1 | // =============================================================== // |
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2 | // // |
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3 | // File : PARS_main.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 "pars_main.hxx" |
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12 | #include "pars_dtree.hxx" |
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13 | #include "pars_klprops.hxx" |
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14 | #include "ap_tree_nlen.hxx" |
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15 | |
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16 | #include <aw_awars.hxx> |
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17 | #include <aw_preset.hxx> |
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18 | #include <aw_msg.hxx> |
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19 | |
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20 | #include <awt.hxx> |
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21 | #include <ColumnStat.hxx> |
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22 | #include <nds.h> |
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23 | #include <awt_sel_boxes.hxx> |
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24 | #include <awt_filter.hxx> |
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25 | #include <arb_progress.h> |
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26 | #include <aw_root.hxx> |
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27 | #include <aw_question.hxx> |
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28 | #include <gui_aliview.hxx> |
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29 | |
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30 | #include <TreeCallbacks.hxx> |
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31 | |
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32 | #include <list> |
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33 | |
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34 | #if defined(DEBUG) |
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35 | # define TESTMENU |
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36 | #endif // DEBUG |
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37 | |
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38 | using namespace std; |
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39 | |
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40 | AW_HEADER_MAIN |
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41 | |
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42 | #define AWAR_COLUMNSTAT_BASE "tmp/pars/colstat" |
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43 | #define AWAR_COLUMNSTAT_NAME AWAR_COLUMNSTAT_BASE "/name" |
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44 | |
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45 | GBDATA *GLOBAL_gb_main; // global gb_main for arb_pars |
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46 | |
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47 | #if defined(WARN_TODO) |
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48 | #warning make GLOBAL_PARS static! |
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49 | #endif |
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50 | PARS_global *GLOBAL_PARS; |
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51 | |
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52 | // waaah more globals :( |
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53 | AP_main *ap_main; |
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54 | |
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55 | static void pars_saveNrefresh_changed_tree(AWT_canvas *ntw) { |
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56 | ap_assert((AWT_TREE(ntw) == GLOBAL_PARS->tree)); |
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57 | |
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58 | GB_ERROR error = GLOBAL_PARS->tree->save(ntw->gb_main, 0, 0, 0); |
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59 | if (error) aw_message(error); |
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60 | |
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61 | ntw->zoom_reset_and_refresh(); |
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62 | } |
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63 | |
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64 | static void pars_export_tree() { |
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65 | GB_ERROR error = GLOBAL_PARS->tree->save(0, 0, 0, 0); |
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66 | if (error) aw_message(error); |
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67 | } |
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68 | |
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69 | STATIC_ATTRIBUTED(__ATTR__NORETURN, void pars_exit(AW_window *aww)) { |
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70 | aww->get_root()->unlink_awars_from_DB(GLOBAL_gb_main); |
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71 | #if defined(DEBUG) |
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72 | AWT_browser_forget_db(GLOBAL_gb_main); |
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73 | #endif // DEBUG |
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74 | GB_close(GLOBAL_gb_main); |
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75 | exit(0); |
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76 | } |
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77 | |
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78 | static void PARS_export_cb(AW_window *aww, AWT_canvas *, AW_CL mode) { |
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79 | if (mode &1) { // export tree |
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80 | pars_export_tree(); |
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81 | } |
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82 | if (mode &2) { |
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83 | // quit |
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84 | pars_exit(aww); |
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85 | } |
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86 | } |
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87 | |
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88 | static void AP_user_push_cb(AW_window *aww, AWT_canvas *) |
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89 | { |
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90 | ap_main->user_push(); |
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91 | aww->get_root()->awar(AWAR_STACKPOINTER)->write_int(ap_main->get_user_push_counter()); |
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92 | } |
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93 | |
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94 | static void AP_user_pop_cb(AW_window *aww, AWT_canvas *ntw) |
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95 | { |
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96 | if (ap_main->get_user_push_counter()<=0) { |
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97 | aw_message("No tree on stack."); |
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98 | return; |
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99 | } |
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100 | ap_main->user_pop(); |
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101 | rootNode()->compute_tree(GLOBAL_gb_main); |
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102 | ASSERT_VALID_TREE(rootNode()); |
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103 | aww->get_root()->awar(AWAR_STACKPOINTER)->write_int(ap_main->get_user_push_counter()); |
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104 | |
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105 | pars_saveNrefresh_changed_tree(ntw); |
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106 | |
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107 | if (ap_main->get_user_push_counter() <= 0) { // last tree was popped => push again |
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108 | AP_user_push_cb(aww, ntw); |
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109 | } |
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110 | } |
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111 | |
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112 | class InsertData { |
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113 | int abort_flag; |
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114 | long currentspecies; |
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115 | |
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116 | arb_progress progress; |
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117 | |
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118 | public: |
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119 | |
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120 | bool quick_add_flag; |
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121 | InsertData(bool quick, long spec_count) |
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122 | : abort_flag(false), |
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123 | currentspecies(0), |
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124 | progress(GBS_global_string("Inserting %li species", spec_count), spec_count), |
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125 | quick_add_flag(quick) |
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126 | { |
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127 | } |
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128 | |
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129 | bool every_sixteenth() { return (currentspecies & 0xf) == 0; } |
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130 | |
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131 | bool aborted() const { return abort_flag; } |
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132 | void set_aborted(bool aborted_) { abort_flag = aborted_; } |
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133 | |
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134 | void inc() { |
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135 | ++currentspecies; |
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136 | progress.inc(); |
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137 | abort_flag = progress.aborted(); |
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138 | } |
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139 | }; |
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140 | |
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141 | static long insert_species_in_tree_test(const char *key, long val, void *cd_isits) { |
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142 | if (!val) return val; |
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143 | |
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144 | InsertData *isits = (InsertData*)cd_isits; |
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145 | if (isits->aborted()) return val; |
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146 | |
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147 | GBDATA *gb_node = (GBDATA *)val; |
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148 | |
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149 | #if defined(WARN_TODO) |
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150 | #warning following code could be a method .. |
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151 | // ARB_tree *ARB_tree_root::create_linked_leaf(GBDATA *gb_species, const char *name) |
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152 | #endif |
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153 | |
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154 | AP_tree *tree = rootNode(); |
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155 | AP_tree *leaf = tree->dup(); |
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156 | leaf->gb_node = gb_node; |
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157 | leaf->name = strdup(key); |
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158 | leaf->is_leaf = true; |
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159 | |
