1 | // ================================================================ // |
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2 | // // |
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3 | // File : ST_window.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 "st_ml.hxx" |
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12 | #include "st_quality.hxx" |
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13 | |
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14 | #include <gui_aliview.hxx> |
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15 | #include <ColumnStat.hxx> |
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16 | |
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17 | #include <aw_awars.hxx> |
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18 | #include <aw_root.hxx> |
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19 | #include <aw_msg.hxx> |
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20 | #include <item_sel_list.h> |
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21 | #include <awt_filter.hxx> |
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22 | |
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23 | #define ST_ML_AWAR "tmp/st_ml/" |
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24 | |
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25 | #define ST_ML_AWAR_COLSTAT_PREFIX ST_ML_AWAR "colstat/" |
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26 | #define ST_ML_AWAR_COLSTAT_NAME ST_ML_AWAR_COLSTAT_PREFIX "name" |
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27 | |
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28 | #define ST_ML_AWAR_FILTER_PREFIX ST_ML_AWAR "filter/" |
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29 | #define ST_ML_AWAR_FILTER_ALIGNMENT ST_ML_AWAR_FILTER_PREFIX "alignment" |
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30 | #define ST_ML_AWAR_FILTER_NAME ST_ML_AWAR_FILTER_PREFIX "name" |
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31 | #define ST_ML_AWAR_FILTER_FILTER ST_ML_AWAR_FILTER_PREFIX "filter" |
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32 | #define ST_ML_AWAR_FILTER_SIMPLIFY ST_ML_AWAR_FILTER_PREFIX "simplify" |
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33 | |
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34 | #define ST_ML_AWAR_CQ_BUCKET_SIZE ST_ML_AWAR "bucket_size" |
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35 | #define ST_ML_AWAR_CQ_MARKED_ONLY ST_ML_AWAR "marked_only" |
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36 | #define ST_ML_AWAR_CQ_DEST_FIELD ST_ML_AWAR "dest_field" |
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37 | #define ST_ML_AWAR_CQ_REPORT ST_ML_AWAR "report" |
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38 | #define ST_ML_AWAR_CQ_KEEP_REPORTS ST_ML_AWAR "keep_reports" |
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39 | |
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40 | static void st_ok_cb(AW_window *aww, ST_ML *st_ml) { |
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41 | AW_root *root = aww->get_root(); |
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42 | char *alignment_name = root->awar_string(AWAR_DEFAULT_ALIGNMENT, "-none-", st_ml->get_gb_main())->read_string(); |
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43 | char *tree_name = root->awar_string(AWAR_TREE, "", st_ml->get_gb_main())->read_string(); |
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44 | int marked_only = root->awar_int(ST_ML_AWAR_CQ_MARKED_ONLY)->read_int(); |
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45 | |
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46 | GB_ERROR error = GB_push_transaction(st_ml->get_gb_main()); |
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47 | if (!error) { |
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48 | error = st_ml->calc_st_ml(tree_name, alignment_name, NULL, marked_only, st_ml->get_column_statistic(), NULL); |
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49 | if (!error) st_ml->do_postcalc_callback(); |
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50 | } |
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51 | |
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52 | error = GB_end_transaction(st_ml->get_gb_main(), error); |
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53 | aww->hide_or_notify(error); |
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54 | |
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55 | free(tree_name); |
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56 | free(alignment_name); |
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57 | } |
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58 | |
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59 | void STAT_set_postcalc_callback(ST_ML *st_ml, AW_CB0 postcalc_cb, AW_window *cb_win) { |
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60 | st_ml->set_postcalc_callback(postcalc_cb, cb_win); |
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61 | } |
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62 | |
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63 | AW_window *STAT_create_main_window(AW_root *root, ST_ML *st_ml) { |
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64 | AW_window_simple *aws = new AW_window_simple; |
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65 | aws->init(root, "COLUMN_STATISTIC", "COLUMN STATISTIC"); |
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66 | |
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67 | aws->load_xfig("stat_main.fig"); |
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68 | |
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69 | aws->callback(AW_POPDOWN); |
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70 | aws->at("close"); |
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71 | aws->create_button("CLOSE", "CLOSE", "C"); |
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72 | |
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73 | aws->callback(makeHelpCallback("st_ml.hlp")); |
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74 | aws->at("help"); |
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75 | aws->create_button("HELP", "HELP", "H"); |
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76 | |
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77 | root->awar_string(ST_ML_AWAR_COLSTAT_NAME, ""); |
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78 | root->awar_int(ST_ML_AWAR_CQ_MARKED_ONLY, 1); |
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79 | |
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80 | AW_awar *awar_default_alignment = root->awar_string(AWAR_DEFAULT_ALIGNMENT, "-none-", st_ml->get_gb_main()); |
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81 | root->awar_string(AWAR_TREE, "", st_ml->get_gb_main()); |
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82 | |
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83 | st_ml->create_column_statistic(root, ST_ML_AWAR_COLSTAT_NAME, awar_default_alignment); |
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84 | |
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85 | aws->at("GO"); |
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86 | aws->callback(makeWindowCallback(st_ok_cb, st_ml)); |
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87 | aws->create_button("GO", "GO", "G"); |
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88 | |
