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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/egglib/egglib-2.1.5/include/egglib-cpp/ParamSet.hpp	Fri Jul 10 04:39:30 2015 -0400
@@ -0,0 +1,279 @@
+/*
+    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_PARAMSET_HPP
+#define EGGLIB_PARAMSET_HPP
+
+
+#include "DataMatrix.hpp"
+
+
+namespace egglib {
+
+    class Change;
+    class Controller;
+
+
+   /** \brief Set of parameters
+    *
+    * \ingroup coalesce
+    *
+    */
+    class ParamSet {
+
+        public:
+    
+           /** \brief Default constructor
+            *
+            * Initializes all parameters to reasonnable values (except
+            * that the sample size is null: 1 population, 0 samples,
+            * selfing rate of 0, recombination rate of 0, growth rate of
+            * 0, population size of 1 and no changes.
+            *
+            */
+            ParamSet();
+
+           /** \brief Destructor
+            * 
+            */
+            ~ParamSet();
+            
+           /** \brief Copy constructor
+            * 
+            */
+            ParamSet(const ParamSet&);
+            
+           /** \brief Assignment operator
+            * 
+            */
+            ParamSet& operator=(const ParamSet&);
+
+           /** \brief Restores default value of all parameters
+            * 
+            */
+            void reset();
+
+           /** \brief Gets the number of populations
+            * 
+            */
+            unsigned int numberOfPopulations() const;
+            
+           /** \brief Gets a pairwise migration rate
+            * 
+            * It is allowed to access a diagonal value. Diagonal
+            * values contain the sum of values of the corresponding
+            * line (diagonal cell excepted, of course).
+            * 
+            */
+            double pairwiseMigrationRate(unsigned int source, unsigned int dest) const;
+            
+           /** \brief Sets a pairwise migration rate
+            * 
+            * It is not allowed to set a value on the diagonal (this
+            * would raise an exception). The method takes care of
+            * modifying the diagonal accordingly (still this is not
+            * relevant for the client);
+            * 
+            */
+            void pairwiseMigrationRate(unsigned int source, unsigned int dest, double value);
+            
+           /** \brief Sets the migration rate for all matrix
+            * 
+            */
+            void migrationRate(double value);
+            
+           /** \brief Gets a population size
+            * 
+            */
+            double populationSize(unsigned int populationIndex) const;
+            
+           /** \brief Sets a population size
+            * 
+            * The size must be strictly positive.
+            * 
+            */
+            void populationSize(unsigned int populationIndex, double value);
+            
+           /** \brief Gets a growth rate
+            * 
+            */
+            double growthRate(unsigned int populationIndex) const;
+            
+           /** \brief Sets a growth rate
+            * 
+            */
+            void growthRate(unsigned int populationIndex, double value);
+            
+           /** \brief Gets the recombination rate
+            * 
+            */
+            double recombinationRate() const;
+            
+           /** \brief Sets the recombination rate
+            * 
+            */
+            void recombinationRate(double value);
+
+           /** \brief Gets the number of recombining segments
+            * 
+            */
+            unsigned int numberOfSegments() const;
+            
+           /** \brief Sets the number of recombining segments
+            * 
+            */
+            void numberOfSegments(unsigned int value);
+
+           /** \brief Gets the selfing rate
+            * 
+            */
+            double selfingRate() const;
+            
+           /** \brief Sets the selfing rate
+            * 
+            */
+            void selfingRate(double value);
+            
+           /** \brief Adds a population to the model
+            * 
+            * \param migr pairwise migration rate between other
+            * population and the new one.
+            *
+            * The parameters for the new population are equivalent to
+            * the default parameters.
+            * 
+            */
+            void addPopulation(double migr);
+            
+           /** \brief Adds a change
+            * 
+            * The change can be of any type derived from Change. A
+            * const Change* must be passed, so ParamSet will neither
+            * modify or delete the object itself. All passed Change
+            * object must be kept available for use by ParamSet.
+            *
+            */
+            void addChange(const Change* change);
+
+           /** \brief Gets the date of the next change
+            * 
+            * Returns -1 if no change is planned.
+            * 
+            */
+            double nextChangeDate() const;
+            
+           /** \brief Applies the next change event
+            * 
+            * \param controller the Change event might need to have
+            * access to simulation controller (to trigger coalescent
+            * events, for example).
+            * 
+            */
+            void nextChangeDo(Controller* controller);
+            
+           /** \brief Gets the number of single sample from a population
+            * 
+            */
+            unsigned int singles(unsigned int populationIndex) const;
+
+           /** \brief Sets the number of single sample from a population
+            * 
+            */
+            void singles(unsigned int populationIndex, unsigned int value);
+
+           /** \brief Gets the number of double sample from a population
+            * 
+            */
+            unsigned int doubles(unsigned int populationIndex) const;
+
+           /** \brief Sets the number of double sample from a population
+            * 
+            */
+            void doubles(unsigned int populationIndex, unsigned int value);
+            
+           /** \brief Computes the total number of samples
+            * 
+            */
+            unsigned int numberOfSamples() const;
+            
+           /** \brief Gives the date of the last size change
+            * 
+            * \param populationIndex the index of the population.
+            * \return The date where the last change occurred, or 0. if
+            * no change occurred during the simulation.
+            *
+            */
+            double dateOfLastChange(unsigned int populationIndex) const;
+
+
+           /** \brief Sets the date of the last size change
+            * 
+            * \param populationIndex the index of the population.
+            * \param date the date where the last change occurred, or 0.
+            * if no change occurred during the simulation.
+            *
+            */
+            void dateOfLastChange(unsigned int populationIndex, double date) const;
+
+            
+           /** \brief Set groups labels
+            * 
+            * Sets the group labels of the DataMatrix, according to the
+            * current state of population structure, and assuming that
+            * the DataMatrix was generated by the class Arg.
+            * 
+            * \param dataMatrix the DataMatrix object to modify. The
+            * number of sequences must match the total number of samples
+            * defined by the ParamSet object this method is called on.
+            * 
+            * \param labelIndividuals by default, labels the different
+            * samples depending on the population they come from (0
+            * being the label of the first population). If this flag is
+            * set to true, then the samples are labelled depending on
+            * the individual they come from, regardless of populations.
+            * In that case there can be only one or two genes for a
+            * given group label.
+            * 
+            */
+            void setGroups(DataMatrix& dataMatrix, bool labelIndividuals=false);
+
+        private:
+
+            void clear();
+            void init();
+            void copy(const ParamSet&);
+        
+            double _selfingRate;
+            double _recombinationRate;
+            unsigned int _numberOfSegments;
+            unsigned int _numberOfPopulations;
+            unsigned int* _singles;
+            unsigned int* _doubles;
+            double* _growthRates;
+            double* _populationSize;
+            double* _dateOfLastChange;
+            double** migrationMatrix;
+            unsigned int _numberOfChanges;
+            unsigned int nextChangeIndex;
+            Change const** changes;
+    };
+
+}
+
+#endif