1 | // This file is a part of Framsticks SDK. http://www.framsticks.com/ |
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2 | // Copyright (C) 1999-2019 Maciej Komosinski and Szymon Ulatowski. |
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3 | // See LICENSE.txt for details. |
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4 | |
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5 | #include <frams/util/sstring.h> |
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6 | #include <vector> |
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7 | #include <frams/param/param.h> |
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8 | #include "fB_conv.h" |
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9 | #include "fB_general.h" |
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10 | #include "fB_oper.h" |
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11 | #include "../fH/fH_oper.h" |
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12 | |
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13 | #define FIELDSTRUCT Geno_fB |
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14 | |
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15 | static ParamEntry GENOfBparam_tab[] = |
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16 | { |
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17 | { "Genetics: fB", 3, FB_MUT_COUNT + FB_XOVER_COUNT, }, |
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18 | { "Genetics: fB: Mutation", }, |
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19 | { "Genetics: fB: Crossover", }, |
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20 | { "fB_mut_substitution", 1, 0, "Substitution", "f 0 1 0.6", FIELD(mutationprobs[FB_SUBSTITUTION]), "Probability of mutation by changing single random letter in genotype", }, |
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21 | { "fB_mut_insertion", 1, 0, "Insertion", "f 0 1 0.095", FIELD(mutationprobs[FB_INSERTION]), "Probability of mutation by inserting characters in random place of genotype", }, |
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22 | { "fB_mut_nclassins", 1, 0, "Insertion of neuron class definition", "f 0 1 0.005", FIELD(mutationprobs[FB_NCLASSINS]), "Probability of mutation by inserting neuron class definition in random place of genotype", }, |
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23 | { "fB_mut_deletion", 1, 0, "Deletion", "f 0 1 0.1", FIELD(mutationprobs[FB_DELETION]), "Probability of mutation by deleting random characters in genotype", }, |
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24 | { "fB_mut_duplication", 1, 0, "Duplication", "f 0 1 0.0", FIELD(mutationprobs[FB_DUPLICATION]), "Probability of mutation by copying single *gene* of genotype and appending it to the beginning of this genotype", }, |
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25 | { "fB_mut_translocation", 1, 0, "Translocation", "f 0 1 0.15", FIELD(mutationprobs[FB_TRANSLOCATION]), "Probability of mutation by replacing two substrings in genotype", }, |
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26 | { "fB_cross_gene_transfer", 2, 0, "Horizontal gene transfer", "f 0 1 0.0", FIELD(crossoverprobs[FB_GENE_TRANSFER]), "Probability of crossing over by transferring single genes from both parents to beginning of each other", }, |
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27 | { "fB_cross_crossover", 2, 0, "Crossing over", "f 0 1 1.0", FIELD(crossoverprobs[FB_CROSSING_OVER]), "Probability of crossing over by random distribution of genes from both parents to both children", }, |
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28 | { 0, }, |
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29 | }; |
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30 | |
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31 | #undef FIELDSTRUCT |
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32 | |
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33 | Geno_fB::Geno_fB() |
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34 | { |
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35 | par.setParamTab(GENOfBparam_tab); |
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36 | par.select(this); |
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37 | par.setDefault(); |
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38 | supported_format = 'B'; |
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39 | } |
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40 | |
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41 | bool Geno_fB::hasStick(const SString &genotype) |
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42 | { |
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43 | for (int i = 0; i < fB_GenoHelpers::geneCount(genotype); i++) |
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44 | { |
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45 | int start, end; |
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46 | SString gene = fB_GenoHelpers::getGene(i, genotype, start, end); |
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47 | int endoffset = 0; |
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48 | if (gene.indexOf("zz", 0) != -1) endoffset = 2; |
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49 | if (gene.len() - endoffset < 3) |
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50 | { |
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51 | return true; // genes with length < 3 are always sticks |
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52 | } |
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53 | else if (gene[2] >= 'a' && gene[2] <= 'i') |
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54 | { |
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55 | return true; // gene within this range is stick |
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56 | } |
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57 | } |
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58 | return false; |
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59 | } |
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60 | |
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61 | int Geno_fB::checkValidity(const char *geno, const char *genoname) |
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62 | { |
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63 | // load genotype |
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64 | SString genotype(geno); |
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65 | SString line; |
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66 | int pos = 0; |
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67 | // if there is no genotype to load, then return error |
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68 | if (!genotype.getNextToken(pos, line, '\n')) |
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69 | { |
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70 | return pos + 1; |
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71 | } |
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72 | // extract dimensions |
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73 | int dims = 0; |
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74 | if (!ExtValue::parseInt(line.c_str(), dims, true, false)) |
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75 | { |