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160 | leaf->set_seq(leaf->get_tree_root()->get_seqTemplate()->dup()); |
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161 | GB_ERROR error = leaf->get_seq()->bind_to_species(gb_node); |
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162 | |
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163 | if (error) { |
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164 | aw_message(error); |
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165 | return val; |
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166 | } |
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167 | |
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168 | if (leaf->get_seq()->weighted_base_count() < MIN_SEQUENCE_LENGTH) { |
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169 | aw_message(GBS_global_string("Species %s has too short sequence (%f, minimum is %i)", |
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170 | key, |
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171 | leaf->get_seq()->weighted_base_count(), |
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172 | MIN_SEQUENCE_LENGTH)); |
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173 | delete leaf; |
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174 | return val; |
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175 | } |
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176 | |
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177 | isits->inc(); |
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178 | |
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179 | { |
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180 | AP_FLOAT best_val = 9999999999999.0; |
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181 | AP_FLOAT this_val; |
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182 | int cnt = 0; |
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183 | |
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184 | while (cnt<2) { |
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185 | this_val = rootEdge()->nni_rek(-1, false, AP_BL_NNI_ONLY, NULL); |
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186 | if (this_val<best_val) { |
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187 | best_val = this_val; |
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188 | cnt = 0; |
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189 | } |
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190 | else if (this_val==best_val) { |
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191 | cnt++; |
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192 | } |
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193 | else { |
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194 | cnt = 0; |
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195 | } |
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196 | } |
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197 | } |
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198 | |
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199 | rootEdge()->dumpNNI=2; |
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200 | |
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201 | AP_tree **blist; |
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202 | AP_tree_nlen *bl, *blf; |
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203 | long bsum = 0; |
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204 | long counter = 0; |
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205 | |
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206 | tree->buildBranchList(blist, bsum, true, -1); // get all branches |
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207 | |
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208 | #if defined(DEBUG) |
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209 | long prevCombineCount = AP_sequence::combine_count(); |
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210 | #endif // DEBUG |
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211 | |
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212 | AP_tree *bestposl = tree->get_leftson(); |
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213 | AP_tree *bestposr = tree->get_rightson(); |
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214 | leaf->insert(bestposl); |
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215 | AP_FLOAT best_parsimony, akt_parsimony; |
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216 | best_parsimony = akt_parsimony = rootNode()->costs(); |
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217 | |
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218 | for (counter = 0; !isits->aborted() && blist[counter]; counter += 2) |
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219 | { |
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220 | bl = (AP_tree_nlen *)blist[counter]; |
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221 | blf = (AP_tree_nlen *)blist[counter+1]; |
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222 | if (blf->father == bl) |
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223 | { |
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224 | bl = (AP_tree_nlen *)blist[counter+1]; |
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225 | blf = (AP_tree_nlen *)blist[counter]; |
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226 | } |
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227 | |
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228 | if (bl->father) bl->set_root(); |
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229 | |
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230 | leaf->moveTo(bl, 0.5); |
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231 | akt_parsimony = rootNode()->costs(); |
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232 | |
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233 | if (akt_parsimony<best_parsimony) |
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234 | { |
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235 | best_parsimony = akt_parsimony; |
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236 | bestposl = bl; |
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237 | bestposr = blf; |
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238 | } |
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239 | } |
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240 | delete blist; |
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241 | blist = 0; |
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242 | if (bestposl->father != bestposr) bestposl = bestposr; |
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243 | leaf->moveTo(bestposl, 0.5); |
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244 | |
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245 | // calculate difference in father-sequence |
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246 | |
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247 | int baseDiff = 0; |
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248 | |
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249 | { |
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250 | AP_tree_nlen *fath = ((AP_tree_nlen*)bestposl)->get_father()->get_father(); |
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251 | |
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252 | char *seq_with_leaf; |
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253 | char *seq_without_leaf; |
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254 | long i; |
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255 | |
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256 | // Note: removed sequence length code here, |
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257 | // cause "sequence_len" is always filter-length (i.e. constant until filter changes) |
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258 | // ralf 10/2009 |
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259 | |
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260 | seq_with_leaf = fath->getSequenceCopy(); |
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261 | |
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262 | ap_main->push(); |
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263 | |
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264 | leaf->remove(); |
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265 | seq_without_leaf = fath->getSequenceCopy(); |
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266 | |
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267 | ap_main->pop(); |
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268 | |
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269 | for (i=0; seq_with_leaf[i]; i++) { |
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270 | if (seq_with_leaf[i]!=seq_without_leaf[i]) { |
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271 | baseDiff++; |
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272 | } |
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273 | |
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274 | } |
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275 | |
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276 | delete [] seq_with_leaf; |
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277 | delete [] seq_without_leaf; |
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278 | } |
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279 | |
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280 | rootEdge()->countSpecies(); |
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281 | |
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282 | #if defined(DEBUG) |
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283 | printf("Combines: %li\n", AP_sequence::combine_count()-prevCombineCount); |
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284 | #endif // DEBUG |
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285 | |
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286 | if (!isits->quick_add_flag) { |
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287 | int deep = -1; |
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288 | AP_tree_nlen *bestpos = (AP_tree_nlen*)bestposl; |
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289 | AP_tree_edge *e = bestpos->edgeTo(bestpos->get_father()); |
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290 | |
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291 | if (isits->every_sixteenth()) deep = -1; |
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292 | |
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293 | arb_progress progress("optimization"); |
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294 | e->dumpNNI = 1; |
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295 | e->distInsertBorder = e->distanceToBorder(INT_MAX, (AP_tree_nlen*)leaf); |
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296 | e->basesChanged = baseDiff; |
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297 | e->nni_rek(deep, false, AP_BL_NNI_ONLY, NULL); |
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298 | e->dumpNNI = 0; |
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299 | } |
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300 | |
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301 | return val; |
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302 | } |
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303 | |
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304 | static int sort_sequences_by_length(const char*, long leaf0_ptr, const char*, long leaf1_ptr) { |
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305 | AP_tree *leaf0 = (AP_tree*)leaf0_ptr; |
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306 | AP_tree *leaf1 = (AP_tree*)leaf1_ptr; |
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307 | |
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308 | AP_FLOAT len0 = leaf0->get_seq()->weighted_base_count(); |
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309 | AP_FLOAT len1 = leaf1->get_seq()->weighted_base_count(); |
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310 | |
