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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_PARAMSET_HPP
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21 #define EGGLIB_PARAMSET_HPP
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22
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23
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24 #include "DataMatrix.hpp"
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25
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26
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27 namespace egglib {
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28
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29 class Change;
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30 class Controller;
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31
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32
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33 /** \brief Set of parameters
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34 *
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35 * \ingroup coalesce
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36 *
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37 */
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38 class ParamSet {
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39
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40 public:
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41
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42 /** \brief Default constructor
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43 *
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44 * Initializes all parameters to reasonnable values (except
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45 * that the sample size is null: 1 population, 0 samples,
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46 * selfing rate of 0, recombination rate of 0, growth rate of
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47 * 0, population size of 1 and no changes.
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48 *
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49 */
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50 ParamSet();
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51
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52 /** \brief Destructor
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53 *
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54 */
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55 ~ParamSet();
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56
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57 /** \brief Copy constructor
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58 *
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59 */
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60 ParamSet(const ParamSet&);
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61
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62 /** \brief Assignment operator
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63 *
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64 */
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65 ParamSet& operator=(const ParamSet&);
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66
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67 /** \brief Restores default value of all parameters
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68 *
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69 */
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70 void reset();
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71
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72 /** \brief Gets the number of populations
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73 *
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74 */
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75 unsigned int numberOfPopulations() const;
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76
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77 /** \brief Gets a pairwise migration rate
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78 *
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79 * It is allowed to access a diagonal value. Diagonal
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80 * values contain the sum of values of the corresponding
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81 * line (diagonal cell excepted, of course).
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82 *
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83 */
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84 double pairwiseMigrationRate(unsigned int source, unsigned int dest) const;
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85
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86 /** \brief Sets a pairwise migration rate
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87 *
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88 * It is not allowed to set a value on the diagonal (this
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89 * would raise an exception). The method takes care of
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90 * modifying the diagonal accordingly (still this is not
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91 * relevant for the client);
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92 *
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93 */
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94 void pairwiseMigrationRate(unsigned int source, unsigned int dest, double value);
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95
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96 /** \brief Sets the migration rate for all matrix
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97 *
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98 */
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99 void migrationRate(double value);
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100
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101 /** \brief Gets a population size
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102 *
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103 */
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104 double populationSize(unsigned int populationIndex) const;
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105
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106 /** \brief Sets a population size
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107 *
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108 * The size must be strictly positive.
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109 *
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110 */
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111 void populationSize(unsigned int populationIndex, double value);
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112
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113 /** \brief Gets a growth rate
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114 *
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115 */
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116 double growthRate(unsigned int populationIndex) const;
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117
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118 /** \brief Sets a growth rate
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119 *
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120 */
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121 void growthRate(unsigned int populationIndex, double value);
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122
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123 /** \brief Gets the recombination rate
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124 *
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125 */
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126 double recombinationRate() const;
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127
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128 /** \brief Sets the recombination rate
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129 *
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130 */
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131 void recombinationRate(double value);
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132
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133 /** \brief Gets the number of recombining segments
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134 *
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135 */
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136 unsigned int numberOfSegments() const;
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137
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138 /** \brief Sets the number of recombining segments
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139 *
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140 */
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141 void numberOfSegments(unsigned int value);
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142
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143 /** \brief Gets the selfing rate
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144 *
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145 */
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146 double selfingRate() const;
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147
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148 /** \brief Sets the selfing rate
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149 *
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150 */
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151 void selfingRate(double value);
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152
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153 /** \brief Adds a population to the model
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154 *
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155 * \param migr pairwise migration rate between other
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156 * population and the new one.
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157 *
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158 * The parameters for the new population are equivalent to
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159 * the default parameters.
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160 *
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161 */
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162 void addPopulation(double migr);
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163
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164 /** \brief Adds a change
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165 *
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166 * The change can be of any type derived from Change. A
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167 * const Change* must be passed, so ParamSet will neither
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168 * modify or delete the object itself. All passed Change
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169 * object must be kept available for use by ParamSet.
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170 *
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171 */
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172 void addChange(const Change* change);
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173
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174 /** \brief Gets the date of the next change
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175 *
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176 * Returns -1 if no change is planned.
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177 *
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178 */
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179 double nextChangeDate() const;
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180
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181 /** \brief Applies the next change event
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182 *
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183 * \param controller the Change event might need to have
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184 * access to simulation controller (to trigger coalescent
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185 * events, for example).
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186 *
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187 */
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188 void nextChangeDo(Controller* controller);
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189
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190 /** \brief Gets the number of single sample from a population
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191 *
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192 */
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193 unsigned int singles(unsigned int populationIndex) const;
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194
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195 /** \brief Sets the number of single sample from a population
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196 *
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197 */
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198 void singles(unsigned int populationIndex, unsigned int value);
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199
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200 /** \brief Gets the number of double sample from a population
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201 *
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202 */
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203 unsigned int doubles(unsigned int populationIndex) const;
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204
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205 /** \brief Sets the number of double sample from a population
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206 *
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207 */
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208 void doubles(unsigned int populationIndex, unsigned int value);
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209
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210 /** \brief Computes the total number of samples
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211 *
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212 */
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213 unsigned int numberOfSamples() const;
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214
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215 /** \brief Gives the date of the last size change
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216 *
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217 * \param populationIndex the index of the population.
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218 * \return The date where the last change occurred, or 0. if
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219 * no change occurred during the simulation.
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220 *
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221 */
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222 double dateOfLastChange(unsigned int populationIndex) const;
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223
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224
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225 /** \brief Sets the date of the last size change
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226 *
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227 * \param populationIndex the index of the population.
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228 * \param date the date where the last change occurred, or 0.
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229 * if no change occurred during the simulation.
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230 *
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231 */
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232 void dateOfLastChange(unsigned int populationIndex, double date) const;
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233
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234
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235 /** \brief Set groups labels
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236 *
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237 * Sets the group labels of the DataMatrix, according to the
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238 * current state of population structure, and assuming that
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239 * the DataMatrix was generated by the class Arg.
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240 *
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241 * \param dataMatrix the DataMatrix object to modify. The
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242 * number of sequences must match the total number of samples
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243 * defined by the ParamSet object this method is called on.
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244 *
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245 * \param labelIndividuals by default, labels the different
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246 * samples depending on the population they come from (0
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247 * being the label of the first population). If this flag is
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248 * set to true, then the samples are labelled depending on
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249 * the individual they come from, regardless of populations.
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250 * In that case there can be only one or two genes for a
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251 * given group label.
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252 *
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253 */
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254 void setGroups(DataMatrix& dataMatrix, bool labelIndividuals=false);
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255
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256 private:
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257
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258 void clear();
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259 void init();
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260 void copy(const ParamSet&);
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261
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262 double _selfingRate;
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263 double _recombinationRate;
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264 unsigned int _numberOfSegments;
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265 unsigned int _numberOfPopulations;
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266 unsigned int* _singles;
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267 unsigned int* _doubles;
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268 double* _growthRates;
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269 double* _populationSize;
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270 double* _dateOfLastChange;
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271 double** migrationMatrix;
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272 unsigned int _numberOfChanges;
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273 unsigned int nextChangeIndex;
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274 Change const** changes;
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275 };
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276
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277 }
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278
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279 #endif
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