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76 | return 1; |
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77 | } |
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78 | // extract next token in order to check if next line starts with "aa" |
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79 | int genstart = genotype.indexOf("aa", 0); |
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80 | if (genstart != pos) |
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81 | { |
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82 | return pos + 1; |
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83 | } |
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84 | // check if rest of characters are lowercase |
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85 | for (int i = genstart; i < genotype.len(); i++) |
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86 | { |
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87 | if (!islower(genotype[i])) |
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88 | { |
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89 | if (genotype[i] == '"') |
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90 | { |
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91 | SString neuclassdef; |
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92 | int nextid = i + 1; |
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93 | if (!genotype.getNextToken(nextid, neuclassdef, '"')) |
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94 | { |
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95 | return i + 1; |
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96 | } |
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97 | Neuro *neu = new Neuro(); |
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98 | neu->setDetails(neuclassdef); |
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99 | |
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100 | bool isclass = neu->getClass() ? true : false; |
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101 | delete neu; |
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102 | if (!isclass) |
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103 | { |
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104 | return i + 1; |
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105 | } |
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106 | i = nextid; |
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107 | } |
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108 | else |
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109 | { |
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110 | return i + 1; |
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111 | } |
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112 | } |
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113 | } |
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114 | if (!hasStick(genotype)) |
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115 | { |
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116 | return 1; |
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117 | } |
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118 | return GENOPER_OK; |
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119 | } |
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120 | |
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121 | int Geno_fB::validate(char *&geno, const char *genoname) |
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122 | { |
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123 | // load genotype |
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124 | SString genotype(geno); |
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125 | SString strdims; |
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126 | int pos = 0; |
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127 | if (!genotype.getNextToken(pos, strdims, '\n')) |
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128 | { |
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129 | return GENOPER_OPFAIL; |
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130 | } |
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131 | // parse dimension |
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132 | int dims = 0; |
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133 | if (!ExtValue::parseInt(strdims.c_str(), dims, true, false)) |
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134 | { |
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135 | return GENOPER_OPFAIL; |
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136 | } |
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137 | SString line; |
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138 | bool fix = false; |
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139 | int genstart = genotype.indexOf("aa", 0); |
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140 | // if there is no "aa" codon in the beginning of a genotype, then add it |
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141 | if (genstart != pos) |
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142 | { |
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143 | genotype = strdims + "\naa" + genotype.substr(pos); |
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144 | fix = true; |
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145 | } |
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146 | for (int i = pos; i < genotype.len(); i++) |
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147 | { |
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148 | // if character is not alphabetic - error |
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149 | if (!isalpha(genotype[i])) |
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150 | { |
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151 | if (genotype[i] == '"') |
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152 | { |
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153 | SString neuclassdef; |
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154 | int nextid = i + 1; |
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155 | if (!genotype.getNextToken(nextid, neuclassdef, '"')) |
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156 | { |
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157 | return i + 1; |
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158 | } |
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159 | Neuro *neu = new Neuro(); |
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160 | neu->setDetails(neuclassdef); |
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161 | |
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162 | bool isclass = neu->getClass() ? true : false; |
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163 | delete neu; |
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164 | if (!isclass) |
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165 | { |
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166 | return i + 1; |
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167 | } |
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168 | i = nextid; |
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169 | } |
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170 | else |
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171 | { |
