1 | // =============================================================== // |
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2 | // // |
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3 | // File : AP_tree_edge.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in Summer 1995 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // =============================================================== // |
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11 | |
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12 | #include "ap_tree_nlen.hxx" |
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13 | |
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14 | #include <AP_filter.hxx> |
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15 | #include <arb_progress.h> |
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16 | |
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17 | #include <cmath> |
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18 | #include <iomanip> |
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19 | |
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20 | using namespace std; |
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21 | |
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22 | long AP_tree_edge::timeStamp = 0; |
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23 | |
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24 | AP_tree_edge::AP_tree_edge(AP_tree_nlen *node1, AP_tree_nlen *node2) |
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25 | { |
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26 | // not really necessary, but why not clear all: |
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27 | memset((char *)this, 0, sizeof(AP_tree_edge)); |
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28 | age = timeStamp++; |
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29 | |
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30 | // link the nodes: |
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31 | |
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32 | relink(node1, node2); |
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33 | } |
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34 | |
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35 | AP_tree_edge::~AP_tree_edge() |
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36 | { |
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37 | unlink(); |
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38 | } |
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39 | |
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40 | static void buildSonEdges(AP_tree_nlen *node) { |
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41 | /*! Builds edges between a node and his two sons. |
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42 | * We assume there is already an edge to node's father and there are |
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43 | * no edges to his sons. |
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44 | */ |
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45 | |
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46 | if (!node->is_leaf) { |
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47 | buildSonEdges(node->get_leftson()); |
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48 | buildSonEdges(node->get_rightson()); |
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49 | |
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50 | // to ensure the nodes contain the correct distance to the border |
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51 | // we MUST build all son edges before creating the father edge |
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52 | |
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53 | new AP_tree_edge(node, node->get_leftson()); |
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54 | new AP_tree_edge(node, node->get_rightson()); |
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55 | } |
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56 | } |
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57 | |
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58 | void AP_tree_edge::initialize(AP_tree_nlen *tree) { |
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59 | /*! Builds all edges in the whole tree. |
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60 | * The root node is skipped - instead his two sons are connected with an edge |
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61 | */ |
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62 | while (tree->get_father()) tree = tree->get_father(); // go up to root |
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63 | buildSonEdges(tree->get_leftson()); // link left subtree |
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64 | buildSonEdges(tree->get_rightson()); // link right subtree |
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65 | |
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66 | // to ensure the nodes contain the correct distance to the border |
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67 | // we MUST build all son edges before creating the root edge |
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68 | |
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69 | new AP_tree_edge(tree->get_leftson(), tree->get_rightson()); // link brothers |
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70 | } |
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71 | |
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72 | void AP_tree_edge::destroy(AP_tree_nlen *tree) { |
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73 | /*! Destroys all edges in the whole tree */ |
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74 | AP_tree_edge *edge = tree->nextEdge(NULL); |
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75 | if (!edge) { |
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76 | ap_assert(tree->is_root_node()); |
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77 | edge = tree->get_leftson()->edgeTo(tree->get_rightson()); |
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78 | } |
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79 | ap_assert(edge); // got no edges? |
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80 | |
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81 | edge->buildChain(-1); |
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82 | while (edge) { |
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83 | AP_tree_edge *next = edge->Next(); |
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84 | delete edge; |
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85 | edge = next; |
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86 | } |
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87 | } |
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88 | |
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89 | |
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90 | void AP_tree_edge::tailDistance(AP_tree_nlen *n) |
