--- trunk/gadget/optinfo.h	2015/07/23 19:00:38	11
+++ trunk/gadget/optinfo.h	2015/07/24 18:36:24	12
@@ -41,9 +41,14 @@
    * \brief This is the function used to call the optimisation algorithms
    */
   virtual void OptimiseLikelihood() {};
-  //FIXME doc
+  /**
+   * \brief This is the function used to call the optimisation algorithms parallelized with OpenMP of the reproducible version
+   */
   virtual void OptimiseLikelihoodOMP() {};
-  //FIXME doc
+  /**
+   * \brief This function set the seeds used in SA
+   * \param val array of unsigned int with the seeds
+   */
   void setSeed(unsigned* val) {seed = val[0]; seedM =  val[1]; seedP = val[2];};
   /**
    * \brief This will return the type of optimisation class
@@ -67,9 +72,17 @@
    * \brief This denotes what type of optimisation class has been created
    */
   OptType type;
-  //FIXME doc
+  /**
+   * \brief This is the seed used for the calculation of the new value of the parameters
+   */
   unsigned seed;
+  /**
+   * \brief This is the seed used for the acceptance of the metropolis
+   */
   unsigned seedM;
+  /**
+   * \brief This is the seed used to change the order of the parameters
+   */
   unsigned seedP;
 };
 
@@ -109,7 +122,9 @@
    */
   virtual void OptimiseLikelihood();
 #ifdef GADGET_OPENMP
-  //TODO doc
+  /**
+   * \brief This is the function that will calculate the likelihood score using the Hooke & Jeeves optimiser parallelized with the reproducible version implemented OpenMP
+   */
   virtual void OptimiseLikelihoodOMP();
 #endif
 private:
@@ -122,8 +137,23 @@
    * \return the best function value found from the search
    */
   double bestNearby(DoubleVector& delta, DoubleVector& point, double prevbest, IntVector& param);
-  //TODO doc
+  /**
+   * \brief This function implemented the reproducible version with OpenMP will calculate the best point that can be found close to the current point
+   * \param delta is the DoubleVector of the steps to take when looking for the best point
+   * \param point is the DoubleVector that will contain the parameters corresponding to the best function value found from the search
+   * \param prevbest is the current best point value
+   * \param param is the IntVector containing the order that the parameters should be searched in
+   * \return the best function value found from the search
+   */
   double bestNearbyOMP(DoubleVector& delta, DoubleVector& point, double prevbest, IntVector& param);
+  /**
+     * \brief This function implemented the speculative version with OpenMP will calculate the best point that can be found close to the current point
+     * \param delta is the DoubleVector of the steps to take when looking for the best point
+     * \param point is the DoubleVector that will contain the parameters corresponding to the best function value found from the search
+     * \param prevbest is the current best point value
+     * \param param is the IntVector containing the order that the parameters should be searched in
+     * \return the best function value found from the search
+     */
   double bestNearbyOMP2(DoubleVector& delta, DoubleVector& point, double prevbest, IntVector& param);
   /**
    * \brief This is the maximum number of iterations for the Hooke & Jeeves optimisation
@@ -181,17 +211,25 @@
    * \brief This is the function that will calculate the likelihood score using the Simulated Annealing optimiser
    */
   virtual void OptimiseLikelihood();
-  //FIXME doc
 #ifdef GADGET_OPENMP
+  /**
+   * \brief This is the function that will calculate the likelihood score using the Simulated Annealing optimiser parallelized with the reproducible version implemented OpenMP
+   */
   virtual void OptimiseLikelihoodOMP();
 #endif
-//FIXME doc
+  /**
+   * \brief This function calculate a new valor for the parameter l
+   * \param nvars the number of variables to be optimised
+   * \param l the parameter to change
+   * \param param IntVector with the order of the parameters
+   * \param trialx DoubleVector that storage the values of the parameters to evaluate during this iteration
+   * \param x DoubleVector that storage the best values of the parameters
+   * \param lowerb DoubleVector with the lower bounds of the variables to be optimised
+   * \param upperb DoubleVector with the upper bounds of the variables to be optimised
+   * \param vm DoubleVector with the value for the maximum step length for each parameter
+   */
   virtual void newValue(int nvars, int l, IntVector& param, DoubleVector& trialx,
   		DoubleVector& x, DoubleVector& lowerb, DoubleVector& upperb, DoubleVector& vm);
-//  //FIXME doc
-//  virtual void buildNewParams_f(Siman& seed, DoubleVector& params);
-//  virtual void adjustVm(Siman& seed);
-//  virtual void temperature(Siman& seed);
 private:
   /**
    * \brief This is the temperature reduction factor
@@ -277,8 +315,10 @@
    * \brief This is the function that will calculate the likelihood score using the BFGS optimiser
    */
   virtual void OptimiseLikelihood();
-  //FIXME doc
 #ifdef GADGET_OPENMP
+  /**
+  * \brief This function call the sequential function. BFGS isn't implemented with OpenMP
+  */
   virtual void OptimiseLikelihoodOMP();
 #endif
 private: