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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_POPULATION_HPP
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21 #define EGGLIB_POPULATION_HPP
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22
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23
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24 #include "Edge.hpp"
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25
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26 namespace egglib {
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27
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28 class Random;
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29
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30 /** \brief Handles a single population
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31 *
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32 * \ingroup coalesce
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33 *
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34 */
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35 class Population {
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36
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37 public:
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38
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39 /** \brief Default constructor
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40 *
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41 * Generates an empty population.
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42 *
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43 */
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44 Population();
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45
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46 /** \brief Copy constructor
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47 *
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48 */
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49 Population(const Population& source);
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50
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51 /** \brief Assignment operator
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52 *
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53 */
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54 Population& operator=(const Population& source);
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55
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56 /** \brief Destructor
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57 *
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58 * The object only cleans Edge objects currently stored in it.
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59 *
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60 */
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61 ~Population();
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62
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63 /** \brief Standard constructor
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64 *
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65 * The Edge instances will be handled by address and they
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66 * MUST be passed using the method set().
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67 *
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68 * \param numberOfSegments number of recombining segments.
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69 *
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70 * \param numberOfLineages the number of lineages contained
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71 * in this population.
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72 *
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73 * \param firstIndex the absolute index (or ID) of the first
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74 * lineage (the other will have consecutive incremented
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75 * ID's).
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76 *
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77 */
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78 Population(unsigned int numberOfSegments,
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79 unsigned int numberOfLineages, unsigned firstIndex);
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80
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81 /** \brief Gets the number of lineages
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82 *
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83 */
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84 unsigned int numberOfLineages() const;
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85
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86 /** \brief Gets the efficient number of lineages
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87 *
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88 * The number of lineages is multiplied by the number of
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89 * covered segments of each lineages.
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90 *
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91 */
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92 unsigned int efficientNumberOfLineages() const;
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93
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94 /** \brief Sets the Edge of a lineage
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95 *
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96 * \param index the index of the lineage within the
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97 * population.
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98 * \param edge the address of the Edge instance representing
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99 * the lineage.
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100 *
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101 */
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102 void set(unsigned int index, Edge* edge);
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103
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104 /** \brief Removes and returns a random lineage.
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105 *
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106 * \param random pointer to simulator's random generator
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107 * instance.
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108 *
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109 */
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110 Edge* extractRandomly(Random* random);
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111
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112 /** \brief Removes and returns a given lineage.
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113 *
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114 * \param index the relative index of the lineage.
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115 *
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116 */
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117 Edge* extractByIndex(unsigned int index);
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118
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119 /** \brief Appends a lineage to the object
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120 *
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121 */
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122 void push(Edge* edge);
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123
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124 /** \brief Gets coverage
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125 *
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126 */
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127 unsigned int coverage(unsigned int edgeIndex) const;
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128
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129
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130 private:
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131
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132 void copy(const Population& source);
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133 void clear();
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134 Edge* pick(unsigned int index);
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135 void init();
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136 unsigned int _numberOfLineages;
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137 unsigned int _efficientNumberOfLineages;
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138 Edge** lineages;
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139 };
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140
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141 }
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142
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143 #endif
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