1 | #include <stdlib.h> |
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2 | #include <arbdb.h> |
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3 | #include <arbdbt.h> |
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4 | #include <string.h> |
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5 | #include <stdio.h> |
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6 | #include <memory.h> |
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7 | // #include <malloc.h> |
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8 | #include <iostream.h> |
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9 | #include "AP_buffer.hxx" |
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10 | #include "parsimony.hxx" |
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11 | #include "ap_tree_nlen.hxx" |
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12 | #include "GA_genetic.hxx" |
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13 | |
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14 | void tree_init(AP_tree *tree0); |
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15 | GA_genetic * GAgenetic; |
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16 | void parsimony_func(AP_tree *); |
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17 | |
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18 | void buildRandomTreeRek(AP_tree *tree,AP_tree **list,int *num) { |
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19 | // builds a list of all species |
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20 | if (tree->is_leaf == AP_TRUE) { |
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21 | AP_tree_nlen *pntr = new AP_tree_nlen; |
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22 | pntr->copy((AP_tree_nlen*)tree); |
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23 | pntr->father = 0; |
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24 | list[*num] = (AP_tree *)pntr; |
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25 | (*num)++; |
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26 | return; |
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27 | } |
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28 | buildRandomTreeRek(tree->leftson,list,num); |
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29 | buildRandomTreeRek(tree->rightson,list,num); |
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30 | return; |
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31 | } |
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32 | |
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33 | |
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34 | AP_tree * buildRandomTree(AP_tree *root) { |
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35 | // function returns a random constructed tree |
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36 | // root is tree with species (needed to build a list of species) |
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37 | AP_tree **list; |
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38 | |
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39 | if (root->sequence_proto == 0) tree_init(root); |
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40 | |
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41 | AP_tree_nlen *ntree; |
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42 | AP_tree *tree1,*tree0; |
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43 | int num; |
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44 | int count = 0; |
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45 | |
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46 | root->arb_tree_leafsum(); |
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47 | |
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48 | list = (AP_tree **)calloc(root->gr.leave_sum +1,sizeof(AP_tree *)); |
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49 | |
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50 | buildRandomTreeRek(root,list,&count); |
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51 | count--; |
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52 | while (count >1) { |
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53 | // choose two random numbers |
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54 | num = (int)random()%(count+1); |
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55 | tree0 = list[num]; |
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56 | list[num] = list[count]; |
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57 | count --; |
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58 | num = (int)random()%(count+1); |
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59 | tree1 = list[num]; |
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60 | ntree = new AP_tree_nlen; |
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61 | ntree->leftson = tree0; |
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62 | ntree->rightson = tree1; |
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63 | ntree->sequence = 0; |
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64 | tree0->father = ntree; |
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65 | tree1->father = ntree; |
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66 | ntree->is_leaf = GB_FALSE; |
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67 | // ################## Laengenberechnung #################3 |
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68 | ntree->leftlen = .5; |
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69 | ntree->rightlen = .5; |
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70 | list[num] = (AP_tree *)ntree; |
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71 | } |
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72 | tree0 = list[0]; |
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73 | delete list; |
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74 | //tree0->sequence_proto = root->sequence_proto->dup(); |
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75 | //tree0->sequence_proto = root->sequence_proto; |
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76 | //tree0->sequence_proto = (AP_sequence *)new AP_sequence_parsimony; |
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77 | return tree0; |
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78 | } |
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79 | |
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80 | void kernighan_lin(AP_tree_nlen *tree) { |
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81 | if (tree ==0) new AP_ERR("kernighan_lin","No tree !"); |
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82 | // ruft kernighan auf |
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83 | } |
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84 | |
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85 | AP_tree_nlen *crossover(AP_tree_nlen *tree0,AP_tree_nlen *tree1) { |
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86 | int size1,size0; |
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87 | AP_CO_LIST *list0,*list1; |
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88 | |
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89 | if (tree0 ==0 || tree1 == 0) { |
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90 | new AP_ERR("crossover","Needs two tress as argument"); |
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91 | return 0; |
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92 | } |
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93 | list0 = tree0->createList(&size0); |
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94 | list1 = tree1->createList(&size1); |
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95 | |
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96 | fprintf(GAgenetic->fout,"\ncrossover tree %d %d size %d %d", |
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97 | tree0,tree1,size0,size1); |
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98 | |
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99 | // ruft crossover auf |
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100 | return tree0; |
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101 | } |
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102 | |
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103 | int randomCluster() { |
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104 | int maxcluster = GAgenetic->getMaxCluster(); |
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105 | int cluster; |
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106 | cluster = (int)random()%maxcluster; |
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107 | cout << cluster << "clust\n"; |
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108 | return cluster; |
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109 | } |
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110 | AP_ERR * make_start_population(GBDATA *gbmain,AP_tree *tree) { |
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111 | // makes random startpopultation |
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112 | // (at least two trees in each cluster) |
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113 | static int msp = 0; |
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114 | msp ++; |