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91 | { |
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92 | ap_assert(!n->is_leaf); // otherwise call was not necessary! |
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93 | |
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94 | int i0 = n->indexOf(this); // index of this |
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95 | int i1 = i0==0 ? 1 : 0; // the indices of the other two nodes (beside n) |
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96 | int i2 = i1==1 ? 2 : (i0==1 ? 2 : 1); |
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97 | AP_tree_edge *e1 = n->edge[i1]; // edges to the other two nodes |
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98 | AP_tree_edge *e2 = n->edge[i2]; |
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99 | |
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100 | cout << "tail n=" << n << " d(n)=" << n->distance << " "; |
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101 | |
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102 | if (e1 && e2) |
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103 | { |
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104 | AP_tree_nlen *n1 = e1->node[1-n->index[i1]]; // the other two nodes |
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105 | AP_tree_nlen *n2 = e2->node[1-n->index[i2]]; |
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106 | |
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107 | cout << "n1=" << n1 << " d(n1)=" << n1->distance << |
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108 | " n2=" << n2 << " d(n2)=" << n2->distance << " "; |
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109 | |
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110 | if (n1->distance==n2->distance) |
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111 | { |
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112 | if (n1->distance>n->distance && n2->distance>n->distance) |
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113 | { |
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114 | // both distances (of n1 and n2) are greather that distance of n |
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115 | // so its possible that the nearest connection the border was |
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116 | // via node n and we must recalculate the distance into the other |
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117 | // directions |
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118 | |
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119 | ap_assert(n1->distance==n2->distance); |
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120 | |
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121 | cout << "special tailDistance-case\n"; |
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122 | e1->tailDistance(n1); |
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123 | e2->tailDistance(n2); |
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124 | |
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125 | if (n1->distance<n2->distance) |
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126 | { |
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127 | n->distance = n1->distance+1; |
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128 | if (!e2->distanceOK()) e2->calcDistance(); |
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129 | } |
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130 | else |
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131 | { |
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132 | n->distance = n2->distance+1; |
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133 | if (!e1->distanceOK()) e1->calcDistance(); |
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134 | } |
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135 | } |
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136 | else |
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137 | { |
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138 | cout << "tail case 2\n"; |
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139 | n->distance = n1->distance+1; |
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140 | } |
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141 | } |
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142 | else |
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143 | { |
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144 | ap_assert(n1->distance != n2->distance); |
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145 | |
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146 | if (n1->distance<n2->distance) |
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147 | { |
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148 | if (n1->distance<n->distance) |
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149 | { |
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150 | // in this case the distance via n1 is the same as |
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151 | // the distance via the cutted edge - so we do nothing |
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152 | |
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153 | cout << "tail case 3\n"; |
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154 | ap_assert(n1->distance==(n->distance-1)); |
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155 | } |
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156 | else |
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157 | { |
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158 | cout << "tail case 4\n"; |
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159 | ap_assert(n1->distance==n->distance); |
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160 | ap_assert(n2->distance==(n->distance+1)); |
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161 | |
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162 | n->distance = n1->distance+1; |
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163 | e2->tailDistance(n2); |
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164 | } |
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165 | } |
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166 | else |
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167 | { |
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168 | ap_assert(n2->distance<n1->distance); |
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169 | |
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170 | if (n2->distance<n->distance) |
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171 | { |
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172 | // in this case the distance via n2 is the same as |
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173 | // the distance via the cutted edge - so we do nothing |
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174 | |
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175 | cout << "tail case 5\n"; |
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176 | ap_assert(n2->distance==(n->distance-1)); |
