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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/ChangeTypes.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,428 @@
+/*
+    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_CHANGETYPES_HPP
+#define EGGLIB_CHANGETYPES_HPP
+
+#include "ParamSet.hpp"
+#include "Controller.hpp"
+
+namespace egglib {
+
+/**********************************************************************/
+
+   /** \brief Pure virtual base class for parameter changes
+    *
+    * \ingroup coalesce
+    *
+    */
+    class Change {
+        public:
+    
+           /** \brief Default constructor
+            *
+            * The default date is 0.
+            *
+            */
+            Change();
+            
+           /** \brief Standard constructor
+            *
+            * \param date the event date.
+            *
+            */
+            Change(double date);
+
+            /// Gets the event date value
+            double date() const;
+            
+            /// Sets the event date value
+            void date(double value);
+            
+           /** \brief Applies the event
+            *
+            * \param paramSet the ParamSet instance to which the Change
+            * instance is attached.
+            * \param controller the Controller instance of the
+            * simulation.
+            *
+            */
+            virtual void apply(ParamSet* paramSet, Controller* controller) const = 0;
+        
+        protected:
+            double _date;
+    
+    };
+
+/**********************************************************************/
+
+   /** \brief Pure virtual base class for single parameter changes
+    *
+    * \ingroup coalesce
+    *
+    */
+    class SingleParamChange : public Change {
+        public:
+    
+           /** \brief Default constructor
+            *
+            * The default date is 0., the default parameter value is 0.
+            *
+            */
+            SingleParamChange();
+            
+           /** \brief Standard constructor
+            *
+            * \param date the event date.
+            * \param value the parameter value.
+            *
+            */
+            SingleParamChange(double date, double value);
+
+            /// Gets the parameter value
+            double value() const;
+            
+            /// Sets the parameter value
+            void value(double value);
+
+        protected:
+            double _value;
+
+    };
+
+/**********************************************************************/
+
+   /** \brief Single parameter changes applied to a single population
+    *
+    * \ingroup coalesce
+    *
+    */
+    class PopulationParamChange : public SingleParamChange {
+        public:
+
+           /** \brief Default constructor
+            *
+            * The default date is 0., the default parameter value is 0.,
+            * the  default population is 0
+            *
+            */
+            PopulationParamChange();
+            
+           /** \brief Standard constructor
+            *
+            * \param date the event date.
+            * \param population the population index.
+            * \param value the parameter value.
+            *
+            */
+            PopulationParamChange(double date, unsigned int population, double value);
+
+            /// Gets the population index
+            unsigned int population() const;
+            
+            /// Sets the population index
+            void population(unsigned int value);
+    
+        protected:
+        
+            unsigned int _population;
+
+    };
+
+            
+/**********************************************************************/
+    
+   /** \brief Bottleneck event
+    *
+    * \ingroup coalesce
+    * 
+    * The bottleneck parameter is its strength, corresponding to an
+    * amount of time where time is locked and only coalescences are
+    * allowed (resulting in a given - and random - number of
+    * instantaneous coalescence with branches).
+    *
+    */
+    class Bottleneck : public SingleParamChange {
+        public:
+            Bottleneck(double date, double param) : SingleParamChange(date, param) {}
+            void apply(ParamSet* paramSet, Controller* controller) const;
+    };
+
+/**********************************************************************/
+    
+   /** \brief Population-specific bottleneck event
+    *
+    * \ingroup coalesce
+    *
+    */
+    class PopulationBottleneck : public PopulationParamChange {
+        public:
+            PopulationBottleneck(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {}
+            void apply(ParamSet* paramSet, Controller* controller) const;
+    };
+
+
+/**********************************************************************/
+    
+   /** \brief Change of the size of all populations
+    *
+    * The parameter is the new size (applied to all populations)
+    *
+    * \ingroup coalesce
+    *
+    */
+    class AllPopulationSizeChange : public SingleParamChange {
+        public:
+            AllPopulationSizeChange(double date, double value) : SingleParamChange(date, value) {}
+            void apply(ParamSet* paramSet, Controller* controller) const; 
+    };
+    
+    
+/**********************************************************************/
+    
+   /** \brief Change of a single population size
+    *
+    * \ingroup coalesce
+    *
+    */
+    class SinglePopulationSizeChange : public PopulationParamChange {
+        public:
+            SinglePopulationSizeChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {}
+            void apply(ParamSet* paramSet, Controller* controller) const;    
+    };
+    
+
+    
+/**********************************************************************/
+    
+   /** \brief Change of the growth rate of all populations
+    *
+    * The parameter is the new rate (applied to all populations)
+    *
+    * \ingroup coalesce
+    *
+    */
+    class GrowthRateChange : public SingleParamChange {
+        public:
+            GrowthRateChange(double date, double value) : SingleParamChange(date, value) {}
+            void apply(ParamSet* paramSet, Controller* controller) const;
+    };
+    
+    
+/**********************************************************************/
+    
+   /** \brief Change of a single population's growth rate
+    *
+    * \ingroup coalesce
+    *
+    */
+    class PopulationGrowthRateChange : public PopulationParamChange {
+        public:
+            PopulationGrowthRateChange(double date, unsigned int population, double value) : PopulationParamChange(date, population, value) {}
+            void apply(ParamSet* paramSet, Controller* controller) const;
+    };
+    
+/**********************************************************************/
+    
+   /** \brief Change of the selfing rate
+    *
+    * The parameter is the new rate
+    *
+    * \ingroup coalesce
+    *
+    */
+    class SelfingRateChange : public SingleParamChange {
+        public:
+            SelfingRateChange(double date, double value) : SingleParamChange(date, value) {}
+            void apply(ParamSet* paramSet, Controller* controller) const;
+    };
+    
+/**********************************************************************/
+    
+   /** \brief Fusion of two populations
+    *
+    * \ingroup coalesce
+    *
+    */
+    class PopulationFusion : public Change {
+        public:
+           /** \brief Default constructor
+            *
+            * The default date is 0., the default mother is 0, the
+            * default daughter is 0.