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172 | return GENOPER_OPFAIL; |
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173 | } |
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174 | } |
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175 | // if character is uppercase, then convert it to lowercase |
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176 | else if (isupper(genotype[i])) |
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177 | { |
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178 | genotype.directWrite()[i] = tolower(genotype[i]); |
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179 | fix = true; |
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180 | } |
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181 | } |
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182 | // if the genotype does not contain any stick - add it |
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183 | if (!hasStick(genotype)) |
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184 | { |
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185 | genotype = SString("aaazz") + genotype; |
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186 | } |
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187 | // if there were any changes - save them |
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188 | if (fix) |
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189 | { |
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190 | free(geno); |
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191 | geno = strdup(genotype.c_str()); |
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192 | } |
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193 | return GENOPER_OK; |
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194 | } |
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195 | |
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196 | SString Geno_fB::detokenizeSequence(std::list<SString> *tokenlist) |
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197 | { |
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198 | SString res = ""; |
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199 | for (std::list<SString>::iterator it = tokenlist->begin(); it != tokenlist->end(); it++) |
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200 | { |
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201 | res += (*it); |
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202 | } |
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203 | return res; |
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204 | } |
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205 | |
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206 | std::list<SString> Geno_fB::tokenizeSequence(const SString &genotype) |
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207 | { |
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208 | std::list<SString> res; |
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209 | int i = 0; |
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210 | while (i < genotype.len()) |
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211 | { |
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212 | // if character is not alphabetic - error |
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213 | if (isalpha(genotype[i])) |
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214 | { |
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215 | SString el = ""; |
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216 | el += genotype[i]; |
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217 | res.push_back(el); |
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218 | i++; |
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219 | } |
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220 | else |
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221 | { |
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222 | SString neuclassdef; |
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223 | i++; |
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224 | genotype.getNextToken(i, neuclassdef, '"'); |
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225 | SString ndef = "\""; |
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226 | ndef += neuclassdef; |
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227 | ndef += "\""; |
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228 | res.push_back(ndef); |
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229 | } |
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230 | } |
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231 | return res; |
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232 | } |
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233 | |
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234 | int Geno_fB::mutate(char *&geno, float &chg, int &method) |
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235 | { |
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236 | SString genotype(geno); |
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237 | SString strdims; |
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238 | int pos = 0; |
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239 | genotype.getNextToken(pos, strdims, '\n'); |
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240 | SString line; |
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241 | genotype.getNextToken(pos, line, '\n'); |
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242 | method = roulette(mutationprobs, FB_MUT_COUNT); |
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243 | switch (method) |
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244 | { |
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245 | case FB_SUBSTITUTION: |
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246 | { |
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247 | std::list<SString> tokenized = tokenizeSequence(line); |
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248 | int rndid = rndUint(tokenized.size()); // select random letter from genotype |
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249 | // increment/decrement character - when overflow happens, this method |
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250 | // uses reflect method |
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251 | std::list<SString>::iterator it = tokenized.begin(); |
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252 | std::advance(it, rndid); |
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253 | SString t = (*it); |
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254 | if ((*it).len() == 1) |
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255 | { |
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256 | if (rndUint(2) == 0) |
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257 | { |
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258 | if ((*it)[0] == 'a') (*it).directWrite()[0] = 'b'; |
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259 | else (*it).directWrite()[0] = (*it)[0] - 1; |
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260 | } |
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261 | else |
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262 | { |
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263 | if ((*it)[0] == 'z') (*it).directWrite()[0] = 'y'; |