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177 | } |
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178 | else |
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179 | { |
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180 | cout << "tail case 6\n"; |
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181 | ap_assert(n2->distance==n->distance); |
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182 | ap_assert(n1->distance==(n->distance+1)); |
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183 | |
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184 | n->distance = n2->distance+1; |
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185 | e1->tailDistance(n1); |
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186 | } |
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187 | } |
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188 | } |
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189 | |
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190 | cout << "d(n)=" << n->distance << |
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191 | " d(n1)=" << n1->distance << |
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192 | " d(n2)=" << n2->distance << |
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193 | " D(e1)=" << e1->Distance() << |
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194 | " D(e2)=" << e2->Distance() << |
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195 | " dtb(e1)=" << e1->distanceToBorder(INT_MAX, n) << |
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196 | " dtb(e2)=" << e2->distanceToBorder(INT_MAX, n) << endl; |
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197 | } |
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198 | else |
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199 | { |
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200 | if (e1) |
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201 | { |
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202 | AP_tree_nlen *n1 = e1->node[1-n->index[i1]]; |
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203 | |
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204 | cout << "tail case 7\n"; |
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205 | ap_assert(n1!=0); |
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206 | if (n1->distance>n->distance) e1->tailDistance(n1); |
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207 | n->distance = n1->distance+1; |
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208 | |
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209 | cout << "d(n)=" << n->distance << |
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210 | " d(n1)=" << n1->distance << |
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211 | " D(e1)=" << e1->Distance() << |
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212 | " dtb(e1)=" << e1->distanceToBorder(INT_MAX, n) << endl; |
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213 | } |
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214 | else if (e2) |
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215 | { |
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216 | AP_tree_nlen *n2 = e2->node[1-n->index[i2]]; |
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217 | |
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218 | cout << "tail case 8\n"; |
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219 | ap_assert(n2!=0); |
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220 | cout << "d(n2)=" << n2->distance << " d(n)=" << n->distance << endl; |
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221 | |
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222 | if (n2->distance>n->distance) e2->tailDistance(n2); |
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223 | n->distance = n2->distance+1; |
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224 | |
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225 | cout << "d(n)=" << n->distance << |
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226 | " d(n2)=" << n2->distance << |
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227 | " D(e2)=" << e2->Distance() << |
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228 | " dtb(e2)=" << e2->distanceToBorder(INT_MAX, n) << endl; |
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229 | } |
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230 | else |
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231 | { |
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232 | cout << "tail case 9\n"; |
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233 | n->distance = INT_MAX; |
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234 | } |
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235 | } |
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236 | } |
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237 | |
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238 | AP_tree_edge* AP_tree_edge::unlink() |
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239 | { |
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240 | ap_assert(this!=0); |
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241 | |
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242 | node[0]->edge[index[0]] = NULL; |
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243 | node[1]->edge[index[1]] = NULL; |
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244 | |
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245 | node[0] = NULL; |
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246 | node[1] = NULL; |
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247 | |
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248 | return this; |
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249 | } |
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250 | |
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251 | void AP_tree_edge::calcDistance() |
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252 | { |
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253 | ap_assert(!distanceOK()); // otherwise call was not necessary |
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254 | ap_assert (node[0]->distance!=node[1]->distance); |
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255 | |
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256 | if (node[0]->distance < node[1]->distance) // node[1] has wrong distance |
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257 | { |
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258 | cout << "dist(" << node[1] << ") " << node[1]->distance; |
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259 | |
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260 | if (node[1]->distance==INT_MAX) // not initialized -> do not recurse |
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261 | { |
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262 | node[1]->distance = node[0]->distance+1; |
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263 | cout << " -> " << node[1]->distance << endl; |
