1 | // ============================================================= // |
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2 | // // |
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3 | // File : arb_read_tree.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // ============================================================= // |
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10 | |
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11 | #include <TreeRead.h> |
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12 | #include <TreeNode.h> |
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13 | #include <arb_strbuf.h> |
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14 | #include <arb_defs.h> |
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15 | #include <ctime> |
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16 | |
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17 | |
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18 | static void add_bootstrap(TreeNode *node, double hundred) { |
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19 | // add_bootstrap interprets the length of the branches as bootstrap value |
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20 | // (this is needed by Phylip DNAPARS/PROTPARS with bootstrapping) |
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21 | // |
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22 | // 'hundred' specifies which value represents 100% |
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23 | |
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24 | if (node->is_leaf()) { |
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25 | node->remove_remark(); |
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26 | return; |
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27 | } |
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28 | |
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29 | node->leftlen /= hundred; |
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30 | node->rightlen /= hundred; |
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31 | |
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32 | double left_bs = node->leftlen * 100.0; |
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33 | double right_bs = node->rightlen * 100.0; |
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34 | |
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35 | #if defined(DEBUG) && 0 |
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36 | fprintf(stderr, "node->leftlen = %f left_bs = %f\n", node->leftlen, left_bs); |
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37 | fprintf(stderr, "node->rightlen = %f right_bs = %f\n", node->rightlen, right_bs); |
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38 | #endif // DEBUG |
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39 | |
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40 | node->leftson ->set_bootstrap(left_bs); |
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41 | node->rightson->set_bootstrap(right_bs); |
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42 | |
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43 | node->leftlen = DEFAULT_BRANCH_LENGTH; // reset branchlengths |
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44 | node->rightlen = DEFAULT_BRANCH_LENGTH; |
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45 | |
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46 | add_bootstrap(node->get_leftson(), hundred); |
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47 | add_bootstrap(node->get_rightson(), hundred); |
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48 | } |
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49 | |
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50 | static GBDATA *gb_msg_main = NULp; |
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51 | |
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52 | static void show_message(const char *msg) { |
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53 | if (gb_msg_main) { |
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54 | GBT_message(gb_msg_main, msg); |
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55 | } |
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56 | else { |
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57 | fflush(stdout); |
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58 | printf("arb_read_tree: %s\n", msg); |
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59 | } |
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60 | } |
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61 | static void show_error(GB_ERROR error) { |
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62 | if (error) show_message(GBS_global_string("Error running arb_read_tree (%s)", error)); |
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63 | } |
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64 | |
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65 | static void error_with_usage(GB_ERROR error) { |
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66 | fputs("Usage: arb_read_tree [options] tree_name treefile [comment]\n" |
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67 | "Available options:\n" |
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68 | " -db database savename specify database and savename (default is 'running ARB')\n" |
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69 | " -scale factor scale branchlengths by 'factor'\n" |
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70 | " -consense numberOfTrees reinterpret branchlengths as consense values\n" |
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71 | " -commentFromFile file read tree comment from 'file'\n" |
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72 | , stdout); |
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73 | |
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74 | show_error(error); |
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75 | } |
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76 | |
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77 | struct parameters { |
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78 | const char *dbname; |
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79 | const char *dbsavename; |
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80 | const char *tree_name; |
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81 | const char *treefilename; |
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82 | const char *comment; |
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83 | const char *commentFile; |
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84 | |
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85 | bool scale; |
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86 | double scale_factor; |
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87 | |
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88 | bool consense; |
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89 | int calculated_trees; |
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90 | |
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91 | parameters() |
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92 | : dbname(":"), |
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93 | dbsavename(NULp), |
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94 | tree_name(NULp), |
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95 | treefilename(NULp), |
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96 | comment(NULp), |
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97 | commentFile(NULp), |
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98 | scale(false), |
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99 | scale_factor(0.0), |
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100 | consense(false), |
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101 | calculated_trees(0) |
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102 | {} |
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103 | |
