1 | #region License Information
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2 | /* HeuristicLab
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3 | * Copyright (C) 2002-2014 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
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4 | *
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5 | * This file is part of HeuristicLab.
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6 | *
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7 | * HeuristicLab is free software: you can redistribute it and/or modify
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8 | * it under the terms of the GNU General Public License as published by
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9 | * the Free Software Foundation, either version 3 of the License, or
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10 | * (at your option) any later version.
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11 | *
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12 | * HeuristicLab is distributed in the hope that it will be useful,
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13 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 | * GNU General Public License for more details.
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16 | *
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17 | * You should have received a copy of the GNU General Public License
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18 | * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
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19 | */
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20 | #endregion
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21 |
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22 | using System;
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23 | using System.Linq;
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24 | using HeuristicLab.Analysis;
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25 | using HeuristicLab.Common;
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26 | using HeuristicLab.Core;
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27 | using HeuristicLab.Data;
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28 | using HeuristicLab.Operators;
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29 | using HeuristicLab.Optimization;
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30 | using HeuristicLab.Parameters;
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31 | using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
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32 |
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33 | namespace HeuristicLab.EvolutionTracking {
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34 | [StorableClass]
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35 | [Item("GenealogyAnalyzer", "An analyzer which performs the necessary instrumentation to record the evolution of a genetic algorithm.")]
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36 | public class GenealogyAnalyzer<T> : SingleSuccessorOperator, IAnalyzer
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37 | where T : class,IItem {
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38 | #region parameter names
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39 | private const string GenerationsParameterName = "Generations";
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40 | private const string ResultsParameterName = "Results";
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41 | private const string PopulationGraphParameterName = "PopulationGraph";
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42 | public const string QualityParameterName = "Quality";
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43 | public const string PopulationParameterName = "SymbolicExpressionTree";
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44 |
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45 | private const string CrossoverParameterName = "Crossover";
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46 | private const string ManipulatorParameterName = "Mutator";
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47 | private const string SolutionCreatorParameterName = "SolutionCreator";
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48 |
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49 | private const string BeforeCrossoverOperatorParameterName = "BeforeCrossoverOperator";
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50 | private const string AfterCrossoverOperatorParameterName = "AfterCrossoverOperator";
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51 |
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52 | private const string BeforeManipulatorOperatorParameterName = "BeforeManipulatorOperator";
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53 | private const string AfterManipulatorOperatorParameterName = "AfterManipulatorOperator";
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54 |
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55 | private const string EnableCrossoverTrackingParameterName = "EnableCrossoverTracking";
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56 | private const string EnableManipulatorTrackingParameterName = "EnableManipulatorTracking";
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57 | private const string EnableSolutionCreatorTrackingParameterName = "EnableSolutionCreatorTracking"; // should always be enabled. maybe superfluous
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58 | #endregion
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59 |
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60 | #region parameter properties
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61 | public IScopeTreeLookupParameter<DoubleValue> QualityParameter {
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62 | get { return (IScopeTreeLookupParameter<DoubleValue>)Parameters[QualityParameterName]; }
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63 | }
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64 | public IScopeTreeLookupParameter<T> PopulationParameter {
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65 | get { return (IScopeTreeLookupParameter<T>)Parameters[PopulationParameterName]; }
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66 | }
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67 | public IValueParameter<ICrossoverOperator<T>> BeforeCrossoverOperatorParameter {
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68 | get { return (IValueParameter<ICrossoverOperator<T>>)Parameters[BeforeCrossoverOperatorParameterName]; }
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69 | }
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70 | public IValueParameter<ICrossoverOperator<T>> AfterCrossoverOperatorParameter {
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71 | get { return (IValueParameter<ICrossoverOperator<T>>)Parameters[AfterCrossoverOperatorParameterName]; }
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72 | }
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73 | public IValueParameter<IManipulatorOperator<T>> BeforeManipulatorOperatorParameter {
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74 | get { return (IValueParameter<IManipulatorOperator<T>>)Parameters[BeforeManipulatorOperatorParameterName]; }
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75 | }
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76 | public IValueParameter<IManipulatorOperator<T>> AfterManipulatorOperatorParameter {