+            *
+            */
+            PopulationFusion();
+
+           /** \brief Standard constructor
+            *
+            * \param date the date of the event.
+            * \param mother first population to merge.
+            * \param daughter second population to merge.
+            *
+            * A time date, all the lineages from the daughter population
+            * are moved to the mother population and all mutation rates
+            * to the daughter population are cancelled. This functions
+            * emulates a population split (forward in time).
+            *
+            */
+            PopulationFusion(double date, unsigned int mother, unsigned int daughter);
+            
+            void apply(ParamSet* paramSet, Controller* controller) const;
+        
+            /// Sets the daughter population
+            void daughter(unsigned int);
+            
+            /// Gets the daughter population
+            unsigned int daughter() const;
+            
+            /// Sets the mother population
+            void mother(unsigned int);
+            
+            /// Gets the mother population
+            unsigned int mother() const;
+        
+        protected:
+            unsigned int _mother;
+            unsigned int _daughter;
+    };    
+    
+    
+/**********************************************************************/
+    
+   /** \brief Split of a population
+    *
+    * \ingroup coalesce
+    *
+    */
+    class PopulationSplit : public Change {
+        public:
+           /** \brief Default constructor
+            *
+            * The default date is 0., the default population is 0, the
+            * default probability is 0.5.
+            *
+            */
+            PopulationSplit();
+
+           /** \brief Standard constructor
+            *
+            * A the time given by date, the specified population is
+            * split in two. An additional population (whose index is
+            * incremented from the current total number of population)
+            * is created and lineages are randomly picked and moved to
+            * the new population. The parameter proba gives the
+            * probability that a lineage from the population number pop
+            * moves instantly to the new population. If proba is 0,
+            * the program emulates the creation of an empty population
+            * (thinking forward in time, this is a population
+            * extinction). In general, forward in time, this is a
+            * population fusion.
+            * 
+            * \param date the date of the event.
+            * \param pop population index.
+            * \param proba the probability that lineages move to the
+            * new population.
+            *
+            */
+            PopulationSplit(double date, unsigned int pop, double proba);
+            
+            void apply(ParamSet* paramSet, Controller* controller) const;
+            
+            /// Gets the population index
+            unsigned int population() const;
+            
+            /// Sets the population index
+            void population(unsigned int);
+            
+            /// Gets the probability of instant migration
+            double probability() const;
+
+            /// Sets the probability of instant migration
+            void probability(double);
+            
+        protected:
+            unsigned int _population;
+            double _probability;
+    };
+
+/**********************************************************************/
+
+   /** \brief Change of the migration rate of all population pairs
+    *
+    * The parameter is the new rate (applied to all population pairs)
+    *
+    * \ingroup coalesce
+    *
+    */
+    class AllMigrationRateChange : public SingleParamChange {
+        public:
+        AllMigrationRateChange(double date, double value) : SingleParamChange(date, value) {}
+        void apply(ParamSet* paramSet, Controller* controller) const;
+    };
+
+/**********************************************************************/
+    
+   /** \brief Change of a single migration rate
+    *
+    * \ingroup coalesce
+    *
+    */
+    class SingleMigrationRateChange : public SingleParamChange {
+        public:
+           /** \brief Default constructor
+            *
+            * The default date is 0., the default parameter value is 0.,
+            * the  default source population is 0, the default
+            * destination population 1.
+            *
+            */
+            SingleMigrationRateChange();
+
+           /** \brief Standard constructor
+            *
+            * \param date the date of the event.
+            * \param source index of the source population.
+            * \param dest index of the destination population.
+            * \param migr new value of the pairwise migration rate.
+            *
+            */
+            SingleMigrationRateChange(double date, unsigned int source, unsigned int dest, double migr);
+            
+            /// Gets the source population index
+            unsigned source() const;
+            
+            /// Sets the source population index
+            void source(unsigned int);
+
+            /// Gets the dest population index
+            unsigned dest() const;
+            
+            /// Sets the dest population index
+            void dest(unsigned int);
+
+            void apply(ParamSet* paramSet, Controller* controller) const;
+        
+        protected:
+            unsigned int _source;
+            unsigned int _dest;
+    };
+}
+
+#endif