annotate egglib/egglib-2.1.5/include/egglib-cpp/Controller.hpp @ 6:ebb0ac9b6fa9 draft

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author gandres
date Mon, 23 May 2016 17:49:17 -0400
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1 /*
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2 Copyright 2009-2010 Stéphane De Mita, Mathieu Siol
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3
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4 This file is part of the EggLib library.
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5
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6 EggLib is free software: you can redistribute it and/or modify
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7 it under the terms of the GNU General Public License as published by
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8 the Free Software Foundation, either version 3 of the License, or
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9 (at your option) any later version.
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10
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11 EggLib is distributed in the hope that it will be useful,
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12 but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 GNU General Public License for more details.
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15
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16 You should have received a copy of the GNU General Public License
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17 along with EggLib. If not, see <http://www.gnu.org/licenses/>.
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18 */
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19
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20 #ifndef EGGLIB_CONTROLLER_HPP
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21 #define EGGLIB_CONTROLLER_HPP
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22
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23 #include "Current.hpp"
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24 #include "Arg.hpp"
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25 #include "ParamSet.hpp"
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26
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27 namespace egglib {
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28
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29 class Random;
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30
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31 /** \brief Controls a coalescent simulation
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32 *
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33 * \ingroup coalesce
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34 *
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35 * This class generates the gene genealogy, based on the parameters
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36 * stocked in a ParamSet object.
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37 *
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38 */
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39 class Controller {
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40
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41 public:
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42
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43 /** \brief Default constructor
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44 *
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45 * Uses a default ParamSet object that will not allow
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46 * performing simulations.
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47 *
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48 */
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49 Controller();
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50
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51 /** \brief Destructor
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52 *
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53 */
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54 ~Controller();
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55
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56 /** \brief Standard constructor
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57 *
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58 * \param paramSet a ParamSet object containing run
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59 * parameters (it is taken as a reference and stored as this
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60 * so it must not be modified during simulations).
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61 *
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62 * \param random the address of the random number generator.
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63 *
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64 */
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65 Controller(const ParamSet* paramSet, Random* random);
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66
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67 /** \brief Reset for a new simulation
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68 *
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69 * Object is reinitiliazed for a new simulation.
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70 *
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71 */
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72 void reset();
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73
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74 /** \brief Increments the coalescent model
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75 *
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76 * \return The number of lineages.
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77 *
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78 */
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79 unsigned int step();
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80
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81 /** \brief Gets the Ancestral Recombination Graph
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82 *
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83 * \return The address of the ARG contained in the object.
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84 *
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85 */
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86 Arg* getArg();
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87
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88 /** \brief Applies a bottleneck to a given population
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89 *
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90 * The bottleneck is applied following Galtier, Depaulis and
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91 * Barton (Genetics, 2000): the general time counter is
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92 * stopped, and coalescence events are performed during a
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93 * time (of normal coalescent process) given by the parameter
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94 * strength. All coalescent events are instantaneous.
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95 *
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96 * \param populationIndex index of the population concerned
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97 * by the event.
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98 *
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99 * \param strength strength of the bottleneck given by a
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100 * number of time units (2N generations times the size of
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101 * the population).
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102 *
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103 */
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104 void bottleneck(unsigned int populationIndex, double strength);
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105
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106 /** \brief Migrate a complete population
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107 *
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108 * Takes all the lineages currently present in the population
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109 * source to the population dest.
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110 *
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111 */
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112 void moveAllLineages(unsigned int source, unsigned int dest);
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113
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114 /** \brief Migrate a complete population
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115 *
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116 * Takes all the lineages currently present in the population
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117 * source to the population dest.
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118 *
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119 * \param source source population.
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120 * \param dest destination population.
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121 * \param probability the probability that a lineage of
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122 * source migrates to dest.
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123 *
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124 */
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125 void moveSomeLineages(unsigned int source, unsigned int dest, double probability);
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126
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127 /// Adds an empty population
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128 void addPopulation();
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129
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130 private:
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131
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132 /// The copy constructor is disabled
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133 Controller(const Controller& source) {}
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134
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135 /// The assignment operator is disabled
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136 Controller& operator=(const Controller& source) {return *this;}
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137
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138 void diploids();
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139 double getMigrationTime(double& migrationParameterDestination);
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140 void getCoalescenceTime(double& destTime, unsigned int& destPopIndex);
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141 double getCoalescenceTimeForPopulation(unsigned int populationIndex);
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142 double getRecombinationTime() const;
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143 void migrate(double migrationParameter);
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144
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145 const ParamSet* initialParamSet;
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146 ParamSet paramSet;
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147 Current current;
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148 Arg arg;
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149
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150 Random* random;
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151
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152 };
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153
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154 }
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155
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156 #endif