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77 | get { return (IValueParameter<IManipulatorOperator<T>>)Parameters[AfterManipulatorOperatorParameterName]; }
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78 | }
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79 | public ILookupParameter<ResultCollection> ResultsParameter {
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80 | get { return (ILookupParameter<ResultCollection>)Parameters[ResultsParameterName]; }
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81 | }
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82 | public ILookupParameter<IntValue> GenerationsParameter {
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83 | get { return (ILookupParameter<IntValue>)Parameters[GenerationsParameterName]; }
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84 | }
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85 | public IValueParameter<BoolValue> EnableCrossoverTrackingParameter {
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86 | get { return (IValueParameter<BoolValue>)Parameters[EnableCrossoverTrackingParameterName]; }
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87 | }
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88 | public IValueParameter<BoolValue> EnableManipulatorTrackingParameter {
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89 | get { return (IValueParameter<BoolValue>)Parameters[EnableManipulatorTrackingParameterName]; }
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90 | }
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91 | public IValueParameter<BoolValue> EnableSolutionCreatorTrackingParameter {
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92 | get { return (IValueParameter<BoolValue>)Parameters[EnableSolutionCreatorTrackingParameterName]; }
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93 | }
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94 | public ILookupParameter<ICrossover> CrossoverParameter {
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95 | get { return (ILookupParameter<ICrossover>)Parameters[CrossoverParameterName]; }
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96 | }
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97 | public ILookupParameter<IManipulator> ManipulatorParameter {
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98 | get { return (ILookupParameter<IManipulator>)Parameters[ManipulatorParameterName]; }
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99 | }
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100 |
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101 | public ILookupParameter<ISolutionCreator> SolutionCreatorParameter {
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102 | get { return (ILookupParameter<ISolutionCreator>)Parameters[SolutionCreatorParameterName]; }
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103 | }
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104 | #endregion
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105 |
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106 | #region properties
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107 | public ICrossoverOperator<T> BeforeCrossoverOperator {
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108 | get { return BeforeCrossoverOperatorParameter.Value; }
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109 | }
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110 | public ICrossoverOperator<T> AfterCrossoverOperator {
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111 | get { return AfterCrossoverOperatorParameter.Value; }
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112 | }
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113 | public IManipulatorOperator<T> BeforeManipulatorOperator {
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114 | get { return BeforeManipulatorOperatorParameter.Value; }
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115 | }
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116 | public IManipulatorOperator<T> AfterManipulatorOperator {
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117 | get { return AfterManipulatorOperatorParameter.Value; }
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118 | }
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119 | public BoolValue EnableCrossoverTracking {
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120 | get { return EnableCrossoverTrackingParameter.Value; }
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121 | }
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122 | public BoolValue EnableManipulatorTracking {
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123 | get { return EnableManipulatorTrackingParameter.Value; }
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124 | }
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125 | public BoolValue EnableSolutionCreatorTracking {
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126 | get { return EnableSolutionCreatorTrackingParameter.Value; }
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127 | }
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128 |
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129 | public IGenealogyGraph<T> GenealogyGraph {
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130 | get {
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131 | IResult result;
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132 | var results = ResultsParameter.ActualValue;
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133 | if (!results.ContainsKey(PopulationGraphParameterName)) {
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134 | result = new Result(PopulationGraphParameterName, new GenealogyGraph<T>());
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135 | results.Add(result);
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136 | } else {
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137 | result = results[PopulationGraphParameterName];
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138 | }
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139 | var graph = (IGenealogyGraph<T>)result.Value;
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140 | return graph;
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141 | }
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142 | }
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143 | #endregion
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144 |
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145 | public GenealogyAnalyzer() {
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146 | #region add parameters
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147 | // the instrumented operators
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148 | Parameters.Add(new LookupParameter<ICrossover>(CrossoverParameterName, "The crossover operator."));
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149 | Parameters.Add(new LookupParameter<IManipulator>(ManipulatorParameterName, "The manipulator operator."));
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150 | Parameters.Add(new LookupParameter<ISolutionCreator>(SolutionCreatorParameterName, "The solution creator operator."));
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151 | // the analyzer parameters
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152 | Parameters.Add(new ValueParameter<BoolValue>(EnableCrossoverTrackingParameterName, new BoolValue(true)));