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311 | return len0<len1 ? 1 : (len0>len1 ? -1 : 0); // longest sequence first |
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312 | } |
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313 | |
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314 | static long transform_gbd_to_leaf(const char *key, long val, void *) { |
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315 | if (!val) return val; |
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316 | |
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317 | #if defined(WARN_TODO) |
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318 | #warning use create_linked_leaf() when impl |
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319 | #endif |
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320 | |
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321 | GBDATA *gb_node = (GBDATA *)val; |
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322 | AP_tree_root *troot = ap_main->get_tree_root()->tree_static; |
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323 | AP_tree_nlen *leaf = DOWNCAST(AP_tree_nlen*, troot->get_nodeTemplate()->dup()); |
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324 | |
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325 | leaf->gb_node = gb_node; |
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326 | leaf->name = strdup(key); |
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327 | leaf->is_leaf = true; |
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328 | |
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329 | leaf->set_seq(troot->get_seqTemplate()->dup()); |
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330 | GB_ERROR error = leaf->get_seq()->bind_to_species(gb_node); |
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331 | if (error) { |
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332 | aw_message(error); |
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333 | delete leaf; leaf = 0; |
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334 | } |
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335 | return (long)leaf; |
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336 | } |
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337 | |
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338 | static AP_tree_nlen *insert_species_in_tree(const char *key, AP_tree_nlen *leaf, InsertData *isits) { |
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339 | if (!leaf) return leaf; |
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340 | if (isits->aborted()) return leaf; |
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341 | |
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342 | AP_tree_nlen *tree = rootNode(); |
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343 | |
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344 | if (leaf->get_seq()->weighted_base_count() < MIN_SEQUENCE_LENGTH) { |
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345 | aw_message(GBS_global_string("Species %s has too short sequence (%f, minimum is %i)", |
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346 | key, |
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347 | leaf->get_seq()->weighted_base_count(), |
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348 | MIN_SEQUENCE_LENGTH)); |
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349 | delete leaf; |
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350 | return 0; |
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351 | } |
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352 | |
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353 | if (!tree) { // no tree yet |
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354 | static AP_tree_nlen *last_inserted = NULL; // @@@ move 'last_inserted' into 'InsertData' |
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355 | |
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356 | if (!last_inserted) { // store 1st leaf |
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357 | last_inserted = leaf; |
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358 | } |
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359 | else { // 2nd leaf -> create initial tree |
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360 | AP_tree_root *troot = ap_main->get_tree_root()->tree_static; |
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361 | leaf->insert(last_inserted); |
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362 | last_inserted = NULL; |
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363 | |
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364 | AP_tree *initial_tree = leaf->get_father(); |
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365 | troot->change_root(NULL, initial_tree); |
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366 | |
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367 | ASSERT_VALID_TREE(troot->get_root_node()); |
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368 | } |
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369 | } |
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370 | else { |
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371 | ASSERT_VALID_TREE(tree); |
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372 | |
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373 | AP_tree_nlen **branchlist; |
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374 | long bsum = 0; |
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375 | |
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376 | { |
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377 | AP_tree **blist; |
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378 | tree->buildBranchList(blist, bsum, true, -1); // get all branches |
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379 | branchlist = (AP_tree_nlen**)blist; |
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380 | } |
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381 | |
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382 | AP_tree_nlen *bestposl = tree->get_leftson(); |
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383 | AP_tree_nlen *bestposr = tree->get_rightson(); |
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384 | |
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385 | ap_assert(tree == rootNode()); |
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386 | leaf->insert(bestposl); |
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387 | tree = NULL; // tree may have changed |
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388 | |
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389 | { |
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390 | AP_FLOAT curr_parsimony = rootNode()->costs(); |
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391 | AP_FLOAT best_parsimony = curr_parsimony; |
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392 | |
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393 | ASSERT_VALID_TREE(rootNode()); |
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394 | |
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395 | for (long counter = 0; !isits->aborted() && branchlist[counter]; counter += 2) { |
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396 | AP_tree_nlen *bl = branchlist[counter]; |
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397 | AP_tree_nlen *blf = branchlist[counter+1]; |
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398 | |
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399 | if (blf->father == bl) { |
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400 | bl = branchlist[counter+1]; |
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401 | blf = branchlist[counter]; |
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402 | } |
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403 | |
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404 | if (bl->father) { |
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405 | bl->set_root(); |
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406 | } |
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407 | |
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408 | ASSERT_VALID_TREE(rootNode()); |
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409 | |
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410 | leaf->moveTo(bl, 0.5); |
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411 | ASSERT_VALID_TREE(rootNode()); |
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412 | |
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413 | curr_parsimony = rootNode()->costs(); |
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414 | ASSERT_VALID_TREE(rootNode()); |
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415 | |
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416 | if (curr_parsimony < best_parsimony) { |
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417 | best_parsimony = curr_parsimony; |
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418 | bestposl = bl; |
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419 | bestposr = blf; |
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420 | } |
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421 | |
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422 | } |
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423 | } |
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424 | delete branchlist; branchlist = 0; |
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425 | if (bestposl->father != bestposr) { |
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426 | bestposl = bestposr; |
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427 | } |
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428 | |
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429 | ASSERT_VALID_TREE(rootNode()); |
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430 | |
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431 | leaf->moveTo(bestposl, 0.5); |
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432 | |
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433 | ASSERT_VALID_TREE(rootNode()); |
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434 | |
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435 | if (!isits->quick_add_flag) { |
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436 | int deep = 5; |
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437 | if (isits->every_sixteenth()) deep = -1; |
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438 | |
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439 | arb_progress progress("optimization"); |
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440 | bestposl->get_father()->nn_interchange_rek(deep, AP_BL_NNI_ONLY, true); |
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441 | ASSERT_VALID_TREE(rootNode()); |
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442 | } |
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443 | AP_tree_nlen *brother = leaf->get_brother(); |
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444 | if (brother->is_leaf && leaf->father->father) { |
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445 | bool brother_is_short = 2 * brother->get_seq()->weighted_base_count() < leaf->get_seq()->weighted_base_count(); |
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446 | |
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447 | if (brother_is_short) { |
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448 | brother->remove(); |
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449 | leaf->remove(); |
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450 | |
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451 | for (int firstUse = 1; firstUse >= 0; --firstUse) { |
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452 | AP_tree_nlen *to_insert = firstUse ? leaf : brother; |
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453 | const char *format = firstUse ? "2:%s" : "shortseq:%s"; |
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454 | |
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455 | char *label = GBS_global_string_copy(format, to_insert->name); |
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456 | insert_species_in_tree(label, to_insert, isits); |
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457 | free(label); |
