1 | #ifndef ARBDBT_H |
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2 | #define ARBDBT_H |
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3 | |
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4 | #ifndef ARBDB_H |
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5 | #include <arbdb.h> |
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6 | #endif |
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7 | #ifndef DOWNCAST_H |
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8 | #include <downcast.h> |
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9 | #endif |
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10 | |
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11 | #define gb_assert(cond) arb_assert(cond) |
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12 | |
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13 | #define GBT_SPECIES_INDEX_SIZE 10000L |
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14 | #define GBT_SAI_INDEX_SIZE 1000L |
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15 | |
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16 | #define GB_GROUP_NAME_MAX 256 |
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17 | |
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18 | #define DEFAULT_BRANCH_LENGTH 0.1 |
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19 | |
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20 | #define ERROR_CONTAINER_PATH "tmp/message/pending" |
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21 | |
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22 | #define REMOTE_BASE "tmp/remote/" |
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23 | #define MACRO_TRIGGER_CONTAINER REMOTE_BASE "trigger" |
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24 | #define MACRO_TRIGGER_TERMINATED MACRO_TRIGGER_CONTAINER "/terminated" |
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25 | #define MACRO_TRIGGER_RECORDING MACRO_TRIGGER_CONTAINER "/recording" |
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26 | #define MACRO_TRIGGER_ERROR MACRO_TRIGGER_CONTAINER "/error" |
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27 | #define MACRO_TRIGGER_TRACKED MACRO_TRIGGER_CONTAINER "/tracked" |
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28 | |
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29 | #define DEFINE_SIMPLE_TREE_RELATIVES_ACCESSORS(TreeType) \ |
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30 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_father, father); \ |
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31 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_leftson, leftson); \ |
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32 | DEFINE_DOWNCAST_ACCESSORS(TreeType, get_rightson, rightson) |
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33 | |
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34 | enum GBT_RemarkType { REMARK_NONE, REMARK_BOOTSTRAP, REMARK_OTHER }; |
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35 | |
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36 | struct GBT_TREE : virtual Noncopyable { |
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37 | bool is_leaf; |
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38 | GBT_TREE *father, *leftson, *rightson; |
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39 | GBT_LEN leftlen, rightlen; |
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40 | GBDATA *gb_node; |
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41 | char *name; |
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42 | |
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43 | private: |
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44 | char *remark_branch; // remark_branch normally contains some bootstrap value in format 'xx%' |
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45 | // if you store other info there, please make sure that this info does not start with digits!! |
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46 | // Otherwise the tree export routines will not work correctly! |
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47 | |
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48 | GBT_LEN& length_ref() { return is_leftson() ? father->leftlen : father->rightlen; } |
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49 | const GBT_LEN& length_ref() const { return const_cast<GBT_TREE*>(this)->length_ref(); } |
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50 | |
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51 | protected: |
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52 | GBT_TREE*& self_ref() { |
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53 | return is_leftson() ? father->leftson : father->rightson; |
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54 | } |
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55 | void unlink_from_father() { |
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56 | if (father) { |
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57 | self_ref() = NULL; |
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58 | father = NULL; |
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59 | } |
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60 | } |
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61 | |
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62 | char *swap_remark(char *new_remark) { |
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63 | char *result = remark_branch; |
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64 | remark_branch = new_remark; |
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65 | return result; |
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66 | } |
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67 | |
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68 | public: |
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69 | GBT_TREE() |
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70 | : is_leaf(false), |
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71 | father(NULL), leftson(NULL), rightson(NULL), |
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72 | leftlen(0.0), rightlen(0.0), |
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73 | gb_node(NULL), |
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74 | name(NULL), |
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75 | remark_branch(NULL) |
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76 | {} |
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77 | virtual ~GBT_TREE() { |
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78 | delete leftson; gb_assert(!leftson); |
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79 | delete rightson; gb_assert(!rightson); |
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80 | |
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81 | unlink_from_father(); |
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82 | |
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83 | free(name); |
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84 | free(remark_branch); |
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85 | } |
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86 | |
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87 | DEFINE_SIMPLE_TREE_RELATIVES_ACCESSORS(GBT_TREE); |
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88 | |
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89 | virtual void announce_tree_constructed() { |