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153 | Parameters.Add(new ValueParameter<BoolValue>(EnableManipulatorTrackingParameterName, new BoolValue(true)));
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154 | Parameters.Add(new ValueParameter<BoolValue>(EnableSolutionCreatorTrackingParameterName, new BoolValue(true)));
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155 | // parameters required by the analyzer to do its work
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156 | Parameters.Add(new LookupParameter<IntValue>(GenerationsParameterName, "The number of generations so far."));
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157 | Parameters.Add(new LookupParameter<ResultCollection>(ResultsParameterName));
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158 | Parameters.Add(new ScopeTreeLookupParameter<T>(PopulationParameterName, "The population of individuals."));
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159 | Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>(QualityParameterName, "The individual qualities."));
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160 | Parameters.Add(new ValueParameter<ICrossoverOperator<T>>(BeforeCrossoverOperatorParameterName));
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161 | Parameters.Add(new ValueParameter<ICrossoverOperator<T>>(AfterCrossoverOperatorParameterName));
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162 | Parameters.Add(new ValueParameter<IManipulatorOperator<T>>(BeforeManipulatorOperatorParameterName));
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163 | Parameters.Add(new ValueParameter<IManipulatorOperator<T>>(AfterManipulatorOperatorParameterName));
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164 | #endregion
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165 | }
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166 | public override IDeepCloneable Clone(Cloner cloner) {
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167 | return new GenealogyAnalyzer<T>(this, cloner);
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168 | }
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169 | protected GenealogyAnalyzer(GenealogyAnalyzer<T> original, Cloner cloner)
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170 | : base(original, cloner) {
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171 | }
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172 |
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173 | [StorableConstructor]
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174 | protected GenealogyAnalyzer(bool deserializing) : base(deserializing) { }
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175 |
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176 | [StorableHook(HookType.AfterDeserialization)]
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177 | private void AfterDeserialization() {
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178 | // the instrumented operators
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179 | if (!Parameters.ContainsKey(CrossoverParameterName))
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180 | Parameters.Add(new LookupParameter<ICrossover>(CrossoverParameterName, "The crossover operator."));
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181 | if (!Parameters.ContainsKey(ManipulatorParameterName))
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182 | Parameters.Add(new LookupParameter<IManipulator>(ManipulatorParameterName, "The manipulator operator."));
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183 | if (!Parameters.ContainsKey(SolutionCreatorParameterName))
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184 | Parameters.Add(new LookupParameter<ISolutionCreator>(SolutionCreatorParameterName, "The solution creator operator."));
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185 | // the analyzer parameters
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186 | if (!Parameters.ContainsKey(EnableCrossoverTrackingParameterName))
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187 | Parameters.Add(new ValueParameter<BoolValue>(EnableCrossoverTrackingParameterName, new BoolValue(true)));
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188 | if (!Parameters.ContainsKey(EnableManipulatorTrackingParameterName))
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189 | Parameters.Add(new ValueParameter<BoolValue>(EnableManipulatorTrackingParameterName, new BoolValue(true)));
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190 | if (!Parameters.ContainsKey(EnableSolutionCreatorTrackingParameterName))
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191 | Parameters.Add(new ValueParameter<BoolValue>(EnableSolutionCreatorTrackingParameterName, new BoolValue(true)));
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192 | // parameters required by the analyzer to do its work
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193 | if (!Parameters.ContainsKey(GenerationsParameterName))
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194 | Parameters.Add(new LookupParameter<IntValue>(GenerationsParameterName, "The number of generations so far."));
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195 | if (!Parameters.ContainsKey(ResultsParameterName))
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196 | Parameters.Add(new LookupParameter<ResultCollection>(ResultsParameterName));
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197 | if (!Parameters.ContainsKey(PopulationParameterName)) {
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198 | Parameters.Add(new ScopeTreeLookupParameter<T>(PopulationParameterName, "The population of individuals."));
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199 | }
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200 | if (!Parameters.ContainsKey(QualityParameterName)) {
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201 | Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>(QualityParameterName, "The individual qualities."));
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202 | }
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203 | }
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204 |
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205 | public bool EnabledByDefault {
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206 | get { return false; }
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207 | }
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208 |
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209 | private void ConfigureTrackingOperators() {
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210 | // at the beginning we add the before/after operators to the instrumented operators
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211 | var crossover = CrossoverParameter.ActualValue;
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212 | if (crossover != null) {
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213 | var instrumentedCrossover = (InstrumentedOperator)crossover;
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214 | instrumentedCrossover.AfterExecutionOperators.Clear();
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215 | instrumentedCrossover.BeforeExecutionOperators.Clear();
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216 |
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217 | if (EnableCrossoverTracking.Value) {
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218 | if (BeforeCrossoverOperator != null) {
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219 | instrumentedCrossover.BeforeExecutionOperators.Add(BeforeCrossoverOperator);
