1 | // =============================================================== // |
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2 | // // |
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3 | // File : AP_tree_nlen.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 | #include "ap_main.hxx" |
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14 | |
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15 | #include <AP_seq_dna.hxx> |
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16 | #include <aw_root.hxx> |
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17 | |
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18 | using namespace std; |
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19 | |
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20 | // --------------------------------- |
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21 | // Section base operations: |
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22 | // --------------------------------- |
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23 | |
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24 | AP_UPDATE_FLAGS AP_pars_root::check_update() { |
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25 | // disables load if tree changes in DB |
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26 | // (ignore changes performed in arb_ntree while tree is loaded in arb_pars) |
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27 | AP_UPDATE_FLAGS res = AP_tree_root::check_update(); |
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28 | return res == AP_UPDATE_RELOADED ? AP_UPDATE_OK : res; |
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29 | } |
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30 | |
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31 | ostream& operator<<(ostream& out, const AP_tree_nlen *node) { |
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32 | out << ' '; |
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33 | |
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34 | if (!node) { |
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35 | out << "NULp"; |
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36 | } |
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37 | if (node->is_leaf()) { |
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38 | out << ((void *)node) << '(' << node->name << ')'; |
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39 | } |
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40 | else { |
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41 | static int notTooDeep; |
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42 | |
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43 | if (notTooDeep) { |
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44 | out << ((void *)node); |
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45 | if (!node->father) out << " (ROOT)"; |
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46 | } |
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47 | else { |
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48 | notTooDeep = 1; |
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49 | |
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50 | out << "NODE(" << ((void *)node); |
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51 | |
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52 | if (!node->father) { |
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53 | out << " (ROOT)"; |
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54 | } |
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55 | else { |
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56 | out << ", father=" << node->father; |
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57 | } |
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58 | |
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59 | out << ", leftson=" << node->leftson |
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60 | << ", rightson=" << node->rightson |
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61 | << ", edge[0]=" << node->edge[0] |
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62 | << ", edge[1]=" << node->edge[1] |
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63 | << ", edge[2]=" << node->edge[2] |
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64 | << ")"; |
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65 | |
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66 | notTooDeep = 0; |
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67 | } |
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68 | } |
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69 | |
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70 | return out << ' '; |
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71 | } |
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72 | |
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73 | int AP_tree_nlen::unusedEdgeIndex() const { |
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74 | for (int e=0; e<3; e++) if (!edge[e]) return e; |
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75 | return -1; |
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76 | } |
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77 | |
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78 | AP_tree_edge* AP_tree_nlen::edgeTo(const AP_tree_nlen *neighbour) const { |
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79 | for (int e=0; e<3; e++) { |
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80 | if (edge[e] && edge[e]->node[1-index[e]]==neighbour) { |
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81 | return edge[e]; |
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82 | } |
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83 | } |
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84 | return NULp; |
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85 | } |
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86 | |
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87 | AP_tree_edge* AP_tree_nlen::nextEdge(const AP_tree_edge *afterThatEdge) const { |
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88 | /*! @return one edge of 'this' |
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89 | * |
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90 | * @param afterThatEdge |
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91 | * - if == NULp -> returns the "first" edge (edge[0]) |
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92 | * - otherwise -> returns the next edge following 'afterThatEdge' in the array edge[] |
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93 | */ |
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94 | return edge[afterThatEdge ? ((indexOf(afterThatEdge)+1) % 3) : 0]; |
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95 | } |
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96 | |
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97 | void AP_tree_nlen::unlinkAllEdges(AP_tree_edge **edgePtr1, AP_tree_edge **edgePtr2, AP_tree_edge **edgePtr3) { |
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98 | ap_assert(edge[0]); |
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99 | ap_assert(edge[1]); |
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100 | ap_assert(edge[2]); |
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101 | |
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102 | *edgePtr1 = edge[0]->unlink(); |
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103 | *edgePtr2 = edge[1]->unlink(); |
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104 | *edgePtr3 = edge[2]->unlink(); |
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105 | } |
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106 | |
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107 | void AP_tree_nlen::linkAllEdges(AP_tree_edge *edge1, AP_tree_edge *edge2, AP_tree_edge *edge3) { |
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108 | ap_assert(!edge[0]); |
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109 | ap_assert(!edge[1]); |
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110 | ap_assert(!edge[2]); |
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111 | |
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112 | edge1->relink(this, get_father()->get_father() ? get_father() : get_brother()); |
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113 | edge2->relink(this, get_leftson()); |
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114 | edge3->relink(this, get_rightson()); |
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115 | } |
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116 | |
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117 | // ----------------------------- |
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118 | // Check tree structure |
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119 | |
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120 | #if defined(PROVIDE_TREE_STRUCTURE_TESTS) |
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121 | |
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122 | #if defined(DEBUG) |
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123 | #define DUMP_INVALID_SUBTREES |
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124 | #endif |
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125 | |
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126 | #if defined(DEVEL_RALF) |