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104 | #define SHIFT_ARGS(off) do { argc -= off; argv += off; } while (0) |
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105 | #define SHIFT_NONSWITCHES(off) do { nonSwitches -= off; nonSwitch += off; } while (0) |
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106 | |
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107 | GB_ERROR scan(int argc, char **argv) { |
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108 | GB_ERROR error = NULp; |
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109 | |
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110 | const char *nonSwitch_buf[20]; |
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111 | const char **nonSwitch = nonSwitch_buf; |
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112 | int nonSwitches = 0; |
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113 | |
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114 | SHIFT_ARGS(1); // position onto first argument |
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115 | |
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116 | while (argc>0 && !error) { |
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117 | if (strcmp("-scale", argv[0]) == 0) { |
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118 | scale = true; |
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119 | if (argc<2) error = "-scale expects a 2nd argument (scale factor)"; |
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120 | else { |
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121 | scale_factor = atof(argv[1]); |
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122 | SHIFT_ARGS(2); |
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123 | } |
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124 | } |
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125 | else if (strcmp("-consense", argv[0]) == 0) { |
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126 | consense = true; |
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127 | if (argc<2) error = "-consense expects a 2nd argument (number of trees)"; |
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128 | else { |
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129 | calculated_trees = atoi(argv[1]); |
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130 | if (calculated_trees < 1) { |
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131 | error = GBS_global_string("Illegal # of trees (%i) for -consense (minimum is 1)", calculated_trees); |
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132 | } |
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133 | else SHIFT_ARGS(2); |
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134 | } |
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135 | } |
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136 | else if (strcmp("-commentFromFile", argv[0]) == 0) { |
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137 | if (argc<2) error = "-commentFromFile expects a 2nd argument (file containing comment)"; |
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138 | else { |
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139 | commentFile = argv[1]; |
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140 | SHIFT_ARGS(2); |
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141 | } |
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142 | } |
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143 | else if (strcmp("-db", argv[0]) == 0) { |
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144 | if (argc<3) error = "-db expects two arguments (database and savename)"; |
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145 | else { |
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146 | dbname = argv[1]; |
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147 | dbsavename = argv[2]; |
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148 | SHIFT_ARGS(3); |
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149 | } |
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150 | } |
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151 | else { |
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152 | nonSwitch[nonSwitches++] = argv[0]; |
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153 | SHIFT_ARGS(1); |
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154 | } |
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155 | } |
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156 | |
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157 | if (!error) { |
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158 | if (!nonSwitches) error = "Missing argument 'tree_name'"; |
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159 | else { |
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160 | tree_name = nonSwitch[0]; |
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161 | SHIFT_NONSWITCHES(1); |
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162 | } |
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163 | } |
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164 | if (!error) { |
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165 | if (!nonSwitches) error = "Missing argument 'treefile'"; |
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166 | else { |
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167 | treefilename = nonSwitch[0]; |
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168 | SHIFT_NONSWITCHES(1); |
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169 | } |
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170 | } |
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171 | if (!error && nonSwitches>0) { |
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172 | comment = nonSwitch[0]; |
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173 | SHIFT_NONSWITCHES(1); |
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174 | } |
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175 | |
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176 | if (!error && nonSwitches>0) { |
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177 | error = GBS_global_string("unexpected argument(s): %s ..", nonSwitch[0]); |
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178 | } |
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179 | return error; |
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180 | } |
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181 | }; |
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182 | |
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183 | int main(int argc, char **argv) { |
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184 | parameters param; |
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185 | GB_ERROR error = param.scan(argc, argv); |
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186 | |
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187 | GBDATA *gb_main = NULp; |
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188 | bool connectToArb = strcmp(param.dbname, ":") == 0; |
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189 | GB_shell shell; |
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190 | |
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191 | if (!error || connectToArb) { |
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192 | gb_main = GB_open(param.dbname, connectToArb ? "r" : "rw"); |
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193 | if (connectToArb) gb_msg_main = gb_main; |
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194 | } |
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195 | |
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196 | if (error) error_with_usage(error); |
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197 | else { |
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198 | if (!gb_main) { |
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199 | if (connectToArb) error = "you have to start an arbdb server first"; |
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200 | else error = GBS_global_string("can't open db (Reason: %s)", GB_await_error()); |
