.
+ *
+ * @see eoStats
+ * @see eoMonitor
+ * @see eoUpdater
+ *
+ * @ingroup Utilities
+ *
+ * @{
+ */
 
 /** eoCheckPoint is a container class.
     It contains std::vectors of (pointers to) 
@@ -161,4 +176,5 @@ std::string eoCheckPoint<EOT>::allClassNames() const
     return s;
 }
 
+/** @} */
 #endif

eo/src/utils/eoDistance.h

@@ -27,9 +27,14 @@
 #define _eoDistance_H
 
 #include <eoFunctor.h>
+
+/** @addtogroup Stats 
+ * @{
+ * */
+
 /** 
     This is a generic class for distance functors:
-    takes 2 things ane returns a double
+    takes 2 things and returns a double
 */
 template< class EOT >
 class eoDistance : public eoBF<const EOT &, const EOT &, double>
@@ -94,5 +99,6 @@ public:
 };
 
 
+/** @} */
 	
 #endif

eo/src/utils/eoFDCStat.h

@@ -32,8 +32,12 @@
 #include <utils/eoFileSnapshot.h>
 
 /**
-    The FDC computation - stores the values into eoValueParam<EOT,double>
+    The Fitness Distance Correlation computation.
+    
+    Stores the values into eoValueParam<EOT,double>
 so they can be snapshot by some eoGnuplotSnapshot ...
+
+@ingroup Stats
 */
 template <class EOT>
 class eoFDCStat : public eoStat<EOT, double>
@@ -106,6 +110,8 @@ private:
  *  As I failed to have FDC stat as an eoStat, this is the trick
  *  to put the 2 eoParam<std::vector<double> > into a monitor
  *  This class does nothing else.
+
+@ingroup Stats
  */
 template <class EOT>
 class eoFDCFileSnapshot : public eoFileSnapshot	// is an eoMonitor

eo/src/utils/eoFeasibleRatioStat.h

@@ -34,7 +34,10 @@ Authors:
 
 #include "eoStat.h"
 
-//! Ratio of the number of individuals with a feasible dual fitness in the population (@see eoDualFitness)
+/** Ratio of the number of individuals with a feasible dual fitness in the population (@see eoDualFitness)
+ *
+ * @ingroup Stats
+ */
 template<class EOT>
 class eoFeasibleRatioStat : public eoStat< EOT, double >
 {

eo/src/utils/eoFileMonitor.h

@@ -34,12 +34,14 @@
 #include "utils/eoMonitor.h"
 #include "eoObject.h"
 
+
 /** Prints statistics to file
 
 Modified the default behavior, so that it erases existing files. Can
 be modified in the ctor.
 
 @version MS 25/11/00
+@ingroup Monitors
 */
 class eoFileMonitor : public eoMonitor
 {

eo/src/utils/eoFileSnapshot.h

@@ -48,8 +48,9 @@ so that you can pass e.g. an evalcounter (minor)
 
 I failed to templatize everything so that it can handle eoParam<std::vector<T> >
 for any type T, simply calling their getValue method ...
-*/
 
+@ingroup Monitors
+*/
 class eoFileSnapshot : public eoMonitor
 {
 public :

eo/src/utils/eoFuncPtrStat.h

@@ -1,9 +1,16 @@
+
 #ifndef eoFuncPtrStat_h
 #define eoFuncPtrStat_h
 
 #include <eoFunctorStore.h>
 #include <utils/eoStat.h>
 
+/** Wrapper to turn any stand-alone function and into an eoStat.
+ *
+ * The function should take an eoPop as argument.
+ *
+ * @ingroup Stats
+ */
 template <class EOT, class T>
 class eoFuncPtrStat : public eoStat<EOT, T>
 {
@@ -25,6 +32,9 @@ private:
     func_t func;
 };
 
+/** 
+ * @ingroup Stats
+ */
 template <class EOT, class T>
 eoFuncPtrStat<EOT, T>& makeFuncPtrStat( T (*func)(const eoPop<EOT>&), eoFunctorStore& store, std::string description = "func") {
     return store.storeFunctor(

eo/src/utils/eoGnuplot.h

@@ -34,6 +34,8 @@ calls to plots what is already written by some eoMonitor into a file
 