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127 | #define CHECK_CORRECT_INVALIDATION // recombines all up-to-date nodes to find missing invalidations (VERY slow) |
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128 | #endif |
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129 | |
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130 | |
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131 | #if defined(DUMP_INVALID_SUBTREES) |
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132 | inline void dumpSubtree(const char *msg, const AP_tree_nlen *node) { |
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133 | fprintf(stderr, "%s:\n", msg); |
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134 | char *printable = GBT_tree_2_newick(node, NewickFormat(nSIMPLE|nWRAP), true); |
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135 | fputs(printable, stderr); |
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136 | fputc('\n', stderr); |
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137 | free(printable); |
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138 | } |
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139 | #endif |
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140 | |
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141 | inline const AP_tree_edge *edge_between(const AP_tree_nlen *node1, const AP_tree_nlen *node2) { |
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142 | AP_tree_edge *edge_12 = node1->edgeTo(node2); |
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143 | |
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144 | #if defined(ASSERTION_USED) |
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145 | AP_tree_edge *edge_21 = node2->edgeTo(node1); |
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146 | ap_assert(edge_12 == edge_21); // nodes should agree about their edge |
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147 | #endif |
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148 | |
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149 | return edge_12; |
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150 | } |
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151 | |
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152 | inline const char *no_valid_edge_between(const AP_tree_nlen *node1, const AP_tree_nlen *node2) { |
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153 | AP_tree_edge *edge_12 = node1->edgeTo(node2); |
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154 | AP_tree_edge *edge_21 = node2->edgeTo(node1); |
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155 | |
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156 | if (edge_12 == edge_21) { |
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157 | return edge_12 ? NULp : "edge missing"; |
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158 | } |
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159 | return "edge inconsistent"; |
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160 | } |
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161 | |
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162 | #if defined(DUMP_INVALID_SUBTREES) |
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163 | #define PRINT_BAD_EDGE(msg,node) dumpSubtree(msg,node) |
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164 | #else // !defined(DUMP_INVALID_SUBTREES) |
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165 | #define PRINT_BAD_EDGE(msg,node) fprintf(stderr, "Warning: %s (at node=%p)\n", (msg), (node)) |
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166 | #endif |
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167 | |
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168 | #define SHOW_BAD_EDGE(format,str,node) do{ \ |
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169 | char *msg = GBS_global_string_copy(format,str); \ |
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170 | PRINT_BAD_EDGE(msg, node); \ |
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171 | free(msg); \ |
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172 | }while(0) |
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173 | |
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174 | Validity AP_tree_nlen::has_valid_edges() const { |
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175 | Validity valid; |
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176 | if (get_father()) { // root has no edges |
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177 | if (get_father()->is_root_node()) { // sons of root have one edge between them |
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178 | if (is_leftson()) { // test root-edge only from one son |
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179 | const char *invalid = no_valid_edge_between(this, get_brother()); |
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180 | if (invalid) { |
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181 | SHOW_BAD_EDGE("root-%s. root", invalid, get_father()); |
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182 | valid = Validity(false, "no valid edge between sons of root"); |
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183 | } |
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184 | } |
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185 | const char *invalid = no_valid_edge_between(this, get_father()); |
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186 | if (!invalid || !strstr(invalid, "missing")) { |
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187 | SHOW_BAD_EDGE("unexpected edge (%s) between root and son", invalid ? invalid : "valid", this); |
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188 | valid = Validity(false, "unexpected edge between son-of-root and root"); |
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189 | } |
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190 | } |
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191 | else { |
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192 | const char *invalid = no_valid_edge_between(this, get_father()); |
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193 | if (invalid) { |
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194 | SHOW_BAD_EDGE("son-%s. father", invalid, get_father()); |
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195 | SHOW_BAD_EDGE("parent-%s. son", invalid, this); |
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196 | valid = Validity(false, "invalid edge between son and father"); |
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197 | } |
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198 | } |
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199 | } |
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200 | |
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201 | if (!is_leaf()) { |
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202 | if (valid) valid = get_leftson()->has_valid_edges(); |
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203 | if (valid) valid = get_rightson()->has_valid_edges(); |
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204 | } |
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205 | return valid; |
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206 | } |
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207 | |
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208 | Validity AP_tree_nlen::sequence_state_valid() const { |
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209 | // if some node has a sequence, all son-nodes have to have sequences! |
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210 | |
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211 | Validity valid; |
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212 | |
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213 | const AP_combinableSeq *sequence = get_seq(); |
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214 | if (sequence) { |
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215 | if (sequence->hasSequence()) { |
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216 | if (!is_leaf()) { |
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217 | bool leftson_hasSequence = get_leftson()->hasSequence(); |
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218 | bool rightson_hasSequence = get_rightson()->hasSequence(); |
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219 | |
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220 | #if defined(DUMP_INVALID_SUBTREES) |
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221 | if (!leftson_hasSequence) dumpSubtree("left subtree has no sequence", get_leftson()); |
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222 | if (!rightson_hasSequence) dumpSubtree("right subtree has no sequence", get_rightson()); |
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223 | if (!(leftson_hasSequence && rightson_hasSequence)) { |
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224 | dumpSubtree("while father HAS sequence", this); |
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225 | } |
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226 | #endif |
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227 | |
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228 | valid = Validity(leftson_hasSequence && rightson_hasSequence, "node has sequence and son w/o sequence"); |
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229 | |
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230 | #if defined(CHECK_CORRECT_INVALIDATION) |