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458 | } |
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459 | } |
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460 | } |
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461 | |
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462 | ASSERT_VALID_TREE(rootNode()); |
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463 | } |
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464 | |
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465 | return leaf; |
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466 | } |
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467 | |
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468 | static long hash_insert_species_in_tree(const char *key, long leaf, void *cd_isits) { |
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469 | InsertData *isits = (InsertData*)cd_isits; |
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470 | long result = (long)insert_species_in_tree(key, (AP_tree_nlen*)leaf, isits); |
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471 | isits->inc(); |
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472 | return result; |
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473 | } |
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474 | |
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475 | static long count_hash_elements(const char *, long val, void *cd_count) { |
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476 | if (val) { |
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477 | long *count = (long*)cd_count; |
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478 | (*count)++; |
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479 | } |
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480 | return val; |
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481 | } |
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482 | |
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483 | enum AddWhat { |
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484 | NT_ADD_MARKED, |
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485 | NT_ADD_SELECTED, |
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486 | }; |
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487 | |
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488 | static void nt_add(AW_window *, AWT_canvas *ntw, AddWhat what, bool quick, int test) |
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489 | { |
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490 | GB_ERROR error = 0; |
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491 | |
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492 | AP_tree *oldrootleft = NULL; |
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493 | AP_tree *oldrootright = NULL; |
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494 | { |
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495 | AP_tree *root = rootNode(); |
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496 | if (root) { |
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497 | oldrootleft = root->get_leftson(); |
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498 | oldrootright = root->get_rightson(); |
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499 | } |
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500 | } |
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501 | |
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502 | GB_HASH *hash = 0; |
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503 | { |
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504 | GB_transaction ta(GLOBAL_gb_main); |
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505 | switch (what) { |
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506 | case NT_ADD_SELECTED: { |
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507 | char *name = GBT_readOrCreate_string(GLOBAL_gb_main, AWAR_SPECIES_NAME, ""); |
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508 | if (name && strlen(name)) { |
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509 | GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main, name); |
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510 | if (gb_species) { |
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511 | hash = GBS_create_hash(1, GB_MIND_CASE); |
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512 | GBS_write_hash(hash, name, (long)gb_species); |
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513 | } |
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514 | else error = GBS_global_string("Selected Species (%s) not found", name); |
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515 | } |
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516 | else error = "Please select a species"; |
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517 | free(name); |
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518 | break; |
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519 | } |
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520 | case NT_ADD_MARKED: { |
---|
521 | hash = GBT_create_marked_species_hash(GLOBAL_gb_main); |
---|
522 | break; |
---|
523 | } |
---|
524 | } |
---|
525 | } |
---|
526 | |
---|
527 | if (!error) { |
---|
528 | ap_assert(hash); |
---|
529 | |
---|
530 | NT_remove_species_in_tree_from_hash(rootNode(), hash); |
---|
531 | |
---|
532 | long max_species = 0; |
---|
533 | GBS_hash_do_loop(hash, count_hash_elements, &max_species); |
---|
534 | InsertData isits(quick, max_species); |
---|
535 | |
---|
536 | if (test) { |
---|
537 | GBS_hash_do_loop(hash, insert_species_in_tree_test, &isits); |
---|
538 | } |
---|
539 | else { |
---|
540 | GB_begin_transaction(GLOBAL_gb_main); |
---|
541 | GBS_hash_do_loop(hash, transform_gbd_to_leaf, NULL); |
---|
542 | GB_commit_transaction(GLOBAL_gb_main); |
---|
543 | GBS_hash_do_sorted_loop(hash, hash_insert_species_in_tree, sort_sequences_by_length, &isits); |
---|
544 | } |
---|
545 | if (!quick) { |
---|
546 | rootEdge()->nni_rek(-1, false, AP_BL_NNI_ONLY, NULL); |
---|
547 | } |
---|
548 | |
---|
549 | if (rootNode()) { |
---|
550 | rootEdge()->calc_branchlengths(); |
---|
551 | |
---|
552 | ASSERT_VALID_TREE(rootNode()); |
---|
553 | rootNode()->compute_tree(GLOBAL_gb_main); |
---|
554 | |
---|
555 | if (oldrootleft) { |
---|
556 | if (oldrootleft->father == oldrootright) oldrootleft->set_root(); |
---|
557 | else oldrootright->set_root(); |
---|
558 | } |
---|
559 | else { |
---|
560 | ARB_edge innermost = rootNode()->get_tree_root()->find_innermost_edge(); |
---|
561 | DOWNCAST(AP_tree*, innermost.son())->set_root(); |
---|
562 | } |
---|
563 | } |
---|
564 | else { |
---|
565 | error = "Tree lost (no leafs left)"; |
---|
566 | } |
---|
567 | } |
---|
568 | |
---|
569 | if (hash) GBS_free_hash(hash); |
---|
570 | if (error) aw_message(error); |
---|
571 | |
---|
572 | AWT_TREE(ntw)->resort_tree(0); |
---|
573 | pars_saveNrefresh_changed_tree(ntw); |
---|
574 | } |
---|
575 | |
---|
576 | // ----------------------------------------- |
---|
577 | // Adding partial sequences to tree |
---|
578 | // ----------------------------------------- |
---|
579 | |
---|
580 | class PartialSequence { |
---|
581 | GBDATA *gb_species; |
---|
582 | mutable AP_tree_nlen *self; // self converted to leaf (ready for insertion) |
---|
583 | const AP_tree_nlen *best_full_match; // full sequence position which matched best |
---|
584 | long overlap; // size of overlapping region |
---|
585 | long penalty; // weighted mismatches |
---|
586 | bool released; |
---|
587 | bool multi_match; |
---|
588 | string multi_list; // list of equal-rated insertion-points (not containing self) |
---|
589 | |
---|
590 | AP_tree_nlen *get_self() const { |
---|
591 | if (!self) { |
---|
592 | ap_assert(!released); // request not possible, because leaf has already been released! |
---|
593 | |
---|
594 | self = (AP_tree_nlen*)transform_gbd_to_leaf(GBT_read_name(gb_species), (long)gb_species, NULL); |
---|
595 | ap_assert(self); |
---|
596 | } |
---|
597 | return self; |
---|
598 | } |
---|
599 | |
---|
600 | public: |
---|
601 | PartialSequence(GBDATA *gb_species_) |
---|
602 | : gb_species(gb_species_), self(0), best_full_match(0) |
---|
603 | , overlap(0), penalty(LONG_MAX), released(false), multi_match(false) |
---|
604 | { |
---|
605 | } |
---|
606 | PartialSequence(const PartialSequence& other) |
---|
607 | : gb_species(other.gb_species), |
---|
608 | self(other.self), |
---|
609 | best_full_match(other.best_full_match), |
---|
610 | overlap(other.overlap), |
---|
611 | penalty(other.penalty), |
---|
612 | released(other.released), |
---|
613 | multi_match(other.multi_match), |
---|
614 | multi_list(other.multi_list) |
---|
615 | { |
---|
616 | ap_assert(self == 0); // copying self not implemented |
---|
617 | } |
---|
618 | DECLARE_ASSIGNMENT_OPERATOR(PartialSequence); |
---|
619 | ~PartialSequence() { ap_assert(self == 0); } |
---|
620 | |
---|
621 | GBDATA *get_species() const { return gb_species; } |
---|
622 | const AP_tree_nlen *get_best_match() const { return best_full_match; } |
---|
623 | AP_FLOAT get_branchlength() const { return AP_FLOAT(penalty)/overlap; } |
---|
624 | void test_match(const AP_tree_nlen *leaf_full); |
---|
625 | bool is_multi_match() const { return multi_match; } |
---|
626 | |
---|
627 | const char *get_name() const { |
---|
628 | const char *name = get_self()->name; |
---|
629 | ap_assert(name); |
---|
630 | return name; |
---|
631 | } |
---|
632 | |
---|
633 | string get_multilist() const { |
---|
634 | ap_assert(is_multi_match()); |
---|
635 | return string(best_full_match->name)+multi_list; |
---|
636 | } |
---|
637 | |
---|
638 | AP_tree_nlen *release() { |
---|
639 | AP_tree_nlen *s = self; |
---|
640 | self = 0; |
---|
641 | released = true; |
---|
642 | return s; |
---|
643 | } |
---|
644 | |
---|
645 | void dump() const { |
---|
646 | printf("best match for '%s' is '%s' (overlap=%li penalty=%li)\n", |
---|
647 | get_name(), best_full_match->name, |
---|
648 | overlap, penalty); |
---|
649 | } |
---|
650 | |
---|
651 | }; |
---|
652 | |
---|
653 | void PartialSequence::test_match(const AP_tree_nlen *leaf_full) { |
---|
654 | long curr_overlap; |
---|
655 | long curr_penalty; |
---|
656 | |
---|
657 | leaf_full->get_seq()->partial_match(get_self()->get_seq(), &curr_overlap, &curr_penalty); |
---|
658 | |
---|
659 | bool better = false; |
---|
660 | |
---|
661 | if (curr_overlap > overlap) { |
---|
662 | better = true; |
---|
663 | } |
---|
664 | else if (curr_overlap == overlap) { |
---|
665 | if (curr_penalty<penalty) { |
---|
666 | better = true; |
---|
667 | } |
---|
668 | else if (curr_penalty == penalty) { |
---|
669 | // found two equal-rated insertion points -> store data for warning |
---|
670 | #if defined(DEBUG) |
---|
671 | if (!multi_match) dump(); |
---|
672 | printf("Another equal match is against '%s' (overlap=%li penalty=%li)\n", leaf_full->name, curr_overlap, curr_penalty); |
---|
673 | #endif // DEBUG |
---|
674 | |
---|
675 | multi_match = true; |
---|
676 | multi_list.append(1, '/'); |
---|
677 | multi_list.append(leaf_full->name); |
---|
678 | } |
---|
679 | } |
---|
680 | |
---|
681 | if (better) { |
---|
682 | overlap = curr_overlap; |
---|
683 | penalty = curr_penalty; |
---|
684 | best_full_match = leaf_full; |
---|
685 | multi_match = false; |
---|
686 | multi_list = ""; |
---|
687 | } |
---|
688 | } |
---|
689 | |
---|
690 | static GB_ERROR nt_best_partial_match_rek(list<PartialSequence>& partial, const AP_tree_nlen *tree) { |
---|
691 | GB_ERROR error = 0; |
---|
692 | |
---|
693 | if (tree) { |
---|
694 | if (tree->is_leaf && tree->name) { |
---|
695 | if (tree->gb_node) { |
---|
696 | int is_partial = GBT_is_partial(tree->gb_node, 0, true); // marks undef as 'full sequence' |
---|
697 | if (is_partial == 0) { // do not consider other partial sequences |
---|
698 | list<PartialSequence>::iterator i = partial.begin(); |
---|
699 | list<PartialSequence>::iterator e = partial.end(); |
---|
700 | for (; i != e; ++i) { |
---|
701 | i->test_match(tree); |
---|
702 | } |
---|
703 | } |
---|
704 | else if (is_partial == -1) { |
---|
705 | error = GB_await_error(); |
---|
706 | } |
---|
707 | } |
---|
708 | } |
---|
709 | else { |
---|
710 | error = nt_best_partial_match_rek(partial, tree->get_leftson()); |
---|