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115 | if (msp > 1) return new AP_ERR("make_start_population","Only call it once !"); |
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116 | int name=0,i =0,maxcluster; |
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117 | |
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118 | AP_tree_nlen* rtree; |
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119 | |
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120 | if (GAgenetic == 0) { |
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121 | GAgenetic = new GA_genetic; |
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122 | GAgenetic->init(gbmain); |
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123 | } |
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124 | |
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125 | maxcluster = GAgenetic->getMaxCluster(); |
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126 | while (i<maxcluster) { |
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127 | rtree = (AP_tree_nlen *)buildRandomTree(tree); |
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128 | rtree->parsimony_rek(); |
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129 | GAgenetic->put_start_tree((AP_tree *)rtree,name,i); |
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130 | name ++; |
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131 | fprintf(GAgenetic->fout,"\ncluster %d put Starttree %d",i,name-1); |
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132 | rtree = (AP_tree_nlen *)buildRandomTree(tree); |
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133 | rtree->parsimony_rek(); |
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134 | GAgenetic->put_start_tree((AP_tree *)rtree,name,i); |
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135 | name ++; |
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136 | fprintf(GAgenetic->fout,"\nCluster %d put Starttree %d",i,name-1); |
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137 | i ++; |
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138 | } |
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139 | return 0; |
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140 | } |
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141 | |
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142 | void quit_genetic() { |
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143 | fclose(GAgenetic->fout); |
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144 | } |
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145 | |
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146 | void start_genetic(GBDATA *gbmain) { |
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147 | // |
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148 | // the genetic algorithm is implemented here |
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149 | // |
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150 | |
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151 | GA_tree * starttree; |
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152 | GA_job *job; |
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153 | int cluster; |
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154 | |
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155 | |
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156 | if (GAgenetic == 0) { |
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157 | GAgenetic = new GA_genetic; |
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158 | GAgenetic->init(gbmain); |
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159 | } |
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160 | fprintf(GAgenetic->fout,"\n**** Genetic ALGORITHEM *****\n"); |
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161 | make_start_population(gbmain,ap_main->tree_root); |
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162 | |
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163 | // |
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164 | // get starttree and optimize it |
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165 | // |
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166 | |
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167 | int i = 0; |
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168 | |
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169 | while (i<GAgenetic->getMaxCluster()) { |
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170 | cluster = i; |
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171 | while ((starttree = GAgenetic->get_start_tree(cluster)) != 0){ |
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172 | if (starttree != 0) { |
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173 | kernighan_lin(starttree->tree); |
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174 | GAgenetic->put_optimized(starttree,cluster); |
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175 | fprintf(GAgenetic->fout,"\nStarttree %d optimized in cluster %d", |
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176 | starttree->id, |
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177 | cluster); |
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178 | delete starttree; |
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179 | } else { |
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180 | fprintf(GAgenetic->fout,"\nNo starttree found in cluster %d",cluster); |
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181 | } |
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182 | } |
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183 | i ++; |
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184 | } |
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185 | |
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186 | // |
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187 | // get job and do it |
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188 | // |
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189 | i =0; |
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190 | while (i++ <20) { |
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191 | cluster = randomCluster(); |
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192 | job = GAgenetic->get_job(cluster); |
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193 | if (job != 0) { |
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194 | switch(job->modus) { |
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195 | case GA_CROSSOVER: { |
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196 | GA_tree * gaTree = new GA_tree; |
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197 | gaTree->tree = crossover(job->tree0->tree,job->tree1->tree); |
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198 | |
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199 | GB_push_transaction(gb_main); |
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200 | char *use =GBT_get_default_alignment(gb_main); |
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201 | gaTree->tree->load_sequences_rek(0,use); |
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202 | GB_pop_transaction(gb_main); |
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203 | |
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204 | parsimony_func(gaTree->tree); |
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205 | |
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206 | gaTree->criteria = gaTree->tree->mutation_rate; |
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207 | gaTree->id = -1; |
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208 | GAgenetic->put_optimized(gaTree,job->cluster0); |
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209 | delete gaTree; |
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210 | delete use; |
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211 | break; } |
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212 | case GA_KERNIGHAN: |
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213 | kernighan_lin(job->tree0->tree); |
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214 | break; |
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215 | case GA_NNI: |
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216 | break; |
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217 | case GA_CREATEJOBS: |
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218 | break; |
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219 | case GA_NONE: |
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220 | default: |
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221 | break; |
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222 | } |
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223 | fprintf(GAgenetic->fout,"\njob %d in cluster %d : %d executed, mode %d" |
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224 | ,job,job->cluster0,job->cluster1,job->modus); |
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225 | GAgenetic->put_optimized(job->tree0,cluster); |
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226 | } else { |
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227 | fprintf(GAgenetic->fout,"\nno job found"); |
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228 | } |
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229 | } |
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230 | } |
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