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231 | if (valid) { |
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232 | // check for missing invalidations |
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233 | // (if recalculating a node (via combine) does not reproduce the current sequence, it should have been invalidated) |
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234 | |
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235 | AP_combinableSeq *recombined = sequence->dup(); |
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236 | Mutations mutations_from_combine = recombined->noncounting_combine_seq(get_leftson()->get_seq(), get_rightson()->get_seq()); |
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237 | |
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238 | valid = Validity(recombined->combinedEquals(sequence), "recombining changed existing sequence (missing invalidation?)"); |
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239 | if (valid) { |
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240 | Mutations expected_mutrate = mutations_from_combine + get_leftson()->mutations + get_rightson()->mutations; |
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241 | valid = Validity(expected_mutrate == mutations, "invalid mutation_rate"); |
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242 | } |
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243 | |
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244 | delete recombined; |
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245 | |
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246 | #if defined(DUMP_INVALID_SUBTREES) |
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247 | if (!valid) { |
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248 | dumpSubtree(valid.why_not(), this); |
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249 | } |
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250 | #endif |
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251 | } |
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252 | #endif |
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253 | } |
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254 | } |
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255 | #if defined(ASSERTION_USED) |
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256 | else { |
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257 | if (is_leaf()) ap_assert(sequence->is_bound_to_species()); // can do lazy load if needed |
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258 | } |
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259 | #endif |
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260 | } |
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261 | |
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262 | if (!is_leaf()) { |
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263 | if (valid) valid = get_leftson()->sequence_state_valid(); |
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264 | if (valid) valid = get_rightson()->sequence_state_valid(); |
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265 | } |
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266 | |
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267 | return valid; |
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268 | } |
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269 | |
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270 | Validity AP_tree_nlen::is_valid() const { |
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271 | ap_assert(knownNonNull(this)); |
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272 | |
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273 | Validity valid = AP_tree::is_valid(); |
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274 | if (valid) valid = has_valid_edges(); |
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275 | if (valid) valid = sequence_state_valid(); |
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276 | |
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277 | return valid; |
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278 | } |
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279 | |
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280 | #endif // PROVIDE_TREE_STRUCTURE_TESTS |
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281 | |
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282 | // ------------------------- |
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283 | // Tree operations: |
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284 | // |
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285 | // insert |
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286 | // remove |
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287 | // swap |
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288 | // set_root |
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289 | // move |
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290 | // costs |
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291 | |
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292 | |
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293 | inline void push_all_upnode_sequences(AP_tree_nlen *nodeBelow) { |
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294 | for (AP_tree_nlen *upnode = nodeBelow->get_father(); |
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295 | upnode; |
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296 | upnode = upnode->get_father()) |
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297 | { |
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298 | ap_main->push_node(upnode, SEQUENCE); |
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299 | } |
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300 | } |
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301 | |
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302 | inline void sortOldestFirst(AP_tree_edge **e1, AP_tree_edge **e2) { |
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303 | if ((*e1)->Age() > (*e2)->Age()) { |
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304 | swap(*e1, *e2); |
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305 | } |
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306 | } |
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307 | |
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308 | inline void sortOldestFirst(AP_tree_edge **e1, AP_tree_edge **e2, AP_tree_edge **e3) { |
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309 | sortOldestFirst(e1, e2); |
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310 | sortOldestFirst(e2, e3); |
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311 | sortOldestFirst(e1, e2); |
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312 | } |
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313 | |
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314 | void AP_tree_nlen::initial_insert(AP_tree_nlen *newBrother, AP_pars_root *troot) { |
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315 | // construct initial tree from 'this' and 'newBrother' |
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316 | // (both have to be leafs) |
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317 | |
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318 | ap_assert(newBrother); |
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319 | ap_assert(is_leaf()); |
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320 | ap_assert(newBrother->is_leaf()); |
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321 | |
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322 | AP_tree::initial_insert(newBrother, troot); |
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323 | makeEdge(newBrother, this); // build the root edge |
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324 | |
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325 | ASSERT_VALID_TREE(this->get_father()); |
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326 | } |
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327 | |
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328 | void AP_tree_nlen::insert(AP_tree_nlen *newBrother) { |
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329 | // inserts 'this' (a new node) at the father-edge of 'newBrother' |
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330 | ap_assert(newBrother); |
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331 | |
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332 | ASSERT_VALID_TREE(this); |
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333 | ASSERT_VALID_TREE(newBrother); |
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334 | |
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335 | ap_main->push_node(this, STRUCTURE); |
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336 | ap_main->push_node(newBrother, STRUCTURE); |
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337 | |
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338 | AP_tree_nlen *brothersFather = newBrother->get_father(); |
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339 | if (brothersFather) { |
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340 | ap_main->push_node(brothersFather, BOTH); |
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341 | push_all_upnode_sequences(brothersFather); |
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342 | |
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343 | if (brothersFather->get_father()) { |