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264 | else (*it).directWrite()[0] = (*it)[0] + 1; |
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265 | } |
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266 | chg = 1.0 / line.len(); |
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267 | } |
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268 | else |
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269 | { |
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270 | // first method needs to extract quotes |
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271 | SString def = (*it); |
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272 | def = def.substr(1, def.len() - 2); |
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273 | Geno_fH::mutateNeuronProperties(def); |
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274 | SString res = "\""; |
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275 | res += def; |
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276 | res += "\""; |
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277 | (*it) = res; |
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278 | chg = (double)def.len() / line.len(); |
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279 | } |
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280 | line = detokenizeSequence(&tokenized); |
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281 | break; |
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282 | } |
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283 | case FB_NCLASSINS: |
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284 | { |
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285 | std::list<SString> tokenized = tokenizeSequence(line); |
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286 | std::list<SString>::iterator it = tokenized.begin(); |
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287 | int rndid = rndUint(tokenized.size()); // select random insertion point |
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288 | std::advance(it, rndid); |
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289 | NeuroClass *cls = getRandomNeuroClass(); |
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290 | if (cls) |
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291 | { |
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292 | SString classdef = cls->getName(); |
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293 | Geno_fH::mutateNeuronProperties(classdef); |
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294 | SString res = "\""; |
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295 | res += classdef; |
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296 | res += "\""; |
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297 | tokenized.insert(it, res); |
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298 | chg = (double)classdef.len() / line.len(); |
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299 | line = detokenizeSequence(&tokenized); |
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300 | break; |
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301 | } |
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302 | } |
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303 | [[fallthrough]]; |
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304 | case FB_INSERTION: |
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305 | { |
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306 | chg = 1.0 / line.len(); |
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307 | std::list<SString> tokenized = tokenizeSequence(line); |
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308 | int rndid = rndUint(tokenized.size()); // select random insertion point |
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309 | std::list<SString>::iterator it = tokenized.begin(); |
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310 | std::advance(it, rndid); |
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311 | SString letter = "a"; |
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312 | letter.directWrite()[0] = 'a' + rndUint(26); |
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313 | tokenized.insert(it, letter); |
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314 | line = detokenizeSequence(&tokenized); |
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315 | break; |
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316 | } |
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317 | case FB_DELETION: |
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318 | { |
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319 | chg = 1.0 / line.len(); |
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320 | std::list<SString> tokenized = tokenizeSequence(line); |
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321 | std::list<SString>::iterator it = tokenized.begin(); |
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322 | int rndid = rndUint(tokenized.size()); // select random deletion point |
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323 | std::advance(it, rndid); |
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324 | tokenized.erase(it); |
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325 | line = detokenizeSequence(&tokenized); |
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326 | break; |
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327 | } |
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328 | case FB_DUPLICATION: |
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329 | { |
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330 | int rndgene = rndUint(fB_GenoHelpers::geneCount(line)); |
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331 | int start, end; |
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332 | SString gene = fB_GenoHelpers::getGene(rndgene, line, start, end); |
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333 | if (gene.indexOf("zz", 0) == -1) gene += "zz"; |
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334 | chg = (float)gene.len() / line.len(); |
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335 | line = gene + line; |
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336 | break; |
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337 | } |
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338 | case FB_TRANSLOCATION: |
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339 | { |
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340 | std::list<SString> tokenized = tokenizeSequence(line); |
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341 | std::vector<unsigned int> cuts(4); |
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342 | for (int i = 0; i < 4; i++) |
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343 | { |
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344 | cuts[i] = rndUint(tokenized.size()); |
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345 | } |
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346 | std::sort(cuts.begin(), cuts.end()); |
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347 | std::vector<std::list<SString>::iterator> iters(4); |
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348 | for (int i = 0; i < 4; i++) |
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349 | { |
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350 | iters[i] = tokenized.begin(); |
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351 | std::advance(iters[i], cuts[i]); |
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352 | } |
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353 | |
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354 | std::list<SString> res; |
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355 | res.insert(res.end(), tokenized.begin(), iters[0]); |
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356 | res.insert(res.end(), iters[2], iters[3]); |
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357 | res.insert(res.end(), iters[1], iters[2]); |
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358 | res.insert(res.end(), iters[0], iters[1]); |
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359 | res.insert(res.end(), iters[3], tokenized.end()); |
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360 | |
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361 | // SString first = line.substr(cuts[0], cuts[1] - cuts[0]); |
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362 | // SString second = line.substr(cuts[2], cuts[3] - cuts[2]); |
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363 | // SString result = line.substr(0, cuts[0]) + second + |
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364 | // line.substr(cuts[1], cuts[2] - cuts[1]) + first + line.substr(cuts[3]); |
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365 | line = detokenizeSequence(&res); |
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366 | chg = (float)(cuts[3] - cuts[2] + cuts[1] - cuts[0]) / line.len(); |
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367 | break; |
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368 | } |
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369 | } |
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370 | SString result = strdims + "\n" + line; |
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371 | free(geno); |
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372 | geno = strdup(result.c_str()); |
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373 | return GENOPER_OK; |
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374 | } |
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375 | |
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376 | int Geno_fB::crossOver(char *&g1, char *&g2, float& chg1, float& chg2) |
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377 | { |
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378 | SString p1(g1); |
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379 | SString p2(g2); |
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380 | |
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381 | int dims1 = 0, dims2 = 0; |
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382 | int pos = 0; |
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383 | SString strdims; |
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384 | p1.getNextToken(pos, strdims, '\n'); |
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385 | ExtValue::parseInt(strdims.c_str(), dims1, true, false); |
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386 | SString parent1; |
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387 | p1.getNextToken(pos, parent1, '\n'); |
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388 | |
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389 | pos = 0; |
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390 | p2.getNextToken(pos, strdims, '\n'); |
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391 | ExtValue::parseInt(strdims.c_str(), dims2, true, false); |
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392 | |
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393 | if (dims1 != dims2) |
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394 | { |
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395 | return GENOPER_OPFAIL; |
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396 | } |
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397 | |
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398 | SString parent2; |
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399 | p2.getNextToken(pos, parent2, '\n'); |
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400 | |
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401 | SString child1 = ""; |
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402 | SString child2 = ""; |
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403 | |
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404 | switch (roulette(crossoverprobs, FB_XOVER_COUNT)) |
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405 | { |
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406 | case FB_GENE_TRANSFER: |
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407 | { |
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408 | // get random gene from first parent |
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409 | int choice = rndUint(fB_GenoHelpers::geneCount(parent1)); |
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410 | int start, end; |
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411 | SString gene = fB_GenoHelpers::getGene(choice, parent1, start, end); |
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412 | // add this gene to the beginning of the second parent genotype |
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413 | child2 = gene + parent2; |
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414 | chg2 = (float)parent2.len() / (float)child2.len(); |
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415 | // do the same for second parent |
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416 | choice = rndUint(fB_GenoHelpers::geneCount(parent2)); |
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417 | gene = fB_GenoHelpers::getGene(choice, parent2, start, end); |
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418 | child1 = gene + parent1; |
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419 | chg1 = (float)parent1.len() / (float)child1.len(); |
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420 | break; |
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421 | } |
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422 | // case FB_CROSSING_OVER: |
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423 | // { |
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424 | // // iterate through all genes of the first parent and assign them |
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425 | // // randomly to children |
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426 | // for (int i = 0; i < fB_GenoHelpers::geneCount(parent1); i++) |
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427 | // { |
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428 | // int start, end; |
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429 | // SString gene = fB_GenoHelpers::getGene(i, parent1, start, end); |
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430 | // if (rndUint(2) == 0) |
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431 | // { |
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432 | // child1 += gene; |
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433 | // chg1 += 1.0f; |
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434 | // } |
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435 | // else |
