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