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344 | AP_tree_edge *oldEdge = newBrother->edgeTo(newBrother->get_father())->unlink(); |
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345 | AP_tree::insert(newBrother); |
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346 | oldEdge->relink(get_father(), get_father()->get_father()); |
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347 | } |
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348 | else { // insert to son of root |
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349 | AP_tree_nlen *brothersOldBrother = newBrother->get_brother(); |
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350 | ap_main->push_node(brothersOldBrother, STRUCTURE); |
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351 | |
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352 | AP_tree_edge *oldEdge = newBrother->edgeTo(brothersOldBrother)->unlink(); |
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353 | AP_tree::insert(newBrother); |
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354 | oldEdge->relink(get_father(), get_father()->get_brother()); |
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355 | } |
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356 | |
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357 | makeEdge(this, get_father()); |
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358 | makeEdge(get_father(), newBrother); |
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359 | |
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360 | ASSERT_VALID_TREE(get_father()->get_father()); |
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361 | } |
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362 | else { // insert at root |
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363 | ap_assert(!newBrother->is_leaf()); // either swap 'this' and 'newBrother' or use initial_insert() to construct the initial tree |
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364 | |
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365 | AP_tree_nlen *lson = newBrother->get_leftson(); |
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366 | AP_tree_nlen *rson = newBrother->get_rightson(); |
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367 | |
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368 | ap_main->push_node(lson, STRUCTURE); |
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369 | ap_main->push_node(rson, STRUCTURE); |
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370 | |
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371 | AP_tree_edge *oldEdge = lson->edgeTo(rson)->unlink(); |
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372 | |
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373 | AP_tree::insert(newBrother); |
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374 | |
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375 | oldEdge->relink(this, newBrother); |
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376 | makeEdge(newBrother, rson); |
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377 | makeEdge(newBrother, lson); |
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378 | |
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379 | ASSERT_VALID_TREE(get_father()); |
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380 | } |
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381 | } |
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382 | |
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383 | AP_tree_nlen *AP_tree_nlen::REMOVE() { |
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384 | // Removes 'this' and its father from the tree: |
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385 | // |
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386 | // grandpa grandpa |
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387 | // / / |
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388 | // / / |
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389 | // father => brother |
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390 | // / \ . |
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391 | // / \ . |
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392 | // this brother |
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393 | // |
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394 | // One of the edges is relinked between brother and grandpa. |
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395 | // 'father' is destroyed, 'this' is returned. |
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396 | |
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397 | AP_tree_nlen *oldBrother = get_brother(); |
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398 | |
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399 | ASSERT_VALID_TREE(this); |
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400 | |
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401 | ap_assert(father); // can't remove complete tree, |
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402 | |
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403 | ap_main->push_node(this, STRUCTURE); |
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404 | ap_main->push_node(oldBrother, STRUCTURE); |
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405 | push_all_upnode_sequences(get_father()); |
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406 | |
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407 | AP_tree_edge *oldEdge; |
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408 | AP_tree_nlen *grandPa = get_father()->get_father(); |
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409 | if (grandPa) { |
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410 | ASSERT_VALID_TREE(grandPa); |
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411 | |
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412 | ap_main->push_node(get_father(), BOTH); |
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413 | ap_main->push_node(grandPa, STRUCTURE); |
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414 | |
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415 | destroyEdge(edgeTo(get_father())->unlink()); |
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416 | destroyEdge(get_father()->edgeTo(oldBrother)->unlink()); |
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417 | |
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418 | if (grandPa->father) { |
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419 | oldEdge = get_father()->edgeTo(grandPa)->unlink(); |
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420 | AP_tree::REMOVE(); |
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421 | oldEdge->relink(oldBrother, grandPa); |
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422 | } |
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423 | else { // remove grandson of root |
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424 | AP_tree_nlen *uncle = get_father()->get_brother(); |
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425 | ap_main->push_node(uncle, STRUCTURE); |
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426 | |
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427 | oldEdge = get_father()->edgeTo(uncle)->unlink(); |
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428 | AP_tree::REMOVE(); |
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429 | oldEdge->relink(oldBrother, uncle); |
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430 | } |
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431 | ASSERT_VALID_TREE(grandPa); |
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432 | } |
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433 | else { // remove son of root |
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434 | AP_tree_nlen *oldRoot = get_father(); |
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435 | ASSERT_VALID_TREE(oldRoot); |
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436 | |
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437 | if (oldBrother->is_leaf()) { |
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438 | // root |
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439 | // oo |
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440 | // o o |
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441 | // o o |
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442 | // oldBrother --- this -----> NULp |
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443 | // |
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444 | ap_main->push_node(oldRoot, ROOT); |
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445 | |
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446 | destroyEdge(edgeTo(oldBrother)->unlink()); |
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447 | |
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448 | #if defined(ASSERTION_USED) |
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449 | AP_pars_root *troot = get_tree_root(); |
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450 | #endif // ASSERTION_USED |
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451 | AP_tree::REMOVE(); |
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452 | ap_assert(!troot->get_root_node()); // tree should have been removed |
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453 | } |
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454 | else { |
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455 | // |
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456 | // root |