711 | if (!error) error = nt_best_partial_match_rek(partial, tree->get_rightson()); |
---|
712 | } |
---|
713 | } |
---|
714 | return error; |
---|
715 | } |
---|
716 | |
---|
717 | static void count_partial_and_full(const AP_tree_nlen *at, int *partial, int *full, int *zombies, int default_value, int define_if_undef) { |
---|
718 | if (at->is_leaf) { |
---|
719 | if (at->gb_node) { |
---|
720 | int is_partial = GBT_is_partial(at->gb_node, default_value, define_if_undef); |
---|
721 | if (is_partial) ++(*partial); |
---|
722 | else ++(*full); |
---|
723 | } |
---|
724 | else { |
---|
725 | ++(*zombies); |
---|
726 | } |
---|
727 | } |
---|
728 | else { |
---|
729 | count_partial_and_full(at->get_leftson(), partial, full, zombies, default_value, define_if_undef); |
---|
730 | count_partial_and_full(at->get_rightson(), partial, full, zombies, default_value, define_if_undef); |
---|
731 | } |
---|
732 | } |
---|
733 | |
---|
734 | static const AP_tree_nlen *find_least_deep_leaf(const AP_tree_nlen *at, int depth, int *min_depth) { |
---|
735 | if (depth >= *min_depth) { |
---|
736 | return 0; // already found better or equal |
---|
737 | } |
---|
738 | |
---|
739 | if (at->is_leaf) { |
---|
740 | if (at->gb_node) { |
---|
741 | *min_depth = depth; |
---|
742 | return at; |
---|
743 | } |
---|
744 | return 0; |
---|
745 | } |
---|
746 | |
---|
747 | const AP_tree_nlen *left = find_least_deep_leaf(at->get_leftson(), depth+1, min_depth); |
---|
748 | const AP_tree_nlen *right = find_least_deep_leaf(at->get_rightson(), depth+1, min_depth); |
---|
749 | |
---|
750 | return right ? right : left; |
---|
751 | } |
---|
752 | inline AP_tree_nlen *find_least_deep_leaf(AP_tree_nlen *at, int depth, int *min_depth) { |
---|
753 | return const_cast<AP_tree_nlen*>(find_least_deep_leaf(const_cast<const AP_tree_nlen*>(at), depth, min_depth)); |
---|
754 | } |
---|
755 | |
---|
756 | static long push_partial(const char *, long val, void *cd_partial) { |
---|
757 | list<PartialSequence> *partial = reinterpret_cast<list<PartialSequence> *>(cd_partial); |
---|
758 | partial->push_back(PartialSequence((GBDATA*)val)); |
---|
759 | return val; |
---|
760 | } |
---|
761 | |
---|
762 | static void nt_add_partial(AW_window * /* aww */, AWT_canvas *ntw) { |
---|
763 | GB_begin_transaction(GLOBAL_gb_main); |
---|
764 | GB_ERROR error = 0; |
---|
765 | int full_marked_sequences = 0; |
---|
766 | int partial_marked_sequences = 0; |
---|
767 | int no_data = 0; // no data in alignment |
---|
768 | |
---|
769 | arb_progress("Adding partial sequences"); |
---|
770 | |
---|
771 | { |
---|
772 | list<PartialSequence> partial; |
---|
773 | { |
---|
774 | GB_HASH *partial_hash = GBS_create_hash(GBT_get_species_count(GLOBAL_gb_main), GB_MIND_CASE); |
---|
775 | int marked_found = 0; |
---|
776 | |
---|
777 | for (GBDATA *gb_marked = GBT_first_marked_species(GLOBAL_gb_main); |
---|
778 | !error && gb_marked; |
---|
779 | gb_marked = GBT_next_marked_species(gb_marked)) |
---|
780 | { |
---|
781 | ++marked_found; |
---|
782 | |
---|
783 | if (GBT_read_sequence(gb_marked, ap_main->get_aliname())) { // species has sequence in alignment |
---|
784 | const char *name = GBT_read_name(gb_marked); |
---|
785 | |
---|
786 | switch (GBT_is_partial(gb_marked, 1, true)) { // marks undef as 'partial sequence' |
---|
787 | case 0: { // full sequences |
---|
788 | aw_message(GBS_global_string("'%s' is a full sequence (cannot add partial)", name)); |
---|
789 | ++full_marked_sequences; |
---|
790 | break; |
---|
791 | } |
---|
792 | case 1: // partial sequences |
---|
793 | ++partial_marked_sequences; |
---|
794 | GBS_write_hash(partial_hash, name, (long)gb_marked); |
---|
795 | break; |
---|
796 | case -1: // error |
---|
797 | error = GB_await_error(); |
---|
798 | break; |
---|
799 | default: |
---|
800 | ap_assert(0); |
---|
801 | break; |
---|
802 | } |
---|
803 | } |
---|
804 | else { |
---|
805 | no_data++; |
---|
806 | } |
---|
807 | } |
---|
808 | |
---|
809 | if (!error && !marked_found) error = "There are no marked species"; |
---|
810 | |
---|
811 | if (!error) { |
---|
812 | NT_remove_species_in_tree_from_hash(rootNode(), partial_hash); // skip all species which are in tree |
---|
813 | GBS_hash_do_loop(partial_hash, push_partial, &partial); // build partial list from hash |
---|
814 | |
---|
815 | int partials_already_in_tree = partial_marked_sequences - partial.size(); |
---|
816 | |
---|
817 | if (no_data>0) aw_message(GBS_global_string("%i marked species have no data in '%s'", no_data, ap_main->get_aliname())); |
---|
818 | if (full_marked_sequences>0) aw_message(GBS_global_string("%i marked species are declared full sequences", full_marked_sequences)); |
---|
819 | if (partials_already_in_tree>0) aw_message(GBS_global_string("%i marked species are already in tree", partials_already_in_tree)); |
---|
820 | |
---|
821 | if (partial.empty()) error = "No species left to add"; |
---|
822 | } |
---|
823 | } |
---|
824 | |
---|
825 | if (!error) { |
---|
826 | // find best matching full sequence for each partial sequence |
---|
827 | error = nt_best_partial_match_rek(partial, rootNode()); |
---|
828 | |
---|
829 | list<PartialSequence>::iterator i = partial.begin(); |
---|
830 | list<PartialSequence>::iterator e = partial.end(); |
---|
831 | |
---|
832 | arb_progress part_insert_progress(partial.size()); |
---|
833 | |
---|
834 | #if defined(DEBUG) |
---|
835 | // show results : |
---|
836 | for (; i != e; ++i) i->dump(); |
---|
837 | i = partial.begin(); |
---|
838 | #endif // DEBUG |
---|
839 | |
---|
840 | for (; i != e && !error; ++i) { |
---|
841 | const char *name = i->get_name(); |
---|
842 | |
---|
843 | if (i->is_multi_match()) { |
---|
844 | aw_message(GBS_global_string("Insertion of '%s' is ambiguous.\n" |
---|
845 | "(took first of equal scored insertion points: %s)", |
---|
846 | name, i->get_multilist().c_str())); |
---|
847 | } |
---|
848 | |
---|
849 | AP_tree_nlen *part_leaf = i->release(); |
---|
850 | AP_tree_nlen *full_seq = const_cast<AP_tree_nlen*>(i->get_best_match()); |
---|
851 | AP_tree_nlen *brother = full_seq->get_brother(); |
---|
852 | int is_partial = 0; |
---|
853 | AP_tree_nlen *target = 0; |
---|
854 | |
---|
855 | if (brother->is_leaf) { |
---|
856 | if (brother->gb_node) { |
---|
857 | is_partial = GBT_is_partial(brother->gb_node, 0, 1); |
---|
858 | |
---|
859 | if (is_partial) { // brother is partial sequence |
---|
860 | target = brother; // insert as brother of brother |
---|
861 | } |
---|
862 | else { |
---|
863 | target = full_seq; // insert as brother of full_seq |
---|
864 | } |
---|
865 | } |
---|
866 | else { |
---|
867 | error = "There are zombies in your tree - please remove them"; |
---|
868 | } |
---|
869 | } |
---|
870 | else { |
---|
871 | int partial_count = 0; |
---|
872 | int full_count = 0; |
---|
873 | int zombie_count = 0; |
---|
874 | |
---|
875 | count_partial_and_full(brother, &partial_count, &full_count, &zombie_count, 0, 1); |
---|
876 | |
---|
877 | if (zombie_count) { |
---|
878 | error = "There are zombies in your tree - please remove them"; |
---|
879 | } |
---|
880 | else if (full_count) { |
---|
881 | // brother is a subtree containing full sequences |
---|
882 | // -> add new brother to full_seq found above |
---|
883 | target = full_seq; |
---|
884 | } |
---|
885 | else { // brother subtree only contains partial sequences |
---|
886 | // find one of the least-deep leafs |
---|
887 | int depth = INT_MAX; |
---|
888 | target = find_least_deep_leaf(brother, 0, &depth); |
---|
889 | is_partial = 1; |
---|
890 | } |
---|
891 | } |
---|
892 | |
---|
893 | |
---|
894 | if (!error) { |
---|
895 | #if defined(DEBUG) |
---|
896 | printf("inserting '%s'\n", name); |
---|
897 | #endif // DEBUG |
---|
898 | part_leaf->insert(target); |
---|
899 | |
---|
900 | // we need to create the sequence of the father node! |
---|
901 | AP_tree_nlen *father = part_leaf->get_father(); |
---|
902 | father->costs(); |
---|
903 | |
---|
904 | // ensure full-sequence is always on top |
---|
905 | if (father->rightson == target) { |
---|
906 | father->swap_sons(); |
---|
907 | } |
---|
908 | |
---|
909 | if (!error) { |
---|
910 | // now correct the branch lengths. |
---|
911 | // First calc the original branchlen |
---|
912 | GBT_LEN orglen = father->get_branchlength()+target->get_branchlength(); |
---|
913 | |
---|
914 | if (is_partial) { // we now have a subtree of partial sequences |
---|
915 | brother->set_branchlength(orglen); // each partial sequence has it's branchlength. |
---|
916 | father->set_branchlength(0); // all father branches are zero length |
---|
917 | } |
---|
918 | else { // we have a subtree of one full+one partial sequence |
---|
919 | father->set_branchlength(orglen); // father branch represents original length (w/o partial seq) |
---|
920 | full_seq->set_branchlength(0); // full seq has no sub-branch length |
---|
921 | } |
---|
922 | part_leaf->set_branchlength(i->get_branchlength()); |
---|
923 | printf("Adding with branchlength=%f\n", i->get_branchlength()); |
---|
924 | } |
---|
925 | } |
---|
926 | else { |
---|
927 | delete part_leaf; |
---|
928 | } |
---|
929 | |
---|
930 | part_insert_progress.inc_and_check_user_abort(error); |
---|
931 | } |
---|
932 | } |
---|
933 | } |
---|
934 | |
---|
935 | if (full_marked_sequences) { |
---|
936 | aw_message(GBS_global_string("%i marked full sequences were not added", full_marked_sequences)); |
---|
937 | } |
---|
938 | |
---|
939 | if (error) { |
---|
940 | aw_message(error); |
---|
941 | GB_abort_transaction(GLOBAL_gb_main); |
---|
942 | } |
---|
943 | else { |
---|
944 | GB_commit_transaction(GLOBAL_gb_main); |
---|
945 | } |
---|
946 | |
---|
947 | pars_saveNrefresh_changed_tree(ntw); |
---|
948 | } |
---|
949 | |
---|
950 | // ----------------------------- |
---|
951 | // add marked / selected |
---|
952 | // ----------------------------- |
---|
953 | |
---|
954 | // normal versions : |
---|
955 | |
---|
956 | static void NT_add (AW_window * aww, AWT_canvas *ntw, AddWhat what) { nt_add(aww, ntw, what, false, 0); } |
---|
957 | static void NT_quick_add(AW_window * aww, AWT_canvas *ntw, AddWhat what) { nt_add(aww, ntw, what, true, 0); } |
---|
958 | |
---|
959 | // test versions : |
---|
960 | |
---|
961 | #if defined(TESTMENU) |
---|
962 | static void TESTMENU_add (AW_window * aww, AWT_canvas *ntw, AddWhat what) { nt_add(aww, ntw, what, false, 1); } |
---|
963 | static void TESTMENU_quick_add(AW_window * aww, AWT_canvas *ntw, AddWhat what) { nt_add(aww, ntw, what, true, 1); } |
---|
964 | #endif // TESTMENU |
---|
965 | |
---|
966 | // ----------------------------------------- |
---|
967 | // remove and add marked / selected |
---|
968 | // ----------------------------------------- |
---|
969 | |
---|
970 | static void NT_radd_internal(AW_window * aww, AWT_canvas *ntw, AddWhat what, bool quick, int test) { |
---|
971 | AW_awar *awar_best_pars = aww->get_root()->awar(AWAR_BEST_PARSIMONY); |
---|
972 | int oldparsval = awar_best_pars->read_int(); |
---|
973 | |
---|
974 | AWT_graphic_tree *agt = AWT_TREE(ntw); |
---|
975 | if (agt->get_root_node()) { |
---|
976 | agt->tree_static->remove_leafs(AWT_REMOVE_BUT_DONT_FREE|AWT_REMOVE_MARKED); |
---|
977 | } |
---|
978 | |
---|
979 | // restore old parsimony value (otherwise the state where species were removed would count) : |
---|
980 | awar_best_pars->write_int(oldparsval); |
---|
981 | |
---|
982 | nt_add(aww, ntw, what, quick, test); |
---|
983 | } |
---|
984 | |
---|
985 | // normal versions : |
---|
986 | |
---|
987 | static void NT_radd (AW_window * aww, AWT_canvas *ntw, AddWhat what) { NT_radd_internal(aww, ntw, what, false, 0); } |
---|
988 | static void NT_rquick_add(AW_window * aww, AWT_canvas *ntw, AddWhat what) { NT_radd_internal(aww, ntw, what, true, 0); } |
---|
989 | |
---|
990 | // test versions : |
---|
991 | |
---|
992 | #if defined(TESTMENU) |
---|
993 | static void TESTMENU_radd (AW_window * aww, AWT_canvas *ntw, AddWhat what) { NT_radd_internal(aww, ntw, what, false, 1); } |
---|
994 | static void TESTMENU_rquick_add_test(AW_window * aww, AWT_canvas *ntw, AddWhat what) { NT_radd_internal(aww, ntw, what, true, 1); } |
---|
995 | #endif // TESTMENU |
---|
996 | |
---|
997 | // -------------------------------------------------------------------------------- |
---|
998 | // Add Partial sequences |
---|
999 | // -------------------------------------------------------------------------------- |
---|
1000 | |
---|
1001 | |
---|