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220 | }
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221 | if (AfterCrossoverOperator != null) {
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222 | instrumentedCrossover.AfterExecutionOperators.Add(AfterCrossoverOperator);
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223 | }
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224 | }
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225 | }
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226 | var manipulator = ManipulatorParameter.ActualValue;
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227 | if (manipulator != null) {
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228 | var instrumentedManipulator = (InstrumentedOperator)manipulator;
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229 | instrumentedManipulator.AfterExecutionOperators.Clear();
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230 | instrumentedManipulator.BeforeExecutionOperators.Clear();
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231 |
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232 | if (EnableManipulatorTracking.Value) {
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233 | if (BeforeManipulatorOperator != null) {
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234 | instrumentedManipulator.BeforeExecutionOperators.Add(BeforeManipulatorOperator);
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235 | }
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236 | if (AfterManipulatorOperator != null) {
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237 | instrumentedManipulator.AfterExecutionOperators.Add(AfterManipulatorOperator);
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238 | }
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239 | }
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240 | }
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241 | }
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242 |
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243 | public override IOperation Apply() {
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244 | var population = PopulationParameter.ActualValue;
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245 | var qualities = QualityParameter.ActualValue.ToList();
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246 |
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247 | int generation = GenerationsParameter.ActualValue.Value;
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248 | if (generation == 0) {
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249 | ConfigureTrackingOperators();
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250 |
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251 | for (int i = 0; i < population.Length; ++i) {
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252 | var individual = population[i];
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253 | var vertex = new GenealogyGraphNode<T>(individual) { Rank = generation };
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254 | GenealogyGraph.AddVertex(vertex);
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255 | // save the vertex id in the individual scope (so that we can identify graph indices)
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256 | ExecutionContext.Scope.SubScopes[i].Variables.Add(new Variable("Id", new StringValue(vertex.Id)));
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257 | }
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258 | } else {
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259 | int index = 0;
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260 | T elite = null;
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261 |
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262 | for (int i = 0; i < population.Length; ++i) {
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263 | if (GenealogyGraph.GetByContent(population[i]).Rank.Equals(generation - 1)) {
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264 | elite = population[i];
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265 | index = i;
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266 | break;
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267 | }
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268 | }
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269 |
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270 | #region add elite in the graph and connect it with the previous elite
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271 | if (elite != null) {
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272 | var prevVertex = (IGenealogyGraphNode<T>)GenealogyGraph.GetByContent(elite);
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273 | prevVertex.IsElite = true; // mark elites in the graph retroactively
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274 | var w = (IGenealogyGraphNode<T>)prevVertex.Clone();
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275 | var v = new GenealogyGraphNode<T>(prevVertex.Data) {
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276 | Rank = generation,
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277 | Quality = prevVertex.Quality,
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278 | IsElite = false
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279 | };
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280 |
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281 | object data = null;
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282 | if (prevVertex.InArcs.Any())
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283 | data = prevVertex.InArcs.Last().Data;
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284 | var children = prevVertex.Children.ToList();
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285 | var parents = prevVertex.Parents.ToList();
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286 |
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287 | GenealogyGraph.RemoveVertex(prevVertex);
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288 | GenealogyGraph.AddVertex(w);
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289 | GenealogyGraph.AddVertex(v);
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290 | GenealogyGraph.AddArc(w, v); // connect current elite with previous elite
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291 |
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292 | // recreate connections after prevVertex was replaced with w
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293 | foreach (var c in children) GenealogyGraph.AddArc(w, c);
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294 | foreach (var p in parents) GenealogyGraph.AddArc(p, w);
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295 |
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296 | v.InArcs.Last().Data = data;
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297 |
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298 | if (w.InArcs.Any())
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299 | w.InArcs.Last().Data = data;
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300 |
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301 | // inject the graph node unique id to the scope
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302 | ExecutionContext.Scope.SubScopes[index].Variables["Id"].Value = new StringValue(v.Id);
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303 | }
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304 | #endregion
