diff egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp @ 1:420b57c3c185 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,156 @@
+/*
+    Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
+
+    This file is part of the EggLib library.
+
+    EggLib is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    EggLib is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with EggLib.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef EGGLIB_CONTROLLER_HPP
+#define EGGLIB_CONTROLLER_HPP
+
+#include "Current.hpp"
+#include "Arg.hpp"
+#include "ParamSet.hpp"
+
+namespace egglib {
+    
+    class Random;
+
+   /** \brief Controls a coalescent simulation
+    *
+    * \ingroup coalesce
+    * 
+    * This class generates the gene genealogy, based on the parameters
+    * stocked in a ParamSet object.
+    *
+    */
+    class Controller {
+
+        public:
+    
+           /** \brief Default constructor
+            *
+            * Uses a default ParamSet object that will not allow
+            * performing simulations.
+            *
+            */
+            Controller();
+
+           /** \brief Destructor
+            * 
+            */
+            ~Controller();
+            
+           /** \brief Standard constructor
+            * 
+            * \param paramSet a ParamSet object containing run
+            * parameters (it is taken as a reference and stored as this
+            * so it must not be modified during simulations).
+            * 
+            * \param random the address of the random number generator.
+            *
+            */
+            Controller(const ParamSet* paramSet, Random* random);
+            
+          /** \brief Reset for a new simulation
+           * 
+           * Object is reinitiliazed for a new simulation.
+           * 
+           */
+           void reset();
+            
+           /** \brief Increments the coalescent model
+            * 
+            * \return The number of lineages.
+            *
+            */
+            unsigned int step();
+            
+           /** \brief Gets the Ancestral Recombination Graph
+            * 
+            * \return The address of the ARG contained in the object.
+            * 
+            */
+            Arg* getArg();
+
+           /** \brief Applies a bottleneck to a given population
+            * 
+            * The bottleneck is applied following Galtier, Depaulis and
+            * Barton (Genetics, 2000): the general time counter is
+            * stopped, and coalescence events are performed during a
+            * time (of normal coalescent process) given by the parameter
+            * strength. All coalescent events are instantaneous.
+            * 
+            * \param populationIndex index of the population concerned
+            * by the event.
+            * 
+            * \param strength strength of the bottleneck given by a
+            * number of time units (2N generations times the size of
+            * the population).
+            * 
+            */
+            void bottleneck(unsigned int populationIndex, double strength);
+
+           /** \brief Migrate a complete population
+            * 
+            * Takes all the lineages currently present in the population
+            * source to the population dest.
+            * 
+            */
+            void moveAllLineages(unsigned int source, unsigned int dest);
+            
+           /** \brief Migrate a complete population
+            * 
+            * Takes all the lineages currently present in the population
+            * source to the population dest.
+            * 
+            * \param source source population.
+            * \param dest destination population.
+            * \param probability the probability that a lineage of
+            * source migrates to dest.
+            * 
+            */
+            void moveSomeLineages(unsigned int source, unsigned int dest, double probability);
+
+            /// Adds an empty population
+            void addPopulation();
+
+        private:
+        
+            /// The copy constructor is disabled
+            Controller(const Controller& source) {}
+            
+            /// The assignment operator is disabled
+            Controller& operator=(const Controller& source) {return *this;}
+
+            void diploids();
+            double getMigrationTime(double& migrationParameterDestination);
+            void getCoalescenceTime(double& destTime, unsigned int& destPopIndex);
+            double getCoalescenceTimeForPopulation(unsigned int populationIndex);
+            double getRecombinationTime() const;
+            void migrate(double migrationParameter);
+
+            const ParamSet* initialParamSet;
+            ParamSet paramSet;
+            Current current;
+            Arg arg;
+            
+            Random* random;
+
+    };
+
+}
+
+#endif