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90 | // (has to be) called after tree has been constructed |
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91 | gb_assert(!father); // has to be called with root-node! |
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92 | } |
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93 | |
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94 | bool is_son_of(const GBT_TREE *Father) const { |
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95 | return father == Father && |
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96 | (father->leftson == this || father->rightson == this); |
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97 | } |
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98 | bool is_leftson() const { |
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99 | gb_assert(is_son_of(get_father())); // do only call with sons! |
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100 | return father->leftson == this; |
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101 | } |
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102 | bool is_rightson() const { |
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103 | gb_assert(is_son_of(get_father())); // do only call with sons! |
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104 | return father->rightson == this; |
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105 | } |
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106 | |
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107 | bool is_root_node() const { return !father; } |
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108 | |
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109 | bool is_inside(const GBT_TREE *subtree) const { |
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110 | return this == subtree || (father && get_father()->is_inside(subtree)); |
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111 | } |
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112 | bool is_anchestor_of(const GBT_TREE *descendant) const { |
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113 | return !is_leaf && descendant != this && descendant->is_inside(this); |
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114 | } |
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115 | const GBT_TREE *ancestor_common_with(const GBT_TREE *other) const; |
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116 | GBT_TREE *ancestor_common_with(GBT_TREE *other) { return const_cast<GBT_TREE*>(ancestor_common_with(other)); } |
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117 | |
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118 | GBT_TREE *fixDeletedSon(); |
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119 | |
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120 | GBT_LEN get_branchlength() const { return length_ref(); } |
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121 | void set_branchlength(GBT_LEN newlen) { |
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122 | gb_assert(!is_nan_or_inf(newlen)); |
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123 | length_ref() = newlen; |
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124 | } |
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125 | |
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126 | GBT_LEN get_branchlength_unrooted() const { |
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127 | //! like get_branchlength, but root-edge is treated correctly |
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128 | if (father->is_root_node()) { |
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129 | return father->leftlen+father->rightlen; |
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130 | } |
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131 | return get_branchlength(); |
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132 | } |
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133 | void set_branchlength_unrooted(GBT_LEN newlen) { |
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134 | //! like set_branchlength, but root-edge is treated correctly |
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135 | if (father->is_root_node()) { |
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136 | father->leftlen = father->rightlen = newlen/2; |
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137 | } |
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138 | else { |
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139 | set_branchlength(newlen); |
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140 | } |
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141 | } |
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142 | |
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143 | GBT_LEN sum_child_lengths() const; |
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144 | GBT_LEN root_distance() const { |
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145 | //! returns distance from node to root (including nodes own length) |
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146 | return father ? get_branchlength()+father->root_distance() : 0.0; |
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147 | } |
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148 | GBT_LEN intree_distance_to(const GBT_TREE *other) const { |
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149 | const GBT_TREE *ancestor = ancestor_common_with(other); |
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150 | return root_distance() + other->root_distance() - 2*ancestor->root_distance(); |
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151 | } |
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152 | |
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153 | enum bs100_mode { BS_UNDECIDED, BS_REMOVE, BS_INSERT }; |
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154 | bs100_mode toggle_bootstrap100(bs100_mode mode = BS_UNDECIDED); // toggle bootstrap '100%' <-> '' |
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155 | void remove_bootstrap(); // remove bootstrap values from subtree |
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156 | |
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157 | void reset_branchlengths(); // reset branchlengths of subtree to tree_defaults::LENGTH |
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158 | void scale_branchlengths(double factor); |
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159 | |
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160 | void bootstrap2branchlen(); // copy bootstraps to branchlengths |
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161 | void branchlen2bootstrap(); // copy branchlengths to bootstraps |
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162 | |
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163 | GBT_RemarkType parse_bootstrap(double& bootstrap) const { |
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164 | /*! analyse 'remark_branch' and return GBT_RemarkType. |
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165 | * If result is REMARK_BOOTSTRAP, 'bootstrap' contains the bootstrap value |
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166 | */ |
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167 | if (!remark_branch) return REMARK_NONE; |
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168 | |
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169 | const char *end = 0; |
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170 | bootstrap = strtod(remark_branch, (char**)&end); |