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436 | // { |
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437 | // child2 += gene; |
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438 | // } |
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439 | // } |
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440 | // chg1 /= fB_GenoHelpers::geneCount(parent1); |
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441 | // |
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442 | // // do the same with second parent |
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443 | // for (int i = 0; i < fB_GenoHelpers::geneCount(parent2); i++) |
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444 | // { |
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445 | // int start, end; |
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446 | // SString gene = fB_GenoHelpers::getGene(i, parent2, start, end); |
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447 | // if (rndUint(2) == 0) |
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448 | // { |
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449 | // child1 += gene; |
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450 | // } |
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451 | // else |
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452 | // { |
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453 | // child2 += gene; |
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454 | // chg2 += 1.0f; |
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455 | // } |
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456 | // } |
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457 | // chg2 /= fB_GenoHelpers::geneCount(parent2); |
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458 | // break; |
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459 | // } |
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460 | case FB_CROSSING_OVER: |
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461 | { |
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462 | // get maximal count of genes from both parents |
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463 | int maxgenecount = max(fB_GenoHelpers::geneCountNoNested(parent1), |
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464 | fB_GenoHelpers::geneCountNoNested(parent2)); |
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465 | |
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466 | // while there are genes in at least one genotype |
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467 | for (int i = 0; i < maxgenecount; i++) |
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468 | { |
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469 | SString to1 = "", to2 = ""; |
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470 | int start = 0, end = 0; |
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471 | |
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472 | // if both parents have genes available, then distribute them |
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473 | if (i < fB_GenoHelpers::geneCountNoNested(parent1) && |
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474 | i < fB_GenoHelpers::geneCountNoNested(parent2)) |
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475 | { |
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476 | if (rndUint(2) == 0) |
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477 | { |
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478 | to1 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); |
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479 | to2 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); |
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480 | chg1 += 1.0f; |
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481 | chg2 += 1.0f; |
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482 | } |
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483 | else |
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484 | { |
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485 | to1 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); |
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486 | to2 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); |
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487 | } |
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488 | } |
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489 | else if (i < fB_GenoHelpers::geneCountNoNested(parent1)) |
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490 | { |
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491 | if (rndUint(2) == 0) |
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492 | { |
---|
493 | to1 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); |
---|
494 | chg1 += 1.0f; |
---|
495 | } |
---|
496 | else |
---|
497 | { |
---|
498 | to2 = fB_GenoHelpers::getNonNestedGene(i, parent1, start, end); |
---|
499 | } |
---|
500 | } |
---|
501 | else // if (i < fB_GenoHelpers::geneCountNoNested(parent2)) |
---|
502 | { |
---|
503 | if (rndUint(2) == 0) |
---|
504 | { |
---|
505 | to1 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); |
---|
506 | } |
---|
507 | else |
---|
508 | { |
---|
509 | to2 = fB_GenoHelpers::getNonNestedGene(i, parent2, start, end); |
---|
510 | chg2 += 1.0f; |
---|
511 | } |
---|
512 | } |
---|
513 | child1 += to1; |
---|
514 | child2 += to2; |
---|
515 | } |
---|
516 | |
---|
517 | chg1 /= fB_GenoHelpers::geneCountNoNested(parent1); |
---|
518 | chg2 /= fB_GenoHelpers::geneCountNoNested(parent2); |
---|
519 | break; |
---|
520 | } |
---|
521 | } |
---|
522 | |
---|
523 | free(g1); |
---|
524 | free(g2); |
---|
525 | if (child1.len() > 0 && child2.len() == 0) |
---|
526 | { |
---|
527 | child1 = strdims + "\n" + child1; |
---|
528 | g1 = strdup(child1.c_str()); |
---|
529 | g2 = strdup(""); |
---|
530 | } |
---|
531 | else if (child2.len() > 0 && child1.len() == 0) |
---|
532 | { |
---|
533 | child2 = strdims + "\n" + child2; |
---|
534 | g1 = strdup(child2.c_str()); |
---|
535 | g2 = strdup(""); |
---|
536 | } |
---|
537 | else |
---|
538 | { |
---|
539 | child1 = strdims + "\n" + child1; |
---|
540 | child2 = strdims + "\n" + child2; |
---|
541 | g1 = strdup(child1.c_str()); |
---|
542 | g2 = strdup(child2.c_str()); |
---|
543 | } |
---|
544 | return GENOPER_OK; |
---|
545 | } |
---|
546 | |
---|
547 | uint32_t Geno_fB::style(const char *geno, int pos) |
---|
548 | { |
---|
549 | char ch = geno[pos]; |
---|
550 | if (isdigit(ch)) |
---|
551 | { |
---|
552 | while (pos > 0) |
---|
553 | { |
---|
554 | pos--; |
---|
555 | if (isdigit(geno[pos]) == 0) |
---|
556 | { |
---|
557 | return GENSTYLE_CS(0, GENSTYLE_INVALID); |
---|
558 | } |
---|
559 | } |
---|
560 | return GENSTYLE_RGBS(0, 0, 200, GENSTYLE_BOLD); |
---|
561 | } |
---|
562 | if (islower(ch) == 0) |
---|
563 | { |
---|
564 | return GENSTYLE_CS(0, GENSTYLE_INVALID); |
---|
565 | } |
---|
566 | uint32_t style = GENSTYLE_CS(GENCOLOR_TEXT, GENSTYLE_NONE); |
---|
567 | if (ch == 'a' && pos > 0 && (geno[pos - 1] == 'a' || geno[pos - 1] == '\n')) |
---|
568 | { |
---|
569 | style = GENSTYLE_RGBS(0, 200, 0, GENSTYLE_BOLD); |
---|
570 | } |
---|
571 | else if (ch == 'z' && pos > 0 && geno[pos - 1] == 'z') |
---|
572 | { |
---|
573 | style = GENSTYLE_RGBS(200, 0, 0, GENSTYLE_BOLD); |
---|
574 | } |
---|
575 | return style; |
---|
576 | } |
---|