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201 | } |
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202 | |
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203 | char *comment_from_file = NULp; |
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204 | char *comment_from_treefile = NULp; |
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205 | TreeNode *tree = NULp; |
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206 | |
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207 | if (!error) { |
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208 | if (param.commentFile) { |
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209 | comment_from_file = GB_read_file(param.commentFile); |
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210 | if (!comment_from_file) { |
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211 | comment_from_file = GBS_global_string_copy("Error reading from comment-file '%s':\n%s", param.commentFile, GB_await_error()); |
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212 | } |
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213 | } |
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214 | |
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215 | show_message(GBS_global_string("Reading tree from '%s' ..", param.treefilename)); |
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216 | { |
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217 | char *warnings = NULp; |
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218 | bool allow_length_scaling = !param.consense && !param.scale; |
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219 | |
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220 | tree = TREE_load(param.treefilename, new SimpleRoot, &comment_from_treefile, allow_length_scaling, &warnings); |
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221 | if (!tree) { |
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222 | error = GB_await_error(); |
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223 | } |
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224 | else if (warnings) { |
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225 | show_message(warnings); |
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226 | free(warnings); |
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227 | } |
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228 | } |
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229 | } |
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230 | |
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231 | if (!error) { |
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232 | if (param.scale) { |
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233 | show_message(GBS_global_string("Scaling branch lengths by factor %f", param.scale_factor)); |
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234 | TREE_scale(tree, param.scale_factor, 1.0); |
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235 | } |
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236 | |
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237 | if (param.consense) { |
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238 | if (param.calculated_trees < 1) { |
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239 | error = "Minimum for -consense is 1"; |
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240 | } |
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241 | else { |
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242 | show_message(GBS_global_string("Reinterpreting branch lengths as consense values (%i trees)", param.calculated_trees)); |
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243 | add_bootstrap(tree, param.calculated_trees); |
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244 | } |
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245 | } |
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246 | } |
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247 | |
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248 | if (!error) { |
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249 | error = GB_begin_transaction(gb_main); |
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250 | |
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251 | if (!error && tree->is_leaf()) error = "Cannot load tree (need at least 2 leafs)"; |
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252 | if (!error) error = GBT_write_tree(gb_main, param.tree_name, tree); |
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253 | |
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254 | if (!error) { |
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255 | // write tree comment |
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256 | const char *comments[] = { |
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257 | param.comment, |
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258 | comment_from_file, |
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259 | comment_from_treefile, |
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260 | }; |
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261 | |
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262 | GBS_strstruct tree_remark(5000); |
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263 | bool empty = true; |
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264 | |
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265 | for (size_t c = 0; c<ARRAY_ELEMS(comments); c++) { |
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266 | if (comments[c]) { |
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267 | if (!empty) tree_remark.put('\n'); |
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268 | tree_remark.cat(comments[c]); |
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269 | empty = false; |
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270 | } |
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271 | } |
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272 | |
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273 | error = GBT_write_tree_remark(gb_main, param.tree_name, tree_remark.get_data()); |
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274 | } |
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275 | |
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276 | error = GB_end_transaction(gb_main, error); |
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277 | } |
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278 | |
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279 | if (error) show_error(error); |
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280 | else show_message(GBS_global_string("Tree %s read into the database", param.tree_name)); |
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281 | |
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282 | UNCOVERED(); |
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283 | destroy(tree); |
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284 | free(comment_from_file); |
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285 | free(comment_from_treefile); |
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286 | } |
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287 | |
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288 | if (gb_main) { |
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289 | if (!error && !connectToArb) { |
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290 | error = GB_save_as(gb_main, param.dbsavename, "a"); |
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291 | if (error) show_error(error); |
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292 | } |
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293 | GB_close(gb_main); |
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294 | } |
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295 | |
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296 | return error ? EXIT_FAILURE : EXIT_SUCCESS; |
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297 | } |
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