1 | // ==================================================================== // |
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2 | // // |
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3 | // File : SQ_main.cxx // |
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4 | // Purpose : Entrypoint to Seq. Quality analysis; calls functions // |
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5 | // // |
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6 | // // |
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7 | // Coded by Juergen Huber in July 2003 - February 2004 // |
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8 | // Coded by Kai Bader (baderk@in.tum.de) in 2007 - 2008 // |
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9 | // Copyright Department of Microbiology (Technical University Munich) // |
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10 | // // |
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11 | // Visit our web site at: http://www.arb-home.de/ // |
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12 | // // |
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13 | // ==================================================================== // |
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14 | |
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15 | #include "seq_quality.h" |
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16 | #include "SQ_functions.h" |
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17 | |
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18 | #include <awt_filter.hxx> |
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19 | #include <awt_sel_boxes.hxx> |
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20 | |
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21 | #include <aw_awars.hxx> |
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22 | #include <aw_msg.hxx> |
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23 | #include <aw_root.hxx> |
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24 | |
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25 | #include <arb_progress.h> |
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26 | #include <arbdbt.h> |
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27 | #include <arb_global_defs.h> |
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28 | |
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29 | // -------------------------------------------------------------------------------- |
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30 | |
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31 | #define AWAR_SQ_PERM "seq_quality/" // saved in properties |
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32 | #define AWAR_SQ_TEMP "tmp/seq_quality/" // not saved in properties |
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33 | #define AWAR_SQ_WEIGHT_BASES AWAR_SQ_PERM "weight_bases" |
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34 | #define AWAR_SQ_WEIGHT_DEVIATION AWAR_SQ_PERM "weight_deviation" |
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35 | #define AWAR_SQ_WEIGHT_HELIX AWAR_SQ_PERM "weight_helix" |
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36 | #define AWAR_SQ_WEIGHT_CONSENSUS AWAR_SQ_PERM "weight_consensus" |
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37 | #define AWAR_SQ_WEIGHT_IUPAC AWAR_SQ_PERM "weight_iupac" |
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38 | #define AWAR_SQ_WEIGHT_GC AWAR_SQ_PERM "weight_gc" |
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39 | |
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40 | #define AWAR_SQ_MARK_ONLY_FLAG AWAR_SQ_PERM "mark_only_flag" |
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41 | #define AWAR_SQ_MARK_FLAG AWAR_SQ_PERM "mark_flag" |
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42 | #define AWAR_SQ_MARK_BELOW AWAR_SQ_PERM "mark_below" |
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43 | #define AWAR_SQ_REEVALUATE AWAR_SQ_PERM "reevaluate" |
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44 | |
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45 | #define AWAR_FILTER_PREFIX AWAR_SQ_TEMP "filter/" |
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46 | #define AWAR_FILTER_NAME AWAR_FILTER_PREFIX "name" |
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47 | #define AWAR_FILTER_FILTER AWAR_FILTER_PREFIX "filter" |
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48 | #define AWAR_FILTER_ALI AWAR_FILTER_PREFIX "alignment" |
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49 | |
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50 | void SQ_create_awars(AW_root * aw_root, AW_default aw_def) { |
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51 | aw_root->awar_int(AWAR_SQ_WEIGHT_BASES, 5, aw_def); |
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52 | aw_root->awar_int(AWAR_SQ_WEIGHT_DEVIATION, 15, aw_def); |
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53 | aw_root->awar_int(AWAR_SQ_WEIGHT_HELIX, 15, aw_def); |
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54 | aw_root->awar_int(AWAR_SQ_WEIGHT_CONSENSUS, 50, aw_def); |
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55 | aw_root->awar_int(AWAR_SQ_WEIGHT_IUPAC, 5, aw_def); |
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56 | aw_root->awar_int(AWAR_SQ_WEIGHT_GC, 10, aw_def); |
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57 | aw_root->awar_int(AWAR_SQ_MARK_ONLY_FLAG, 0, aw_def); |
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58 | aw_root->awar_int(AWAR_SQ_MARK_FLAG, 1, aw_def); |
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59 | aw_root->awar_int(AWAR_SQ_MARK_BELOW, 40, aw_def); |
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60 | aw_root->awar_int(AWAR_SQ_REEVALUATE, 0, aw_def); |
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61 | aw_root->awar_string(AWAR_FILTER_NAME, "none", aw_def); |
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62 | aw_root->awar_string(AWAR_FILTER_FILTER, "", aw_def); |
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63 | AW_awar *awar_ali = aw_root->awar_string(AWAR_FILTER_ALI, "", aw_def); |
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64 | awar_ali->map(AWAR_DEFAULT_ALIGNMENT); |
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65 | } |
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66 | |
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67 | // -------------------------------------------------------------------------------- |
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68 | |
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69 | |
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70 | static void sq_calc_seq_quality_cb(AW_window * aww, AW_CL res_from_awt_create_select_filter, AW_CL cl_gb_main) { |
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71 | GBDATA *gb_main = (GBDATA*)cl_gb_main; |
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72 | AW_root *aw_root = aww->get_root(); |
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73 | GB_ERROR error = 0; |
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74 | GBT_TREE *tree = 0; |
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75 | bool marked_only = (aw_root->awar(AWAR_SQ_MARK_ONLY_FLAG)->read_int() > 0); |
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76 | |
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77 | arb_progress main_progress("Calculating sequence quality"); |
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78 | |
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79 | { |
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80 | char *treename = aw_root->awar(AWAR_TREE)->read_string(); |
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81 | |
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82 | if (treename && strcmp(treename, NO_TREE_SELECTED) != 0) { |
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83 | error = GB_push_transaction(gb_main); |
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84 | |
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85 | if (!error) { |
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86 | tree = GBT_read_tree(gb_main, treename, GBT_TREE_NodeFactory()); |
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87 | if (!tree) error = GB_await_error(); |
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88 | else { |