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264 | } |
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265 | else |
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266 | { |
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267 | node[1]->distance = node[0]->distance+1; |
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268 | cout << " -> " << node[1]->distance << endl; |
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269 | |
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270 | if (!node[1]->is_leaf) |
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271 | { |
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272 | for (int e=0; e<3; e++) // recursively correct distance where necessary |
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273 | { |
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274 | AP_tree_edge *ed = node[1]->edge[e]; |
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275 | if (ed && ed!=this && !ed->distanceOK()) ed->calcDistance(); |
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276 | } |
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277 | } |
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278 | } |
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279 | } |
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280 | else // node[0] has wrong distance |
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281 | { |
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282 | cout << "dist(" << node[0] << ") " << node[0]->distance; |
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283 | |
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284 | if (node[0]->distance==INT_MAX) // not initialized -> do not recurse |
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285 | { |
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286 | node[0]->distance = node[1]->distance+1; |
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287 | cout << " -> " << node[0]->distance << endl; |
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288 | } |
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289 | else |
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290 | { |
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291 | node[0]->distance = node[1]->distance+1; |
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292 | cout << " -> " << node[0]->distance << endl; |
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293 | |
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294 | if (!node[0]->is_leaf) |
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295 | { |
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296 | for (int e=0; e<3; e++) // recursively correct distance where necessary |
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297 | { |
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298 | AP_tree_edge *ed = node[0]->edge[e]; |
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299 | if (ed && ed!=this && !ed->distanceOK()) ed->calcDistance(); |
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300 | } |
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301 | } |
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302 | } |
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303 | } |
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304 | |
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305 | ap_assert(distanceOK()); // invariant of AP_tree_edge (if fully constructed) |
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306 | } |
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307 | |
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308 | void AP_tree_edge::relink(AP_tree_nlen *node1, AP_tree_nlen *node2) { |
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309 | node[0] = node1; |
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310 | node[1] = node2; |
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311 | |
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312 | node1->edge[index[0] = node1->unusedEdgeIndex()] = this; |
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313 | node2->edge[index[1] = node2->unusedEdgeIndex()] = this; |
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314 | |
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315 | node1->index[index[0]] = 0; |
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316 | node2->index[index[1]] = 1; |
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317 | } |
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318 | |
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319 | int AP_tree_edge::test() const |
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320 | { |
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321 | int ok = 1; // result is used by |
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322 | int n; |
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323 | |
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324 | for (n=0; n<2; n++) |
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325 | { |
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326 | if (node[n]->edge[index[n]]!=this) |
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327 | { |
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328 | int i; |
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329 | |
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330 | for (i=0; i<3; i++) |
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331 | { |
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332 | if (node[n]->edge[i]==this) break; |
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333 | } |
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334 | |
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335 | if (i==3) |
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336 | { |
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337 | cout << *this << " points to wrong node " << node[n] |
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338 | << '\n'; |
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339 | ok = 0; |
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340 | } |
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341 | else |
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342 | { |
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343 | cout << *this << " has wrong index (" |
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344 | << index[n] << "instead of " << i << ")\n"; |
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345 | ok = 0; |
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346 | } |
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347 | } |
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348 | } |
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349 | |
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350 | if (!distanceOK() || |
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351 | (node[0]->is_leaf && node[0]->distance!=0) || |
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352 | (node[1]->is_leaf && node[1]->distance!=0)) |
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353 | { |