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305 |
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306 | ComputeSuccessRatios();
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307 | }
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308 | // update qualities
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309 | for (int i = 0; i < population.Length; ++i) {
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310 | var vertex = GenealogyGraph.GetByContent(population[i]);
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311 | vertex.Quality = qualities[i].Value;
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312 | }
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313 |
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314 | // remove extra graph nodes (added by the instrumented operators in the case of offspring selection)
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315 | RemoveUnsuccessfulOffspring();
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316 |
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317 | return base.Apply();
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318 | }
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319 |
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320 | private void RemoveUnsuccessfulOffspring() {
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321 | int generation = GenerationsParameter.ActualValue.Value;
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322 | var population = PopulationParameter.ActualValue;
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323 | var discardedOffspring = GenealogyGraph.Ranks[generation].Select(x => (T)x.Data).Except(population).ToList();
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324 | foreach (var vertex in discardedOffspring.Select(individual => GenealogyGraph.GetByContent(individual))) {
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325 | if (vertex.InDegree == 1) {
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326 | var p = vertex.Parents.First();
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327 | if (!p.Rank.Equals(generation - 0.5))
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328 | throw new InvalidOperationException("Parent must be an intermediate vertex");
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329 | GenealogyGraph.RemoveVertex(p);
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330 | }
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331 | GenealogyGraph.RemoveVertex(vertex);
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332 | }
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333 | }
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334 |
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335 | private void ComputeSuccessRatios() {
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336 | const string successfulOffspringRatioTableHistoryName = "Successful offspring ratio";
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337 | const string successfulOffspringRatioHeatMapName = "Successful offspring ratio heatmap";
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338 |
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339 | var population = PopulationParameter.ActualValue;
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340 | var generation = GenerationsParameter.ActualValue.Value;
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341 | // compute the weight of each genealogy graph node as the ratio (produced offspring) / (surviving offspring)
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342 | foreach (var ind in population) {
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343 | var v = GenealogyGraph.GetByContent(ind);
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344 | foreach (var p in v.Parents)
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345 | p.Weight++;
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346 | }
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347 | foreach (var v in GenealogyGraph.Ranks[generation - 1]) {
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348 | if (v.OutDegree > 0)
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349 | v.Weight /= v.OutDegree;
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350 | }
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351 |
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352 | var results = ResultsParameter.ActualValue;
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353 |
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354 | DataTableHistory history;
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355 | if (!results.ContainsKey(successfulOffspringRatioTableHistoryName)) {
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356 | history = new DataTableHistory();
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357 | results.Add(new Result(successfulOffspringRatioTableHistoryName, history));
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358 | } else {
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359 | history = (DataTableHistory)results[successfulOffspringRatioTableHistoryName].Value;
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360 | }
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361 | var table = new DataTable();
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362 | var row = new DataRow("Successful Offspring") {
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363 | VisualProperties = { ChartType = DataRowVisualProperties.DataRowChartType.Columns, StartIndexZero = true }
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364 | };
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365 | row.Values.Replace(GenealogyGraph.Ranks[generation - 1].OrderByDescending(x => x.Quality).Select(x => x.Weight));
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366 | table.Rows.Add(row);
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367 | history.Add(table);
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368 | double[,] elements = new double[population.Length, history.Count];
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369 | var col = history.AsReadOnly().ToList();
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370 | for (int i = 0; i < col.Count; ++i) {
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371 | var values = col[i].Rows.First().Values;
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372 | for (int j = 0; j < values.Count; ++j) {
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373 | elements[j, i] = values[j];
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374 | }
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375 | }
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376 |
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377 | var heatmap = new HeatMap(elements);
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378 | if (!results.ContainsKey(successfulOffspringRatioHeatMapName)) {
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379 | results.Add(new Result(successfulOffspringRatioHeatMapName, heatmap));
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380 | } else {
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381 | results[successfulOffspringRatioHeatMapName].Value = heatmap;
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382 | }
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383 | }
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384 | }
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385 | }
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