1002 | static void NT_partial_add(AW_window *aww, AW_CL cl_ntw, AW_CL) { |
---|
1003 | AWT_canvas *ntw = (AWT_canvas*)cl_ntw; |
---|
1004 | nt_add_partial(aww, ntw); |
---|
1005 | } |
---|
1006 | |
---|
1007 | // -------------------------------------------------------------------------------- |
---|
1008 | |
---|
1009 | static void NT_branch_lengths(AW_window *, AWT_canvas *ntw) { |
---|
1010 | arb_progress progress("Calculating Branch Lengths"); |
---|
1011 | rootEdge()->calc_branchlengths(); |
---|
1012 | AWT_TREE(ntw)->resort_tree(0); |
---|
1013 | pars_saveNrefresh_changed_tree(ntw); |
---|
1014 | } |
---|
1015 | |
---|
1016 | static void NT_bootstrap(AW_window *, AWT_canvas *ntw, AW_CL limit_only) { |
---|
1017 | arb_progress progress("Calculating Bootstrap Limit"); |
---|
1018 | AP_BL_MODE mode = AP_BL_MODE((limit_only ? AP_BL_BOOTSTRAP_LIMIT : AP_BL_BOOTSTRAP_ESTIMATE)|AP_BL_BL_ONLY); |
---|
1019 | rootEdge()->nni_rek(-1, false, mode, NULL); |
---|
1020 | AWT_TREE(ntw)->resort_tree(0); |
---|
1021 | AWT_TREE(ntw)->tree_root_display = AWT_TREE(ntw)->get_root_node(); |
---|
1022 | pars_saveNrefresh_changed_tree(ntw); |
---|
1023 | } |
---|
1024 | |
---|
1025 | static void NT_optimize(AW_window *, AWT_canvas *ntw) { |
---|
1026 | arb_progress progress("Optimizing Tree"); |
---|
1027 | PARS_optimizer_cb(rootNode(), progress); |
---|
1028 | ASSERT_VALID_TREE(rootNode()); |
---|
1029 | rootEdge()->calc_branchlengths(); |
---|
1030 | AWT_TREE(ntw)->resort_tree(0); |
---|
1031 | rootNode()->compute_tree(GLOBAL_gb_main); |
---|
1032 | pars_saveNrefresh_changed_tree(ntw); |
---|
1033 | } |
---|
1034 | |
---|
1035 | static void NT_recursiveNNI(AW_window *, AWT_canvas *ntw) { |
---|
1036 | arb_progress progress("Recursive NNI"); |
---|
1037 | AP_FLOAT orgPars = rootNode()->costs(); |
---|
1038 | AP_FLOAT prevPars = orgPars; |
---|
1039 | progress.subtitle(GBS_global_string("Old parsimony: %.1f", orgPars)); |
---|
1040 | while (!progress.aborted()) { |
---|
1041 | AP_FLOAT currPars = rootEdge()->nni_rek(-1, true, AP_BL_NNI_ONLY, NULL); |
---|
1042 | if (currPars == prevPars) break; // no improvement -> abort |
---|
1043 | progress.subtitle(GBS_global_string("New parsimony: %.1f (gain: %.1f)", currPars, orgPars-currPars)); |
---|
1044 | prevPars = currPars; |
---|
1045 | } |
---|
1046 | rootEdge()->calc_branchlengths(); |
---|
1047 | AWT_TREE(ntw)->resort_tree(0); |
---|
1048 | rootNode()->compute_tree(GLOBAL_gb_main); |
---|
1049 | pars_saveNrefresh_changed_tree(ntw); |
---|
1050 | } |
---|
1051 | |
---|
1052 | static AW_window *NT_create_tree_setting(AW_root *aw_root) |
---|
1053 | { |
---|
1054 | static AW_window_simple *aws = 0; |
---|
1055 | if (aws) return (AW_window *)aws; |
---|
1056 | |
---|
1057 | aws = new AW_window_simple; |
---|
1058 | aws->init(aw_root, "SAVE_DB", "SAVE ARB DB"); |
---|
1059 | aws->load_xfig("awt/tree_settings.fig"); |
---|
1060 | |
---|
1061 | aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN); |
---|
1062 | aws->create_button("CLOSE", "CLOSE", "C"); |
---|
1063 | |
---|
1064 | aws->at("help"); aws->callback(AW_POPUP_HELP, (AW_CL)"nt_tree_settings.hlp"); |
---|
1065 | aws->create_button("HELP", "HELP", "H"); |
---|
1066 | |
---|
1067 | aws->at("button"); |
---|
1068 | aws->auto_space(10, 10); |
---|
1069 | aws->label_length(30); |
---|
1070 | |
---|
1071 | aws->label("Base Line Width"); |
---|
1072 | aws->create_input_field(AWAR_DTREE_BASELINEWIDTH, 4); |
---|
1073 | aws->at_newline(); |
---|
1074 | |
---|
1075 | aws->label("Relative vert. Dist"); |
---|
1076 | aws->create_input_field(AWAR_DTREE_VERICAL_DIST, 4); |
---|
1077 | aws->at_newline(); |
---|
1078 | |
---|
1079 | aws->label("Auto Jump (list tree)"); |
---|
1080 | aws->create_toggle(AWAR_DTREE_AUTO_JUMP); |
---|
1081 | aws->at_newline(); |
---|
1082 | |
---|
1083 | |
---|
1084 | return (AW_window *)aws; |
---|
1085 | |
---|
1086 | } |
---|
1087 | |
---|
1088 | static void PA_focus_cb(AW_window *, GBDATA *gb_main_par) |
---|
1089 | { |
---|
1090 | GB_transaction dummy(gb_main_par); |
---|
1091 | } |
---|
1092 | |
---|
1093 | // ----------------------- |
---|
1094 | // test functions |
---|
1095 | |
---|
1096 | #if defined(TESTMENU) |
---|
1097 | static void refreshTree(AWT_canvas *ntw) { |
---|
1098 | GB_transaction gb_dummy(ntw->gb_main); |
---|
1099 | |
---|
1100 | AWT_TREE(ntw)->check_update(ntw->gb_main); |
---|
1101 | GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, 0, 0, 0); |
---|
1102 | if (error) aw_message(error); |
---|
1103 | ntw->zoom_reset_and_refresh(); |
---|
1104 | } |
---|
1105 | #endif // TESTMENU |
---|
1106 | |
---|
1107 | static void setBranchlens(AP_tree_nlen *node, double newLen) |
---|
1108 | { |
---|
1109 | node->setBranchlen(newLen, newLen); |
---|
1110 | |
---|
1111 | if (!node->is_leaf) |
---|
1112 | { |
---|
1113 | setBranchlens(node->get_leftson(), newLen); |
---|
1114 | setBranchlens(node->get_rightson(), newLen); |
---|
1115 | } |
---|
1116 | } |
---|
1117 | #if defined(TESTMENU) |
---|
1118 | static void TESTMENU_setBranchlen(AW_window *, AWT_canvas *ntw) |
---|
1119 | { |
---|
1120 | AP_tree_nlen *root = rootNode(); |
---|
1121 | |
---|
1122 | setBranchlens(root, 1.0); |
---|
1123 | refreshTree(ntw); |
---|
1124 | } |
---|
1125 | |
---|
1126 | static void TESTMENU_treeStats(AW_window *, AWT_canvas *) { |
---|
1127 | ARB_tree_info tinfo; |
---|
1128 | AP_tree_nlen *root = rootNode(); |
---|
1129 | |
---|
1130 | { |
---|
1131 | GB_transaction ta(root->get_tree_root()->get_gb_main()); |
---|
1132 | root->calcTreeInfo(tinfo); |
---|
1133 | } |
---|
1134 | |
---|
1135 | puts("Tree stats:"); |
---|
1136 | |
---|
1137 | printf("nodes =%6zu\n", tinfo.nodes()); |
---|
1138 | printf(" inner =%6zu\n", tinfo.innerNodes); |
---|
1139 | printf(" groups =%6zu\n", tinfo.groups); |
---|
1140 | printf(" leafs =%6zu\n", tinfo.leafs); |
---|
1141 | printf(" unlinked =%6zu (zombies?)\n", tinfo.unlinked); |
---|
1142 | printf(" linked =%6zu\n", tinfo.linked()); |
---|
1143 | printf(" marked =%6zu\n", tinfo.marked); |
---|
1144 | } |
---|
1145 | |
---|
1146 | static void TESTMENU_mixTree(AW_window *, AWT_canvas *ntw) |
---|
1147 | { |
---|
1148 | rootEdge()->mixTree(100); |
---|
1149 | refreshTree(ntw); |
---|
1150 | } |
---|
1151 | |
---|
1152 | static void TESTMENU_sortTreeByName(AW_window *, AWT_canvas *ntw) |
---|
1153 | { |
---|
1154 | AP_tree_nlen *root = rootNode(); |
---|
1155 | |
---|
1156 | root->sortByName(); |
---|
1157 | refreshTree(ntw); |
---|
1158 | } |
---|
1159 | |
---|
1160 | static void TESTMENU_buildAndDumpChain(AW_window *, AWT_canvas *) |
---|
1161 | { |
---|
1162 | AP_tree_nlen *root = rootNode(); |
---|
1163 | |
---|
1164 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(2); |
---|
1165 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(3); |
---|
1166 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(4); |
---|
1167 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(5); |
---|
1168 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(6); |
---|
1169 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(7); |
---|
1170 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(8); |
---|
1171 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(9); |
---|
1172 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(10); |
---|
1173 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(11); |
---|
1174 | root->get_leftson()->edgeTo(root->get_rightson())->testChain(-1); |
---|
1175 | } |
---|
1176 | |
---|
1177 | static void init_TEST_menu(AW_window_menu_modes *awm, AWT_canvas *ntw) |
---|
1178 | { |
---|
1179 | awm->create_menu("Test[debug]", "T", AWM_ALL); |
---|
1180 | |
---|
1181 | awm->insert_menu_topic(0, "Mix tree", "M", "", AWM_ALL, (AW_CB)TESTMENU_mixTree, (AW_CL)ntw, 0); |
---|
1182 | awm->insert_menu_topic(0, "Tree statistics", "s", "", AWM_ALL, (AW_CB)TESTMENU_treeStats, (AW_CL)ntw, 0); |
---|
1183 | awm->insert_menu_topic(0, "Set branchlens", "b", "", AWM_ALL, (AW_CB)TESTMENU_setBranchlen, (AW_CL)ntw, 0); |
---|
1184 | awm->insert_menu_topic(0, "Sort tree by name", "o", "", AWM_ALL, (AW_CB)TESTMENU_sortTreeByName, (AW_CL)ntw, 0); |
---|
1185 | awm->insert_menu_topic(0, "Build & dump chain", "c", "", AWM_ALL, (AW_CB)TESTMENU_buildAndDumpChain, (AW_CL)ntw, 0); |
---|
1186 | awm->sep______________(); |
---|
1187 | awm->insert_menu_topic(0, "Add marked species", "A", "pa_quick.hlp", AWM_ALL, (AW_CB)TESTMENU_quick_add, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1188 | awm->insert_menu_topic(0, "Add marked species + NNI", "N", "pa_add.hlp", AWM_ALL, (AW_CB)TESTMENU_add, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1189 | awm->insert_menu_topic(0, "Remove & add marked species", "o", "pa_add.hlp", AWM_ALL, (AW_CB)TESTMENU_rquick_add_test, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1190 | awm->insert_menu_topic(0, "Remove & add marked + NNI", "v", "pa_add.hlp", AWM_ALL, (AW_CB)TESTMENU_radd, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1191 | awm->sep______________(); |
---|
1192 | awm->insert_menu_topic(0, "Add selected species", "l", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)TESTMENU_quick_add, (AW_CL)ntw, NT_ADD_SELECTED); |
---|
1193 | awm->insert_menu_topic(0, "Add selected species + NNI", "I", "pa_add_sel.hlp", AWM_ALL, (AW_CB)TESTMENU_add, (AW_CL)ntw, NT_ADD_SELECTED); |
---|
1194 | } |
---|
1195 | #endif // TESTMENU |
---|
1196 | |
---|
1197 | static GB_ERROR pars_check_size(AW_root *awr) { |
---|
1198 | char *tree_name = awr->awar(AWAR_TREE)->read_string(); |
---|
1199 | char *filter = awr->awar(AWAR_FILTER_FILTER)->read_string(); |
---|
1200 | GB_ERROR error = 0; |
---|
1201 | long ali_len = 0; |
---|
1202 | if (strlen(filter)) { |
---|
1203 | int i; |
---|
1204 | for (i=0; filter[i]; i++) { |
---|
1205 | if (filter[i] != '0') ali_len++; |
---|
1206 | } |
---|
1207 | } |
---|
1208 | else { |
---|
1209 | char *ali_name = awr->awar(AWAR_ALIGNMENT)->read_string(); |
---|
1210 | ali_len = GBT_get_alignment_len(GLOBAL_gb_main, ali_name); |
---|
1211 | delete ali_name; |
---|
1212 | } |
---|
1213 | |
---|
1214 | long tree_size = GBT_size_of_tree(GLOBAL_gb_main, tree_name); |
---|
1215 | if (tree_size == -1) { |
---|
1216 | error = "Please select an existing tree"; |
---|
1217 | } |
---|
1218 | else { |
---|
1219 | unsigned long expected_memuse = (ali_len * tree_size * 4 / 1000); |
---|
1220 | if (expected_memuse > GB_get_physical_memory()) { |
---|
1221 | error = GBS_global_string("Estimated memory usage (%s) exceeds physical memory (will swap)\n" |
---|
1222 | "(did you specify a filter?)", |
---|
1223 | GBS_readable_size(expected_memuse, "b")); |
---|
1224 | } |
---|
1225 | } |
---|
1226 | free(filter); |
---|
1227 | free(tree_name); |
---|
1228 | return error; |
---|
1229 | } |
---|
1230 | |
---|
1231 | static void pars_reset_optimal_parsimony(AW_window *aww, AW_CL *cl_ntw) { |
---|
1232 | AW_root *awr = aww->get_root(); |
---|
1233 | awr->awar(AWAR_BEST_PARSIMONY)->write_int(awr->awar(AWAR_PARSIMONY)->read_int()); |
---|
1234 | |
---|
1235 | AWT_canvas *ntw = (AWT_canvas*)cl_ntw; |
---|
1236 | ntw->refresh(); |
---|
1237 | } |
---|
1238 | |
---|
1239 | |
---|
1240 | static void pars_start_cb(AW_window *aw_parent, AW_CL cd_weightedFilter, AW_CL cl_cmds) { |
---|
1241 | WeightedFilter *wfilt = (WeightedFilter*)cd_weightedFilter; |
---|
1242 | PARS_commands *cmds = (PARS_commands*)cl_cmds; |
---|
1243 | AW_root *awr = aw_parent->get_root(); |
---|
1244 | GB_begin_transaction(GLOBAL_gb_main); |
---|
1245 | { |
---|
1246 | GB_ERROR warning = pars_check_size(awr); |
---|
1247 | if (warning) { |
---|
1248 | char *question = GBS_global_string_copy("%s\nDo you want to continue?", warning); |
---|
1249 | bool cont = aw_ask_sure("swap_warning", question); |
---|
1250 | free(question); |
---|
1251 | |
---|
1252 | if (!cont) { |
---|
1253 | GB_commit_transaction(GLOBAL_gb_main); |
---|
1254 | return; |
---|
1255 | } |
---|
1256 | } |
---|
1257 | } |
---|
1258 | |
---|
1259 | |
---|
1260 | AW_window_menu_modes *awm = new AW_window_menu_modes(); |
---|
1261 | awm->init(awr, "ARB_PARSIMONY", "ARB_PARSIMONY", 400, 200); |
---|
1262 | |
---|
1263 | AW_gc_manager aw_gc_manager = 0; |
---|
1264 | |
---|
1265 | GLOBAL_PARS->tree = PARS_generate_tree(awr, wfilt); |
---|
1266 | |
---|
1267 | AWT_canvas *ntw; |
---|
1268 | { |
---|
1269 | AP_tree_sort old_sort_type = GLOBAL_PARS->tree->tree_sort; |
---|
1270 | GLOBAL_PARS->tree->set_tree_type(AP_LIST_SIMPLE, NULL); // avoid NDS warnings during startup |