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457 | // oo . |
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458 | // o o root (=oldBrother) |
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459 | // o o oo . |
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460 | // oldBrother --- this -----> o o . |
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461 | // /\ o o . |
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462 | // / \ lson ----- rson |
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463 | // / \ . |
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464 | // lson rson |
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465 | // |
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466 | AP_tree_nlen *lson = oldBrother->get_leftson(); |
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467 | AP_tree_nlen *rson = oldBrother->get_rightson(); |
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468 | |
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469 | ap_assert(lson && rson); |
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470 | |
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471 | ap_main->push_node(lson, STRUCTURE); |
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472 | ap_main->push_node(rson, STRUCTURE); |
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473 | ap_main->push_node(oldRoot, ROOT); |
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474 | |
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475 | destroyEdge(edgeTo(oldBrother)->unlink()); |
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476 | destroyEdge(oldBrother->edgeTo(lson)->unlink()); |
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477 | |
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478 | oldEdge = oldBrother->edgeTo(rson)->unlink(); |
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479 | AP_tree::REMOVE(); |
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480 | oldEdge->relink(lson, rson); |
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481 | |
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482 | ap_assert(lson->get_tree_root()->get_root_node() == oldBrother); |
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483 | ASSERT_VALID_TREE(oldBrother); |
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484 | } |
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485 | } |
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486 | |
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487 | father = NULp; |
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488 | set_tree_root(NULp); |
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489 | |
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490 | ASSERT_VALID_TREE(this); |
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491 | return this; |
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492 | } |
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493 | |
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494 | void AP_tree_nlen::swap_sons() { |
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495 | ap_assert(!is_leaf()); // cannot swap sons at leafs |
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496 | |
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497 | ap_main->push_node(this, STRUCTURE); |
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498 | AP_tree::swap_sons(); |
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499 | } |
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500 | |
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501 | void AP_tree_nlen::swap_assymetric(AP_TREE_SIDE mode) { |
---|
502 | // mode AP_LEFT exchanges leftson with brother |
---|
503 | // mode AP_RIGHT exchanges rightson with brother |
---|
504 | |
---|
505 | // @@@ "NNI" works really bad for keeled groups (fixable?; #785) |
---|
506 | |
---|
507 | ap_assert(!is_leaf()); // cannot swap leafs |
---|
508 | ap_assert(father); // cannot swap root (has no brother) |
---|
509 | ap_assert(mode == AP_LEFT || mode == AP_RIGHT); // illegal mode |
---|
510 | |
---|
511 | AP_tree_nlen *oldBrother = get_brother(); |
---|
512 | AP_tree_nlen *movedSon = mode == AP_LEFT ? get_leftson() : get_rightson(); |
---|
513 | |
---|
514 | if (!father->father) { |
---|
515 | // son of root case |
---|
516 | // take leftson of brother to exchange with |
---|
517 | |
---|
518 | if (!oldBrother->is_leaf()) { // swap needed ? |
---|
519 | AP_tree_nlen *nephew = oldBrother->get_leftson(); |
---|
520 | |
---|
521 | ap_main->push_node(this, BOTH); |
---|
522 | ap_main->push_node(movedSon, STRUCTURE); |
---|
523 | ap_main->push_node(get_father(), SEQUENCE); |
---|
524 | ap_main->push_node(nephew, STRUCTURE); |
---|
525 | ap_main->push_node(oldBrother, BOTH); |
---|
526 | |
---|
527 | AP_tree_edge *edge1 = edgeTo(movedSon)->unlink(); |
---|
528 | AP_tree_edge *edge2 = oldBrother->edgeTo(nephew)->unlink(); |
---|
529 | |
---|
530 | if (mode == AP_LEFT) { |
---|
531 | swap(leftson->father, nephew->father); |
---|
532 | swap(leftson, oldBrother->leftson); |
---|
533 | } |
---|
534 | else { |
---|
535 | swap(rightson->father, nephew->father); |
---|
536 | swap(rightson, oldBrother->leftson); |
---|
537 | } |
---|
538 | |
---|
539 | edge2->relink(this, nephew); |
---|
540 | edge1->relink(oldBrother, movedSon); |
---|
541 | |
---|
542 | if (nephew->gr.mark_sum != movedSon->gr.mark_sum) { |
---|
543 | get_brother()->recalc_marked_from_sons(); |
---|
544 | this->recalc_marked_from_sons_and_forward_upwards(); |
---|
545 | } |
---|
546 | } |
---|
547 | } |
---|
548 | else { |
---|
549 | ap_main->push_node(this, BOTH); |
---|
550 | ap_main->push_node(get_father(), BOTH); |
---|
551 | ap_main->push_node(oldBrother, STRUCTURE); |
---|
552 | ap_main->push_node(movedSon, STRUCTURE); |
---|
553 | |
---|
554 | push_all_upnode_sequences(get_father()); |
---|
555 | |
---|
556 | AP_tree_edge *edge1 = edgeTo(movedSon)->unlink(); |
---|
557 | AP_tree_edge *edge2 = get_father()->edgeTo(oldBrother)->unlink(); |
---|
558 | |
---|
559 | if (mode == AP_LEFT) { // swap leftson with brother |
---|
560 | swap(leftson->father, oldBrother->father); |
---|
561 | if (father->leftson == this) { |
---|
562 | swap(leftson, father->rightson); |
---|
563 | } |
---|
564 | else { |
---|
565 | swap(leftson, father->leftson); |
---|
566 | } |
---|
567 | } |
---|
568 | else { // swap rightson with brother |
---|
569 | swap(rightson->father, oldBrother->father); |
---|
570 | if (father->leftson == this) { |
---|
571 | swap(rightson, father->rightson); |
---|
572 | } |
---|
573 | else { |
---|
574 | swap(rightson, father->leftson); |
---|
575 | } |
---|
576 | } |
---|
577 | |
---|
578 | edge2->relink(this, oldBrother); |
---|
579 | edge1->relink(get_father(), movedSon); |
---|
580 | |
---|
581 | if (oldBrother->gr.mark_sum != movedSon->gr.mark_sum) { |
---|
582 | recalc_marked_from_sons_and_forward_upwards(); // father is done implicit |
---|
583 | } |
---|
584 | } |
---|
585 | } |
---|
586 | |
---|
587 | void AP_tree_nlen::set_root() { |
---|
588 | if (at_root()) return; // already root |
---|
589 | |
---|
590 | // from this to root buffer the nodes |
---|
591 | ap_main->push_node(this, STRUCTURE); |
---|
592 | |
---|
593 | AP_tree_nlen *son_of_root = NULp; // in previous topology 'this' was contained inside 'son_of_root' |
---|
594 | AP_tree_nlen *old_root = NULp; |
---|
595 | { |
---|
596 | AP_tree_nlen *pntr; |
---|
597 | for (pntr = get_father(); pntr->father; pntr = pntr->get_father()) { |
---|
598 | ap_main->push_node(pntr, BOTH); |
---|
599 | son_of_root = pntr; |
---|
600 | } |
---|
601 | old_root = pntr; |
---|
602 | } |
---|
603 | |
---|
604 | ap_assert(son_of_root); // always true |
---|
605 | |
---|
606 | { |
---|
607 | AP_tree_nlen *other_son_of_root = son_of_root->get_brother(); |
---|
608 | ap_main->push_node(other_son_of_root, STRUCTURE); |
---|
609 | } |
---|
610 | |
---|
611 | ap_main->push_node(old_root, ROOT); |
---|
612 | AP_tree::set_root(); |
---|
613 | |
---|
614 | for (AP_tree_nlen *node = son_of_root; node ; node = node->get_father()) { |
---|
615 | node->recalc_marked_from_sons(); |
---|
616 | } |
---|
617 | } |
---|
618 | |
---|
619 | void AP_tree_nlen::moveNextTo(AP_tree_nlen *newBrother, AP_FLOAT rel_pos) { |
---|
620 | // Note: see http://bugs.arb-home.de/ticket/627#comment:8 for an experimental |
---|
621 | // replacement of moveNextTo with REMOVE() + insert() |
---|
622 | |
---|
623 | ap_assert(father); |
---|
624 | ap_assert(newBrother); |
---|
625 | ap_assert(newBrother->father); |
---|
626 | ap_assert(newBrother->father != father); // already there |
---|
627 | ap_assert(newBrother != father); // already there |
---|
628 | |
---|
629 | ASSERT_VALID_TREE(rootNode()); |
---|
630 | |
---|
631 | // push everything that will be modified onto stack |
---|
632 | ap_main->push_node(this, STRUCTURE); |
---|
633 | ap_main->push_node(get_brother(), STRUCTURE); |
---|
634 | |
---|
635 | if (father->father) { |
---|
636 | AP_tree_nlen *grandpa = get_father()->get_father(); |
---|
637 | |
---|
638 | ap_main->push_node(get_father(), BOTH); |
---|
639 | |
---|
640 | if (grandpa->father) { |
---|
641 | ap_main->push_node(grandpa, BOTH); |
---|
642 | push_all_upnode_sequences(grandpa); |
---|
643 | } |
---|
644 | else { // 'this' is grandson of root |
---|
645 | ap_main->push_node(grandpa, ROOT); |
---|
646 | ap_main->push_node(get_father()->get_brother(), STRUCTURE); |
---|
647 | } |
---|
648 | } |
---|
649 | else { // 'this' is son of root |
---|
650 | ap_main->push_node(get_father(), ROOT); |
---|
651 | |
---|
652 | if (!get_brother()->is_leaf()) { |