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89 | aws->at("awt_csp"); |
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90 | aws->callback(makeCreateWindowCallback(COLSTAT_create_selection_window, st_ml->get_column_statistic())); |
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91 | aws->button_length(20); |
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92 | aws->create_button("SELECT_CSP", ST_ML_AWAR_COLSTAT_NAME); |
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93 | |
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94 | aws->at("marked"); |
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95 | aws->create_toggle_field(ST_ML_AWAR_CQ_MARKED_ONLY, "Calculate for ..", ""); |
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96 | aws->insert_toggle("All species", "A", 0); |
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97 | aws->insert_toggle("Marked species", "M", 1); |
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98 | aws->update_toggle_field(); |
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99 | |
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100 | return aws; |
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101 | } |
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102 | |
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103 | ST_ML *STAT_create_ST_ML(GBDATA *gb_main) { |
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104 | return new ST_ML(gb_main); |
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105 | } |
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106 | |
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107 | ST_ML_Color *STAT_get_color_string(ST_ML *st_ml, char *species_name, AP_tree *node, int start_ali_pos, int end_ali_pos) { |
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108 | return st_ml->get_color_string(species_name, node, start_ali_pos, end_ali_pos); |
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109 | } |
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110 | |
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111 | bool STAT_update_ml_likelihood(ST_ML *st_ml, char *result[4], int& latest_update, const char *species_name, AP_tree *node) { |
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112 | //! @see ST_ML::update_ml_likelihood() |
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113 | return st_ml->update_ml_likelihood(result, latest_update, species_name, node); |
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114 | } |
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115 | |
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116 | AP_tree *STAT_find_node_by_name(ST_ML *st_ml, const char *species_name) { |
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117 | return st_ml->find_node_by_name(species_name); |
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118 | } |
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119 | |
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120 | struct st_check_cb_data : public Noncopyable { |
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121 | GBDATA *gb_main; |
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122 | ColumnStat *colstat; |
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123 | WeightedFilter *filter; |
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124 | |
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125 | st_check_cb_data(GBDATA *gb_main_, AW_root *root, const char *columnStatAwarName, const char *filterAwarName, AW_awar *awar_default_alignment) { |
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126 | gb_main = gb_main_; |
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127 | colstat = new ColumnStat(gb_main, root, columnStatAwarName, awar_default_alignment); |
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128 | filter = new WeightedFilter(gb_main, root, filterAwarName, NULL, awar_default_alignment); |
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129 | } |
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130 | }; |
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131 | |
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132 | static void st_check_cb(AW_window *aww, st_check_cb_data *data) { |
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133 | GB_transaction ta(data->gb_main); |
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134 | |
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135 | AW_root *r = aww->get_root(); |
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136 | |
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137 | char *alignment_name = r->awar(ST_ML_AWAR_FILTER_ALIGNMENT)->read_string(); |
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138 | int bucket_size = r->awar(ST_ML_AWAR_CQ_BUCKET_SIZE)->read_int(); |
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139 | char *tree_name = r->awar(AWAR_TREE)->read_string(); |
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140 | char *dest_field = r->awar(ST_ML_AWAR_CQ_DEST_FIELD)->read_string(); |
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141 | int marked_only = r->awar(ST_ML_AWAR_CQ_MARKED_ONLY)->read_int(); |
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142 | |
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143 | st_report_enum report = (st_report_enum) r->awar(ST_ML_AWAR_CQ_REPORT)->read_int(); |
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144 | |
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145 | GB_ERROR error = st_ml_check_sequence_quality(data->gb_main, tree_name, alignment_name, data->colstat, data->filter, bucket_size, marked_only, report, dest_field); |
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146 | |
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147 | free(dest_field); |
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148 | free(alignment_name); |
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149 | free(tree_name); |
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150 | |
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151 | error = ta.close(error); |
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152 | if (error) aw_message(error); |
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153 | } |
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154 | |
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155 | static void STAT_create_awars(AW_root *root, GBDATA *gb_main) { |
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156 | root->awar_string(AWAR_DEFAULT_ALIGNMENT, "-none-", gb_main); |
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157 | root->awar_string(AWAR_TREE, "", gb_main); |
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158 | |
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159 | root->awar_string(ST_ML_AWAR_COLSTAT_NAME, "none"); |
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160 | |
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161 | root->awar_string(ST_ML_AWAR_FILTER_ALIGNMENT, "none"); |
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162 | root->awar_string(ST_ML_AWAR_FILTER_NAME, "none"); |
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163 | root->awar_string(ST_ML_AWAR_FILTER_FILTER, ""); |
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164 | root->awar_int (ST_ML_AWAR_FILTER_SIMPLIFY, 0); |
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165 | |
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166 | root->awar_int (ST_ML_AWAR_CQ_BUCKET_SIZE, 300); |