---|
1271 | ntw = new AWT_canvas(GLOBAL_gb_main, (AW_window *)awm, GLOBAL_PARS->tree, aw_gc_manager, AWAR_TREE); |
---|
1272 | GLOBAL_PARS->tree->set_tree_type(old_sort_type, ntw); |
---|
1273 | } |
---|
1274 | |
---|
1275 | { |
---|
1276 | GB_ERROR error = 0; |
---|
1277 | arb_progress progress("loading tree"); |
---|
1278 | NT_reload_tree_event(awr, ntw, 0); // load tree (but do not expose - first zombies need to be removed) |
---|
1279 | if (!GLOBAL_PARS->tree->get_root_node()) { |
---|
1280 | error = "I cannot load the selected tree"; |
---|
1281 | } |
---|
1282 | else { |
---|
1283 | AP_tree_edge::initialize(rootNode()); // builds edges |
---|
1284 | long removed = GLOBAL_PARS->tree->tree_static->remove_leafs(AWT_REMOVE_DELETED); |
---|
1285 | |
---|
1286 | PARS_tree_init(GLOBAL_PARS->tree); |
---|
1287 | removed += GLOBAL_PARS->tree->tree_static->remove_leafs(AWT_REMOVE_DELETED | AWT_REMOVE_NO_SEQUENCE); |
---|
1288 | |
---|
1289 | if (!GLOBAL_PARS->tree->get_root_node()) { |
---|
1290 | const char *aliname = GLOBAL_PARS->tree->tree_static->get_aliview()->get_aliname(); |
---|
1291 | error = GBS_global_string("Less than 2 species contain data in '%s'\n" |
---|
1292 | "Tree vanished", aliname); |
---|
1293 | } |
---|
1294 | else if (removed) { |
---|
1295 | aw_message(GBS_global_string("Removed %li leafs (zombies or species w/o data in alignment)", removed)); |
---|
1296 | } |
---|
1297 | |
---|
1298 | error = GB_end_transaction(ntw->gb_main, error); |
---|
1299 | if (!error) { |
---|
1300 | progress.subtitle("Calculating inner nodes"); |
---|
1301 | GLOBAL_PARS->get_root_node()->costs(); |
---|
1302 | } |
---|
1303 | } |
---|
1304 | if (error) aw_popup_exit(error); |
---|
1305 | } |
---|
1306 | |
---|
1307 | awr->awar(AWAR_COLOR_GROUPS_USE)->add_callback((AW_RCB)NT_recompute_cb, (AW_CL)ntw, 0); |
---|
1308 | |
---|
1309 | if (cmds->add_marked) NT_quick_add(awm, ntw, NT_ADD_MARKED); |
---|
1310 | if (cmds->add_selected) NT_quick_add(awm, ntw, NT_ADD_SELECTED); |
---|
1311 | if (cmds->calc_branch_lengths) NT_branch_lengths(awm, ntw); |
---|
1312 | if (cmds->calc_bootstrap) NT_bootstrap(awm, ntw, 0); |
---|
1313 | if (cmds->quit) pars_exit(awm); |
---|
1314 | |
---|
1315 | GB_transaction dummy(ntw->gb_main); |
---|
1316 | |
---|
1317 | GBDATA *gb_arb_presets = GB_search(ntw->gb_main, "arb_presets", GB_CREATE_CONTAINER); |
---|
1318 | GB_add_callback(gb_arb_presets, GB_CB_CHANGED, (GB_CB)AWT_expose_cb, (int *)ntw); |
---|
1319 | |
---|
1320 | #if defined(DEBUG) |
---|
1321 | AWT_create_debug_menu(awm); |
---|
1322 | #endif // DEBUG |
---|
1323 | |
---|
1324 | awm->create_menu("File", "F", AWM_ALL); |
---|
1325 | { |
---|
1326 | awm->insert_menu_topic("print_tree", "Print Tree ...", "P", "tree2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0); |
---|
1327 | awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, (AW_CB)PARS_export_cb, (AW_CL)ntw, 2); |
---|
1328 | } |
---|
1329 | |
---|
1330 | awm->create_menu("Species", "S", AWM_ALL); |
---|
1331 | { |
---|
1332 | NT_insert_mark_submenus(awm, ntw, 0); |
---|
1333 | |
---|
1334 | } |
---|
1335 | awm->create_menu("Tree", "T", AWM_ALL); |
---|
1336 | { |
---|
1337 | |
---|
1338 | awm->insert_menu_topic("nds", "NDS (Node Display Setup) ...", "N", "props_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_create_nds_window, (AW_CL)ntw->gb_main); |
---|
1339 | |
---|
1340 | awm->sep______________(); |
---|
1341 | awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG ...", "E", "tree2file.hlp", AWM_ALL, AWT_popup_tree_export_window, (AW_CL)ntw, 0); |
---|
1342 | awm->insert_menu_topic("tree_print", "Print tree ...", "P", "tree2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0); |
---|
1343 | awm->sep______________(); |
---|
1344 | awm->insert_sub_menu("Collapse/Expand Tree", "C"); |
---|
1345 | { |
---|
1346 | awm->insert_menu_topic("tree_group_all", "Group All", "A", "tgroupall.hlp", AWM_ALL, (AW_CB)NT_group_tree_cb, (AW_CL)ntw, 0); |
---|
1347 | awm->insert_menu_topic("tree_group_not_marked", "Group All Except Marked", "M", "tgroupnmrkd.hlp", AWM_ALL, (AW_CB)NT_group_not_marked_cb, (AW_CL)ntw, 0); |
---|
1348 | awm->insert_menu_topic("tree_ungroup_all", "Ungroup All", "U", "tungroupall.hlp", AWM_ALL, (AW_CB)NT_ungroup_all_cb, (AW_CL)ntw, 0); |
---|
1349 | awm->sep______________(); |
---|
1350 | NT_insert_color_collapse_submenu(awm, ntw); |
---|
1351 | } |
---|
1352 | awm->close_sub_menu(); |
---|
1353 | awm->sep______________(); |
---|
1354 | awm->insert_sub_menu("Remove Species from Tree", "R"); |
---|
1355 | { |
---|
1356 | awm->insert_menu_topic("tree_remove_deleted", "Remove Zombies", "Z", "trm_del.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_DELETED|AWT_REMOVE_BUT_DONT_FREE); |
---|
1357 | awm->insert_menu_topic("tree_remove_marked", "Remove Marked", "M", "trm_mrkd.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_MARKED|AWT_REMOVE_BUT_DONT_FREE); |
---|
1358 | awm->insert_menu_topic("tree_keep_marked", "Keep Marked", "K", "tkeep_mrkd.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_NOT_MARKED|AWT_REMOVE_DELETED|AWT_REMOVE_BUT_DONT_FREE); |
---|
1359 | } |
---|
1360 | awm->close_sub_menu(); |
---|
1361 | awm->insert_sub_menu("Add Species to Tree", "A"); |
---|
1362 | { |
---|
1363 | awm->insert_menu_topic("add_marked", "Add Marked Species", "M", "pa_quick.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1364 | awm->insert_menu_topic("add_marked_nni", "Add Marked Species + Local Optimization (NNI)", "N", "pa_add.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1365 | awm->insert_menu_topic("rm_add_marked", "Remove & Add Marked Species", "R", "pa_add.hlp", AWM_ALL, (AW_CB)NT_rquick_add, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1366 | awm->insert_menu_topic("rm_add_marked_nni|", "Remove & Add Marked + Local Optimization (NNI)", "L", "pa_add.hlp", AWM_ALL, (AW_CB)NT_radd, (AW_CL)ntw, NT_ADD_MARKED); |
---|
1367 | awm->sep______________(); |
---|
1368 | awm->insert_menu_topic("add_marked_partial", "Add Marked Partial Species", "P", "pa_partial.hlp", AWM_ALL, NT_partial_add, (AW_CL)ntw, (AW_CL)0); |
---|
1369 | awm->sep______________(); |
---|
1370 | awm->insert_menu_topic("add_selected", "Add Selected Species", "S", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, NT_ADD_SELECTED); |
---|
1371 | awm->insert_menu_topic("add_selected_nni", "Add Selected Species + Local Optimization (NNI)", "O", "pa_add_sel.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, NT_ADD_SELECTED); |
---|
1372 | } |
---|
1373 | awm->close_sub_menu(); |
---|
1374 | awm->sep______________(); |
---|
1375 | awm->insert_sub_menu("Tree Optimization", "O"); |
---|
1376 | { |
---|
1377 | awm->insert_menu_topic("nni", "Local Optimization (NNI) of Marked Visible Nodes", "L", "", AWM_ALL, (AW_CB)NT_recursiveNNI, (AW_CL)ntw, 0); |
---|
1378 | awm->insert_menu_topic("kl_optimization", "Global Optimization of Marked Visible Nodes", "G", "pa_optimizer.hlp", AWM_ALL, (AW_CB)NT_optimize, (AW_CL)ntw, 0); |
---|
1379 | } |
---|
1380 | awm->close_sub_menu(); |
---|
1381 | awm->insert_menu_topic("reset", "Reset optimal parsimony", "s", "", AWM_ALL, (AW_CB)pars_reset_optimal_parsimony, (AW_CL)ntw, 0); |
---|
1382 | awm->sep______________(); |
---|
1383 | awm->insert_menu_topic("beautify_tree", "Beautify Tree", "B", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 0); |
---|
1384 | awm->insert_menu_topic("calc_branch_lengths", "Calculate Branch Lengths", "L", "pa_branchlengths.hlp", AWM_ALL, (AW_CB)NT_branch_lengths, (AW_CL)ntw, 0); |
---|
1385 | awm->sep______________(); |
---|
1386 | awm->insert_menu_topic("calc_upper_bootstrap_indep", "Calculate Upper Bootstrap Limit (dependent NNI)", "d", "pa_bootstrap.hlp", AWM_ALL, (AW_CB)NT_bootstrap, (AW_CL)ntw, 0); |
---|
1387 | awm->insert_menu_topic("calc_upper_bootstrap_dep", "Calculate Upper Bootstrap Limit (independent NNI)", "i", "pa_bootstrap.hlp", AWM_ALL, (AW_CB)NT_bootstrap, (AW_CL)ntw, 1); |
---|
1388 | awm->insert_menu_topic("tree_remove_remark", "Remove Bootstrap Values", "V", "trm_boot.hlp", AWM_ALL, (AW_CB)NT_remove_bootstrap, (AW_CL)ntw, 0); |
---|
1389 | } |
---|
1390 | |
---|
1391 | #if defined(TESTMENU) |
---|
1392 | init_TEST_menu(awm, ntw); |
---|
1393 | #endif // TESTMENU |
---|
1394 | |
---|
1395 | awm->create_menu("Reset", "R", AWM_ALL); |
---|
1396 | { |
---|
1397 | awm->insert_menu_topic("reset_logical_zoom", "Logical Zoom", "L", "rst_log_zoom.hlp", AWM_ALL, (AW_CB)NT_reset_lzoom_cb, (AW_CL)ntw, 0); |
---|
1398 | awm->insert_menu_topic("reset_physical_zoom", "Physical Zoom", "P", "rst_phys_zoom.hlp", AWM_ALL, (AW_CB)NT_reset_pzoom_cb, (AW_CL)ntw, 0); |
---|
1399 | } |
---|
1400 | |
---|
1401 | awm->create_menu("Properties", "r", AWM_ALL); |
---|
1402 | { |
---|
1403 | awm->insert_menu_topic("props_menu", "Menu: Colors and Fonts ...", "M", "props_frame.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_preset_window, 0); |
---|
1404 | awm->insert_menu_topic("props_tree", "Tree: Colors and Fonts ...", "C", "pars_props_data.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_create_gc_window, (AW_CL)aw_gc_manager); |
---|
1405 | awm->insert_menu_topic("props_tree2", "Tree: Settings ...", "T", "nt_tree_settings.hlp", AWM_ALL, AW_POPUP,(AW_CL)NT_create_tree_setting, (AW_CL)ntw); |
---|
1406 | awm->insert_menu_topic("props_kl", "KERN. LIN ...", "K", "kernlin.hlp", AWM_ALL, AW_POPUP,(AW_CL)create_kernighan_window, 0); |
---|
1407 | awm->sep______________(); |
---|
1408 | AW_insert_common_property_menu_entries(awm); |
---|
1409 | awm->sep______________(); |
---|
1410 | awm->insert_menu_topic("save_props", "Save Defaults (pars.arb)", "D", "savedef.hlp", AWM_ALL, (AW_CB)AW_save_properties, 0, 0); |
---|
1411 | } |
---|
1412 | awm->button_length(5); |
---|
1413 | |
---|
1414 | awm->insert_help_topic("How to use Help", "H", "help.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"help.hlp", 0); |
---|
1415 | awm->insert_help_topic("ARB Help", "A", "arb.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"arb.hlp", 0); |
---|
1416 | awm->insert_help_topic("ARB PARSIMONY Help", "N", "arb_pars.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"arb_pars.hlp", 0); |
---|
1417 | |
---|
1418 | awm->create_mode("select.bitmap", "mode_select.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SELECT); |
---|
1419 | awm->create_mode("mark.bitmap", "mode_mark.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_MARK); |
---|
1420 | awm->create_mode("group.bitmap", "mode_group.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_GROUP); |
---|
1421 | awm->create_mode("pzoom.bitmap", "mode_pzoom.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_ZOOM); |
---|
1422 | awm->create_mode("lzoom.bitmap", "mode_lzoom.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_LZOOM); |
---|
1423 | awm->create_mode("swap.bitmap", "mode_swap.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SWAP); |
---|
1424 | awm->create_mode("move.bitmap", "mode_move.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_MOVE); |
---|
1425 | #ifdef NNI_MODES |
---|
1426 | awm->create_mode("nearestn.bitmap", "mode_nni.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_NNI); |
---|
1427 | awm->create_mode("kernlin.bitmap", "mode_kernlin.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_KERNINGHAN); |
---|
1428 | awm->create_mode("optimize.bitmap", "mode_optimize.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_OPTIMIZE); |
---|
1429 | #endif // NNI_MODES |
---|
1430 | awm->create_mode("setroot.bitmap", "mode_set_root.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SETROOT); |
---|
1431 | awm->create_mode("reset.bitmap", "mode_reset.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_RESET); |
---|
1432 | |
---|
1433 | awm->at(5, 2); |
---|
1434 | awm->auto_space(0, -2); |
---|
1435 | awm->shadow_width(1); |
---|
1436 | |
---|
1437 | |
---|
1438 | int db_treex, db_treey; |
---|
1439 | awm->get_at_position(&db_treex, &db_treey); |
---|
1440 | awm->callback(AW_POPUP_HELP, (AW_CL)"nt_tree_select.hlp"); |
---|
1441 | awm->button_length(16); |
---|
1442 | awm->help_text("nt_tree_select.hlp"); |
---|
1443 | awm->create_button(0, AWAR_TREE); |
---|
1444 | |
---|
1445 | |
---|
1446 | int db_stackx, db_stacky; |
---|
1447 | awm->label_length(8); |
---|
1448 | awm->label("Stored"); |
---|
1449 | awm->get_at_position(&db_stackx, &db_stacky); |
---|
1450 | awm->button_length(6); |
---|