 @author Marc Schoenauer
 @version 0.0 (2001)
+
+@ingroup Monitors
 */
 class eoGnuplot
 {

eo/src/utils/eoGnuplot1DMonitor.h

@@ -43,6 +43,8 @@ eoGnuplot1DMonitor plots stats through gnuplot
 
 Assumes that the same file is appened every so and so, and replots it
 everytime
+
+@ingroup Monitors
 */
 class eoGnuplot1DMonitor : public eoFileMonitor, public eoGnuplot
 {

eo/src/utils/eoGnuplot1DSnapshot.h

@@ -47,6 +47,8 @@ This class plots through gnuplot the eoStat given as argument
 
 Assumes that the same file is re-written every so and so, and plots it
 from scratch everytime it's called
+
+@ingroup Monitors
  */
 class eoGnuplot1DSnapshot: public eoFileSnapshot, public eoGnuplot
 {

eo/src/utils/eoHowMany.h

@@ -29,6 +29,11 @@ Contact: http://eodev.sourceforge.net
 #ifndef eoHowMany_h
 #define eoHowMany_h
 
+#include <sstream>
+
+#include <utils/eoLogger.h>
+
+
 /** A helper class, to determine a number of individuals from another one
  *  Typically, is used in selection / replacement procedures, e.g.
  *             the number of offspring from the number of parents, or
@@ -65,12 +70,9 @@ Contact: http://eodev.sourceforge.net
  *    eoG3Repalcement)
  *
  * It is an eoPersistent because we need to be able to use eoParamValue<eoHowMany>
+ *
+ * @ingroup Core
  */
-
-#include <sstream>
-
-#include <utils/eoLogger.h>
-
 class eoHowMany : public eoPersistent
 {
 public:

eo/src/utils/eoIntBounds.h

@@ -31,14 +31,15 @@
 #include <utils/eoRNG.h>
 
 /**
-\defgroup EvolutionStrategies
+\defgroup Real
 
 */
 
 
 /**
 \class eoIntBounds eoIntBounds.h es/eoIntBounds.h
-\ingroup EvolutionStrategies
+\ingroup Real
+\ingroup Bounds
 
     Defines bound classes for real numbers.
 
@@ -149,6 +150,9 @@ public:
 };
 
 /** A default class for unbounded variables
+ *
+ * @ingroup Real
+ * @ingroup Bounds
  */
 class eoIntNoBounds : public eoIntBounds
 {
@@ -221,11 +225,18 @@ public:
 
 };
 
-// one object for all - see eoIntBounds.cpp
+/** one object for all - see eoIntBounds.cpp
+ *
+ * @ingroup Real
+ * @ingroup Bounds
+ */
 extern eoIntNoBounds eoDummyIntNoBounds;
 
 /**
  * fully bounded eoIntBound == interval
+ *
+ * @ingroup Real
+ * @ingroup Bounds
  */
 class eoIntInterval : public eoIntBounds
 {
@@ -349,6 +360,9 @@ private :
 
 /**
  * an eoIntBound bounded from below only
+ *
+ * @ingroup Real
+ * @ingroup Bounds
  */
 class eoIntBelowBound : public eoIntBounds
 {
@@ -453,6 +467,9 @@ private :
 
 /**
 An eoIntBound bounded from above only
+ *
+ * @ingroup Real
+ * @ingroup Bounds
 */
 class eoIntAboveBound : public eoIntBounds
 {
@@ -560,6 +577,9 @@ private :
 
 /** A class that encapsulate all possible eoIntBounds.
  *  Mandatory in order to read through the parser
+ *
+ * @ingroup Real
+ * @ingroup Bounds
  */
 class eoGeneralIntBounds : public eoIntBounds
 {

eo/src/utils/eoLogger.h

@@ -25,8 +25,12 @@ Caner Candan <caner.candan@thalesgroup.com>
 
 */
 
-/** Here's an example explaning how to use eoLogger:
+/** @defgroup Logging Logging
 
+ Global logger for EO.
+
+ Here's an example explaning how to use eoLogger:
+\code
     #include <iostream>
     #include <utils/eoLogger.h>
     #include <utils/eoParserLogger.h>
@@ -77,7 +81,9 @@ Caner Candan <caner.candan@thalesgroup.com>
 
     return 0;
     }
+\endcode
 
+@{
 */
 
 #ifndef eoLogger_h
@@ -249,4 +255,7 @@ namespace	eo
     extern eoLogger	log;
 }
 
+
+/** @} */
+
 #endif // !eoLogger_h

eo/src/utils/eoMonitor.h

@@ -1,7 +1,5 @@
 // -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
 
-//-----------------------------------------------------------------------------
-// eoMonitor.h
 // (c) Marc Schoenauer, Maarten Keijzer and GeNeura Team, 2000
 /* 
     This library is free software; you can redistribute it and/or
@@ -21,10 +19,7 @@
     Contact: todos@geneura.ugr.es, http://geneura.ugr.es
              Marc.Schoenauer@polytechnique.fr
              mak@dhi.dk
-CVS Info: $Date: 2010-03-18 12:44:45 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/utils/eoMonitor.h,v 1.13 2010-03-18 12:44:45 paradiseo Exp $ $Author: paradiseo $ 
-
  */
-//-----------------------------------------------------------------------------
 