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354 | cout << "distance not set correctly at" << *this << '\n'; |
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355 | } |
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356 | else if (Distance()!=distanceToBorder()) |
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357 | { |
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358 | cout << "Distance() != distanceToBorder()" << endl; |
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359 | } |
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360 | |
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361 | return ok; |
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362 | } |
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363 | |
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364 | void AP_tree_edge::testChain(int deep) |
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365 | { |
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366 | cout << "Building chain (deep=" << deep << ")\n"; |
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367 | buildChain(deep, false); |
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368 | int inChain = dumpChain(); |
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369 | cout << "Edges in Chain = " << inChain << '\n'; |
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370 | } |
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371 | |
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372 | int AP_tree_edge::dumpChain() const |
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373 | { |
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374 | return next ? 1+next->dumpChain() : 1; |
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375 | } |
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376 | |
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377 | AP_tree_edge* AP_tree_edge::buildChain(int deep, bool skip_hidden, |
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378 | int distanceToInsert, |
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379 | const AP_tree_nlen *skip, |
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380 | AP_tree_edge *comesFrom) |
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381 | { |
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382 | AP_tree_edge *last = this; |
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383 | |
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384 | data.distance = distanceToInsert++; |
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385 | if (comesFrom) comesFrom->next = this; |
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386 | this->next = NULL; |
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387 | if (skip_hidden) { |
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388 | if (node[0]->gr.hidden) return last; |
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389 | if (node[1]->gr.hidden) return last; |
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390 | if ((!node[0]->gr.has_marked_children) && (!node[1]->gr.has_marked_children)) return last; |
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391 | } |
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392 | |
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393 | if (deep--) |
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394 | for (int n=0; n<2; n++) |
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395 | if (node[n]!=skip && !node[n]->is_leaf) { |
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396 | for (int e=0; e<3; e++) { |
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397 | if (node[n]->edge[e]!=this) { |
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398 | last = node[n]->edge[e]->buildChain(deep, skip_hidden, distanceToInsert, node[n], last); |
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399 | } |
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400 | } |
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401 | } |
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402 | |
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403 | return last; |
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404 | } |
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405 | |
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406 | long AP_tree_edge::sizeofChain() { |
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407 | AP_tree_edge *f; |
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408 | long c = 0; |
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409 | for (f=this; f; f = f->next) c++; |
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410 | return c; |
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411 | } |
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412 | |
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413 | int AP_tree_edge::distanceToBorder(int maxsearch, AP_tree_nlen *skipNode) const { |
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414 | /*! @return the minimal distance to the borders of the tree (aka leafs). |
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415 | * a return value of 0 means: one of the nodes is a leaf |
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416 | * |
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417 | * @param maxsearch max search depth |
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418 | * @param skipNode do not descent into that part of the tree |
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419 | */ |
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420 | |
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421 | if ((node[0] && node[0]->is_leaf) || (node[1] && node[1]->is_leaf)) |
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422 | { |
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423 | return 0; |
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424 | } |
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425 | |
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426 | for (int n=0; n<2 && maxsearch; n++) |
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427 | { |
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428 | if (node[n] && node[n]!=skipNode) |
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429 | { |
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430 | for (int e=0; e<3; e++) |
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431 | { |
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432 | AP_tree_edge *ed = node[n]->edge[e]; |
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433 | |
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434 | if (ed && ed!=this) |
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435 | { |
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436 | int dist = ed->distanceToBorder(maxsearch-1, node[n])+1; |
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437 | if (dist<maxsearch) maxsearch = dist; |
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438 | } |
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439 | } |
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440 | } |