1451 | awm->callback(AW_POPUP_HELP, (AW_CL)"ap_stack.hlp"); |
---|
1452 | awm->help_text("ap_stack.hlp"); |
---|
1453 | awm->create_button(0, AWAR_STACKPOINTER); |
---|
1454 | |
---|
1455 | int db_parsx, db_parsy; |
---|
1456 | awm->label_length(14); |
---|
1457 | awm->label("Current Pars:"); |
---|
1458 | awm->get_at_position(&db_parsx, &db_parsy); |
---|
1459 | |
---|
1460 | awm->button_length(10); |
---|
1461 | awm->create_button(0, AWAR_PARSIMONY); |
---|
1462 | |
---|
1463 | awm->button_length(0); |
---|
1464 | |
---|
1465 | awm->callback((AW_CB)NT_jump_cb, (AW_CL)ntw, 1); |
---|
1466 | awm->help_text("tr_jump.hlp"); |
---|
1467 | awm->create_button("JUMP", "#pjump.bitmap", 0); |
---|
1468 | |
---|
1469 | awm->callback(AW_POPUP_HELP, (AW_CL)"arb_pars.hlp"); |
---|
1470 | awm->help_text("help.hlp"); |
---|
1471 | awm->create_button("HELP", "HELP", "H"); |
---|
1472 | |
---|
1473 | awm->at_newline(); |
---|
1474 | |
---|
1475 | awm->button_length(8); |
---|
1476 | awm->at_x(db_stackx); |
---|
1477 | awm->callback((AW_CB1)AP_user_pop_cb, (AW_CL)ntw); |
---|
1478 | awm->help_text("ap_stack.hlp"); |
---|
1479 | awm->create_button("POP", "RESTORE", 0); |
---|
1480 | |
---|
1481 | awm->button_length(6); |
---|
1482 | awm->callback((AW_CB1)AP_user_push_cb, (AW_CL)ntw); |
---|
1483 | awm->help_text("ap_stack.hlp"); |
---|
1484 | awm->create_button("PUSH", "STORE", 0); |
---|
1485 | |
---|
1486 | awm->button_length(7); |
---|
1487 | |
---|
1488 | awm->at_x(db_treex); |
---|
1489 | awm->callback((AW_CB)NT_set_tree_style, (AW_CL)ntw, (AW_CL)AP_TREE_RADIAL); |
---|
1490 | awm->help_text("tr_type_radial.hlp"); |
---|
1491 | awm->create_button("RADIAL_TREE", "#radial.bitmap", 0); |
---|
1492 | |
---|
1493 | awm->callback((AW_CB)NT_set_tree_style, (AW_CL)ntw, (AW_CL)AP_TREE_NORMAL); |
---|
1494 | awm->help_text("tr_type_list.hlp"); |
---|
1495 | awm->create_button("LIST_TREE", "#list.bitmap", 0); |
---|
1496 | |
---|
1497 | awm->at_x(db_parsx); |
---|
1498 | awm->label_length(14); |
---|
1499 | awm->label("Optimal Pars:"); |
---|
1500 | |
---|
1501 | awm->button_length(10); |
---|
1502 | awm->create_button(0, AWAR_BEST_PARSIMONY); |
---|
1503 | |
---|
1504 | awm->at_newline(); |
---|
1505 | |
---|
1506 | { |
---|
1507 | AW_at_maxsize maxSize; // store size (so AWAR_FOOTER does not affect min. window size) |
---|
1508 | maxSize.store(awm->_at); |
---|
1509 | awm->button_length(AWAR_FOOTER_MAX_LEN); |
---|
1510 | awm->create_button(0, AWAR_FOOTER); |
---|
1511 | awm->at_newline(); |
---|
1512 | maxSize.restore(awm->_at); |
---|
1513 | } |
---|
1514 | |
---|
1515 | awm->get_at_position(&db_treex, &db_treey); |
---|
1516 | awm->set_info_area_height(db_treey+6); |
---|
1517 | |
---|
1518 | awm->set_bottom_area_height(0); |
---|
1519 | awm->set_focus_callback((AW_CB)PA_focus_cb, (AW_CL)ntw->gb_main, 0); |
---|
1520 | |
---|
1521 | aw_parent->hide(); // hide parent |
---|
1522 | awm->show(); |
---|
1523 | |
---|
1524 | AP_user_push_cb(aw_parent, ntw); // push initial tree |
---|
1525 | } |
---|
1526 | |
---|
1527 | static AW_window *create_pars_init_window(AW_root *awr, const PARS_commands *cmds) { |
---|
1528 | AW_window_simple *aws = new AW_window_simple; |
---|
1529 | aws->init(awr, "PARS_PROPS", "SET PARSIMONY OPTIONS"); |
---|
1530 | aws->load_xfig("pars/init.fig"); |
---|
1531 | |
---|
1532 | aws->button_length(10); |
---|
1533 | aws->label_length(10); |
---|
1534 | |
---|
1535 | aws->callback(pars_exit); |
---|
1536 | aws->at("close"); |
---|
1537 | aws->create_button("ABORT", "ABORT", "A"); |
---|
1538 | |
---|
1539 | aws->callback(AW_POPUP_HELP, (AW_CL)"arb_pars_init.hlp"); |
---|
1540 | aws->at("help"); |
---|
1541 | aws->create_button("HELP", "HELP", "H"); |
---|
1542 | |
---|
1543 | WeightedFilter *weighted_filter = // do NOT free (bound to callbacks) |
---|
1544 | new WeightedFilter(GLOBAL_gb_main, aws->get_root(), AWAR_FILTER_NAME, AWAR_COLUMNSTAT_NAME, aws->get_root()->awar_string(AWAR_ALIGNMENT)); |
---|
1545 | |
---|
1546 | aws->at("filter"); |
---|
1547 | aws->callback(AW_POPUP, (AW_CL)awt_create_select_filter_win, (AW_CL)weighted_filter->get_adfiltercbstruct()); |
---|
1548 | aws->create_button("SELECT_FILTER", AWAR_FILTER_NAME); |
---|
1549 | |
---|
1550 | aws->at("weights"); |
---|
1551 | aws->callback(AW_POPUP, (AW_CL)COLSTAT_create_selection_window, (AW_CL)weighted_filter->get_column_stat()); |
---|
1552 | aws->sens_mask(AWM_EXP); |
---|
1553 | aws->create_button("SELECT_CSP", AWAR_COLUMNSTAT_NAME); |
---|
1554 | aws->sens_mask(AWM_ALL); |
---|
1555 | |
---|
1556 | aws->at("alignment"); |
---|
1557 | awt_create_selection_list_on_alignments(GLOBAL_gb_main, (AW_window *)aws, AWAR_ALIGNMENT, "*="); |
---|
1558 | |
---|
1559 | aws->at("tree"); |
---|
1560 | awt_create_selection_list_on_trees(GLOBAL_gb_main, (AW_window *)aws, AWAR_TREE); |
---|
1561 | |
---|
1562 | aws->callback(pars_start_cb, (AW_CL)weighted_filter, (AW_CL)cmds); |
---|
1563 | aws->at("go"); |
---|
1564 | aws->create_button("GO", "GO", "G"); |
---|
1565 | |
---|
1566 | return aws; |
---|
1567 | } |
---|
1568 | |
---|
1569 | static void create_parsimony_variables(AW_root *aw_root, AW_default def) |
---|
1570 | { |
---|
1571 | // parsimony |
---|
1572 | #if 0 |
---|
1573 | aw_root->awar_float("genetic/m_rate", 0, def); |
---|
1574 | aw_root->awar_int("genetic/input_1", 0, def); |
---|
1575 | aw_root->awar_int("genetic/input_2", 0, def); |
---|
1576 | aw_root->awar_float("genetic/input_3", 0, def); |
---|
1577 | aw_root->awar_float("genetic/input_4", 0, def); |
---|
1578 | aw_root->awar_float("genetic/input_5", 0, def); |
---|
1579 | aw_root->awar_float("genetic/input_6", 0, def); |
---|
1580 | aw_root->awar_float("genetic/input_7", 0, def); |
---|
1581 | aw_root->awar_float("genetic/input_8", 0, def); |
---|
1582 | aw_root->awar_float("genetic/input_9", 0, def); |
---|
1583 | aw_root->awar_float("genetic/input_10", 0, def); |
---|
1584 | aw_root->awar_float("genetic/input_11", 0, def); |
---|
1585 | aw_root->awar_int("genetic/out_1", 0, def); |
---|
1586 | aw_root->awar_float("genetic/out_2", 0, def); |
---|
1587 | aw_root->awar_float("genetic/out_3", 0, def); |
---|
1588 | aw_root->awar_float("genetic/out_4", 0, def); |
---|
1589 | aw_root->awar_float("genetic/out_5", 0, def); |
---|
1590 | aw_root->awar_float("genetic/out_6", 0, def); |
---|
1591 | aw_root->awar_float("genetic/out_7", 0, def); |
---|
1592 | aw_root->awar_float("genetic/out_8", 0, def); |
---|
1593 | #endif |
---|
1594 | // kernighan |
---|
1595 | |
---|
1596 | aw_root->awar_float("genetic/kh/nodes", 1.7, def); |
---|
1597 | aw_root->awar_int("genetic/kh/maxdepth", 15, def); |
---|
1598 | aw_root->awar_int("genetic/kh/incdepth", 5, def); |
---|
1599 | |
---|
1600 | aw_root->awar_int("genetic/kh/static/enable", 1, def); |
---|
1601 | aw_root->awar_int("genetic/kh/static/depth0", 2, def); |
---|
1602 | aw_root->awar_int("genetic/kh/static/depth1", 2, def); |
---|
1603 | aw_root->awar_int("genetic/kh/static/depth2", 2, def); |
---|
1604 | aw_root->awar_int("genetic/kh/static/depth3", 2, def); |
---|
1605 | aw_root->awar_int("genetic/kh/static/depth4", 1, def); |
---|
1606 | |
---|
1607 | aw_root->awar_int("genetic/kh/dynamic/enable", 1, def); |
---|
1608 | aw_root->awar_int("genetic/kh/dynamic/start", 100, def); |
---|
1609 | aw_root->awar_int("genetic/kh/dynamic/maxx", 6, def); |
---|
1610 | aw_root->awar_int("genetic/kh/dynamic/maxy", 150, def); |
---|
1611 | |
---|
1612 | aw_root->awar_int("genetic/kh/function_type", AP_QUADRAT_START, def); |
---|
1613 | |
---|
1614 | awt_create_dtree_awars(aw_root, def); |
---|
1615 | } |
---|
1616 | |
---|
1617 | static void pars_create_all_awars(AW_root *awr, AW_default aw_def) |
---|
1618 | { |
---|
1619 | awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL_gb_main); |
---|
1620 | awr->awar_string(AWAR_FOOTER, "", aw_def); |
---|
1621 | awr->awar_string(AWAR_FILTER_NAME, "none", GLOBAL_gb_main); |
---|
1622 | |
---|
1623 | { |
---|
1624 | GB_transaction ta(GLOBAL_gb_main); |
---|
1625 | char *dali = GBT_get_default_alignment(GLOBAL_gb_main); |
---|
1626 | |
---|
1627 | awr->awar_string(AWAR_ALIGNMENT, dali, GLOBAL_gb_main)->write_string(dali); |
---|
1628 | free(dali); |
---|
1629 | } |
---|
1630 | |
---|
1631 | awt_set_awar_to_valid_filter_good_for_tree_methods(GLOBAL_gb_main, awr, AWAR_FILTER_NAME); |
---|
1632 | |
---|
1633 | awr->awar_string(AWAR_FILTER_FILTER, "", GLOBAL_gb_main); |
---|
1634 | awr->awar_string(AWAR_FILTER_ALIGNMENT, "", aw_def); |
---|
1635 | |
---|
1636 | awr->awar(AWAR_FILTER_ALIGNMENT)->map(AWAR_ALIGNMENT); |
---|
1637 | |
---|
1638 | awr->awar_int(AWAR_PARS_TYPE, PARS_WAGNER, GLOBAL_gb_main); |
---|
1639 | |
---|
1640 | { |
---|
1641 | GB_transaction ta(GLOBAL_gb_main); |
---|
1642 | GBDATA *gb_tree_name = GB_search(GLOBAL_gb_main, AWAR_TREE, GB_STRING); |
---|
1643 | char *tree_name = GB_read_string(gb_tree_name); |
---|
1644 | |
---|
1645 | awr->awar_string(AWAR_TREE, 0, aw_def)->write_string(tree_name); |
---|
1646 | free(tree_name); |
---|
1647 | } |
---|
1648 | |
---|
1649 | awr->awar_int(AWAR_PARSIMONY, 0, aw_def); |
---|
1650 | awr->awar_int(AWAR_BEST_PARSIMONY, 0, aw_def); |
---|
1651 | awr->awar_int(AWAR_STACKPOINTER, 0, aw_def); |
---|
1652 | |
---|
1653 | create_parsimony_variables(awr, GLOBAL_gb_main); |
---|
1654 | create_nds_vars(awr, aw_def, GLOBAL_gb_main); |
---|
1655 | |
---|
1656 | #if defined(DEBUG) |
---|
1657 | AWT_create_db_browser_awars(awr, aw_def); |
---|
1658 | #endif // DEBUG |
---|
1659 | |
---|
1660 | GB_ERROR error = ARB_init_global_awars(awr, aw_def, GLOBAL_gb_main); |
---|
1661 | if (error) aw_message(error); |
---|
1662 | } |
---|
1663 | |
---|
1664 | static AW_root *AD_map_viewer_aw_root = 0; |
---|
1665 | |
---|
1666 | void PARS_map_viewer(GBDATA *gb_species, AD_MAP_VIEWER_TYPE vtype) { |
---|
1667 | if (vtype == ADMVT_SELECT && AD_map_viewer_aw_root && gb_species) { |
---|
1668 | AD_map_viewer_aw_root->awar(AWAR_SPECIES_NAME)->write_string(GBT_read_name(gb_species)); |
---|
1669 | } |
---|
1670 | } |
---|
1671 | |
---|
1672 | int ARB_main(int argc, const char *argv[]) { |
---|
1673 | aw_initstatus(); |
---|
1674 | |
---|
1675 | GB_shell shell; |
---|
1676 | AW_root *aw_root = AWT_create_root("pars.arb", "ARB_PARS"); |
---|
1677 | AD_map_viewer_aw_root = aw_root; |
---|
1678 | |
---|
1679 | ap_main = new AP_main; |
---|
1680 | |
---|
1681 | GLOBAL_PARS = (PARS_global *)calloc(sizeof(PARS_global), 1); |
---|
1682 | GLOBAL_PARS->awr = aw_root; |
---|
1683 | |
---|
1684 | const char *db_server = ":"; |
---|
1685 | |
---|
1686 | PARS_commands cmds; |
---|
1687 | |
---|
1688 | while (argc>=2 && argv[1][0] == '-') { |
---|
1689 | argc--; |
---|
1690 | argv++; |
---|
1691 | if (!strcmp(argv[0], "-quit")) cmds.quit = 1; |
---|
1692 | else if (!strcmp(argv[0], "-add_marked")) cmds.add_marked = 1; |
---|
1693 | else if (!strcmp(argv[0], "-add_selected")) cmds.add_selected = 1; |
---|
1694 | else if (!strcmp(argv[0], "-calc_branchlengths")) cmds.calc_branch_lengths = 1; |
---|
1695 | else if (!strcmp(argv[0], "-calc_bootstrap")) cmds.calc_bootstrap = 1; |
---|
1696 | else { |
---|
1697 | fprintf(stderr, "Unknown option '%s'\n", argv[0]); |
---|
1698 | |
---|
1699 | printf(" Options: Meaning:\n" |
---|
1700 | "\n" |
---|
1701 | " -add_marked add marked species (without changing topology)\n" |
---|
1702 | " -add_selected add selected species (without changing topology)\n" |
---|
1703 | " -calc_branchlengths calculate branch lengths only\n" |
---|
1704 | " -calc_bootstrap estimate bootstrap values\n" |
---|
1705 | " -quit quit after performing operations\n" |
---|
1706 | ); |
---|
1707 | |
---|
1708 | exit(EXIT_FAILURE); |
---|
1709 | } |
---|
1710 | } |
---|
1711 | |
---|
1712 | |
---|
1713 | if (argc==2) { |
---|
1714 | db_server = argv[1]; |
---|
1715 | } |
---|
1716 | |
---|
1717 | GLOBAL_gb_main = GBT_open(db_server, "rw"); |
---|
1718 | if (!GLOBAL_gb_main) aw_popup_exit(GB_await_error()); // exits |
---|
1719 | |
---|
1720 | #if defined(DEBUG) |
---|
1721 | AWT_announce_db_to_browser(GLOBAL_gb_main, GBS_global_string("ARB-database (%s)", db_server)); |
---|
1722 | #endif // DEBUG |
---|
1723 | |
---|
1724 | pars_create_all_awars(aw_root, AW_ROOT_DEFAULT); |
---|
1725 | |
---|
1726 | AW_window *aww = create_pars_init_window(aw_root, &cmds); |
---|
1727 | aww->show(); |
---|
1728 | |
---|
1729 | AWT_install_cb_guards(); |
---|
1730 | aw_root->main_loop(); |
---|
1731 | return EXIT_SUCCESS; |
---|
1732 | } |
---|
1733 | |
---|