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89 | error = GBT_link_tree(tree, gb_main, false, NULL, NULL); |
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90 | if (!error) { |
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91 | GBT_TreeRemoveType mode = marked_only ? GBT_KEEP_MARKED : GBT_REMOVE_ZOMBIES; |
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92 | tree = GBT_remove_leafs(tree, mode, NULL, NULL, NULL); |
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93 | if (!tree || tree->is_leaf) { |
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94 | error = GBS_global_string("Tree contains less than 2 species after removing zombies%s", |
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95 | marked_only ? " and non-marked" : ""); |
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96 | } |
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97 | } |
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98 | } |
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99 | } |
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100 | |
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101 | error = GB_end_transaction(gb_main, error); |
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102 | } |
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103 | free(treename); |
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104 | } |
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105 | |
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106 | // if tree == 0 -> do basic quality calculations that are possible without tree information |
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107 | // otherwise -> use all groups found in tree and compare sequences against the groups they are contained in |
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108 | |
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109 | if (!error) { |
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110 | struct SQ_weights weights; |
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111 | |
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112 | weights.bases = aw_root->awar(AWAR_SQ_WEIGHT_BASES)->read_int(); |
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113 | weights.diff_from_average = aw_root->awar(AWAR_SQ_WEIGHT_DEVIATION)->read_int(); |
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114 | weights.helix = aw_root->awar(AWAR_SQ_WEIGHT_HELIX)->read_int(); |
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115 | weights.consensus = aw_root->awar(AWAR_SQ_WEIGHT_CONSENSUS)->read_int(); |
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116 | weights.iupac = aw_root->awar(AWAR_SQ_WEIGHT_IUPAC)->read_int(); |
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117 | weights.gc = aw_root->awar(AWAR_SQ_WEIGHT_GC)->read_int(); |
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118 | |
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119 | int mark_flag = aw_root->awar(AWAR_SQ_MARK_FLAG)->read_int(); |
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120 | int mark_below = aw_root->awar(AWAR_SQ_MARK_BELOW)->read_int(); |
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121 | int reevaluate = aw_root->awar(AWAR_SQ_REEVALUATE)->read_int(); |
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122 | |
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123 | // Load and use Sequence-Filter |
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124 | AP_filter *filter = awt_get_filter((adfiltercbstruct*)res_from_awt_create_select_filter); |
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125 | error = awt_invalid_filter(filter); |
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126 | |
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127 | /* |
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128 | SQ_evaluate() generates the final estimation for the quality of an alignment. |
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129 | It takes the values from the different containers, which are generated by the other functions, weights them |
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130 | and calculates a final value. The final value is stored in "value_of_evaluation" (see options). |
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131 | With the values stored in "weights" one can customize how important a value stored in a container becomes |
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132 | for the final result. |
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133 | */ |
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134 | |
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135 | if (!error) { |
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136 | if (tree == 0) { |
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137 | if (reevaluate) { |
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138 | SQ_mark_species(gb_main, mark_below, marked_only); |
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139 | } |
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140 | else { |
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141 | arb_progress progress(GBT_get_species_count(gb_main)*2); |
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142 | SQ_GroupData *globalData = new SQ_GroupData_RNA; |
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143 | |
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144 | progress.subtitle("pass1"); |
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145 | error = SQ_pass1_no_tree(globalData, gb_main, filter, progress); |
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146 | if (!error) { |
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147 | progress.subtitle("pass2"); |
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148 | error = SQ_pass2_no_tree(globalData, gb_main, filter, progress); |
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149 | if (!error) { |
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150 | error = SQ_evaluate(gb_main, weights, marked_only); |
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151 | if (mark_flag && !error) { |
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152 | SQ_mark_species(gb_main, mark_below, marked_only); |
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153 | } |
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154 | } |
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155 | } |
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156 | if (error) progress.done(); |
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157 | delete globalData; |
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158 | } |
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159 | } |
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160 | else { |
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161 | SQ_TREE_ERROR check = SQ_check_tree_structure(tree); |
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162 | if (check != NONE) { |
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163 | switch (check) { |
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164 | case ZOMBIE: |
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165 | error = "Found one or more zombies in the tree.\n" |
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166 | "Please remove them or use another tree before running the quality check tool."; |
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167 | break; |
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168 | case MISSING_NODE: |
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169 | error = "Missing node(s) or unusable tree structure.\n" |
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170 | "Please fix the tree before running the quality check tool."; |
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171 | break; |
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172 | default: |
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173 | error = "An error occurred while traversing the tree.\n" |
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174 | "Please fix the tree before running the quality check tool."; |
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175 | break; |
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176 | } |
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177 | } |
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178 | else if (reevaluate) { |