---|
653 | ap_main->push_node(get_brother()->get_leftson(), STRUCTURE); |
---|
654 | ap_main->push_node(get_brother()->get_rightson(), STRUCTURE); |
---|
655 | } |
---|
656 | } |
---|
657 | |
---|
658 | ap_main->push_node(newBrother, STRUCTURE); |
---|
659 | if (newBrother->father) { |
---|
660 | AP_tree_nlen *newBrothersFather = newBrother->get_father(); |
---|
661 | ap_main->push_node(newBrothersFather, BOTH); |
---|
662 | if (!newBrothersFather->father) { // move to son of root |
---|
663 | ap_main->push_node(newBrother->get_brother(), STRUCTURE); |
---|
664 | } |
---|
665 | push_all_upnode_sequences(newBrothersFather); |
---|
666 | } |
---|
667 | |
---|
668 | AP_tree_nlen *thisFather = get_father(); |
---|
669 | AP_tree_nlen *grandFather = thisFather->get_father(); |
---|
670 | AP_tree_nlen *oldBrother = get_brother(); |
---|
671 | AP_tree_nlen *newBrothersFather = newBrother->get_father(); |
---|
672 | AP_tree_edge *e1, *e2, *e3; |
---|
673 | |
---|
674 | if (thisFather==newBrothersFather->get_father()) { // son -> son of brother |
---|
675 | if (grandFather) { |
---|
676 | if (grandFather->get_father()) { |
---|
677 | // covered by test at PARS_main.cxx@COVER3 |
---|
678 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
679 | AP_tree_edge *e4 = newBrother->edgeTo(oldBrother)->unlink(); |
---|
680 | |
---|
681 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
682 | |
---|
683 | sortOldestFirst(&e1, &e2, &e3); |
---|
684 | e1->relink(oldBrother, grandFather); // use oldest edge at remove position |
---|
685 | thisFather->linkAllEdges(e2, e3, e4); |
---|
686 | } |
---|
687 | else { // grandson of root -> son of brother |
---|
688 | // covered by test at PARS_main.cxx@COVER2 |
---|
689 | AP_tree_nlen *uncle = thisFather->get_brother(); |
---|
690 | |
---|
691 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
692 | AP_tree_edge *e4 = newBrother->edgeTo(oldBrother)->unlink(); |
---|
693 | |
---|
694 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
695 | |
---|
696 | sortOldestFirst(&e1, &e2, &e3); |
---|
697 | e1->relink(oldBrother, uncle); |
---|
698 | thisFather->linkAllEdges(e2, e3, e4); |
---|
699 | } |
---|
700 | } |
---|
701 | else { // son of root -> grandson of root |
---|
702 | // covered by test at PARS_main.cxx@COVER1 |
---|
703 | oldBrother->unlinkAllEdges(&e1, &e2, &e3); |
---|
704 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
705 | thisFather->linkAllEdges(e1, e2, e3); |
---|
706 | } |
---|
707 | } |
---|
708 | else if (grandFather==newBrothersFather) { // son -> brother of father |
---|
709 | if (grandFather->father) { |
---|
710 | // covered by test at PARS_main.cxx@COVER4 |
---|
711 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
712 | AP_tree_edge *e4 = grandFather->edgeTo(newBrother)->unlink(); |
---|
713 | |
---|
714 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
715 | |
---|
716 | sortOldestFirst(&e1, &e2, &e3); |
---|
717 | e1->relink(oldBrother, grandFather); |
---|
718 | thisFather->linkAllEdges(e2, e3, e4); |
---|
719 | } |
---|
720 | else { // no edges change if we move grandson of root -> son of root |
---|
721 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
722 | } |
---|
723 | } |
---|
724 | else { |
---|
725 | // now we are sure, the minimal distance |
---|
726 | // between 'this' and 'newBrother' is 4 edges |
---|
727 | // or if the root-edge is between them, the |
---|
728 | // minimal distance is 3 edges |
---|
729 | |
---|
730 | if (!grandFather) { // son of root |
---|
731 | oldBrother->unlinkAllEdges(&e1, &e2, &e3); |
---|
732 | AP_tree_edge *e4 = newBrother->edgeTo(newBrothersFather)->unlink(); |
---|
733 | |
---|
734 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
735 | |
---|
736 | sortOldestFirst(&e1, &e2, &e3); |
---|
737 | e1->relink(oldBrother->get_leftson(), oldBrother->get_rightson()); // new root-edge |
---|
738 | thisFather->linkAllEdges(e2, e3, e4); // old root |
---|
739 | } |
---|
740 | else if (!grandFather->get_father()) { // grandson of root |
---|
741 | if (!newBrothersFather->get_father()->get_father()) { // grandson of root -> grandson of root |
---|
742 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
743 | AP_tree_edge *e4 = newBrother->edgeTo(newBrothersFather)->unlink(); |
---|
744 | |
---|
745 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
746 | |
---|
747 | sortOldestFirst(&e1, &e2, &e3); |
---|
748 | e1->relink(oldBrother, newBrothersFather); // new root-edge |
---|
749 | thisFather->linkAllEdges(e2, e3, e4); |
---|
750 | } |
---|
751 | else { |
---|
752 | AP_tree_nlen *uncle = thisFather->get_brother(); |
---|
753 | |
---|
754 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
755 | AP_tree_edge *e4 = newBrother->edgeTo(newBrothersFather)->unlink(); |
---|
756 | |
---|
757 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
758 | |
---|
759 | sortOldestFirst(&e1, &e2, &e3); |
---|
760 | e1->relink(oldBrother, uncle); |
---|
761 | thisFather->linkAllEdges(e2, e3, e4); |
---|
762 | } |
---|
763 | } |
---|
764 | else { |
---|
765 | if (!newBrothersFather->get_father()) { // move to son of root |
---|
766 | AP_tree_nlen *newBrothersBrother = newBrother->get_brother(); |
---|
767 | |
---|
768 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
769 | AP_tree_edge *e4 = newBrother->edgeTo(newBrothersBrother)->unlink(); |
---|
770 | |
---|
771 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
772 | |
---|
773 | sortOldestFirst(&e1, &e2, &e3); |
---|
774 | e1->relink(oldBrother, grandFather); |
---|
775 | thisFather->linkAllEdges(e2, e3, e4); |
---|
776 | } |
---|
777 | else { // simple independent move |
---|
778 | thisFather->unlinkAllEdges(&e1, &e2, &e3); |
---|
779 | AP_tree_edge *e4 = newBrother->edgeTo(newBrothersFather)->unlink(); |
---|
780 | |
---|
781 | AP_tree::moveNextTo(newBrother, rel_pos); |
---|
782 | |
---|
783 | sortOldestFirst(&e1, &e2, &e3); |
---|
784 | e1->relink(oldBrother, grandFather); |
---|
785 | thisFather->linkAllEdges(e2, e3, e4); |
---|
786 | } |
---|
787 | } |
---|
788 | } |
---|
789 | |
---|
790 | ASSERT_VALID_TREE(this); |
---|
791 | ASSERT_VALID_TREE(rootNode()); |
---|
792 | |
---|
793 | ap_assert(is_leftson()); |
---|
794 | ap_assert(get_brother() == newBrother); |
---|
795 | } |
---|
796 | |
---|
797 | void AP_tree_nlen::unhash_sequence() { |
---|
798 | /*! removes the parsimony sequence from an inner node |
---|
799 | * (has no effect for leafs) |
---|
800 | */ |
---|
801 | |
---|
802 | AP_sequence *sequence = get_seq(); |
---|
803 | if (sequence && !is_leaf()) sequence->forget_sequence(); |
---|
804 | } |
---|
805 | |
---|
806 | bool AP_tree_nlen::acceptCurrentState(Level frame_level) { |
---|
807 | // returns |
---|
808 | // - true if the top state has been removed |
---|
809 | // - false if the top state was kept/extended for possible revert at lower frame_level |
---|
810 | |
---|
811 | if (remembered_for_frame != frame_level) { |
---|
812 | ap_assert(0); // internal control number check failed |
---|
813 | return false; |
---|
814 | } |
---|
815 | |
---|
816 | NodeState *state = states.pop(); |
---|
817 | bool removed = true; |
---|
818 | |
---|
819 | Level next_frame_level = frame_level-1; |
---|
820 | Level stored_frame_level = state->frameNr; |
---|
821 | |
---|
822 | if (!next_frame_level) { // accept() called at top-level |
---|
823 | delete state; |
---|
824 | } |
---|
825 | else if (stored_frame_level == next_frame_level) { |
---|
826 | // node already is buffered for next_frame_level |
---|
827 | |
---|
828 | // if the currently accepted state->mode is not completely covered by previous state->mode |
---|
829 | // => a future revert() would only restore partially |
---|
830 | // To avoid that, move missing state information to previous NodeState |
---|
831 | { |
---|
832 | NodeState *prev_state = states.top(); |
---|
833 | AP_STACK_MODE prev_mode = prev_state->mode; |
---|
834 | AP_STACK_MODE common = AP_STACK_MODE(prev_mode & state->mode); |
---|
835 | |
---|
836 | if (common != state->mode) { |
---|
837 | AP_STACK_MODE missing = AP_STACK_MODE(state->mode & ~common); // previous is missing this state information |
---|
838 | |
---|
839 | ap_assert((prev_mode&missing) == NOTHING); |
---|
840 | state->move_info_to(*prev_state, missing); |
---|
841 | } |
---|
842 | } |
---|
843 | |
---|
844 | delete state; |
---|
845 | } |
---|
846 | else { |
---|
847 | // keep state for future revert |
---|
848 | states.push(state); |
---|
849 | removed = false; |
---|
850 | } |
---|
851 | remembered_for_frame = next_frame_level; |
---|
852 | |
---|
853 | return removed; |
---|
854 | } |
---|
855 | |
---|
856 | |
---|
857 | bool AP_tree_nlen::rememberState(AP_STACK_MODE mode, Level frame_level) { |
---|
858 | // according to mode |
---|
859 | // tree_structure or sequence is buffered in the node |
---|
860 | |
---|
861 | NodeState *store; |
---|
862 | bool ret; |
---|
863 | |
---|
864 | if (is_leaf() && !(STRUCTURE & mode)) return false; // tips push only structure |
---|
865 | |
---|
866 | if (remembered_for_frame == frame_level) { // node already has a push (at current frame_level) |
---|
867 | NodeState *is_stored = states.top(); |
---|
868 | |
---|
869 | if (0 == (mode & ~is_stored->mode)) { // already buffered |
---|
870 | AP_sequence *sequence = get_seq(); |
---|
871 | if (sequence && (mode & SEQUENCE)) sequence->forget_sequence(); |
---|
872 | return false; |
---|
873 | } |
---|
874 | store = is_stored; |
---|
875 | ret = false; |
---|
876 | } |
---|
877 | else { // first push for this node (in current stack frame) |
---|
878 | store = new NodeState(remembered_for_frame); |
---|
879 | states.push(store); |