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167 | root->awar_int (ST_ML_AWAR_CQ_MARKED_ONLY, 0); |
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168 | root->awar_string(ST_ML_AWAR_CQ_DEST_FIELD, "tmp"); |
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169 | root->awar_int (ST_ML_AWAR_CQ_REPORT, 0); |
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170 | root->awar_int (ST_ML_AWAR_CQ_KEEP_REPORTS, 0); |
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171 | |
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172 | root->awar_string(ST_ML_AWAR_FILTER_ALIGNMENT)->map(AWAR_DEFAULT_ALIGNMENT); |
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173 | } |
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174 | |
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175 | static void st_remove_entries(AW_window */*aww*/) { |
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176 | // @@@ shall remove created all entries (from current alignment) |
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177 | } |
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178 | |
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179 | AW_window *STAT_create_chimera_check_window(AW_root *root, GBDATA *gb_main) { |
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180 | static AW_window_simple *aws = 0; |
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181 | if (!aws) { |
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182 | aws = new AW_window_simple; |
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183 | aws->init(root, "CHIMERA_CHECK", "Chimera Check of marked sequences"); |
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184 | aws->load_xfig("chimera_check.fig"); |
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185 | |
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186 | STAT_create_awars(root, gb_main); |
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187 | |
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188 | aws->callback(AW_POPDOWN); |
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189 | aws->at("close"); |
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190 | aws->create_button("CLOSE", "CLOSE", "C"); |
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191 | |
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192 | aws->callback(makeHelpCallback("chimera_check.hlp")); |
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193 | aws->at("help"); |
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194 | aws->create_button("HELP", "HELP", "H"); |
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195 | |
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196 | AW_awar *awar_default_alignment = root->awar_string(AWAR_DEFAULT_ALIGNMENT, "-none-", gb_main); |
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197 | st_check_cb_data *cb_data = new st_check_cb_data(gb_main, root, ST_ML_AWAR_COLSTAT_NAME, ST_ML_AWAR_FILTER_NAME, awar_default_alignment); // bound to cb (not freed) |
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198 | |
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199 | aws->at("which"); |
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200 | { |
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201 | aws->create_option_menu(ST_ML_AWAR_CQ_MARKED_ONLY, true); |
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202 | aws->insert_option("All in tree", "t", 0); |
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203 | aws->insert_option("Only marked and in tree", "m", 1); |
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204 | aws->update_option_menu(); |
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205 | } |
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206 | |
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207 | aws->at("colstat"); |
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208 | aws->callback(makeCreateWindowCallback(COLSTAT_create_selection_window, cb_data->colstat)); |
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209 | aws->create_button("SELECT_CSP", ST_ML_AWAR_COLSTAT_NAME); |
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210 | |
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211 | |
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212 | aws->at("filter"); |
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213 | aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, cb_data->filter->get_adfiltercbstruct())); |
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214 | aws->create_button("SELECT_FILTER", ST_ML_AWAR_FILTER_NAME); |
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215 | |
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216 | aws->at("sb"); |
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217 | aws->create_input_field(ST_ML_AWAR_CQ_BUCKET_SIZE); |
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218 | |
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219 | create_selection_list_on_itemfields(gb_main, aws, ST_ML_AWAR_CQ_DEST_FIELD, true, 1 << GB_STRING, "dest", 0, SPECIES_get_selector(), 20, 10, SF_STANDARD, "SELECT_REPORT_FIELD"); |
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220 | |
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221 | aws->at("report"); |
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222 | { |
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223 | aws->create_option_menu(ST_ML_AWAR_CQ_REPORT, true); |
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224 | aws->insert_option("No", "N", 0); |
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225 | aws->insert_option("to temporary entry", "t", 1); |
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226 | aws->insert_option("to permanent entry", "p", 2); |
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227 | aws->update_option_menu(); |
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228 | } |
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229 | |
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230 | { // @@@ not implemented yet |
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231 | aws->sens_mask(AWM_DISABLED); |
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232 | |
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233 | aws->at("keep"); |
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234 | aws->create_toggle(ST_ML_AWAR_CQ_KEEP_REPORTS); |
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235 | |
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236 | aws->at("del"); |
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237 | aws->callback(st_remove_entries); |
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238 | aws->create_button("DEL_ENTRIES", "Remove them now!", "R"); |
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239 | |
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240 | aws->sens_mask(AWM_ALL); |
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241 | } |
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242 | |
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243 | aws->at("GO"); |
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244 | aws->callback(makeWindowCallback(st_check_cb, cb_data)); |
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245 | aws->create_button("GO", "GO", "G"); |
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246 | } |
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247 | return aws; |
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248 | } |
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