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441 | } |
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442 | |
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443 | return maxsearch; |
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444 | } |
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445 | |
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446 | void AP_tree_edge::countSpecies(int deep, const AP_tree_nlen *skip) |
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447 | { |
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448 | if (!skip) |
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449 | { |
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450 | speciesInTree = 0; |
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451 | nodesInTree = 0; |
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452 | } |
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453 | |
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454 | if (deep--) |
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455 | { |
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456 | for (int n=0; n<2; n++) |
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457 | { |
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458 | if (node[n]->is_leaf) |
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459 | { |
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460 | speciesInTree++; |
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461 | nodesInTree++; |
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462 | } |
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463 | else if (node[n]!=skip) |
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464 | { |
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465 | nodesInTree++; |
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466 | |
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467 | for (int e=0; e<3; e++) |
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468 | { |
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469 | if (node[n]->edge[e]!=this) |
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470 | { |
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471 | node[n]->edge[e]->countSpecies(deep, node[n]); |
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472 | } |
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473 | } |
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474 | } |
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475 | } |
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476 | } |
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477 | } |
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478 | |
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479 | class MutationsPerSite : virtual Noncopyable { |
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480 | char *Data; |
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481 | size_t length; |
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482 | |
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483 | public: |
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484 | MutationsPerSite(size_t len) |
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485 | : Data((char*)GB_calloc(sizeof(char), len*3)) |
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486 | , length(len) |
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487 | {} |
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488 | ~MutationsPerSite() { |
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489 | free(Data); |
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490 | } |
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491 | |
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492 | char *data(int block) { |
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493 | ap_assert(block >= 0 && block<3); |
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494 | return Data+block*length; |
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495 | } |
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496 | const char *data(int block) const { |
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497 | return const_cast<MutationsPerSite*>(this)->data(block); |
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498 | } |
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499 | }; |
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500 | |
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501 | static double ap_calc_bootstrap_remark_sub(int seq_len, const char *old, const char *ne) { |
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502 | int sum[3] = { 0, 0, 0 }; |
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503 | for (int i=0; i<seq_len; i++) { |
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504 | int diff = ne[i] - old[i]; |
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505 | if (diff > 1 || diff < -1) { |
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506 | #if defined(DEBUG) |
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507 | fprintf(stderr, "diff by nni at one position not in [-1,1]: %i:%i - %i", diff, old[i], ne[i]); |
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508 | #endif // DEBUG |
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509 | continue; |
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510 | } |
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511 | sum[diff+1] ++; |
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512 | } |
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513 | |
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514 | double prob = 0; |
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515 | { |
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516 | int asum = 0; |
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517 | for (int i=0; i<3; i++) asum += sum[i]; |
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518 | |
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519 | double freq[3]; |
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520 | double log_freq[3]; |
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521 | for (int i=0; i<3; i++) { |
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522 | freq[i] = sum[i] / double(asum); // relative frequencies of -1, 0, 1 |
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523 | if (sum[i] >0) { |
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524 | log_freq[i] = log(freq[i]); |
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525 | } |
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526 | else { |
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527 | log_freq[i] = -1e100; // minus infinit |
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528 | } |
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529 | } |
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530 | |
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531 | int max = seq_len; // bootstrap can select seq_len ones maximum |
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532 | double log_fak_seq_len = GB_log_fak(seq_len); |