---|
880 | |
---|
881 | remembered_for_frame = frame_level; |
---|
882 | ret = true; |
---|
883 | } |
---|
884 | |
---|
885 | if ((mode & (STRUCTURE|SEQUENCE)) && !(store->mode & (STRUCTURE|SEQUENCE))) { |
---|
886 | store->mark_sum = gr.mark_sum; |
---|
887 | } |
---|
888 | if ((mode & STRUCTURE) && !(store->mode & STRUCTURE)) { |
---|
889 | store->father = get_father(); |
---|
890 | store->leftson = get_leftson(); |
---|
891 | store->rightson = get_rightson(); |
---|
892 | store->leftlen = leftlen; |
---|
893 | store->rightlen = rightlen; |
---|
894 | store->root = get_tree_root(); |
---|
895 | store->gb_node = gb_node; |
---|
896 | store->keelState = keeledStateInfo(); |
---|
897 | |
---|
898 | for (int e=0; e<3; e++) { |
---|
899 | store->edge[e] = edge[e]; |
---|
900 | store->edgeIndex[e] = index[e]; |
---|
901 | } |
---|
902 | } |
---|
903 | |
---|
904 | if (mode & SEQUENCE) { |
---|
905 | ap_assert(!is_leaf()); // only allowed to push SEQUENCE for inner nodes |
---|
906 | if (!(store->mode & SEQUENCE)) { |
---|
907 | AP_sequence *sequence = take_seq(); |
---|
908 | store->sequence = sequence; |
---|
909 | store->mutations = mutations; |
---|
910 | mutations = 0; |
---|
911 | } |
---|
912 | else { |
---|
913 | AP_sequence *sequence = get_seq(); |
---|
914 | if (sequence) sequence->forget_sequence(); |
---|
915 | } |
---|
916 | } |
---|
917 | |
---|
918 | store->mode = (AP_STACK_MODE)(store->mode|mode); |
---|
919 | |
---|
920 | return ret; |
---|
921 | } |
---|
922 | |
---|
923 | void NodeState::move_info_to(NodeState& target, AP_STACK_MODE what) { |
---|
924 | // rescue partial NodeState information |
---|
925 | |
---|
926 | ap_assert((mode&what) == what); // this has to contain 'what' is moved |
---|
927 | ap_assert((target.mode&what) == NOTHING); // target shall not already contain 'what' is moved |
---|
928 | |
---|
929 | if ((what & (STRUCTURE|SEQUENCE)) && !(target.mode & (STRUCTURE|SEQUENCE))) { |
---|
930 | target.mark_sum = mark_sum; |
---|
931 | } |
---|
932 | if (what & STRUCTURE) { |
---|
933 | target.father = father; |
---|
934 | target.leftson = leftson; |
---|
935 | target.rightson = rightson; |
---|
936 | target.leftlen = leftlen; |
---|
937 | target.rightlen = rightlen; |
---|
938 | target.root = root; |
---|
939 | target.gb_node = gb_node; |
---|
940 | target.keelState = keelState; |
---|
941 | |
---|
942 | for (int e=0; e<3; e++) { |
---|
943 | target.edge[e] = edge[e]; |
---|
944 | target.edgeIndex[e] = edgeIndex[e]; |
---|
945 | } |
---|
946 | } |
---|
947 | if (what & SEQUENCE) { |
---|
948 | target.sequence = sequence; |
---|
949 | target.mutations = mutations; |
---|
950 | sequence = NULp; |
---|
951 | |
---|
952 | } |
---|
953 | // nothing needs to be done for ROOT |
---|
954 | target.mode = AP_STACK_MODE(target.mode|what); |
---|
955 | } |
---|
956 | |
---|
957 | void AP_tree_nlen::restore_structure(const NodeState& state) { |
---|
958 | father = state.father; |
---|
959 | leftson = state.leftson; |
---|
960 | rightson = state.rightson; |
---|
961 | leftlen = state.leftlen; |
---|
962 | rightlen = state.rightlen; |
---|
963 | set_tree_root(state.root); |
---|
964 | gb_node = state.gb_node; |
---|
965 | setKeeledState(state.keelState); |
---|
966 | |
---|
967 | gr.mark_sum = state.mark_sum; |
---|
968 | |
---|
969 | for (int e=0; e<3; e++) { |
---|
970 | edge[e] = state.edge[e]; |
---|
971 | index[e] = state.edgeIndex[e]; |
---|
972 | if (edge[e]) { |
---|
973 | edge[e]->index[index[e]] = e; |
---|
974 | edge[e]->node[index[e]] = this; |
---|
975 | } |
---|
976 | } |
---|
977 | } |
---|
978 | void AP_tree_nlen::restore_sequence(NodeState& state) { |
---|
979 | replace_seq(state.sequence); |
---|
980 | state.sequence = NULp; |
---|
981 | mutations = state.mutations; |
---|
982 | gr.mark_sum = state.mark_sum; |
---|
983 | } |
---|
984 | void AP_tree_nlen::restore_sequence_nondestructive(const NodeState& state) { |
---|
985 | replace_seq(state.sequence ? state.sequence->dup() : NULp); |
---|
986 | mutations = state.mutations; |
---|
987 | } |
---|
988 | void AP_tree_nlen::restore_root(const NodeState& state) { |
---|
989 | state.root->change_root(state.root->get_root_node(), this); |
---|
990 | } |
---|
991 | |
---|
992 | void AP_tree_nlen::restore(NodeState& state) { |
---|
993 | //! restore 'this' from NodeState (cheap; only call once for each 'state') |
---|
994 | AP_STACK_MODE mode = state.mode; |
---|
995 | if (mode&STRUCTURE) restore_structure(state); |
---|
996 | if (mode&SEQUENCE) restore_sequence(state); |
---|
997 | if (ROOT==mode) restore_root(state); |
---|
998 | } |
---|
999 | void AP_tree_nlen::restore_nondestructive(const NodeState& state) { |
---|
1000 | //! restore 'this' from NodeState (expensive; may be called multiple times for each 'state') |
---|
1001 | AP_STACK_MODE mode = state.mode; |
---|
1002 | if (mode&STRUCTURE) restore_structure(state); |
---|
1003 | if (mode&SEQUENCE) restore_sequence_nondestructive(state); |
---|
1004 | if (ROOT==mode) restore_root(state); |
---|
1005 | } |
---|
1006 | |
---|
1007 | void AP_tree_nlen::revertToPreviousState(Level IF_ASSERTION_USED(curr_frameLevel), bool& IF_ASSERTION_USED(rootPopped)) { // pop old tree costs |
---|
1008 | ap_assert(remembered_for_frame == curr_frameLevel); // error in node stack (node wasnt remembered in current frame!) |
---|
1009 | |
---|
1010 | NodeState *previous = states.pop(); |
---|
1011 | #if defined(ASSERTION_USED) |
---|
1012 | if (previous->mode == ROOT) { // @@@ remove test code later |
---|
1013 | ap_assert(!rootPopped); // only allowed once |
---|
1014 | rootPopped = true; |
---|
1015 | } |
---|
1016 | #endif |
---|
1017 | restore(*previous); |
---|
1018 | |
---|
1019 | remembered_for_frame = previous->frameNr; |
---|
1020 | delete previous; |
---|
1021 | } |
---|
1022 | |
---|
1023 | void AP_tree_nlen::parsimony_rec(char *mutPerSite) { |
---|
1024 | AP_combinableSeq *sequence = get_seq(); |
---|
1025 | |
---|
1026 | if (is_leaf()) { |
---|
1027 | ap_assert(sequence); // tree w/o aliview? |
---|
1028 | sequence->ensure_sequence_loaded(); |
---|
1029 | } |
---|
1030 | else { |
---|
1031 | if (!sequence) { |
---|
1032 | sequence = set_seq(get_tree_root()->get_seqTemplate()->dup()); |
---|
1033 | ap_assert(sequence); |
---|
1034 | } |
---|
1035 | |
---|
1036 | if (!sequence->hasSequence()) { |
---|
1037 | AP_tree_nlen *lson = get_leftson(); |
---|
1038 | AP_tree_nlen *rson = get_rightson(); |
---|
1039 | |
---|
1040 | ap_assert(lson); |
---|
1041 | ap_assert(rson); |
---|
1042 | |
---|
1043 | lson->parsimony_rec(mutPerSite); |
---|
1044 | rson->parsimony_rec(mutPerSite); |
---|
1045 | |
---|
1046 | AP_combinableSeq *lseq = lson->get_seq(); |
---|
1047 | AP_combinableSeq *rseq = rson->get_seq(); |
---|
1048 | |
---|
1049 | ap_assert(lseq); |
---|
1050 | ap_assert(rseq); |
---|
1051 | |
---|
1052 | Mutations mutations_for_combine = sequence->combine_seq(lseq, rseq, mutPerSite); |
---|
1053 | mutations = lson->mutations + rson->mutations + mutations_for_combine; |
---|
1054 | } |
---|
1055 | } |
---|
1056 | } |
---|
1057 | |
---|
1058 | Mutations AP_tree_nlen::costs(char *mutPerSite) { |
---|
1059 | // returns costs of a tree ( = number of mutations) |
---|
1060 | |
---|
1061 | ap_assert(get_tree_root()->get_seqTemplate()); // forgot to set_seqTemplate() ? (previously returned 0.0 in this case) |
---|
1062 | ap_assert(sequence_state_valid()); |
---|
1063 | |
---|
1064 | parsimony_rec(mutPerSite); |
---|
1065 | return mutations; |
---|
1066 | } |
---|
1067 | |
---|
1068 | Mutations AP_tree_nlen::nn_interchange_rec(EdgeSpec whichEdges, AP_BL_MODE mode) { |
---|
1069 | if (!father) { |
---|
1070 | return rootEdge()->nni_rec(whichEdges, mode, NULp, true); |
---|
1071 | } |
---|
1072 | if (!father->father) { |
---|
1073 | AP_tree_edge *e = rootEdge(); |
---|
1074 | return e->nni_rec(whichEdges, mode, e->otherNode(this), false); |
---|
1075 | } |
---|
1076 | return edgeTo(get_father())->nni_rec(whichEdges, mode, get_father(), false); |
---|
1077 | } |
---|
1078 | |
---|
1079 | CONSTEXPR_INLINE AP_TREE_SIDE idx2side(const int idx) { |
---|
1080 | return idx&1 ? AP_RIGHT : AP_LEFT; |
---|
1081 | } |
---|
1082 | |
---|
1083 | bool AP_tree_edge::kl_rec(const KL_params& KL, const int rec_depth, Mutations pars_best) { |
---|
1084 | /*! does K.L. recursion |
---|
1085 | * @param KL parameters defining how recursion is done |
---|
1086 | * @param rec_depth current recursion depth (starts with 0) |
---|
1087 | * @param pars_best current parsimony value of topology |
---|
1088 | */ |
---|
1089 | |
---|
1090 | ap_assert(!is_leaf_edge()); |
---|
1091 | if (rec_depth >= KL.max_rec_depth) return false; |
---|
1092 | |
---|
1093 | ap_assert(implicated(rec_depth>0, kl_visited)); |
---|
1094 | |
---|
1095 | int order[8]; |
---|
1096 | AP_tree_edge *descend[8]; |
---|
1097 | |
---|
1098 | { |
---|
1099 | if (rec_depth == 0) { |
---|
1100 | descend[0] = this; |
---|
1101 | descend[2] = NULp; |
---|
1102 | descend[4] = NULp; |
---|
1103 | descend[6] = NULp; |
---|
1104 | } |
---|
1105 | else { |
---|
1106 | AP_tree_nlen *son = sonNode(); |
---|
1107 | AP_tree_nlen *notSon = otherNode(son); // brother or father |
---|
1108 | |
---|
1109 | descend[0] = notSon->nextEdge(this); |
---|
1110 | descend[2] = notSon->nextEdge(descend[0]); |
---|
1111 | |
---|
1112 | ap_assert(descend[2] != this); |
---|
1113 | |
---|
1114 | descend[4] = son->nextEdge(this); |
---|
1115 | descend[6] = son->nextEdge(descend[4]); |
---|
1116 | |
---|
1117 | ap_assert(descend[6] != this); |
---|
1118 | } |
---|
1119 | |
---|
1120 | descend[1] = descend[0]; |
---|
1121 | descend[3] = descend[2]; |
---|
1122 | descend[5] = descend[4]; |