 #ifndef _eoMonitor_h
 #define _eoMonitor_h
@@ -34,6 +29,20 @@ CVS Info: $Date: 2010-03-18 12:44:45 $ $Header: /home/nojhan/dev/eodev/eodev_cvs
 #include <iostream>
 #include <eoFunctor.h>
 
+/** @defgroup Monitors Monitoring
+ *
+ * Monitors take a set of value parameters (eoValueParam) objects and 
+ * output them on a given stream, file, pipe, etc.
+ *
+ * They can be called from within an eoCheckPoint, to print different values
+ * of parameters or of eoStat at each generation.
+ *
+ * @see eoCheckPoint
+ * @see eoStat
+ * @ingroup Utilities
+ */
+
+
 class eoParam;
 template <class EOT> class eoCheckPoint;
 
@@ -43,6 +52,8 @@ template <class EOT> class eoCheckPoint;
     Derived classes will then implement the operator()(void) which
     will stream or pipe the current values of the parameters to wherever you
     want it streamed or piped to.
+
+    @ingroup Monitors
 */
 class eoMonitor : public eoF<eoMonitor&>
 {

eo/src/utils/eoOStreamMonitor.h

@@ -25,8 +25,6 @@ Authors:
 	 Johann Dréo <johann.dreo@thalesgroup.com>
 */
 
-
-
 #ifndef _eoOStreamMonitor_h_
 #define _eoOStreamMonitor_h_
 
@@ -39,6 +37,8 @@ Authors:
 
 /**
     Prints statistics to stdout
+
+    @ingroup Monitors
 */
 class eoOStreamMonitor : public eoMonitor
 {

eo/src/utils/eoParam.h

@@ -35,6 +35,15 @@
 #include <vector>
 #include <eoScalarFitness.h>
 
+/** @defgroup Parameters Parameters management
+ *
+ * A parameter is basically an object that stores a value and that can read/print it from/on streams.
+ *
+ * It is mainly used for command-line options (see eoParser) and eoStat.
+ *
+ * @ingroup Utilities
+ * @{
+ */
 
 /**
    eoParam: Base class for monitoring and parsing parameters
@@ -126,8 +135,9 @@ private:
 
 /**
    eoValueParam<ValueType>: templatized derivation of eoParam. Can be used to contain
-   any scalar value type. It makes use of std::strstream to get and set values. This
-   should be changed to std::stringstream when that class is available in g++.
+   any scalar value type. It makes use of std::strstream to get and set values. 
+   
+   @todo This should be changed to std::stringstream when that class is available in g++.
 
    Note also that there is a template specialization for std::pair<double, double> and
    for std::vector<double>. These stream their contents delimited with whitespace.
@@ -458,4 +468,6 @@ public:
 std::ostream & operator<<(std::ostream & _os, const eoParamParamType & _rate);
 std::istream & operator>>(std::istream & _is,  eoParamParamType & _rate);
 
+/** @} */
 #endif
+

eo/src/utils/eoParser.h

@@ -36,6 +36,8 @@ Contact: http://eodev.sourceforge.net
 eoParameterLoader is an abstract class that can be used as a base for your own
 parameter loading and saving. The command line parser eoParser is derived from
 this class.
+
+@ingroup Parameters
 */
 class eoParameterLoader
 {
@@ -96,6 +98,8 @@ private :
     eoParser: command line parser and configuration file reader
     This class is persistent, so it can be stored and reloaded to restore
     parameter settings.
+
+    @ingroup Parameters
 */
 class eoParser : public eoParameterLoader, public eoObject, public eoPersistent
 {

eo/src/utils/eoParserLogger.h

@@ -29,6 +29,9 @@ Authors:
 
 /**
  * A parser that use the advanced logging system (@see eoLogger)
+ *
+ * @ingroup Parameters
+ * @ingroup Logging
  */
 class	eoParserLogger : public eoParser
 {

eo/src/utils/eoPopStat.h

@@ -46,6 +46,8 @@ This is the plain version - see eoPopString for the Sorted version
 
 Note: this Stat should probably be used only within eoStdOutMonitor, and not
 inside an eoFileMonitor, as the eoState construct will work much better there.
+
+@ingroup Stats
 */
 template <class EOT>
 class eoPopStat : public eoStat<EOT, std::string>
@@ -91,6 +93,8 @@ This is the Sorted version - see eoPopString for the plain version
 
 Note: this Stat should probably be used only within eoStdOutMonitor, and not
 inside an eoFileMonitor, as the eoState construct will work much better there.
+
+@ingroup Stats
 */
 template <class EOT>
 class eoSortedPopStat : public eoSortedStat<EOT, std::string>