---|
533 | double log_eps = log(1e-11); |
---|
534 | |
---|
535 | // loop over all delta_mutations, begin in the middle |
---|
536 | for (int tsum_add = 1; tsum_add >= -1; tsum_add -= 2) { |
---|
537 | int tsum = sum[2]-sum[0]; |
---|
538 | if (tsum <= 0) tsum = 1; |
---|
539 | for (; tsum < max && tsum > 0; tsum += tsum_add) { // sum of mutations in bootstrap sample, loop over all possibilities |
---|
540 | if (tsum_add < 0 && tsum == sum[2]-sum[0]) continue; // don't double count tsum |
---|
541 | |
---|
542 | |
---|
543 | |
---|
544 | int max_minus = max; // we need tsum + n_minus ones, we cannot have more than max_minux minus, reduce also |
---|
545 | for (int minus_add = 1; minus_add>=-1; minus_add-=2) { |
---|
546 | int first_minus = 1; |
---|
547 | for (int n_minus = sum[0]; n_minus<max_minus && n_minus>=0; first_minus = 0, n_minus+=minus_add) { |
---|
548 | if (minus_add < 0 && first_minus) continue; // don't double count center |
---|
549 | int n_zeros = seq_len - n_minus * 2 - tsum; // number of minus |
---|
550 | int n_plus = tsum + n_minus; // number of plus ones (n_ones + n_minus + n_zeros = seq_len) |
---|
551 | |
---|
552 | double log_a = |
---|
553 | n_minus * log_freq[0] + |
---|
554 | n_zeros * log_freq[1] + |
---|
555 | n_plus * log_freq[2] + |
---|
556 | log_fak_seq_len - GB_log_fak(n_minus) - GB_log_fak(n_zeros) - GB_log_fak(n_plus); |
---|
557 | |
---|
558 | if (log_a < log_eps) { |
---|
559 | if (first_minus && minus_add>0) goto end; |
---|
560 | break; // cannot go with so many minus, try next |
---|
561 | } |
---|
562 | double a = exp(log_a); |
---|
563 | prob += a; |
---|
564 | } |
---|
565 | } |
---|
566 | } |
---|
567 | end :; |
---|
568 | } |
---|
569 | } |
---|
570 | return prob; |
---|
571 | } |
---|
572 | |
---|
573 | static void ap_calc_bootstrap_remark(AP_tree_nlen *son_node, AP_BL_MODE mode, const MutationsPerSite& mps) { |
---|
574 | if (!son_node->is_leaf) { |
---|
575 | size_t seq_len = son_node->get_seq()->get_sequence_length(); |
---|
576 | float one = ap_calc_bootstrap_remark_sub(seq_len, mps.data(0), mps.data(1)); |
---|
577 | float two = ap_calc_bootstrap_remark_sub(seq_len, mps.data(0), mps.data(2)); |
---|
578 | |
---|
579 | if ((mode & AP_BL_BOOTSTRAP_ESTIMATE) == AP_BL_BOOTSTRAP_ESTIMATE) { |
---|
580 | one = one * two; // assume independent bootstrap values for both nnis |
---|
581 | } |
---|
582 | else { |
---|
583 | if (two<one) one = two; // dependent bootstrap values, take minimum (safe) |
---|
584 | } |
---|
585 | |
---|
586 | double bootstrap = one<1.0 ? 100.0 * one : 100.0; |
---|
587 | son_node->set_bootstrap(bootstrap); |
---|
588 | son_node->get_brother()->set_remark(son_node->get_remark()); |
---|
589 | } |
---|
590 | } |
---|
591 | |
---|
592 | |
---|
593 | static void ap_calc_leaf_branch_length(AP_tree_nlen *leaf) { |
---|
594 | AP_FLOAT Seq_len = leaf->get_seq()->weighted_base_count(); |
---|
595 | if (Seq_len <= 1.0) Seq_len = 1.0; |
---|
596 | |
---|
597 | AP_FLOAT parsbest = rootNode()->costs(); |
---|
598 | ap_main->push(); |
---|
599 | leaf->remove(); |
---|
600 | AP_FLOAT Blen = parsbest - rootNode()->costs(); |
---|
601 | ap_main->pop(); |
---|
602 | double blen = Blen/Seq_len; |
---|
603 | |
---|
604 | if (!leaf->father->father) { // at root |
---|
605 | leaf->father->leftlen = blen*.5; |
---|
606 | leaf->father->rightlen = blen*.5; |
---|
607 | } |
---|
608 | else { |
---|
609 | if (leaf->father->leftson == leaf) { |
---|
610 | leaf->father->leftlen = blen; |
---|
611 | } |
---|
612 | else { |
---|
613 | leaf->father->rightlen = blen; |
---|
614 | } |
---|
615 | } |
---|
616 | } |
---|
617 | |
---|
618 | |
---|
619 | |
---|
620 | |
---|
621 | static void ap_calc_branch_lengths(AP_tree_nlen * /* root */, AP_tree_nlen *son, double /* parsbest */, double blen) { |
---|
622 | AP_FLOAT seq_len = son->get_seq()->weighted_base_count(); |
---|
623 | if (seq_len <= 1.0) seq_len = 1.0; |
---|
624 | blen *= 0.5 / seq_len * 2.0; // doubled counted sum * corr |
---|
625 | |
---|
626 | AP_tree_nlen *fathr = son->get_father(); |
---|
627 | if (!fathr->father) { // at root |
---|
628 | fathr->leftlen = blen *.5; |
---|
629 | fathr->rightlen = blen *.5; |
---|
630 | } |
---|
631 | else { |
---|
632 | if (fathr->leftson == son) { |
---|
633 | fathr->leftlen = blen; |
---|
634 | } |
---|
635 | else { |
---|
636 | fathr->rightlen = blen; |
---|
637 | } |
---|
638 | } |
---|
639 | |
---|
640 | if (son->leftson->is_leaf) { |
---|
641 | ap_calc_leaf_branch_length(son->get_leftson()); |
---|
642 | } |
---|
643 | |
---|
644 | if (son->rightson->is_leaf) { |
---|
645 | ap_calc_leaf_branch_length(son->get_rightson()); |
---|
646 | } |
---|
647 | } |
---|
648 | const double ap_undef_bl = 10.5; |
---|
649 | |
---|
650 | static void ap_check_leaf_bl(AP_tree_nlen *node) { |
---|
651 | if (node->is_leaf) { |
---|
652 | if (!node->father->father) { |
---|
653 | if (node->father->leftlen + node->father->rightlen == ap_undef_bl) { |
---|
654 | ap_calc_leaf_branch_length(node); |
---|
655 | } |
---|
656 | } |
---|
657 | else if (node->father->leftson == node) { |
---|
658 | if (node->father->leftlen == ap_undef_bl) { |
---|
659 | ap_calc_leaf_branch_length(node); |
---|
660 | } |
---|
661 | } |
---|
662 | else { |
---|
663 | if (node->father->rightlen == ap_undef_bl) { |
---|
664 | ap_calc_leaf_branch_length(node); |
---|
665 | } |
---|
666 | } |
---|
667 | return; |
---|
668 | } |
---|
669 | else { |
---|
670 | if (node->leftlen == ap_undef_bl) ap_calc_leaf_branch_length(node->get_leftson()); |
---|
671 | if (node->rightlen == ap_undef_bl) ap_calc_leaf_branch_length(node->get_rightson()); |
---|
672 | } |
---|
673 | } |
---|
674 | |
---|
675 | AP_FLOAT AP_tree_edge::nni_rek(int deep, bool skip_hidden, AP_BL_MODE mode, AP_tree_nlen *skipNode) { |
---|
676 | if (!rootNode()) return 0.0; |
---|
677 | if (rootNode()->is_leaf) return rootNode()->costs(); |
---|
678 | |
---|
679 | AP_tree_edge *oldRootEdge = rootEdge(); |
---|
680 | |
---|
681 | if (deep>=0) set_root(); |
---|
682 | |
---|
683 | AP_FLOAT old_parsimony = rootNode()->costs(); |
---|
684 | AP_FLOAT new_parsimony = old_parsimony; |
---|
685 | |
---|
686 | buildChain(deep, skip_hidden, 0, skipNode); |
---|
687 | long cs = sizeofChain(); |
---|
688 | arb_progress progress(cs*2); |
---|
689 | AP_tree_edge *follow; |
---|
690 | { |
---|
691 | // set all branch lengths to undef |
---|
692 | for (follow = this; follow; follow = follow->next) { |
---|
693 | follow->node[0]->leftlen = ap_undef_bl; |
---|
694 | follow->node[0]->rightlen = ap_undef_bl; |
---|
695 | follow->node[1]->leftlen = ap_undef_bl; |
---|
696 | follow->node[1]->rightlen = ap_undef_bl; |
---|
697 | follow->node[0]->father->leftlen = ap_undef_bl; |
---|
698 | follow->node[0]->father->rightlen = ap_undef_bl; |
---|
699 | } |
---|
700 | rootNode()->leftlen = ap_undef_bl *.5; |
---|
701 | rootNode()->rightlen = ap_undef_bl *.5; |
---|
702 | } |
---|
703 | |
---|
704 | for (follow = this; follow && !progress.aborted(); follow = follow->next) { |
---|
705 | AP_tree_nlen *son = follow->sonNode(); |
---|
706 | AP_tree_nlen *fath = son; |
---|
707 | |
---|
708 | if (follow->otherNode(fath)==fath->get_father()) fath = fath->get_father(); |