---|
1123 | descend[7] = descend[6]; |
---|
1124 | } |
---|
1125 | |
---|
1126 | // --------------------------------- |
---|
1127 | // detect parsimony values |
---|
1128 | |
---|
1129 | ap_main->remember(); // @@@ i think this is unneeded. better reset root after all done in caller |
---|
1130 | set_root(); |
---|
1131 | rootNode()->costs(); |
---|
1132 | |
---|
1133 | int rec_width_dynamic = 0; |
---|
1134 | int visited_subtrees = 0; |
---|
1135 | int better_subtrees = 0; |
---|
1136 | |
---|
1137 | Mutations pars[8]; // eight parsimony values (produced by 2*swap_assymetric at each adjacent edge) |
---|
1138 | |
---|
1139 | #if defined(ASSERTION_USED) |
---|
1140 | int forbidden_descends = 0; |
---|
1141 | #endif |
---|
1142 | { |
---|
1143 | AP_FLOAT schwellwert = KL.thresFunctor.calculate(rec_depth); // @@@ skip if not needed |
---|
1144 | for (int i = 0; i < 8; i++) { |
---|
1145 | order[i] = i; |
---|
1146 | AP_tree_edge * const subedge = descend[i]; |
---|
1147 | |
---|
1148 | if (subedge && |
---|
1149 | !subedge->is_leaf_edge() && |
---|
1150 | !subedge->kl_visited && |
---|
1151 | (!KL.stopAtFoldedGroups || !subedge->next_to_folded_group()) |
---|
1152 | ) |
---|
1153 | { |
---|
1154 | ap_main->remember(); |
---|
1155 | subedge->sonNode()->swap_assymetric(idx2side(i)); |
---|
1156 | pars[i] = rootNode()->costs(); |
---|
1157 | if (pars[i] < pars_best) { |
---|
1158 | better_subtrees++; |
---|
1159 | pars_best = pars[i]; // @@@ do not overwrite yet; store and overwrite when done with this loop |
---|
1160 | } |
---|
1161 | if (pars[i] < schwellwert) { |
---|
1162 | rec_width_dynamic++; |
---|
1163 | } |
---|
1164 | ap_main->revert(); |
---|
1165 | visited_subtrees++; |
---|
1166 | } |
---|
1167 | else { |
---|
1168 | pars[i] = -1; |
---|
1169 | #if defined(ASSERTION_USED) |
---|
1170 | if (subedge && subedge->kl_visited) { |
---|
1171 | forbidden_descends++; |
---|
1172 | } |
---|
1173 | #endif |
---|
1174 | } |
---|
1175 | } |
---|
1176 | } |
---|
1177 | |
---|
1178 | // bubblesort pars[]+order[], such that pars[0] contains best (=smallest) parsimony value |
---|
1179 | { |
---|
1180 | for (int i=7, t=0; t<i; t++) { // move negative (=unused) parsimony values to the end |
---|
1181 | if (pars[t] <0) { |
---|
1182 | pars[t] = pars[i]; |
---|
1183 | order[t] = i; |
---|
1184 | t--; |
---|
1185 | i--; |
---|
1186 | } |
---|
1187 | } |
---|
1188 | |
---|
1189 | for (int t = visited_subtrees - 1; t > 0; t--) { |
---|
1190 | bool bubbled = false; |
---|
1191 | for (int i = 0; i < t; i++) { |
---|
1192 | if (pars[i] > pars[i+1]) { |
---|
1193 | std::swap(order[i], order[i+1]); |
---|
1194 | std::swap(pars[i], pars[i+1]); |
---|
1195 | bubbled = true; |
---|
1196 | } |
---|
1197 | } |
---|
1198 | if (!bubbled) break; |
---|
1199 | } |
---|
1200 | } |
---|
1201 | |
---|
1202 | #if defined(ASSERTION_USED) |
---|
1203 | // rec_depth == 0 (called with start-node) |
---|
1204 | // rec_depth == 1 (called twice with start-node (swap_assymetric AP_LEFT + AP_RIGHT)) |
---|
1205 | // rec_depth == 2 (called twice with each adjacent node -> 8 calls) |
---|
1206 | // rec_depth == 3 (called twice with each adjacent node, but not with those were recursion came from -> 6 calls) |
---|
1207 | |
---|
1208 | if (!is_root_edge()) { |
---|
1209 | switch (rec_depth) { |
---|
1210 | case 0: |
---|
1211 | ap_assert(visited_subtrees == 2); |
---|
1212 | ap_assert(forbidden_descends == 0); |
---|
1213 | break; |
---|
1214 | case 1: |
---|
1215 | ap_assert(visited_subtrees <= 8); |
---|
1216 | ap_assert(forbidden_descends == 0); |
---|
1217 | break; |
---|
1218 | default: |
---|
1219 | ap_assert(visited_subtrees <= 6); |
---|
1220 | ap_assert(forbidden_descends == 2); |
---|
1221 | break; |
---|
1222 | } |
---|
1223 | } |
---|
1224 | else { // at root |
---|
1225 | switch (rec_depth) { |
---|
1226 | case 0: |
---|
1227 | ap_assert(visited_subtrees <= 2); |
---|
1228 | break; |
---|
1229 | case 1: |
---|
1230 | ap_assert(visited_subtrees <= 8); |
---|
1231 | ap_assert(forbidden_descends <= 2); // in case of subtree-optimization, 2 descends may be forbidden |
---|
1232 | break; |
---|
1233 | default: |
---|
1234 | ap_assert(visited_subtrees <= 8); |
---|
1235 | break; |
---|
1236 | } |
---|
1237 | } |
---|
1238 | #endif |
---|
1239 | |
---|
1240 | int rec_width; |
---|
1241 | if (better_subtrees) { |
---|
1242 | rec_width = better_subtrees; // @@@ wrong if static/dynamic reduction would allow more |
---|
1243 | |
---|
1244 | // @@@ IMO the whole concept of incrementing depth when a better topology was found has no positive effect |
---|
1245 | // (the better topology is kept anyway and next recursive KL will do a full optimization starting from that edge as well) |
---|
1246 | |
---|
1247 | } |
---|
1248 | else { |
---|
1249 | rec_width = visited_subtrees; |
---|
1250 | if (KL.rec_type & AP_STATIC) { |
---|
1251 | int rec_width_static = (rec_depth < CUSTOM_DEPTHS) ? KL.rec_width[rec_depth] : 1; |
---|
1252 | rec_width = std::min(rec_width, rec_width_static); |
---|
1253 | } |
---|
1254 | if (KL.rec_type & AP_DYNAMIK) { |
---|
1255 | rec_width = std::min(rec_width, rec_width_dynamic); |
---|
1256 | } |
---|
1257 | } |
---|
1258 | ap_assert(rec_width<=visited_subtrees); |
---|
1259 | |
---|
1260 | bool found_better = false; |
---|
1261 | for (int i=0; i<rec_width && !found_better; i++) { |
---|
1262 | AP_tree_edge * const subedge = descend[order[i]]; |
---|
1263 | |
---|
1264 | ap_main->remember(); |
---|
1265 | subedge->kl_visited = true; // mark |
---|
1266 | subedge->sonNode()->swap_assymetric(idx2side(order[i])); // swap |
---|
1267 | rootNode()->parsimony_rec(); |
---|
1268 | |
---|
1269 | if (better_subtrees) { |
---|
1270 | KL_params modified = KL; |
---|
1271 | modified.rec_type = AP_STATIC; |
---|
1272 | modified.max_rec_depth += KL.inc_rec_depth; |
---|
1273 | |
---|
1274 | subedge->kl_rec(modified, rec_depth+1, pars_best); |
---|
1275 | found_better = true; |
---|
1276 | } |
---|
1277 | else { |
---|
1278 | found_better = subedge->kl_rec(KL, rec_depth+1, pars_best); |
---|
1279 | } |
---|
1280 | |
---|
1281 | subedge->kl_visited = false; // unmark |
---|
1282 | ap_main->accept_if(found_better); // revert |
---|
1283 | } |
---|
1284 | |
---|
1285 | ap_main->accept_if(found_better); // undo set_root otherwise |
---|
1286 | return found_better; |
---|
1287 | } |
---|
1288 | |
---|
1289 | void AP_tree_nlen::exchange(AP_tree_nlen *other) { |
---|
1290 | // exchange 'this' with other |
---|
1291 | // 'this' has to be in tree; other has to be a "single node" |
---|
1292 | // |
---|
1293 | // Used by quick-add. |
---|
1294 | |
---|
1295 | AP_tree_root *root = get_tree_root(); |
---|
1296 | ap_assert(root); |
---|
1297 | ap_assert(!other->get_tree_root()); |
---|
1298 | |
---|
1299 | ASSERT_VALID_TREE(rootNode()); |
---|
1300 | ASSERT_VALID_TREE(other); |
---|
1301 | |
---|
1302 | ap_main->push_node(this, STRUCTURE); |
---|
1303 | ap_main->push_node(other, STRUCTURE); |
---|
1304 | ap_main->push_node(get_father(), BOTH); |
---|
1305 | push_all_upnode_sequences(get_father()); |
---|
1306 | |
---|
1307 | AP_tree_edge *myEdge = nextEdge(NULp); |
---|
1308 | AP_tree_nlen *connected = myEdge->otherNode(this); |
---|
1309 | myEdge->unlink(); |
---|
1310 | |
---|
1311 | if (is_leftson()) { |
---|
1312 | father->leftson = other; |
---|
1313 | } |
---|
1314 | else { |
---|
1315 | father->rightson = other; |
---|
1316 | } |
---|
1317 | other->father = father; |
---|
1318 | father = NULp; |
---|
1319 | |
---|
1320 | other->set_tree_root(root); |
---|
1321 | set_tree_root(NULp); |
---|
1322 | |
---|
1323 | myEdge->relink(other, connected); |
---|
1324 | |
---|
1325 | ASSERT_VALID_TREE(rootNode()); |
---|
1326 | ASSERT_VALID_TREE(this); |
---|
1327 | } |
---|
1328 | |
---|
1329 | const char* AP_tree_nlen::sortByName() { |
---|
1330 | if (name) return name; // leafs |
---|
1331 | |
---|
1332 | const char *n1 = get_leftson()->sortByName(); |
---|
1333 | const char *n2 = get_rightson()->sortByName(); |
---|
1334 | |
---|
1335 | if (strcmp(n1, n2)<0) return n1; |
---|
1336 | |
---|
1337 | AP_tree::swap_sons(); |
---|
1338 | |
---|
1339 | return n2; |
---|
1340 | } |
---|
1341 | |
---|
1342 | const char *AP_tree_nlen::fullname() const { |
---|
1343 | if (!name) { |
---|
1344 | static char *buffer; |
---|
1345 | char *lName = ARB_strdup(get_leftson()->fullname()); |
---|
1346 | char *rName = ARB_strdup(get_rightson()->fullname()); |
---|
1347 | int len = strlen(lName)+strlen(rName)+4; |
---|
1348 | |
---|
1349 | if (buffer) free(buffer); |
---|
1350 | |
---|
1351 | ARB_alloc(buffer, len); |
---|
1352 | |
---|
1353 | strcpy(buffer, "["); |
---|
1354 | strcat(buffer, lName); |
---|
1355 | strcat(buffer, ","); |
---|
1356 | strcat(buffer, rName); |
---|
1357 | strcat(buffer, "]"); |
---|
1358 | |
---|
1359 | free(lName); |
---|
1360 | free(rName); |
---|
1361 | |
---|
1362 | return buffer; |
---|
1363 | } |
---|
1364 | |
---|
1365 | return name; |
---|
1366 | } |
---|
1367 | |
---|
1368 | |
---|
1369 | char* AP_tree_nlen::getSequenceCopy() { |
---|
1370 | costs(); |
---|
1371 | |
---|
1372 | AP_sequence_parsimony *pseq = DOWNCAST(AP_sequence_parsimony*, get_seq()); |
---|
1373 | ap_assert(pseq->hasSequence()); |
---|
1374 | |
---|
1375 | size_t len = pseq->get_sequence_length(); |
---|
1376 | char *s = new char[len]; |
---|
1377 | memcpy(s, pseq->get_sequence(), len); |
---|
1378 | |
---|
1379 | return s; |
---|
1380 | } |
---|
1381 | |
---|
1382 | |
---|
1383 | GB_ERROR AP_pars_root::saveToDB() { |
---|
1384 | has_been_saved = true; |
---|
1385 | return AP_tree_root::saveToDB(); |
---|
1386 | } |
---|
1387 | |
---|