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171 | |
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172 | bool is_bootstrap = end[0] == '%' && end[1] == 0; |
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173 | return is_bootstrap ? REMARK_BOOTSTRAP : REMARK_OTHER; |
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174 | } |
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175 | const char *get_remark() const { return remark_branch; } |
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176 | void use_as_remark(char *newRemark) { freeset(remark_branch, newRemark); } |
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177 | void set_remark(const char *newRemark) { freedup(remark_branch, newRemark); } |
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178 | void set_bootstrap(double bootstrap) { use_as_remark(GBS_global_string_copy("%i%%", int(bootstrap+0.5))); } // @@@ protect against "100%"? |
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179 | void remove_remark() { use_as_remark(NULL); } |
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180 | }; |
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181 | |
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182 | struct TreeNodeFactory { |
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183 | virtual ~TreeNodeFactory() {} |
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184 | virtual GBT_TREE *makeNode() const = 0; |
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185 | }; |
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186 | |
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187 | struct GBT_TREE_NodeFactory : public TreeNodeFactory { |
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188 | GBT_TREE *makeNode() const OVERRIDE { return new GBT_TREE; } |
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189 | }; |
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190 | |
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191 | enum GBT_TreeRemoveType { |
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192 | GBT_REMOVE_MARKED = 1, |
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193 | GBT_REMOVE_UNMARKED = 2, |
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194 | GBT_REMOVE_ZOMBIES = 4, |
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195 | |
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196 | // please keep AWT_RemoveType in sync with GBT_TreeRemoveType |
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197 | // see ../SL/AP_TREE/AP_Tree.hxx@sync_GBT_TreeRemoveType__AWT_RemoveType |
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198 | |
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199 | // combined defines: |
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200 | GBT_KEEP_MARKED = GBT_REMOVE_UNMARKED|GBT_REMOVE_ZOMBIES, |
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201 | }; |
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202 | |
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203 | enum GBT_ORDER_MODE { |
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204 | GBT_BEHIND, |
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205 | GBT_INFRONTOF, |
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206 | }; |
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207 | |
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208 | enum TreeModel { ROOTED = 0, UNROOTED = 1 }; |
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209 | |
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210 | inline CONSTEXPR_RETURN int nodes_2_edges(int nodes) { return nodes-1; } |
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211 | inline CONSTEXPR_RETURN int edges_2_nodes(int nodes) { return nodes+1; } |
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212 | |
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213 | inline CONSTEXPR_RETURN int leafs_2_nodes(int leafs, TreeModel model) { |
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214 | //! calculate the number of nodes (leaf- plus inner-nodes) in a tree with 'leafs' leafs |
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215 | return 2*leafs-1-int(model); |
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216 | } |
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217 | inline CONSTEXPR_RETURN int nodes_2_leafs(int nodes, TreeModel model) { |
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218 | //! calculate the number of leafs in a tree with 'nodes' nodes |
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219 | return (nodes+1+int(model))/2; |
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220 | } |
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221 | inline CONSTEXPR_RETURN int leafs_2_edges(int leafs, TreeModel model) { |
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222 | //! calculate the number of edges in a tree with 'leafs' leafs |
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223 | return nodes_2_edges(leafs_2_nodes(leafs, model)); |
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224 | } |
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225 | inline CONSTEXPR_RETURN int edges_2_leafs(int edges, TreeModel model) { |
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226 | //! calculate the number of leafs in a tree with 'edges' edges |
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227 | return nodes_2_leafs(edges_2_nodes(edges), model); |
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228 | } |
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229 | |
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230 | #define GBT_TREE_AWAR_SRT " = :\n=:*=tree_*1:tree_tree_*=tree_*1" |
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231 | #define GBT_ALI_AWAR_SRT " =:\n=:*=ali_*1:ali_ali_*=ali_*1" |
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232 | |
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233 | typedef GB_ERROR (*species_callback)(GBDATA *gb_species, int *clientdata); |
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234 | |
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235 | #include <ad_t_prot.h> |
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236 | |
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237 | #define CHANGE_KEY_PATH "presets/key_data" |
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238 | #define CHANGE_KEY_PATH_GENES "presets/gene_key_data" |
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239 | #define CHANGE_KEY_PATH_EXPERIMENTS "presets/experiment_key_data" |
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240 | |
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241 | #define CHANGEKEY "key" |
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242 | #define CHANGEKEY_NAME "key_name" |
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243 | #define CHANGEKEY_TYPE "key_type" |
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244 | #define CHANGEKEY_HIDDEN "key_hidden" |
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245 | |
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246 | |
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247 | #else |
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248 | #error arbdbt.h included twice |
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249 | #endif |
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250 | |
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251 | |
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