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179 | SQ_mark_species(gb_main, mark_below, marked_only); |
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180 | } |
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181 | else { |
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182 | arb_progress progress(SQ_count_nodes(tree)*2); |
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183 | SQ_GroupData *globalData = new SQ_GroupData_RNA; |
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184 | |
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185 | progress.subtitle("pass1"); |
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186 | SQ_calc_and_apply_group_data(tree, gb_main, globalData, filter, progress); |
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187 | progress.subtitle("pass2"); |
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188 | SQ_calc_and_apply_group_data2(tree, gb_main, globalData, filter, progress); |
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189 | SQ_evaluate(gb_main, weights, marked_only); |
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190 | if (mark_flag) SQ_mark_species(gb_main, mark_below, marked_only); |
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191 | delete globalData; |
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192 | } |
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193 | } |
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194 | } |
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195 | awt_destroy_filter(filter); |
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196 | } |
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197 | |
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198 | if (error) aw_message(error); |
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199 | |
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200 | SQ_clear_group_dictionary(); |
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201 | delete tree; |
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202 | } |
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203 | |
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204 | static void sq_remove_quality_entries_cb(AW_window *, AW_CL cl_gb_main) { |
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205 | GBDATA *gb_main = (GBDATA*)cl_gb_main; |
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206 | SQ_remove_quality_entries(gb_main); |
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207 | } |
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208 | |
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209 | AW_window *SQ_create_seq_quality_window(AW_root *aw_root, GBDATA *gb_main) { |
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210 | // create window for sequence quality calculation (called only once) |
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211 | |
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212 | AW_window_simple *aws = new AW_window_simple; |
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213 | |
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214 | aws->init(aw_root, "CALC_SEQ_QUALITY", "CALCULATE SEQUENCE QUALITY"); |
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215 | aws->load_xfig("seq_quality.fig"); |
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216 | |
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217 | aws->at("close"); |
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218 | aws->callback((AW_CB0) AW_POPDOWN); |
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219 | aws->create_button("CLOSE", "CLOSE", "C"); |
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220 | |
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221 | aws->at("help"); |
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222 | aws->callback(makeHelpCallback("seq_quality.hlp")); |
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223 | aws->create_button("HELP", "HELP", "H"); |
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224 | |
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225 | aws->at("base"); |
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226 | aws->create_input_field(AWAR_SQ_WEIGHT_BASES, 3); |
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227 | |
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228 | aws->at("deviation"); |
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229 | aws->create_input_field(AWAR_SQ_WEIGHT_DEVIATION, 3); |
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230 | |
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231 | aws->at("no_helices"); |
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232 | aws->create_input_field(AWAR_SQ_WEIGHT_HELIX, 3); |
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233 | |
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234 | aws->at("consensus"); |
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235 | aws->create_input_field(AWAR_SQ_WEIGHT_CONSENSUS, 3); |
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236 | |
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237 | aws->at("iupac"); |
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238 | aws->create_input_field(AWAR_SQ_WEIGHT_IUPAC, 3); |
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239 | |
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240 | aws->at("gc_proportion"); |
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241 | aws->create_input_field(AWAR_SQ_WEIGHT_GC, 3); |
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242 | |
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243 | aws->at("monly"); |
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244 | aws->create_toggle(AWAR_SQ_MARK_ONLY_FLAG); |
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245 | |
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246 | aws->at("mark"); |
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247 | aws->create_toggle(AWAR_SQ_MARK_FLAG); |
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248 | |
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249 | aws->at("mark_below"); |
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250 | aws->create_input_field(AWAR_SQ_MARK_BELOW, 3); |
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251 | |
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252 | aws->at("tree"); |
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253 | awt_create_TREE_selection_list(gb_main, aws, AWAR_TREE, true); |
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254 | |
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255 | aws->at("filter"); |
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256 | adfiltercbstruct *adfilter = awt_create_select_filter(aws->get_root(), gb_main, AWAR_FILTER_NAME); |
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257 | aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, adfilter)); |
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258 | aws->create_button("SELECT_FILTER", AWAR_FILTER_NAME); |
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259 | |
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260 | aws->at("go"); |
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261 | aws->callback(sq_calc_seq_quality_cb, (AW_CL)adfilter, (AW_CL)gb_main); |
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262 | aws->highlight(); |
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263 | aws->create_button("GO", "GO", "G"); |
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264 | |
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265 | aws->at("remove"); |
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266 | aws->callback(sq_remove_quality_entries_cb, (AW_CL)gb_main); |
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267 | aws->create_button("Remove", "Remove", "R"); |
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268 | |
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269 | aws->at("reevaluate"); |
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270 | aws->label("Re-Evaluate only"); |
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271 | aws->create_toggle(AWAR_SQ_REEVALUATE); |
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272 | |
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273 | return aws; |
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274 | } |
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