---|
709 | if (fath->father) { |
---|
710 | if (fath->father->father) { |
---|
711 | fath->set_root(); |
---|
712 | new_parsimony = rootNode()->costs(); |
---|
713 | } |
---|
714 | } |
---|
715 | if (mode & AP_BL_BOOTSTRAP_LIMIT) { |
---|
716 | if (fath->father) { |
---|
717 | son->set_root(); |
---|
718 | new_parsimony = rootNode()->costs(); |
---|
719 | } |
---|
720 | |
---|
721 | MutationsPerSite mps(son->get_seq()->get_sequence_length()); |
---|
722 | new_parsimony = follow->nni_mutPerSite(new_parsimony, mode, &mps); |
---|
723 | ap_calc_bootstrap_remark(son, mode, mps); |
---|
724 | } |
---|
725 | else { |
---|
726 | new_parsimony = follow->nni(new_parsimony, mode); |
---|
727 | } |
---|
728 | |
---|
729 | progress.inc(); |
---|
730 | } |
---|
731 | |
---|
732 | for (follow = this; follow && !progress.aborted(); follow = follow->next) { |
---|
733 | ap_check_leaf_bl(follow->node[0]); |
---|
734 | ap_check_leaf_bl(follow->node[1]); |
---|
735 | progress.inc(); |
---|
736 | } |
---|
737 | oldRootEdge->set_root(); |
---|
738 | new_parsimony = rootNode()->costs(); |
---|
739 | |
---|
740 | return new_parsimony; |
---|
741 | } |
---|
742 | |
---|
743 | int AP_tree_edge::dumpNNI = 0; |
---|
744 | int AP_tree_edge::distInsertBorder; |
---|
745 | int AP_tree_edge::basesChanged; |
---|
746 | int AP_tree_edge::speciesInTree; |
---|
747 | int AP_tree_edge::nodesInTree; |
---|
748 | |
---|
749 | AP_FLOAT AP_tree_edge::nni_mutPerSite(AP_FLOAT pars_one, AP_BL_MODE mode, MutationsPerSite *mps) |
---|
750 | { |
---|
751 | AP_tree_nlen *root = rootNode(); |
---|
752 | |
---|
753 | if (node[0]->is_leaf || node[1]->is_leaf) { // a son at root |
---|
754 | #if 0 |
---|
755 | // calculate branch lengths at root |
---|
756 | if (mode&AP_BL_BL_ONLY) { |
---|
757 | AP_tree_nlen *tip, *brother; |
---|
758 | |
---|
759 | if (node[0]->is_leaf) { |
---|
760 | tip = node[0]; brother = node[1]; |
---|
761 | } |
---|
762 | else { |
---|
763 | tip = node[1]; brother = node[0]; |
---|
764 | } |
---|
765 | |
---|
766 | AP_FLOAT Blen = pars_one - brother->costs(); |
---|
767 | AP_FLOAT Seq_len = tip->sequence->real_len(); |
---|
768 | |
---|
769 | node[0]->father->leftlen = node[0]->father->rightlen = Blen/Seq_len*.5; |
---|
770 | } |
---|
771 | #endif |
---|
772 | return pars_one; |
---|
773 | } |
---|
774 | |
---|
775 | AP_tree_edge_data oldData = data; |
---|
776 | |
---|
777 | AP_FLOAT parsbest = pars_one, |
---|
778 | pars_two, |
---|
779 | pars_three; |
---|
780 | AP_tree_nlen *son = sonNode(); |
---|
781 | int betterValueFound = 0; |
---|
782 | { // ******** original tree |
---|
783 | if ((mode & AP_BL_BOOTSTRAP_LIMIT)) { |
---|
784 | root->costs(); |
---|
785 | son->unhash_sequence(); |
---|
786 | son->get_father()->unhash_sequence(); |
---|
787 | ap_assert(!son->father->father); |
---|
788 | AP_tree_nlen *brother = son->get_brother(); |
---|
789 | brother->unhash_sequence(); |
---|
790 | |
---|
791 | ap_assert(mps); |
---|
792 | pars_one = root->costs(mps->data(0)); |
---|
793 | } |
---|
794 | else if (pars_one==0.0) { |
---|
795 | pars_one = root->costs(); |
---|
796 | } |
---|
797 | } |
---|
798 | { // ********* first nni |
---|
799 | ap_main->push(); |
---|
800 | son->swap_assymetric(AP_LEFT); |
---|
801 | pars_two = root->costs(mps ? mps->data(1) : NULL); |
---|
802 | |
---|
803 | if (pars_two <= parsbest) { |
---|
804 | if ((mode & AP_BL_NNI_ONLY) == 0) ap_main->pop(); |
---|
805 | else ap_main->clear(); |
---|
806 | |
---|
807 | parsbest = pars_two; |
---|
808 | betterValueFound = (int)(pars_one-pars_two); |
---|
809 | } |
---|
810 | else { |
---|
811 | ap_main->pop(); |
---|
812 | } |
---|
813 | } |
---|
814 | { // ********** second nni |
---|
815 | ap_main->push(); |
---|
816 | son->swap_assymetric(AP_RIGHT); |
---|
817 | pars_three = root->costs(mps ? mps->data(2) : NULL); |
---|
818 | |
---|
819 | if (pars_three <= parsbest) { |
---|
820 | if ((mode & AP_BL_NNI_ONLY) == 0) ap_main->pop(); |
---|
821 | else ap_main->clear(); |
---|
822 | |
---|
823 | parsbest = pars_three; |
---|
824 | betterValueFound = (int)(pars_one-pars_three); |
---|
825 | } |
---|
826 | else { |
---|
827 | ap_main->pop(); |
---|
828 | } |
---|
829 | } |
---|
830 | |
---|
831 | if (mode & AP_BL_BL_ONLY) { // ************* calculate branch lengths ************** |
---|
832 | AP_FLOAT blen = (pars_one + pars_two + pars_three) - (3.0 * parsbest); |
---|
833 | if (blen <0) blen = 0; |
---|
834 | ap_calc_branch_lengths(root, son, parsbest, blen); |
---|
835 | } |
---|
836 | |
---|
837 | // zu Auswertungszwecken doch unsortiert uebernehmen: |
---|
838 | |
---|
839 | data.parsValue[0] = pars_one; |
---|
840 | data.parsValue[1] = pars_two; |
---|
841 | data.parsValue[2] = pars_three; |
---|
842 | |
---|
843 | |
---|
844 | if (dumpNNI) { |
---|
845 | if (dumpNNI==2) GBK_terminate("NNI called between optimize and statistics"); |
---|
846 | |
---|
847 | AP_tree_nlen *node0 = this->node[0]; |
---|
848 | AP_tree_nlen *node1 = this->node[1]; |
---|
849 | if (node0->gr.leaf_sum > node1->gr.leaf_sum) { // node0 is final son |
---|
850 | node0 = node1; |
---|
851 | } |
---|
852 | |
---|
853 | static int num = 0; |
---|
854 | |
---|
855 | node0->use_as_remark(GBS_global_string_copy("%i %4.0f:%4.0f:%4.0f %4.0f:%4.0f:%4.0f\n", |
---|
856 | num++, |
---|
857 | oldData.parsValue[0], oldData.parsValue[1], oldData.parsValue[2], |
---|
858 | data.parsValue[0], data.parsValue[1], data.parsValue[2])); |
---|
859 | |
---|
860 | cout |
---|
861 | << setw(4) << distInsertBorder |
---|
862 | << setw(6) << basesChanged |
---|
863 | << setw(4) << distanceToBorder() |
---|
864 | << setw(4) << data.distance |
---|
865 | << setw(4) << betterValueFound |
---|
866 | << setw(8) << oldData.parsValue[0] |
---|
867 | << setw(8) << oldData.parsValue[1] |
---|
868 | << setw(8) << oldData.parsValue[2] |
---|
869 | << setw(8) << data.parsValue[0] |
---|
870 | << setw(8) << data.parsValue[1] |
---|
871 | << setw(8) << data.parsValue[2] |
---|
872 | << '\n'; |
---|
873 | } |
---|
874 | |
---|
875 | return parsbest; |
---|
876 | } |
---|
877 | |
---|
878 | ostream& operator<<(ostream& out, const AP_tree_edge& e) |
---|
879 | { |
---|
880 | static int notTooDeep; |
---|
881 | |
---|
882 | out << ' '; |
---|
883 | |
---|
884 | if (notTooDeep || &e==NULL) { |
---|
885 | out << e; |
---|
886 | } |
---|
887 | else { |
---|
888 | notTooDeep = 1; |
---|
889 | out << "AP_tree_edge(" << e |
---|
890 | << ", node[0]=" << *(e.node[0]) |
---|
891 | << ", node[1]=" << *(e.node[1]) |
---|
892 | << ")"; |
---|
893 | notTooDeep = 0; // cppcheck-suppress redundantAssignment |
---|
894 | } |
---|
895 | |
---|
896 | return out << ' '; |
---|
897 | } |
---|
898 | |
---|
899 | void AP_tree_edge::mixTree(int cnt) |
---|
900 | { |
---|
901 | buildChain(-1); |
---|
902 | |
---|
903 | while (cnt--) |
---|
904 | { |
---|
905 | AP_tree_edge *follow = this; |
---|
906 | |
---|
907 | while (follow) { |
---|
908 | AP_tree_nlen *son = follow->sonNode(); |
---|
909 | if (!son->is_leaf) son->swap_assymetric(GB_random(2) ? AP_LEFT : AP_RIGHT); |
---|
910 | follow = follow->next; |
---|
911 | } |
---|
912 | } |
---|
913 | } |
---|
914 | |
---|